Metware developers

This page is intended to contain information for developers on the Metware project.

SVN

To check out the latest version of the Metware code, use:

svn co https://metware.svn.sourceforge.net/svnroot/metware metware

svn co http://metware.svn.sourceforge.net/svnroot/metware/MetBeans/trunk MetBeans
svn co http://metware.svn.sourceforge.net/svnroot/metware/BigMet/trunk BigMet
svn co http://metware.svn.sourceforge.net/svnroot/metware/MetWeb/trunk MetWeb

Requirements

Java version 1.5
PostgreSQL
Tomcat version 5.5.25
ANT 1.7.0

Libraries

There are a bunch of libraries necessary to compile everything, here a short list:

Xerces (xercesImpl.jar) for XML-parsing
Servlet API (servlet.jar) shipped with Java EE/Tomcat/WebLogic

Installation

The following steps have to be made to install Metware on your system:

Download the latest stable version of Metware (via SVN)
Database setup
Tomcat setup
Several modules have to be compiled:
- 1. BigMet
- 2. MetBeans
- 3. MetWeb Core (.WAR creation)
- 4. MetDriver

Database setup

When PostgreSQL is installed you can make use of the tool createdb to create the database for Metware. If you run into problems, you might take a look at the PostgreSQL createdb tutorial

Create the database

#createdb metware_db

Import SQL dump from file in Metware directory into PostgreSQL

#psql metware_db < metware/BigMet/trunk/onto/metware.sql

Tomcat setup

You will need the PostgreSQL JDBC drivers, located in tomcat/common/lib for any database connectivity. The driver can be downloaded from http://jdbc.postgresql.org/

Furthermore you have to add the connection information to the Tomcat-configuration file, which is often located in a directory like /etc/tomcat/server.xml. There should be added a section (replace the following variables; $metware_db=database name, $metware_user=database user, $metware_host=url to machine)

<Resource name="jdbc/$metware_db" auth="Container" type="javax.sql.DataSource"
               maxActive="100" maxIdle="30" maxWait="10000"
               username="$metware_user" driverClassName="org.postgresql.Driver"
               url="jdbc:postgresql://$metware_host:3306/$metware_db"/>

1. Compiling & Installing BigMet

Step into the Bigmet trunk directory

#cd metware/BigMet/trunk

Use ANT to compile the source code (might be necessarry to pass the location of Xerces), it will automatically look for the build.xml file and try to compile the Java sources

#ant -DxercesImpl.jar=path/to/java/lib/xercesImpl.jar -Dsqltarget=pgsql

If everything goes fine, you should see a succesful build

Buildfile: build.xml

compileSQLGenerator:

checkXerces:
     [echo] Xerces2 found: true

runSQLGenerator:
     [java] Creating SQL for MySQL...
     [java] SKOSifying: src/main/onto/metware.skos
     [java] Found file.

build:

jarLibrary:

make:

BUILD SUCCESSFUL
Total time: 0 seconds

The next step is installing the compiled JAR and documentation into a directory (default is /usr/local/)

#ant install -Dprefix=/usr/local

If everything goes fine, you should see a succesful installation (something like this)

Buildfile: build.xml

install:
     [echo] Installing in: /usr/local
    [mkdir] Created dir: /usr/local/share/doc/metware/bigmet
     [copy] Copying 3 files to usr/local/share/doc/metware/bigmet
    [mkdir] Created dir:  /usr/local/share/doc/metware/bigmet/onto
     [copy] Copying 3 files to /usr/local/metware/bigmet/onto
     [copy] Copying 1 file to /usr/local/share/java

BUILD SUCCESSFUL
Total time: 0 seconds

2. Compiling MetBeans

Step into the MetBeans trunk directory

#cd metware/MetBeans/trunk

Use ANT again to compile the source code (might be necessarry to pass the location of Xerces), it will automatically look for the build.xml file and try to compile the Java sources (default directory is /usr/local)

