From francois@flymine.org Thu Aug 15 15:59:40 2002 Received: from purple.csi.cam.ac.uk ([131.111.8.4]) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 17fM68-0003FS-00 for ; Thu, 15 Aug 2002 15:59:40 +0100 Received: from flywall.gen.cam.ac.uk ([131.111.146.25] helo=flymine.org) by purple.csi.cam.ac.uk with esmtp (Exim 4.10) id 17fM67-0007c3-00 for flymine-dev@flymine.org; Thu, 15 Aug 2002 15:59:39 +0100 Message-ID: <3D5BC1DB.1080303@flymine.org> Date: Thu, 15 Aug 2002 15:59:39 +0100 From: Francois GUILLIER User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.1b) Gecko/20020722 X-Accept-Language: en, fr, en-us MIME-Version: 1.0 To: flymine-dev Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Subject: [Flymine-dev] This is a test Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.11 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers List-Unsubscribe: , List-Archive: Message #1 -- Francois. ----------------- Systems Administrator Flymine project - Department of Genetics University of Cambridge - Downing Site - Cambridge - CB2 3EH - UK From francois@flymine.org Thu Aug 15 16:57:21 2002 Received: from purple.csi.cam.ac.uk ([131.111.8.4]) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 17fMzw-0003Lz-00; Thu, 15 Aug 2002 16:57:20 +0100 Received: from flywall.gen.cam.ac.uk ([131.111.146.25] helo=flymine.org) by purple.csi.cam.ac.uk with esmtp (Exim 4.10) id 17fMzw-0002sm-00; Thu, 15 Aug 2002 16:57:20 +0100 Message-ID: <3D5BCF60.8010302@flymine.org> Date: Thu, 15 Aug 2002 16:57:20 +0100 From: Francois GUILLIER User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.1b) Gecko/20020722 X-Accept-Language: en, fr, en-us MIME-Version: 1.0 To: flymine-dev , flymine-announce@flymine.org Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Subject: [Flymine-dev] Test Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.11 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers List-Unsubscribe: , List-Archive: This is the second test... -- Francois. ----------------- Systems Administrator Flymine project - Department of Genetics University of Cambridge - Downing Site - Cambridge - CB2 3EH - UK From andy@flymine.org Mon Nov 11 09:03:29 2002 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 18BATh-0004Tu-00 for ; Mon, 11 Nov 2002 09:03:29 +0000 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 18BATh-0000dL-00 for ; Mon, 11 Nov 2002 09:03:29 +0000 Date: Fri, 25 Oct 2002 18:44:12 +0100 From: Andrew Varley To: richard@flymine.org, matthew@flymine.org, Mark Woodbridge Message-ID: <20021025174412.GD8426@flymine.org> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4i Resent-From: andy@flymine.org Resent-Date: Mon, 11 Nov 2002 09:03:28 +0000 Resent-To: flymine-dev@flymine.org Resent-Message-Id: Subject: [flymine-dev] next 2 weeks Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: So, to summarise: We have agreed that a Query object will contain some kind of tree structure with QueryNodes representing classes and QueryLinks either between classes, or between fields of classes, or between a class field and a constant. These links representing concepts such as "contains/contained in", "equals", "not equals", "less than" etc, and aggregates. A QueryNode object will be constructed by passing a Class (eg. qnode = new QueryNode(Gene.class)). We have agreed that a "Results" object will be a "FlyMineCollectionImpl" of ResultsRows. The FlyMineResultsImpl will be the really clever thing that is doing the transparent caching of queries to SQL tables to allow quick reordering without rerunning the entire Query. Each ResultsRow will contain a collection/array of (business objects, Field or Aggregate). Field and Aggregate are objects that have two attributes: value and Collection, where the collection is a collection of the objects which have been aggregated or the objects to which the field applies. The same pre/lazy-loading applies to these collections as to a Collection in a regular business object. We have agreed that there needs to be some concept of a "ResultsView" that specifies what objects we want to see in the output. For performance reasons, this may act as a "hint" to the class that actually runs the query, so that it knows what Collection fields to pre-fill. This is verging on the presentation layer. We have also agreed that there needs to be some concept of ordering of results that is separate from a query object (because ordering does not affect the joins and constaints in SQL terms). Again, this may be passed to the class that runs the query as a hint, or probably even better to the FlyMineCollectionImpl object in the Results class (The FlyMineCollectionImpl will probably have a method such as setOrdering(OrderByObject order). These are the things that you could do over the next 2 weeks. I am not saying do them all, but there should be enough here to keep you busy. i) In discussion, concentrate on the graphical query representation. Go through the use-cases and see if each use-case can be represented fully in the proposed graphical query language. Do not get too hung up about the business-object model - ask Gos if you need help with that. Think of as many other query scenarios as you can and try them out - like we have been doing. Try and separate this discussion from anything related to how the Query will actually be run/objects persisted - that is a separate discussion for when I get back. ii) Refine the drawing that we had that had objects such as QueryNode, QueryLink. What are the possible objects that the QueryLinks link (QueryField->QueryField, QueryField->constant, .....? This is in effect the structure of a Query object. iii) Investigate in as much detail as you like the things on the list I sent earlier. iv) Set up the internal web site in conjunction with Francois. Use the same ant method of producing/releasing the pages. Use the same stylesheet as for the main site (ie. exactly the same one - not a copy). v) Delve a bit into the source code of OJB to ascertain the following: a) How they implement the client-server persistence broker architecture - remember that bioinformatics users will be using FlyMine in a client-server kind of way. b) How difficult it would be to bolt-on calls to the query planner. I think we can learn a lot from the OJB code, even if we don't actually use OJB itself. vi) Look at ways that we can actually implement the graphical part of the query builder (Swing.....). The ArgoUML code would be a good place to start. Attempt to build a standalone prototype if you are really keen!! The most important thing is not to get bogged down. We are still at a very early stage in the project, and I think we have made a lot of progress over the last 2 weeks. This early on we are bound to talk ourselves round in circles at times, but time spent discussing/arguing/debating now will reap huge dividends 6 months down the line. I have asked Richard to decide when to have team discussions and when to do stuff on your own for the next 2 weeks. Hope this makes some sort of sense!! Enjoy yourselves!!! Andy From andy@flymine.org Mon Nov 11 09:04:10 2002 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 18BAUM-0004U9-00 for ; Mon, 11 Nov 2002 09:04:10 +0000 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 18BAUI-0000da-00 for ; Mon, 11 Nov 2002 09:04:06 +0000 Received: from [192.168.128.105] (helo=flymine.org ident=rns) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 186XN9-0005nH-00; Tue, 29 Oct 2002 14:29:35 +0000 Message-ID: <3DBE9B4F.40803@flymine.org> Date: Tue, 29 Oct 2002 14:29:35 +0000 From: Richard Smith User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.1) Gecko/20020913 Debian/1.1-1 X-Accept-Language: en MIME-Version: 1.0 To: andy@flymine.org, richard@flymine.org, mark@flymine.org, matthew@flymine.org Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Resent-From: andy@flymine.org Resent-Date: Mon, 11 Nov 2002 09:04:06 +0000 Resent-To: flymine-dev@flymine.org Resent-Message-Id: Subject: [flymine-dev] Kaleidoquery Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: A paper about visual query languages for object databases, quite interesting. One of the authors (Carole Goble) is now involved with the myGrid project. www.nicve.salford.ac.uk/~norman/kaleidoquery.pdf Richard. From andy@flymine.org Mon Nov 11 09:04:42 2002 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 18BAUs-0004UH-00 for ; Mon, 11 Nov 2002 09:04:42 +0000 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 18BAUs-0000dl-00 for ; Mon, 11 Nov 2002 09:04:42 +0000 Received: from [192.168.128.105] (helo=flymine.org ident=rns) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 188fpd-0003ys-00; Mon, 04 Nov 2002 11:55:49 +0000 Message-ID: <3DC66045.70900@flymine.org> Date: Mon, 04 Nov 2002 11:55:49 +0000 From: Richard Smith User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.1) Gecko/20020913 Debian/1.1-1 X-Accept-Language: en MIME-Version: 1.0 To: matthew@flymine.org, mark@flymine.org, andy@flymine.org, richard@flymine.org Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Resent-From: andy@flymine.org Resent-Date: Mon, 11 Nov 2002 09:04:42 +0000 Resent-To: flymine-dev@flymine.org Resent-Message-Id: Subject: [flymine-dev] Query Representation - summary Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Hi, Below is a summary of thoughts about query representation taken from Andy's mail and conclusions from our discussions last week. It sounds rather confusing but hopefully everything is mentioned - we can change/add things that I have missed out. If we are happy about these conclusions and there are no outstanding topics we could move the discussion on to structure of the Query objects in java terms. We have a basic model of QueryNodes, QueryLinks, QueryNodeFields, etc - is this still valid, what further contstraints now need to be applied. Perhaps we could start talking about that this afternoon. Richard. Query Representation -------------------- * Queries will be displayed on screen with boxes representing business objects and lines showing relationships between them. Boxes will list the fields/collections belonging to them, it should be clear which are business objects themselves and hence can be dragged out to form a new box. * Two types of lines: 1) From a collection in one object to the title or corresponding collection in another business object (to be decided). This represents contains/contained in. 2) Between fields in different objects to show direct comparason of those fields (equals, less than, not equals, etc). * If possible we should avoid having two boxes representing the same instance of an object - this may be difficult in some cases. * Left/right joins should be represented by e.g. dashed lines with a direction or opaque boxes. This allows additional information to be added to ouput if it is present, otherwise a blank entry will be displayed. Outer joins may/will also need to be represented - how? * In representing aggregates there were problems with associativity in some examples. It is not sufficient to display aggregations on links, instead boxes (dashed lines) must be placed around business objects to determine order/scope of aggregation. These can be nested. * Aggegates will be defined as objects where fields are the aggregate types. The types to be computed/displayed will be drawn in the dashed box, constraints can be placed on these fields. * In some cases the query system will have to infer and run additional queries. e.g. if a field is part of an aggregate (inside a dashed box) but the user selects it for display one query must be run to compute the aggregate (e.g. returns a count of five) and a second to find all results for that field (the five individual values). * OR relationships need to be represented in some way. It is not sufficient to place these on links. OR relationships will need in some way to point to fields within objects and fields of aggregates. Do they sometimes need to point at links?? Sometimes more complex AND/OR relationships may be required (i.e if (A or B) and (C or D)). These could be displayed as lines superimposed on the box diagram and/or by using different colours. * Field objects will be used where a field of a business object needs to behave like a business object itself. It will have a value and a collection of objects defined by that value. This collection could be heterogeneous? (not very well described). * Propogation of objects (a la Voodoo) was mentioned but not really discussed. i.e any object can appear as a field in one that is derived from it (?). Should we look into this further? From andy@flymine.org Mon Nov 11 09:05:12 2002 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 18BAVM-0004Us-00 for ; Mon, 11 Nov 2002 09:05:12 +0000 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 18BAVM-0000ds-00 for ; Mon, 11 Nov 2002 09:05:12 +0000 Received: from [192.168.128.105] (helo=flymine.org ident=rns) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 18A6su-00051G-00; Fri, 08 Nov 2002 11:01:08 +0000 Message-ID: <3DCB9974.7050502@flymine.org> Date: Fri, 08 Nov 2002 11:01:08 +0000 From: Richard Smith User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.1) Gecko/20020913 Debian/1.1-1 X-Accept-Language: en MIME-Version: 1.0 To: mark@flymine.org, matthew@flymine.org, richard@flymine.org, andy@flymine.org Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Resent-From: andy@flymine.org Resent-Date: Mon, 11 Nov 2002 09:05:12 +0000 Resent-To: flymine-dev@flymine.org Resent-Message-Id: Subject: [flymine-dev] more questions than conclusions Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: We have been discussing various aspects of the implementing a flymineQuery. It has become apparent that this needs to interact very closely with the query builder display and a flymineResults object. We have talked around these topics without reaching any real conclusions. A summary of what these discussions covered is given below (rather vague). I think we decided/reiterated that flymine query/results should form a very distinct layer, decoupled from interface(s) above and object/db accessor below. To continue today I think we should focus just on this layer and test the flymineQuery model against the interface we discussed last week. Richard. Representing a business object as a node in our visual query builder: --------------------------------------------------------------------- * What object does a box in our visual query representation correspond to? - queryNode(gene.class) - displayableQueryNode(gene.class) - drawableGene [drawable in terms of query not output] - queryDisplayHelper(gene.class) * The object needs to know: - How the business object behaves in the data model (reflection) - extra info about how to render the business object - dropdowns (+contents), - text boxes, etc * we want to separate the display (in query builder) info from query data. FlymineQuery and Results: ------------------------- * A FlymineQuery needs to be a query representation that translates easily to our graphical representation and to a 'concrete' query that can talk to an object repository/database. - how well does it translate to other access methods - html, xml, etc?? * The Results object will be linked very closely to a FlymineQuery. Should Results contain a FlymineQuery? Should it contain a translation of FlymineQuery? Changes to results view could change query (e.g. adding a column) -- should this change the original query object? * do we need to track/store changes to a flymineQuery throughout a session. From andy@flymine.org Mon Nov 11 13:37:21 2002 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 18BEkj-0004y7-00 for ; Mon, 11 Nov 2002 13:37:21 +0000 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 18BEkj-0001M2-00 for ; Mon, 11 Nov 2002 13:37:21 +0000 Received: from [192.168.128.103] (helo=aragorn.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 17x9AG-00064G-00; Thu, 03 Oct 2002 17:49:28 +0100 Received: from mnw21 (helo=localhost) by aragorn.flymine.org with local-esmtp (Exim 3.35 #1 (Debian)) id 17x9AF-000791-00; Thu, 03 Oct 2002 17:49:27 +0100 Date: Thu, 3 Oct 2002 17:49:27 +0100 (BST) From: Matthew Wakeling X-X-Sender: mnw21@aragorn.flymine.org To: gos@flymine.org, cc: matthew@flymine.org Message-ID: MIME-Version: 1.0 Content-Type: MULTIPART/MIXED; BOUNDARY="-1463785600-266887628-1033663767=:10809" Resent-From: andy@flymine.org Resent-Date: Mon, 11 Nov 2002 13:37:21 +0000 Resent-To: flymine-dev@flymine.org Resent-Message-Id: Subject: [flymine-dev] Statistics for precomputed joins. Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. Send mail to mime@docserver.cac.washington.edu for more info. ---1463785600-266887628-1033663767=:10809 Content-Type: TEXT/PLAIN; charset=US-ASCII Attached is a summary of some performance tests I did on my workstation of large tables, and joins between them. I set up three tables, each with one million rows - call them 1, 2, and 3. I then set up two more tables - call them m1 and m2, which represent a many-to-many relationship between the rows of 1 and 2, or 2 and 3 respectively. m1 and m2 both have two million rows. I then set up a precomputed join of 1-m1-2 (2 million rows), a precomputed join of m2-3 (2 million rows), and of 1-m1-2-m2-3 (4 million rows). I added as many indexes as possible, and clustered the tables on the indexes, and tested the performance of joins. Generally, you should be able to get a performance increase of around 20 times by using a precomputed join instead of an explicit join. On one of my tests, the query planner made a bad choice, so I will send a bug report to the developers of postgres. I managed to force a more efficient query plan by using a subquery. I performed each test twice, to get results before and after the cache had been populated. Anyway, the results are attached. Matthew ---1463785600-266887628-1033663767=:10809 Content-Type: TEXT/PLAIN; charset=US-ASCII; name=insert1M_jointest2_results4_summary Content-Transfer-Encoding: BASE64 Content-ID: Content-Description: summary Content-Disposition: attachment; filename=insert1M_jointest2_results4_summary IC0gaW5kaWNhdGVzIGpvaW5zLg0KID0gaW5kaWNhdGVzIHRoYXQgdGhlIERC IGRpZCBhIG1lcmdlIGpvaW4uIElmIHRoZXJlIGFyZW4ndCB0d28gYXJyb3dz LCB0aGVuIGl0IGhhZCB0byBkbyBhIHNvcnQgZmlyc3QuIDw9PiBpbmRpY2F0 ZXMgYSBtZXJnZSBqb2luIHdpdGhvdXQgbmVlZGluZyB0byBzb3J0Lg0KIC0+ IGluZGljYXRlcyBqb2luIHdpdGggdGhlIGhlbHAgb2YgYSBjbHVzdGVyZWQg aW5kZXggKGhlbHBzIHdpdGggbWVyZ2Ugam9pbikuDQogKCkgaW5kaWNhdGVz IHByZWNhbGN1bGF0ZWQgam9pbi4NCg0KVGltZXMgaW4gbWlsbGlzZWNvbmRz DQoNCldpdGhvdXQJCVdpdGgJCUpvaW4gcGF0dGVybg0KY2FjaGUJCWNhY2hl DQoNCjEyMDg1Ni4yNgkxMDU0NjUuNDkJMTw9Pm0xLT4yDQo1MDQ3Ljc4CQkz NTQzLjM5CQkoMS1tMS0yKQkJCQkJCVNwZWVkIGltcHJvdmVtZW50OiAyNCB0 byAzMA0KMTM0ODYxLjY5CTExNjU0Mi40NgkyPT5tMi0+Mw0KMzU4MTEuODgJ MjgxNzEuMzEJMj0+KG0yLTMpCQkJCQkJU3BlZWQgaW1wcm92ZW1lbnQ6IDMu NyB0byA0LjINCjQ2NDI5NC44MgkzODU4MjMuMTMJMTw9Pm0xLT4yPT5tMi0+ Mw0KMjA4Mjg1LjQ3CTIwODIwMy44MQkoMS1tMS0yKTw9Pm0yLT4zCQkJCQlT cGVlZCBpbXByb3ZlbWVudDogMS44IHRvIDIuMg0KMzM2MDUuMDEJMzAyMjcu NzIJKDEtbTEtMik8PT4obTItMykJCQkJCVNwZWVkIGltcHJvdmVtZW50OiAx MiB0byAxNA0KMTE1MzkuNjMJMTEwNDguMjkJKDEtbTEtMi1tMi0zKQkJCQkJ CVNwZWVkIGltcHJvdmVtZW50OiAzNSB0byA0MA0KDQoyMDA3LjM2CQkyNi41 MwkJMTwtPm0xLT4yLCB3aXRoIHJlc3RyaWN0aW9uICJpbmZvYSA9IDEyMzQi DQozMy43MwkJNi43NgkJKDEtbTEtMiksIHdpdGggcmVzdHJpY3Rpb24JCQkJ U3BlZWQgaW1wcm92ZW1lbnQ6IDQgdG8gNjANCjI5NDQwLjg5CTI5NjY0LjEx CTI9Pm0yLT4zLCB3aXRoIHJlc3RyaWN0aW9uICJpbmZvYyA9IDEyMzQiCSAg IDwtLS0gQmFkIHBsYW5uZXIgZGVjaXNpb24gdG8gc29ydCB0YWJsZSAyDQoo MjU2Ni44OAkyNy40NAkJd2l0aCBhbHRlcm5hdGl2ZSBwbGFuKQ0KMTEzMS4x OQkJMTkuNjcJCTItPihtMi0zKSwgd2l0aCByZXN0cmljdGlvbgkJCQlTcGVl ZCBpbXByb3ZlbWVudDogMjYgdG8gMTUwMA0KMTY1MjEuNTkJODIuNTYJCTE8 LT5tMS0+Mi0+bTItPjMsIHdpdGggcmVzdHJpY3Rpb24gImluZm9hID0gMTIz NCINCjQ1Ny4yNAkJNTUuNzQJCSgxLW0xLTIpPC0+bTItPjMsIHdpdGggcmVz dHJpY3Rpb24JCQlTcGVlZCBpbXByb3ZlbWVudDogMS41IHRvIDM2DQoxMzc2 LjQ5CQkyMy4xNwkJKDEtbTEtMik8LT4obTItMyksIHdpdGggcmVzdHJpY3Rp b24JCQlTcGVlZCBpbXByb3ZlbWVudDogMy41IHRvIDEyDQoyNDIuMTkJCTYu NjUJCSgxLW0xLTItbTItMyksIHdpdGggcmVzdHJpY3Rpb24JCQkJU3BlZWQg aW1wcm92ZW1lbnQ6IDEyIHRvIDY4DQoNCg== ---1463785600-266887628-1033663767=:10809-- From andy@flymine.org Mon Nov 11 18:03:15 2002 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 18BIu3-0005bS-00 for ; Mon, 11 Nov 2002 18:03:15 +0000 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 18BIu3-00023O-00 for ; Mon, 11 Nov 2002 18:03:15 +0000 Date: Mon, 11 Nov 2002 18:03:15 +0000 From: Andrew Varley To: flymine-dev@flymine.org Message-ID: <20021111180315.GH2262@flymine.org> Mail-Followup-To: flymine-dev@flymine.org Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4i Subject: [flymine-dev] FlyMine internal website Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Hi, There is now an internal website for FlyMine staff eyes only. Access is from www.flymine.org and is restricted to machines in the flymine.org domain. We may implement password access if there is a need for external machines to access this part of the site in the future. This is the place to put internal documents. The source is the flymine-private/doc directory in CVS. Andy From andy@flymine.org Mon Nov 18 10:16:19 2002 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 18Dix1-0006dh-00 for ; Mon, 18 Nov 2002 10:16:19 +0000 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 18Dix0-0004TX-00 for ; Mon, 18 Nov 2002 10:16:18 +0000 Date: Mon, 18 Nov 2002 10:16:18 +0000 From: Andrew Varley To: FlyMine Developers Message-ID: <20021118101618.GA16058@flymine.org> Mail-Followup-To: FlyMine Developers Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4i Subject: [flymine-dev] Final query meeting Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Hi, Let's have a meeting today at 2pm in G3 to: 1) Finalise the Query/Results objects 2) Discuss the overall system architecture in more detail than we've already done. I have written 2 documents - one is on the internal website (documentation -> system architecture) and I think covers things we've already discussed but had not spelled out in full. The other is a UML diagram available on the same menu as an ArgoUML file. Again, I think this documents the things we've already discussed. It would be good to have your thoughts on these and we can make as many alterations as needed and then call this version 1.0 of the FlyMine Query/Results API!! Andy From andy@flymine.org Tue Nov 19 12:05:16 2002 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 18E780-0001Ks-00; Tue, 19 Nov 2002 12:05:16 +0000 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 18E780-0006ow-00; Tue, 19 Nov 2002 12:05:16 +0000 Date: Tue, 19 Nov 2002 12:05:16 +0000 From: Andrew Varley To: flymine-dev@flymine.org Message-ID: <20021119120516.GA25060@flymine.org> Mail-Followup-To: flymine-dev@flymine.org Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4i Subject: [flymine-dev] CVS Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: The CVS repository has now moved onto a machine in the internal network (cvs-internal.flymine.org). The old alias cvs.flymine.org still points to this machine for the time being so everything should still work. However, when you have not got much checked out, you should delete/rename your working copies of flymine and flymine-private and check out another copy, using CVSROOT=:ext:cvs-internal.flymine.org/cvs (this will get set automatically if you open a new xterm). Then copy back in to this new working copy any files you have changed. The by product of this location change is that the "cvsmove" script will now work. This is used for moving or renaming files in CVS and is on your path. Andy From mrw34@cam.ac.uk Tue Nov 26 16:11:00 2002 Received: from rose.csi.cam.ac.uk ([131.111.8.13]) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 18GiIe-0002bs-00 for ; Tue, 26 Nov 2002 16:11:00 +0000 Received: from orange.csi.cam.ac.uk ([131.111.8.77] ident=exim) by rose.csi.cam.ac.uk with esmtp (Exim 4.10) id 18GiIe-0004BZ-00 for flymine-dev@flymine.org; Tue, 26 Nov 2002 16:11:00 +0000 Received: from boromir.gen.cam.ac.uk ([131.111.146.53] helo=localhost.localdomain) by orange.csi.cam.ac.uk with esmtp (Exim 4.10) id 18GiIe-0000AE-00 for flymine-dev@flymine.org; Tue, 26 Nov 2002 16:11:00 +0000 From: Mark Woodbridge To: flymine-dev@flymine.org Content-Type: text/plain Content-Transfer-Encoding: 7bit X-Mailer: Ximian Evolution 1.0.8 Date: 26 Nov 2002 16:11:00 +0000 Message-Id: <1038327060.13429.235.camel@boromir> Mime-Version: 1.0 Subject: [flymine-dev] Default persistance layer Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: The "build-db" task now uses hibernate. "build-db-ojb" is available as an alternative. This has required the renaming of two build properties (db.type and db.type.torque). These are case sensitive. The relevent section of your local build.properties.flymine should look something like: db.url=jdbc\:mysql\://localhost/test db.driver=com.mysql.jdbc.Driver db.type.torque=mysql db.type=MySQL db.user=mark db.password= The relevent database (eg. test) should be cleared before switching to/from hibernate. Mark. From andy@flymine.org Mon Dec 02 12:28:39 2002 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 18Ipgl-0000dF-00; Mon, 02 Dec 2002 12:28:39 +0000 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 18Ipgl-0006Qc-00; Mon, 02 Dec 2002 12:28:39 +0000 Date: Mon, 2 Dec 2002 12:28:39 +0000 From: Andrew Varley To: FlyMine Developers , rachel@flymine.org, raj@flymine.org Message-ID: <20021202122839.GA24568@flymine.org> Mail-Followup-To: FlyMine Developers , rachel@flymine.org, raj@flymine.org Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4i Subject: [flymine-dev] FlyMine prototype evaluation Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Hi, As I think everyone knows, we are currently developing a prototype of the FlyMine backend system. Already a number of issues have arisen, and I think it would be good to meet as an extended group to talk about what we have done in the prototype and whether we want to go with this for the real thing, or make big changes, and what is going to take loads of time to implement and what is easy. This should be relevant to everyone, not just the developers, as we have already had a first stab at a simple data model. How about setting aside a whole morning (or day, even?) for this, say Monday 6th January (9.30-12.30)? I think it would be good if everyone could be prepared to talk about the tasks they have done in the prototype (say for 10-15 minutes), together with a bit of technical background to the task (eg. what is JAXB, Castor, ....) and why we chose such-and-such to do in the prototype. Suggested programme: Andy - overview of prototype FlyMine Richard - the data model Andy - the Query/Results/Objectstore interface Mark - implementing the interface with an existing product Matthew - JDBC intecepting and parsing Richard - loading genomic data Andy - loading microarray data Let me know if you can't make this date. I have booked the Bateson Room (or will it be ours anyway by then???!!) as that is a better room for discussion than G3. I will make sure that we can use the projector with our laptop. Andy From andy@flymine.org Tue Dec 03 10:05:02 2002 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 18J9vK-0003Du-00; Tue, 03 Dec 2002 10:05:02 +0000 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 18J9vK-00013w-00; Tue, 03 Dec 2002 10:05:02 +0000 Date: Tue, 3 Dec 2002 10:05:01 +0000 From: Andrew Varley To: FlyMine Developers Cc: raj@flymine.org Message-ID: <20021203100501.GC502@flymine.org> Mail-Followup-To: FlyMine Developers , raj@flymine.org Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4i Subject: [flymine-dev] External resources web page Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Hi, I've put a web page up on which we can list external resources. If you come across anything (work-related!) that you think might be of interest to everyone (eg. tutorials, references, etc), please list it on here: flymine/www/developer/resources.xml Cheers, Andy From andy@flymine.org Thu Dec 05 11:54:09 2002 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 18Jua1-0000kd-00 for ; Thu, 05 Dec 2002 11:54:09 +0000 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 18Jua1-0008Nb-00 for ; Thu, 05 Dec 2002 11:54:09 +0000 Date: Thu, 5 Dec 2002 11:54:09 +0000 From: Andrew Varley To: flymine-dev@flymine.org Message-ID: <20021205115409.GB14579@flymine.org> Mail-Followup-To: flymine-dev@flymine.org Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4i Subject: [flymine-dev] Prototype progress Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Hi, The timetable for finishing the prototype is: Tuesday 10th December: main coding effort ends. Wed 11th - Fri 20th: correct any integration issues and write suite of genuine test queries. Mon 23rd Dec - Fri 3rd Jan: Performance testing and preparation of short presentations Mon 6th Jan: Meeting to review prototype and the proposed main system. Andy From andy@flymine.org Tue Dec 24 14:57:00 2002 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 18QqUO-0004JK-00; Tue, 24 Dec 2002 14:57:00 +0000 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 18QqUN-0004Ve-00; Tue, 24 Dec 2002 14:56:59 +0000 Date: Tue, 24 Dec 2002 14:56:59 +0000 From: Andrew Varley To: FlyMine Developers Cc: raj@flymine.org Message-ID: <20021224145659.GA13021@flymine.org> Mail-Followup-To: FlyMine Developers , raj@flymine.org Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4i Subject: [flymine-dev] prototype building instructions Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Dear All, With a huge amount of hackery, the prototype is now working, as far as I can tell. Here are the steps needed to build a working database from scratch. Run "ant clean". Comment out the line: module_flatten=org.flymine.p6flatten.P6FlattenSpyDriver near the beginning of the file resources/spy.properties Run "ant build-db" to build a new database from scratch (takes approx 4 hours). This can be speeded up slightly by running "VACUUM ANALYSE" regularly during the loading process. Uncomment the line in the above file. Run "VACUUM ANALYSE" in the database. Run "ant test-system" to run the sample queries. System configuration (eg. logging levels) can be found in the file resources/org/flymine/common/flymine.properties User configuration (eg. database url, username, password) should be in the file ~/build.properties.flymine in your home directory. This may need updating to contain the property db.realdriver (see build.properties file in main flymine directory). Precomputed tables can be found in the file resources/FlyMine.manual_precomp. Add to this anything you feel necessary. Andy From andy@flymine.org Tue Dec 24 15:08:28 2002 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 18QqfU-0004Kx-00; Tue, 24 Dec 2002 15:08:28 +0000 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 18QqfU-0004Xf-00; Tue, 24 Dec 2002 15:08:28 +0000 Date: Tue, 24 Dec 2002 15:08:28 +0000 From: Andrew Varley To: FlyMine Developers , rachel@flymine.org Subject: Re: [flymine-dev] FlyMine prototype evaluation Message-ID: <20021224150828.GB13021@flymine.org> Mail-Followup-To: FlyMine Developers , rachel@flymine.org References: <20021202122839.GA24568@flymine.org> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <20021202122839.GA24568@flymine.org> User-Agent: Mutt/1.4i Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: I have booked a video projector for us to use. Also the laptop has openoffice.org installed if you wanted to make any slides. If you do, please make sure that they are copied on to the laptop before the meeting, as we may not have network connectivity in that room. In fact, the best thing might be to rsync your whole home directory to the laptop so you can show any code etc. Rachel - can we use the laptop for the whole day, please? Cheers, Andy From andy@flymine.org Tue Dec 24 16:00:20 2002 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 18QrTg-0004Rb-00 for ; Tue, 24 Dec 2002 16:00:20 +0000 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 18QrTf-0004wu-00 for ; Tue, 24 Dec 2002 16:00:19 +0000 Date: Tue, 24 Dec 2002 16:00:19 +0000 From: Andrew Varley To: FlyMine Developers Subject: Re: [flymine-dev] prototype building instructions Message-ID: <20021224160019.GC13021@flymine.org> Mail-Followup-To: FlyMine Developers References: <20021224145659.GA13021@flymine.org> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <20021224145659.GA13021@flymine.org> User-Agent: Mutt/1.4i Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: In fact, I now have a dump file of the database which you can use which can replace all the steps up to and including "ant build-db". Find it at /shared/data/flymine.sql. It was created with pg_dump and can be loaded using pg_restore. Using this dump should be a lot quicker than running via ant. Cheers, Andy From francois@flymine.org Tue Dec 24 16:51:09 2002 Received: from brown.csi.cam.ac.uk ([131.111.8.14]) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 18QsGr-0004ZZ-00 for ; Tue, 24 Dec 2002 16:51:09 +0000 Received: from [213.228.0.169] (helo=postfix3-2.free.fr) by brown.csi.cam.ac.uk with esmtp (Exim 4.10) id 18QsGr-0005jQ-00 for flymine-dev@flymine.org; Tue, 24 Dec 2002 16:51:09 +0000 Received: from localhero.guillier.org (nantes-1-a7-62-147-41-155.dial.proxad.net [62.147.41.155]) by postfix3-2.free.fr (Postfix) with ESMTP id 8AB4DC127 for ; Tue, 24 Dec 2002 17:51:08 +0100 (CET) Received: from localhost.localdomain ([127.0.0.1]) by localhero.guillier.org with esmtp (Exim 4.10) id 18QsGl-0000nt-00 for flymine-dev@flymine.org; Tue, 24 Dec 2002 17:51:03 +0100 Received: from flymine.org (localhero.guillier.org [192.168.100.5]) by localhero.guillier.org (AvMailGate-2.0.1.5) id 03087-35F62959; Tue, 24 Dec 2002 17:51:02 +0100 Message-ID: <3E089076.1060207@flymine.org> Date: Tue, 24 Dec 2002 17:51:02 +0100 From: Francois GUILLIER User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.3a) Gecko/20021123 X-Accept-Language: en, fr MIME-Version: 1.0 To: flymine-dev@flymine.org Subject: Re: [flymine-dev] prototype building instructions Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-AntiVirus: checked by AntiVir MailGate (version: 2.0.1.5; AVE: 6.17.0.2; VDF: 6.17.0.9; host: localhero.guillier.org) Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Andrew Varley wrote: > Dear All, > > With a huge amount of hackery, the prototype is now working, as far as > I can tell. > > Before Christmas!? Congratulation everybody!!!! Joyeux Noël.... François. From gm263@mole.bio.cam.ac.uk Tue Dec 24 20:23:56 2002 Received: from rose.csi.cam.ac.uk ([131.111.8.13]) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 18Qvam-0004y6-00; Tue, 24 Dec 2002 20:23:56 +0000 Received: from mole.bio.cam.ac.uk ([131.111.36.9] ident=exim) by rose.csi.cam.ac.uk with esmtp (Exim 4.10) id 18Qvam-0006YP-00; Tue, 24 Dec 2002 20:23:56 +0000 Received: from gm263 by mole.bio.cam.ac.uk with local (Exim 3.33 #2 (SGI IRIX)) id 18Qvam-000xBu-00; Tue, 24 Dec 2002 20:23:56 +0000 Date: Tue, 24 Dec 2002 20:23:56 +0000 From: Gos Micklem To: FlyMine Developers , raj@flymine.org Subject: Re: [flymine-dev] prototype building instructions Message-ID: <20021224202356.A31486@mole.bio.cam.ac.uk> References: <20021224145659.GA13021@flymine.org> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5i In-Reply-To: <20021224145659.GA13021@flymine.org>; from andy@flymine.org on Tue, Dec 24, 2002 at 02:56:59PM +0000 Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Great stuff ! Have a good Christmas and New Year, Gos On Tue, Dec 24, 2002 at 02:56:59PM +0000, Andrew Varley wrote: > Dear All, > > With a huge amount of hackery, the prototype is now working, as far as > I can tell. > > Here are the steps needed to build a working database from scratch. > > Run "ant clean". > > Comment out the line: > module_flatten=org.flymine.p6flatten.P6FlattenSpyDriver > near the beginning of the file resources/spy.properties > > Run "ant build-db" to build a new database from scratch (takes approx > 4 hours). This can be speeded up slightly by running "VACUUM ANALYSE" > regularly during the loading process. > > Uncomment the line in the above file. > > Run "VACUUM ANALYSE" in the database. > > Run "ant test-system" to run the sample queries. > > System configuration (eg. logging levels) can be found in the file > resources/org/flymine/common/flymine.properties > > User configuration (eg. database url, username, password) should be in the > file ~/build.properties.flymine in your home directory. This may need > updating to contain the property db.realdriver (see build.properties > file in main flymine directory). > > Precomputed tables can be found in the file > resources/FlyMine.manual_precomp. Add to this anything you feel > necessary. > > Andy > > _______________________________________________ > flymine-dev mailing list > flymine-dev@flymine.org > http://mailman.flymine.org/listinfo/flymine-dev -- Gos Micklem Ph.D. gos@gen.cam.ac.uk Genetics Department, Cambridge University, Downing Street, Cambridge CB2 3EH, UK +44 (0) 1223 765 281 +44 (0) 1223 333 992 fax http://www.flymine.org http://www.flychip.org.uk From andy@flymine.org Thu Jan 02 14:22:52 2003 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 18U6FI-0003ni-00 for ; Thu, 02 Jan 2003 14:22:52 +0000 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 18U6FI-0004S9-00 for ; Thu, 02 Jan 2003 14:22:52 +0000 Date: Thu, 2 Jan 2003 14:22:52 +0000 From: Andrew Varley To: FlyMine Developers Message-ID: <20030102142249.GA13546@flymine.org> Mail-Followup-To: FlyMine Developers Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4i Subject: [flymine-dev] Automated build daemon Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: There is now an automated build daemon running that will attempt to build and test the whole of FlyMine after every CVS commit. After 5 minutes from commiting any changes to CVS you will receive an email saying whether the master build was successful or not. If not, then it is up to you to mend it straight away!! (Successful=compiles+all unit tests pass). The automated build results can be viewed at: http://www1.flymine.org:8080/cruisecontrol/buildresults Cheers, Andy From andy@flymine.org Thu Jan 02 17:04:16 2003 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 18U8lU-00047n-00 for ; Thu, 02 Jan 2003 17:04:16 +0000 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 18U8lU-0005GE-00 for ; Thu, 02 Jan 2003 17:04:16 +0000 Date: Thu, 2 Jan 2003 17:04:16 +0000 From: Andrew Varley To: FlyMine Developers Subject: Re: [flymine-dev] FlyMine prototype evaluation Message-ID: <20030102170416.GB13546@flymine.org> Mail-Followup-To: FlyMine Developers References: <20021202122839.GA24568@flymine.org> <20021224150828.GB13021@flymine.org> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <20021224150828.GB13021@flymine.org> User-Agent: Mutt/1.4i Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: There is a Openoffice presentation template in CVS (flymine-private/templates/openoffice/flymine.sti) that you could use for your presentations, if you wish. It features the lovely purple colour scheme!! Andy From andy@flymine.org Thu Jan 02 17:20:32 2003 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 18U91E-0004AA-00 for ; Thu, 02 Jan 2003 17:20:32 +0000 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 18U91E-0005Ky-00 for ; Thu, 02 Jan 2003 17:20:32 +0000 Date: Thu, 2 Jan 2003 17:20:32 +0000 From: Andrew Varley To: FlyMine Developers Subject: Re: [flymine-dev] FlyMine prototype evaluation Message-ID: <20030102172031.GC13546@flymine.org> Mail-Followup-To: FlyMine Developers References: <20021202122839.GA24568@flymine.org> <20021224150828.GB13021@flymine.org> <20030102170416.GB13546@flymine.org> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <20030102170416.GB13546@flymine.org> User-Agent: Mutt/1.4i Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: ...and a directory in flymine-private for completed presentations: flymine-private/doc/prototype/ From andy@flymine.org Wed Jan 08 18:21:46 2003 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 18WKpm-0004jL-00 for ; Wed, 08 Jan 2003 18:21:46 +0000 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 18WKpm-0007QM-00 for ; Wed, 08 Jan 2003 18:21:46 +0000 Date: Wed, 8 Jan 2003 18:21:46 +0000 From: Andrew Varley To: FlyMine Developers Message-ID: <20030108182135.GA28301@flymine.org> Mail-Followup-To: FlyMine Developers Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4i Subject: [flymine-dev] Technology reviews Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Hi, I thought it would be a good idea to have some regular meetings where we talk about a particular piece of software/technique/issue that is not directly related to what we are doing on the project, but of potential interest to everyone, the aim being to try and make it easier to keep abreast of new developments in the field and incorporate things into FlyMine where appropriate. Examples that I can think of off the top of my head are: JUnit JBoss/Application servers Apache sub-projects (eg. Cocoon, batik, velocity, ...) Postgres Java 1.5 ?? A tutorial on a particular part of the Java API (eg. Swing, EJBs, ...) These would take the form of a monthly meeting (no longer than an hour) where one person will have researched a topic (of their choice, but agreed in advance with me) and presents it to the rest in a 20-30 minute talk. After that, questions and discussion. As there are 5 or 6 of us, there will be no need for each person to do it more than twice a year!! To start the ball rolling, how about the following: Friday 31st Jan Andy Extreme programming Friday 28th Feb Richard Friday 28th Mar Matthew Friday 25th Apr Raj Friday 30th May Mark Andy From raj@flymine.org Thu Jan 09 13:28:00 2003 Received: from [192.168.128.107] (helo=flymine.org ident=raj) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 18Wcj2-0006ke-00 for ; Thu, 09 Jan 2003 13:28:00 +0000 Message-ID: <3E1D78DF.9050103@flymine.org> Date: Thu, 09 Jan 2003 13:27:59 +0000 From: Raj Paidi User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.1) Gecko/20020913 Debian/1.1-1 MIME-Version: 1.0 To: flymine-dev@flymine.org Subject: Re: [flymine-dev] Technology reviews References: <20030108182135.GA28301@flymine.org> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: hi, i can takeup Postgres cheers raj Andrew Varley wrote: >Hi, > >I thought it would be a good idea to have some regular meetings where >we talk about a particular piece of software/technique/issue that is >not directly related to what we are doing on the project, but of >potential interest to everyone, the aim being to try and make it >easier to keep abreast of new developments in the field and >incorporate things into FlyMine where appropriate. Examples that I >can think of off the top of my head are: > >JUnit >JBoss/Application servers >Apache sub-projects (eg. Cocoon, batik, velocity, ...) >Postgres >Java 1.5 ?? >A tutorial on a particular part of the Java API (eg. Swing, EJBs, ...) > >These would take the form of a monthly meeting (no longer than an >hour) where one person will have researched a topic (of their choice, >but agreed in advance with me) and presents it to the rest in a 20-30 >minute talk. After that, questions and discussion. As there are 5 or 6 >of us, there will be no need for each person to do it more than twice >a year!! > >To start the ball rolling, how about the following: > >Friday 31st Jan Andy Extreme programming >Friday 28th Feb Richard >Friday 28th Mar Matthew >Friday 25th Apr Raj >Friday 30th May Mark > >Andy > > >_______________________________________________ >flymine-dev mailing list >flymine-dev@flymine.org >http://mailman.flymine.org/listinfo/flymine-dev > > From andy@flymine.org Mon Jan 13 12:23:51 2003 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 18Y3d9-0001HU-00 for ; Mon, 13 Jan 2003 12:23:51 +0000 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 18Y3d9-0005Ta-00 for ; Mon, 13 Jan 2003 12:23:51 +0000 Date: Mon, 13 Jan 2003 12:23:51 +0000 From: Andrew Varley To: FlyMine Developers Message-ID: <20030113122351.GB18843@flymine.org> Mail-Followup-To: FlyMine Developers Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4i Subject: [flymine-dev] CVS changes and rules Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: The CVS source has been reorganised. The prototype is now in a directory flymine-prototype, which you can checkout using the command "cvs co flymine-prototype". The "flymine" directory will contain the production system as we write it. At the moment, only the static website exists in there. The reason for these changes is that it we are starting the main system from a clean sheet, so as not to be burdened by the prototype code. The rules for checking in code to the flymine directory: 1. Code must adhere to the FlyMine coding standards. 