LMS-916 overriding task in openbis build.xml for phosphonetx

SVN: 11278

rtd_phosphonetx/build/build.xml

@@ -23,4 +23,35 @@
         // Task for continuous integration server.
         -->
         <target name="ci" depends="build-common.ci, dist, check-dependencies"/>
+	
+        <!--
+        // Compiles the javascript using GWT compiler.
+        -->
+        <target name="compile-javascript"
+                depends="prepare-web-client"
+                description="Compiles the javascript using GWT compiler.">
+                <!--antcall target="compile-gwt-module">
+                        <param name="gwt.module.name" value="ch.systemsx.cisd.openbis.plugin.phosphonetx.OpenBIS" />
+                </antcall-->
+        </target>
+
+        <!--
+        // Creates WAR file.
+        -->
+        <target name="war" depends="openbis.war" description="Creates project war file.">
+        	<war warfile="${webapp.file}" update="true">
+                        <fileset prefix="WEB-INF/classes/phosphonetx" dir="source">
+                                <include name="**/*.sql" />
+                        </fileset>
+                        <classes dir="../openbis/${sources}">
+                                <include name="**/*.xml" />
+                        </classes>
+                        <lib dir="${lib}/jaxb">
+                                <include name="*.jar" />
+                        </lib>
+                        <lib dir="${lib}/eodsql">
+                                <include name="*.jar" />
+                        </lib>
+        	</war>
+        </target>
 </project>
\ No newline at end of file

rtd_phosphonetx/dist/etc/log.xml

+<?xml version="1.0" encoding="UTF-8" ?>
+<!DOCTYPE log4j:configuration SYSTEM "log4j.dtd">
+
+<log4j:configuration xmlns:log4j='http://jakarta.apache.org/log4j/'>
+
+    <appender name="DEFAULT" class="org.apache.log4j.DailyRollingFileAppender">
+
+        <param name="File" value="logs/openbis_log.txt" />
+        <param name="DatePattern" value="'.'yyyy-MM-dd" />
+
+        <layout class="org.apache.log4j.PatternLayout">
+            <!--
+                // %d: outputs the date of the logging event.
+                // %-5p: priority (i.e. level) of the logging event should be left justified to
+                //       a width of five characters.
+                // %t: outputs the name of the thread that generated the logging event.
+                // %c: outputs the category of the logging event.
+                // %m: outputs the application supplied message associated with the logging event.
+                // %X: outputs the MDC (mapped diagnostic context) associated with the thread that generated the logging event.
+            -->
+            <param name="ConversionPattern" value="%d %-5p [%t]%X{sessionInfo} %c - %m%n" />
+        </layout>
+
+    </appender>
+    <appender name="AUTH" class="org.apache.log4j.DailyRollingFileAppender">
+
+        <param name="File" value="logs/openbis_auth_log.txt" />
+        <param name="DatePattern" value="'.'yyyy-MM-dd" />
+
+        <layout class="org.apache.log4j.PatternLayout">
+            <param name="ConversionPattern" value="%d %-5p [%t]%X{sessionInfo} %c - %m%n" />
+        </layout>
+    </appender>
+
+    <appender name="USAGE" class="org.apache.log4j.DailyRollingFileAppender">
+
+        <param name="File" value="logs/openbis_usage_log.txt" />
+        <param name="DatePattern" value="'.'yyyy-MM-dd" />
+
+        <layout class="org.apache.log4j.PatternLayout">
+            <param name="ConversionPattern" value="%d %-5p [%t]%X{sessionInfo} %c - %m%n" />
+        </layout>
+    </appender>
+
+    <appender name="STDOUT" class="org.apache.log4j.ConsoleAppender">
+        <layout class="org.apache.log4j.PatternLayout">
+            <param name="ConversionPattern" value="%d %-5p [%t] %c - %m%n" />
+        </layout>
+    </appender>
+
+    <!--
+        // Defined but not used right now.
+    -->
+    <appender name="NULL" class="org.apache.log4j.varia.NullAppender" />
+
+    <appender name="EMAIL" class="org.apache.log4j.net.SMTPAppender">
+
+        <param name="BufferSize" value="512" />
+        <param name="SMTPHost" value="localhost" />
+        <param name="From" value="dmc@localhost" />
+        <param name="To" value="root@localhost" />
+        <param name="Subject" value="ATTENTION: openBIS Server" />
+        <param name="EvaluatorClass"
+            value="ch.systemsx.cisd.common.logging.AlwaysTrueTriggeringEventEvaluator" />
+
+        <layout class="org.apache.log4j.PatternLayout">
+            <param name="ConversionPattern" value="%d %-5p [%t] %c - %m%n" />
+        </layout>
+
+    </appender>
+
+    <!--
+        // If we have the category 'NOTIFY' and we send a logging event with priority 'info', then an email will be sent.
+    -->
+    <category name="NOTIFY">
+        <priority value="info" />
+        <appender-ref ref="EMAIL" />
+    </category>
+    
+    <!--
+        // If we have the category 'AUTH' and we send a logging event with priority 'info', then log to AUTH and USAGE.
+    -->
+    <category name="AUTH">
+        <priority value="info" />
+        <appender-ref ref="AUTH" />
+        <appender-ref ref="USAGE" />
+    </category>
+
+    <!--
+        // If we have the category 'TRACKING' and we send a logging event with priority 'info', then log to USAGE.
+    -->
+    <category name="TRACKING">
+        <priority value="info" />
+        <appender-ref ref="USAGE" />
+    </category>
+
+    <!--
+        // If we have the category 'ACCESS' and we send a logging event with priority 'info', then log to USAGE.
+    -->
+    <category name="ACCESS">
+        <priority value="info" />
+        <appender-ref ref="USAGE" />
+    </category>
+    
+    <!-- 
+        // Do not use log level debug otherwise plain passwords are readable.
+    -->
+    <logger name="httpclient.wire">
+        <level value="ERROR" />
+    </logger>
+
+    <root>
+        <priority value="info" />
+        <appender-ref ref="DEFAULT" />
+    </root>
+
+</log4j:configuration>

