Merge branch 'shell-fix' into biodiversity
diff --git a/pom.xml b/pom.xml
index 690c494..6415d34 100644
--- a/pom.xml
+++ b/pom.xml
@@ -9,10 +9,10 @@
</parent>
<groupId>net.sf.taverna.t2.taverna-workbench</groupId>
<artifactId>taverna-workbench-${edition}</artifactId>
- <name>Taverna Workbench Core</name>
+ <name>Taverna Workbench Biodiversity</name>
<properties>
- <edition>core</edition>
+ <edition>biodiversity</edition>
<raven.app.name>taverna-workbench-${edition}-${project.version}-${buildNumber}</raven.app.name>
<m2Repository />
</properties>
@@ -502,13 +502,13 @@
<scope>test</scope>
</dependency>
+ -->
<dependency>
<groupId>net.sf.taverna.t2.activities</groupId>
<artifactId>webdav-activity</artifactId>
<version>${t2.activities.version}</version>
<scope>test</scope>
</dependency>
- -->
<dependency>
<groupId>net.sf.taverna.t2.component</groupId>
@@ -560,13 +560,13 @@
<scope>test</scope>
</dependency>
+ -->
<dependency>
<groupId>net.sf.taverna.t2.ui-activities</groupId>
<artifactId>webdav-activity-ui</artifactId>
<version>${t2.ui.activities.version}</version>
<scope>test</scope>
</dependency>
- -->
<dependency>
<groupId>net.sf.taverna.t2.ui-activities</groupId>
<artifactId>component-activity-ui</artifactId>
@@ -673,6 +673,189 @@
-->
+
+ <artifactItem>
+ <groupId>com.github.lookfirst</groupId>
+ <artifactId>sardine</artifactId>
+ <version>5.0_1_6</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/com/github/lookfirst/sardine/5.0_1_6</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>com.github.lookfirst</groupId>
+ <artifactId>sardine</artifactId>
+ <version>5.0_1_6</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/com/github/lookfirst/sardine/5.0_1_6</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>commons-codec</groupId>
+ <artifactId>commons-codec</artifactId>
+ <version>1.8</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/commons-codec/commons-codec/1.8</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>commons-codec</groupId>
+ <artifactId>commons-codec</artifactId>
+ <version>1.8</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/commons-codec/commons-codec/1.8</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>commons-codec</groupId>
+ <artifactId>commons-codec</artifactId>
+ <version>1.7</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/commons-codec/commons-codec/1.7</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>commons-codec</groupId>
+ <artifactId>commons-codec</artifactId>
+ <version>1.7</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/commons-codec/commons-codec/1.7</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>commons-logging</groupId>
+ <artifactId>commons-logging</artifactId>
+ <version>1.1.3</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/commons-logging/commons-logging/1.1.3</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>commons-logging</groupId>
+ <artifactId>commons-logging</artifactId>
+ <version>1.1.3</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/commons-logging/commons-logging/1.1.3</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>commons-logging</groupId>
+ <artifactId>commons-logging</artifactId>
+ <version>1.1.2</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/commons-logging/commons-logging/1.1.2</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>commons-logging</groupId>
+ <artifactId>commons-logging</artifactId>
+ <version>1.1.2</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/commons-logging/commons-logging/1.1.2</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>org.apache.httpcomponents</groupId>
+ <artifactId>project</artifactId>
+ <version>4.0</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/org/apache/httpcomponents/project/4.0</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>org.apache.httpcomponents</groupId>
+ <artifactId>project</artifactId>
+ <version>7</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/org/apache/httpcomponents/project/7</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>org.apache.httpcomponents</groupId>
+ <artifactId>httpcomponents-core</artifactId>
+ <version>4.3.1</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/org/apache/httpcomponents/httpcomponents-core/4.3.1</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>org.apache.httpcomponents</groupId>