2. New code must have either i) been jointly designed with another developer (preferred) ii) reviewed by another team member before committing to CVS. 3. Code must have a full set of unit tests, which pass at 100%. 4. Modules must have a set of functional tests, using test data, which must pass at 100%. Cheers, Andy From andy@flymine.org Wed Jan 29 11:57:00 2003 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 18dqpw-0004MH-00 for ; Wed, 29 Jan 2003 11:57:00 +0000 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 18dqpv-0000Gd-00 for ; Wed, 29 Jan 2003 11:56:59 +0000 Date: Wed, 29 Jan 2003 11:56:59 +0000 From: Andrew Varley To: FlyMine Developers Message-ID: <20030129115659.GC31111@flymine.org> Mail-Followup-To: FlyMine Developers Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4i Subject: [flymine-dev] Talk - 31 Jan Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: The first in the series of FlyMine technology review meetings is entitled "Extreme Programming - what is it and what's in it for us?" and will be at 2pm on Friday 31st January in the Bateson Room. Andy From andy@flymine.org Fri Feb 07 11:31:09 2003 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 18h6ir-0007qd-00; Fri, 07 Feb 2003 11:31:09 +0000 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 18h6ir-0006fx-00; Fri, 07 Feb 2003 11:31:09 +0000 Date: Fri, 7 Feb 2003 11:31:09 +0000 From: Andrew Varley To: FlyMine Developers , Gos Micklem , Rachel Lyne Message-ID: <20030207113109.GB24167@flymine.org> Mail-Followup-To: FlyMine Developers , Gos Micklem , Rachel Lyne Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4i Subject: [flymine-dev] FlyMine front end Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Thursday 20th February 9-12 Bateson Room To spur discussion of the FlyMine front end, there will be a mornings meeting, the aim of which will be to agree some requirements for this part of the system, and the order in which they need to be implemented. Rachel and Gos will be demonstrating the Ace and SRS user interfaces and functionality. Gos - can we use your laptop for these demos as it will work on the department network? Andy From gm263@mole.bio.cam.ac.uk Fri Feb 07 11:35:29 2003 Received: from rose.csi.cam.ac.uk ([131.111.8.13]) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 18h6n3-0007rO-00 for ; Fri, 07 Feb 2003 11:35:29 +0000 Received: from mole.bio.cam.ac.uk ([131.111.36.9] ident=exim) by rose.csi.cam.ac.uk with esmtp (Exim 4.10) id 18h6n3-0008Pl-00 for flymine-dev@flymine.org; Fri, 07 Feb 2003 11:35:29 +0000 Received: from gm263 by mole.bio.cam.ac.uk with local (Exim 3.33 #2 (SGI IRIX)) id 18h6n2-00JmRN-00; Fri, 07 Feb 2003 11:35:28 +0000 Date: Fri, 7 Feb 2003 11:35:28 +0000 From: Gos Micklem To: FlyMine Developers , Rachel Lyne Message-ID: <20030207113528.M4463616@mole.bio.cam.ac.uk> References: <20030207113109.GB24167@flymine.org> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5i In-Reply-To: <20030207113109.GB24167@flymine.org>; from andy@flymine.org on Fri, Feb 07, 2003 at 11:31:09AM +0000 Subject: [flymine-dev] Re: FlyMine front end Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: On Fri, Feb 07, 2003 at 11:31:09AM +0000, Andrew Varley wrote: > Thursday 20th February 9-12 > Bateson Room > > To spur discussion of the FlyMine front end, there will be a mornings > meeting, the aim of which will be to agree some requirements for this > part of the system, and the order in which they need to be > implemented. > > Rachel and Gos will be demonstrating the Ace and SRS user interfaces > and functionality. > > Gos - can we use your laptop for these demos as it will work on the > department network? May have to use the IBM laptop - can't it work on the network ? Will also try and cover filemaker quickly if we can get that running. Gos From andy@flymine.org Mon Feb 17 13:27:56 2003 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 3.22 #1 (Red Hat Linux)) id 18klJM-0006ly-00; Mon, 17 Feb 2003 13:27:56 +0000 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 18klJM-0006wZ-00; Mon, 17 Feb 2003 13:27:56 +0000 Date: Mon, 17 Feb 2003 13:27:56 +0000 From: Andrew Varley To: FlyMine Developers , Gos Micklem , Rachel Lyne Subject: Re: [flymine-dev] FlyMine front end Message-ID: <20030217132756.GB24770@flymine.org> Mail-Followup-To: FlyMine Developers , Gos Micklem , Rachel Lyne References: <20030207113109.GB24167@flymine.org> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <20030207113109.GB24167@flymine.org> User-Agent: Mutt/1.4i Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: This will now be on Thursday February 27th 9-12 instead. Andy On Fri, Feb 07, 2003 at 11:31:09AM +0000, Andrew Varley wrote: > Thursday 20th February 9-12 > Bateson Room > > To spur discussion of the FlyMine front end, there will be a mornings > meeting, the aim of which will be to agree some requirements for this > part of the system, and the order in which they need to be > implemented. > > Rachel and Gos will be demonstrating the Ace and SRS user interfaces > and functionality. > > Gos - can we use your laptop for these demos as it will work on the > department network? > > Andy > > _______________________________________________ > flymine-dev mailing list > flymine-dev@flymine.org > http://mailman.flymine.org/listinfo/flymine-dev From francois@flymine.org Fri Feb 21 13:25:50 2003 Received: from [192.168.128.101] (helo=flymine.org) by flymine.flymine.org with esmtp (Exim 4.12) id 18mDBW-0002MK-00 for flymine-dev@flymine.org; Fri, 21 Feb 2003 13:25:50 +0000 Message-ID: <3E5628DE.6000008@flymine.org> Date: Fri, 21 Feb 2003 13:25:50 +0000 From: Francois GUILLIER User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.3a) Gecko/20021212 X-Accept-Language: en, fr, en-us MIME-Version: 1.0 To: flymine-dev Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Subject: [flymine-dev] TEST Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Just a quick test really... François. ----------------- Systems Administrator Flymine project - Department of Genetics University of Cambridge - Downing Site - Cambridge - CB2 3EH - UK From andy@flymine.org Mon Feb 24 16:40:02 2003 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 18nLe6-0003MY-00 for flymine-dev@flymine.org; Mon, 24 Feb 2003 16:40:02 +0000 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 18nLe6-0005Ln-00 for ; Mon, 24 Feb 2003 16:40:02 +0000 Date: Mon, 24 Feb 2003 16:40:02 +0000 From: Andrew Varley To: FlyMine Developers Message-ID: <20030224164002.GA15082@flymine.org> Mail-Followup-To: FlyMine Developers Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4i Subject: [flymine-dev] properties change Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: The properties for the database have changed. See build.properties file for examples. Cheers, Andy From andy@flymine.org Mon Feb 24 16:42:56 2003 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 18nLgu-0003N7-00 for flymine-dev@flymine.org; Mon, 24 Feb 2003 16:42:56 +0000 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 18nLgu-0005MK-00 for ; Mon, 24 Feb 2003 16:42:56 +0000 Date: Mon, 24 Feb 2003 16:42:56 +0000 From: Andrew Varley To: FlyMine Developers Message-ID: <20030224164256.GB15082@flymine.org> Mail-Followup-To: FlyMine Developers Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4i Subject: [flymine-dev] Postgres talk Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: On 7th March, 2pm, Raj will be giving a talk on PostgreSQL, specifically aimed at the application development side of things. If you have any specific topics you would like him to include, let him know ASAP. Andy From andy@flymine.org Thu Feb 27 11:43:58 2003 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 18oMSE-0003c3-00 for flymine-dev@flymine.org; Thu, 27 Feb 2003 11:43:58 +0000 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 18oMSE-0004jL-00 for ; Thu, 27 Feb 2003 11:43:58 +0000 Date: Thu, 27 Feb 2003 11:43:58 +0000 From: Andrew Varley To: FlyMine Developers Message-ID: <20030227114358.GB16943@flymine.org> Mail-Followup-To: FlyMine Developers Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4i Subject: [flymine-dev] Talk - 28th Feb Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: The next talk in our series of technology reviews will be on the subject of EJBs and be given by Richard, tomorrow, Friday 28th Feb, 2pm, Bateson Room. Andy From richard@flymine.org Wed Mar 19 14:37:43 2003 Received: from [192.168.128.105] (helo=flymine.org ident=rns) by flymine.flymine.org with esmtp (Exim 4.12) id 18vehL-0000Q3-00 for flymine-dev@flymine.org; Wed, 19 Mar 2003 14:37:43 +0000 Message-ID: <3E7880B7.4030601@flymine.org> Date: Wed, 19 Mar 2003 14:37:43 +0000 From: Richard Smith User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.1) Gecko/20020913 Debian/1.1-1 MIME-Version: 1.0 To: flymine-dev@flymine.org Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Subject: [flymine-dev] build.properties.flymine Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: I have now checked in the changes I have made to run explains before executing queries. The checking relies on some properties. Until the properties mechanism is sorted out these will reside in our own local build.properties.flymine files. You will need to add the following properties: # ObjectStore os.query.max-rows=100000 os.query.max-time=1000000000 os.query.max-limit=10000 os.query.max-offset=10000 Richard. From andy@flymine.org Tue Mar 25 10:57:31 2003 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 18xm7X-0001Rp-00 for flymine-dev@flymine.org; Tue, 25 Mar 2003 10:57:31 +0000 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 18xm7D-0007ml-00 for ; Tue, 25 Mar 2003 10:57:11 +0000 Date: Tue, 25 Mar 2003 10:57:11 +0000 From: Andrew Varley To: FlyMine Developers Message-ID: <20030325105711.GB29075@flymine.org> Mail-Followup-To: FlyMine Developers Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4i Subject: [flymine-dev] Talk - 28th March 2003 Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Talk - "What's new in Java 1.5" Friday 28th March 2003, 2pm Part II classroom, Genetics Department Matthew will be giving an overview of the new features expected in the next release of Java. From andy@flymine.org Wed Apr 02 13:41:04 2003 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 190hY8-0001Sf-00; Wed, 02 Apr 2003 13:41:04 +0100 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 190hY8-0000vb-00; Wed, 02 Apr 2003 13:41:04 +0100 Date: Wed, 2 Apr 2003 13:41:04 +0100 From: Andrew Varley To: flymine-dev@flymine.org, Rachel Lyne , Gos Micklem , Debashis Rana Message-ID: <20030402124104.GA3016@flymine.org> Mail-Followup-To: flymine-dev@flymine.org, Rachel Lyne , Gos Micklem , Debashis Rana Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4i Subject: [flymine-dev] FlyMine front end Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Wednesday 23rd April, 9.30am - 12 We will be having another full-group meeting to discuss the front end of FlyMine - basically carrying on from where we left off last time. It would be good if everyone could be familiar with: http://www.flymine.org/system/query_spec/spec http://www.flymine.org/user/usage_scenarios/ http://www.flymine.org/internal/design/other_projects before the meeting, then we have something to build on. Cheers, Andy From mrw34@cam.ac.uk Thu Apr 03 17:20:03 2003 Received: from brown.csi.cam.ac.uk ([131.111.8.14]) by flymine.flymine.org with esmtp (Exim 4.12) id 1917Rb-00057j-00 for flymine-dev@flymine.org; Thu, 03 Apr 2003 17:20:03 +0100 Received: from red.csi.cam.ac.uk ([131.111.8.70] ident=exim) by brown.csi.cam.ac.uk with esmtp (Exim 4.12) id 1917Rb-0003ro-00 for flymine-dev@flymine.org; Thu, 03 Apr 2003 17:20:03 +0100 Received: from boromir.gen.cam.ac.uk ([131.111.146.53] helo=localhost.localdomain) by red.csi.cam.ac.uk with esmtp (Exim 4.12) id 1917Rb-0000QQ-00 for flymine-dev@flymine.org; Thu, 03 Apr 2003 17:20:03 +0100 From: Mark Woodbridge To: flymine-dev@flymine.org Content-Type: text/plain Content-Transfer-Encoding: 7bit X-Mailer: Ximian Evolution 1.0.5 Date: 03 Apr 2003 17:20:02 +0100 Message-Id: <1049386803.23761.109.camel@boromir> Mime-Version: 1.0 Subject: [flymine-dev] Local properties Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: All runtime properties should now be specified in $HOME/flymine.properties. This mean that build.properties.flymine only contains settings used in the build process. Examples of the two files are given below. The db, user and password need to be set before use. Mark. $HOME/flymine.properties: os.unittest.class=org.flymine.objectstore.ojb.ObjectStoreOjbImpl os.unittest.alias=ojb os.unittest.ojb.model=testmodel os.unittest.ojb.db=db.unittest os.query.max-rows=100000 os.query.max-time=1000000000 os.query.max-limit=10000 os.query.max-offset=10000 db.unittest.datasource.class=org.postgresql.jdbc3.Jdbc3PoolingDataSource db.unittest.datasource.dataSourceName=db.unittest db.unittest.datasource.serverName=localhost db.unittest.datasource.databaseName=test db.unittest.datasource.user= db.unittest.datasource.password= db.unittest.datasource.maxConnections=10 db.unittest.driver=org.postgresql.Driver db.unittest.platform=PostgreSQL $HOME/build.properties.flymine: www.serverlocation=mark@www.flymine.org:public_html/flymine www.location=http://www.flymine.org/~mark/flymine From matthew@flymine.org Fri Apr 04 16:04:14 2003 Received: from [192.168.128.103] (helo=aragorn.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 191Sjm-00089F-00 for flymine-dev@flymine.org; Fri, 04 Apr 2003 16:04:14 +0100 Received: from mnw21 (helo=localhost) by aragorn.flymine.org with local-esmtp (Exim 3.36 #1 (Debian)) id 191Sjl-0002ju-00 for ; Fri, 04 Apr 2003 16:04:13 +0100 Date: Fri, 4 Apr 2003 16:04:13 +0100 (BST) From: Matthew Wakeling To: flymine-dev@flymine.org Subject: Re: [flymine-dev] Local properties In-Reply-To: <1049386803.23761.109.camel@boromir> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: An update to the properties. On 3 Apr 2003, Mark Woodbridge wrote: > $HOME/flymine.properties: ... > os.query.max-rows=100000 > os.query.max-time=1000000000 > os.query.max-limit=10000 > os.query.max-offset=10000 os.query.max-rows is defunct, so remove it from the properties. In addition, the system needs another property, named os.queue-len, which is the JVM-wide batch flush queue length. This is effectively the number of Results object batches which are held in memory as a cache. A suitable number is probably 100, so this will ensure that the last 100 batches fetched from the database remain in memory as a cache. So, that properties block changes into: os.query.max-time=1000000000 os.query.max-limit=10000 os.query.max-offset=10000 os.queue-len=100 Matthew -- Bashir: What's that you're chewing? O'Brien: Gum. It's kind of traditional. I got the replicator to make some for me. They used to infuse it with different flavourings. Bashir: Oh? And what did you infuse it with? O'Brien: Scotch. Here, you want some? From richard@flymine.org Mon Apr 14 11:54:56 2003 Received: from [192.168.128.105] (helo=flymine.org ident=rns) by flymine.flymine.org with esmtp (Exim 4.12) id 1951c0-00058T-00 for flymine-dev@flymine.org; Mon, 14 Apr 2003 11:54:56 +0100 Message-ID: <3E9A9380.4090102@flymine.org> Date: Mon, 14 Apr 2003 11:54:56 +0100 From: Richard Smith User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.3) Gecko/20030312 X-Accept-Language: en MIME-Version: 1.0 To: flymine-dev Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Subject: [flymine-dev] flymine.properties Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Some DataLoader code is now checked in, for the tests to work the lines given below need to be added to $HOME/flymine.properties. Richard. dataloader.unittest.integration=org.flymine.dataloader.IntegrationWriterSingleSourceImpl dataloader.unittest.osw=osw.unittest osw.unittest.class=org.flymine.objectstore.ojb.ObjectStoreWriterOjbImpl From andy@flymine.org Thu Apr 17 09:39:19 2003 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 1964vP-0006DD-00; Thu, 17 Apr 2003 09:39:19 +0100 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 1964vP-0003jC-00; Thu, 17 Apr 2003 09:39:19 +0100 Date: Thu, 17 Apr 2003 09:39:19 +0100 From: Andrew Varley To: flymine-dev@flymine.org, Rachel Lyne , Gos Micklem , Debashis Rana Subject: Re: [flymine-dev] FlyMine front end Message-ID: <20030417083914.GA14253@flymine.org> Mail-Followup-To: flymine-dev@flymine.org, Rachel Lyne , Gos Micklem , Debashis Rana References: <20030402124104.GA3016@flymine.org> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <20030402124104.GA3016@flymine.org> User-Agent: Mutt/1.5.3i Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Due to room booking constraints, there will now be 2 meetings. We thought it would be good, before we talk about the front end, to fill everyone in in the discussions Gos, Rachel and I have been having about the data model, as one or two things might affect the front end design (and maybe the back end as well). So, here is the new proposal: Wednesday 23rd April 9-11: Proposals for FlyMine data model Thursday 24th April 9-11: Update on where we are now on coding and more detailed roadmap for next few months. Can I propose that the following do a quick 5-10 minute summary/explaination of these areas (if there's anything I've forgotton, let me know...): Andy - general overview Richard - data loading/data integration Matthew - paging, optimiser Mark - proxies Following week (in our new room!!): FlyMine front end Andy From andy@flymine.org Thu Apr 17 16:18:30 2003 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 196B9i-0007Cw-00; Thu, 17 Apr 2003 16:18:30 +0100 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 196B9h-0007aQ-00; Thu, 17 Apr 2003 16:18:29 +0100 Date: Thu, 17 Apr 2003 16:18:29 +0100 From: Andrew Varley To: FlyMine Developers Cc: Rachel Lyne , Debashis Rana Message-ID: <20030417151829.GB14253@flymine.org> Mail-Followup-To: FlyMine Developers , Rachel Lyne , Debashis Rana Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.5.3i Subject: [flymine-dev] Next talk - Demystifying XML Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: The next talk in our series will be entitled "Demystifying XML", where Mark will explain XML/XSLT/XPath/etc,etc. Friday 25th April, 2pm, Part II room. From mark@flymine.org Tue Apr 22 11:03:19 2003 Received: from [192.168.128.104] (helo=localhost.localdomain ident=mark) by flymine.flymine.org with esmtp (Exim 4.12) id 197ucR-0004k0-00 for flymine-dev@flymine.org; Tue, 22 Apr 2003 11:03:19 +0100 From: Mark Woodbridge To: FlyMine Developers Content-Type: text/plain Content-Transfer-Encoding: 7bit X-Mailer: Ximian Evolution 1.0.5 Date: 22 Apr 2003 11:03:19 +0100 Message-Id: <1051005799.12281.86.camel@boromir> Mime-Version: 1.0 Subject: [flymine-dev] OJB Presentation Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Vaguely interesting Atlanta Java Users Group presentation on OJB including comparison of O/R mapping approaches and (crude) performance tests... http://cvs.apache.org/viewcvs.cgi/*checkout*/db-ojb/contrib/cavaness-ajug-slides.pdf?rev=HEAD From mark@flymine.org Tue Apr 22 11:45:05 2003 Received: from [192.168.128.104] (helo=localhost.localdomain ident=mark) by flymine.flymine.org with esmtp (Exim 4.12) id 197vGr-0004qh-00; Tue, 22 Apr 2003 11:45:05 +0100 Subject: Re: [flymine-dev] Next talk - Demystifying XML From: Mark Woodbridge To: flymine-dev@flymine.org Cc: Rachel Lyne , Debashis Rana In-Reply-To: <20030417151829.GB14253@flymine.org> References: <20030417151829.GB14253@flymine.org> Content-Type: text/plain Content-Transfer-Encoding: 7bit X-Mailer: Ximian Evolution 1.0.5 Date: 22 Apr 2003 11:45:05 +0100 Message-Id: <1051008305.12281.96.camel@boromir> Mime-Version: 1.0 Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: If anyone has any special requests regarding the content of my talk then let me know. I'm going to start from the beginning...but after that it will be what i think is interesting, unless anyone tells me otherwise. Especially if you've heard of any exciting XML-related biological things. mark. On Thu, 2003-04-17 at 16:18, Andrew Varley wrote: > The next talk in our series will be entitled "Demystifying XML", where > Mark will explain XML/XSLT/XPath/etc,etc. > > Friday 25th April, 2pm, Part II room. > > _______________________________________________ > flymine-dev mailing list > flymine-dev@flymine.org > http://mailman.flymine.org/listinfo/flymine-dev > From andy@flymine.org Fri Apr 25 10:18:02 2003 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 198zLG-0006GI-00; Fri, 25 Apr 2003 10:18:02 +0100 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 198zLG-0006MI-00; Fri, 25 Apr 2003 10:18:02 +0100 Date: Fri, 25 Apr 2003 10:18:02 +0100 From: Andrew Varley To: flymine-dev@flymine.org Cc: Rachel Lyne , Debashis Rana Message-ID: <20030425091802.GB23684@flymine.org> Mail-Followup-To: flymine-dev@flymine.org, Rachel Lyne , Debashis Rana References: <20030417151829.GB14253@flymine.org> <1051008305.12281.96.camel@boromir> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <1051008305.12281.96.camel@boromir> User-Agent: Mutt/1.5.3i Subject: [flymine-dev] RESCHEDULED - Demystifying XML Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Today's talk has had to be cancelled due to Mark being ill. Rescheduled for Friday 2nd March 2-3pm. On Tue, Apr 22, 2003 at 11:45:05AM +0100, Mark Woodbridge wrote: > If anyone has any special requests regarding the content of my talk then > let me know. I'm going to start from the beginning...but after that it > will be what i think is interesting, unless anyone tells me otherwise. > Especially if you've heard of any exciting XML-related biological > things. > > mark. > > On Thu, 2003-04-17 at 16:18, Andrew Varley wrote: > > The next talk in our series will be entitled "Demystifying XML", where > > Mark will explain XML/XSLT/XPath/etc,etc. > > > > Friday 25th April, 2pm, Part II room. > > > > _______________________________________________ > > flymine-dev mailing list > > flymine-dev@flymine.org > > http://mailman.flymine.org/listinfo/flymine-dev > > > > > > _______________________________________________ > flymine-dev mailing list > flymine-dev@flymine.org > http://mailman.flymine.org/listinfo/flymine-dev > From andy@flymine.org Fri Apr 25 10:23:12 2003 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 198zQG-0006I0-00; Fri, 25 Apr 2003 10:23:12 +0100 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 198zQG-0006NJ-00; Fri, 25 Apr 2003 10:23:12 +0100 Date: Fri, 25 Apr 2003 10:23:12 +0100 From: Andrew Varley To: flymine-dev@flymine.org, Rachel Lyne , Debashis Rana Subject: Re: [flymine-dev] RESCHEDULED - Demystifying XML Message-ID: <20030425092312.GD23684@flymine.org> Mail-Followup-To: flymine-dev@flymine.org, Rachel Lyne , Debashis Rana References: <20030417151829.GB14253@flymine.org> <1051008305.12281.96.camel@boromir> <20030425091802.GB23684@flymine.org> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <20030425091802.GB23684@flymine.org> User-Agent: Mutt/1.5.3i Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: On Fri, Apr 25, 2003 at 10:18:02AM +0100, Andrew Varley wrote: > Today's talk has had to be cancelled due to Mark being ill. > > Rescheduled for Friday 2nd March 2-3pm. The year is going too fast -- of couse I meant Friday 2nd May. From francois@flymine.org Fri Apr 25 13:38:38 2003 Received: from [192.168.128.101] (helo=flymine.org) by flymine.flymine.org with esmtp (Exim 4.12) id 1992TN-0006sR-00 for flymine-dev@flymine.org; Fri, 25 Apr 2003 13:38:38 +0100 Message-ID: <3EA92C4D.1070909@flymine.org> Date: Fri, 25 Apr 2003 13:38:37 +0100 From: Francois Guillier User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.3) Gecko/20030312 X-Accept-Language: en-us, en MIME-Version: 1.0 To: flymine-dev@flymine.org References: <20030417151829.GB14253@flymine.org> <1051008305.12281.96.camel@boromir> <20030425091802.GB23684@flymine.org> <20030425092312.GD23684@flymine.org> In-Reply-To: <20030425092312.GD23684@flymine.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Subject: [flymine-dev] PNG (again) Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: http://www.alistapart.com/stories/pngopacity/ François. ----------------- Systems Administrator Flymine project - Department of Genetics University of Cambridge - Downing Site - Cambridge - CB2 3EH - UK From andy@flymine.org Thu May 01 14:23:35 2003 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 19BE2B-0000eL-00 for flymine-dev@flymine.org; Thu, 01 May 2003 14:23:35 +0100 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 19BE2B-0003WJ-00 for ; Thu, 01 May 2003 14:23:35 +0100 Date: Thu, 1 May 2003 14:23:35 +0100 From: Andrew Varley To: FlyMine Developers Message-ID: <20030501132335.GB7421@flymine.org> Mail-Followup-To: FlyMine Developers Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.5.3i Subject: [flymine-dev] Initial webapp Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: The trial webapp is now checked in to cvs. To release you need to set a property in ~/build.properties.flymine: # Web application server webapp.serverlocation=yourname@yourmachine.flymine.org:webapps/query also create the above directory and type "ant release-webapp" You also need to make sure tomcat has a symbolic link from its webapps directory (/usr/share/tomcat4/webapps on Debian) to the directory mentioned above and is re-started (or release direct to the tomcat webapps directory). The webapp can then be accessed at http://localhost:8080/query. Pretty rudimentary at the moment but lots of scope for improvements..... The queries are SQL queries on the db.unittest (for the moment). Available in English and French, by setting browser preferences!! From andy@flymine.org Wed May 14 11:53:54 2003 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 19FttS-00077m-00 for flymine-dev@flymine.org; Wed, 14 May 2003 11:53:54 +0100 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 19FttS-00064Q-00 for ; Wed, 14 May 2003 11:53:54 +0100 Date: Wed, 14 May 2003 11:53:54 +0100 From: Andrew Varley To: FlyMine Developers Message-ID: <20030514105354.GB19052@flymine.org> Mail-Followup-To: FlyMine Developers Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.5.3i Subject: [flymine-dev] webapp deployment etc. Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: I've made a couple of changes to the webapp deployment. To take advantage of them, you need the tomcat manager application configured (install package tomcat4-admin and edit /usr/share/tomcat4/conf/tomcat-users.xml). Also remove any flymine webapp from being picked up by tomcat on startup (eg. if you have a link in /usr/share/tomcat4/webapps to the flymine webapp). The relevant ant tasks are: remove-webapp: Removes the webapp from the server test-webapp: Builds a testable version of the webapp, install to server, tests, removes from server (no testing actually done on the server yet, though). jar-testmodel: Builds a flymine-testmodel.jar release-webapp: Builds and releases the webapp to the server. The test classes will not be in there (except if you have not run the distclean target for a while). Used together, these targets will build either a testable webapp, or a production quality webapp, with no need to restart tomcat each time. The following need to be added to your personal build.properties: # Web application server webapp.serverlocation=user@mymachine.flymine.org:webapps/query webapp.filelocation=/home/user/webapps/query webapp.managerurl=http://mymachine.flymine.org:8180/manager webapp.path=/query webapp.manager=user webapp.password=secret Andy From andy@flymine.org Wed May 28 16:41:45 2003 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 19L33h-0002AI-00 for flymine-dev@flymine.org; Wed, 28 May 2003 16:41:45 +0100 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 19L33h-0006vy-00 for ; Wed, 28 May 2003 16:41:45 +0100 Date: Wed, 28 May 2003 16:41:45 +0100 From: Andrew Varley To: FlyMine Developers Message-ID: <20030528154145.GF15637@flymine.org> Mail-Followup-To: FlyMine Developers Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.5.4i Subject: [flymine-dev] Next tech-talk Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Tuesday 3rd June 2pm, FlyMine Room (postponed from this Friday). Francois will giving a talk about network firewalls. From mark@flymine.org Thu Jun 05 16:37:33 2003 Received: from [192.168.128.104] (helo=localhost.localdomain ident=mark) by flymine.flymine.org with esmtp (Exim 4.12) id 19Nwo0-0002fO-00 for flymine-dev@flymine.org; Thu, 05 Jun 2003 16:37:33 +0100 From: Mark Woodbridge To: flymine-dev@flymine.org Content-Type: text/plain Content-Transfer-Encoding: 7bit X-Mailer: Ximian Evolution 1.0.5 Date: 05 Jun 2003 16:37:32 +0100 Message-Id: <1054827452.24910.218.camel@boromir> Mime-Version: 1.0 Subject: [flymine-dev] flymine.properties Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: This time the "dataloader" and "osw" sections have changed to reflect modifications to the IntegrationWriter and ObjectStoreWriter factories. A complete set of properties is given below. Mark. db.unittest.datasource.class=org.postgresql.jdbc3.Jdbc3PoolingDataSource db.unittest.datasource.dataSourceName=db.unittest db.unittest.datasource.serverName=localhost db.unittest.datasource.databaseName=test db.unittest.datasource.user=mark db.unittest.datasource.password= db.unittest.datasource.maxConnections=10 db.unittest.driver=org.postgresql.Driver db.unittest.platform=PostgreSQL os.unittest.class=org.flymine.objectstore.ojb.ObjectStoreOjbImpl os.unittest.alias=ojb os.unittest.ojb.db=db.unittest os.unittest.model=testmodel os.query.max-time=1000000000 os.query.max-limit=10000 os.query.max-offset=10000 os.queue-len=100 osw.unittest.class=org.flymine.objectstore.ojb.ObjectStoreWriterOjbImpl osw.unittest.os=os.unittest integration.unittest.class=org.flymine.dataloader.IntegrationWriterSingleSourceImpl integration.unittest.osw=osw.unittest From richard@flymine.org Mon Jun 09 11:51:14 2003 Received: from [192.168.128.105] (helo=flymine.org ident=rns) by flymine.flymine.org with esmtp (Exim 4.12) id 19PKF8-0006Db-00 for flymine-dev@flymine.org; Mon, 09 Jun 2003 11:51:14 +0100 Message-ID: <3EE466A2.4080000@flymine.org> Date: Mon, 09 Jun 2003 11:51:14 +0100 From: Richard Smith User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.3) Gecko/20030312 X-Accept-Language: en MIME-Version: 1.0 To: flymine-dev Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Subject: [flymine-dev] build.properties.flymine Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Needs to have the following added to it, where username and password are saceserver login details. # Acedb acedb.user=username acedb.password=password acedb.host=localhost acedb.port=23100 From richard@flymine.org Mon Jun 09 11:56:53 2003 Received: from [192.168.128.105] (helo=flymine.org ident=rns) by flymine.flymine.org with esmtp (Exim 4.12) id 19PKKb-0006El-00 for flymine-dev@flymine.org; Mon, 09 Jun 2003 11:56:53 +0100 Message-ID: <3EE467F5.4090704@flymine.org> Date: Mon, 09 Jun 2003 11:56:53 +0100 From: Richard Smith User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.3) Gecko/20030312 X-Accept-Language: en MIME-Version: 1.0 To: flymine-dev Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Subject: [flymine-dev] flymine.properties Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: For the build-production ant target to work (creates flymine from ace model and inserts data) all unittest properties need to be duplicated replacing instances "unittest" and "testmodel" with "acedb". Example below. Richard. # acedb properties os.acedb.class=org.flymine.objectstore.ojb.ObjectStoreOjbImpl os.acedb.alias=ojb os.acedb.ojb.db=db.acedb os.acedb.model=acedb osw.acedb.class=org.flymine.objectstore.ojb.ObjectStoreWriterOjbImpl osw.acedb.os=os.acedb integration.acedb.class=org.flymine.dataloader.IntegrationWriterSingleSourceImpl integration.acedb.osw=osw.acedb db.acedb.datasource.class=org.postgresql.jdbc3.Jdbc3PoolingDataSource db.acedb.datasource.dataSourceName=db.acedb db.acedb.datasource.serverName=localhost db.acedb.datasource.databaseName=acedb db.acedb.datasource.user=user db.acedb.datasource.password=password db.acedb.datasource.maxConnections=10 db.acedb.driver=org.postgresql.Driver db.acedb.platform=PostgreSQL From richard@flymine.org Tue Jun 17 18:22:11 2003 Received: from [192.168.128.105] (helo=flymine.org ident=rns) by flymine.flymine.org with esmtp (Exim 4.12) id 19SK9r-0008Eq-00 for flymine-dev@flymine.org; Tue, 17 Jun 2003 18:22:11 +0100 Message-ID: <3EEF4E43.7040307@flymine.org> Date: Tue, 17 Jun 2003 18:22:11 +0100 From: Richard Smith User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.3) Gecko/20030312 X-Accept-Language: en MIME-Version: 1.0 To: flymine-dev Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Subject: [flymine-dev] Licenses Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: 1. I have checked in two files relating to licenses: LICENSE - details the FlyMine LGPL license. LICENSE.LIBS - contains license information for all jars distrbuted with FlyMine (i.e. those in the lib/ directory). This should be modified when any new jars are added to the distribution. 2. All java source files now have the following comment at the beginning, this needs to be added to any new java files before they are checked in: /* * Copyright (C) 2002-2003 FlyMine * * This code may be freely distributed and modified under the * terms of the GNU Lesser General Public Licence. This should * be distributed with the code. See the LICENSE file for more * information or http://www.gnu.org/copyleft/lesser.html. * */ Richard. From andy@flymine.org Wed Jul 16 12:36:40 2003 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 19ckaO-00077R-00 for flymine-dev@flymine.org; Wed, 16 Jul 2003 12:36:40 +0100 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 19ckaO-0004WW-00 for ; Wed, 16 Jul 2003 12:36:40 +0100 Date: Wed, 16 Jul 2003 12:36:40 +0100 From: Andrew Varley To: FlyMine Developers Message-ID: <20030716113640.GB13131@flymine.org> Mail-Followup-To: FlyMine Developers Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.5.4i Subject: [flymine-dev] more property changes Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: I've added and changed some of the webapp properties, now that we have 2 webapps, both being built as WARs. These are examples of the necessary properties # Web application webapp.serverlocation=user@appserver.mydomain.org:webapps webapp.warfileurl=jar:file:/home/user/webapps/flymine.war!/ webapp.managerurl=http://appserver.mydomain.org:8180/manager webapp.path=/query webapp.manager=username webapp.password=secret # Web service webservice.serverlocation=user@appserver.mydomain.org:webapps webservice.warfileurl=jar:file:/home/user/webapps/webservice.war!/ webservice.managerurl=http://appserver.mydomain.org:8180/manager webservice.path=/webservice webservice.manager=username webservice.password=secret From mark@flymine.org Thu Jul 17 11:44:39 2003 Received: from [192.168.128.104] (helo=flymine.org ident=mark) by flymine.flymine.org with esmtp (Exim 4.12) id 19d6Fb-00021w-00 for flymine-dev@flymine.org; Thu, 17 Jul 2003 11:44:39 +0100 Message-ID: <3F167E17.6050909@flymine.org> Date: Thu, 17 Jul 2003 11:44:39 +0100 From: Mark Woodbridge User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4b) Gecko/20030717 X-Accept-Language: en MIME-Version: 1.0 To: flymine-dev@flymine.org Subject: Re: [flymine-dev] more property changes References: <20030716113640.GB13131@flymine.org> In-Reply-To: <20030716113640.GB13131@flymine.org> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Should "webapp.path=/flymine"? My tomcat will only allow you to deploy to a directory of the same name as the .war... mark. Andrew Varley wrote: >I've added and changed some of the webapp properties, now that we have >2 webapps, both being built as WARs. > >These are examples of the necessary properties > ># Web application >webapp.serverlocation=user@appserver.mydomain.org:webapps >webapp.warfileurl=jar:file:/home/user/webapps/flymine.war!/ >webapp.managerurl=http://appserver.mydomain.org:8180/manager >webapp.path=/query >webapp.manager=username >webapp.password=secret > ># Web service >webservice.serverlocation=user@appserver.mydomain.org:webapps >webservice.warfileurl=jar:file:/home/user/webapps/webservice.war!/ >webservice.managerurl=http://appserver.mydomain.org:8180/manager >webservice.path=/webservice >webservice.manager=username >webservice.password=secret > >_______________________________________________ >flymine-dev mailing list >flymine-dev@flymine.org >http://mailman.flymine.org/listinfo/flymine-dev > > > From andy@flymine.org Fri Aug 08 16:49:27 2003 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 19l9Ud-0008NK-00; Fri, 08 Aug 2003 16:49:27 +0100 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 19l9Ud-00048f-00; Fri, 08 Aug 2003 16:49:27 +0100 Date: Fri, 8 Aug 2003 16:49:27 +0100 From: Andrew Varley To: FlyMine Developers , Rachel Lyne , Gos Micklem Message-ID: <20030808154927.GA15889@flymine.org> Mail-Followup-To: FlyMine Developers , Rachel Lyne , Gos Micklem Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.5.4i Subject: [flymine-dev] FlyMine "production" query site Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: There is now a site where we will keep the latest version of the FlyMine query web site. Currently it is using a test model and a set of test data, but this will evolve over the coming weeks. http://www.flymine.org/query At the moment, this is only accessible from within flymine.org and gen.cam.ac.uk. Gos + Rachel: Please keep trying it out and give us feedback. Andy From andy@flymine.org Tue Sep 02 13:23:52 2003 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 19uACO-0002Nj-00 for flymine-dev@flymine.org; Tue, 02 Sep 2003 13:23:52 +0100 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 19uACO-0005m1-00 for ; Tue, 02 Sep 2003 13:23:52 +0100 Date: Tue, 2 Sep 2003 13:23:52 +0100 From: Andrew Varley To: FlyMine Developers Message-ID: <20030902122352.GD18250@flymine.org> Mail-Followup-To: FlyMine Developers Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.5.4i Subject: [flymine-dev] default ObjectStore property Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: There is a new property "os.default" which specifies the default ObjectStore that should be used when no alias is given. There are now 2 methods of getting an ObjectStore: i) ObjectStoreFactory.getObjectStore(String alias) - get the ObjectStore with the given alias. ii) ObjectStoreFactory.getObjectStore() - get the default ObjectStore configured by the property os.default. This new property replaces the objectstoreserver.os property. Example of use: os.default=os.unittest Andy From mark@flymine.org Tue Sep 09 12:12:54 2003 Received: from [192.168.128.104] (helo=flymine.org ident=mark) by flymine.flymine.org with esmtp (Exim 4.12) id 19wgQY-0000pC-00 for flymine-dev@flymine.org; Tue, 09 Sep 2003 12:12:54 +0100 Message-ID: <3F5DB5B6.1060409@flymine.org> Date: Tue, 09 Sep 2003 12:12:54 +0100 From: Mark Woodbridge User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.5b) Gecko/20030903 Thunderbird/0.2 X-Accept-Language: en-us, en MIME-Version: 1.0 To: flymine-dev@flymine.org Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Subject: [flymine-dev] properties files Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: The properties for the webapps have changed. build.properties.flymine should look something like this (though your port number and username/password may be different): # Web application webapp.baseurl=http://localhost:8080 webapp.path=/query webapp.manager=manager webapp.password=manager # Web service webservice.baseurl=http://localhost:8080 webservice.path=/webservice webservice.manager=manager webservice.password=manager and flymine.properties needs an extra section for the webservice tests (again perhaps with a different port): os.unittest-client.class=org.flymine.objectstore.webservice.ObjectStoreClient os.unittest-client.alias=client os.unittest-client.model=testmodel os.unittest-client.client.url=http://localhost:8080/webservice/services/ObjectStore Mark. From andy@flymine.org Fri Sep 12 11:32:05 2003 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 19xlDh-0000Pq-00 for flymine-dev@flymine.org; Fri, 12 Sep 2003 11:32:05 +0100 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 19xlDh-0000UH-00 for ; Fri, 12 Sep 2003 11:32:05 +0100 Date: Fri, 12 Sep 2003 11:32:05 +0100 From: Andrew Varley To: FlyMine Developers Message-ID: <20030912103205.GA1853@flymine.org> Mail-Followup-To: FlyMine Developers Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.5.4i Subject: [flymine-dev] Automatic build results Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: The automatic build results (cruisecontrol) are now available outside (and inside!) the flymine.org domain at www.flymine.org/autobuild. An automatic build is run every time a file or group of files is checked into the CVS server. Cheers, Andy From matthew@flymine.org Fri Sep 26 10:36:21 2003 Received: from [192.168.128.103] (helo=aragorn.