rtd_phosphonetx/dist/etc/passwd

+a:a@admins.com:A:The Admin:J3fII6Pex7jnCBwF+uXz2mFuB1QVhPUi
+u:u@users.com:U:The User:dmbGKaGRmbX8YKfslMxUHObmYfjywkuT
+o:o@observers.com:O:The Observer:t53ADCnFnEFhBvHB7FPoHhbHeW2O1KJc
+etlserver::::SHGHSPawL/B3NKXD5nsu4fSrj5LwR2MX

rtd_phosphonetx/dist/server/service.properties

+# Supported: 'file-authentication-service' and 'crowd-authentication-service'
+authentication-service = file-authentication-service
+
+# The time after which an inactive session is expired by the service (in minutes).
+session-timeout = 720
+
+# Authorization
+# Supported: 'no-authorization' and 'active-authorization'
+authorization-component-factory = active-authorization
+
+script-folder = .
+
+# Supported: currently only 'postgresql' is supported
+database.engine = postgresql
+database.create-from-scratch = false
+# For debugging set this value to true.
+database.script-single-step-mode = false
+database.url-host-part =
+database.kind = demo
+database.owner =
+database.owner-password =
+database.admin-user = 
+database.admin-password =
+
+phosphonetx.database.engine = postgresql
+phosphonetx.database.create-from-scratch = false
+phosphonetx.database.script-single-step-mode = false
+phosphonetx.database.url-host-part =
+phosphonetx.database.kind = demo
+phosphonetx.database.owner =
+phosphonetx.database.owner-password =
+phosphonetx.database.admin-user = 
+phosphonetx.database.admin-password =
+phosphonetx.script-folder = phosphonetx
+
+crowd.service.host = crowd.systemsx.ch
+crowd.service.port = 8443
+crowd.application.name = openbis
+crowd.application.password =
+
+# The database instance local unique identifier. Used when the new database is created.
+database-instance = TEST
+
+# Base URL of the Data Store Server. 
+# Will be used only for data sets registered in an openBIS server version before 14.04.2009 (or revision 10665)
+data-store-server-base-url = 
+
+# The URL of the CIFEX server
+cifex-url = https://cifex.ethz.ch:443
+
+# Hibernate Search
+# The working directory.
+hibernate.search.index-base = ./indices
+# One of NO_INDEX, SKIP_IF_MARKER_FOUND, INDEX_FROM_SCRATCH.
+# If not specified, default (SKIP_IF_MARKER_FOUND) is taken.
+hibernate.search.index-mode = SKIP_IF_MARKER_FOUND
+# Defines the maximum number of elements indexed before flushing the transaction-bound queue.
+# Default is 1000.
+hibernate.search.batch-size = 1000
\ No newline at end of file