+ <artifactId>httpcomponents-core</artifactId>
+ <version>4.0.1</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/org/apache/httpcomponents/httpcomponents-core/4.0.1</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>org.apache.httpcomponents</groupId>
+ <artifactId>httpcomponents-client</artifactId>
+ <version>4.0.1</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/org/apache/httpcomponents/httpcomponents-client/4.0.1</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>org.apache.httpcomponents</groupId>
+ <artifactId>httpcomponents-client</artifactId>
+ <version>4.3.2</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/org/apache/httpcomponents/httpcomponents-client/4.3.2</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>org.apache.httpcomponents</groupId>
+ <artifactId>httpclient</artifactId>
+ <version>4.0.1</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/org/apache/httpcomponents/httpclient/4.0.1</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>org.apache.httpcomponents</groupId>
+ <artifactId>httpclient</artifactId>
+ <version>4.0.1</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/org/apache/httpcomponents/httpclient/4.0.1</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>org.apache.httpcomponents</groupId>
+ <artifactId>httpclient</artifactId>
+ <version>4.3.2</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/org/apache/httpcomponents/httpclient/4.3.2</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>org.apache.httpcomponents</groupId>
+ <artifactId>httpclient</artifactId>
+ <version>4.3.2</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/org/apache/httpcomponents/httpclient/4.3.2</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>org.apache.httpcomponents</groupId>
+ <artifactId>httpcore</artifactId>
+ <version>4.3.1</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/org/apache/httpcomponents/httpcore/4.3.1</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>org.apache.httpcomponents</groupId>
+ <artifactId>httpcore</artifactId>
+ <version>4.3.1</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/org/apache/httpcomponents/httpcore/4.3.1</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>org.apache.httpcomponents</groupId>
+ <artifactId>httpcore</artifactId>
+ <version>4.0.1</version>
+ <type>jar</type>
+ <outputDirectory>${project.build.directory}/repository/org/apache/httpcomponents/httpcore/4.0.1</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>org.apache.httpcomponents</groupId>
+ <artifactId>httpcore</artifactId>
+ <version>4.0.1</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/org/apache/httpcomponents/httpcore/4.0.1</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>commons-parent</artifactId>
+ <version>28</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/org/apache/commons/commons-parent/28</outputDirectory>
+ </artifactItem>
+ <artifactItem>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>commons-parent</artifactId>
+ <version>26</version>
+ <type>pom</type>
+ <outputDirectory>${project.build.directory}/repository/org/apache/commons/commons-parent/26</outputDirectory>
+ </artifactItem>
<artifactItem>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
@@ -2134,8 +2317,26 @@
</snapshots>
<id>aduna-opensource.releases</id>
<name>Aduna Open Source - Maven releases</name>
+<!--
<url>http://repo.aduna-software.org/maven2/releases</url>
+-->
+ <url>http://build.mygrid.org.uk/maven/aduna</url>
</repository>
+ <repository>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <id>aduna-software</id>
+ <name>Aduna Open Source - Maven releases</name>
+<!--
+ <url>http://repo.aduna-software.org/maven2/releases</url>
+-->
+ <url>http://build.mygrid.org.uk/maven/aduna</url>
+ </repository>
+
</repositories>
<scm>
diff --git a/src/main/install4j/taverna-workbench.install4j b/src/main/install4j/taverna-workbench.install4j
index d72f19c..623aa84 100644
--- a/src/main/install4j/taverna-workbench.install4j
+++ b/src/main/install4j/taverna-workbench.install4j
@@ -1,7 +1,7 @@
<?xml version="1.0" encoding="UTF-8"?>
<install4j version="5.1.11" transformSequenceNumber="4">
<directoryPresets config="../../../target/taverna-workbench-dist/taverna.sh" />