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 1A2p1R-0008B5-00 for flymine-dev@flymine.org; Fri, 26 Sep 2003 10:36:21 +0100 Received: from mnw21 (helo=localhost) by aragorn.flymine.org with local-esmtp (Exim 3.36 #1 (Debian)) id 1A2p1R-0008Fq-00 for ; Fri, 26 Sep 2003 10:36:21 +0100 Date: Fri, 26 Sep 2003 10:36:21 +0100 (BST) From: Matthew Wakeling X-X-Sender: mnw21@aragorn.flymine.org To: flymine-dev@flymine.org Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Subject: [flymine-dev] Testmodel Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: The testmodel is now no longer mastered by the testmodel.zargo file. Instead, it is mastered by the model/flymine/testmodel_model.xml file, in Flymine XML model format. The old testmodel.zargo file has been moved to model/uml/xmitest.zargo, and is the subject of a test that verifies that xmi to flymine model translation works. Matthew -- ... I am Hamlet of Borg: prepare to be, or not to be... From andy@flymine.org Fri Sep 26 16:06:34 2003 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 1A2uB0-0000X7-00 for flymine-dev@flymine.org; Fri, 26 Sep 2003 16:06:34 +0100 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 1A2uAy-0006yQ-00 for ; Fri, 26 Sep 2003 16:06:32 +0100 Date: Fri, 26 Sep 2003 16:06:32 +0100 From: Andrew Varley To: flymine-dev@flymine.org Subject: Re: [flymine-dev] Testmodel Message-ID: <20030926150632.GE23521@flymine.org> Mail-Followup-To: flymine-dev@flymine.org References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: User-Agent: Mutt/1.5.4i Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: I've slightly re-organised the model directory. It now has subdirectories corresponding to the model name, rather than the type of model. This is because the webapp can incorporate model-specific pages and configuration. The file Matthew refers to is now in model/testmodel/ and the original .zargo file in model/xmitest/. Cheers, Andy On Fri, Sep 26, 2003 at 10:36:21AM +0100, Matthew Wakeling wrote: > > The testmodel is now no longer mastered by the testmodel.zargo file. > Instead, it is mastered by the model/flymine/testmodel_model.xml file, in > Flymine XML model format. > > The old testmodel.zargo file has been moved to model/uml/xmitest.zargo, > and is the subject of a test that verifies that xmi to flymine model > translation works. > > Matthew > From andy@flymine.org Tue Oct 14 17:06:14 2003 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 1A9Rgc-0001fs-00 for flymine-dev@flymine.org; Tue, 14 Oct 2003 17:06:14 +0100 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 1A9Rgc-0006Ut-00 for ; Tue, 14 Oct 2003 17:06:14 +0100 Date: Tue, 14 Oct 2003 17:06:14 +0100 From: Andrew Varley To: FlyMine Developers Message-ID: <20031014160614.GC17603@flymine.org> Mail-Followup-To: FlyMine Developers Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.5.4i Subject: [flymine-dev] CVS branch Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: We are phasing out the use of OJB as the backend for the FlyMine ObjectStore. The CVS tree has been branched (OJB_END_OF_LINE branch) to enable bug fixes to take place. The trunk is being used for development of the new backend (ObjectStoreFlyMineImpl), which will have support for multiple inheritence and other nifty features that are just not possible with OJB. Therefore, for the next few weeks the main CVS trunk will not work as a fully functioning system. Andy From andy@flymine.org Mon Nov 17 17:35:28 2003 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 1ALnHc-0004UK-00 for flymine-dev@flymine.org; Mon, 17 Nov 2003 17:35:28 +0000 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 1ALnHc-0004Af-00 for ; Mon, 17 Nov 2003 17:35:28 +0000 Date: Mon, 17 Nov 2003 17:35:28 +0000 From: Andrew Varley To: flymine-dev@flymine.org Message-ID: <20031117173528.GF8392@flymine.org> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.5.4i Subject: [flymine-dev] Metadata Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: > On Mon, Nov 17, 2003, Mullen-Schultz, Gary L. wrote: > > - How easy/difficult would you think pulling the metadata code out > and using in another application? I bascially need to maintain > metadata on classes, fields and relationships. It should be fairly easy. It's all in the org.flymine.metadata package, plus the XML parsing of the metadata XML representation in the org.flymine.modelproduction.xml package. All of this gets into the flymine.jar file built using the command "ant jar". > - Have you any plans to do any xDoclet metadata definition work? We have no plans to do this, although I can't think of any reason why it wouldn't work. The reason we are not planning to do this is that for our own use, we generate the metadata XML format from external sources and auto-generate Java classes (and database schema etc) from that. Of course if you wanted to do it, you would always be welcome to contribute it back....!!!! Best wishes, Andy From mark@flymine.org Wed Nov 26 15:46:18 2003 Received: from [192.168.128.104] (helo=flymine.org ident=mark) by flymine.flymine.org with esmtp (Exim 4.12) id 1AP1ru-0000oY-00 for flymine-dev@flymine.org; Wed, 26 Nov 2003 15:46:18 +0000 Message-ID: <3FC4CAC9.7060905@flymine.org> Date: Wed, 26 Nov 2003 15:46:17 +0000 From: Mark Woodbridge User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.6b) Gecko/20031112 Thunderbird/0.4a X-Accept-Language: en-us, en MIME-Version: 1.0 To: flymine-dev@flymine.org Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Subject: [flymine-dev] flymine.properties Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: The new datatracking tests require the following additions to your flymine.properties file: os.datatrackingtest.class=org.flymine.objectstore.flymine.ObjectStoreFlyMineImpl os.datatrackingtest.alias=flymine os.datatrackingtest.flymine.db=db.unittest os.datatrackingtest.model=datatracking osw.datatrackingtest.class=org.flymine.objectstore.flymine.ObjectStoreWriterFlyMineImpl osw.datatrackingtest.os=os.datatrackingtest Mark. From mark@flymine.org Wed Jan 21 11:08:55 2004 Received: from [192.168.128.104] (helo=flymine.org ident=mark) by flymine.flymine.org with esmtp (Exim 4.12) id 1AjGEB-0005Pc-00 for flymine-dev@flymine.org; Wed, 21 Jan 2004 11:08:55 +0000 Message-ID: <400E5DC1.8080307@flymine.org> Date: Wed, 21 Jan 2004 11:08:49 +0000 From: Mark Woodbridge User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.6b) Gecko/20031205 Thunderbird/0.4 X-Accept-Language: en-us, en MIME-Version: 1.0 To: flymine-dev@flymine.org Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Subject: [flymine-dev] Common unit test properties Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: I have put a properties file (default.flymine.properties) in resources/test. This contains the properties that should (at the moment) be present in everyone's flymine.properties in order to run the unit tests. It is copied onto the classpath when the tests are run and loaded by PropertiesUtil before your own flymine.properties so you can subsequently override the defaults. You don't need to change your properties at all - everything will still work. But all you really need in your own file (apart from the various datasource properties) is something like: os.unittest-client.alias=impl os.unittest-client.impl.url=http://localhost:8080/webservice/services/ObjectStore db.unittest.datasource.serverName=localhost db.unittest.datasource.databaseName=test db.unittest.datasource.user=mark db.unittest.datasource.password=password db.datatrackingtest.datasource.serverName=localhost db.datatrackingtest.datasource.databaseName=datatrackingtest db.datatrackingtest.datasource.user=mark db.datatrackingtest.datasource.password=password because these are only ones for which defaults aren't provided. Mark. From matthew@flymine.org Tue Feb 24 16:17:22 2004 Received: from [192.168.128.103] (helo=aragorn.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 1AvfFK-0002f9-00 for flymine-dev@flymine.org; Tue, 24 Feb 2004 16:17:22 +0000 Received: from mnw21 (helo=localhost) by aragorn.flymine.org with local-esmtp (Exim 3.36 #1 (Debian)) id 1AvfFK-0004RG-00 for ; Tue, 24 Feb 2004 16:17:22 +0000 Date: Tue, 24 Feb 2004 16:17:21 +0000 (GMT) From: Matthew Wakeling X-X-Sender: mnw21@aragorn.flymine.org To: flymine-dev@flymine.org Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Subject: [flymine-dev] New properties for ObjectStoreFastCollectionsImpl Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: This is a new objectstore, and its properties are as follows: os.objectstoreName.class=org.flymine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl os.objectstoreName.alias=flymine os.objectstoreName.model= os.objectstoreName.flymine.os=os.subObjectstoreName For example, in my flymine.properties I have the following: osw.chado-items.class=org.flymine.objectstore.flymine.ObjectStoreWriterFlyMineImpl osw.chado-items.os=os.chado-items-slow os.chado-items-slow.class=org.flymine.objectstore.flymine.ObjectStoreFlyMineImpl os.chado-items-slow.alias=flymine os.chado-items-slow.flymine.db=db.chado-items os.chado-items-slow.model=fulldata os.chado-items.class=org.flymine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl os.chado-items.alias=flymine os.chado-items.model=fulldata os.chado-items.flymine.os=os.chado-items-slow Matthew -- I wouldn't be so paranoid if you weren't all out to get me!! From andy@flymine.org Mon Mar 29 18:10:57 2004 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 1B80Hp-0004cg-00 for flymine-dev@flymine.org; Mon, 29 Mar 2004 18:10:57 +0100 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 1B80Hp-0003Xx-00 for ; Mon, 29 Mar 2004 18:10:57 +0100 Date: Mon, 29 Mar 2004 18:10:57 +0100 From: Andrew Varley To: flymine-dev@flymine.org Message-ID: <20040329171056.GR16313@flymine.org> Mail-Followup-To: flymine-dev@flymine.org Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.5.4i Subject: [flymine-dev] Code split Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Tomorrow (Tuesday 30th April) we will be splitting the FlyMine code into two parts - the core system and the genomic/fly specific parts. The CVS repository should be treated as vunerable all day. It would be best to check in all you can by 10am tomorrow as the repository structure will change significantly after that. Cheers, Andy From matthew@flymine.org Mon Mar 29 21:40:49 2004 Received: from [192.168.128.103] (helo=aragorn.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 1B83Yv-000594-00 for flymine-dev@flymine.org; Mon, 29 Mar 2004 21:40:49 +0100 Received: from mnw21 (helo=localhost) by aragorn.flymine.org with local-esmtp (Exim 3.36 #1 (Debian)) id 1B83Yp-0007tj-00 for ; Mon, 29 Mar 2004 21:40:43 +0100 Date: Mon, 29 Mar 2004 21:40:43 +0100 (BST) From: Matthew Wakeling X-X-Sender: mnw21@aragorn.flymine.org To: flymine-dev@flymine.org Subject: Re: [flymine-dev] Code split In-Reply-To: <20040329171056.GR16313@flymine.org> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: On Mon, 29 Mar 2004, Andrew Varley wrote: > Tomorrow (Tuesday 30th April) we will be splitting the FlyMine code > into two parts - the core system and the genomic/fly specific > parts. The CVS repository should be treated as vunerable all day. It > would be best to check in all you can by 10am tomorrow as the > repository structure will change significantly after that. I trust that we will be using CVS changes that preserve the history of the repository correctly. Matthew -- Now you see why I said that the first seven minutes of this section will have you looking for the nearest brick wall to beat your head against. This is why I do it at the end of the lecture - so I can run. -- Computer Science lecturer From francois@flymine.org Mon Mar 29 21:49:10 2004 Received: from gold.csi.cam.ac.uk ([131.111.8.12]) by flymine.flymine.org with esmtp (Exim 4.12) id 1B83h0-0005Aj-00 for flymine-dev@flymine.org; Mon, 29 Mar 2004 21:49:10 +0100 Received: from [62.253.162.48] (helo=mta08-svc.ntlworld.com) by gold.csi.cam.ac.uk with esmtp (Exim 4.20) id 1B83gk-0000Ku-3g for flymine-dev@flymine.org; Mon, 29 Mar 2004 21:48:54 +0100 Received: from avalon.guillier.org ([81.104.196.195]) by mta08-svc.ntlworld.com (InterMail vM.4.01.03.37 201-229-121-137-20020806) with ESMTP id <20040329204848.KNRM5004.mta08-svc.ntlworld.com@avalon.guillier.org> for ; Mon, 29 Mar 2004 21:48:48 +0100 Received: from localhost.localdomain ([127.0.0.1]) by avalon.guillier.org with esmtp (Exim 4.22) id 1B83gc-0000fc-No for flymine-dev@flymine.org; Mon, 29 Mar 2004 21:48:46 +0100 Received: from flymine.org (localhost.localdomain [127.0.0.1]) by localhost.localdomain (AvMailGate-2.0.1.10) id 02575-1DCF5BFB; Mon, 29 Mar 2004 21:47:47 +0100 Message-ID: <40688B73.80207@flymine.org> Date: Mon, 29 Mar 2004 21:47:47 +0100 From: Francois GUILLIER User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4.1) Gecko/20031008 X-Accept-Language: en, en-gb, fr, en-us MIME-Version: 1.0 To: flymine-dev@flymine.org Subject: Re: [flymine-dev] Code split References: In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-AntiVirus: checked by AntiVir MailGate (version: 2.0.1.10; AVE: 6.24.0.7; VDF: 6.24.0.75; host: avalon) X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: scanned, SpamAssassin (score=-2.1, EMAIL_ATTRIBUTION -0.50, IN_REP_TO -0.50, REFERENCES -0.50, REPLY_WITH_QUOTES -0.50, USER_AGENT_MOZILLA_UA 0.00, X_ACCEPT_LANG -0.10) Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Matthew Wakeling wrote: >On Mon, 29 Mar 2004, Andrew Varley wrote: > > >>Tomorrow (Tuesday 30th April) we will be splitting the FlyMine code >>into two parts - the core system and the genomic/fly specific >>parts. The CVS repository should be treated as vunerable all day. It >>would be best to check in all you can by 10am tomorrow as the >>repository structure will change significantly after that. >> >> > >I trust that we will be using CVS changes that preserve the history of the >repository correctly. > The history probably but AFAIK the name of the files will be changed as the classnames will change. So dealing with a non-checked file after that will mean: - Identify the right directory/repository then The File - Check the history - (Probably) check it out - Diff/Patch the new file - Committing the change... François. ----------------- Systems Administrator Flymine project - Department of Genetics University of Cambridge - Downing Site - Cambridge - CB2 3EH - UK From matthew@flymine.org Mon Mar 29 22:08:51 2004 Received: from [192.168.128.103] (helo=aragorn.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 1B8403-0005Dc-00 for flymine-dev@flymine.org; Mon, 29 Mar 2004 22:08:51 +0100 Received: from mnw21 (helo=localhost) by aragorn.flymine.org with local-esmtp (Exim 3.36 #1 (Debian)) id 1B8402-00081o-00 for ; Mon, 29 Mar 2004 22:08:50 +0100 Date: Mon, 29 Mar 2004 22:08:50 +0100 (BST) From: Matthew Wakeling X-X-Sender: mnw21@aragorn.flymine.org To: flymine-dev@flymine.org Subject: Re: [flymine-dev] Code split In-Reply-To: <40688B73.80207@flymine.org> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: > >I trust that we will be using CVS changes that preserve the history of the > >repository correctly. > > > The history probably but AFAIK the name of the files will be changed as > the classnames > will change. So dealing with a non-checked file after that will mean: > - Identify the right directory/repository then The File > - Check the history > - (Probably) check it out > - Diff/Patch the new file > - Committing the change... What I mean is: will one be able to call "cvs update -D " and get a valid working directory? This will involve at least 1. Copying file from old location to new 2. Modifying the file to make it work again 3. Removing the old file 4. CVS removing the old file 5. CVS adding the new file 6. CVS committing the whole lot Alternatively, stages 1 and 4 can be replaced with a cvsmove operation if you really wish, but that is messy and unreliable. Matthew -- Note: some countries impose serious penalties for a conspiracy to overthrow the political system. THIS DOES NOT FIX THE VULNERABILITY. From francois@flymine.org Mon Mar 29 22:29:03 2004 Received: from brown.csi.cam.ac.uk ([131.111.8.14]) by flymine.flymine.org with esmtp (Exim 4.12) id 1B84Jb-0005GM-00 for flymine-dev@flymine.org; Mon, 29 Mar 2004 22:29:03 +0100 Received: from [62.253.162.48] (helo=mta08-svc.ntlworld.com) by brown.csi.cam.ac.uk with esmtp (Exim 4.20) id 1B84JI-0002dY-Es for flymine-dev@flymine.org; Mon, 29 Mar 2004 22:28:44 +0100 Received: from avalon.guillier.org ([81.104.196.195]) by mta08-svc.ntlworld.com (InterMail vM.4.01.03.37 201-229-121-137-20020806) with ESMTP id <20040329212844.NSJP5004.mta08-svc.ntlworld.com@avalon.guillier.org> for ; Mon, 29 Mar 2004 22:28:44 +0100 Received: from localhost.localdomain ([127.0.0.1]) by avalon.guillier.org with esmtp (Exim 4.22) id 1B84JG-0000rT-9W for flymine-dev@flymine.org; Mon, 29 Mar 2004 22:28:42 +0100 Received: from flymine.org (localhost.localdomain [127.0.0.1]) by localhost.localdomain (AvMailGate-2.0.1.10) id 03310-0B800382; Mon, 29 Mar 2004 22:28:28 +0100 Message-ID: <406894FB.8030901@flymine.org> Date: Mon, 29 Mar 2004 22:28:27 +0100 From: Francois GUILLIER User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4.1) Gecko/20031008 X-Accept-Language: en, en-gb, fr, en-us MIME-Version: 1.0 To: flymine-dev@flymine.org Subject: Re: [flymine-dev] Code split References: In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-AntiVirus: checked by AntiVir MailGate (version: 2.0.1.10; AVE: 6.24.0.7; VDF: 6.24.0.75; host: avalon) X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: scanned, SpamAssassin (score=-1.1, IN_REP_TO -0.50, REFERENCES -0.50, USER_AGENT_MOZILLA_UA 0.00, X_ACCEPT_LANG -0.10) Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: >What I mean is: will one be able to call >"cvs update -D " and get a valid working directory? > Good question... probably not... (maybe with a tag?) subversion has been conceived to deal with copy/move etc... cvs not really... I don't know how good is Dr Andy's script for that... François. ----------------- Systems Administrator Flymine project - Department of Genetics University of Cambridge - Downing Site - Cambridge - CB2 3EH - UK From richard@flymine.org Tue Apr 06 15:55:23 2004 Received: from [192.168.128.105] (helo=flymine.org ident=rns) by flymine.flymine.org with esmtp (Exim 4.12) id 1BArz1-0004YR-00 for flymine-dev@flymine.org; Tue, 06 Apr 2004 15:55:23 +0100 Message-ID: <4072C4DA.308@flymine.org> Date: Tue, 06 Apr 2004 15:55:22 +0100 From: Richard Smith User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.5) Gecko/20031007 X-Accept-Language: en MIME-Version: 1.0 To: flymine-dev@flymine.org Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Subject: [flymine-dev] intermine/flymine lib Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: I have checked in a change to the InterMine jar target that adds all essential library jars to a second jar file - intermine-all.jar. This is now referenced by FlyMine allowing us to avoid duplicating these jars in the FlyMine lib directory. Richard. From matthew@flymine.org Mon Apr 19 17:12:19 2004 Received: from [192.168.128.103] (helo=aragorn.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 1BFbNb-0004FZ-00 for flymine-dev@flymine.org; Mon, 19 Apr 2004 17:12:19 +0100 Received: from mnw21 (helo=localhost) by aragorn.flymine.org with local-esmtp (Exim 3.36 #1 (Debian)) id 1BFbNa-0001ag-00 for ; Mon, 19 Apr 2004 17:12:18 +0100 Date: Mon, 19 Apr 2004 17:12:18 +0100 (BST) From: Matthew Wakeling X-X-Sender: mnw21@aragorn.flymine.org To: flymine-dev@flymine.org Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Subject: [flymine-dev] Properties changes Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: The format for the properties for data tracking has changed. In fact, the DataTrackerFactory no longer exists. All datatracker properties have been moved into the IntegrationWriterDataTrackingImpl properties. So, where once before you had: --------- BEGIN old integration.unittestmulti.class=org.intermine.dataloader.IntegrationWriterDataTrackingImpl integration.unittestmulti.osw=osw.unittest integration.unittestmulti.datatracker=dt.datatrackingtest dt.datatrackingtest.db=db.unittest dt.datatrackingtest.maxSize=30 dt.datatrackingtest.commitSize=10 --------- END old you should now have --------- BEGIN new integration.unittestmulti.class=org.intermine.dataloader.IntegrationWriterDataTrackingImpl integration.unittestmulti.osw=osw.unittest integration.unittestmulti.datatrackerMaxSize=30 integration.unittestmulti.datatrackerCommitSize=10 --------- END new Matthew -- I would like to think that in this day and age people would know better than to open executables in an e-mail. I'd also like to be able to flap my arms and fly to the moon. -- Tim Mullen From matthew@flymine.org Tue Apr 20 11:42:39 2004 Received: from [192.168.128.103] (helo=aragorn.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 1BFsi7-0006Xw-00 for flymine-dev@flymine.org; Tue, 20 Apr 2004 11:42:39 +0100 Received: from mnw21 (helo=localhost) by aragorn.flymine.org with local-esmtp (Exim 3.36 #1 (Debian)) id 1BFsi7-0006af-00 for ; Tue, 20 Apr 2004 11:42:39 +0100 Date: Tue, 20 Apr 2004 11:42:39 +0100 (BST) From: Matthew Wakeling X-X-Sender: mnw21@aragorn.flymine.org To: flymine-dev@flymine.org Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Subject: [flymine-dev] Postgres on Gollum Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: I have set up an alternative location for databases to be stored on Gollum (for performance reasons). Until recently, there were three separate /export/db directories, each mounted on a separate RAID system, each with a database data directory. These were: /export/db1/postgres - OLD postgres 7.3 on Gollum (now defunct) /export/db2/postgres - NEW postgres 7.4 on Gollum /export/db3/postgres - postgres 7.4 on Smeagol Now, it is possible to tell postgres to put database data in a different location with gollum, when creating a database with "createdb". This is good, because it allows us to have gollum accessing several independent RAID arrays, allowing independent database performance. The new location I have set up is: /export/db1/gollum_second_location - NEW postgres 7.4 on Gollum To create a new database in the alternative location, add "-D PGDATA2" to the "createdb" command, like so: createdb -D PGDATA2 -U flymine -h gollum chado-src-items As such, I have placed chado-src-items on Gollum in the alternative location. Francois: you may wish to look at the change I made to /sbin/init.d/postgresql on Gollum, and possibly do this properly (ie allow both Smeagol and Gollum to access all three/four RAID arrays). Matthew -- Psychotics are consistently inconsistent. The essence of sanity is to be inconsistently inconsistent. From francois@flymine.org Tue Apr 20 15:33:38 2004 Received: from plum.csi.cam.ac.uk ([131.111.8.3]) by flymine.flymine.org with esmtp (Exim 4.12) id 1BFwJe-0007Dv-00 for flymine-dev@flymine.org; Tue, 20 Apr 2004 15:33:38 +0100 Received: from [62.253.162.48] (helo=mta08-svc.ntlworld.com) by plum.csi.cam.ac.uk with esmtp (Exim 4.20) id 1BFwJI-0006xx-VY for flymine-dev@flymine.org; Tue, 20 Apr 2004 15:33:16 +0100 Received: from avalon.guillier.org ([81.104.196.195]) by mta08-svc.ntlworld.com (InterMail vM.4.01.03.37 201-229-121-137-20020806) with ESMTP id <20040420143317.VALT4673.mta08-svc.ntlworld.com@avalon.guillier.org> for ; Tue, 20 Apr 2004 15:33:17 +0100 Received: from localhost.localdomain ([127.0.0.1]) by avalon.guillier.org with esmtp (Exim 4.22) id 1BFwIl-0004Ge-Dm for flymine-dev@flymine.org; Tue, 20 Apr 2004 15:32:43 +0100 Received: from flymine.org (localhost.localdomain [127.0.0.1]) by localhost.localdomain (AvMailGate-2.0.1.10) id 16403-18625710; Tue, 20 Apr 2004 15:32:43 +0100 Message-ID: <4085348B.3030308@flymine.org> Date: Tue, 20 Apr 2004 15:32:43 +0100 From: Francois GUILLIER User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4.1) Gecko/20031008 X-Accept-Language: en, en-gb, fr, en-us MIME-Version: 1.0 To: flymine-dev@flymine.org Subject: Re: [flymine-dev] Postgres on Gollum References: In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-AntiVirus: checked by AntiVir MailGate (version: 2.0.1.10; AVE: 6.25.0.2; VDF: 6.25.0.10; host: avalon) X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: scanned, SpamAssassin (score=-1.1, IN_REP_TO -0.50, REFERENCES -0.50, USER_AGENT_MOZILLA_UA 0.00, X_ACCEPT_LANG -0.10) Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: >Francois: you may wish to look at the change I made to >/sbin/init.d/postgresql on Gollum, > >and possibly do this properly (ie allow >both Smeagol and Gollum to access all three/four RAID arrays). > What do you mean? Smeagol & Gollum see the same thing. (Only the /sbin/init.d/postgresql are different). François. ----------------- Systems Administrator Flymine project - Department of Genetics University of Cambridge - Downing Site - Cambridge - CB2 3EH - UK From matthew@flymine.org Tue Apr 20 15:47:00 2004 Received: from [192.168.128.103] (helo=aragorn.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 1BFwWa-0007GQ-00 for flymine-dev@flymine.org; Tue, 20 Apr 2004 15:47:00 +0100 Received: from mnw21 (helo=localhost) by aragorn.flymine.org with local-esmtp (Exim 3.36 #1 (Debian)) id 1BFwWZ-0007o0-00 for ; Tue, 20 Apr 2004 15:46:59 +0100 Date: Tue, 20 Apr 2004 15:46:59 +0100 (BST) From: Matthew Wakeling X-X-Sender: mnw21@aragorn.flymine.org To: flymine-dev@flymine.org Subject: Re: [flymine-dev] Postgres on Gollum In-Reply-To: <4085348B.3030308@flymine.org> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: > >Francois: you may wish to look at the change I made to > >/sbin/init.d/postgresql on Gollum, > > >and possibly do this properly (ie allow > >both Smeagol and Gollum to access all three/four RAID arrays). > > What do you mean? Smeagol & Gollum see the same thing. > (Only the /sbin/init.d/postgresql are different). Yeah. /sbin/init.d/postgresql contains an environment variable at the top called PGDATA, which points to a directory where postgres stores its main "location". On gollum, I have defined (and exported) another environment variable called PGDATA2, pointing to a directory mounted from a different RAID array. When one creates a new database on Gollum, one can tell postgres on Gollum to use the alternative location defined by that environment variable - hence postgres on Gollum can use two different RAID arrays. What I mean is for us to set up postgres on both Gollum and Smeagol so that they can both use all of the available RAID arrays for database storage. Matthew -- I've run DOOM more in the last few days than I have the last few months. I just love debugging ;-) -- Linus Torvalds From matthew@flymine.org Wed May 05 14:57:02 2004 Received: from [192.168.128.103] (helo=aragorn.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 1BLMtS-0006E3-00 for flymine-dev@flymine.org; Wed, 05 May 2004 14:57:02 +0100 Received: from mnw21 (helo=localhost) by aragorn.flymine.org with local-esmtp (Exim 3.36 #1 (Debian)) id 1BLMtR-0007wL-00 for ; Wed, 05 May 2004 14:57:01 +0100 Date: Wed, 5 May 2004 14:57:01 +0100 (BST) From: Matthew Wakeling X-X-Sender: mnw21@aragorn.flymine.org To: flymine-dev@flymine.org Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Subject: [flymine-dev] New property, and new service class Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: There is a new property for ObjectStoreInterMineImpl, called "logfile". Set it to the name of a file, and the objectstore will log all execute operations that are explained to that file. For example: os.unittest.class=org.intermine.objectstore.intermine.ObjectStoreInterMineImpl os.unittest.alias=intermine os.unittest.intermine.db=db.unittest os.unittest.intermine.logfile=executeLog os.unittest.model=testmodel In addition, there is a new service class for handling all shutdown-related operations. It is org.intermine.util.ShutdownHook, and you can register an object to be cleanly shut down with ShutdownHook.registerObject(Object). The hook will handle java.io.Writer, java.io.OutputStream, and ObjectStoreWriterInterMineImpl. You can wrap your objects in WeakReference if you wish. It is useful for if you wish to have a log being written by a BufferedWriter or BufferedOutputStream, but still wish the buffer to be flushed on exit. Matthew -- No trees were killed in the sending of this message. However a large number of electrons were terribly inconvenienced. From richard@flymine.org Thu May 27 17:21:44 2004 Received: from [192.168.128.105] (helo=flymine.org ident=rns) by flymine.flymine.org with esmtp (Exim 4.12) id 1BTNdY-0006j6-00 for flymine-dev@flymine.org; Thu, 27 May 2004 17:21:44 +0100 Message-ID: <40B61597.6040705@flymine.org> Date: Thu, 27 May 2004 17:21:43 +0100 From: Richard Smith User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.5) Gecko/20031007 X-Accept-Language: en MIME-Version: 1.0 To: flymine-dev Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Subject: [flymine-dev] FlyMine default.intermine.properties Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: We have checked in a common default.intermine.properties (in resources/runtime/) file for the FlyMine build. This includes definitions of all ObjectStores mentioned in flymine build.xml. For each database one only needs to define the four properties (but there is only need to define these if intending to build a FlyMine database: db.some_database.datasource.serverName=server_name db.some_database.datasource.databaseName=db_name db.some_database.datasource.user=user db.some_database.datasource.password=password No ObjectStore definitions should be required for the current targets. There is also a default.intermine.properties in resouces/test/ for flymine tests. I have added a database called genomic-test to this. For all tests to work the following are required personal intermine.properties: db.genomic-test.datasource.serverName=server_name db.genomic-test.datasource.databaseName=db_name db.genomic-test.datasource.user=user db.genomic-test.datasource.password=password Cheers, Richard. From matthew@flymine.org Wed Jun 02 12:55:11 2004 Received: from [192.168.128.103] (helo=aragorn.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 1BVUKt-0008Ou-00 for flymine-dev@flymine.org; Wed, 02 Jun 2004 12:55:11 +0100 Received: from mnw21 (helo=localhost) by aragorn.flymine.org with local-esmtp (Exim 3.36 #1 (Debian)) id 1BVUKt-0007tt-00 for ; Wed, 02 Jun 2004 12:55:11 +0100 Date: Wed, 2 Jun 2004 12:55:11 +0100 (BST) From: Matthew Wakeling X-X-Sender: mnw21@aragorn.flymine.org To: flymine-dev@flymine.org Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Subject: [flymine-dev] New properties required, and other changes Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: I am just about to check in my change that allows truncated classes in an ObjectStore, which will allow us to support models with many classes. However, in order to do this, the build-db task has been changed: Before, one would write an ANT target like the following to perform the build-db stuff: ------------- BEGIN old target ------------- END old target A new property needs to be passed to build-model.xml, like this: ------------- BEGIN new target ------------- END new target In addition, new properties are required in intermine.properties in order to support new tests for the truncated class. A whole new objectstore called "os.truncunittest" is required, and it should have properties like this: ------------- BEGIN new properties db.truncunittest.datasource.class=org.postgresql.jdbc3.Jdbc3PoolingDataSource db.truncunittest.datasource.dataSourceName=db.truncunittest db.truncunittest.datasource.serverName= db.truncunittest.datasource.databaseName=trunctest db.truncunittest.datasource.user= db.truncunittest.datasource.password= db.truncunittest.datasource.maxConnections=10 db.truncunittest.driver=org.postgresql.Driver db.truncunittest.platform=PostgreSQL os.truncunittest.class=org.intermine.objectstore.intermine.ObjectStoreInterMineImpl os.truncunittest.alias=intermine os.truncunittest.intermine.db=db.truncunittest os.truncunittest.intermine.logfile=executeLog os.truncunittest.intermine.truncatedClasses=org.intermine.model.InterMineObject os.truncunittest.model=testmodel osw.truncunittest.class=org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl osw.truncunittest.os=os.truncunittest osw.truncunittest.batchWriter=org.intermine.sql.writebatch.BatchWriterSimpleImpl ------------- END new properties The new objectstore particularly needs to have its own database separate from db.unittest. It is also recommended that os.unittest has a separate database from os.fulldatatest. I have set this up in the default properties, so you should only need to add the following to your intermine.properties: ------------- BEGIN new properties db.truncunittest.datasource.servername= db.truncunittest.datasource.user= db.truncunittest.datasource.password= db.fulldatatest.datasource.servername= db.fulldatatest.datasource.user= db.fulldatatest.datasource.password= ------------- END new properties You will also need to createdb trunctest and fulldatatest. Matthew -- "Argue not with dragons, for thou art crunchy and go well with brie." -- Unknown From andy@flymine.org Wed Jun 02 16:26:33 2004 Received: from [192.168.128.102] (helo=galadriel.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 1BVXdR-0000ZU-00 for flymine-dev@flymine.org; Wed, 02 Jun 2004 16:26:33 +0100 Received: from andy by galadriel.flymine.org with local (Exim 3.36 #1 (Debian)) id 1BVXdP-0002Jz-00 for ; Wed, 02 Jun 2004 16:26:31 +0100 Date: Wed, 2 Jun 2004 16:26:31 +0100 From: Andrew Varley To: flymine-dev@flymine.org Subject: Re: [flymine-dev] New properties required, and other changes Message-ID: <20040602152631.GC8395@flymine.org> Mail-Followup-To: flymine-dev@flymine.org References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: User-Agent: Mutt/1.5.4i Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: On Wed, Jun 02, 2004 at 12:55:11PM +0100, Matthew Wakeling wrote: > > > > db.truncunittest.datasource.servername= I think this needs to be: db.truncunittest.datasource.serverName= ie. serverName with a capital 'N' From mark@flymine.org Fri Jun 04 16:44:33 2004 Received: from host104 ([192.168.128.104] ident=mark) by flymine.flymine.org with esmtp (Exim 4.12) id 1BWGrw-0002m4-00 for flymine-dev@flymine.org; Fri, 04 Jun 2004 16:44:32 +0100 Message-ID: <40C098E0.3020403@flymine.org> Date: Fri, 04 Jun 2004 16:44:32 +0100 From: Mark Woodbridge User-Agent: Mozilla Thunderbird 0.6 (X11/20040502) X-Accept-Language: en-us, en MIME-Version: 1.0 To: flymine-dev@flymine.org Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Subject: [flymine-dev] Properties Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: An intermine.properties file sufficient to perform a successful fulltest can be found below. Obviously you need to createdb for each database. Properties aren't added to jars anymore. --- os.query.max-time=100000000 os.query.max-limit=100000 os.query.max-offset=100000 os.queue-len=100 os.unittest-client.alias=impl os.unittest-client.impl.url=http://localhost:8080/webservice/services/ObjectStore db.unittest.datasource.serverName=localhost db.unittest.datasource.databaseName=unittest db.unittest.datasource.user=user db.unittest.datasource.password=password db.truncunittest.datasource.serverName=localhost db.truncunittest.datasource.databaseName=truncunittest db.truncunittest.datasource.user=user db.truncunittest.datasource.password=password db.fulldatatest.datasource.serverName=localhost db.fulldatatest.datasource.databaseName=fulldatatest db.fulldatatest.datasource.user=user db.fulldatatest.datasource.password=pasword db.userprofile.datasource.serverName=localhost db.userprofile.datasource.databaseName=userprofile db.userprofile.datasource.user=user db.userprofile.datasource.password=password From mark@flymine.org Fri Jun 04 17:18:37 2004 Received: from host104 ([192.168.128.104] ident=mark) by flymine.flymine.org with esmtp (Exim 4.12) id 1BWHOv-0002uV-00 for flymine-dev@flymine.org; Fri, 04 Jun 2004 17:18:37 +0100 Message-ID: <40C0A0DD.9020706@flymine.org> Date: Fri, 04 Jun 2004 17:18:37 +0100 From: Mark Woodbridge User-Agent: Mozilla Thunderbird 0.6 (X11/20040502) X-Accept-Language: en-us, en MIME-Version: 1.0 To: flymine-dev@flymine.org Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Subject: [flymine-dev] Properties (cont...) Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: The properties in the previous mail correspond to those that are now commented out in resources/test/default.intermine.properties. In particular, defaults are no longer provided for database names. This should make it clearer that you need to create the relevant databases. The new format for the default properties should make it easier for new users: if you want to do a fulltest you just need to consult the default properties and provide values for those that are commented out. From wenyan@flymine.org Thu Jun 10 09:08:40 2004 Received: from host111 ([192.168.128.111] helo=flymine.org ident=wenyan) by flymine.flymine.org with esmtp (Exim 4.12) id 1BYKc4-0001oD-00 for flymine-dev@flymine.org; Thu, 10 Jun 2004 09:08:40 +0100 Message-ID: <40C816FF.6060800@flymine.org> Date: Thu, 10 Jun 2004 09:08:31 +0100 From: Wenyan Ji User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.6) Gecko/20040413 Debian/1.6-5 X-Accept-Language: zh-cn MIME-Version: 1.0 To: flymine-dev@flymine.org Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Subject: [flymine-dev] add tutorial db in intermine.properties Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: we have added the following lines in intermine.properties in order to have a tutorial work. <<<<<<<<<<<<<<<< db.tutorial.datasource.serverName= db.tutorial.datasource.databaseName=tutorial db.tutorial.datasource.user= db.tutorial.datasource.password= >>>>>>>>>>>>>>>> From mark@flymine.org Tue Jun 29 18:26:31 2004 Received: from host104 ([192.168.128.104] ident=mark) by flymine.flymine.org with esmtp (Exim 4.12) id 1BfMNL-0004Hp-00 for flymine-dev@flymine.org; Tue, 29 Jun 2004 18:26:31 +0100 Message-ID: <40E1A647.4020204@flymine.org> Date: Tue, 29 Jun 2004 18:26:31 +0100 From: Mark Woodbridge User-Agent: Mozilla Thunderbird 0.7.1 (X11/20040626) X-Accept-Language: en-us, en MIME-Version: 1.0 To: flymine-dev@flymine.org Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Subject: [flymine-dev] Web properties Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: If you want to release a production webapp, or the flymine website, you no longer need a default.properties.flymine-www in your home directory. The required properties should now be put in default.properties.flymine, an example of which is shown below. The new webapp.prefix is necessary so that the website knows how to resolve links to webapp pages. Mark ----- webapp.baseurl=http://boromir:8080 webapp.path=/flymine webapp.manager=manager webapp.password=manager webapp.prefix=http://boromir:8080/flymine www.serverlocation=mark@www.flymine.org:public_html/flymine www.location=http://www.flymine.org/~mark/flymine From matthew@flymine.org Tue Sep 21 15:06:46 2004 Received: from host103 ([192.168.128.103] helo=aragorn.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 1C9lI6-0004nu-00 for flymine-dev@flymine.org; Tue, 21 Sep 2004 15:06:46 +0100 Received: from mnw21 (helo=localhost) by aragorn.flymine.org with local-esmtp (Exim 3.36 #1 (Debian)) id 1C9lI4-0003Mx-00 for ; Tue, 21 Sep 2004 15:06:44 +0100 Date: Tue, 21 Sep 2004 15:06:44 +0100 (BST) From: Matthew Wakeling X-X-Sender: mnw21@aragorn.flymine.org To: flymine-dev@flymine.org Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Subject: [flymine-dev] New properties for uniprot Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: It seems sensible to separate out the source items database for uniprot, in a similar way to the ensembl database, because it takes about a day to transfer the 6GB of uniprot XML into a 100GB source items database. Therefore, there is a set of new properties for db.uniprot-src-items (which os.uniprot-src-items uses). You will need to supply server name, database name, user name, and password in your own properties files in order to build uniprot. Matthew -- "Beware the lightning that lurketh in an undischarged capacitor, lest it cause thee to be bounced upon thy buttocks in a most ungentlemanly manner." -- The Ten Commandments of Electronics From matthew@flymine.org Sat Nov 20 13:07:14 2004 Received: from host103 ([192.168.128.103] helo=aragorn.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 1CVUxO-0003k1-00 for flymine-dev@flymine.org; Sat, 20 Nov 2004 13:07:14 +0000 Received: from mnw21 (helo=localhost) by aragorn.flymine.org with local-esmtp (Exim 3.36 #1 (Debian)) id 1CVUxO-0004C2-00 for ; Sat, 20 Nov 2004 13:07:14 +0000 Date: Sat, 20 Nov 2004 13:07:14 +0000 (GMT) From: Matthew Wakeling X-X-Sender: mnw21@aragorn.flymine.org To: flymine-dev@flymine.org Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Subject: [flymine-dev] Bug in java Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Once upon a time, we wrote a workaround for the bug in Java that allows large Strings to be encoded/decoded to/from byte arrays. This bug is now fixed in the beta Java 6.0. http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4949631 Matthew -- Doctor: Are you okay? You appear to be injured. Neelix: Aaaaaaah! Doctor: It's okay, it looks superficial. Neelix: Am I going to die? Doctor: Not unless you are allergic to tomatoes. This appears to be a sauce some kind. From matthew@flymine.org Thu Apr 14 13:12:29 2005 Received: from host103 ([192.168.128.103] helo=aragorn.