[flymine-dev] XML

[Thomas Riley]

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out of date.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*)
>
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