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Posted to commits@taverna.apache.org by st...@apache.org on 2018/06/29 12:43:07 UTC
[1/4] incubator-taverna-plugin-bioinformatics git commit: Clarify
CacheImpl remains LGPL 2.1
Repository: incubator-taverna-plugin-bioinformatics
Updated Branches:
refs/heads/master 4d67ab4a1 -> 0cd19f59c
Clarify CacheImpl remains LGPL 2.1
.. as it might not have been part of the software grant to Apache
signed by Univ of Manchester, as it does not seem that Martin Senger
had signed a Software Grant Agreement with Manchester.
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/commit/aa249b29
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/tree/aa249b29
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/diff/aa249b29
Branch: refs/heads/master
Commit: aa249b298e802c611d08b4f00999ef72491ae9ab
Parents: 4d67ab4
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Fri Jun 29 13:39:41 2018 +0100
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Fri Jun 29 13:39:41 2018 +0100
----------------------------------------------------------------------
LICENSE | 9 +++++++++
NOTICE | 3 ++-
.../t2/activities/biomoby/query/CacheImpl.java | 17 ++---------------
3 files changed, 13 insertions(+), 16 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/aa249b29/LICENSE
----------------------------------------------------------------------
diff --git a/LICENSE b/LICENSE
index d645695..13c1a54 100644
--- a/LICENSE
+++ b/LICENSE
@@ -200,3 +200,12 @@
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
+
+-------------------------------------------------
+taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/CacheImpl.java
+
+ This file is a component of the Taverna project,
+ and is licensed under the GNU LGPL.
+ Copyright Edward Kawas, Martin Senger, The BioMoby Project
+
+https://www.gnu.org/licenses/old-licenses/lgpl-2.1.en.html
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/aa249b29/NOTICE
----------------------------------------------------------------------
diff --git a/NOTICE b/NOTICE
index 077276c..8199955 100644
--- a/NOTICE
+++ b/NOTICE
@@ -11,4 +11,5 @@ These have been licensed to the Apache Software Foundation under a software gran
---------------------------------------------------------
TODO: taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/CacheImpl.java
says (c) Martin Senger and is licensed as LGPL - did University of Manchester
-have a ICLA from Senger so that this file can relicensed as Apache License?
+have a ICLA from Senger so that this file could have been relicensed as Apache License 2.0
+as part of their software grant?
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/aa249b29/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/CacheImpl.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/CacheImpl.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/CacheImpl.java
index ef88d2d..49f808f 100644
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/CacheImpl.java
+++ b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/CacheImpl.java
@@ -2,24 +2,11 @@
* This file is a component of the Taverna project,
* and is licensed under the GNU LGPL.
* Copyright Edward Kawas, Martin Senger, The BioMoby Project
- */
-package net.sf.taverna.t2.activities.biomoby.query;
-/*
- * Licensed to the Apache Software Foundation (ASF) under one or more
- * contributor license agreements. See the NOTICE file distributed with
- * this work for additional information regarding copyright ownership.
- * The ASF licenses this file to You under the Apache License, Version 2.0
- * (the "License"); you may not use this file except in compliance with
- * the License. You may obtain a copy of the License at
*
- * http://www.apache.org/licenses/LICENSE-2.0
+ * https://www.gnu.org/licenses/old-licenses/lgpl-2.1.en.html
*
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
*/
+package net.sf.taverna.t2.activities.biomoby.query;
import java.io.BufferedOutputStream;
import java.io.BufferedReader;
[4/4] incubator-taverna-plugin-bioinformatics git commit: ignore
Posted by st...@apache.org.
ignore
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/commit/0cd19f59
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/tree/0cd19f59
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/diff/0cd19f59
Branch: refs/heads/master
Commit: 0cd19f59c159f0f8cc078b4b50a3e39d5538f5fe
Parents: c3d7326
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Fri Jun 29 13:42:54 2018 +0100
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Fri Jun 29 13:42:54 2018 +0100
----------------------------------------------------------------------
.gitignore | 1 +
1 file changed, 1 insertion(+)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/0cd19f59/.gitignore
----------------------------------------------------------------------
diff --git a/.gitignore b/.gitignore
index f736862..2b764c5 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,3 +3,4 @@
.classpath
target
.gitignore
+.factorypath
[2/4] incubator-taverna-plugin-bioinformatics git commit: retired
from ASF to taverna-extras
Posted by st...@apache.org.