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 1DM3Cv-0002nx-00 for flymine-dev@flymine.org; Thu, 14 Apr 2005 13:12:29 +0100 Received: from mnw21 (helo=localhost) by aragorn.flymine.org with local-esmtp (Exim 3.36 #1 (Debian)) id 1DM3Cy-0007qU-00 for ; Thu, 14 Apr 2005 13:12:32 +0100 Date: Thu, 14 Apr 2005 13:12:32 +0100 (BST) From: Matthew Wakeling X-X-Sender: mnw21@aragorn.flymine.org To: flymine-dev@flymine.org Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Subject: [flymine-dev] New property for objectstore Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: I have now checked in my (quite pervasive) changes to how the ObjectStoreInterMineImpl works. It is now capable of storing the notxml in only the InterMineObject table, possibly leading to performance improvements. However - some operations will be slower. The new behaviour is now the default behaviour, but can be switched off with a property. The new behaviour is incompatible with objectstores that have a missing table of InterMineObject (so all the items databases), so all such objectstores must have a property switching the new behaviour off. The new property is (for example): os.unittest.noNotXml=true True is the default, false sets the old behaviour. I have updated the intermine default properties for the unit tests, but I have not updated any of the flymine properties. In addition, you will need to create a new database for unit tests, and add properties for it, like this: db.notxmlunittest.datasource.serverName= db.notxmlunittest.datasource.databaseName=notxmltest db.notxmlunittest.datasource.user= db.notxmlunittest.datasource.password=----- Matthew -- I pause for breath to allow you to get over your shock that I really did cover all that in only five minutes... -- Computer Science Lecturer From matthew@flymine.org Thu Apr 21 13:47:52 2005 Received: from host103 ([192.168.128.103] helo=aragorn.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 1DOb60-0000sn-00 for flymine-dev@flymine.org; Thu, 21 Apr 2005 13:47:52 +0100 Received: from mnw21 (helo=localhost) by aragorn.flymine.org with local-esmtp (Exim 3.36 #1 (Debian)) id 1DOb64-0004PP-00 for ; Thu, 21 Apr 2005 13:47:56 +0100 Date: Thu, 21 Apr 2005 13:47:56 +0100 (BST) From: Matthew Wakeling X-X-Sender: mnw21@aragorn.flymine.org To: flymine-dev@flymine.org Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Subject: [flymine-dev] Another change to properties and a new database Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: I have checked in some changes to the ObjectStore system, to include a new "flat mode" when notxml is missing, and the intermineobject table is missing. It is not complete, and is not tested. Anyway, you will need to add some properties to your intermine.properties file, like this: db.flatmodeunittest.datasource.serverName= db.flatmodeunittest.datasource.databaseName=flatmodetest db.flatmodeunittest.datasource.user= db.flatmodeunittest.datasource.password=<> You will also need to create a database for this new objectstore. Matthew -- I'd try being be a pessimist, but it probably wouldn't work anyway. From matthew@flymine.org Thu May 26 16:46:06 2005 Received: from host103 ([192.168.128.103] helo=aragorn.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 1DbKYg-00083Y-00 for flymine-dev@flymine.org; Thu, 26 May 2005 16:46:06 +0100 Received: from mnw21 (helo=localhost) by aragorn.flymine.org with local-esmtp (Exim 3.36 #1 (Debian)) id 1DbKYm-0003RX-00 for ; Thu, 26 May 2005 16:46:12 +0100 Date: Thu, 26 May 2005 16:46:11 +0100 (BST) From: Matthew Wakeling X-X-Sender: mnw21@aragorn.flymine.org To: flymine-dev@flymine.org Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Subject: [flymine-dev] New test database, properties Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: I have created a new objectstore "mode," which doesn't use an OBJECT column in the database, and a new set of tests for it. You will need to create a new database in order to run intermine tests, and properties to match. For example, add: db.flatmodeunittest.datasource.serverName= db.flatmodeunittest.datasource.databaseName=flatmodetest db.flatmodeunittest.datasource.user= db.flatmodeunittest.datasource.password= to your intermine.properties file, and create the flatmodetest database. This change means that we can remove the "noNotXml=false" properties from the flymine items databases, which will (hopefully) make them run faster. I have not done this. Matthew -- Q: What's the difference between ignorance and apathy? A: I don't know, and I don't care. From tom@flymine.org Mon Jun 06 13:14:13 2005 Received: from host109 ([192.168.128.109]) by flymine.flymine.org with esmtp (Exim 4.12) id 1DfGUf-00071k-00 for flymine-dev@flymine.org; Mon, 06 Jun 2005 13:14:13 +0100 Mime-Version: 1.0 (Apple Message framework v730) Content-Transfer-Encoding: 7bit Message-Id: <4DA262D2-9DC3-4EBC-BAAD-4FEEFB707520@flymine.org> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed To: flymine-dev@flymine.org From: Thomas Riley Date: Mon, 6 Jun 2005 13:14:18 +0100 X-Mailer: Apple Mail (2.730) Subject: [flymine-dev] combined javadoc Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: I've added a project at imbuild/javadoc that produces javadoc for objectstore, integrate and web projects combined (to imbuild/javadoc/ build/javadoc). tom From tom@flymine.org Tue Jun 07 10:20:28 2005 Received: from host109 ([192.168.128.109]) by flymine.flymine.org with esmtp (Exim 4.12) id 1DfaG4-00020w-00 for flymine-dev@flymine.org; Tue, 07 Jun 2005 10:20:28 +0100 Mime-Version: 1.0 (Apple Message framework v730) Content-Transfer-Encoding: 7bit Message-Id: <45CCC160-1E92-4AD7-994F-0575C66FED75@flymine.org> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed To: flymine-dev@flymine.org From: Thomas Riley Date: Tue, 7 Jun 2005 10:20:34 +0100 X-Mailer: Apple Mail (2.730) Subject: [flymine-dev] build properties Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Hello everyone, As well as renaming build.properties.intermine to build.properties.testmodel-webapp there are some changes to the property names. Since the contents of build.properties.whatever is appended to web.properties in the webapp there doesn't seem much point in doing a token replace with ant and repeating the same properties. So my build.properties.testmodel-webapp now looks like this: #www.location=http://theoden.flymine.org/intermine www.serverlocation=tom@theoden:/Library/Apache2/htdocs/intermine/ #www.help.location=http://theoden.flymine.org/flymine/doc webapp.deploy.url=http://theoden.flymine.org:8080 webapp.path=intermine-app2 webapp.manager=manager webapp.password=manager #webapp.superuser=tom@flymine.org webapp.logdir=/Users/tom/Library/Logs webapp.os.alias=os.unittest webapp.userprofile.os.alias=osw.userprofile-test #webapp.release.version=1.0 superuser.account=tom@flymine.org project.helpLocation=http://theoden.flymine.org/flymine/doc project.sitePrefix=http://theoden.flymine.org/intermine project.releaseVersion=1.0 with the last 4 lines being added and the equivalents above being commented out. Anyway, this only applied to building and releasing the testmodel webapp. It's a bit of a mess so I need to sort it out. tom From tom@flymine.org Mon Jul 11 16:30:39 2005 Received: from host109 ([192.168.128.109]) by flymine.flymine.org with esmtp (Exim 4.12) id 1Ds0Ex-0005wR-00 for flymine-dev@flymine.org; Mon, 11 Jul 2005 16:30:39 +0100 Mime-Version: 1.0 (Apple Message framework v730) Content-Transfer-Encoding: 7bit Message-Id: Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed To: flymine-dev@flymine.org From: Thomas Riley Date: Mon, 11 Jul 2005 16:30:48 +0100 X-Mailer: Apple Mail (2.730) Subject: [flymine-dev] priorities Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: I've just reformatted the genomic_priorities.properties file. You'll probably want to update before making changes to your local copy or you are guaranteed to have merge conflicts. tom p.s. kim, i hope i merged your drosdel changes in with mine properly - you might want to check it. From tom@flymine.org Fri Jul 29 11:55:59 2005 Received: from host109 ([192.168.128.109]) by flymine.flymine.org with esmtp (Exim 4.12) id 1DySX1-0000DT-00 for flymine-dev@flymine.org; Fri, 29 Jul 2005 11:55:59 +0100 Mime-Version: 1.0 (Apple Message framework v733) Content-Transfer-Encoding: 7bit Message-Id: <3D416C36-4085-4B10-AA4F-4A21D7B8AE5E@flymine.org> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed To: flymine-dev@flymine.org From: Thomas Riley Date: Fri, 29 Jul 2005 11:56:09 +0100 X-Mailer: Apple Mail (2.733) Subject: [flymine-dev] code coverage reports Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Good day to you, EMMA code coverage reports are now generated when running unit tests. The reports are generated to build/coverage/index.html. It looks like they will be quite useful. Tom From tom@flymine.org Thu Aug 11 12:41:58 2005 Received: from host109 ([192.168.128.109]) by flymine.flymine.org with esmtp (Exim 4.12) id 1E3BRe-00060K-00 for flymine-dev@flymine.org; Thu, 11 Aug 2005 12:41:58 +0100 Mime-Version: 1.0 (Apple Message framework v733) Content-Transfer-Encoding: 7bit Message-Id: <367F3AD3-0497-4B5C-8328-C2133DFAFE01@flymine.org> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed To: flymine-dev@flymine.org From: Thomas Riley Date: Thu, 11 Aug 2005 12:42:08 +0100 X-Mailer: Apple Mail (2.733) Subject: [flymine-dev] global build.properties Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: I've updated the imbuild/library.xml (the base build script for all projects) to import properties from /build.properties early in the build process. So now you can override properties globally over all projects in your checkout. For example, my build.properties looks like: javac.compiler = jikes emma.enabled = false Also, emma code coverage is on by default but you can disable it for all test projects, as I've done above. Tom From tom@flymine.org Tue Sep 20 10:49:26 2005 Received: from host109 ([192.168.128.109]) by flymine.flymine.org with esmtp (Exim 4.12) id 1EHekg-0002h1-00 for flymine-dev@flymine.org; Tue, 20 Sep 2005 10:49:26 +0100 Mime-Version: 1.0 (Apple Message framework v733) Content-Transfer-Encoding: 7bit Message-Id: <7C1C89FF-6CFD-4CA9-AE3E-DF5CCE279CBE@flymine.org> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed To: flymine-dev@flymine.org From: Thomas Riley Date: Tue, 20 Sep 2005 10:49:40 +0100 X-Mailer: Apple Mail (2.733) Subject: [flymine-dev] home directory property files and branching, proposal Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: We need to come up with a nice solution for the case where someone has several flymine/t1dmine/etc releases (branches) checked out and they are all trying to use the same properties files from the user's home directory. I think we should rearrange things a bit and support different sets of properties files for different branches under the same user account. Maybe home directories should look like this: ~/ .flymine/ 1.0/ build.properties.flymine flymine.properties 2.0/ build.properties.flymine flymine.properties 2.1/ build.properties.flymine flymine.properties 3.0/ <--- used by checkouts of branches build.properties.flymine flymine.properties dev/ <--- used by a checkout of the trunk build.properties.flymine flymine.properties .testmodel-webapp/ dev/ build.properties.testmodel-webapp testmodel-webapp.properties .t1dmine/ ... etc This would be combined with a change to the branching process. After branching, the branch would be immediately modified so that checkouts read properties from the correct subdirectory (e.g. '3.0' rather than 'dev') when building/releasing. We should also have a way to override the directory used on the command line when building. E.g.: and build-production-webapp release-webapp -Dhome.properties.dir=~/ flymine/dev2 What do you think? Tom From AlexanderP@gmx.at Fri Dec 02 13:40:18 2005 Received: from ppsw-1.csi.cam.ac.uk ([131.111.8.131]) by flymine.flymine.org with esmtp (Exim 4.12) id 1EiB98-0000P4-00 for flymine-dev@flymine.org; Fri, 02 Dec 2005 13:40:18 +0000 X-Cam-SpamScore: ss X-Cam-SpamDetails: scanned, SpamAssassin (score=2.777, FORGED_RCVD_HELO 0.05, NO_REAL_NAME 0.18, UNIQUE_WORDS 2.55) X-Cam-AntiVirus: No virus found X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Received: from mail.gmx.de ([213.165.64.20]:53138 helo=mail.gmx.net) by ppsw-1.csi.cam.ac.uk (mx.cam.ac.uk [131.111.8.141]:25) with smtp (csa=unknown) id 1EiB9Q-0003ie-4o (Exim 4.54) for flymine-dev@flymine.org (return-path ); Fri, 02 Dec 2005 13:40:36 +0000 Received: (qmail 18234 invoked by uid 0); 2 Dec 2005 13:40:35 -0000 Received: from 141.244.134.112 by www54.gmx.net with HTTP; Fri, 2 Dec 2005 14:40:35 +0100 (MET) Date: Fri, 2 Dec 2005 14:40:35 +0100 (MET) From: AlexanderP@gmx.at To: flymine-dev@flymine.org MIME-Version: 1.0 X-Priority: 3 (Normal) X-Authenticated: #6910802 Message-ID: <31508.1133530835@www54.gmx.net> X-Mailer: WWW-Mail 1.6 (Global Message Exchange) X-Flags: 0001 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Subject: [flymine-dev] XML Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Hello, (its my first mail on this group, hopefully right placed) the documentation of flymine exists as many xml-files, how can they best be browsed? (opera, IE and firefox don't look so great...) regards, Alexander -- Lust, ein paar Euro nebenbei zu verdienen? Ohne Kosten, ohne Risiko! Satte Provisionen für GMX Partner: http://www.gmx.net/de/go/partner From tom@flymine.org Fri Dec 02 14:29:50 2005 Received: from host109 ([192.168.128.109]) by flymine.flymine.org with esmtp (Exim 4.12) id 1EiBv4-0000YW-00 for flymine-dev@flymine.org; Fri, 02 Dec 2005 14:29:50 +0000 In-Reply-To: <31508.1133530835@www54.gmx.net> References: <31508.1133530835@www54.gmx.net> Mime-Version: 1.0 (Apple Message framework v746.2) X-Priority: 3 (Normal) Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Message-Id: Content-Transfer-Encoding: quoted-printable From: Thomas Riley Subject: Re: [flymine-dev] XML Date: Fri, 2 Dec 2005 14:30:11 +0000 To: flymine-dev@flymine.org X-Mailer: Apple Mail (2.746.2) Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Hi Alexander, All the XML documents (most of which are in docbook format ) are transformed into html when we release the =20 websites, http://www.flymine.org and http://www.intermine.org - have =20 a look at them for the FlyMine user manual and documentation relating =20= to InterMine as a generic data warehouse toolkit. Yes, this is =20 definitely the right place to ask questions about flymine/intermine =20 development. Good luck! Tom On 2 Dec 2005, at 13:40, AlexanderP@gmx.at wrote: > Hello, > (its my first mail on this group, hopefully right placed) > > the documentation of flymine exists as many xml-files, > how can they best be browsed? > (opera, IE and firefox don't look so great...) > > regards, > Alexander > > --=20 > Lust, ein paar Euro nebenbei zu verdienen? Ohne Kosten, ohne Risiko! > Satte Provisionen f=FCr GMX Partner: http://www.gmx.net/de/go/partner > > _______________________________________________ > flymine-dev mailing list > flymine-dev@flymine.org > http://mailman.flymine.org/listinfo/flymine-dev > From AlexanderP@gmx.at Fri Dec 02 18:02:00 2005 Received: from ppsw-9.csi.cam.ac.uk ([131.111.8.139]) by flymine.flymine.org with esmtp (Exim 4.12) id 1EiFEO-0001OQ-00 for flymine-dev@flymine.org; Fri, 02 Dec 2005 18:02:00 +0000 X-Cam-SpamDetails: scanned, SpamAssassin (score=0.228, FORGED_RCVD_HELO 0.05, NO_REAL_NAME 0.18) X-Cam-AntiVirus: No virus found X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Received: from mail.gmx.de ([213.165.64.20]:52936 helo=mail.gmx.net) by ppsw-9.csi.cam.ac.uk (mx.cam.ac.uk [131.111.8.149]:25) with smtp (csa=unknown) id 1EiFEW-0006Gi-TP (Exim 4.54) for flymine-dev@flymine.org (return-path ); Fri, 02 Dec 2005 18:02:08 +0000 Received: (qmail 22005 invoked by uid 0); 2 Dec 2005 18:02:07 -0000 Received: from 83.65.73.2 by www36.gmx.net with HTTP; Fri, 2 Dec 2005 19:02:07 +0100 (MET) Date: Fri, 2 Dec 2005 19:02:07 +0100 (MET) From: AlexanderP@gmx.at To: flymine-dev@flymine.org MIME-Version: 1.0 References: Subject: Re: [flymine-dev] XML X-Priority: 3 (Normal) X-Authenticated: #6910802 Message-ID: <4476.1133546527@www36.gmx.net> X-Mailer: WWW-Mail 1.6 (Global Message Exchange) X-Flags: 0001 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Hello! uhm... maybe I have misunderstood it, or I haven't it written right... I want to build flymine, and run it locally... in the package there are only xml-files... the docu at flymine.org is good, but only for using the webservice of flymine.org (?) (is there maybe somewhere a good docbook viewer?) intermine has html with it, but it isn't the same as flymine...? thanks in advance, (and excuse the bad english...) Alex > --- Ursprüngliche Nachricht --- > Von: Thomas Riley > An: flymine-dev@flymine.org > Betreff: Re: [flymine-dev] XML > Datum: Fri, 2 Dec 2005 14:30:11 +0000 > > Hi Alexander, > > All the XML documents (most of which are in docbook format www.docbook.org/>) are transformed into html when we release the > websites, http://www.flymine.org and http://www.intermine.org - have > a look at them for the FlyMine user manual and documentation relating > to InterMine as a generic data warehouse toolkit. Yes, this is > definitely the right place to ask questions about flymine/intermine > development. > > Good luck! > > Tom > > > On 2 Dec 2005, at 13:40, AlexanderP@gmx.at wrote: > > > Hello, > > (its my first mail on this group, hopefully right placed) > > > > the documentation of flymine exists as many xml-files, > > how can they best be browsed? > > (opera, IE and firefox don't look so great...) > > > > regards, > > Alexander > > > > -- > > Lust, ein paar Euro nebenbei zu verdienen? Ohne Kosten, ohne Risiko! > > Satte Provisionen für GMX Partner: http://www.gmx.net/de/go/partner > > > > _______________________________________________ > > flymine-dev mailing list > > flymine-dev@flymine.org > > http://mailman.flymine.org/listinfo/flymine-dev -- Lust, ein paar Euro nebenbei zu verdienen? Ohne Kosten, ohne Risiko! Satte Provisionen für GMX Partner: http://www.gmx.net/de/go/partner From AlexanderP@gmx.at Fri Dec 02 18:15:46 2005 Received: from ppsw-0.csi.cam.ac.uk ([131.111.8.130]) by flymine.flymine.org with esmtp (Exim 4.12) id 1EiFRi-0001Sf-00 for flymine-dev@flymine.org; Fri, 02 Dec 2005 18:15:46 +0000 X-Cam-SpamDetails: scanned, SpamAssassin (score=0.178, NO_REAL_NAME 0.18) X-Cam-AntiVirus: No virus found X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Received: from mail.gmx.net ([213.165.64.20]:56698) by ppsw-0.csi.cam.ac.uk (mx.cam.ac.uk [131.111.8.140]:25) with smtp (csa=unknown) id 1EiFRw-00026k-1U (Exim 4.54) for flymine-dev@flymine.org (return-path ); Fri, 02 Dec 2005 18:16:00 +0000 Received: (qmail 31774 invoked by uid 0); 2 Dec 2005 18:15:59 -0000 Received: from 83.65.73.2 by www36.gmx.net with HTTP; Fri, 2 Dec 2005 19:15:59 +0100 (MET) Date: Fri, 2 Dec 2005 19:15:59 +0100 (MET) From: AlexanderP@gmx.at To: flymine-dev@flymine.org MIME-Version: 1.0 References: Subject: Re: [flymine-dev] XML X-Priority: 3 (Normal) X-Authenticated: #6910802 Message-ID: <11434.1133547359@www36.gmx.net> X-Mailer: WWW-Mail 1.6 (Global Message Exchange) X-Flags: 0001 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: hmm... the last mail was not planned to go on the group... (or should it? *g*) -- Lust, ein paar Euro nebenbei zu verdienen? Ohne Kosten, ohne Risiko! Satte Provisionen für GMX Partner: http://www.gmx.net/de/go/partner From tom@flymine.org Mon Dec 05 11:12:16 2005 Received: from host109 ([192.168.128.109]) by flymine.flymine.org with esmtp (Exim 4.12) id 1EjEGW-0008Jv-00 for flymine-dev@flymine.org; Mon, 05 Dec 2005 11:12:16 +0000 In-Reply-To: <11434.1133547359@www36.gmx.net> References: <11434.1133547359@www36.gmx.net> Mime-Version: 1.0 (Apple Message framework v746.2) X-Priority: 3 (Normal) Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Message-Id: Content-Transfer-Encoding: quoted-printable From: Thomas Riley Subject: Re: [flymine-dev] XML Date: Mon, 5 Dec 2005 11:12:36 +0000 To: flymine-dev@flymine.org X-Mailer: Apple Mail (2.746.2) Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Hi Alexander, I think everything that you might find in XML format is in the web. =20 I'm afraid most of the docs for getting started using InterMine are =20 out of date. Also, there is practically on documentation on setting =20 up to perform a FlyMine build (FlyMine being an actual application =20 built on top of InterMine). If you've checked out from our subversion repository you will see =20 three main directories, intermine, flymine and testmodel. The =20 intermine directory contains all of the reusable code and the generic =20= web application. 'flymine' and 'testmodel' are actual applications =20 built on top of intermine. testmodel just contains some dummy test =20 data that we use, unsurprisingly, for testing. Getting the testmodel =20 webapp built and running is fairy straightforward. Building flymine =20 is not. Which one you want to base your application on depends on =20 whether you want to include a lot of the data that flymine includes. =20 If so, you may want to base your application on the flymine directory =20= and unfortunately, you will be in for a lot of work. If you just want =20= to build an application with your own data, you could just duplicate =20 and modify the testmodel directory accordingly (I can give you help =20 with this). Unfortunately, the testmodel and flymine applications use =20= two different build systems, where testmodel is quite modular and =20 flymine is one big lump and hard to modify. In the near future =20 (hopefully starting before the end of the year), we want to split =20 everything in the flymine directory into manageable pieces. Then =20 you'll be able to start building your InterMine based application, =20 easily take the data you need from FlyMine and extend it any way you =20 like. In brief, to build and run the testmodel application, you need to =20 create two files in your *home* directory. The first is called =20 testmodel-webapp.properties and contains something like: db.userprofile-test.datasource.serverName=3Dlocalhost db.userprofile-test.datasource.databaseName=3Dtestmodel-webapp-userprofile= db.userprofile-test.datasource.user=3Dtom db.userprofile-test.datasource.password=3Dpassword db.unittest.datasource.serverName=3Dlocalhost db.unittest.datasource.databaseName=3Dtestmodel-webapp db.unittest.datasource.user=3Dtom db.unittest.datasource.password=3Dpassword Adjust according to your own database settings. and the other is called build.properties.testmodel-webapp and looks =20 like this: # You don't really need to change these project.helpLocation=3Dhttp://www.flymine.org/flymine/doc project.sitePrefix=3Dhttp://www.flymine.org/flymine project.releaseVersion=3D1.0 # You will want to change the following 6 properties: webapp.deploy.url=3Dhttp://localhost:8080 webapp.path=3Dmy-app webapp.manager=3Dmanager webapp.password=3Dmanager webapp.logdir=3D/Users/tom/Library/Logs superuser.account=3Dyou@yourdomain.com # You don't need to change these webapp.os.alias=3Dos.unittest webapp.userprofile.os.alias=3Dosw.userprofile-test webapp.deploy.url should point to your tomcat server, webapp.path is =20 the tomcat context to deploy to. webapp.manager and webapp.password =20 specify a tomcat user with the 'manager' role. Now run createdb to create the 'testmodel-webapp-userprofile' and =20 'testmodel-webapp' (the ant build files won't do this for you). Now initialise intermine's build system by executing 'ant' in imbuild/=20= ant-tasks/. If this fails, check that you have a fairly up-to-date =20 version of ant installed. Now go into testmodel/dbmodel and execute 'ant insert-data-=20 testmodel'. This will initialise the database and insert the test data. Now you can build and release the web application by going into =20 testmodel/webapp/main and running: ant ant release-webapp Let me know if you get stuck. Tom On 2 Dec 2005, at 18:15, AlexanderP@gmx.at wrote: > hmm... the last mail was not planned to go on the group... (or =20 > should it? > *g*) > > --=20 > Lust, ein paar Euro nebenbei zu verdienen? Ohne Kosten, ohne Risiko! > Satte Provisionen f=FCr GMX Partner: http://www.gmx.net/de/go/partner > > _______________________________________________ > flymine-dev mailing list > flymine-dev@flymine.org > http://mailman.flymine.org/listinfo/flymine-dev > From richard@flymine.org Mon Dec 05 15:09:38 2005 Received: from [192.168.128.190] (helo=[192.168.128.190]) by flymine.flymine.org with esmtp (Exim 4.12) id 1EjHyE-0000pl-00; Mon, 05 Dec 2005 15:09:38 +0000 Message-ID: <43945847.3030801@flymine.org> Date: Mon, 05 Dec 2005 15:09:59 +0000 From: Richard Smith User-Agent: Mozilla Thunderbird 1.0.6 (Macintosh/20050716) X-Accept-Language: en-us, en MIME-Version: 1.0 To: AlexanderP@gmx.at CC: flymine-dev@flymine.org References: <31034.1133780877@www84.gmx.net> In-Reply-To: <31034.1133780877@www84.gmx.net> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Subject: [flymine-dev] Re: Flymine Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Alex, I hope Tom's e-mail cleared up a few issues. Let us know how you get on. I'm afraid you are the first group to attempt to set up InterMine/FlyMine externally but we will do our best to help. As Tom says all documentation that is in the docbook XML files is available as pages on the www.intermine.org website. Some of it is, however, out of date. We also have an internal wiki (and bug tracking system) that has some additional documentation and more that we will added as soon as possible. Do you usually access from the same IP address? If so we can set up access to the wiki from that address. It may help us if we knew a bit more about your plans. From my discussion with David it sounds like you would be using the FlyMine data model and adding additional data. Do you know at this stage what types of data you hope to include? Regards, Richard. AlexanderP@gmx.at wrote: >Dear Richard, > >(it's Alex the diploma student of Dr. Kreil) > >I have some questions about flymine. > >the build of flymine (ant build-db-testmodel) stops with >'build-model.xml:...: database attribute is not set or database is not >present' >(line is (file is modified, some 'echo' is added): >build-db database="${db.name}" destdir="${build.model}/${model.name}" >what is missing? (the prerequisites are all installed) >(the name of the database is 'db.unittest', what does this mean? (should a >database be created with that name, should there another name written?)) > >the build of the tutorial ('ant run'; is it depending on the build of >flymine-src?) stops with: >/bi/common/src/flymine-tutorial-1.01/flymine-tutorial-1.01/build.xml:100: >java.lang.reflect.InvocationTargetException >there is a maybe important error on the way, the path of the >repository.dtd is not found (db.apache.org/ojb/dtds/1.0/repository.dtd), if >I change it before building on the right path, in at least one file >(repository_tutorial.xml) it is reseted to the old one, I haven't found >where is the reason... > >Is there somewhere a documentation for building flymine, other than in >xml-form? (or a good viewer for the xmls?) > >excuse my probably bad english, and the maybe not necessary questions, I am >not used to it (ant, xml, ...), (most of the time I was/am a >C++-programmer) > >thanks in advance and kind regards, > Alexander > > From AlexanderP@gmx.at Thu Dec 08 13:33:56 2005 Received: from ppsw-9.csi.cam.ac.uk ([131.111.8.139]) by flymine.flymine.org with esmtp (Exim 4.12) id 1EkLuG-0001dA-00 for flymine-dev@flymine.org; Thu, 08 Dec 2005 13:33:56 +0000 X-Cam-SpamDetails: scanned, SpamAssassin (score=0.228, FORGED_RCVD_HELO 0.05, NO_REAL_NAME 0.18) X-Cam-AntiVirus: No virus found X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Received: from mail.gmx.de ([213.165.64.20]:41054 helo=mail.gmx.net) by ppsw-9.csi.cam.ac.uk (mx.cam.ac.uk [131.111.8.149]:25) with smtp (csa=unknown) id 1EkLuT-0001N8-VD (Exim 4.54) for flymine-dev@flymine.org (return-path ); Thu, 08 Dec 2005 13:34:09 +0000 Received: (qmail 11598 invoked by uid 0); 8 Dec 2005 13:34:05 -0000 Received: from 83.65.73.2 by www30.gmx.net with HTTP; Thu, 8 Dec 2005 14:34:05 +0100 (MET) Date: Thu, 8 Dec 2005 14:34:05 +0100 (MET) From: AlexanderP@gmx.at To: flymine-dev@flymine.org MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="========GMXBoundary88771134048845" Subject: Re: [flymine-dev] XML X-Priority: 3 (Normal) X-Authenticated: #6910802 Message-ID: <8877.1134048845@www30.gmx.net> X-Mailer: WWW-Mail 1.6 (Global Message Exchange) X-Flags: 0001 Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: This is a MIME encapsulated multipart message - please use a MIME-compliant e-mail program to open it. Dies ist eine mehrteilige Nachricht im MIME-Format - bitte verwenden Sie zum Lesen ein MIME-konformes Mailprogramm. --========GMXBoundary88771134048845 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit ok, output is attached (output2 are the error-messages) kind regards, Alex > --- Ursprüngliche Nachricht --- > Von: Thomas Riley > An: AlexanderP@gmx.at > Betreff: Re: [flymine-dev] XML > Datum: Thu, 8 Dec 2005 10:32:01 +0000 > > Hi Alex, > > That's a bit odd. the org.apache.xpath package is part of xalan.jar > in imbuild/ant-tasks/lib. Everything inside that lib directory should > be on the classpath when compiling ant-tasks. Can you run 'ant -v' in > imbuild/ant-tasks and email me the output? If you want to, you can > post all these emails to the flymine-dev list - it's useful to have a > public archive. > > cheers, > tom > > On 8 Dec 2005, at 01:46, AlexanderP@gmx.at wrote: > > > Hello Tom, > > > > we got stuck at... javac. > > > > the error message: > > [javac] > > /bi/common/src/flymine-3.0-checkout/flymine_release_3_0_branch/ > > imbuild/ant-tasks/src/org/intermine/task/XPathSelect.java:16: > > package org.apache.xpath does not exist > > [javac] > > /bi/common/src/flymine-3.0-checkout/flymine_release_3_0_branch/ > > imbuild/ant-tasks/src/org/intermine/task/XPathSelect.java:90: > > cannot find symbol > > > > well, looks like a normal java-problem (not somethink with flymine); > > but this class should be installed (we have installed the jdk1.5.0), > > even if I change the CLASSPATH, its the same (and I have tried > > 'property > > name="javac.compilerargs" value="-classpath (path)' in library.xml); > > is there something that override all the parameters? (in jdk1.5.0 > > it is as a > > .jar container, but the path I set points to a extracted > > structure... (looks > > right)) > > (ok, maybe its only some easy thing...) > > > > kind regards, > > Alex -- GMX DSL-Flatrate 1 Jahr kostenlos* + WLAN-Router ab 0,- Euro* Bis 31.12.2005 einsteigen! 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Zy5hcGFjaGUudG9vbHMuYW50Lk1haW4uc3RhcnRBbnQoTWFpbi5qYXZhOjE4NykNCglhdCBvcmcu YXBhY2hlLnRvb2xzLmFudC5sYXVuY2guTGF1bmNoZXIucnVuKExhdW5jaGVyLmphdmE6MjQ2KQ0K CWF0IG9yZy5hcGFjaGUudG9vbHMuYW50LmxhdW5jaC5MYXVuY2hlci5tYWluKExhdW5jaGVyLmph dmE6NjcpDQoNClRvdGFsIHRpbWU6IDEgc2Vjb25kDQo= --========GMXBoundary88771134048845-- From tom@flymine.org Thu Dec 08 13:57:53 2005 Received: from host109 ([192.168.128.109]) by flymine.flymine.org with esmtp (Exim 4.12) id 1EkMHR-0001h5-00 for flymine-dev@flymine.org; Thu, 08 Dec 2005 13:57:53 +0000 In-Reply-To: <8877.1134048845@www30.gmx.net> References: <8877.1134048845@www30.gmx.net> Mime-Version: 1.0 (Apple Message framework v746.2) X-Priority: 3 (Normal) Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Message-Id: Content-Transfer-Encoding: quoted-printable From: Thomas Riley Subject: Re: [flymine-dev] XML Date: Thu, 8 Dec 2005 13:58:13 +0000 To: flymine-dev@flymine.org X-Mailer: Apple Mail (2.746.2) Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Okay, I see what the problem is. For some reason the xalan.jar was =20 missing from both the 3.0 and 3.1 branches. I have just updated both =20 so run 'svn up' in ant-tasks and it should start to work (you might =20 have to wait a few minutes while out internal repository syncs with =20 the public one). tom On 8 Dec 2005, at 13:34, AlexanderP@gmx.at wrote: > ok, > > output is attached (output2 are the error-messages) > > kind regards, > Alex > > > > >> --- Urspr=FCngliche Nachricht --- >> Von: Thomas Riley >> An: AlexanderP@gmx.at >> Betreff: Re: [flymine-dev] XML >> Datum: Thu, 8 Dec 2005 10:32:01 +0000 >> >> Hi Alex, >> >> That's a bit odd. the org.apache.xpath package is part of xalan.jar >> in imbuild/ant-tasks/lib. Everything inside that lib directory should >> be on the classpath when compiling ant-tasks. Can you run 'ant -v' in >> imbuild/ant-tasks and email me the output? If you want to, you can >> post all these emails to the flymine-dev list - it's useful to have a >> public archive. >> >> cheers, >> tom >> >> On 8 Dec 2005, at 01:46, AlexanderP@gmx.at wrote: >> >>> Hello Tom, >>> >>> we got stuck at... javac. >>> >>> the error message: >>> [javac] >>> /bi/common/src/flymine-3.0-checkout/flymine_release_3_0_branch/ >>> imbuild/ant-tasks/src/org/intermine/task/XPathSelect.java:16: >>> package org.apache.xpath does not exist >>> [javac] >>> /bi/common/src/flymine-3.0-checkout/flymine_release_3_0_branch/ >>> imbuild/ant-tasks/src/org/intermine/task/XPathSelect.java:90: >>> cannot find symbol >>> >>> well, looks like a normal java-problem (not somethink with flymine); >>> but this class should be installed (we have installed the jdk1.5.0), >>> even if I change the CLASSPATH, its the same (and I have tried >>> 'property >>> name=3D"javac.compilerargs" value=3D"-classpath (path)' in = library.xml); >>> is there something that override all the parameters? (in jdk1.5.0 >>> it is as a >>> .jar container, but the path I set points to a extracted >>> structure... (looks >>> right)) >>> (ok, maybe its only some easy thing...) >>> >>> kind regards, >>> Alex > > --=20 > GMX DSL-Flatrate 1 Jahr kostenlos* + WLAN-Router ab 0,- Euro* > Bis 31.12.2005 einsteigen! Infos unter: http://www.gmx.net/de/go/dsl > > From AlexanderP@gmx.at Thu Dec 08 13:59:28 2005 Received: from ppsw-9.csi.cam.ac.uk ([131.111.8.139]) by flymine.flymine.org with esmtp (Exim 4.12) id 1EkMIy-0001ht-00 for flymine-dev@flymine.org; Thu, 08 Dec 2005 13:59:28 +0000 X-Cam-SpamDetails: scanned, SpamAssassin (score=0.178, NO_REAL_NAME 0.18) X-Cam-AntiVirus: No virus found X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Received: from mail.gmx.net ([213.165.64.20]:34607) by ppsw-9.csi.cam.ac.uk (mx.cam.ac.uk [131.111.8.149]:25) with smtp (csa=unknown) id 1EkMJF-0003fi-UV (Exim 4.54) for flymine-dev@flymine.org (return-path ); Thu, 08 Dec 2005 13:59:45 +0000 Received: (qmail 4278 invoked by uid 0); 8 Dec 2005 13:59:45 -0000 Received: from 83.65.73.2 by www30.gmx.net with HTTP; Thu, 8 Dec 2005 14:59:45 +0100 (MET) Date: Thu, 8 Dec 2005 14:59:45 +0100 (MET) From: AlexanderP@gmx.at To: flymine-dev@flymine.org MIME-Version: 1.0 References: Subject: Re: [flymine-dev] XML X-Priority: 3 (Normal) X-Authenticated: #6910802 Message-ID: <9971.1134050385@www30.gmx.net> X-Mailer: WWW-Mail 1.6 (Global Message Exchange) X-Flags: 0001 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: (well, I have been invited to lunch today, I know ists short timed... hopefully your read this in short time...) ok, next thing, in testmodel/dbmodel exists no target insert-data-testmodel for ant, (so I have tried simply 'ant' -> BUILD FAILED /bi/common/src/flymine-3.0-checkout/flymine_release_3_0_branch/imbuild/objectstore.xml:54: java.sql.SQLException: ERROR: relation "intermine_metadata" does not exist is it something simple? thanks in advance, Alex -- GMX DSL-Flatrate 1 Jahr kostenlos* + WLAN-Router ab 0,- Euro* Bis 31.12.2005 einsteigen! Infos unter: http://www.gmx.net/de/go/dsl From tom@flymine.org Thu Dec 08 14:08:53 2005 Received: from host109 ([192.168.128.109]) by flymine.flymine.org with esmtp (Exim 4.12) id 1EkMS5-0001jn-00 for flymine-dev@flymine.org; Thu, 08 Dec 2005 14:08:53 +0000 In-Reply-To: <9971.1134050385@www30.gmx.net> References: <9971.1134050385@www30.gmx.net> Mime-Version: 1.0 (Apple Message framework v746.2) X-Priority: 3 (Normal) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Message-Id: Content-Transfer-Encoding: 7bit From: Thomas Riley Date: Thu, 8 Dec 2005 14:09:14 +0000 To: flymine-dev@flymine.org X-Mailer: Apple Mail (2.746.2) Subject: [flymine-dev] testmodel/dbmodel Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: On 8 Dec 2005, at 13:59, AlexanderP@gmx.at wrote: > (well, I have been invited to lunch today, I know ists short timed... > hopefully your read this in short time...) > ok, next thing, > > in > testmodel/dbmodel > exists no target insert-data-testmodel for ant, > (so I have tried simply 'ant' > -> > BUILD > FAILED > /bi/common/src/flymine-3.0-checkout/flymine_release_3_0_branch/ > imbuild/objectstore.xml:54: > java.sql.SQLException: ERROR: relation "intermine_metadata" does > not exist Apologies - my original instructions probably weren't quite right. What the default ant target in dbmodel does is look at an initialised database, pull the model out of the database and build a jar containing the model that is added to the final webapp. So the error you get is because the database has not been initialised so run: ant build-db ant insert-data-unittest in dbmodel to get the database set up. (The default target will be run automatically when you build the testmodel web-app.) After that, run ant in testmodel/webapp/main to build the final war file. tom From AlexanderP@gmx.at Thu Dec 08 14:09:18 2005 Received: from ppsw-9.csi.cam.ac.uk ([131.111.8.139]) by flymine.flymine.org with esmtp (Exim 4.12) id 1EkMSU-0001kW-00 for flymine-dev@flymine.org; Thu, 08 Dec 2005 14:09:18 +0000 X-Cam-SpamDetails: scanned, SpamAssassin (score=0.228, FORGED_RCVD_HELO 0.05, NO_REAL_NAME 0.18) X-Cam-AntiVirus: No virus found X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Received: from mail.gmx.de ([213.165.64.20]:43365 helo=mail.gmx.net) by ppsw-9.csi.cam.ac.uk (mx.cam.ac.uk [131.111.8.149]:25) with smtp (csa=unknown) id 1EkMSP-0007Zx-T6 (Exim 4.54) for flymine-dev@flymine.org (return-path ); Thu, 08 Dec 2005 14:09:13 +0000 Received: (qmail 28226 invoked by uid 0); 8 Dec 2005 14:09:12 -0000 Received: from 83.65.73.2 by www30.gmx.net with HTTP; Thu, 8 Dec 2005 15:09:12 +0100 (MET) Date: Thu, 8 Dec 2005 15:09:12 +0100 (MET) From: AlexanderP@gmx.at To: flymine-dev@flymine.org MIME-Version: 1.0 References: Subject: Re: [flymine-dev] XML X-Priority: 3 (Normal) X-Authenticated: #6910802 Message-ID: <14809.1134050952@www30.gmx.net> X-Mailer: WWW-Mail 1.6 (Global Message Exchange) X-Flags: 0001 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: once more, before running 'ant' in testmodel/dbmodel, there is 'ant build-db' necessary (there was this hint in the output...) > --- Ursprüngliche Nachricht --- > Von: Thomas Riley > An: flymine-dev@flymine.org > Betreff: Re: [flymine-dev] XML > Datum: Thu, 8 Dec 2005 13:58:13 +0000 > > Okay, I see what the problem is. For some reason the xalan.jar was > missing from both the 3.0 and 3.1 branches. I have just updated both > so run 'svn up' in ant-tasks and it should start to work (you might > have to wait a few minutes while out internal repository syncs with > the public one). > > tom > > On 8 Dec 2005, at 13:34, AlexanderP@gmx.at wrote: > > > ok, > > > > output is attached (output2 are the error-messages) > > > > kind regards, > > Alex > > > > > > > > > >> --- Ursprüngliche Nachricht --- > >> Von: Thomas Riley > >> An: AlexanderP@gmx.at > >> Betreff: Re: [flymine-dev] XML > >> Datum: Thu, 8 Dec 2005 10:32:01 +0000 > >> > >> Hi Alex, > >> > >> That's a bit odd. the org.apache.xpath package is part of xalan.jar > >> in imbuild/ant-tasks/lib. Everything inside that lib directory should > >> be on the classpath when compiling ant-tasks. Can you run 'ant -v' in > >> imbuild/ant-tasks and email me the output? If you want to, you can > >> post all these emails to the flymine-dev list - it's useful to have a > >> public archive. > >> > >> cheers, > >> tom > >> > >> On 8 Dec 2005, at 01:46, AlexanderP@gmx.at wrote: > >> > >>> Hello Tom, > >>> > >>> we got stuck at... javac. > >>> > >>> the error message: > >>> [javac] > >>> /bi/common/src/flymine-3.0-checkout/flymine_release_3_0_branch/ > >>> imbuild/ant-tasks/src/org/intermine/task/XPathSelect.java:16: > >>> package org.apache.xpath does not exist > >>> [javac] > >>> /bi/common/src/flymine-3.0-checkout/flymine_release_3_0_branch/ > >>> imbuild/ant-tasks/src/org/intermine/task/XPathSelect.java:90: > >>> cannot find symbol > >>> > >>> well, looks like a normal java-problem (not somethink with flymine); > >>> but this class should be installed (we have installed the jdk1.5.0), > >>> even if I change the CLASSPATH, its the same (and I have tried > >>> 'property > >>> name="javac.compilerargs" value="-classpath (path)' in library.xml); > >>> is there something that override all the parameters? (in jdk1.5.0 > >>> it is as a > >>> .jar container, but the path I set points to a extracted > >>> structure... (looks > >>> right)) > >>> (ok, maybe its only some easy thing...) > >>> > >>> kind regards, > >>> Alex -- Telefonieren Sie schon oder sparen Sie noch? NEU: GMX Phone_Flat http://www.gmx.net/de/go/telefonie From richard@flymine.org Thu Dec 15 11:13:23 2005 Received: from [192.168.128.190] (helo=[192.168.128.190]) by flymine.flymine.org with esmtp (Exim 4.12) id 1Emr35-00054R-00; Thu, 15 Dec 2005 11:13:23 +0000 Message-ID: <43A14FE8.3000104@flymine.org> Date: Thu, 15 Dec 2005 11:13:44 +0000 From: Richard Smith User-Agent: Mozilla Thunderbird 1.0.6 (Macintosh/20050716) X-Accept-Language: en-us, en MIME-Version: 1.0 To: AlexanderP@gmx.at CC: flymine-dev@flymine.org References: <2032.1134608116@www40.gmx.net> In-Reply-To: <2032.1134608116@www40.gmx.net> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Subject: [flymine-dev] Re: [release 3.1 webapp build] Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Yes, that is exactly the problem. We have our max time set to 1000000000 but in your case I think that still wouldn't help. This limit is imposed to prevent poorly constrained queries run in a production environment from clogging up the database server for too long. When releasing the webapp it could be set as high as you like. A better option is to get the query to run a bit faster. Have you done an analyse on the restored dump? We set our default_statistics_target to 200. Explanation if you haven't done much with postgres before: Statistics are stored about each table (number of rows, etc) and are used by the postgres query planner to choose sensible queriy methods. Whenever you restore a dump or significantly alter the contents of the database you should run "analyse;" in psql. default_statistics_target is a number between 1 and 1000 that governs how precise the statistics are (default is 10). High numbers lead to slightly longer spent planning but should result in more efficient queries. So, you should try: > set default_statistics_target 200; > analyse; The value is set only for a particular session, to see value: > show default_statistics_target; It is better to set the in postgresql.conf and restart postgres. Then try building the webapp again. Hope this helps, Richard. AlexanderP@gmx.at wrote: >here it is, > >ausgabe is the normal output >errausgabe are the error messages... >(attached) > >maybe it's only the Estimated time to run query greater than maximum...? > >from command: >nice nohup ant -v build-production-webapp >ausgabe.dat 2>errausgabe.dat > >kind regards, > alex > > > > From AlexanderP@gmx.at Thu Dec 15 13:55:33 2005 Received: from ppsw-0.csi.cam.ac.uk ([131.111.8.130]) by flymine.flymine.org