Changes between Initial Version and Version 1 of MolgenisApps

Timestamp:

2011-07-21T21:36:24+02:00 (13 years ago)

Author:

Morris Swertz

Comment:

--

MolgenisApps

@@ +1 @@
+= MOLGENIS 'Apps'project =
+[[TOC()]]
+
+Welcome to the MOLGENIS apps project. MOLGENIS apps is a suite of integrated biomedical research tools born from the MOLGENIS community.
+
+== For researchers ==
+
+Find more information at the app homepages:
+
+* [animaldb AnimaldbStart] -- for tracking research animals
+* [xgap XgapStart] -- for genotype and phenotype experiments
+* [ngs NgsStart] -- LIMS and pipelines for illumina sequencing
+* [mutation MutationStart] -- for rare diseases and mutations
+* [compute ComputeStart] -- for bioinformatics computational workflows
+
+== For developers ==
+
+Developers can download all code as open source at:
+http://www.molgenis.org/svn/molgenis_apps/trunk
+
+The MOLGENIS apps project is structured as follows:
+* /apps -- apps in the suite
+* /modules -- pieces of reusable software shared between apps
+* /generated -- autogenerated code by MOLGENIS (svn:ignore)
+* /dist -- result of the build process (svn:ignore)
+* /WebContent -- images, style sheets and scripts for on the web 
+* /build_xyz.xml -- script to automatically build a complete app from above
+
+Each app is automatically build every night.
+
+Detailed descriptions below:
+
+=== build_xyz automatic build scripts ===
+Each app can be build automatically by running {{{ant build_xyz.xml}}} or in eclipse, right-click and choose 'run as'->'Ant build'. 
+For example: build_xgap.xml builds a runnable version of xgap. 
+
+The build script defines all settings for the app. For example:
+
+{{{
+!#xml
+<project>
+        <!-- this name is used to name the war file -->
+        <property name="app_name" value="col7a1" />
+
+        <!-- this holds all the settings for the generator -->
+        <property name="app_properties" value="apps/${app_name}/org/molgenis/${app_name}/${app_name}.properties"/>
+        
+        <!-- this determines what additional modules should be loaded -->
+        <path id="app.class.path">
+                <pathelement location="apps/${app_name}" />
+                <pathelement location="modules/datamodel" />
+                <pathelement location="modules/auth" />
+                <pathelement location="modules/pheno" />
+                <pathelement location="modules/search" />       
+        </path>
+
+        <!-- import all tasks from build_common: clean, generate, compile, test, war, standalone-jar -->
+        <import file="build_common.xml" />
+
+</project>
+}}}
+
+The build scripts provide the following standard methods:
+* clean -- cleans the generated folders
+* generate -- generates all code using MOLGENIS
+* compile -- compile generated code and imported modules
+* test -- run the test cases defined in this app + dependent modules
+* update-eclipse -- update Eclipse to only show selected app + modules
+* (todo) create-jar -- create a standalone executable jar of this app
+* (todo) create-war -- create a mysql + tomcat deployable war of this app
+
+At every change in SVN, hudson will run clean-generate-compile-test and sent emails if errors are found.
+
+=== /apps ===
+Apps are applications designed to be used by an end-user. For example: /apps/xgap. 
+
+Each app is structured as follows: 
+* root package org.molgenis.<appname> contains specific sources and resourses
+* <appname>.properties file has settings for this app [move to build.xml?]
+* <appname>.testng.xml files lists all tests for this app (see hudson)
+* <appname>_ui.xml lists the user interface design for this app
+
+Developers of apps have complete freedom to do what they want within their app as other apps will ignore any code in these folders.
+
+=== /modules ===
+Modules are bundles of code that are shared between two or more apps. For example: /modules/auth.
+
+Each module is structured as follows:
+* root package org.molgenis.<modulename> contains specific sources and resourses
+* <modulename>.properties file has settings to setup a test molgenis for this module only (see hudson)
+* <modulemame>.testng.xml files lists all tests for this module (see hudson)
+* <modulename>_ui.xml lists a user interface design for this module; apps may choose to [ref] import this ui design into their application.
+
+Developers of modules are required to:
+* ensure stability of the modules by providing sufficient tests and stable programming interfaces. 
+* mark yet unstable modules with a suffix as '-dev'. For example /modules/matrix-dev. 
+* when changing an existing module copy it into a -dev version and develop on that until the code is stable before promoting it to stable
+* monitor the tests of all dependent apps on hudson and fix or undo any problems they you may have caused.
+
+=== /generated (svn:ignore) ===
+This folder contains all program resources autogenerated by the build script.
+Typically, there are:
+* /java -- generated java
+* /python -- generated python
+* /
+
+[[BIG POINT: I want new generators not immediately in MOLGENIS core but instead as separate modules; we need a 'registerGenerator' method to make this easy ]]
+
+
+=== /WebContent ===
+All resources for the web, such as images, css and javascript, can be stored in /WebContent. 
+Each app or module will create subfolders. For example:
+
+* /res -- contains resource files that are created by hand
+  * /css -- contains css files
+    * /xgap -- contains xgap specific css files
+  * /img -- contains images
+    * /xgap -- contains xgap specific css files
+  * /scritps -- contains scripts.
+    * /xgap -- contains xgap specific css files
+* /generated-res -- contains generator produced resource files (svn:ignore).
+
+=== /dist (svn:ignore) ===
+
+