rtd_phosphonetx/resource/server/web.xml

@@ -10,6 +10,12 @@
 
     &common;
 
+    <context-param>
+        <param-name>contextConfigLocation</param-name>
+        <param-value>classpath:phosphonetx-applicationContext.xml</param-value>
+        <description>File for Spring beans.</description>
+    </context-param>
+
     <listener>
         <listener-class>
             ch.systemsx.cisd.openbis.generic.server.GenericHttpSessionListener

rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xmlns:tx="http://www.springframework.org/schema/tx"
+    xsi:schemaLocation="http://www.springframework.org/schema/beans
+                        http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
+                        http://www.springframework.org/schema/tx
+                        http://www.springframework.org/schema/tx/spring-tx-2.5.xsd">
+
+    <import resource="applicationContext.xml"/>
+    
+    <bean id="phosphonetx-db-configuration-context"
+        class="ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext">
+        <property name="basicDatabaseName" value="phosphonetx" />
+        <property name="createFromScratch" value="${phosphonetx.database.create-from-scratch}" />
+        <property name="scriptSingleStepMode" value="${phosphonetx.database.script-single-step-mode}" />
+        <property name="sequenceNameMapper">
+            <bean class="ch.systemsx.cisd.openbis.generic.server.dataaccess.db.SequenceNameMapper" />
+        </property>
+        <property name="urlHostPart" value="${phosphonetx.database.url-host-part}" />
+        <property name="adminUser" value="${phosphonetx.database.admin-user}" />
+        <property name="owner" value="${phosphonetx.database.owner}" />
+        <property name="readOnlyGroup" value="openbis_readonly" />
+        <property name="password" value="${phosphonetx.database.owner-password}" />
+        <property name="adminPassword" value="${phosphonetx.database.admin-password}" />
+        <property name="databaseKind" value="${phosphonetx.database.kind}" />
+        <property name="databaseEngineCode" value="${phosphonetx.database.engine}" />
+        <property name="scriptFolder" value="${phosphonetx.script-folder}/sql" />
+        <property name="databaseInstance" value="${phosphonetx.database-instance}" />
+    </bean>
+    
+    <bean id="phosphonetx-data-source" factory-bean="phosphonetx-db-configuration-context" factory-method="getDataSource" />
+
+</beans>
\ No newline at end of file

rtd_phosphonetx/source/java/service.properties

@@ -25,6 +25,17 @@ database.owner-password =
 database.admin-user = 
 database.admin-password =
 
+phosphonetx.database.engine = postgresql
+phosphonetx.database.create-from-scratch = false
+phosphonetx.database.script-single-step-mode = false
+phosphonetx.database.url-host-part =
+phosphonetx.database.kind = dev
+phosphonetx.database.owner =
+phosphonetx.database.owner-password =
+phosphonetx.database.admin-user = 
+phosphonetx.database.admin-password =
+phosphonetx.script-folder = source
+
 crowd.service.host = crowd.systemsx.ch
 crowd.service.port = 8443
 crowd.application.name = lims