with esmtp (Exim 4.12) id 1Emta1-0005Rb-00 for flymine-dev@flymine.org; Thu, 15 Dec 2005 13:55:33 +0000 X-Cam-SpamDetails: scanned, SpamAssassin (score=0.228, FORGED_RCVD_HELO 0.05, NO_REAL_NAME 0.18) X-Cam-AntiVirus: No virus found X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Received: from mail.gmx.de ([213.165.64.21]:54787 helo=mail.gmx.net) by ppsw-0.csi.cam.ac.uk (mx.cam.ac.uk [131.111.8.140]:25) with smtp (csa=unknown) id 1EmtaA-0005Dk-37 (Exim 4.54) for flymine-dev@flymine.org (return-path ); Thu, 15 Dec 2005 13:55:43 +0000 Received: (qmail 1473 invoked by uid 0); 15 Dec 2005 13:55:42 -0000 Received: from 141.244.134.112 by www4.gmx.net with HTTP; Thu, 15 Dec 2005 14:55:42 +0100 (MET) Date: Thu, 15 Dec 2005 14:55:42 +0100 (MET) From: AlexanderP@gmx.at To: flymine-dev@flymine.org MIME-Version: 1.0 References: <43A14FE8.3000104@flymine.org> Subject: Re: [flymine-dev] Re: [release 3.1 webapp build] X-Priority: 3 (Normal) X-Authenticated: #6910802 Message-ID: <29421.1134654942@www4.gmx.net> X-Mailer: WWW-Mail 1.6 (Global Message Exchange) X-Flags: 0001 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: it's now only a little bit faster, not fast enough... how do I set the max time? > --- Ursprüngliche Nachricht --- > Von: Richard Smith > An: AlexanderP@gmx.at > Kopie: flymine-dev@flymine.org > Betreff: [flymine-dev] Re: [release 3.1 webapp build] > Datum: Thu, 15 Dec 2005 11:13:44 +0000 > > Yes, that is exactly the problem. We have our max time set to > 1000000000 but in your case I think that still wouldn't help. > This limit is imposed to prevent poorly constrained queries run > in a production environment from clogging up the database > server for too long. When releasing the webapp it could be set > as high as you like. > > A better option is to get the query to run a bit faster. Have > you done an analyse on the restored dump? We set our > default_statistics_target to 200. > > Explanation if you haven't done much with postgres before: > Statistics are stored about each table (number of rows, etc) > and are used by the postgres query planner to choose sensible > queriy methods. Whenever you restore a dump or significantly > alter the contents of the database you should run "analyse;" in > psql. > > default_statistics_target is a number between 1 and 1000 that > governs how precise the statistics are (default is 10). High > numbers lead to slightly longer spent planning but should > result in more efficient queries. > > So, you should try: > > set default_statistics_target 200; > > analyse; > > The value is set only for a particular session, to see value: > > show default_statistics_target; > > It is better to set the in postgresql.conf and restart postgres. > > > Then try building the webapp again. Hope this helps, > Richard. > > > > > AlexanderP@gmx.at wrote: > > >here it is, > > > >ausgabe is the normal output > >errausgabe are the error messages... > >(attached) > > > >maybe it's only the Estimated time to run query greater than maximum...? > > > >>from command: > >nice nohup ant -v build-production-webapp >ausgabe.dat 2>errausgabe.dat > > > > >kind regards, > > alex > > > > > > > > > > > _______________________________________________ > flymine-dev mailing list > flymine-dev@flymine.org > http://mailman.flymine.org/listinfo/flymine-dev -- 10 GB Mailbox, 100 FreeSMS/Monat http://www.gmx.net/de/go/topmail +++ GMX - die erste Adresse für Mail, Message, More +++ From richard@flymine.org Thu Dec 15 14:05:21 2005 Received: from [192.168.128.190] (helo=[192.168.128.190]) by flymine.flymine.org with esmtp (Exim 4.12) id 1EmtjV-0005Ub-00 for flymine-dev@flymine.org; Thu, 15 Dec 2005 14:05:21 +0000 Message-ID: <43A17837.2070701@flymine.org> Date: Thu, 15 Dec 2005 14:05:43 +0000 From: Richard Smith User-Agent: Mozilla Thunderbird 1.0.6 (Macintosh/20050716) X-Accept-Language: en-us, en MIME-Version: 1.0 To: flymine-dev@flymine.org Subject: Re: [flymine-dev] Re: [release 3.1 webapp build] References: <43A14FE8.3000104@flymine.org> <29421.1134654942@www4.gmx.net> In-Reply-To: <29421.1134654942@www4.gmx.net> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Set values in flymine.properties, e.g: os.query.max-time=1000000000 os.query.max-limit=100000000 os.query.max-offset=100000000 os.queue-len=100 These should override corresponding default properties in: flymine/resources/runtime/default.intermine.properties Richard. AlexanderP@gmx.at wrote: >it's now only a little bit faster, not fast enough... > >how do I set the max time? > > > > > >>--- Ursprüngliche Nachricht --- >>Von: Richard Smith >>An: AlexanderP@gmx.at >>Kopie: flymine-dev@flymine.org >>Betreff: [flymine-dev] Re: [release 3.1 webapp build] >>Datum: Thu, 15 Dec 2005 11:13:44 +0000 >> >>Yes, that is exactly the problem. We have our max time set to >>1000000000 but in your case I think that still wouldn't help. >>This limit is imposed to prevent poorly constrained queries run >>in a production environment from clogging up the database >>server for too long. When releasing the webapp it could be set >>as high as you like. >> >>A better option is to get the query to run a bit faster. Have >>you done an analyse on the restored dump? We set our >>default_statistics_target to 200. >> >>Explanation if you haven't done much with postgres before: >>Statistics are stored about each table (number of rows, etc) >>and are used by the postgres query planner to choose sensible >>queriy methods. Whenever you restore a dump or significantly >>alter the contents of the database you should run "analyse;" in >>psql. >> >>default_statistics_target is a number between 1 and 1000 that >>governs how precise the statistics are (default is 10). High >>numbers lead to slightly longer spent planning but should >>result in more efficient queries. >> >>So, you should try: >> > set default_statistics_target 200; >> > analyse; >> >>The value is set only for a particular session, to see value: >> > show default_statistics_target; >> >>It is better to set the in postgresql.conf and restart postgres. >> >> >>Then try building the webapp again. Hope this helps, >>Richard. >> >> >> >> >>AlexanderP@gmx.at wrote: >> >> >>>here it is, >>> >>>ausgabe is the normal output >>>errausgabe are the error messages... >>>(attached) >>> >>>maybe it's only the Estimated time to run query greater than maximum...? >>> >>>>from command: >>>nice nohup ant -v build-production-webapp >ausgabe.dat 2>errausgabe.dat >>>>> >>>kind regards, >>> alex >>> >>> >>> >>> >>> >> >>_______________________________________________ >>flymine-dev mailing list >>flymine-dev@flymine.org >>http://mailman.flymine.org/listinfo/flymine-dev >> > From AlexanderP@gmx.at Fri Dec 16 11:15:02 2005 Received: from ppsw-1.csi.cam.ac.uk ([131.111.8.131]) by flymine.flymine.org with esmtp (Exim 4.12) id 1EnDYE-0002Bi-00 for flymine-dev@flymine.org; Fri, 16 Dec 2005 11:15:02 +0000 X-Cam-SpamDetails: scanned, SpamAssassin (score=0.178, NO_REAL_NAME 0.18) X-Cam-AntiVirus: No virus found X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Received: from mail.gmx.net ([213.165.64.21]:57111) by ppsw-1.csi.cam.ac.uk (mx.cam.ac.uk [131.111.8.141]:25) with smtp (csa=unknown) id 1EnDYW-0000pG-4p (Exim 4.54) for flymine-dev@flymine.org (return-path ); Fri, 16 Dec 2005 11:15:20 +0000 Received: (qmail 9745 invoked by uid 0); 16 Dec 2005 11:15:19 -0000 Received: from 83.65.73.2 by www61.gmx.net with HTTP; Fri, 16 Dec 2005 12:15:19 +0100 (MET) Date: Fri, 16 Dec 2005 12:15:19 +0100 (MET) From: AlexanderP@gmx.at To: flymine-dev@flymine.org MIME-Version: 1.0 References: <43A17837.2070701@flymine.org> Subject: Re: [flymine-dev] Re: [release 3.1 webapp build] X-Priority: 3 (Normal) X-Authenticated: #6910802 Message-ID: <1769.1134731719@www61.gmx.net> X-Mailer: WWW-Mail 1.6 (Global Message Exchange) X-Flags: 0001 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: thanks! it is running... alex > --- Ursprüngliche Nachricht --- > Von: Richard Smith > An: flymine-dev@flymine.org > Betreff: Re: [flymine-dev] Re: [release 3.1 webapp build] > Datum: Thu, 15 Dec 2005 14:05:43 +0000 > > Set values in flymine.properties, e.g: > > os.query.max-time=1000000000 > os.query.max-limit=100000000 > os.query.max-offset=100000000 > os.queue-len=100 > > These should override corresponding default properties in: > flymine/resources/runtime/default.intermine.properties > > Richard. > > > > > > AlexanderP@gmx.at wrote: > > >it's now only a little bit faster, not fast enough... > > > >how do I set the max time? > > > > > > > > > > > >>--- Ursprüngliche Nachricht --- > >>Von: Richard Smith > >>An: AlexanderP@gmx.at > >>Kopie: flymine-dev@flymine.org > >>Betreff: [flymine-dev] Re: [release 3.1 webapp build] > >>Datum: Thu, 15 Dec 2005 11:13:44 +0000 > >> > >>Yes, that is exactly the problem. We have our max time set to > >>1000000000 but in your case I think that still wouldn't help. > >>This limit is imposed to prevent poorly constrained queries run > >>in a production environment from clogging up the database > >>server for too long. When releasing the webapp it could be set > >>as high as you like. > >> > >>A better option is to get the query to run a bit faster. Have > >>you done an analyse on the restored dump? We set our > >>default_statistics_target to 200. > >> > >>Explanation if you haven't done much with postgres before: > >>Statistics are stored about each table (number of rows, etc) > >>and are used by the postgres query planner to choose sensible > >>queriy methods. Whenever you restore a dump or significantly > >>alter the contents of the database you should run "analyse;" in > >>psql. > >> > >>default_statistics_target is a number between 1 and 1000 that > >>governs how precise the statistics are (default is 10). High > >>numbers lead to slightly longer spent planning but should > >>result in more efficient queries. > >> > >>So, you should try: > >> > set default_statistics_target 200; > >> > analyse; > >> > >>The value is set only for a particular session, to see value: > >> > show default_statistics_target; > >> > >>It is better to set the in postgresql.conf and restart postgres. > >> > >> > >>Then try building the webapp again. Hope this helps, > >>Richard. > >> > >> > >> > >> > >>AlexanderP@gmx.at wrote: > >> > >> > >>>here it is, > >>> > >>>ausgabe is the normal output > >>>errausgabe are the error messages... > >>>(attached) > >>> > >>>maybe it's only the Estimated time to run query greater than > maximum...? > >>> > >>>>>from command: > >>>nice nohup ant -v build-production-webapp >ausgabe.dat 2>errausgabe.dat > >>> >>> > >>>kind regards, > >>> alex > >>> > >>> > >>> > >>> > >>> > >> > >>_______________________________________________ > >>flymine-dev mailing list > >>flymine-dev@flymine.org > >>http://mailman.flymine.org/listinfo/flymine-dev -- Lust, ein paar Euro nebenbei zu verdienen? Ohne Kosten, ohne Risiko! Satte Provisionen für GMX Partner: http://www.gmx.net/de/go/partner From AlexanderP@gmx.at Fri Dec 16 11:48:15 2005 Received: from ppsw-9.csi.cam.ac.uk ([131.111.8.139]) by flymine.flymine.org with esmtp (Exim 4.12) id 1EnE4N-0002LN-00 for flymine-dev@flymine.org; Fri, 16 Dec 2005 11:48:15 +0000 X-Cam-SpamDetails: scanned, SpamAssassin (score=0.228, FORGED_RCVD_HELO 0.05, NO_REAL_NAME 0.18) X-Cam-AntiVirus: No virus found X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Received: from mail.gmx.de ([213.165.64.21]:39542 helo=mail.gmx.net) by ppsw-9.csi.cam.ac.uk (mx.cam.ac.uk [131.111.8.149]:25) with smtp (csa=unknown) id 1EnE4d-0005lc-UE (Exim 4.54) for flymine-dev@flymine.org (return-path ); Fri, 16 Dec 2005 11:48:31 +0000 Received: (qmail 28833 invoked by uid 0); 16 Dec 2005 11:48:30 -0000 Received: from 83.65.73.2 by www61.gmx.net with HTTP; Fri, 16 Dec 2005 12:48:30 +0100 (MET) Date: Fri, 16 Dec 2005 12:48:30 +0100 (MET) From: AlexanderP@gmx.at To: flymine-dev@flymine.org MIME-Version: 1.0 X-Priority: 3 (Normal) X-Authenticated: #6910802 Message-ID: <24938.1134733710@www61.gmx.net> X-Mailer: WWW-Mail 1.6 (Global Message Exchange) X-Flags: 0001 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Subject: [flymine-dev] instruction Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: hmm... is there maybe somewhere a step for step instruction for putting own data in flymine(-local-database)? (own data from the local machine... given as file...) alex -- 10 GB Mailbox, 100 FreeSMS/Monat http://www.gmx.net/de/go/topmail +++ GMX - die erste Adresse für Mail, Message, More +++ From kmr@flymine.org Fri Dec 16 14:28:00 2005 Received: from host110 ([192.168.128.110] helo=merry.flymine.org) by flymine.flymine.org with esmtp (Exim 4.12) id 1EnGYy-00034g-00; Fri, 16 Dec 2005 14:28:00 +0000 Received: from kmr by merry.flymine.org with local (Exim 3.36 #1 (Debian)) id 1EnGZK-0007Qp-00; Fri, 16 Dec 2005 14:28:22 +0000 From: Kim Rutherford MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="H4SiwxFQJZ" Content-Transfer-Encoding: 7bit Message-ID: <17314.52997.755940.510986@merry.flymine.org> Date: Fri, 16 Dec 2005 14:28:21 +0000 To: AlexanderP@gmx.at CC: flymine-dev@flymine.org Subject: Re: [flymine-dev] instruction In-Reply-To: <24938.1134733710@www61.gmx.net> References: <24938.1134733710@www61.gmx.net> X-Mailer: VM 7.19 under Emacs 21.3.50.1 X-PGP-Key: 0x1BF31C43 (1998-11-01) X-PGP-Fingerprint: 1F7E 46F2 3347 3C51 E9CF ED16 9E63 6029 1BF3 1C43 Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org X-Reply-To: kmr@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: --H4SiwxFQJZ Content-Type: text/plain; charset=us-ascii Content-Description: message body text Content-Transfer-Encoding: 7bit On Fri, 16 Dec 2005 12:48:30 +0100 (MET), AlexanderP wrote: > hmm... is there maybe somewhere a step for step instruction for > putting own data in flymine(-local-database)? (own data from the > local machine... given as file...) Hi. Unfortunately, we don't have a good tutorial at the moment. I understand that you would like to do things like create new ProteinFeature objects attached to existing Proteins. One way to do what you want is to write an ANT task that reads a file and creates ProteinFeature objects in your copy of the FlyMine database. I've attached a possible implementation that you could use as a starting point. To try it, you'll need to copy the file to: flymine/model/genomic/src/java/org/flymine/task/SimpleLoadTask.java And add this target to build.xml in the flymine directory: The Task reads files that look like: A32CD_DROME protein_feature_1_identifier protein_feature_1_long_name A33A_DROME protein_feature_2_identifier protein_feature_2_long_name (etc...) The first column of each line is the protein identifier, the second is the identifier of the new ProteinFeature and the third is the longName field for the new ProteinFeature. The command: ant simple-load-test should be all you need to test things. It's possible you'll have some problems with properties - let me know go it goes. Kim. --H4SiwxFQJZ Content-Type: text/plain Content-Description: SimpleLoadTask.java Content-Disposition: inline; filename="SimpleLoadTask.java" Content-Transfer-Encoding: 7bit package org.flymine.task; /* * Copyright (C) 2002-2005 FlyMine * * This code may be freely distributed and modified under the * terms of the GNU Lesser General Public Licence. This should * be distributed with the code. See the LICENSE file for more * information or http://www.gnu.org/copyleft/lesser.html. * */ import org.intermine.objectstore.query.ConstraintOp; import org.intermine.objectstore.query.Query; import org.intermine.objectstore.query.QueryClass; import org.intermine.objectstore.query.QueryField; import org.intermine.objectstore.query.QueryValue; import org.intermine.objectstore.query.Results; import org.intermine.objectstore.query.ResultsRow; import org.intermine.objectstore.query.SimpleConstraint; import org.intermine.objectstore.ObjectStoreException; import org.intermine.objectstore.ObjectStoreWriter; import org.intermine.objectstore.ObjectStoreWriterFactory; import org.intermine.util.DynamicUtil; import org.intermine.util.StringUtil; import org.flymine.model.genomic.Protein; import org.flymine.model.genomic.ProteinFeature; import java.io.BufferedReader; import java.io.File; import java.io.FileNotFoundException; import java.io.FileReader; import java.io.IOException; import java.util.ArrayList; import java.util.Collections; import java.util.HashSet; import java.util.Iterator; import java.util.List; import java.util.Set; import org.apache.tools.ant.BuildException; import org.apache.tools.ant.DirectoryScanner; import org.apache.tools.ant.Task; import org.apache.tools.ant.types.FileSet; /** * * @author Kim Rutherford */ public class SimpleLoadTask extends Task { private String oswAlias; private List fileSets = new ArrayList(); private ObjectStoreWriter osw; /** * The ObjectStoreWriter alias to use when querying and creating objects. * @param oswAlias the ObjectStoreWriter alias */ public void setOswAlias(String oswAlias) { this.oswAlias = oswAlias; } /** * Return the oswAlias set by setOswAlias() * @return the object store alias */ public String getOswAlias() { return oswAlias; } /** * Return the set of files that should be read from. * @return the List of FileSets */ public List getFileSets() { return fileSets; } /** * Return the ObjectStoreWriter given by oswAlias. * @return the ObjectStoreWriter * @throws BuildException if there is an error while processing */ protected ObjectStoreWriter getObjectStoreWriter() throws BuildException { if (oswAlias == null) { throw new BuildException("oswAlias attribute is not set"); } if (osw == null) { try { osw = ObjectStoreWriterFactory.getObjectStoreWriter(oswAlias); } catch (ObjectStoreException e) { throw new BuildException("cannot get ObjectStoreWriter for: " + oswAlias, e); } } return osw; } /** * Add a FileSet to read from * @param fileSet the FileSet */ public void addFileSet(FileSet fileSet) { fileSets.add(fileSet); } /** * Load data into the ObjectStoire given by oswAlias. * @throws BuildException if an ObjectStore method fails */ public void execute() throws BuildException { if (getOswAlias() == null) { throw new BuildException("oswAlias not set"); } try { getObjectStoreWriter().beginTransaction(); } catch (ObjectStoreException e) { throw new BuildException("cannot begin a transaction", e); } Iterator fileSetIter = getFileSets().iterator(); while (fileSetIter.hasNext()) { FileSet fileSet = (FileSet) fileSetIter.next(); DirectoryScanner ds = fileSet.getDirectoryScanner(getProject()); String[] files = ds.getIncludedFiles(); for (int i = 0; i < files.length; i++) { File file = new File(ds.getBasedir(), files[i]); processFile(file); } } try { getObjectStoreWriter().commitTransaction(); } catch (ObjectStoreException e) { throw new BuildException("cannot begin a transaction", e); } } private void processFile(File file) { try { BufferedReader reader = new BufferedReader(new FileReader(file)); String line; while ((line = reader.readLine()) != null) { if (line.trim().length() == 0) { continue; } String bits[] = StringUtil.split(line, " "); String proteinName = bits[0]; Set proteins = getProteinsForName(proteinName); String proteinFeatureIdentifier = bits[1]; String proteinFeatureName = bits[2]; ProteinFeature proteinFeature = (ProteinFeature) DynamicUtil.createObject(Collections.singleton(ProteinFeature.class)); proteinFeature.setIdentifier(proteinFeatureIdentifier); proteinFeature.setName(proteinFeatureName); proteinFeature.setProteins(proteins); osw.store(proteinFeature); } } catch (FileNotFoundException e) { throw new BuildException("problem reading file - file not found: " + file, e); } catch (IOException e) { throw new BuildException("problem reading file - I/O exception for:" + file, e); } catch (ObjectStoreException e) { throw new BuildException("problem storing object", e); } } private Set getProteinsForName(String proteinIdentifier) { Query q = new Query(); QueryClass qc = new QueryClass(Protein.class); q.addFrom(qc); q.addToSelect(qc); QueryValue qv = new QueryValue(proteinIdentifier); QueryField qf = new QueryField(qc, "identifier"); SimpleConstraint sc = new SimpleConstraint(qf, ConstraintOp.EQUALS, qv); q.setConstraint(sc); Set returnList = new HashSet(); try { Results res = osw.execute(q); Iterator resIter = res.iterator(); while (resIter.hasNext()) { ResultsRow rr = (ResultsRow) resIter.next(); returnList.add(rr.get(0)); } } catch (ObjectStoreException e) { throw new BuildException("cannot query Protein objects from database", e); } return returnList; } } --H4SiwxFQJZ-- From AlexanderP@gmx.at Wed Dec 21 23:11:37 2005 Received: from ppsw-1.csi.cam.ac.uk ([131.111.8.131]) by flymine.flymine.org with esmtp (Exim 4.12) id 1EpD7R-0006VS-00 for flymine-dev@flymine.org; Wed, 21 Dec 2005 23:11:37 +0000 X-Cam-SpamDetails: scanned, SpamAssassin (score=0.228, FORGED_RCVD_HELO 0.05, NO_REAL_NAME 0.18) X-Cam-AntiVirus: No virus found X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Received: from mail.gmx.de ([213.165.64.21]:40527 helo=mail.gmx.net) by ppsw-1.csi.cam.ac.uk (mx.cam.ac.uk [131.111.8.141]:25) with smtp (csa=unknown) id 1EpD7Z-0001pv-55 (Exim 4.54) for flymine-dev@flymine.org (return-path ); Wed, 21 Dec 2005 23:11:45 +0000 Received: (qmail 6275 invoked by uid 0); 21 Dec 2005 23:11:45 -0000 Received: from 83.65.73.2 by www81.gmx.net with HTTP; Thu, 22 Dec 2005 00:11:45 +0100 (MET) Date: Thu, 22 Dec 2005 00:11:45 +0100 (MET) From: AlexanderP@gmx.at To: flymine-dev@flymine.org MIME-Version: 1.0 X-Priority: 3 (Normal) X-Authenticated: #6910802 Message-ID: <26292.1135206705@www81.gmx.net> X-Mailer: WWW-Mail 1.6 (Global Message Exchange) X-Flags: 0001 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Subject: [flymine-dev] Query Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: (the last thing I have still not tried...) how do I make a query? (out of some program..) is there the possibility to query out of a program over the net? (maybe you have an example?) I have heard of a loader for some other databases (human, mouse,...), how is this working? for the xml, what favourite editor you have? (I should say I don't know good xml editors) (this time it isn't to hurriedly, Christmas is near :) regards, alex -- GMX DSL-Flatrate 1 Jahr kostenlos* + WLAN-Router ab 0,- Euro* Bis 31.12.2005 einsteigen! Infos unter: http://www.gmx.net/de/go/dsl From kmr@flymine.org Thu Dec 22 11:15:32 2005 Received: from host110 ([192.168.128.110] helo=merry.flymine.org) by flymine.flymine.org with esmtp (Exim 4.12) id 1EpOQ0-00008K-00; Thu, 22 Dec 2005 11:15:32 +0000 Received: from kmr by merry.flymine.org with local (Exim 3.36 #1 (Debian)) id 1EpOQM-0000Up-00; Thu, 22 Dec 2005 11:15:54 +0000 From: Kim Rutherford MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <17322.35562.875826.431888@merry.flymine.org> Date: Thu, 22 Dec 2005 11:15:54 +0000 To: flymine-dev@flymine.org CC: AlexanderP@gmx.at Subject: Re: [flymine-dev] Query In-Reply-To: <26292.1135206705@www81.gmx.net> References: <26292.1135206705@www81.gmx.net> X-Mailer: VM 7.19 under Emacs 21.3.50.1 X-PGP-Key: 0x1BF31C43 (1998-11-01) X-PGP-Fingerprint: 1F7E 46F2 3347 3C51 E9CF ED16 9E63 6029 1BF3 1C43 Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org X-Reply-To: kmr@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: On Thu, 22 Dec 2005 00:11:45 +0100 (MET), AlexanderP wrote: > (the last thing I have still not tried...) > how do I make a query? (out of some program..) Hi. There's an example of how to make a query in the SimpleLoadTask code I sent on Friday. See the getProteinsForName() method: http://subversion.flymine.org/trunk/flymine/doc/examples/simple_loader/SimpleLoadTask.java?rev=8190&view=markup There's another example here: http://www.intermine.org/doc/software/java_query/spec.html And a bit more of a description here: http://www.intermine.org/doc/software/howto_query.html For code example from FlyMine, have a look in: http://subversion.flymine.org/trunk/flymine/model/genomic/src/java/org/flymine/postprocess/PostProcessUtil.java?rev=8125&view=markup and the other classes in the org.flymine.postprocess package. > is there the possibility to query out of a program over the net? > (maybe you have an example?) Your client code doesn't have to be on the same machine as your postgres server. Is that what you mean? > I have heard of a loader for some other databases (human, mouse,...), > how is this working? We have another database for human genome stuff (http://www.flymine.org/t1dmine-preview/begin.do). That database is built in the same way as FlyMine, but from different database sources. The data model is very similar to FlyMine. Kim. From kmr@flymine.org Tue Jan 03 14:06:33 2006 Received: from host110 ([192.168.128.110] helo=merry.flymine.org) by flymine.flymine.org with esmtp (Exim 4.12) id 1Etmo5-0006nC-00; Tue, 03 Jan 2006 14:06:33 +0000 Received: from kmr by merry.flymine.org with local (Exim 3.36 #1 (Debian)) id 1EtmoR-0002nq-00; Tue, 03 Jan 2006 14:06:55 +0000 From: Kim Rutherford MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <17338.34047.104275.537367@merry.flymine.org> Date: Tue, 3 Jan 2006 14:06:55 +0000 To: AlexanderP@gmx.at CC: flymine-dev@flymine.org Subject: Re: [flymine-dev] instruction In-Reply-To: <26162.1136294918@www5.gmx.net> References: <26162.1136294918@www5.gmx.net> X-Mailer: VM 7.19 under Emacs 21.3.50.1 X-PGP-Key: 0x1BF31C43 (1998-11-01) X-PGP-Fingerprint: 1F7E 46F2 3347 3C51 E9CF ED16 9E63 6029 1BF3 1C43 Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org X-Reply-To: kmr@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: On Tue, 3 Jan 2006 14:28:38 +0100 (MET), AlexanderP wrote: > Hi, Hi. > I have done it (hopefully right), Excellent. > and at end there is written successfull, but it isn't > (the verbose output is attached) > the content of my_file is (I have named it so...): > 128UP_DROME temp_feature 1 > 14331_CAEEL temp_feature 2 > 18C_DROME temp_feature 3 > there are more than one thing in the output, that doesn't sound running > perfect, but especially the line: > compile-java: > [javac] my_file skipped - don't know how to handle it > (maybe I have forgotten some other easy thing?) I don't think that warning is a problem - my_file is in a directory that javac is trying to compile. It shouldn't matter. If you check the database with the webapp, are the extra objects in the database? > one other thing, how could I add a feature with more than one field? > (so: id featurename featurestart featureend ....) Unfortunately, ProteinFeature doesn't have a start or end field at the moment. In the rest of FlyMine we model start and end positions by having a separate Location object. For example, in a Gene there is a chromosomeLocation reference that contains the location information. http://www.flymine.org/release-3.1/objectDetails.do?id=18000931 I'll change the SimpleLoadTask to make a Location for each feature and get back to you. >> > is there the possibility to query out of a program over the net? >> > (maybe you have an example?) >> Your client code doesn't have to be on the same machine as your >> postgres server. Is that what you mean? > not exactly; running postgresql and have installed flymine on one > machine (or on two), and the querying program on one other > machine... (like browsing it, but maybe some smaller code... and > possible to change data...) When you say "installed flymine" do you mean installing the webapp? The postgres database can be accessed and changed from anywhere the intermine code is running (ie. the code in intermine-objectstore.jar). The webapp is just one example application. SimpleLoadTask is another application. SimpleLoadTask can run anywhere you have a copy of the flymine/intermine code and the right flymine.properties file. Kim. From kmr@flymine.org Tue Jan 03 15:18:40 2006 Received: from host110 ([192.168.128.110] helo=merry.flymine.org) by flymine.flymine.org with esmtp (Exim 4.12) id 1Etnvs-000719-00; Tue, 03 Jan 2006 15:18:40 +0000 Received: from kmr by merry.flymine.org with local (Exim 3.36 #1 (Debian)) id 1EtnwE-0003AN-00; Tue, 03 Jan 2006 15:19:02 +0000 From: Kim Rutherford MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="z7TRQ2N66q" Content-Transfer-Encoding: 7bit Message-ID: <17338.38374.341538.326815@merry.flymine.org> Date: Tue, 3 Jan 2006 15:19:02 +0000 To: AlexanderP@gmx.at, flymine-dev@flymine.org Subject: Re: [flymine-dev] instruction In-Reply-To: <17338.34047.104275.537367@merry.flymine.org> References: <26162.1136294918@www5.gmx.net> <17338.34047.104275.537367@merry.flymine.org> X-Mailer: VM 7.19 under Emacs 21.3.50.1 X-PGP-Key: 0x1BF31C43 (1998-11-01) X-PGP-Fingerprint: 1F7E 46F2 3347 3C51 E9CF ED16 9E63 6029 1BF3 1C43 Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org X-Reply-To: kmr@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: --z7TRQ2N66q Content-Type: text/plain; charset=us-ascii Content-Description: message body text Content-Transfer-Encoding: 7bit On Tue, 3 Jan 2006 14:06:55 +0000, Kim Rutherford wrote: >> one other thing, how could I add a feature with more than one field? >> (so: id featurename featurestart featureend ....) > Unfortunately, ProteinFeature doesn't have a start or end field at the > moment. In the rest of FlyMine we model start and end positions by > having a separate Location object. For example, in a Gene there is a > chromosomeLocation reference that contains the location information. > http://www.flymine.org/release-3.1/objectDetails.do?id=18000931 > I'll change the SimpleLoadTask to make a Location for each feature and > get back to you. Here is the updated version. Note that the code in processFile() might be a little more complicated than it needs to be because of the possibility that the protein identifier (ie. the first column) matches more than one Protein. processFile() creates a Location object that connects each matching Protein with the new ProteinFeature. Please let me know if there is a problem. Kim. --z7TRQ2N66q Content-Type: text/plain Content-Description: SimpleLoadTask.java Content-Disposition: inline; filename="SimpleLoadTask.java" Content-Transfer-Encoding: 7bit package org.flymine.task; /* * Copyright (C) 2002-2005 FlyMine * * This code may be freely distributed and modified under the * terms of the GNU Lesser General Public Licence. This should * be distributed with the code. See the LICENSE file for more * information or http://www.gnu.org/copyleft/lesser.html. * */ import org.intermine.objectstore.query.ConstraintOp; import org.intermine.objectstore.query.Query; import org.intermine.objectstore.query.QueryClass; import org.intermine.objectstore.query.QueryField; import org.intermine.objectstore.query.QueryValue; import org.intermine.objectstore.query.Results; import org.intermine.objectstore.query.ResultsRow; import org.intermine.objectstore.query.SimpleConstraint; import org.intermine.objectstore.ObjectStoreException; import org.intermine.objectstore.ObjectStoreWriter; import org.intermine.objectstore.ObjectStoreWriterFactory; import org.intermine.util.DynamicUtil; import org.intermine.util.StringUtil; import org.flymine.model.genomic.Location; import org.flymine.model.genomic.Protein; import org.flymine.model.genomic.ProteinFeature; import java.io.BufferedReader; import java.io.File; import java.io.FileNotFoundException; import java.io.FileReader; import java.io.IOException; import java.util.ArrayList; import java.util.Collections; import java.util.HashSet; import java.util.Iterator; import java.util.List; import java.util.Set; import org.apache.tools.ant.BuildException; import org.apache.tools.ant.DirectoryScanner; import org.apache.tools.ant.Task; import org.apache.tools.ant.types.FileSet; /** * An example Task that creates ProteinFeature objects using data from a flat file. * @author Kim Rutherford */ public class SimpleLoadTask extends Task { private String oswAlias; private List fileSets = new ArrayList(); private ObjectStoreWriter osw; /** * The ObjectStoreWriter alias to use when querying and creating objects. * @param oswAlias the ObjectStoreWriter alias */ public void setOswAlias(String oswAlias) { this.oswAlias = oswAlias; } /** * Return the oswAlias set by setOswAlias() * @return the object store alias */ public String getOswAlias() { return oswAlias; } /** * Return the set of files that should be read from. * @return the List of FileSets */ public List getFileSets() { return fileSets; } /** * Return the ObjectStoreWriter given by oswAlias. * @return the ObjectStoreWriter * @throws BuildException if there is an error while processing */ protected ObjectStoreWriter getObjectStoreWriter() throws BuildException { if (oswAlias == null) { throw new BuildException("oswAlias attribute is not set"); } if (osw == null) { try { osw = ObjectStoreWriterFactory.getObjectStoreWriter(oswAlias); } catch (ObjectStoreException e) { throw new BuildException("cannot get ObjectStoreWriter for: " + oswAlias, e); } } return osw; } /** * Add a FileSet to read from * @param fileSet the FileSet */ public void addFileSet(FileSet fileSet) { fileSets.add(fileSet); } /** * Load data into the ObjectStoire given by oswAlias. * @throws BuildException if an ObjectStore method fails */ public void execute() throws BuildException { if (getOswAlias() == null) { throw new BuildException("oswAlias not set"); } try { getObjectStoreWriter().beginTransaction(); } catch (ObjectStoreException e) { throw new BuildException("cannot begin a transaction", e); } Iterator fileSetIter = getFileSets().iterator(); while (fileSetIter.hasNext()) { FileSet fileSet = (FileSet) fileSetIter.next(); DirectoryScanner ds = fileSet.getDirectoryScanner(getProject()); String[] files = ds.getIncludedFiles(); for (int i = 0; i < files.length; i++) { File file = new File(ds.getBasedir(), files[i]); processFile(file); } } try { getObjectStoreWriter().commitTransaction(); } catch (ObjectStoreException e) { throw new BuildException("cannot begin a transaction", e); } } private void processFile(File file) { try { BufferedReader reader = new BufferedReader(new FileReader(file)); String line; while ((line = reader.readLine()) != null) { if (line.trim().length() == 0) { continue; } String bits[] = StringUtil.split(line, " "); String proteinName = bits[0]; Set proteins = getProteinsForName(proteinName); String proteinStart = bits[1]; String proteinEnd = bits[2]; String proteinFeatureIdentifier = bits[3]; String proteinFeatureName = bits[4]; ProteinFeature proteinFeature = (ProteinFeature) DynamicUtil.createObject(Collections.singleton(ProteinFeature.class)); proteinFeature.setIdentifier(proteinFeatureIdentifier); proteinFeature.setName(proteinFeatureName); proteinFeature.setProteins(proteins); Iterator proteinIter = proteins.iterator(); while (proteinIter.hasNext()) { Protein thisProtein = (Protein) proteinIter.next(); Location featureLocation = (Location) DynamicUtil.createObject(Collections.singleton(Location.class)); try { featureLocation.setStart(new Integer(Integer.parseInt(proteinStart))); } catch (NumberFormatException e) { throw new RuntimeException("failed to parse start position: " + proteinStart, e); } try { featureLocation.setEnd(new Integer(Integer.parseInt(proteinEnd))); } catch (NumberFormatException e) { throw new RuntimeException("failed to parse end position: " + proteinEnd, e); } featureLocation.setSubject(proteinFeature); featureLocation.setObject(thisProtein); osw.store(featureLocation); } osw.store(proteinFeature); } } catch (FileNotFoundException e) { throw new BuildException("problem reading file - file not found: " + file, e); } catch (IOException e) { throw new BuildException("problem reading file - I/O exception for:" + file, e); } catch (ObjectStoreException e) { throw new BuildException("problem storing object", e); } } private Set getProteinsForName(String proteinIdentifier) { Query q = new Query(); QueryClass qc = new QueryClass(Protein.class); q.addFrom(qc); q.addToSelect(qc); QueryValue qv = new QueryValue(proteinIdentifier); QueryField qf = new QueryField(qc, "identifier"); SimpleConstraint sc = new SimpleConstraint(qf, ConstraintOp.EQUALS, qv); q.setConstraint(sc); Set returnList = new HashSet(); try { Results res = osw.execute(q); Iterator resIter = res.iterator(); while (resIter.hasNext()) { ResultsRow rr = (ResultsRow) resIter.next(); returnList.add(rr.get(0)); } } catch (ObjectStoreException e) { throw new BuildException("cannot query Protein objects from database", e); } return returnList; } } --z7TRQ2N66q-- From kmr@flymine.org Tue Jan 03 17:07:45 2006 Received: from host110 ([192.168.128.110] helo=merry.flymine.org) by flymine.flymine.org with esmtp (Exim 4.12) id 1EtpdR-0007K3-00; Tue, 03 Jan 2006 17:07:45 +0000 Received: from kmr by merry.flymine.org with local (Exim 3.36 #1 (Debian)) id 1Etpdn-0003Xv-00; Tue, 03 Jan 2006 17:08:07 +0000 From: Kim Rutherford MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <17338.44919.404281.406572@merry.flymine.org> Date: Tue, 3 Jan 2006 17:08:07 +0000 To: AlexanderP@gmx.at CC: flymine-dev@flymine.org Subject: Re: [flymine-dev] instruction In-Reply-To: <31360.1136307732@www72.gmx.net> References: <17338.38374.341538.326815@merry.flymine.org> <31360.1136307732@www72.gmx.net> X-Mailer: VM 7.19 under Emacs 21.3.50.1 X-PGP-Key: 0x1BF31C43 (1998-11-01) X-PGP-Fingerprint: 1F7E 46F2 3347 3C51 E9CF ED16 9E63 6029 1BF3 1C43 Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org X-Reply-To: kmr@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: On Tue, 3 Jan 2006 18:02:12 +0100 (MET), AlexanderP wrote: > ok, I have done it with the new one, > my_file is now: > 128UP_DROME 1 2 temp_feature 1 > 14331_CAEEL 3 4 temp_feature 2 > 18C_DROME 5 6 temp_feature 3 > in the end of build is written successfull, > but I can't find changes in browsing the data (I looked for the special > protein, but no new feature is added...) > (the first time it was the same) Perhaps you could try querying the database directly. Try this query against your PostgreSQL database: select * from proteinfeature where identifier = 'temp_feature'; Kim. From kmr@flymine.org Wed Jan 04 14:50:48 2006 Received: from host110 ([192.168.128.110] helo=merry.flymine.org) by flymine.flymine.org with esmtp (Exim 4.12) id 1Eu9yS-0001ye-00; Wed, 04 Jan 2006 14:50:48 +0000 Received: from kmr by merry.flymine.org with local (Exim 3.36 #1 (Debian)) id 1Eu9yo-0006CU-00; Wed, 04 Jan 2006 14:51:10 +0000 From: Kim Rutherford MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <17339.57566.763904.946450@merry.flymine.org> Date: Wed, 4 Jan 2006 14:51:10 +0000 To: AlexanderP@gmx.at CC: flymine-dev@flymine.org Subject: Re: [flymine-dev] instruction In-Reply-To: <25268.1136326960@www2.gmx.net> References: <17338.44919.404281.406572@merry.flymine.org> <25268.1136326960@www2.gmx.net> X-Mailer: VM 7.19 under Emacs 21.3.50.1 X-PGP-Key: 0x1BF31C43 (1998-11-01) X-PGP-Fingerprint: 1F7E 46F2 3347 3C51 E9CF ED16 9E63 6029 1BF3 1C43 Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org X-Reply-To: kmr@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: On Tue, 3 Jan 2006 23:22:40 +0100 (MET), AlexanderP wrote: > hmmm... > if I browsing for it (ProteinFeature=="temp_feature" output Protein) then I > get the right Proteins... > but then if I browse on protein details I see nothing about that (I thought > in the special proteins in their protein-feature-list there will be the new > feature added... why not?) Hi. You are right, the new features should be on the Protein details page. The problem is that the model is slightly incorrect (Protein.proteinFeatures and ProteinFeature.proteins should be declared as reverse references of each other). We will fix that during our next build in a few weeks from now. For now Protein.proteinFeatures and ProteinFeature.proteins both need to be updated. > if I see the code right... it wasn't planned? > (there should be something like > get the feature-list of thisProtein; > add featureLocation to feature-list; > osw.store(thisProtein); > ? ) You are right. Try this change: --- SimpleLoadTask.java (revision 8225) +++ SimpleLoadTask.java (working copy) @@ -176,6 +176,9 @@ public class SimpleLoadTask extends Task while (proteinIter.hasNext()) { Protein thisProtein = (Protein) proteinIter.next(); + thisProtein.addProteinFeatures(proteinFeature); + osw.store(thisProtein); + Location featureLocation = (Location) DynamicUtil.createObject(Collections.singleton(Location.class)); try { Also we've noticed a bug in the original code that may cause the wrong object (ie. the old, unchanged object) to be stored. You should probably make this change: @@ -218,7 +221,7 @@ public class SimpleLoadTask extends Task Set returnList = new HashSet(); try { - Results res = osw.execute(q); + Results res = osw.getObjectStore().execute(q); Iterator resIter = res.iterator(); while (resIter.hasNext()) { ResultsRow rr = (ResultsRow) resIter.next(); Let me know it that works. Kim. From dpkreil@gmail.com Mon Jan 09 20:44:18 2006 Received: from ppsw-7.csi.cam.ac.uk ([131.111.8.137]) by flymine.flymine.org with esmtp (Exim 4.12) id 1Ew3sI-0000sK-00 for flymine-dev@flymine.org; Mon, 09 Jan 2006 20:44:18 +0000 X-Cam-SpamScore: s X-Cam-SpamDetails: scanned, SpamAssassin (score=1.033, HTML_10_20 0.29, HTML_MESSAGE 0.00, HTML_SHORT_LENGTH 0.71, RCVD_BY_IP 0.02) X-Cam-AntiVirus: No virus found X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Received: from zproxy.gmail.com ([64.233.162.207]:39671) by ppsw-7.csi.cam.ac.uk (mx.cam.ac.uk [131.111.8.147]:25) with esmtp (csa=unknown) id 1Ew3sX-0001V1-NP (Exim 4.54) for flymine-dev@flymine.org (return-path ); Mon, 09 Jan 2006 20:44:33 +0000 Received: by zproxy.gmail.com with SMTP id 18so3794659nzp for ; Mon, 09 Jan 2006 12:44:29 -0800 (PST) DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:message-id:date:from:reply-to:to:subject:mime-version:content-type; b=ChHNGdqO8b/KZC9co1gAkYQlVpcJYCHPVznktPoSWMORdNVwysIOR9TtSFnaINzpf+Rq1xonBAiI6S6BGQHenbmFnAN5Lmk/Bi/n29+v1xJ8o9xqgCXPiy+YWOXc6WDYIzaPAMR2CkFEW/S5/2I1WinTzMnj62rKQ6UXrCU7SGs= Received: by 10.65.52.3 with SMTP id e3mr2779232qbk; Mon, 09 Jan 2006 12:44:28 -0800 (PST) Received: by 10.65.155.15 with HTTP; Mon, 9 Jan 2006 12:44:27 -0800 (PST) Message-ID: <20e578260601091244w5d6a24b1n@mail.gmail.com> Date: Mon, 9 Jan 2006 21:44:27 +0100 From: "Dr. D. P. Kreil" To: flymine-dev@flymine.org MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_13247_13375192.1136839467539" Subject: [flymine-dev] 2006! Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org X-Reply-To: boku@kreil.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: ------=_Part_13247_13375192.1136839467539 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dear Flymine Developers, A Happy New Year, and many thanks for all your help and support with FlyMine! Greetings from Vienna, David. ------=_Part_13247_13375192.1136839467539 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dear Flymine Developers,

A Happy New Year, and many thanks for all y= our help and support with FlyMine!

Greetings from Vienna,

Dav= id.