- <application name="${compiler:product-name}" distributionSourceDir="" applicationId="5202-1944-9901-7953" mediaDir="../../../target/media" mediaFilePattern="${compiler:sys.shortName}-${compiler:sys.version}-${compiler:sys.platform}" compression="6" lzmaCompression="false" pack200Compression="false" excludeSignedFromPacking="true" commonExternalFiles="false" createMd5Sums="true" shrinkRuntime="false" shortName="taverna-workbench-${compiler:edition}" publisher="myGrid" publisherWeb="http://www.taverna.org.uk/" version="2.5-SNAPSHOT" allPathsRelative="true" backupOnSave="false" autoSave="true" convertDotsToUnderscores="false" macSignature="????" installerName="" javaMinVersion="1.7" javaMaxVersion="" allowBetaVM="false" jdkMode="runtimeJre" jdkName="">
+ <application name="${compiler:product-name}" distributionSourceDir="" applicationId="5550-8553-0586-0508" mediaDir="../../../target/media" mediaFilePattern="${compiler:sys.shortName}-${compiler:sys.version}-${compiler:sys.platform}" compression="6" lzmaCompression="false" pack200Compression="false" excludeSignedFromPacking="true" commonExternalFiles="false" createMd5Sums="true" shrinkRuntime="false" shortName="taverna-workbench-${compiler:edition}" publisher="myGrid" publisherWeb="http://www.taverna.org.uk/" version="2.5-SNAPSHOT" allPathsRelative="true" backupOnSave="false" autoSave="true" convertDotsToUnderscores="false" macSignature="????" installerName="" javaMinVersion="1.7" javaMaxVersion="" allowBetaVM="false" jdkMode="runtimeJre" jdkName="">
<languages skipLanguageSelection="false" languageSelectionInPrincipalLanguage="false">
<principalLanguage id="en" customLocalizationFile="" />
<additionalLanguages />
@@ -19,7 +19,7 @@
<variable name="edition" value="snapshot" description="" category="" />
</variables>
<mergedProjects />
- <codeSigning macEnabled="false" macPkcs12File="/tmp/code-signing.pfx" windowsEnabled="false" windowsKeySource="pkcs12" windowsPvkFile="" windowsSpcFile="" windowsPkcs12File="/tmp/code-signing.pfx" />
+ <codeSigning macEnabled="true" macPkcs12File="/tmp/code-signing.pfx" windowsEnabled="true" windowsKeySource="pkcs12" windowsPvkFile="" windowsSpcFile="" windowsPkcs12File="/tmp/code-signing.pfx" />
</application>
<files keepModificationTimes="false" missingFilesStrategy="error" globalExcludeSuffixes="" defaultOverwriteMode="3" defaultUninstallMode="0" launcherOverwriteMode="3" defaultFileMode="644" defaultDirMode="755">
<filesets>
diff --git a/src/main/resources/README.txt b/src/main/resources/README.txt
index b8bbf43..1680df4 100644
--- a/src/main/resources/README.txt
+++ b/src/main/resources/README.txt
@@ -1,5 +1,5 @@
=======================
-Taverna workbench 2.5.0
+Taverna Workbench 2.5.0
=======================
http://www.taverna.org.uk/
http://www.mygrid.org.uk/
diff --git a/src/main/resources/conf/default_service_providers.xml b/src/main/resources/conf/default_service_providers.xml
index 3524e22..49f792b 100644
--- a/src/main/resources/conf/default_service_providers.xml
+++ b/src/main/resources/conf/default_service_providers.xml
@@ -1,56 +1,21 @@
<serviceDescriptions xmlns="http://taverna.sf.net/2009/xml/servicedescription">
<providers>
- <!--
- <provider>
- <providerId xmlns="http://taverna.sf.net/2008/xml/t2flow">http://taverna.sf.net/2010/service-provider/biomart</providerId>
- <configBean xmlns="http://taverna.sf.net/2008/xml/t2flow" encoding="xstream">
- <net.sf.taverna.t2.activities.biomart.servicedescriptions.BiomartServiceProviderConfig xmlns="">
- <url>http://www.biomart.org/biomart</url>
- </net.sf.taverna.t2.activities.biomart.servicedescriptions.BiomartServiceProviderConfig>
- </configBean>
- </provider>
- <provider>
- <providerId xmlns="http://taverna.sf.net/2008/xml/t2flow">http://taverna.sf.net/2010/service-provider/wsdl</providerId>
- <configBean xmlns="http://taverna.sf.net/2008/xml/t2flow" encoding="xstream">
- <net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceProviderConfig xmlns="">
- <uri>http://soap.bind.ca/wsdl/bind.wsdl</uri>
- </net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceProviderConfig>
- </configBean>
- </provider>
- <provider>
- <providerId xmlns="http://taverna.sf.net/2008/xml/t2flow">http://taverna.sf.net/2010/service-provider/biomoby</providerId>
- <configBean xmlns="http://taverna.sf.net/2008/xml/t2flow" encoding="xstream">