retired from ASF to taverna-extras
https://lists.apache.org/thread.html/547b87fa93601d42ef77a778f80bf59fe9a300fffd7d3a6bcb7a7d81@%3Cdev.taverna.apache.org%3E
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/commit/d6fbc0d9
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/tree/d6fbc0d9
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/diff/d6fbc0d9
Branch: refs/heads/master
Commit: d6fbc0d9eff778634e0fa10f965db80e32be3ad9
Parents: aa249b2
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Fri Jun 29 13:41:22 2018 +0100
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Fri Jun 29 13:41:22 2018 +0100
----------------------------------------------------------------------
DISCLAIMER | 10 ----------
README.md | 51 ++++++++++++++++-----------------------------------
2 files changed, 16 insertions(+), 45 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/d6fbc0d9/DISCLAIMER
----------------------------------------------------------------------
diff --git a/DISCLAIMER b/DISCLAIMER
deleted file mode 100644
index 3e3a5ce..0000000
--- a/DISCLAIMER
+++ /dev/null
@@ -1,10 +0,0 @@
-Apache Taverna is an effort undergoing incubation at the Apache Software
-Foundation (ASF), sponsored by the Apache Incubator PMC.
-
-Incubation is required of all newly accepted projects until a further review
-indicates that the infrastructure, communications, and decision making process
-have stabilized in a manner consistent with other successful ASF projects.
-
-While incubation status is not necessarily a reflection of the completeness
-or stability of the code, it does indicate that the project has yet to be
-fully endorsed by the ASF.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/d6fbc0d9/README.md
----------------------------------------------------------------------
diff --git a/README.md b/README.md
index 9421ce4..1686202 100644
--- a/README.md
+++ b/README.md
@@ -15,22 +15,28 @@
limitations under the License.
-->
-# Apache Taverna Bioinformatics plugins
+# Bioinformatics plugins for Apache Taverna
Plugins for
-[Apache Taverna](http://taverna.incubator.apache.org/) for
+[Taverna](http://taverna.incubator.apache.org/) for
supporting bioinformatics-specific services.
-Note this module relies on other
-[Apache Taverna modules](http://taverna.incubator.apache.org/code) for
-the actual workflow execution.
+This plugin is **no longer maintained** by the Apache Taverna project, but
+has been made available to [taverna-extras](https://github.com/taverna-extras/)
+for archival purposes, open for third-party contributions.
+
+This module may rely on
+[Apache Taverna modules](http://taverna.incubator.apache.org/code) from Maven Central
+as well as the older Taverna 2 modules from http://www.mygrid.org.uk/maven/repository - do note that Taverna 2 was licensed as LGPL 2.1 or later.
+
+**Note:** This plugins have **not** been updated for [Apache Taverna 3](https://taverna.incubator.apache.org/download/engine/)
## License
(c) 2007-2014 University of Manchester
-(c) 2014-2015 Apache Software Foundation
+(c) 2014-2018 Apache Software Foundation
This product includes software developed at The
[Apache Software Foundation](http://www.apache.org/).
@@ -45,38 +51,13 @@ details about embedded third-party libraries and source code.
# Contribute
-Please subscribe to and contact the
-[dev@taverna](http://taverna.incubator.apache.org/community/lists#dev mailing list)
-for any questions, suggestions and discussions about
-Apache Taverna.
-
-Bugs and feature plannings are tracked in the Jira
-[Issue tracker](https://issues.apache.org/jira/browse/TAVERNA/component/12326818)
-under the `TAVERNA` component _Taverna Plugin Bioinformatics._ Feel free
-to add an issue!
-
-To suggest changes to this source code, feel free to raise a
-[GitHub pull request](https://github.com/apache/incubator-taverna-plugin-bioinformatics/pulls).
-Any contributions received are assumed to be covered by the [Apache License
-2.0](https://www.apache.org/licenses/LICENSE-2.0). We might ask you
-to sign a [Contributor License Agreement](https://www.apache.org/licenses/#clas)
-before accepting a larger contribution.
-
-## Disclaimer
-
-Apache Taverna is an effort undergoing incubation at the
-[Apache Software Foundation (ASF)](http://www.apache.org/),
-sponsored by the [Apache Incubator PMC](http://incubator.apache.org/).
-[Incubation](http://incubator.apache.org/incubation/Process_Description.html)
-is required of all newly accepted projects until a further review
-indicates that the infrastructure, communications, and decision making process
-have stabilized in a manner consistent with other successful ASF projects.
-While incubation status is not necessarily a reflection of the completeness
-or stability of the code, it does indicate that the project has yet to be
-fully endorsed by the ASF.
+This plugin is **not actively maintained**, but feel free to raise a
+[GitHub pull request](https://github.com/taverna-extras/taverna-plugin-bioinformatics/pulls).
+Any contributions received are assumed to be covered by the
+[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0).
## Prerequisites
[3/4] incubator-taverna-plugin-bioinformatics git commit: somewhat
tidy up groupId?
Posted by st...@apache.org.
somewhat tidy up groupId?