------=_Part_13247_13375192.1136839467539-- From AlexanderP@gmx.at Fri Jan 13 00:37:13 2006 Received: from ppsw-7.csi.cam.ac.uk ([131.111.8.137]) by flymine.flymine.org with esmtp (Exim 4.12) id 1ExCwL-0007lG-00 for flymine-dev@flymine.org; Fri, 13 Jan 2006 00:37:13 +0000 X-Cam-SpamDetails: scanned, SpamAssassin (score=0.228, FORGED_RCVD_HELO 0.05, NO_REAL_NAME 0.18) X-Cam-AntiVirus: No virus found X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Received: from mail.gmx.de ([213.165.64.21]:50100 helo=mail.gmx.net) by ppsw-7.csi.cam.ac.uk (mx.cam.ac.uk [131.111.8.147]:25) with smtp (csa=unknown) id 1ExCwe-000692-Pl (Exim 4.54) for flymine-dev@flymine.org (return-path ); Fri, 13 Jan 2006 00:37:33 +0000 Received: (qmail 3226 invoked by uid 0); 13 Jan 2006 00:37:30 -0000 Received: from 83.65.73.2 by www47.gmx.net with HTTP; Fri, 13 Jan 2006 01:37:30 +0100 (MET) Date: Fri, 13 Jan 2006 01:37:30 +0100 (MET) From: AlexanderP@gmx.at To: flymine-dev@flymine.org MIME-Version: 1.0 X-Priority: 3 (Normal) X-Authenticated: #6910802 Message-ID: <30754.1137112650@www47.gmx.net> X-Mailer: WWW-Mail 1.6 (Global Message Exchange) X-Flags: 0001 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Subject: [flymine-dev] Thanks Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: hello all, for all a good year, a good friday and a good weekend; and thanks for all the help and advice (and reading my alien english as well... ;) without that we would never had set up the database so far... kind regards, alex -- 10 GB Mailbox, 100 FreeSMS/Monat http://www.gmx.net/de/go/topmail +++ GMX - die erste Adresse für Mail, Message, More +++ From S.G.Edwards-2@sms.ed.ac.uk Fri Jan 04 14:30:21 2008 Received: from ppsw-1.csi.cam.ac.uk ([131.111.8.131]) by flymine.flymine.org with esmtp (Exim 4.12) id 1JAnYz-0000JY-00 for flymine-dev@flymine.org; Fri, 04 Jan 2008 14:30:21 +0000 X-Cam-SpamDetails: scanned, SpamAssassin-3.2.3 (score=0) X-Cam-AntiVirus: No virus found X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Received: from lmtp2.ucs.ed.ac.uk ([129.215.149.71]:52285) by ppsw-1.csi.cam.ac.uk (mx.cam.ac.uk [131.111.8.141]:25) with esmtp (csa=unknown) id 1JAnYx-0002S5-5F (Exim 4.67) for flymine-dev@flymine.org (return-path ); Fri, 04 Jan 2008 14:30:19 +0000 Received: from smtp.sms.ed.ac.uk (mailfe6.ucs.ed.ac.uk [129.215.149.74]) by lmtp2.ucs.ed.ac.uk (8.13.8/8.13.7) with ESMTP id m04EU9s4015720 for ; Fri, 4 Jan 2008 14:30:14 GMT Received: from 88-107-85-213.dynamic.dsl.as9105.com (88-107-85-213.dynamic.dsl.as9105.com [88.107.85.213]) by www.sms.ed.ac.uk (Horde MIME library) with HTTP; Fri, 04 Jan 2008 14:30:09 +0000 Message-ID: <20080104143009.qbnujh928g0gwgo0@www.sms.ed.ac.uk> Date: Fri, 04 Jan 2008 14:30:09 +0000 From: SG Edwards To: flymine-dev@flymine.org MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Content-Disposition: inline Content-Transfer-Encoding: quoted-printable X-Edinburgh-Scanned: at lmtp2.ucs.ed.ac.uk with MIMEDefang 2.52, Sophie, Sophos Anti-Virus X-Scanned-By: MIMEDefang 2.52 on 129.215.149.71 Subject: [flymine-dev] Large file loading bottleneck Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Hey guys, Hope you had a good Christmas/New Year! I've still been having trouble with very large data files above a =20 certain size. They seem to reach a bottle neck such that the load =20 takes exponentially longer than you would expect given load times for =20 smaller files. You have suggested previously changing the ANT_OPTS settings to: export ANT_OPTS=3D"-server -XX:MaxPermSize=3D256M -Xmx1800m =20 -XX:+UseParallelGC -Xms1800m -XX:SoftRefLRUPolicyMSPerMB=3D1 =20 -XX:MaxHeapFreeRatio=3D99" However, this actually made the loads approx 2-4 times slower than =20 with the original setting of: export ANT_OPTS=3D"-server -XX:MaxPermSize=3D256M -Xmx1800m" Once the running job (e.g. ant -v -Dsource=3Dsentences_con_abs =20 integrate) reaches a java memory of 1.1Gb or above there is a distinct =20 increase in load time (most of the large data sources are custom ones =20 of the type intermine-items-large-xml-file). I suspect this is =20 probably more due to the postgres settings as much as anything? I can =20 get a hold of the postgres settings if you need them (which ones?). My question would be: is it possible to split a large file into two =20 custom files with distinct information in each i.e. sentence IDs from =20 1 -> 1,000,000 in file one; 1,000,001 -> 2,000,000 in file two and =20 load each file separately. Kim had mentioned previously that this =20 wasn't a good idea to try and reload a source that had been already =20 loaded but would it be possible to do this if the data is distinct =20 (i.e. should avoid the error: object already loaded from this source). =20 Would this affect indexing or some other integration process? Cheers, Stephen p.s. I'm still using version 8.2 at the minute as I want to stay =20 compatible with the older style interface. --=20 The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From s0460205@sms.ed.ac.uk Fri Jan 04 20:23:16 2008 Received: from ppsw-9.csi.cam.ac.uk ([131.111.8.139]) by flymine.flymine.org with esmtp (Exim 4.12) id 1JAt4W-0001Ia-00 for flymine-dev@flymine.org; Fri, 04 Jan 2008 20:23:16 +0000 X-Cam-SpamDetails: scanned, SpamAssassin-3.2.3 (score=0) X-Cam-AntiVirus: No virus found X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Received: from lmtp2.ucs.ed.ac.uk ([129.215.149.71]:38827) by ppsw-9.csi.cam.ac.uk (mx.cam.ac.uk [131.111.8.149]:25) with esmtp (csa=unknown) id 1JAt4U-0008Kw-TL (Exim 4.67) for flymine-dev@flymine.org (return-path ); Fri, 04 Jan 2008 20:23:14 +0000 Received: from smtp.sms.ed.ac.uk (mailfe6.ucs.ed.ac.uk [129.215.149.74]) by lmtp2.ucs.ed.ac.uk (8.13.8/8.13.7) with ESMTP id m04KND6m024930 for ; Fri, 4 Jan 2008 20:23:14 GMT Received: from 88-107-85-213.dynamic.dsl.as9105.com (88-107-85-213.dynamic.dsl.as9105.com [88.107.85.213]) by www.sms.ed.ac.uk (Horde MIME library) with HTTP; Fri, 04 Jan 2008 20:23:13 +0000 Message-ID: <20080104202313.8f912a38w040wws4@www.sms.ed.ac.uk> Date: Fri, 04 Jan 2008 20:23:13 +0000 From: SG Edwards To: flymine-dev@flymine.org MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Content-Disposition: inline Content-Transfer-Encoding: quoted-printable X-Edinburgh-Scanned: at lmtp2.ucs.ed.ac.uk with MIMEDefang 2.52, Sophie, Sophos Anti-Virus X-Scanned-By: MIMEDefang 2.52 on 129.215.149.71 Subject: [flymine-dev] Large file loading bottleneck Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Hey guys, Hope you had a good Christmas/New Year! I've still been having trouble with very large data files above a =20 certain size. They seem to reach a bottle neck such that the load =20 takes exponentially longer than you would expect given load times for =20 smaller files. You have suggested previously changing the ANT_OPTS settings to: export ANT_OPTS=3D"-server -XX:MaxPermSize=3D256M -Xmx1800m =20 -XX:+UseParallelGC -Xms1800m -XX:SoftRefLRUPolicyMSPerMB=3D1 =20 -XX:MaxHeapFreeRatio=3D99" However, this actually made the loads approx 2-4 times slower than =20 with the original setting of: export ANT_OPTS=3D"-server -XX:MaxPermSize=3D256M -Xmx1800m" Once the running job (e.g. ant -v -Dsource=3Dsentences_con_abs =20 integrate) reaches a java memory of 1.1Gb or above there is a distinct =20 increase in load time (most of the large data sources are custom ones =20 of the type intermine-items-large-xml-file). I suspect this is =20 probably more due to the postgres settings as much as anything? I can =20 get a hold of the postgres settings if you need them (which ones?). My question would be: is it possible to split a large file into two =20 custom files with distinct information in each i.e. sentence IDs from =20 1 -> 1,000,000 in file one; 1,000,001 -> 2,000,000 in file two and =20 load each file separately. Kim had mentioned previously that this =20 wasn't a good idea to try and reload a source that had been already =20 loaded but would it be possible to do this if the data is distinct =20 (i.e. should avoid the error: object already loaded from this source). =20 Would this affect indexing or some other integration process? Cheers, Stephen p.s. I'm still using version 8.2 at the minute as I want to stay =20 compatible with the older style interface. --=20 The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From richard@flymine.org Tue Jan 08 11:25:02 2008 Received: from [192.168.128.115] (helo=chimp.flymine.org) by flymine.flymine.org with esmtp (Exim 4.12) id 1JCCZq-0005KP-00 for flymine-dev@flymine.org; Tue, 08 Jan 2008 11:25:02 +0000 Message-ID: <47835D8E.4030302@flymine.org> Date: Tue, 08 Jan 2008 11:25:02 +0000 From: Richard Smith User-Agent: Thunderbird 2.0.0.9 (Macintosh/20071031) MIME-Version: 1.0 To: flymine-dev@flymine.org Subject: Re: [flymine-dev] Large file loading bottleneck References: <20080104202313.8f912a38w040wws4@www.sms.ed.ac.uk> In-Reply-To: <20080104202313.8f912a38w040wws4@www.sms.ed.ac.uk> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Hi Stephen, It could be a memory issue. Are you running the java and postgres on the same machine? How much RAM does the machine have? And are there other processes on the machine? How much RAM/cpu is postgres using? If you can let us have the intermine.log from the load then we may be able to spot something. You could try running the data load in the 10.0 branch and see if it is better. I think most performance improvements were completed by 8.2 but we do keep making improvements. Cheers, Richard. SG Edwards wrote: > Hey guys, > > Hope you had a good Christmas/New Year! > > I've still been having trouble with very large data files above a > certain size. They seem to reach a bottle neck such that the load takes > exponentially longer than you would expect given load times for smaller > files. > > You have suggested previously changing the ANT_OPTS settings to: > > export ANT_OPTS="-server -XX:MaxPermSize=256M -Xmx1800m > -XX:+UseParallelGC -Xms1800m -XX:SoftRefLRUPolicyMSPerMB=1 > -XX:MaxHeapFreeRatio=99" > > However, this actually made the loads approx 2-4 times slower than with > the original setting of: > > export ANT_OPTS="-server -XX:MaxPermSize=256M -Xmx1800m" > > Once the running job (e.g. ant -v -Dsource=sentences_con_abs integrate) > reaches a java memory of 1.1Gb or above there is a distinct increase in > load time (most of the large data sources are custom ones of the type > intermine-items-large-xml-file). I suspect this is probably more due to > the postgres settings as much as anything? I can get a hold of the > postgres settings if you need them (which ones?). > > My question would be: is it possible to split a large file into two > custom files with distinct information in each i.e. sentence IDs from 1 > -> 1,000,000 in file one; 1,000,001 -> 2,000,000 in file two and load > each file separately. Kim had mentioned previously that this wasn't a > good idea to try and reload a source that had been already loaded but > would it be possible to do this if the data is distinct (i.e. should > avoid the error: object already loaded from this source). Would this > affect indexing or some other integration process? > > Cheers, > > Stephen > > p.s. I'm still using version 8.2 at the minute as I want to stay > compatible with the older style interface. > From s0460205@sms.ed.ac.uk Tue Jan 08 14:24:22 2008 Received: from ppsw-8.csi.cam.ac.uk ([131.111.8.138]) by flymine.flymine.org with esmtp (Exim 4.12) id 1JCFNO-0005oA-00; Tue, 08 Jan 2008 14:24:22 +0000 X-Cam-SpamScore: s X-Cam-SpamDetails: scanned, SpamAssassin-3.2.0 (score=1.819, MIME_QP_LONG_LINE 1.82) X-Cam-AntiVirus: No virus found X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Received: from lmtp2.ucs.ed.ac.uk ([129.215.149.71]:62606) by ppsw-8.csi.cam.ac.uk (mx.cam.ac.uk [131.111.8.148]:25) with esmtp (csa=unknown) id 1JCFNL-0007dO-Qb (Exim 4.67) (return-path ); Tue, 08 Jan 2008 14:24:19 +0000 Received: from smtp.sms.ed.ac.uk (mailwfe2.ucs.ed.ac.uk [129.215.149.70]) by lmtp2.ucs.ed.ac.uk (8.13.8/8.13.7) with ESMTP id m08EOJQQ006561; Tue, 8 Jan 2008 14:24:19 GMT Received: from 88-107-85-213.dynamic.dsl.as9105.com (88-107-85-213.dynamic.dsl.as9105.com [88.107.85.213]) by www.sms.ed.ac.uk (Horde MIME library) with HTTP; Tue, 08 Jan 2008 14:24:18 +0000 Message-ID: <20080108142418.wgufvr968ow84wo4@www.sms.ed.ac.uk> Date: Tue, 08 Jan 2008 14:24:18 +0000 From: SG Edwards To: Richard Smith Cc: flymine-dev@flymine.org, Shakir Ali Subject: Re: [flymine-dev] Large file loading bottleneck References: <20080104202313.8f912a38w040wws4@www.sms.ed.ac.uk> <47835D8E.4030302@flymine.org> In-Reply-To: <47835D8E.4030302@flymine.org> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Content-Disposition: inline Content-Transfer-Encoding: quoted-printable X-Edinburgh-Scanned: at lmtp2.ucs.ed.ac.uk with MIMEDefang 2.52, Sophie, Sophos Anti-Virus X-Scanned-By: MIMEDefang 2.52 on 129.215.149.71 Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Hi Richard, OK, there are two separate issues here: 1. Up until a couple of weeks ago the loads were going fine except =20 that they were very slow for large sources. 2. Recently, the loads for medium or large sources have slowed right =20 down e.g. UniProt used to take 50 mins to load on our machines but now =20 takes 105 mins? Small sources load in the exact same time as previously. It would seem that something has changed that has caused the second =20 point. As far as we can tell there have been no changes to java, ant =20 or postgres configs recently and the only change is that a small =20 tomcat application has been deployed (SyMBA), however, we don't think =20 this should be the cause, it certainly doesn't appear to be taking any =20 cpu time at all. > It could be a memory issue. Are you running the java and postgres on =20 > the same machine? How much RAM does the machine have? And are there =20 > other processes on the machine? How much RAM/cpu is postgres using? I'm pretty sure it is a memory issue (in regards to problem 2) as the =20 loads were running fine previously. Java, ant and tomcat are running =20 on a separate server to postgres. Both machines are pretty reasonable =20 spec (4Gb RAM). Occasionally people are running other processes on the =20 machines but by and large there are no other processes doing much at =20 all. Here's the 'top' output during a load of the uniprot source, this =20 is a snapshot after about two hours (real time) running, no other =20 significant processes are running: top - 14:10:02 up 47 days, 1:32, 3 users, load average: 0.49, 0.50, 0.39 Tasks: 168 total, 2 running, 166 sleeping, 0 stopped, 0 zombie Cpu(s): 4.1%us, 0.7%sy, 0.0%ni, 94.6%id, 0.5%wa, 0.0%hi, 0.0%si, 0.0%= st Mem: 4151220k total, 3979884k used, 171336k free, 24360k buffers Swap: 8193140k total, 40100k used, 8153040k free, 1386996k cached PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND 15017 s0460205 18 0 2298m 1.9g 46m R 70 48.2 49:03.24 java ...and on the postgres server (postgres processes only).... top - 14:09:25 up 320 days, 21:14, 1 user, load average: 1.42, 1.31, 1.21 Tasks: 130 total, 1 running, 128 sleeping, 1 stopped, 0 zombie Cpu(s): 0.4%us, 0.2%sy, 0.0%ni, 99.3%id, 0.1%wa, 0.0%hi, 0.0%si, 0.0%= st Mem: 4151220k total, 4013228k used, 137992k free, 47696k buffers Swap: 20482864k total, 1607664k used, 18875200k free, 3128772k cached PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND 31670 postgres 17 0 97200 5484 5096 S 0 0.1 0:00.34 postmaster 31671 postgres 15 0 10852 624 244 S 0 0.0 0:00.35 postmaster 31673 postgres 15 0 97432 80m 79m S 0 2.0 0:52.26 postmaster 31674 postgres 15 0 11852 1584 196 S 0 0.0 0:01.84 postmaster 31675 postgres 15 0 12296 1768 276 S 0 0.0 0:21.52 postmaster 2786 postgres 15 0 98356 82m 81m S 0 2.0 0:10.50 postmaster 2789 postgres 15 0 98064 82m 81m S 0 2.0 3:05.32 postmaster 2801 postgres 15 0 98236 81m 79m S 0 2.0 0:15.48 postmaster 2807 postgres 15 0 98308 82m 80m S 0 2.0 1:51.76 postmaster 2808 postgres 16 0 98012 74m 73m S 0 1.8 0:09.79 postmaster 2815 postgres 15 0 98236 6740 5584 S 0 0.2 0:00.02 postmaster 2816 postgres 15 0 99136 83m 81m S 0 2.1 4:02.89 postmaster 2817 postgres 15 0 97916 3848 2976 S 0 0.1 0:00.03 postmaster 2818 postgres 15 0 98052 81m 80m S 0 2.0 2:04.06 postmaster 2819 postgres 15 0 97656 2212 1496 S 0 0.1 0:00.01 postmaster 2820 postgres 16 0 98932 83m 81m S 0 2.0 79:42.95 postmaster 2821 postgres 15 0 98236 4964 3788 S 0 0.1 0:00.01 postmaster 2822 postgres 15 0 98008 8508 7420 S 0 0.2 0:00.03 postmaster Seems to be an awful lot of postmaster processes running, is that =20 normal?! There are five postmaster processes running when there is no =20 activity on the postgres database ? I think there should only be =20 one(?). Looking at it there appears to be a tiny amount of free memory =20 on both machines (~150Mb out of 4Gb) but I think this is normal =20 behaviour where the OS will free up memory as required? Our OS memory settings are as follows: > cat /proc/meminfo MemTotal: 4151220 kB MemFree: 182180 kB Buffers: 26040 kB Cached: 1377780 kB SwapCached: 19808 kB Active: 2579972 kB Inactive: 1275760 kB HighTotal: 3276544 kB HighFree: 42468 kB LowTotal: 874676 kB LowFree: 139712 kB SwapTotal: 8193140 kB SwapFree: 8153040 kB Dirty: 720 kB Writeback: 0 kB AnonPages: 2450680 kB Mapped: 86836 kB Slab: 77724 kB PageTables: 11396 kB NFS_Unstable: 0 kB Bounce: 0 kB CommitLimit: 10268748 kB Committed_AS: 3250984 kB VmallocTotal: 116728 kB VmallocUsed: 11316 kB VmallocChunk: 105140 kB HugePages_Total: 0 HugePages_Free: 0 HugePages_Rsvd: 0 Hugepagesize: 2048 kB > You could try running the data load in the 10.0 branch and see if it is > better. I think most performance improvements were completed by 8.2 > but we do keep making improvements. I have tried an install of version 10 to see if that resets the =20 problem but it?s still struggling as with version 8_2. I?m sure =20 problem 2 is not with the intermine code but with the postgres =20 database or memory. We?ve restarted the postgres database as well but =20 again didn?t fix it. Any suggestions very welcome!! A bit bemused up here as to what has happened= ! Cheers, Stephen > Cheers, > Richard. > > > > SG Edwards wrote: >> Hey guys, >> >> Hope you had a good Christmas/New Year! >> >> I've still been having trouble with very large data files above a =20 >> certain size. They seem to reach a bottle neck such that the load =20 >> takes exponentially longer than you would expect given load times =20 >> for smaller files. >> >> You have suggested previously changing the ANT_OPTS settings to: >> >> export ANT_OPTS=3D"-server -XX:MaxPermSize=3D256M -Xmx1800m =20 >> -XX:+UseParallelGC -Xms1800m -XX:SoftRefLRUPolicyMSPerMB=3D1 =20 >> -XX:MaxHeapFreeRatio=3D99" >> >> However, this actually made the loads approx 2-4 times slower than =20 >> with the original setting of: >> >> export ANT_OPTS=3D"-server -XX:MaxPermSize=3D256M -Xmx1800m" >> >> Once the running job (e.g. ant -v -Dsource=3Dsentences_con_abs =20 >> integrate) reaches a java memory of 1.1Gb or above there is a =20 >> distinct increase in load time (most of the large data sources are =20 >> custom ones of the type intermine-items-large-xml-file). I suspect =20 >> this is probably more due to the postgres settings as much as =20 >> anything? I can get a hold of the postgres settings if you need =20 >> them (which ones?). >> >> My question would be: is it possible to split a large file into two =20 >> custom files with distinct information in each i.e. sentence IDs =20 >> from 1 -> 1,000,000 in file one; 1,000,001 -> 2,000,000 in file two =20 >> and load each file separately. Kim had mentioned previously that =20 >> this wasn't a good idea to try and reload a source that had been =20 >> already loaded but would it be possible to do this if the data is =20 >> distinct (i.e. should avoid the error: object already loaded from =20 >> this source). Would this affect indexing or some other integration =20 >> process? >> >> Cheers, >> >> Stephen >> >> p.s. I'm still using version 8.2 at the minute as I want to stay =20 >> compatible with the older style interface. >> > > > _______________________________________________ > flymine-dev mailing list > flymine-dev@flymine.org > http://mailman.flymine.org/listinfo/flymine-dev --=20 The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From matthew@flymine.org Thu Jan 10 15:56:56 2008 Received: from host103 ([192.168.128.103] helo=aragorn.flymine.org ident=Debian-exim) by flymine.flymine.org with esmtp (Exim 4.12) id 1JCzm4-0004Da-00 for flymine-dev@flymine.org; Thu, 10 Jan 2008 15:56:56 +0000 Received: from mnw21 (helo=localhost) by aragorn.flymine.org with local-esmtp (Exim 4.68) (envelope-from ) id 1JCzlo-0001VY-Rj for flymine-dev@flymine.org; Thu, 10 Jan 2008 15:56:40 +0000 Date: Thu, 10 Jan 2008 15:56:40 +0000 (GMT) From: Matthew Wakeling X-X-Sender: mnw21@aragorn.flymine.org To: flymine-dev@flymine.org Subject: Re: [flymine-dev] Large file loading bottleneck In-Reply-To: <20080104202313.8f912a38w040wws4@www.sms.ed.ac.uk> Message-ID: References: <20080104202313.8f912a38w040wws4@www.sms.ed.ac.uk> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: On Fri, 4 Jan 2008, SG Edwards wrote: > I've still been having trouble with very large data files above a certain > size. They seem to reach a bottle neck such that the load takes exponentially > longer than you would expect given load times for smaller files. Hi. I was wondering if you could send us a copy of an intermine.log that gets generated when you do a data loading run on a slow data source. Send it directly to me, preferably compressed, as it could be big. Thanks, Matthew From kmr@flymine.org Thu Jan 17 15:51:18 2008 Received: from host110 ([192.168.128.110] helo=merry.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 1JFX1S-0002Nf-00; Thu, 17 Jan 2008 15:51:18 +0000 Received: from kmr by merry.flymine.org with local (Exim 3.36 #1 (Debian)) id 1JFX1R-0008Dx-00; Thu, 17 Jan 2008 15:51:17 +0000 From: Kim Rutherford MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <18319.31093.903060.90125@merry.flymine.org> Date: Thu, 17 Jan 2008 15:51:17 +0000 To: flymine-dev@flymine.org X-Mailer: VM 7.19 under Emacs 21.3.50.1 X-PGP-Key: 0x1BF31C43 (1998-11-01) X-PGP-Fingerprint: 1F7E 46F2 3347 3C51 E9CF ED16 9E63 6029 1BF3 1C43 Subject: [flymine-dev] Objectstore summarisation improvements Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org X-Reply-To: kmr@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Hi. We've recently made some improvements to the InterMine code that performs the Object store summarisation (see: http://www.intermine.org/wiki/WebappRelease#Objectstoresummarisation). If you have been making your own build of a webapp you will have seen the message "Summarising object store"... which is followed by long wait. The code has been improved in two ways: The summary is now stored in the database rather than in a file (which was dbmodel/dist/objectstoresummary.properties). This means that if you do a "ant clean-all" command you won't have another long wait for the summary properties file to be recreated - it will be retrieved from the database. The second change is the addition of a post-process task that can be added to the project.xml that will create the summary as part of the build. All that is needed is to add the line: to the end of the section of your project.xml Added the post-process is recommended as it will save time while deploying the webapp as the summarisation will already be done. It also provides a way to re-summarise (needed if any data changes), by running the `summarise-objectstore` post-process (in the /postprocess directory): ant -Daction=summarise-objectstore Note that these changes are currently only on the subversion trunk. We won't be changing older branches. The changes will be in the version 11.0 branch. Kim. From Wolfgang.Lugmayr@imp.ac.at Mon Feb 18 12:27:55 2008 Received: from ppsw-7.csi.cam.ac.uk ([131.111.8.137]) by flymine.flymine.org with esmtp (Exim 4.12) id 1JR56B-0001vm-00 for flymine-dev@flymine.org; Mon, 18 Feb 2008 12:27:55 +0000 X-Cam-SpamDetails: scanned, SpamAssassin-3.2.3 (score=0) X-Cam-AntiVirus: No virus found X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Received: from mordor.imp.ac.at ([193.171.188.3]:6763 helo=mail.imp.univie.ac.at) by ppsw-7.csi.cam.ac.uk (mx.cam.ac.uk [131.111.8.147]:25) with esmtp (csa=unknown) id 1JR560-0002BI-NS (Exim 4.67) for flymine-dev@flymine.org (return-path ); Mon, 18 Feb 2008 12:27:49 +0000 Received: from bioinfo10.imp.univie.ac.at ([10.42.100.10]) by mail.imp.univie.ac.at with Microsoft SMTPSVC(6.0.3790.1830); Mon, 18 Feb 2008 13:27:23 +0100 From: Wolfgang Lugmayr To: flymine-dev@flymine.org Content-Type: multipart/mixed; boundary="=-rH7SK11qRjSLp6QktYC5" Date: Mon, 18 Feb 2008 13:27:23 +0100 Message-Id: <1203337643.3173.23.camel@bioinfo10.imp.univie.ac.at> Mime-Version: 1.0 X-Mailer: Evolution 2.6.3 X-OriginalArrivalTime: 18 Feb 2008 12:27:23.0489 (UTC) FILETIME=[9D182510:01C87229] Subject: [flymine-dev] flymine 11 - ant build-db-userprofile problem Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org X-Reply-To: wolfgang.lugmayr@imp.ac.at List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: --=-rH7SK11qRjSLp6QktYC5 Content-Type: text/plain Content-Transfer-Encoding: 7bit Hi, when building flymine 11 from scratch the following error occurs when calling: (ant build-db-userprofile 2>&1) | tee ant-userprofile.log : [load-default-templates] Adding template "gene_agLifecycleExpression" [load-default-templates] Adding template "gene_downstreamAdjacentgene_FlyAtlas" [invalid] [load-default-templates] Adding template "mRNAlocalisationTerm_Genes" BUILD FAILED /bioinfodev1/flymine/flymine11/imbuild/application.xml:87: java.lang.RuntimeException: unknown class name "org.flymine.model.genomic.Paralogue" while tagging: org.flymine.model.genomic.Paralogue doing some ant compile, jar, war etc. ... and running the same again the error is: /bioinfodev1/flymine/flymine11/imbuild/application.xml:87: java.lang.RuntimeException: unknown class name "org.flymine.model.genomic.ProteinFeature" while tagging: org.flymine.model.genomic.ProteinFeature The classes/tables existed in flymine9 but not in 11? Attached is the logfile of the first run. Is there an error in ./webapp/src/default-template-queries.xml? Cheers, Wolfgang -- Wolfgang Lugmayr Research Institute of Molecular Pathology (IMP) Dr. Bohr-Gasse 7, A-1030 Vienna, Austria Phone: +43 1 797 30 - 3370 Email: wolfgang.lugmayr@imp.ac.at http://www.imp.ac.at/ --=-rH7SK11qRjSLp6QktYC5 Content-Disposition: attachment; filename=ant-userprofile.log Content-Type: text/x-log; name=ant-userprofile.log; charset=UTF-8 Content-Transfer-Encoding: 7bit Buildfile: build.xml -init-project: -check-for-intermine-properties-file: -set-release-suffix-not-exists: -set-release-suffix-exists: -set-release-suffix: library.-pre-pre-init: -pre-pre-init: library.-pre-init: webapp.-pre-init: -pre-init: -pre-define-task-classpath: [delete] Deleting directory /bioinfodev1/flymine/flymine11/flymine/webapp/build/tmp [mkdir] Created dir: /bioinfodev1/flymine/flymine11/flymine/webapp/build/tmp -init-check-for-intermine-properties: -check-for-intermine-properties: -init-properties: [copy] Copying 1 file to /bioinfodev1/flymine/flymine11/flymine/webapp/build/main [copy] Copying 1 file to /bioinfodev1/flymine/flymine11/flymine/webapp/build/main -pre-init-deps: -init-deps: [dependencies] ---- Dependency build order:----------------------- [dependencies] intermine/objectstore/main [dependencies] intermine/integrate/model/fulldata [dependencies] intermine/integrate/main [dependencies] flymine/dbmodel [dependencies] intermine/web/model/userprofile [dependencies] intermine/web/main [dependencies] intermine/webapp/main [dependencies] intermine/webtasks/main [dependencies] bio/core/main [dependencies] bio/core/props [dependencies] bio/postprocess/main [dependencies] bio/tools/main [dependencies] bio/webapp [dependencies] flymine/sitemap [dependencies] --------------------------------------------------- [dependencies] Executing "jar" for source "intermine/objectstore/main" in directory: /bioinfodev1/flymine/flymine11/imbuild/../intermine/objectstore/main -init-project: -pre-pre-init: -pre-init: init: -pre-init-deps: -init-deps: -init-compile: -init-generate: -pre-generate: do-generate: -post-generate: generate: -pre-compile: -init-macrodef-javac: do-compile-with-gen-src: do-compile-without-gen-src: do-compile: -post-compile: compile: -init-jar: -pre-jar: -init-presetdef-jar: do-jar: -post-jar: jar: [dependencies] Executing "jar" for source "intermine/integrate/model/fulldata" in directory: /bioinfodev1/flymine/flymine11/imbuild/../intermine/integrate/model/fulldata -init-project: -pre-pre-init: library.-pre-init: -pre-init: init: -pre-init-deps: -init-deps: -init-compile: library.-init-generate: -pre-define-task-classpath: [delete] Deleting directory /bioinfodev1/flymine/flymine11/intermine/integrate/model/fulldata/build/tmp [mkdir] Created dir: /bioinfodev1/flymine/flymine11/intermine/integrate/model/fulldata/build/tmp -define-task-classpath: -check-task-availability: -load-os-tasks: [echo] Loading objectstore tasks -load-int-tasks: [echo] Loading integration tasks -load-web-tasks: -load-task-taskdefs: -init-macrodef-build-db: -init-task-xml: -init-model-out-of-date: -init-macrodef-model-generation: -init-generate: -pre-generate: build-model-from-xml-in-build-dir: build-model-from-xml-in-project-dir: build-model-from-xmi: build-model-from-zargo: [echo] Found zargo file build-model-from-xmlschema: -generate-model-java-message: [echo] generated model java is up to date - not regenerating -init-macrodef-model-output: generate-model-java: do-generate: -post-generate: generate: -pre-compile: -init-macrodef-javac: do-compile-with-gen-src: do-compile-without-gen-src: do-compile: -post-compile: compile: -init-jar: -pre-jar: -init-presetdef-jar: do-jar: -post-jar: jar: [dependencies] Executing "jar" for source "intermine/integrate/main" in directory: /bioinfodev1/flymine/flymine11/imbuild/../intermine/integrate/main -init-project: -pre-pre-init: -pre-init: init: -pre-init-deps: -init-deps: -init-compile: -init-generate: -pre-generate: do-generate: -post-generate: generate: -pre-compile: -init-macrodef-javac: do-compile-with-gen-src: do-compile-without-gen-src: do-compile: -post-compile: compile: -init-jar: -pre-jar: -init-presetdef-jar: do-jar: -post-jar: jar: [dependencies] Executing "jar" for source "flymine/dbmodel" in directory: /bioinfodev1/flymine/flymine11/imbuild/../flymine/dbmodel -init-project: -pre-pre-init: library.-pre-init: model.-pre-init: -pre-init: init: -pre-init-deps: -init-deps: -init-compile: library.-init-generate: -pre-define-task-classpath: [delete] Deleting directory /bioinfodev1/flymine/flymine11/flymine/dbmodel/build/tmp [mkdir] Created dir: /bioinfodev1/flymine/flymine11/flymine/dbmodel/build/tmp -define-task-classpath: -check-task-availability: -load-os-tasks: [echo] Loading objectstore tasks -load-int-tasks: [echo] Loading integration tasks -load-web-tasks: -load-task-taskdefs: -init-macrodef-build-db: -init-task-xml: -init-model-out-of-date: -init-macrodef-model-generation: model.-init-generate: -init-generate: -check-for-intermine-properties-file: -set-release-suffix-not-exists: -set-release-suffix-exists: -set-release-suffix: -init-check-for-intermine-properties: -check-for-intermine-properties: -init-properties: [copy] Copying 1 file to /bioinfodev1/flymine/flymine11/flymine/dbmodel/build/main [copy] Copying 1 file to /bioinfodev1/flymine/flymine11/flymine/dbmodel/build/main -pre-generate-retrieve: [echo] Retrieving model from os.production... [dependencies] Not writing "genomic_keyDefs.properties" as version in database is identical to local copy [dependencies] Model in database is identical to local model. -pre-generate-properties: -pre-generate: [copy] Warning: Could not find file /bioinfodev1/flymine/flymine11/flymine/dbmodel/resources/genomic_*.properties to copy. build-model-from-xml-in-build-dir: [echo] Found xml file in /bioinfodev1/flymine/flymine11/flymine/dbmodel/build build-model-from-xml-in-project-dir: build-model-from-xmi: build-model-from-zargo: build-model-from-xmlschema: -generate-model-java-message: -init-macrodef-model-output: generate-model-java: [echo] Generating model java code... do-generate: -post-generate: generate: -pre-compile: -init-macrodef-javac: do-compile-with-gen-src: [javac] Compiling 270 source files to /bioinfodev1/flymine/flymine11/flymine/dbmodel/build/classes do-compile-without-gen-src: do-compile: -post-compile: compile: -init-jar: -pre-jar: -init-presetdef-jar: do-jar: [lib:jar] Building jar: /bioinfodev1/flymine/flymine11/flymine/dbmodel/dist/flymine-dbmodel.jar -post-jar: jar: [dependencies] Executing "jar" for source "intermine/web/model/userprofile" in directory: /bioinfodev1/flymine/flymine11/imbuild/../intermine/web/model/userprofile -init-project: -pre-pre-init: library.-pre-init: -pre-init: init: -pre-init-deps: -init-deps: -init-compile: library.-init-generate: -pre-define-task-classpath: [delete] Deleting directory /bioinfodev1/flymine/flymine11/intermine/web/model/userprofile/build/tmp [mkdir] Created dir: /bioinfodev1/flymine/flymine11/intermine/web/model/userprofile/build/tmp -define-task-classpath: -check-task-availability: -load-os-tasks: [echo] Loading objectstore tasks -load-int-tasks: [echo] Loading integration tasks -load-web-tasks: -load-task-taskdefs: -init-macrodef-build-db: -init-task-xml: -init-model-out-of-date: -init-macrodef-model-generation: -init-generate: -pre-generate: build-model-from-xml-in-build-dir: build-model-from-xml-in-project-dir: [echo] Found xml file in project directory build-model-from-xmi: build-model-from-zargo: build-model-from-xmlschema: -generate-model-java-message: [echo] generated model java is up to date - not regenerating -init-macrodef-model-output: generate-model-java: do-generate: -post-generate: generate: -pre-compile: -init-macrodef-javac: do-compile-with-gen-src: do-compile-without-gen-src: do-compile: -post-compile: compile: -init-jar: -pre-jar: -init-presetdef-jar: do-jar: -post-jar: jar: [dependencies] Executing "jar" for source "intermine/web/main" in directory: /bioinfodev1/flymine/flymine11/imbuild/../intermine/web/main -init-project: -pre-pre-init: -pre-init: init: -pre-init-deps: -init-deps: -init-compile: -init-generate: -pre-generate: do-generate: -post-generate: generate: -pre-compile: -init-macrodef-javac: do-compile-with-gen-src: do-compile-without-gen-src: do-compile: -post-compile: compile: -init-jar: -pre-jar: -init-presetdef-jar: do-jar: -post-jar: jar: [dependencies] Executing "jar" for source "intermine/webapp/main" in directory: /bioinfodev1/flymine/flymine11/imbuild/../intermine/webapp/main -init-project: library.-pre-pre-init: -pre-pre-init: library.-pre-init: -pre-init: init: -pre-init-deps: -init-deps: -init-compile: -init-generate: -pre-generate: do-generate: -post-generate: generate: -pre-compile: -init-macrodef-javac: do-compile-with-gen-src: do-compile-without-gen-src: do-compile: -post-compile: compile: -init-jar: -pre-jar: [copy] Copying 1 file to /bioinfodev1/flymine/flymine11/intermine/webapp/main/build/webapp/WEB-INF/lib -init-presetdef-war: do-jar: [war] Building war: /bioinfodev1/flymine/flymine11/intermine/webapp/main/dist/intermine-webapp.war [war] Warning: selected war files include a WEB-INF/web.xml which will be ignored (please use webxml attribute to war task) -post-jar: jar: [dependencies] Executing "jar" for source "intermine/webtasks/main" in directory: /bioinfodev1/flymine/flymine11/imbuild/../intermine/webtasks/main -init-project: -pre-pre-init: -pre-init: init: -pre-init-deps: -init-deps: -init-compile: -init-generate: -pre-generate: do-generate: -post-generate: generate: -pre-compile: -init-macrodef-javac: do-compile-with-gen-src: do-compile-without-gen-src: do-compile: -post-compile: compile: -init-jar: -pre-jar: -init-presetdef-jar: do-jar: -post-jar: jar: [dependencies] Executing "jar" for source "bio/core/main" in directory: /bioinfodev1/flymine/flymine11/imbuild/../bio/core/main -init-project: -pre-pre-init: -pre-init: init: -pre-init-deps: -init-deps: -init-compile: -init-generate: -pre-generate: do-generate: -post-generate: generate: -pre-compile: -init-macrodef-javac: do-compile-with-gen-src: do-compile-without-gen-src: do-compile: -post-compile: compile: -init-jar: -pre-jar: -init-presetdef-jar: do-jar: -post-jar: jar: [dependencies] Executing "jar" for source "bio/core/props" in directory: /bioinfodev1/flymine/flymine11/imbuild/../bio/core/props -init-project: -pre-pre-init: -pre-init: init: -pre-init-deps: -init-deps: -init-compile: -init-generate: -pre-generate: do-generate: -post-generate: generate: -pre-compile: -init-macrodef-javac: do-compile-with-gen-src: do-compile-without-gen-src: do-compile: -post-compile: compile: -init-jar: -pre-jar: -init-presetdef-jar: do-jar: -post-jar: jar: [dependencies] Executing "jar" for source "bio/postprocess/main" in directory: /bioinfodev1/flymine/flymine11/imbuild/../bio/postprocess/main -init-project: -pre-pre-init: -pre-init: init: -pre-init-deps: -init-deps: -init-compile: -init-generate: -pre-generate: do-generate: -post-generate: generate: -pre-compile: -init-macrodef-javac: do-compile-with-gen-src: do-compile-without-gen-src: do-compile: -post-compile: compile: -init-jar: -pre-jar: -init-presetdef-jar: do-jar: -post-jar: jar: [dependencies] Executing "jar" for source "bio/tools/main" in directory: /bioinfodev1/flymine/flymine11/imbuild/../bio/tools/main -init-project: -pre-pre-init: -pre-init: init: -pre-init-deps: -init-deps: -init-compile: -init-generate: -pre-generate: do-generate: -post-generate: generate: -pre-compile: -init-macrodef-javac: do-compile-with-gen-src: do-compile-without-gen-src: do-compile: -post-compile: compile: -init-jar: -pre-jar: -init-presetdef-jar: do-jar: -post-jar: jar: [dependencies] Executing "jar" for source "bio/webapp" in directory: /bioinfodev1/flymine/flymine11/imbuild/../bio/webapp -init-project: library.-pre-pre-init: -pre-pre-init: library.-pre-init: webapp.-pre-init: -pre-init: init: -pre-init-deps: -init-deps: -init-compile: -init-generate: -pre-generate: do-generate: -post-generate: generate: -pre-compile: -init-macrodef-javac: do-compile-with-gen-src: do-compile-without-gen-src: do-compile: -post-compile: compile: -init-jar: -check-for-intermine-properties-file: -set-release-suffix-not-exists: -set-release-suffix-exists: -set-release-suffix: -pre-define-task-classpath: [delete] Deleting directory /bioinfodev1/flymine/flymine11/bio/webapp/build/tmp [mkdir] Created dir: /bioinfodev1/flymine/flymine11/bio/webapp/build/tmp -init-check-for-intermine-properties: -check-for-intermine-properties: -init-properties: -init-check-for-build-properties: -check-for-build-properties: -init-app-properties: -final-app-pre-jar: webapp.-pre-jar: [copy] Copying 1 file to /bioinfodev1/flymine/flymine11/bio/webapp/build/webapp/WEB-INF/lib -pre-jar: [copy] Copying 1 file to /bioinfodev1/flymine/flymine11/bio/webapp/dist -init-presetdef-war: -define-task-classpath: Overriding previous definition of reference to task.class.path -check-task-availability: -load-os-tasks: [echo] Loading objectstore tasks -load-int-tasks: [echo] Loading integration tasks -load-web-tasks: [echo] Loading web tasks -load-task-taskdefs: -init-macrodef-build-db: -init-task-xml: -init-summarise-objectstore: retrieve-objectstore-summary: do-jar: [war] Updating war: /bioinfodev1/flymine/flymine11/bio/webapp/dist/bio-webapp.war -post-jar: jar: [dependencies] Executing "jar" for source "flymine/sitemap" in directory: /bioinfodev1/flymine/flymine11/imbuild/../flymine/sitemap -init-project: -pre-pre-init: -pre-init: init: -pre-init-deps: -init-deps: -init-compile: -init-generate: -pre-generate: do-generate: -post-generate: generate: -pre-compile: -init-macrodef-javac: do-compile-with-gen-src: do-compile-without-gen-src: do-compile: -post-compile: compile: -init-jar: -pre-jar: -pre-define-task-classpath: [delete] Deleting directory /bioinfodev1/flymine/flymine11/flymine/sitemap/build/tmp [mkdir] Created dir: /bioinfodev1/flymine/flymine11/flymine/sitemap/build/tmp -define-task-classpath: -check-task-availability: -load-os-tasks: [echo] Loading objectstore tasks -load-int-tasks: [echo] Loading integration tasks -load-web-tasks: -load-task-taskdefs: -init-macrodef-build-db: -init-task-xml: -check-for-intermine-properties-file: -set-release-suffix-not-exists: -set-release-suffix-exists: -set-release-suffix: -init-check-for-intermine-properties: -check-for-intermine-properties: -init-properties: [copy] Copying 1 file to /bioinfodev1/flymine/flymine11/flymine/sitemap/build/main [copy] Copying 1 file to /bioinfodev1/flymine/flymine11/flymine/sitemap/build/main -set-sitemap-output: -init-generate-sitemap: generate-sitemap: do-jar: -post-jar: jar: -init-check-for-build-properties: -check-for-build-properties: -init-app-properties: init: -define-task-classpath: -check-task-availability: -load-os-tasks: [echo] Loading objectstore tasks [taskdef] java.util.zip.ZipException: error in opening zip file [taskdef] at java.util.zip.ZipFile.open(Native Method) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:114) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:131) [taskdef] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.findNextResource(AntClassLoader.java:126) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.nextElement(AntClassLoader.java:109) [taskdef] at org.apache.tools.ant.util.CollectionUtils$CompoundEnumeration.nextElement(CollectionUtils.java:146) [taskdef] at sun.misc.CompoundEnumeration.nextElement(CompoundEnumeration.java:43) [taskdef] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:215) [taskdef] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [taskdef] at org.apache.tools.ant.Task.perform(Task.java:364) [taskdef] at org.apache.tools.ant.Target.execute(Target.java:341) [taskdef] at org.apache.tools.ant.Target.performTasks(Target.java:369) [taskdef] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [taskdef] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [taskdef] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [taskdef] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [taskdef] at org.apache.tools.ant.Main.runBuild(Main.java:668) [taskdef] at org.apache.tools.ant.Main.startAnt(Main.java:187) [taskdef] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [taskdef] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [taskdef] java.util.zip.ZipException: error in opening zip file [taskdef] at java.util.zip.ZipFile.open(Native Method) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:114) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:131) [taskdef] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.findNextResource(AntClassLoader.java:126) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.nextElement(AntClassLoader.java:109) [taskdef] at org.apache.tools.ant.util.CollectionUtils$CompoundEnumeration.nextElement(CollectionUtils.java:146) [taskdef] at sun.misc.CompoundEnumeration.nextElement(CompoundEnumeration.java:43) [taskdef] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:215) [taskdef] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [taskdef] at org.apache.tools.ant.Task.perform(Task.java:364) [taskdef] at org.apache.tools.ant.Target.execute(Target.java:341) [taskdef] at org.apache.tools.ant.Target.performTasks(Target.java:369) [taskdef] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [taskdef] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [taskdef] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [taskdef] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [taskdef] at org.apache.tools.ant.Main.runBuild(Main.java:668) [taskdef] at org.apache.tools.ant.Main.startAnt(Main.java:187) [taskdef] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [taskdef] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [taskdef] java.util.zip.ZipException: error in opening zip file [taskdef] at java.util.zip.ZipFile.open(Native Method) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:114) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:131) [taskdef] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.findNextResource(AntClassLoader.java:126) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.nextElement(AntClassLoader.java:109) [taskdef] at org.apache.tools.ant.util.CollectionUtils$CompoundEnumeration.nextElement(CollectionUtils.java:146) [taskdef] at sun.misc.CompoundEnumeration.nextElement(CompoundEnumeration.java:43) [taskdef] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:215) [taskdef] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [taskdef] at org.apache.tools.ant.Task.perform(Task.java:364) [taskdef] at org.apache.tools.ant.Target.execute(Target.java:341) [taskdef] at org.apache.tools.ant.Target.performTasks(Target.java:369) [taskdef] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [taskdef] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [taskdef] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [taskdef] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [taskdef] at org.apache.tools.ant.Main.runBuild(Main.java:668) [taskdef] at org.apache.tools.ant.Main.startAnt(Main.java:187) [taskdef] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [taskdef] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [taskdef] java.util.zip.ZipException: error in opening zip file [taskdef] at java.util.zip.ZipFile.open(Native Method) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:114) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:131) [taskdef] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.findNextResource(AntClassLoader.java:126) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.nextElement(AntClassLoader.java:109) [taskdef] at org.apache.tools.ant.util.CollectionUtils$CompoundEnumeration.nextElement(CollectionUtils.java:146) [taskdef] at sun.misc.CompoundEnumeration.nextElement(CompoundEnumeration.java:43) [taskdef] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:215) [taskdef] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [taskdef] at org.apache.tools.ant.Task.perform(Task.java:364) [taskdef] at org.apache.tools.ant.Target.execute(Target.java:341) [taskdef] at org.apache.tools.ant.Target.performTasks(Target.java:369) [taskdef] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [taskdef] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [taskdef] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [taskdef] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [taskdef] at org.apache.tools.ant.Main.runBuild(Main.java:668) [taskdef] at org.apache.tools.ant.Main.startAnt(Main.java:187) [taskdef] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [taskdef] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [taskdef] java.util.zip.ZipException: error in opening zip file [taskdef] at java.util.zip.ZipFile.open(Native Method) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:114) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:131) [taskdef] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.findNextResource(AntClassLoader.java:126) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.nextElement(AntClassLoader.java:109) [taskdef] at org.apache.tools.ant.util.CollectionUtils$CompoundEnumeration.nextElement(CollectionUtils.java:146) [taskdef] at sun.misc.CompoundEnumeration.nextElement(CompoundEnumeration.java:43) [taskdef] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:215) [taskdef] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [taskdef] at org.apache.tools.ant.Task.perform(Task.java:364) [taskdef] at org.apache.tools.ant.Target.execute(Target.java:341) [taskdef] at org.apache.tools.ant.Target.performTasks(Target.java:369) [taskdef] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [taskdef] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [taskdef] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [taskdef] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [taskdef] at org.apache.tools.ant.Main.runBuild(Main.java:668) [taskdef] at org.apache.tools.ant.Main.startAnt(Main.java:187) [taskdef] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [taskdef] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [taskdef] java.util.zip.ZipException: error in opening zip file [taskdef] at java.util.zip.ZipFile.open(Native Method) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:114) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:131) [taskdef] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.findNextResource(AntClassLoader.java:126) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.nextElement(AntClassLoader.java:109) [taskdef] at org.apache.tools.ant.util.CollectionUtils$CompoundEnumeration.nextElement(CollectionUtils.java:146) [taskdef] at sun.misc.CompoundEnumeration.nextElement(CompoundEnumeration.java:43) [taskdef] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:215) [taskdef] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [taskdef] at org.apache.tools.ant.Task.perform(Task.java:364) [taskdef] at org.apache.tools.ant.Target.execute(Target.java:341) [taskdef] at org.apache.tools.ant.Target.performTasks(Target.java:369) [taskdef] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [taskdef] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [taskdef] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [taskdef] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [taskdef] at org.apache.tools.ant.Main.runBuild(Main.java:668) [taskdef] at org.apache.tools.ant.Main.startAnt(Main.java:187) [taskdef] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [taskdef] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [taskdef] java.util.zip.ZipException: error in opening zip file [taskdef] at java.util.zip.ZipFile.open(Native Method) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:114) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:131) [taskdef] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.findNextResource(AntClassLoader.java:126) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.nextElement(AntClassLoader.java:109) [taskdef] at org.apache.tools.ant.util.CollectionUtils$CompoundEnumeration.nextElement(CollectionUtils.java:146) [taskdef] at sun.misc.CompoundEnumeration.nextElement(CompoundEnumeration.java:43) [taskdef] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:215) [taskdef] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [taskdef] at org.apache.tools.ant.Task.perform(Task.java:364) [taskdef] at org.apache.tools.ant.Target.execute(Target.java:341) [taskdef] at org.apache.tools.ant.Target.performTasks(Target.java:369) [taskdef] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [taskdef] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [taskdef] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [taskdef] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [taskdef] at org.apache.tools.ant.Main.runBuild(Main.java:668) [taskdef] at org.apache.tools.ant.Main.startAnt(Main.java:187) [taskdef] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [taskdef] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [antlib] java.util.zip.ZipException: error in opening zip file [antlib] at java.util.zip.ZipFile.open(Native Method) [antlib] at java.util.zip.ZipFile.