#ant -Dprefix=/usr/local -DxercesImpl.jar=path/to/java/lib/xercesImpl.jar

If everything goes fine here too, you should see a succesful compilation

Buildfile: build.xml

compileBeanGenerator:

checkXerces:
     [echo] Xerces2 found: true

runBeanGenerator:
     [java] SKOSifying: /usr/local/share/doc/metware/bigmet/onto/metware.skos
     [java] Found file.
     [java] Found an addon 'metid_metabolites_addon_pubchem' for 'metid_metabolites'.
     [java] Processing table: metchar_putative_metabolites_identities
     [java] Creating java file for MetcharPutativeMetabolitesIdentitiesBean...
     [java] Creating JUnit java file for MetcharPutativeMetabolitesIdentitiesBeanTest...
     [java] Creating java file for MetcharPutativeMetabolitesIdentitiesQueryBean...
     (...etc...)
compileLibrary:
    [javac] Compiling 58 source files to /home/username/metware-metbeans-0.3/build

jarLibrary:
     [jar] Building jar: /home/username/metware-metbeans-0.3/metware-metbeans.jar
javadoc:
     [javadoc] Generating Javadoc
     [javadoc] Javadoc execution
     [javadoc] Loading source files for package net.sf.metware.beans...
test:
    [junit] Running net.sf.metware.BeansTestSuite3
     (...etc...)
BUILD SUCCESSFUL
Total time: 6 seconds

3. Compiling MetWeb Core (.WAR creation)

Step into the MetWeb Core directory

#cd metware/MetWeb/Core

Use ANT again to compile the source code (might be necessarry to pass the location of Xerces and the Servlet API), it will automatically look for the build.xml file and try to compile the Java sources (default directory is /usr/local)

#ant -Dprefix=/usr/local -DxercesImpl.jar=path/to/java/lib/xercesImpl.jar -Dservlet-api.jar=/path/to/lib/servlet.jar

If everything goes fine here too, you should see a succesful compilation (the actual output will be much longer, but just to give you an indication):

Buildfile: build.xml

compileFacesConfigCreator:

runFacesConfigCreator:
     [java] SKOSifying: /usr/local/share/doc/metware/bigmet/onto/metware.skos
     [java] Found file.
     [java] Processing table: metchar_putative_metabolites_identities
     (...)
     [java] Processing table: metmeta_sample

compileSessionBean:
compileJSFGenerator:
checkXerces:
     [echo] Xerces2 found: /var/lib/tomcat5/webapps/axis/WEB-INF/lib/xercesImpl.jar
runJSFGenerator:
    [mkdir] Created dir: /home/user/metware/MetWeb/Core/WebContent/metraw
    [mkdir] Created dir: /home/user/metware/MetWeb/Core/WebContent/metmeta
     [java] Creating SQL database ${metwaredbname}...
    (...)
     [java] SKOSifying: /home/user/metware/share/doc/metware/bigmet/onto/metware.skos
     [java] Found file.
war:
      [war] Building war: /home/user/metware/MetWeb/Core/Core.war

build:
BUILD SUCCESSFUL

4. Compiling MetDriver

Step into the MetDriver trunk directory

#cd metware/MetDriver/trunk

Use ANT to compile the source code (might be necessarry to pass the location of saaj), it will automatically look for the build.xml file and try to compile the Java sources

#ant -Dsaaj.jar=path/to/java/lib/saaj.jar

Metware modules

BigMet
- This module contains the MetWare ontology and SQL design
MetBeans
- Java Beans library to interact with SQL database
MetFlow
MetDriver
MetWeb
- The HTML-based GUI to the datawarehouse
MetRAW
mzMLEditor
ProtoRAW
- the prototype storage facility (currently Python based)

Eclipse EE setup

Download Eclipse EE from Eclipse.org (Europe) and start Eclipse.

Get the important modules via SVN:

svn co https://metware.svn.sourceforge.net/svnroot/metware/BigMet/trunk BigMet
svn co https://metware.svn.sourceforge.net/svnroot/metware/MetBeans/trunk MetBeans
svn co https://metware.svn.sourceforge.net/svnroot/metware/MetWeb/trunk MetWeb

Import the three modules, one by one, by choosing File -> Import -> General -> Existing Project into Workspace, and select as root folder the BigMet and MetBeans folders created in the svn co commands. Also import the Core/ folder from the MetWeb checkout.

Be sure the Build Path is also set correctly by right-clicking on the MetBeans project (which launches Properties). Then select Java Build Path and click on the Projects tab. From there on add BigMet and Core to the Build Path.

Developer tools and reference documentation

Miscellaneous

Metware pastebin
Metware IRC logs
IRC: /join #metware
PGAdmin tunnel:
```
ssh -L 5432:localhost:5432 username@wsx.grid.sara.nl
```
then connect from PGAdmin to localhost port 5432 to use the tunnel.

Metware developers

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SVN

Requirements

Libraries

Installation

Metware modules

Eclipse EE setup

Developer tools and reference documentation

Miscellaneous

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