- <net.sf.taverna.t2.activities.biomoby.servicedescriptions.BiomobyServiceProviderConfig xmlns="">
- <endpoint>http://www.inab.org/cgi-bin/MOBY-Central.pl</endpoint>
- <namespace>http://www.inab.org/MOBY/Central</namespace>
- </net.sf.taverna.t2.activities.biomoby.servicedescriptions.BiomobyServiceProviderConfig>
- </configBean>
- </provider>
- <provider>
- <providerId xmlns="http://taverna.sf.net/2008/xml/t2flow">http://taverna.sf.net/2010/service-provider/wsdl</providerId>
- <configBean xmlns="http://taverna.sf.net/2008/xml/t2flow" encoding="xstream">
- <net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceProviderConfig xmlns="">
- <uri>http://www.ebi.ac.uk/ws/services/urn:Dbfetch?wsdl</uri>
- </net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceProviderConfig>
- </configBean>
- </provider>
- <provider>
- <providerId xmlns="http://taverna.sf.net/2008/xml/t2flow">http://taverna.sf.net/2010/service-provider/soaplab</providerId>
- <configBean xmlns="http://taverna.sf.net/2008/xml/t2flow" encoding="xstream">
- <net.sf.taverna.t2.activities.soaplab.servicedescriptions.SoaplabServiceProviderConfig xmlns="">
- <endpoint>http://wsembnet.vital-it.ch/soaplab2-axis/services/</endpoint>
- </net.sf.taverna.t2.activities.soaplab.servicedescriptions.SoaplabServiceProviderConfig>
- </configBean>
- </provider>
<provider>
<providerId xmlns="http://taverna.sf.net/2008/xml/t2flow">http://taverna.sf.net/2012/service-provider/component</providerId>
<configBean xmlns="http://taverna.sf.net/2008/xml/t2flow" encoding="xstream">
<net.sf.taverna.t2.component.ui.serviceprovider.ComponentServiceProviderConfig xmlns="">
<registryBase>http://www.myexperiment.org</registryBase>
- <familyName>WebDAV test</familyName>
+ <familyName>GBIF</familyName>
</net.sf.taverna.t2.component.ui.serviceprovider.ComponentServiceProviderConfig>
</configBean>
</provider>
- -->
+ <provider>
+ <providerId xmlns="http://taverna.sf.net/2008/xml/t2flow">http://taverna.sf.net/2010/service-provider/wsdl</providerId>
+ <configBean xmlns="http://taverna.sf.net/2008/xml/t2flow" encoding="xstream">
+ <net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceProviderConfig xmlns="">
+ <uri>http://www.marinespecies.org/aphia.php?p=soap&wsdl=1</uri>
+ </net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceProviderConfig>
+ </configBean>
+ </provider>
</providers>
-</serviceDescriptions>
+</serviceDescriptions>
\ No newline at end of file
diff --git a/src/main/resources/conf/workbench-profile.properties b/src/main/resources/conf/workbench-profile.properties
index 5b3c544..7c796eb 100644
--- a/src/main/resources/conf/workbench-profile.properties
+++ b/src/main/resources/conf/workbench-profile.properties
@@ -1,4 +1,4 @@
-servicecatalogue.base.url=https://www.biocatalogue.org
-servicecatalogue.name=BioCatalogue
+servicecatalogue.base.url=https://www.biodiversitycatalogue.org
+servicecatalogue.name=BiodiversityCatalalogue
myexperiment.base.url=http://www.myexperiment.org
-myexperiment.starterpack=254
+myexperiment.starterpack=610
diff --git a/src/main/resources/plugins/plugins.xml b/src/main/resources/plugins/plugins.xml
index 15b96f9..4eff0de 100644
--- a/src/main/resources/plugins/plugins.xml
+++ b/src/main/resources/plugins/plugins.xml
@@ -255,7 +255,6 @@
</application>
</compatibility>
</plugin>
-<!--
<plugin>
<provider>taverna.sf.net</provider>
<identifier>net.sf.taverna.t2.webdav-activity</identifier>
@@ -282,11 +281,9 @@
<artifactId>webdav-activity-ui</artifactId>
<version>${t2.ui.activities.version}</version>
</dependency>
--->
<!-- For backwards compatibility with older
WebDAV local workers the remaining old versions
need to be pulled into the repository: -->
-<!--
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpcore</artifactId>
@@ -302,10 +299,8 @@
<artifactId>sardine</artifactId>
<version>5.0_1_6</version>
</dependency>
--->
<!-- Any future versions of these dependencies also would need to
be listed here: -->
-<!--
</profile>
<compatibility>
<application>
@@ -313,7 +308,6 @@
</application>
</compatibility>
</plugin>
--->
<plugin>
<provider>taverna.sf.net</provider>
@@ -355,7 +349,6 @@
</compatibility>
</plugin>
- <!--
<plugin>
<provider>taverna.sf.net</provider>
<identifier>net.sf.taverna.t2.servicecatalogue</identifier>
@@ -384,8 +377,6 @@
</application>
</compatibility>
</plugin>
- -->
-
</plugins:plugins>