(ZipFile.java:114) [antlib] at java.util.zip.ZipFile.(ZipFile.java:131) [antlib] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [antlib] at org.apache.tools.ant.AntClassLoader.getResource(AntClassLoader.java:832) [antlib] at org.apache.log4j.helpers.Loader.getResource(Loader.java:91) [antlib] at org.apache.log4j.LogManager.(LogManager.java:94) [antlib] at org.apache.log4j.Logger.getLogger(Logger.java:94) [antlib] at org.intermine.task.BuildDbTask.(BuildDbTask.java:47) [antlib] at java.lang.Class.forName0(Native Method) [antlib] at java.lang.Class.forName(Class.java:247) [antlib] at org.apache.tools.ant.taskdefs.Definer.addDefinition(Definer.java:457) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:183) [antlib] at org.apache.tools.ant.taskdefs.Antlib.execute(Antlib.java:161) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.taskdefs.Definer.loadAntlib(Definer.java:330) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:236) [antlib] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.Target.execute(Target.java:341) [antlib] at org.apache.tools.ant.Target.performTasks(Target.java:369) [antlib] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [antlib] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [antlib] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [antlib] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [antlib] at org.apache.tools.ant.Main.runBuild(Main.java:668) [antlib] at org.apache.tools.ant.Main.startAnt(Main.java:187) [antlib] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [antlib] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [antlib] java.util.zip.ZipException: error in opening zip file [antlib] at java.util.zip.ZipFile.open(Native Method) [antlib] at java.util.zip.ZipFile.(ZipFile.java:114) [antlib] at java.util.zip.ZipFile.(ZipFile.java:131) [antlib] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [antlib] at org.apache.tools.ant.AntClassLoader.getResource(AntClassLoader.java:832) [antlib] at org.apache.log4j.helpers.Loader.getResource(Loader.java:91) [antlib] at org.apache.log4j.LogManager.(LogManager.java:94) [antlib] at org.apache.log4j.Logger.getLogger(Logger.java:94) [antlib] at org.intermine.task.BuildDbTask.(BuildDbTask.java:47) [antlib] at java.lang.Class.forName0(Native Method) [antlib] at java.lang.Class.forName(Class.java:247) [antlib] at org.apache.tools.ant.taskdefs.Definer.addDefinition(Definer.java:457) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:183) [antlib] at org.apache.tools.ant.taskdefs.Antlib.execute(Antlib.java:161) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.taskdefs.Definer.loadAntlib(Definer.java:330) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:236) [antlib] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.Target.execute(Target.java:341) [antlib] at org.apache.tools.ant.Target.performTasks(Target.java:369) [antlib] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [antlib] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [antlib] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [antlib] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [antlib] at org.apache.tools.ant.Main.runBuild(Main.java:668) [antlib] at org.apache.tools.ant.Main.startAnt(Main.java:187) [antlib] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [antlib] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [antlib] java.util.zip.ZipException: error in opening zip file [antlib] at java.util.zip.ZipFile.open(Native Method) [antlib] at java.util.zip.ZipFile.(ZipFile.java:114) [antlib] at java.util.zip.ZipFile.(ZipFile.java:131) [antlib] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [antlib] at org.apache.tools.ant.AntClassLoader.getResource(AntClassLoader.java:832) [antlib] at org.apache.log4j.helpers.Loader.getResource(Loader.java:91) [antlib] at org.apache.log4j.LogManager.(LogManager.java:94) [antlib] at org.apache.log4j.Logger.getLogger(Logger.java:94) [antlib] at org.intermine.task.BuildDbTask.(BuildDbTask.java:47) [antlib] at java.lang.Class.forName0(Native Method) [antlib] at java.lang.Class.forName(Class.java:247) [antlib] at org.apache.tools.ant.taskdefs.Definer.addDefinition(Definer.java:457) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:183) [antlib] at org.apache.tools.ant.taskdefs.Antlib.execute(Antlib.java:161) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.taskdefs.Definer.loadAntlib(Definer.java:330) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:236) [antlib] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.Target.execute(Target.java:341) [antlib] at org.apache.tools.ant.Target.performTasks(Target.java:369) [antlib] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [antlib] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [antlib] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [antlib] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [antlib] at org.apache.tools.ant.Main.runBuild(Main.java:668) [antlib] at org.apache.tools.ant.Main.startAnt(Main.java:187) [antlib] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [antlib] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [antlib] java.util.zip.ZipException: error in opening zip file [antlib] at java.util.zip.ZipFile.open(Native Method) [antlib] at java.util.zip.ZipFile.(ZipFile.java:114) [antlib] at java.util.zip.ZipFile.(ZipFile.java:131) [antlib] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [antlib] at org.apache.tools.ant.AntClassLoader.getResource(AntClassLoader.java:832) [antlib] at org.apache.log4j.helpers.Loader.getResource(Loader.java:91) [antlib] at org.apache.log4j.LogManager.(LogManager.java:94) [antlib] at org.apache.log4j.Logger.getLogger(Logger.java:94) [antlib] at org.intermine.task.BuildDbTask.(BuildDbTask.java:47) [antlib] at java.lang.Class.forName0(Native Method) [antlib] at java.lang.Class.forName(Class.java:247) [antlib] at org.apache.tools.ant.taskdefs.Definer.addDefinition(Definer.java:457) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:183) [antlib] at org.apache.tools.ant.taskdefs.Antlib.execute(Antlib.java:161) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.taskdefs.Definer.loadAntlib(Definer.java:330) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:236) [antlib] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.Target.execute(Target.java:341) [antlib] at org.apache.tools.ant.Target.performTasks(Target.java:369) [antlib] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [antlib] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [antlib] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [antlib] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [antlib] at org.apache.tools.ant.Main.runBuild(Main.java:668) [antlib] at org.apache.tools.ant.Main.startAnt(Main.java:187) [antlib] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [antlib] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [antlib] java.util.zip.ZipException: error in opening zip file [antlib] at java.util.zip.ZipFile.open(Native Method) [antlib] at java.util.zip.ZipFile.(ZipFile.java:114) [antlib] at java.util.zip.ZipFile.(ZipFile.java:131) [antlib] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [antlib] at org.apache.tools.ant.AntClassLoader.getResource(AntClassLoader.java:832) [antlib] at org.apache.log4j.helpers.Loader.getResource(Loader.java:91) [antlib] at org.apache.log4j.LogManager.(LogManager.java:94) [antlib] at org.apache.log4j.Logger.getLogger(Logger.java:94) [antlib] at org.intermine.task.BuildDbTask.(BuildDbTask.java:47) [antlib] at java.lang.Class.forName0(Native Method) [antlib] at java.lang.Class.forName(Class.java:247) [antlib] at org.apache.tools.ant.taskdefs.Definer.addDefinition(Definer.java:457) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:183) [antlib] at org.apache.tools.ant.taskdefs.Antlib.execute(Antlib.java:161) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.taskdefs.Definer.loadAntlib(Definer.java:330) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:236) [antlib] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.Target.execute(Target.java:341) [antlib] at org.apache.tools.ant.Target.performTasks(Target.java:369) [antlib] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [antlib] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [antlib] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [antlib] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [antlib] at org.apache.tools.ant.Main.runBuild(Main.java:668) [antlib] at org.apache.tools.ant.Main.startAnt(Main.java:187) [antlib] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [antlib] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [antlib] java.util.zip.ZipException: error in opening zip file [antlib] at java.util.zip.ZipFile.open(Native Method) [antlib] at java.util.zip.ZipFile.(ZipFile.java:114) [antlib] at java.util.zip.ZipFile.(ZipFile.java:131) [antlib] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [antlib] at org.apache.tools.ant.AntClassLoader.getResource(AntClassLoader.java:832) [antlib] at org.apache.log4j.helpers.Loader.getResource(Loader.java:91) [antlib] at org.apache.log4j.LogManager.(LogManager.java:94) [antlib] at org.apache.log4j.Logger.getLogger(Logger.java:94) [antlib] at org.intermine.task.BuildDbTask.(BuildDbTask.java:47) [antlib] at java.lang.Class.forName0(Native Method) [antlib] at java.lang.Class.forName(Class.java:247) [antlib] at org.apache.tools.ant.taskdefs.Definer.addDefinition(Definer.java:457) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:183) [antlib] at org.apache.tools.ant.taskdefs.Antlib.execute(Antlib.java:161) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.taskdefs.Definer.loadAntlib(Definer.java:330) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:236) [antlib] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.Target.execute(Target.java:341) [antlib] at org.apache.tools.ant.Target.performTasks(Target.java:369) [antlib] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [antlib] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [antlib] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [antlib] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [antlib] at org.apache.tools.ant.Main.runBuild(Main.java:668) [antlib] at org.apache.tools.ant.Main.startAnt(Main.java:187) [antlib] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [antlib] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [antlib] java.util.zip.ZipException: error in opening zip file [antlib] at java.util.zip.ZipFile.open(Native Method) [antlib] at java.util.zip.ZipFile.(ZipFile.java:114) [antlib] at java.util.zip.ZipFile.(ZipFile.java:131) [antlib] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [antlib] at org.apache.tools.ant.AntClassLoader.getResource(AntClassLoader.java:832) [antlib] at org.apache.log4j.helpers.Loader.getResource(Loader.java:91) [antlib] at org.apache.log4j.LogManager.(LogManager.java:94) [antlib] at org.apache.log4j.Logger.getLogger(Logger.java:94) [antlib] at org.intermine.task.BuildDbTask.(BuildDbTask.java:47) [antlib] at java.lang.Class.forName0(Native Method) [antlib] at java.lang.Class.forName(Class.java:247) [antlib] at org.apache.tools.ant.taskdefs.Definer.addDefinition(Definer.java:457) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:183) [antlib] at org.apache.tools.ant.taskdefs.Antlib.execute(Antlib.java:161) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.taskdefs.Definer.loadAntlib(Definer.java:330) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:236) [antlib] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.Target.execute(Target.java:341) [antlib] at org.apache.tools.ant.Target.performTasks(Target.java:369) [antlib] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [antlib] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [antlib] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [antlib] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [antlib] at org.apache.tools.ant.Main.runBuild(Main.java:668) [antlib] at org.apache.tools.ant.Main.startAnt(Main.java:187) [antlib] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [antlib] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) -load-int-tasks: [echo] Loading integration tasks [taskdef] java.util.zip.ZipException: error in opening zip file [taskdef] at java.util.zip.ZipFile.open(Native Method) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:114) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:131) [taskdef] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.findNextResource(AntClassLoader.java:126) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.nextElement(AntClassLoader.java:109) [taskdef] at org.apache.tools.ant.util.CollectionUtils$CompoundEnumeration.nextElement(CollectionUtils.java:146) [taskdef] at sun.misc.CompoundEnumeration.nextElement(CompoundEnumeration.java:43) [taskdef] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:215) [taskdef] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [taskdef] at org.apache.tools.ant.Task.perform(Task.java:364) [taskdef] at org.apache.tools.ant.Target.execute(Target.java:341) [taskdef] at org.apache.tools.ant.Target.performTasks(Target.java:369) [taskdef] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [taskdef] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [taskdef] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [taskdef] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [taskdef] at org.apache.tools.ant.Main.runBuild(Main.java:668) [taskdef] at org.apache.tools.ant.Main.startAnt(Main.java:187) [taskdef] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [taskdef] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [taskdef] java.util.zip.ZipException: error in opening zip file [taskdef] at java.util.zip.ZipFile.open(Native Method) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:114) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:131) [taskdef] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.findNextResource(AntClassLoader.java:126) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.nextElement(AntClassLoader.java:109) [taskdef] at org.apache.tools.ant.util.CollectionUtils$CompoundEnumeration.nextElement(CollectionUtils.java:146) [taskdef] at sun.misc.CompoundEnumeration.nextElement(CompoundEnumeration.java:43) [taskdef] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:215) [taskdef] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [taskdef] at org.apache.tools.ant.Task.perform(Task.java:364) [taskdef] at org.apache.tools.ant.Target.execute(Target.java:341) [taskdef] at org.apache.tools.ant.Target.performTasks(Target.java:369) [taskdef] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [taskdef] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [taskdef] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [taskdef] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [taskdef] at org.apache.tools.ant.Main.runBuild(Main.java:668) [taskdef] at org.apache.tools.ant.Main.startAnt(Main.java:187) [taskdef] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [taskdef] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [taskdef] java.util.zip.ZipException: error in opening zip file [taskdef] at java.util.zip.ZipFile.open(Native Method) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:114) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:131) [taskdef] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.findNextResource(AntClassLoader.java:126) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.nextElement(AntClassLoader.java:109) [taskdef] at org.apache.tools.ant.util.CollectionUtils$CompoundEnumeration.nextElement(CollectionUtils.java:146) [taskdef] at sun.misc.CompoundEnumeration.nextElement(CompoundEnumeration.java:43) [taskdef] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:215) [taskdef] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [taskdef] at org.apache.tools.ant.Task.perform(Task.java:364) [taskdef] at org.apache.tools.ant.Target.execute(Target.java:341) [taskdef] at org.apache.tools.ant.Target.performTasks(Target.java:369) [taskdef] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [taskdef] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [taskdef] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [taskdef] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [taskdef] at org.apache.tools.ant.Main.runBuild(Main.java:668) [taskdef] at org.apache.tools.ant.Main.startAnt(Main.java:187) [taskdef] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [taskdef] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [taskdef] java.util.zip.ZipException: error in opening zip file [taskdef] at java.util.zip.ZipFile.open(Native Method) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:114) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:131) [taskdef] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.findNextResource(AntClassLoader.java:126) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.nextElement(AntClassLoader.java:109) [taskdef] at org.apache.tools.ant.util.CollectionUtils$CompoundEnumeration.nextElement(CollectionUtils.java:146) [taskdef] at sun.misc.CompoundEnumeration.nextElement(CompoundEnumeration.java:43) [taskdef] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:215) [taskdef] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [taskdef] at org.apache.tools.ant.Task.perform(Task.java:364) [taskdef] at org.apache.tools.ant.Target.execute(Target.java:341) [taskdef] at org.apache.tools.ant.Target.performTasks(Target.java:369) [taskdef] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [taskdef] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [taskdef] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [taskdef] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [taskdef] at org.apache.tools.ant.Main.runBuild(Main.java:668) [taskdef] at org.apache.tools.ant.Main.startAnt(Main.java:187) [taskdef] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [taskdef] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [taskdef] java.util.zip.ZipException: error in opening zip file [taskdef] at java.util.zip.ZipFile.open(Native Method) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:114) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:131) [taskdef] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.findNextResource(AntClassLoader.java:126) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.nextElement(AntClassLoader.java:109) [taskdef] at org.apache.tools.ant.util.CollectionUtils$CompoundEnumeration.nextElement(CollectionUtils.java:146) [taskdef] at sun.misc.CompoundEnumeration.nextElement(CompoundEnumeration.java:43) [taskdef] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:215) [taskdef] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [taskdef] at org.apache.tools.ant.Task.perform(Task.java:364) [taskdef] at org.apache.tools.ant.Target.execute(Target.java:341) [taskdef] at org.apache.tools.ant.Target.performTasks(Target.java:369) [taskdef] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [taskdef] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [taskdef] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [taskdef] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [taskdef] at org.apache.tools.ant.Main.runBuild(Main.java:668) [taskdef] at org.apache.tools.ant.Main.startAnt(Main.java:187) [taskdef] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [taskdef] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [taskdef] java.util.zip.ZipException: error in opening zip file [taskdef] at java.util.zip.ZipFile.open(Native Method) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:114) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:131) [taskdef] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.findNextResource(AntClassLoader.java:126) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.nextElement(AntClassLoader.java:109) [taskdef] at org.apache.tools.ant.util.CollectionUtils$CompoundEnumeration.nextElement(CollectionUtils.java:146) [taskdef] at sun.misc.CompoundEnumeration.nextElement(CompoundEnumeration.java:43) [taskdef] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:215) [taskdef] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [taskdef] at org.apache.tools.ant.Task.perform(Task.java:364) [taskdef] at org.apache.tools.ant.Target.execute(Target.java:341) [taskdef] at org.apache.tools.ant.Target.performTasks(Target.java:369) [taskdef] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [taskdef] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [taskdef] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [taskdef] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [taskdef] at org.apache.tools.ant.Main.runBuild(Main.java:668) [taskdef] at org.apache.tools.ant.Main.startAnt(Main.java:187) [taskdef] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [taskdef] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [taskdef] java.util.zip.ZipException: error in opening zip file [taskdef] at java.util.zip.ZipFile.open(Native Method) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:114) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:131) [taskdef] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.findNextResource(AntClassLoader.java:126) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.nextElement(AntClassLoader.java:109) [taskdef] at org.apache.tools.ant.util.CollectionUtils$CompoundEnumeration.nextElement(CollectionUtils.java:146) [taskdef] at sun.misc.CompoundEnumeration.nextElement(CompoundEnumeration.java:43) [taskdef] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:215) [taskdef] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [taskdef] at org.apache.tools.ant.Task.perform(Task.java:364) [taskdef] at org.apache.tools.ant.Target.execute(Target.java:341) [taskdef] at org.apache.tools.ant.Target.performTasks(Target.java:369) [taskdef] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [taskdef] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [taskdef] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [taskdef] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [taskdef] at org.apache.tools.ant.Main.runBuild(Main.java:668) [taskdef] at org.apache.tools.ant.Main.startAnt(Main.java:187) [taskdef] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [taskdef] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [antlib] java.util.zip.ZipException: error in opening zip file [antlib] at java.util.zip.ZipFile.open(Native Method) [antlib] at java.util.zip.ZipFile.(ZipFile.java:114) [antlib] at java.util.zip.ZipFile.(ZipFile.java:131) [antlib] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [antlib] at org.apache.tools.ant.AntClassLoader.getResource(AntClassLoader.java:832) [antlib] at org.apache.log4j.helpers.Loader.getResource(Loader.java:91) [antlib] at org.apache.log4j.LogManager.(LogManager.java:94) [antlib] at org.apache.log4j.Logger.getLogger(Logger.java:94) [antlib] at org.intermine.task.CreateIndexesTask.(CreateIndexesTask.java:71) [antlib] at java.lang.Class.forName0(Native Method) [antlib] at java.lang.Class.forName(Class.java:247) [antlib] at org.apache.tools.ant.taskdefs.Definer.addDefinition(Definer.java:457) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:183) [antlib] at org.apache.tools.ant.taskdefs.Antlib.execute(Antlib.java:161) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.taskdefs.Definer.loadAntlib(Definer.java:330) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:236) [antlib] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.Target.execute(Target.java:341) [antlib] at org.apache.tools.ant.Target.performTasks(Target.java:369) [antlib] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [antlib] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [antlib] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [antlib] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [antlib] at org.apache.tools.ant.Main.runBuild(Main.java:668) [antlib] at org.apache.tools.ant.Main.startAnt(Main.java:187) [antlib] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [antlib] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [antlib] java.util.zip.ZipException: error in opening zip file [antlib] at java.util.zip.ZipFile.open(Native Method) [antlib] at java.util.zip.ZipFile.(ZipFile.java:114) [antlib] at java.util.zip.ZipFile.(ZipFile.java:131) [antlib] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [antlib] at org.apache.tools.ant.AntClassLoader.getResource(AntClassLoader.java:832) [antlib] at org.apache.log4j.helpers.Loader.getResource(Loader.java:91) [antlib] at org.apache.log4j.LogManager.(LogManager.java:94) [antlib] at org.apache.log4j.Logger.getLogger(Logger.java:94) [antlib] at org.intermine.task.CreateIndexesTask.(CreateIndexesTask.java:71) [antlib] at java.lang.Class.forName0(Native Method) [antlib] at java.lang.Class.forName(Class.java:247) [antlib] at org.apache.tools.ant.taskdefs.Definer.addDefinition(Definer.java:457) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:183) [antlib] at org.apache.tools.ant.taskdefs.Antlib.execute(Antlib.java:161) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.taskdefs.Definer.loadAntlib(Definer.java:330) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:236) [antlib] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.Target.execute(Target.java:341) [antlib] at org.apache.tools.ant.Target.performTasks(Target.java:369) [antlib] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [antlib] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [antlib] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [antlib] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [antlib] at org.apache.tools.ant.Main.runBuild(Main.java:668) [antlib] at org.apache.tools.ant.Main.startAnt(Main.java:187) [antlib] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [antlib] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [antlib] java.util.zip.ZipException: error in opening zip file [antlib] at java.util.zip.ZipFile.open(Native Method) [antlib] at java.util.zip.ZipFile.(ZipFile.java:114) [antlib] at java.util.zip.ZipFile.(ZipFile.java:131) [antlib] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [antlib] at org.apache.tools.ant.AntClassLoader.getResource(AntClassLoader.java:832) [antlib] at org.apache.log4j.helpers.Loader.getResource(Loader.java:91) [antlib] at org.apache.log4j.LogManager.(LogManager.java:94) [antlib] at org.apache.log4j.Logger.getLogger(Logger.java:94) [antlib] at org.intermine.task.CreateIndexesTask.(CreateIndexesTask.java:71) [antlib] at java.lang.Class.forName0(Native Method) [antlib] at java.lang.Class.forName(Class.java:247) [antlib] at org.apache.tools.ant.taskdefs.Definer.addDefinition(Definer.java:457) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:183) [antlib] at org.apache.tools.ant.taskdefs.Antlib.execute(Antlib.java:161) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.taskdefs.Definer.loadAntlib(Definer.java:330) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:236) [antlib] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.Target.execute(Target.java:341) [antlib] at org.apache.tools.ant.Target.performTasks(Target.java:369) [antlib] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [antlib] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [antlib] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [antlib] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [antlib] at org.apache.tools.ant.Main.runBuild(Main.java:668) [antlib] at org.apache.tools.ant.Main.startAnt(Main.java:187) [antlib] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [antlib] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [antlib] java.util.zip.ZipException: error in opening zip file [antlib] at java.util.zip.ZipFile.open(Native Method) [antlib] at java.util.zip.ZipFile.(ZipFile.java:114) [antlib] at java.util.zip.ZipFile.(ZipFile.java:131) [antlib] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [antlib] at org.apache.tools.ant.AntClassLoader.getResource(AntClassLoader.java:832) [antlib] at org.apache.log4j.helpers.Loader.getResource(Loader.java:91) [antlib] at org.apache.log4j.LogManager.(LogManager.java:94) [antlib] at org.apache.log4j.Logger.getLogger(Logger.java:94) [antlib] at org.intermine.task.CreateIndexesTask.(CreateIndexesTask.java:71) [antlib] at java.lang.Class.forName0(Native Method) [antlib] at java.lang.Class.forName(Class.java:247) [antlib] at org.apache.tools.ant.taskdefs.Definer.addDefinition(Definer.java:457) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:183) [antlib] at org.apache.tools.ant.taskdefs.Antlib.execute(Antlib.java:161) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.taskdefs.Definer.loadAntlib(Definer.java:330) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:236) [antlib] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.Target.execute(Target.java:341) [antlib] at org.apache.tools.ant.Target.performTasks(Target.java:369) [antlib] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [antlib] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [antlib] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [antlib] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [antlib] at org.apache.tools.ant.Main.runBuild(Main.java:668) [antlib] at org.apache.tools.ant.Main.startAnt(Main.java:187) [antlib] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [antlib] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [antlib] java.util.zip.ZipException: error in opening zip file [antlib] at java.util.zip.ZipFile.open(Native Method) [antlib] at java.util.zip.ZipFile.(ZipFile.java:114) [antlib] at java.util.zip.ZipFile.(ZipFile.java:131) [antlib] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [antlib] at org.apache.tools.ant.AntClassLoader.getResource(AntClassLoader.java:832) [antlib] at org.apache.log4j.helpers.Loader.getResource(Loader.java:91) [antlib] at org.apache.log4j.LogManager.(LogManager.java:94) [antlib] at org.apache.log4j.Logger.getLogger(Logger.java:94) [antlib] at org.intermine.task.CreateIndexesTask.(CreateIndexesTask.java:71) [antlib] at java.lang.Class.forName0(Native Method) [antlib] at java.lang.Class.forName(Class.java:247) [antlib] at org.apache.tools.ant.taskdefs.Definer.addDefinition(Definer.java:457) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:183) [antlib] at org.apache.tools.ant.taskdefs.Antlib.execute(Antlib.java:161) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.taskdefs.Definer.loadAntlib(Definer.java:330) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:236) [antlib] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.Target.execute(Target.java:341) [antlib] at org.apache.tools.ant.Target.performTasks(Target.java:369) [antlib] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [antlib] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [antlib] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [antlib] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [antlib] at org.apache.tools.ant.Main.runBuild(Main.java:668) [antlib] at org.apache.tools.ant.Main.startAnt(Main.java:187) [antlib] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [antlib] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [antlib] java.util.zip.ZipException: error in opening zip file [antlib] at java.util.zip.ZipFile.open(Native Method) [antlib] at java.util.zip.ZipFile.(ZipFile.java:114) [antlib] at java.util.zip.ZipFile.(ZipFile.java:131) [antlib] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [antlib] at org.apache.tools.ant.AntClassLoader.getResource(AntClassLoader.java:832) [antlib] at org.apache.log4j.helpers.Loader.getResource(Loader.java:91) [antlib] at org.apache.log4j.LogManager.(LogManager.java:94) [antlib] at org.apache.log4j.Logger.getLogger(Logger.java:94) [antlib] at org.intermine.task.CreateIndexesTask.(CreateIndexesTask.java:71) [antlib] at java.lang.Class.forName0(Native Method) [antlib] at java.lang.Class.forName(Class.java:247) [antlib] at org.apache.tools.ant.taskdefs.Definer.addDefinition(Definer.java:457) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:183) [antlib] at org.apache.tools.ant.taskdefs.Antlib.execute(Antlib.java:161) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.taskdefs.Definer.loadAntlib(Definer.java:330) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:236) [antlib] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.Target.execute(Target.java:341) [antlib] at org.apache.tools.ant.Target.performTasks(Target.java:369) [antlib] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [antlib] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [antlib] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [antlib] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [antlib] at org.apache.tools.ant.Main.runBuild(Main.java:668) [antlib] at org.apache.tools.ant.Main.startAnt(Main.java:187) [antlib] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [antlib] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [antlib] java.util.zip.ZipException: error in opening zip file [antlib] at java.util.zip.ZipFile.open(Native Method) [antlib] at java.util.zip.ZipFile.(ZipFile.java:114) [antlib] at java.util.zip.ZipFile.(ZipFile.java:131) [antlib] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [antlib] at org.apache.tools.ant.AntClassLoader.getResource(AntClassLoader.java:832) [antlib] at org.apache.log4j.helpers.Loader.getResource(Loader.java:91) [antlib] at org.apache.log4j.LogManager.(LogManager.java:94) [antlib] at org.apache.log4j.Logger.getLogger(Logger.java:94) [antlib] at org.intermine.task.CreateIndexesTask.(CreateIndexesTask.java:71) [antlib] at java.lang.Class.forName0(Native Method) [antlib] at java.lang.Class.forName(Class.java:247) [antlib] at org.apache.tools.ant.taskdefs.Definer.addDefinition(Definer.java:457) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:183) [antlib] at org.apache.tools.ant.taskdefs.Antlib.execute(Antlib.java:161) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.taskdefs.Definer.loadAntlib(Definer.java:330) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:236) [antlib] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.Target.execute(Target.java:341) [antlib] at org.apache.tools.ant.Target.performTasks(Target.java:369) [antlib] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [antlib] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [antlib] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [antlib] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [antlib] at org.apache.tools.ant.Main.runBuild(Main.java:668) [antlib] at org.apache.tools.ant.Main.startAnt(Main.java:187) [antlib] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [antlib] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) -load-web-tasks: [echo] Loading web tasks [taskdef] java.util.zip.ZipException: error in opening zip file [taskdef] at java.util.zip.ZipFile.open(Native Method) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:114) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:131) [taskdef] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.findNextResource(AntClassLoader.java:126) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.nextElement(AntClassLoader.java:109) [taskdef] at org.apache.tools.ant.util.CollectionUtils$CompoundEnumeration.nextElement(CollectionUtils.java:146) [taskdef] at sun.misc.CompoundEnumeration.nextElement(CompoundEnumeration.java:43) [taskdef] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:215) [taskdef] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [taskdef] at org.apache.tools.ant.Task.perform(Task.java:364) [taskdef] at org.apache.tools.ant.Target.execute(Target.java:341) [taskdef] at org.apache.tools.ant.Target.performTasks(Target.java:369) [taskdef] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [taskdef] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [taskdef] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [taskdef] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [taskdef] at org.apache.tools.ant.Main.runBuild(Main.java:668) [taskdef] at org.apache.tools.ant.Main.startAnt(Main.java:187) [taskdef] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [taskdef] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [taskdef] java.util.zip.ZipException: error in opening zip file [taskdef] at java.util.zip.ZipFile.open(Native Method) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:114) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:131) [taskdef] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.findNextResource(AntClassLoader.java:126) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.nextElement(AntClassLoader.java:109) [taskdef] at org.apache.tools.ant.util.CollectionUtils$CompoundEnumeration.nextElement(CollectionUtils.java:146) [taskdef] at sun.misc.CompoundEnumeration.nextElement(CompoundEnumeration.java:43) [taskdef] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:215) [taskdef] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [taskdef] at org.apache.tools.ant.Task.perform(Task.java:364) [taskdef] at org.apache.tools.ant.Target.execute(Target.java:341) [taskdef] at org.apache.tools.ant.Target.performTasks(Target.java:369) [taskdef] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [taskdef] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [taskdef] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [taskdef] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [taskdef] at org.apache.tools.ant.Main.runBuild(Main.java:668) [taskdef] at org.apache.tools.ant.Main.startAnt(Main.java:187) [taskdef] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [taskdef] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [taskdef] java.util.zip.ZipException: error in opening zip file [taskdef] at java.util.zip.ZipFile.open(Native Method) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:114) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:131) [taskdef] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.findNextResource(AntClassLoader.java:126) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.nextElement(AntClassLoader.java:109) [taskdef] at org.apache.tools.ant.util.CollectionUtils$CompoundEnumeration.nextElement(CollectionUtils.java:146) [taskdef] at sun.misc.CompoundEnumeration.nextElement(CompoundEnumeration.java:43) [taskdef] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:215) [taskdef] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [taskdef] at org.apache.tools.ant.Task.perform(Task.java:364) [taskdef] at org.apache.tools.ant.Target.execute(Target.java:341) [taskdef] at org.apache.tools.ant.Target.performTasks(Target.java:369) [taskdef] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [taskdef] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [taskdef] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [taskdef] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [taskdef] at org.apache.tools.ant.Main.runBuild(Main.java:668) [taskdef] at org.apache.tools.ant.Main.startAnt(Main.java:187) [taskdef] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [taskdef] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [taskdef] java.util.zip.ZipException: error in opening zip file [taskdef] at java.util.zip.ZipFile.open(Native Method) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:114) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:131) [taskdef] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.findNextResource(AntClassLoader.java:126) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.nextElement(AntClassLoader.java:109) [taskdef] at org.apache.tools.ant.util.CollectionUtils$CompoundEnumeration.nextElement(CollectionUtils.java:146) [taskdef] at sun.misc.CompoundEnumeration.nextElement(CompoundEnumeration.java:43) [taskdef] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:215) [taskdef] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [taskdef] at org.apache.tools.ant.Task.perform(Task.java:364) [taskdef] at org.apache.tools.ant.Target.execute(Target.java:341) [taskdef] at org.apache.tools.ant.Target.performTasks(Target.java:369) [taskdef] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [taskdef] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [taskdef] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [taskdef] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [taskdef] at org.apache.tools.ant.Main.runBuild(Main.java:668) [taskdef] at org.apache.tools.ant.Main.startAnt(Main.java:187) [taskdef] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [taskdef] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [taskdef] java.util.zip.ZipException: error in opening zip file [taskdef] at java.util.zip.ZipFile.open(Native Method) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:114) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:131) [taskdef] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.findNextResource(AntClassLoader.java:126) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.nextElement(AntClassLoader.java:109) [taskdef] at org.apache.tools.ant.util.CollectionUtils$CompoundEnumeration.nextElement(CollectionUtils.java:146) [taskdef] at sun.misc.CompoundEnumeration.nextElement(CompoundEnumeration.java:43) [taskdef] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:215) [taskdef] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [taskdef] at org.apache.tools.ant.Task.perform(Task.java:364) [taskdef] at org.apache.tools.ant.Target.execute(Target.java:341) [taskdef] at org.apache.tools.ant.Target.performTasks(Target.java:369) [taskdef] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [taskdef] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [taskdef] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [taskdef] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [taskdef] at org.apache.tools.ant.Main.runBuild(Main.java:668) [taskdef] at org.apache.tools.ant.Main.startAnt(Main.java:187) [taskdef] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [taskdef] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [taskdef] java.util.zip.ZipException: error in opening zip file [taskdef] at java.util.zip.ZipFile.open(Native Method) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:114) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:131) [taskdef] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.findNextResource(AntClassLoader.java:126) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.nextElement(AntClassLoader.java:109) [taskdef] at org.apache.tools.ant.util.CollectionUtils$CompoundEnumeration.nextElement(CollectionUtils.java:146) [taskdef] at sun.misc.CompoundEnumeration.nextElement(CompoundEnumeration.java:43) [taskdef] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:215) [taskdef] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [taskdef] at org.apache.tools.ant.Task.perform(Task.java:364) [taskdef] at org.apache.tools.ant.Target.execute(Target.java:341) [taskdef] at org.apache.tools.ant.Target.performTasks(Target.java:369) [taskdef] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [taskdef] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [taskdef] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [taskdef] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [taskdef] at org.apache.tools.ant.Main.runBuild(Main.java:668) [taskdef] at org.apache.tools.ant.Main.startAnt(Main.java:187) [taskdef] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [taskdef] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [taskdef] java.util.zip.ZipException: error in opening zip file [taskdef] at java.util.zip.ZipFile.open(Native Method) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:114) [taskdef] at java.util.zip.ZipFile.(ZipFile.java:131) [taskdef] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.findNextResource(AntClassLoader.java:126) [taskdef] at org.apache.tools.ant.AntClassLoader$ResourceEnumeration.nextElement(AntClassLoader.java:109) [taskdef] at org.apache.tools.ant.util.CollectionUtils$CompoundEnumeration.nextElement(CollectionUtils.java:146) [taskdef] at sun.misc.CompoundEnumeration.nextElement(CompoundEnumeration.java:43) [taskdef] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:215) [taskdef] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [taskdef] at org.apache.tools.ant.Task.perform(Task.java:364) [taskdef] at org.apache.tools.ant.Target.execute(Target.java:341) [taskdef] at org.apache.tools.ant.Target.performTasks(Target.java:369) [taskdef] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [taskdef] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [taskdef] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [taskdef] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [taskdef] at org.apache.tools.ant.Main.runBuild(Main.java:668) [taskdef] at org.apache.tools.ant.Main.startAnt(Main.java:187) [taskdef] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [taskdef] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [antlib] java.util.zip.ZipException: error in opening zip file [antlib] at java.util.zip.ZipFile.open(Native Method) [antlib] at java.util.zip.ZipFile.(ZipFile.java:114) [antlib] at java.util.zip.ZipFile.(ZipFile.java:131) [antlib] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [antlib] at org.apache.tools.ant.AntClassLoader.getResource(AntClassLoader.java:832) [antlib] at org.apache.log4j.helpers.Loader.getResource(Loader.java:91) [antlib] at org.apache.log4j.LogManager.(LogManager.java:94) [antlib] at org.apache.log4j.Logger.getLogger(Logger.java:94) [antlib] at org.intermine.web.task.LoadDefaultTemplatesTask.(LoadDefaultTemplatesTask.java:56) [antlib] at java.lang.Class.forName0(Native Method) [antlib] at java.lang.Class.forName(Class.java:247) [antlib] at org.apache.tools.ant.taskdefs.Definer.addDefinition(Definer.java:457) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:183) [antlib] at org.apache.tools.ant.taskdefs.Antlib.execute(Antlib.java:161) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.taskdefs.Definer.loadAntlib(Definer.java:330) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:236) [antlib] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.Target.execute(Target.java:341) [antlib] at org.apache.tools.ant.Target.performTasks(Target.java:369) [antlib] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [antlib] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [antlib] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [antlib] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [antlib] at org.apache.tools.ant.Main.runBuild(Main.java:668) [antlib] at org.apache.tools.ant.Main.startAnt(Main.java:187) [antlib] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [antlib] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [antlib] java.util.zip.ZipException: error in opening zip file [antlib] at java.util.zip.ZipFile.open(Native Method) [antlib] at java.util.zip.ZipFile.(ZipFile.java:114) [antlib] at java.util.zip.ZipFile.(ZipFile.java:131) [antlib] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [antlib] at org.apache.tools.ant.AntClassLoader.getResource(AntClassLoader.java:832) [antlib] at org.apache.log4j.helpers.Loader.getResource(Loader.java:91) [antlib] at org.apache.log4j.LogManager.(LogManager.java:94) [antlib] at org.apache.log4j.Logger.getLogger(Logger.java:94) [antlib] at org.intermine.web.task.LoadDefaultTemplatesTask.(LoadDefaultTemplatesTask.java:56) [antlib] at java.lang.Class.forName0(Native Method) [antlib] at java.lang.Class.forName(Class.java:247) [antlib] at org.apache.tools.ant.taskdefs.Definer.addDefinition(Definer.java:457) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:183) [antlib] at org.apache.tools.ant.taskdefs.Antlib.execute(Antlib.java:161) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.taskdefs.Definer.loadAntlib(Definer.java:330) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:236) [antlib] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.Target.execute(Target.java:341) [antlib] at org.apache.tools.ant.Target.performTasks(Target.java:369) [antlib] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [antlib] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [antlib] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [antlib] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [antlib] at org.apache.tools.ant.Main.runBuild(Main.java:668) [antlib] at org.apache.tools.ant.Main.startAnt(Main.java:187) [antlib] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [antlib] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [antlib] java.util.zip.ZipException: error in opening zip file [antlib] at java.util.zip.ZipFile.open(Native Method) [antlib] at java.util.zip.ZipFile.(ZipFile.java:114) [antlib] at java.util.zip.ZipFile.(ZipFile.java:131) [antlib] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [antlib] at org.apache.tools.ant.AntClassLoader.getResource(AntClassLoader.java:832) [antlib] at org.apache.log4j.helpers.Loader.getResource(Loader.java:91) [antlib] at org.apache.log4j.LogManager.(LogManager.java:94) [antlib] at org.apache.log4j.Logger.getLogger(Logger.java:94) [antlib] at org.intermine.web.task.LoadDefaultTemplatesTask.(LoadDefaultTemplatesTask.java:56) [antlib] at java.lang.Class.forName0(Native Method) [antlib] at java.lang.Class.forName(Class.java:247) [antlib] at org.apache.tools.ant.taskdefs.Definer.addDefinition(Definer.java:457) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:183) [antlib] at org.apache.tools.ant.taskdefs.Antlib.execute(Antlib.java:161) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.taskdefs.Definer.loadAntlib(Definer.java:330) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:236) [antlib] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.Target.execute(Target.java:341) [antlib] at org.apache.tools.ant.Target.performTasks(Target.java:369) [antlib] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [antlib] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [antlib] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [antlib] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [antlib] at org.apache.tools.ant.Main.runBuild(Main.java:668) [antlib] at org.apache.tools.ant.Main.startAnt(Main.java:187) [antlib] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [antlib] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [antlib] java.util.zip.ZipException: error in opening zip file [antlib] at java.util.zip.ZipFile.open(Native Method) [antlib] at java.util.zip.ZipFile.(ZipFile.java:114) [antlib] at java.util.zip.ZipFile.(ZipFile.java:131) [antlib] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [antlib] at org.apache.tools.ant.AntClassLoader.getResource(AntClassLoader.java:832) [antlib] at org.apache.log4j.helpers.Loader.getResource(Loader.java:91) [antlib] at org.apache.log4j.LogManager.(LogManager.java:94) [antlib] at org.apache.log4j.Logger.getLogger(Logger.java:94) [antlib] at org.intermine.web.task.LoadDefaultTemplatesTask.(LoadDefaultTemplatesTask.java:56) [antlib] at java.lang.Class.forName0(Native Method) [antlib] at java.lang.Class.forName(Class.java:247) [antlib] at org.apache.tools.ant.taskdefs.Definer.addDefinition(Definer.java:457) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:183) [antlib] at org.apache.tools.ant.taskdefs.Antlib.execute(Antlib.java:161) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.taskdefs.Definer.loadAntlib(Definer.java:330) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:236) [antlib] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.Target.execute(Target.java:341) [antlib] at org.apache.tools.ant.Target.performTasks(Target.java:369) [antlib] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [antlib] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [antlib] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [antlib] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [antlib] at org.apache.tools.ant.Main.runBuild(Main.java:668) [antlib] at org.apache.tools.ant.Main.startAnt(Main.java:187) [antlib] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [antlib] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [antlib] java.util.zip.ZipException: error in opening zip file [antlib] at java.util.zip.ZipFile.open(Native Method) [antlib] at java.util.zip.ZipFile.(ZipFile.java:114) [antlib] at java.util.zip.ZipFile.(ZipFile.java:131) [antlib] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [antlib] at org.apache.tools.ant.AntClassLoader.getResource(AntClassLoader.java:832) [antlib] at org.apache.log4j.helpers.Loader.getResource(Loader.java:91) [antlib] at org.apache.log4j.LogManager.(LogManager.java:94) [antlib] at org.apache.log4j.Logger.getLogger(Logger.java:94) [antlib] at org.intermine.web.task.LoadDefaultTemplatesTask.(LoadDefaultTemplatesTask.java:56) [antlib] at java.lang.Class.forName0(Native Method) [antlib] at java.lang.Class.forName(Class.java:247) [antlib] at org.apache.tools.ant.taskdefs.Definer.addDefinition(Definer.java:457) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:183) [antlib] at org.apache.tools.ant.taskdefs.Antlib.execute(Antlib.java:161) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.taskdefs.Definer.loadAntlib(Definer.java:330) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:236) [antlib] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.Target.execute(Target.java:341) [antlib] at org.apache.tools.ant.Target.performTasks(Target.java:369) [antlib] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [antlib] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [antlib] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [antlib] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [antlib] at org.apache.tools.ant.Main.runBuild(Main.java:668) [antlib] at org.apache.tools.ant.Main.startAnt(Main.java:187) [antlib] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [antlib] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [antlib] java.util.zip.ZipException: error in opening zip file [antlib] at java.util.zip.ZipFile.open(Native Method) [antlib] at java.util.zip.ZipFile.(ZipFile.java:114) [antlib] at java.util.zip.ZipFile.(ZipFile.java:131) [antlib] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [antlib] at org.apache.tools.ant.AntClassLoader.getResource(AntClassLoader.java:832) [antlib] at org.apache.log4j.helpers.Loader.getResource(Loader.java:91) [antlib] at org.apache.log4j.LogManager.(LogManager.java:94) [antlib] at org.apache.log4j.Logger.getLogger(Logger.java:94) [antlib] at org.intermine.web.task.LoadDefaultTemplatesTask.(LoadDefaultTemplatesTask.java:56) [antlib] at java.lang.Class.forName0(Native Method) [antlib] at java.lang.Class.forName(Class.java:247) [antlib] at org.apache.tools.ant.taskdefs.Definer.addDefinition(Definer.java:457) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:183) [antlib] at org.apache.tools.ant.taskdefs.Antlib.execute(Antlib.java:161) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.taskdefs.Definer.loadAntlib(Definer.java:330) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:236) [antlib] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.Target.execute(Target.java:341) [antlib] at org.apache.tools.ant.Target.performTasks(Target.java:369) [antlib] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [antlib] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [antlib] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [antlib] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [antlib] at org.apache.tools.ant.Main.runBuild(Main.java:668) [antlib] at org.apache.tools.ant.Main.startAnt(Main.java:187) [antlib] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [antlib] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) [antlib] java.util.zip.ZipException: error in opening zip file [antlib] at java.util.zip.ZipFile.open(Native Method) [antlib] at java.util.zip.ZipFile.(ZipFile.java:114) [antlib] at java.util.zip.ZipFile.(ZipFile.java:131) [antlib] at org.apache.tools.ant.AntClassLoader.getResourceURL(AntClassLoader.java:919) [antlib] at org.apache.tools.ant.AntClassLoader.getResource(AntClassLoader.java:832) [antlib] at org.apache.log4j.helpers.Loader.getResource(Loader.java:91) [antlib] at org.apache.log4j.LogManager.(LogManager.java:94) [antlib] at org.apache.log4j.Logger.getLogger(Logger.java:94) [antlib] at org.intermine.web.task.LoadDefaultTemplatesTask.(LoadDefaultTemplatesTask.java:56) [antlib] at java.lang.Class.forName0(Native Method) [antlib] at java.lang.Class.forName(Class.java:247) [antlib] at org.apache.tools.ant.taskdefs.Definer.addDefinition(Definer.java:457) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:183) [antlib] at org.apache.tools.ant.taskdefs.Antlib.execute(Antlib.java:161) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.taskdefs.Definer.loadAntlib(Definer.java:330) [antlib] at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:236) [antlib] at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:275) [antlib] at org.apache.tools.ant.Task.perform(Task.java:364) [antlib] at org.apache.tools.ant.Target.execute(Target.java:341) [antlib] at org.apache.tools.ant.Target.performTasks(Target.java:369) [antlib] at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1216) [antlib] at org.apache.tools.ant.Project.executeTarget(Project.java:1185) [antlib] at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:40) [antlib] at org.apache.tools.ant.Project.executeTargets(Project.java:1068) [antlib] at org.apache.tools.ant.Main.runBuild(Main.java:668) [antlib] at org.apache.tools.ant.Main.startAnt(Main.java:187) [antlib] at org.apache.tools.ant.launch.Launcher.run(Launcher.java:246) [antlib] at org.apache.tools.ant.launch.Launcher.main(Launcher.java:67) -load-task-taskdefs: -init-macrodef-build-db: -init-task-xml: -init-build-db: -do-build-db-userprofile: [build-db] Our new url -> jdbc:postgresql://localhost:5460/userprofile-flymine11 [build-db] Our new url -> jdbc:postgresql://localhost:5460/userprofile-flymine11 -load-default-templates: [load-default-templates] Loading default templates and tags into profile lugmayr@imp.ac.at [load-default-templates] Adding template "A_IdentifierSynonym_Object" [load-default-templates] Adding template "AllGene_Chromosome" [load-default-templates] Adding template "All_Genes_In_Organism_To_Publications" [load-default-templates] Adding template "AnatomyTerm_Region" [invalid] [load-default-templates] Adding template "CDNAClone_To_Protein_Type_Converter" [load-default-templates] Adding template "ChromLocation_AmplimerPrimer" [load-default-templates] Adding template "ChromLocation_AmplimerPrimerPromoter" [load-default-templates] Adding template "ChromLocation_DrosDelDeletion" [load-default-templates] Adding template "ChromLocation_Gene" [load-default-templates] Adding template "ChromLocation_GeneTranscriptExon" [load-default-templates] Adding template "ChromLocation_GeneTranscriptINDAC" [load-default-templates] Adding template "ChromLocation_Region" [invalid] [load-default-templates] Adding template "ChromLocation_RegionOverlappingTFBindingsite" [load-default-templates] Adding template "ChromLocation_TFBindingSiteLocationGeneFactor" [load-default-templates] Adding template "ChromosomeLocation_ESTcluster" [load-default-templates] Adding template "ChromosomeLocation_ESTclusterandESTs" [load-default-templates] Adding template "ChromosomeLocation_Tiffin" [load-default-templates] Adding template "Chromosome_AmplimerLocation" [load-default-templates] Adding template "Chromosome_Gene" [load-default-templates] Adding template "Chromosome_GeneInsertionLocation" [load-default-templates] Adding template "Chromosome_IntergenicSequence" [load-default-templates] Adding template "Chromosome_RegionOverlappingInsertion" [load-default-templates] Adding template "DRSCScreen_ScreenHit" [load-default-templates] Adding template "DRSCamplicon_ScreenHit" [load-default-templates] Adding template "DatasetGiot_ProteinInteractions2" [load-default-templates] Adding template "Dataset_proteinInteractions" [load-default-templates] Adding template "Disease_GeneOrthologue" [load-default-templates] Adding template "Disease_GeneOrthologueEValue" [load-default-templates] Adding template "DrosDel_GeneLocation" [load-default-templates] Adding template "DrosDel_LocationGeneTranscriptINDAC" [load-default-templates] Adding template "ESTaccession_ClusterChromosomelocation" [load-default-templates] Adding template "ESTclone_LocationDMorthologuePathway" [invalid] [load-default-templates] Adding template "ESTclone_LocationOverlappingGene" [load-default-templates] Adding template "ESTclone_LocationOverlappingGeneOrthologue" [invalid] [load-default-templates] Adding template "ESTclone_LocationOverlappingGeneStructure" [load-default-templates] Adding template "ESTclone_clusterLocation" [load-default-templates] Adding template "ESTcluster_DMorthologuePathway" [invalid] [load-default-templates] Adding template "ESTcluster_ESTSchromosomelocation" [load-default-templates] Adding template "ESTclustertype_chromosomelocation" [load-default-templates] Adding template "Exon_To_Gene_Type_Converter" [load-default-templates] Adding template "FlyFish_Genes" [load-default-templates] Adding template "GO_name_Gene" [load-default-templates] Adding template "GOname_GOidentifier" [load-default-templates] Adding template "GOtermidentifier_name" [load-default-templates] Adding template "Gene _adjacent genes" [load-default-templates] Adding template "GeneOrganism1_OrthologueOrganism2" [invalid] [load-default-templates] Adding template "GeneOrganism_OrthologueRNAi" [invalid] [load-default-templates] Adding template "GeneSymbol_Identifier" [load-default-templates] Adding template "GeneTF_TFBindingsites" [load-default-templates] Adding template "GeneTissue_FlyAtlas" [invalid] [load-default-templates] Adding template "Gene_DRSCOrthologueRNAiPhenotype" [invalid] [load-default-templates] Adding template "Gene_DRSCScreenHit" [load-default-templates] Adding template "Gene_DrosDelDeletion" [load-default-templates] Adding template "Gene_DrosDelDeletionAvailable" [load-default-templates] Adding template "Gene_DrosDelDeletionInsertion" [load-default-templates] Adding template "Gene_ExonLocation2" [load-default-templates] Adding template "Gene_FlyAtlas" [invalid] [load-default-templates] Adding template "Gene_FlyAtlasGO" [invalid] [load-default-templates] Adding template "Gene_FlyFish" [load-default-templates] Adding template "Gene_GO" [load-default-templates] Adding template "Gene_INDAC" [load-default-templates] Adding template "Gene_Identifiers" [load-default-templates] Adding template "Gene_Insertion" [load-default-templates] Adding template "Gene_IntronChromosome" [load-default-templates] Adding template "Gene_Orthologue" [invalid] [load-default-templates] Adding template "Gene_OrthologueDisease" [load-default-templates] Adding template "Gene_OrthologueDiseaseEValue" [load-default-templates] Adding template "Gene_OrthologueDiseaseRNAi" [invalid] [load-default-templates] Adding template "Gene_OrthologueGO" [invalid] [load-default-templates] Adding template "Gene_OrthologueOrganism" [invalid] [load-default-templates] Adding template "Gene_OrthologueProteinInteraction" [invalid] [load-default-templates] Adding template "Gene_OrthologueRNAi" [invalid] [load-default-templates] Adding template "Gene_OverlapppingGenes" [load-default-templates] Adding template "Gene_PointMutationLocation" [load-default-templates] Adding template "Gene_Probe" [load-default-templates] Adding template "Gene_Protein" [load-default-templates] Adding template "Gene_ProteinInteractingproteinConfidenceOtherDetails" [load-default-templates] Adding template "Gene_ProteinInteractingproteinPfamdomainStructure" [invalid] [load-default-templates] Adding template "Gene_ProteinStructure" [invalid] [load-default-templates] Adding template "Gene_RNAiOrthologue" [invalid] [load-default-templates] Adding template "Gene_RNAiPhenotype" [load-default-templates] Adding template "Gene_RegionLocation" [invalid] [load-default-templates] Adding template "Gene_RegionOverlappingTFbindingsite" [load-default-templates] Adding template "Gene_TFBindingSiteLocationFactor" [load-default-templates] Adding template "Gene_TFBindingSiteRegionLocation" [load-default-templates] Adding template "Gene_Tiffin" [load-default-templates] Adding template "Gene_TilingPathAmplimersLocation" [load-default-templates] Adding template "Gene_TilingPathSpanAmplimerLocation" [load-default-templates] Adding template "Gene_TilingPathSpanLocation" [load-default-templates] Adding template "Gene_TimeCourseResult" [load-default-templates] Adding template "Gene_TimeCourseResultGeneralStage" [load-default-templates] Adding template "Gene_TimeCourseResultGeneralStageRatio" [load-default-templates] Adding template "Gene_TimeCourseResultSpecificStage" [load-default-templates] Adding template "Gene_TimeCourseResultSpecificStageRatio" [load-default-templates] Adding template "Gene_To_Exon_Type_Converter" [load-default-templates] Adding template "Gene_To_KEGG_Pathway_Id" [load-default-templates] Adding template "Gene_To_MRNA_Type_Converter" [load-default-templates] Adding template "Gene_To_Protein_Type_Converter" [load-default-templates] Adding template "Gene_To_Publications" [load-default-templates] Adding template "Gene_To_Transcript_Type_Converter" [load-default-templates] Adding template "Gene_TranscriptExon" [load-default-templates] Adding template "Gene_TranscriptExonIntron" [load-default-templates] Adding template "Gene_TranscriptExonLocation" [load-default-templates] Adding template "Gene_TranscriptIntronLocation" [load-default-templates] Adding template "Gene_TranscriptOrthologue" [invalid] [load-default-templates] Adding template "Gene_TranscriptTranslation" [load-default-templates] Adding template "Gene_allGOTerms" [load-default-templates] Adding template "Gene_chromosomeLocation" [load-default-templates] Adding template "Gene_paralogues" [invalid] [load-default-templates] Adding template "Gene_particularGoannotation" [load-default-templates] Adding template "Gene_pointMutationsInExons" [load-default-templates] Adding template "Gene_to_upstream_intergenic" [load-default-templates] Adding template "Gene_transposableElementsOverlappingExons" [load-default-templates] Adding template "Gene_upstreamAdjacent_FlyAtlas" [invalid] [load-default-templates] Adding template "Gene_upstreamRegulatoryRegions" [load-default-templates] Adding template "GeneralStageRatio_agLifecycleExpression" [load-default-templates] Adding template "GeneralStage_agLifecycleExpression" [load-default-templates] Adding template "INDAC_GeneLocation" [load-default-templates] Adding template "Insertion_GeneLocation" [load-default-templates] Adding template "InterProDomain_ProteinGene" [invalid] [load-default-templates] Adding template "InterPro_Domain_Family" [invalid] [load-default-templates] Adding template "Intergenic_RegRegion" [load-default-templates] Adding template "MRNA_To_Gene_Type_Converter" [load-default-templates] Adding template "MRNA_To_Protein_Type_Converter" [load-default-templates] Adding template "OrganismGOterm_GenesTEinsertionsite" [load-default-templates] Adding template "OrganismGoterm_genesDrosDelDeletion" [load-default-templates] Adding template "OrganismGoterm_genesPointMutations" [load-default-templates] Adding template "Organism_3UTR" [load-default-templates] Adding template "Organism_5UTR" [load-default-templates] Adding template "Organism_Gene" [load-default-templates] Adding template "Organism_GeneDomain" [invalid] [load-default-templates] Adding template "Organism_GeneLocation" [load-default-templates] Adding template "Organism_GenePointMutation" [load-default-templates] Adding template "Organism_GeneProteinStructure" [invalid] [load-default-templates] Adding template "Organism_GoTermEC_Gene" [load-default-templates] Adding template "Organism_GoTerm_Gene" [load-default-templates] Adding template "Organism_GoTerm_GeneWithannotation" [load-default-templates] Adding template "Organism_Intergenic" [load-default-templates] Adding template "Organism_Interpro" [invalid] [load-default-templates] Adding template "Organism_Protein" [load-default-templates] Adding template "Organism_ProteinDomain" [invalid] [load-default-templates] Adding template "Organism_ProteinInteraction" [load-default-templates] Adding template "Organism_TFBindingSiteLocationFactor" [load-default-templates] Adding template "Organism_Transcript" [load-default-templates] Adding template "PFam_ProteinStructure" [invalid] [load-default-templates] Adding template "Pathway_Genes" [load-default-templates] Adding template "Pathway_GenesOrthol" [invalid] [load-default-templates] Adding template "Pathway_GenesOrtholEST" [invalid] [load-default-templates] Adding template "PointMutation_Gene_Chromosome" [load-default-templates] Adding template "ProbeSet_FlyAtlas" [invalid] [load-default-templates] Adding template "Probe_Gene" [load-default-templates] Adding template "Protein12_GeneTFBindingSite" [load-default-templates] Adding template "ProteinInteractionOrganism_ProteinInteractionOrganism" [invalid] [load-default-templates] Adding template "ProteinInteraction_OrthologueOrganism" [invalid] [load-default-templates] Adding template "Protein_GOterms" [load-default-templates] Adding template "Protein_Gene" [load-default-templates] Adding template "Protein_GeneChromosomeLength" [load-default-templates] Adding template "Protein_Interpro" [invalid] [load-default-templates] Adding template "Protein_Orthologue_RNAi" [invalid] [load-default-templates] Adding template "Protein_PDBStructure" [load-default-templates] Adding template "Protein_ProteinInteraction" [load-default-templates] Adding template "Protein_ProteinInteractionDmRNAi" [invalid] [load-default-templates] Adding template "Protein_ProteinInteractionOrthologue" [invalid] [load-default-templates] Adding template "Protein_ProteinInteractionOrthologueRNAi" [invalid] [load-default-templates] Adding template "Protein_Structure" [invalid] [load-default-templates] Adding template "Protein_To_CDNAclone_Type_Converter" [load-default-templates] Adding template "Protein_To_Gene_Type_Converter" [load-default-templates] Adding template "Protein_To_MRNA_Type_Converter" [load-default-templates] Adding template "Protein_To_Transcript_Type_Converter" [load-default-templates] Adding template "RNAiPhenotype_GeneOrthologue" [invalid] [load-default-templates] Adding template "RNAi_Gene" [load-default-templates] Adding template "SpecificStageRatio_agLifecycleExpression" [load-default-templates] Adding template "SpecificStage_agLifecycleExpression" [load-default-templates] Adding template "Stage_FlyFish" [load-default-templates] Adding template "TFBindingSite_GeneFactor" [load-default-templates] Adding template "Technique_PDBstructure" [load-default-templates] Adding template "TiffinBSmotif_locations" [load-default-templates] Adding template "TilingPathSpan_GeneLocation" [load-default-templates] Adding template "TimeCourseDataGeneralStageRatio_genes" [load-default-templates] Adding template "TimeCourseDataGeneralStage_genes" [load-default-templates] Adding template "TimeCourseDataSpecificStageRatio_genes" [load-default-templates] Adding template "TimeCourseDataSpecificStage_genes" [load-default-templates] Adding template "Tissue_Flyatlas" [invalid] [load-default-templates] Adding template "Transcript_INDAC" [load-default-templates] Adding template "Transcript_To_Gene_Type_Converter" [load-default-templates] Adding template "Transcript_To_Protein_Type_Converter" [load-default-templates] Adding template "TranscriptionFactor_Genes" [load-default-templates] Adding template "Transcriptionfactor_TFBindingSiteChromosomeGene" [load-default-templates] Adding template "Translation_To_Gene_Type_Converter" [load-default-templates] Adding template "Translation_To_Protein_Type_Converter" [load-default-templates] Adding template "Translation_To_Transcript_Type_Converter" [load-default-templates] Adding template "UnalignedESTclusters" [load-default-templates] Adding template "allGO_GeneOrganism" [load-default-templates] Adding template "flyreg_info" [load-default-templates] Adding template "geneGeneralStageRatio_agLifecycleExpression" [load-default-templates] Adding template "geneGeneralStage_agLifecycleExpression" [load-default-templates] Adding template "geneSpecificStageRatio_agLifecycleExpression" [load-default-templates] Adding template "geneSpecificStage_agLifecycleExpression" [load-default-templates] Adding template "gene_adjacentgenes_allflyatlas" [invalid] [load-default-templates] Adding template "gene_agLifecycleExpression" [load-default-templates] Adding template "gene_downstreamAdjacentgene_FlyAtlas" [invalid] [load-default-templates] Adding template "mRNAlocalisationTerm_Genes" BUILD FAILED /bioinfodev1/flymine/flymine11/imbuild/application.xml:87: java.lang.RuntimeException: unknown class name "org.flymine.model.genomic.Paralogue" while tagging: org.flymine.model.genomic.Paralogue Total time: 37 seconds --=-rH7SK11qRjSLp6QktYC5-- From richard@flymine.org Mon Feb 18 17:22:59 2008 Received: from [192.168.128.115] (helo=chimp.flymine.org) by flymine.flymine.org with esmtp (Exim 4.12) id 1JR9hj-0002ov-00 for flymine-dev@flymine.org; Mon, 18 Feb 2008 17:22:59 +0000 Message-ID: <47B9BEF3.9000704@flymine.org> Date: Mon, 18 Feb 2008 17:22:59 +0000 From: Richard Smith User-Agent: Thunderbird 2.0.0.9 (Macintosh/20071031) MIME-Version: 1.0 To: flymine-dev@flymine.org Subject: Re: [flymine-dev] flymine 11 - ant build-db-userprofile problem References: <1203337643.3173.23.camel@bioinfo10.imp.univie.ac.at> In-Reply-To: <1203337643.3173.23.camel@bioinfo10.imp.univie.ac.at> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Hi Wolfgang, Yes, Sorry. The problem was with tags on classes that had been removed from the model appearing in default-template-queries.xml. I've updated it on the branch. In general it is fine to delete invalid tags, we should really change the code to ignore them instead of throwing an exception. We never load that file for FlyMine and instead upgrade the existing userprofile each time. Richard. Wolfgang Lugmayr wrote: > Hi, > > when building flymine 11 from scratch the following error occurs when > calling: > (ant build-db-userprofile 2>&1) | tee ant-userprofile.log > : > [load-default-templates] Adding template "gene_agLifecycleExpression" > [load-default-templates] Adding template > "gene_downstreamAdjacentgene_FlyAtlas" [invalid] > [load-default-templates] Adding template "mRNAlocalisationTerm_Genes" > > BUILD FAILED > /bioinfodev1/flymine/flymine11/imbuild/application.xml:87: > java.lang.RuntimeException: unknown class name > "org.flymine.model.genomic.Paralogue" while tagging: > org.flymine.model.genomic.Paralogue > > > doing some ant compile, jar, war etc. ... > and running the same again the error is: > /bioinfodev1/flymine/flymine11/imbuild/application.xml:87: > java.lang.RuntimeException: unknown class name > "org.flymine.model.genomic.ProteinFeature" while tagging: > org.flymine.model.genomic.ProteinFeature > > The classes/tables existed in flymine9 but not in 11? > > Attached is the logfile of the first run. > > Is there an error in > ./webapp/src/default-template-queries.xml? > > Cheers, > Wolfgang > > From Wolfgang.Lugmayr@imp.ac.at Thu Feb 21 10:20:28 2008 Received: from ppsw-9.csi.cam.ac.uk ([131.111.8.139]) by flymine.flymine.org with esmtp (Exim 4.12) id 1JS8XU-000385-00 for flymine-dev@flymine.org; Thu, 21 Feb 2008 10:20:28 +0000 X-Cam-SpamDetails: scanned, SpamAssassin-3.2.3 (score=0) X-Cam-AntiVirus: No virus found X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Received: from mordor.imp.ac.at ([193.171.188.3]:5324 helo=mail.imp.univie.ac.at) by ppsw-9.csi.cam.ac.uk (mx.cam.ac.uk [131.111.8.149]:25) with esmtp (csa=unknown) id 1JS8XI-0001Jo-TO (Exim 4.67) for flymine-dev@flymine.org (return-path ); Thu, 21 Feb 2008 10:20:21 +0000 Received: from bioinfo10.imp.univie.ac.at ([10.42.100.10]) by mail.imp.univie.ac.at with Microsoft SMTPSVC(6.0.3790.1830); Thu, 21 Feb 2008 11:19:55 +0100 From: Wolfgang Lugmayr To: flymine-dev@flymine.org Content-Type: text/plain Date: Thu, 21 Feb 2008 11:19:55 +0100 Message-Id: <1203589195.2902.29.camel@bioinfo10.imp.univie.ac.at> Mime-Version: 1.0 X-Mailer: Evolution 2.6.3 Content-Transfer-Encoding: 7bit X-OriginalArrivalTime: 21 Feb 2008 10:19:55.0581 (UTC) FILETIME=[4DD33ED0:01C87473] Subject: [flymine-dev] FlyMine GBrowse questions Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org X-Reply-To: wolfgang.lugmayr@imp.ac.at List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: hi, we have flymine 11 running at our site without the gbrowse support. we can access the gbrowse flymine 11 data at our url: http://flymine/cgi-bin/gbrowse/flymine-release-11.0/ and it seems fine. but in the flymine application we see only the url: e.g. zen http://flymine/?source=;label=Genes;name=FlyMineInternalID_1090061028;width=750 instead of http://flymine/cgi-bin/gbrowse/flymine-release-11.0?source=;label=Genes;name=FlyMineInternalID_1090061028;width=750 or http://flymine/cgi-bin/gbrowse_details/... do i miss some configuration settings during the build somewhere? cheers, wolfgang From Wolfgang.Lugmayr@imp.ac.at Thu Feb 21 10:53:16 2008 Received: from ppsw-5.csi.cam.ac.uk ([131.111.8.135]) by flymine.flymine.org with esmtp (Exim 4.12) id 1JS93E-0003Fg-00 for flymine-dev@flymine.org; Thu, 21 Feb 2008 10:53:16 +0000 X-Cam-SpamDetails: scanned, SpamAssassin-3.2.3 (score=0) X-Cam-AntiVirus: No virus found X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Received: from mordor.imp.ac.at ([193.171.188.3]:28271 helo=mail.imp.univie.ac.at) by ppsw-5.csi.cam.ac.uk (mx.cam.ac.uk [131.111.8.145]:25) with esmtp (csa=unknown) id 1JS936-0007oA-JD (Exim 4.67) for flymine-dev@flymine.org (return-path ); Thu, 21 Feb 2008 10:53:14 +0000 Received: from bioinfo10.imp.univie.ac.at ([10.42.100.10]) by mail.imp.univie.ac.at with Microsoft SMTPSVC(6.0.3790.1830); Thu, 21 Feb 2008 11:52:48 +0100 From: Wolfgang Lugmayr To: FlyMine Development List Content-Type: text/plain Date: Thu, 21 Feb 2008 11:52:48 +0100 Message-Id: <1203591168.7996.4.camel@bioinfo10.imp.univie.ac.at> Mime-Version: 1.0 X-Mailer: Evolution 2.6.3 Content-Transfer-Encoding: 7bit X-OriginalArrivalTime: 21 Feb 2008 10:52:48.0356 (UTC) FILETIME=[E5B0D240:01C87477] Subject: [flymine-dev] case sensitive logins Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org X-Reply-To: wolfgang.lugmayr@imp.ac.at List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: hi, due the user migration to flymine 11 we have found out, that we have some duplicated user accounts in the userprofile database. the logins "MyName" and "myname" are two different accounts. can this be unified by using a java towlower() in the login mask? on the long run, this may confuse our users - if they have different settings each time they log in (with different case letters). what do you think? cheers, wolfgang From kmr@flymine.org Thu Feb 21 12:53:14 2008 Received: from host110 ([192.168.128.110] helo=merry.flymine.org ident=mail) by flymine.flymine.org with esmtp (Exim 4.12) id 1JSAvK-0003bx-00; Thu, 21 Feb 2008 12:53:14 +0000 Received: from kmr by merry.flymine.org with local (Exim 3.36 #1 (Debian)) id 1JSAvK-0000qs-00; Thu, 21 Feb 2008 12:53:14 +0000 From: Kim Rutherford MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <18365.29754.393256.484649@merry.flymine.org> Date: Thu, 21 Feb 2008 12:53:14 +0000 To: flymine-dev@flymine.org Subject: Re: [flymine-dev] FlyMine GBrowse questions In-Reply-To: <1203589195.2902.29.camel@bioinfo10.imp.univie.ac.at> References: <1203589195.2902.29.camel@bioinfo10.imp.univie.ac.at> X-Mailer: VM 7.19 under Emacs 21.3.50.1 X-PGP-Key: 0x1BF31C43 (1998-11-01) X-PGP-Fingerprint: 1F7E 46F2 3347 3C51 E9CF ED16 9E63 6029 1BF3 1C43 Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org X-Reply-To: kmr@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: On Thu, 21 Feb 2008 11:19:55 +0100, Wolfgang Lugmayr wrote: > hi, > we have flymine 11 running at our site without the gbrowse support. > we can access the gbrowse flymine 11 data at our url: > http://flymine/cgi-bin/gbrowse/flymine-release-11.0/ > and it seems fine. > but in the flymine application we see only the url: > e.g. zen > http://flymine/?source=;label=Genes;name=FlyMineInternalID_1090061028;width=750 > instead of > http://flymine/cgi-bin/gbrowse/flymine-release-11.0?source=;label=Genes;name=FlyMineInternalID_1090061028;width=750 > or > http://flymine/cgi-bin/gbrowse_details/... > do i miss some configuration settings during the build somewhere? Hi. Sorry for the problems. The documentation wasn't good for GBrowse configuration. The problem you are seeing is probably due to a mis-feature which means that the GBrowse properties need to be in build.properties. and in build.properties.-gbrowse. These are the properties you'll need in both files: gbrowse.database gbrowse.database.adaptor gbrowse.database.source gbrowse.database.host gbrowse.database.user gbrowse.database.password gbrowse.database.write.user gbrowse.database.write.password This has been fixed in trunk so that build.properties.-gbrowse isn't needed anymore - all properties will go in build.properties.. I've updated http://www.intermine.org/wiki/GBrowseConfiguration so I hope it will be clearer for others. Kim. From richard@flymine.org Mon Aug 04 16:51:42 2008 Received: from [192.168.128.115] (helo=chimp.flymine.org) by flymine.flymine.org with esmtp (Exim 4.12) id 1KQ2LW-0007B6-00; Mon, 04 Aug 2008 16:51:42 +0100 Message-ID: <4897258E.90003@flymine.org> Date: Mon, 04 Aug 2008 16:51:42 +0100 From: Richard Smith User-Agent: Thunderbird 2.0.0.16 (Macintosh/20080707) MIME-Version: 1.0 To: flymine-dev@flymine.org Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Subject: [flymine-dev] InterMine workshop Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Hi all, We are planning to run a two day InterMine workshop in late October this year. It will be for existing InterMine users and also an introduction to any groups that are interested in getting started. Hopefully it will be quite hands on, examples of session topics may be writing converters, webapp configuration, widget development, web services and the query API. We will also request suggestions for topics and encourage InterMine users to present what they are working on. It will also be an opportunity for you to spend time with the InterMine developers and other users to discuss ideas for improvements and priorities for development. We have yet to finalise the date but the possibilities are: Thu 23rd & Fri 24th October Thu 30th & Fri 31st October We would really like as many existing InterMine users to come as possible so please let me know as soon as possible if you would like to come and if you have conflicts with either of those dates. The workshop will be in Cambridge and free to attend. Regards, Richard. From richard@flymine.org Tue Aug 05 10:46:55 2008 Received: from [192.168.128.115] (helo=chimp.flymine.org) by flymine.flymine.org with esmtp (Exim 4.12) id 1KQJ83-0000yY-00 for flymine-dev@flymine.org; Tue, 05 Aug 2008 10:46:55 +0100 Message-ID: <4898218F.3050708@flymine.org> Date: Tue, 05 Aug 2008 10:46:55 +0100 From: Richard Smith User-Agent: Thunderbird 2.0.0.16 (Macintosh/20080707) MIME-Version: 1.0 To: flymine-dev@flymine.org Subject: Re: [flymine-dev] InterMine workshop References: <4897258E.90003@flymine.org> In-Reply-To: <4897258E.90003@flymine.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: If anyone coming from outside Cambridge needs help with travel and accommodation costs to come to the workshop we do have limited funds available. Richard. Richard Smith wrote: > Hi all, > We are planning to run a two day InterMine workshop in late October this > year. It will be for existing InterMine users and also an introduction > to any groups that are interested in getting started. > > Hopefully it will be quite hands on, examples of session topics may be > writing converters, webapp configuration, widget development, web > services and the query API. We will also request suggestions for topics > and encourage InterMine users to present what they are working on. > > It will also be an opportunity for you to spend time with the > InterMine developers and other users to discuss ideas for improvements > and priorities for development. > > > We have yet to finalise the date but the possibilities are: > > Thu 23rd & Fri 24th October > Thu 30th & Fri 31st October > > We would really like as many existing InterMine users to come as > possible so please let me know as soon as possible if you would like to > come and if you have conflicts with either of those dates. The workshop > will be in Cambridge and free to attend. > > Regards, > Richard. > > > _______________________________________________ > flymine-dev mailing list > flymine-dev@flymine.org > http://mailman.flymine.org/listinfo/flymine-dev > From richard@flymine.org Thu Sep 04 16:01:56 2008 Received: from [192.168.128.115] (helo=chimp.flymine.org) by flymine.flymine.org with esmtp (Exim 4.12) id 1KbGLM-0002WQ-00 for flymine-dev@flymine.org; Thu, 04 Sep 2008 16:01:56 +0100 Message-ID: <48BFF864.2020000@flymine.org> Date: Thu, 04 Sep 2008 16:01:56 +0100 From: Richard Smith User-Agent: Thunderbird 2.0.0.16 (Macintosh/20080707) MIME-Version: 1.0 To: flymine-dev@flymine.org Subject: Re: [flymine-dev] InterMine workshop References: <4897258E.90003@flymine.org> In-Reply-To: <4897258E.90003@flymine.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Hi everyone, The InterMine workshop date is now confirmed as 30th-31st October. There is a course outline and sign-up system available. Please could you sign up online even if you have already let me know you will be attending: http://www.biomed.cam.ac.uk/gradschool/current/courses/intermine.html We will hopefully provide lunch and an evening meal on Thursday 30th. Please let me know if you have any questions. Thanks, Richard. Richard Smith wrote: > Hi all, > We are planning to run a two day InterMine workshop in late October this > year. It will be for existing InterMine users and also an introduction > to any groups that are interested in getting started. > > Hopefully it will be quite hands on, examples of session topics may be > writing converters, webapp configuration, widget development, web > services and the query API. We will also request suggestions for topics > and encourage InterMine users to present what they are working on. > > It will also be an opportunity for you to spend time with the > InterMine developers and other users to discuss ideas for improvements > and priorities for development. > > > We have yet to finalise the date but the possibilities are: > > Thu 23rd & Fri 24th October > Thu 30th & Fri 31st October > > We would really like as many existing InterMine users to come as > possible so please let me know as soon as possible if you would like to > come and if you have conflicts with either of those dates. The workshop > will be in Cambridge and free to attend. > > Regards, > Richard. > > > _______________________________________________ > flymine-dev mailing list > flymine-dev@flymine.org > http://mailman.flymine.org/listinfo/flymine-dev > From gmodhelp@googlemail.com Fri Oct 17 17:40:09 2008 Received: from ppsw-6.csi.cam.ac.uk ([131.111.8.136]) by flymine.flymine.org with esmtp (Exim 4.12) id 1KqsMz-000540-00 for flymine-dev@flymine.org; Fri, 17 Oct 2008 17:40:09 +0100 X-Cam-AntiVirus: no malware found X-Cam-SpamDetails: score 0.0 from SpamAssassin-3.2.5-699147 X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Received: from ug-out-1314.google.com ([66.249.92.169]:55883) by ppsw-6.csi.cam.ac.uk (mx.cam.ac.uk [131.111.8.146]:25) with esmtp (csa=unknown) id 1KqsMy-0001Zv-Kh (Exim 4.70) for flymine-dev@flymine.org (return-path ); Fri, 17 Oct 2008 17:40:09 +0100 Received: by ug-out-1314.google.com with SMTP id 30so73586ugs.24 for ; Fri, 17 Oct 2008 09:40:08 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=googlemail.com; s=gamma; h=domainkey-signature:received:received:message-id:date:from:reply-to :to:subject:mime-version:content-type:content-transfer-encoding :content-disposition; bh=Vf5ypt/XvybjnBkblTn0+513kWs2r7i5xKHVVhDL4R0=; b=TgHfU49xs9qYwb0/jE3yU+Q6kGdzyM+IyQ47fBcaR953L8/3wZLDFgzezORHT+rKo+ MTSopM0g4pt39UOlqqiY04g0/O8cFii001GGg+11tcVW9j1KCKEhsB2CC66eEegBA01/ OImvHkSmc3tIwrezVjHdCyiav5iqszQHMp+bQ= DomainKey-Signature: a=rsa-sha1; c=nofws; d=googlemail.com; s=gamma; h=message-id:date:from:reply-to:to:subject:mime-version:content-type :content-transfer-encoding:content-disposition; b=Q6hWNKUdO5yolvzlfHjH+rUehcnQo4wK8Zd3E4GZpspCH79UHoTbQOCuNMI4GJZTSe E+Eboxi2prsspF3eJetiAtEY7r6mQmpx7pKh5maS+i9n1c2w4VQgbM1nfAj9AkeYsdDq AFpR6xWtpXSoPZTQOfSwJG47KP2H9dsFjHegE= Received: by 10.66.221.19 with SMTP id t19mr180147ugg.69.1224261607697; Fri, 17 Oct 2008 09:40:07 -0700 (PDT) Received: by 10.67.16.6 with HTTP; Fri, 17 Oct 2008 09:40:07 -0700 (PDT) Message-ID: <71ee57c70810170940o29987008j721406571bf0654d@mail.gmail.com> Date: Fri, 17 Oct 2008 09:40:07 -0700 From: "Dave Clements, GMOD Help Desk" To: "Gbrowse Mailing List" , "GMOD Schema List" , "GMOD CMap List" , "GMOD Announce" , "Apollo Mailing List" , "Modware List" , "BioMart Development List" , "GMOD Architecture List" , "Ergatis Users List" , "Ergatis Developers List" , "GBrowse AJAX List" , "GMOD Developers" , "Natural Diversity List" , "Sybil List" , "Turnkey Developers List" , "Turnkey Users List" , "InterMine List" MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Subject: [flymine-dev] 2008 GMOD Community Survery, or, Win a GMOD T-Shirt or Mug! Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org X-Reply-To: help@gmod.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Hello all, Please take a few minutes to fill out the first annual GMOD Community Survey: http://survey.oit.duke.edu/ViewsFlash/servlet/viewsflash?cmd=page&pollid=NESCent!GMODUserSurvey2008 We are asking all GMOD users and developers to provide input on how GMOD is doing, and how it can be improved. All questions are optional, but please provide as much information as you can. The survey covers GMOD in general, and any GMOD components that you use (and it only asks about components that you indicate you use). *** Three randomly selected survey participants will receive the GMOD T-shirt or mug of their choice (see http://www.cafepress.com/GenericMOD/). Names will be drawn from the first 100 responses we receive, so get your response in early *** Please contact the GMOD Help Desk if you have any questions. Thank you, The GMOD Team http://gmod.org -- Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback From gmodhelp@googlemail.com Fri Oct 24 18:30:35 2008 Received: from ppsw-7.csi.cam.ac.uk ([131.111.8.137]) by flymine.flymine.org with esmtp (Exim 4.12) id 1KtQUd-0003XV-00 for flymine-dev@flymine.org; Fri, 24 Oct 2008 18:30:35 +0100 X-Cam-AntiVirus: no malware found X-Cam-SpamDetails: score 0.0 from SpamAssassin-3.2.5-699147 X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Received: from ug-out-1314.google.com ([66.249.92.173]:27671) by ppsw-7.csi.cam.ac.uk (mx.cam.ac.uk [131.111.8.147]:25) with esmtp (csa=unknown) id 1KtQUb-0007IK-Pb (Exim 4.70) for flymine-dev@flymine.org (return-path ); Fri, 24 Oct 2008 18:30:35 +0100 Received: by ug-out-1314.google.com with SMTP id 30so244556ugs.24 for ; Fri, 24 Oct 2008 10:30:33 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=googlemail.com; s=gamma; h=domainkey-signature:received:received:message-id:date:from:reply-to :to:subject:in-reply-to:mime-version:content-type :content-transfer-encoding:content-disposition:references; bh=SED6PNnsV7e+J0eaaHDLFby28NVDJ2GzIvv1clb0mmI=; b=vhJGax6ZWE1er7aaSyRMgjXaMjBOy2gwr/MJflZm9a6BSlRrzs/7v+n7mHy4BH5iC+ tPooy8vL6xjIwnhhDnY5zsC5KcmjMvLKSBAiAMYvHlQ4CPjT6Pe16OcpctIiywbWGQEV fXnZYeCcvty+rNwDx8kUzXno4knE7dEjnFOoo= DomainKey-Signature: a=rsa-sha1; c=nofws; d=googlemail.com; s=gamma; h=message-id:date:from:reply-to:to:subject:in-reply-to:mime-version :content-type:content-transfer-encoding:content-disposition :references; b=gXnzE/1tj42sgm21L0o9Gf4p9pvr16etY6Z/rUsscjZPb6dTl4XguzIibi7i+wHG7g Geopom1gIQKCZjSvm7VHwVKGNuNereRIZtlwVW2nQq6CCrPI/pwh1t7WuvMlV7iQmBXY utqTVY28siwWZ6y6G8u+lYP0YjC/Tp+GBfoaI= Received: by 10.66.245.2 with SMTP id s2mr865034ugh.80.1224869433592; Fri, 24 Oct 2008 10:30:33 -0700 (PDT) Received: by 10.67.16.6 with HTTP; Fri, 24 Oct 2008 10:30:33 -0700 (PDT) Message-ID: <71ee57c70810241030i16a3214di12b96f35098bd99e@mail.gmail.com> Date: Fri, 24 Oct 2008 10:30:33 -0700 From: "Dave Clements, GMOD Help Desk" To: "InterMine List" In-Reply-To: <71ee57c70810241029i1fc7f496m5de0519be4f8bd93@mail.gmail.com> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline References: <71ee57c70810241018n29f5cbb6lcf3fad56d1fd4e50@mail.gmail.com> <71ee57c70810241024u6f4ffbc0wc3150589ca88d30c@mail.gmail.com> <71ee57c70810241024hedbcc94w5df786253ef91b05@mail.gmail.com> <71ee57c70810241025g1bc86522o9f8231af5d216b5f@mail.gmail.com> <71ee57c70810241026h729015bcye4affc38bc9d8128@mail.gmail.com> <71ee57c70810241026k2ffc6060q2547f4771b1ea317@mail.gmail.com> <71ee57c70810241027rc0bca43xa84063499bd19855@mail.gmail.com> <71ee57c70810241028w128c30d0g7eea3bd9ae5065a1@mail.gmail.com> <71ee57c70810241028i6f35e3d8i5ebb46808f25b35a@mail.gmail.com> <71ee57c70810241029i1fc7f496m5de0519be4f8bd93@mail.gmail.com> Subject: [flymine-dev] 2008 GMOD Community Survery: One Week Left! Sender: flymine-dev-admin@flymine.org Errors-To: flymine-dev-admin@flymine.org X-BeenThere: flymine-dev@flymine.org X-Mailman-Version: 2.0.13 Precedence: bulk Reply-To: flymine-dev@flymine.org X-Reply-To: help@gmod.org List-Help: List-Post: List-Subscribe: , List-Id: FlyMine developers discussion List-Unsubscribe: , List-Archive: Hello all, If you haven't already done so, please take a few minutes to fill out the first annual GMOD Community Survey: http://survey.oit.duke.edu/ViewsFlash/servlet/viewsflash?cmd=page&pollid=NESCent!GMODUserSurvey2008 We'll be running the survey for one more week, until the end of Friday, October 31. If you are in the first 100 responders then you will be enterred to win one of three GMOD T-shirts or mugs. PLEASE NOTE: 1. There are *not* 50 pages of questions in the survey. There are only 38! (I feel 24% better already! ;-) You'll be happy to know that you will see only 8 pages, plus a page for each component you use. 2. Your answers are not recorded until you hit "Submit" on the last page, so please follow through to the last page. Please take a few minutes to help improve and guide GMOD. We really do appreciate and welcome your feedback. Thanks, Dave C GMOD Help Desk -- Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback Fill out the the GMOD Community Survey NOW and win some GMOD Gear: http://gmod.org/wiki/GMOD_News#2008_GMOD_Community_Survey