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/commit/c3d73263
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/tree/c3d73263
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/diff/c3d73263
Branch: refs/heads/master
Commit: c3d73263b6ea7ee243f2d993adf5e05d2052e750
Parents: d6fbc0d
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Fri Jun 29 13:42:18 2018 +0100
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Fri Jun 29 13:42:18 2018 +0100
----------------------------------------------------------------------
pom.xml | 135 ++++++++++++++++++++++++++++---
taverna-biomart-activity-ui/pom.xml | 28 +------
taverna-biomart-activity/pom.xml | 15 +---
taverna-biomart-martservice/pom.xml | 31 +------
taverna-biomoby-activity-ui/pom.xml | 7 +-
taverna-biomoby-activity/pom.xml | 18 ++---
taverna-ncbi-activity-ui/pom.xml | 31 ++-----
taverna-soaplab-activity-ui/pom.xml | 34 +-------
taverna-soaplab-activity/pom.xml | 33 +-------
9 files changed, 155 insertions(+), 177 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/c3d73263/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 604556b..c004358 100644
--- a/pom.xml
+++ b/pom.xml
@@ -20,22 +20,117 @@
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>org.apache.taverna</groupId>
- <artifactId>apache-taverna-parent</artifactId>
- <version>2-incubating</version>
- </parent>
- <groupId>org.apache.taverna.bioinformatics</groupId>
- <artifactId>apache-taverna-plugin-bioinformatics</artifactId>
- <version>3.1.0-incubating-SNAPSHOT</version>
+
+ <groupId>io.github.taverna-extras.bioinformatics</groupId>
+ <artifactId>taverna-plugin-bioinformatics</artifactId>
+ <version>3.1.0-SNAPSHOT</version>
<packaging>pom</packaging>
- <name>Apache Taverna Plugin for Bioinformatics</name>
+ <name>Bioinformatics plugin for Taverna</name>
+ <url>https://github.com/apache/incubator-taverna-plugin-bioinformatics</url>
<properties>
<taverna.language.version>0.15.1-incubating</taverna.language.version>
<taverna.osgi.version>0.2.1-incubating</taverna.osgi.version>
<taverna.engine.version>3.1.0-incubating</taverna.engine.version>
<taverna.commonactivities.version>2.1.0-incubating</taverna.commonactivities.version>
+
+ <!-- TODO: Only keep the versions needed -->
+
+ <activation.version>1.1.1</activation.version>
+ <antlr.version>2.7.7</antlr.version>
+ <apache.commons.csv.version>1.5</apache.commons.csv.version>
+ <apache.httpclient.version>4.5.3</apache.httpclient.version><!-- must be compatibe with jsonld-java/jena -->
+ <apache.httpcore.version>4.4.6</apache.httpcore.version> <!-- must match what httpclient depends on -->
+ <aspectj.version>1.6.9</aspectj.version>
+ <axis.jaxrpc.version>1.4</axis.jaxrpc.version>
+ <axis.sggj.version>1.4</axis.sggj.version>
+ <axis.version>1.4.0</axis.version>
+ <!--<axis.wsdl4j.version>1.5.1</axis.wsdl4j.version>-->
+ <batik.version>1.7.0</batik.version>
+ <bcprov.version>1.54</bcprov.version><!-- bcprov-jdk15on --><!-- bcprov-jdk15on --><!-- bcprov-jdk15on --><!-- bcprov-jdk15on -->
+ <cglib.version>2.1.3</cglib.version>
+ <commons.beanutils.version>1.9.2</commons.beanutils.version>
+ <commons.cli.version>1.4</commons.cli.version>
+ <commons.codec.version>1.10</commons.codec.version>
+ <commons.collections.version>3.2.2</commons.collections.version>
+ <commons.configuration.version>1.10</commons.configuration.version>
+ <commons.dbcp.version>1.4</commons.dbcp.version>
+ <commons.httpclient.version>3.1.0</commons.httpclient.version>
+ <commons.io.version>2.6</commons.io.version>
+ <commons.lang.version>2.6</commons.lang.version>
+ <commons.logging.version>1.1.3</commons.logging.version>
+ <commons.net.version>2.0.0</commons.net.version>
+ <dexx.collection.version>0.6</dexx.collection.version>
+ <dom4j.version>1.6.1</dom4j.version>
+ <geronimo.spec.jta.version>1.0-M1</geronimo.spec.jta.version>
+ <gson.version>1.4</gson.version>
+ <htmlparser.version>1.4</htmlparser.version>
+ <icu4j.version>3.4.4</icu4j.version>
+ <io.airlift.airline.version>0.7</io.airlift.airline.version>
+ <jackson.version>2.9.0</jackson.version> <!-- See also jsonldjava -->
+ <jai.imageio.core.version>1.3.1</jai.imageio.core.version> <!-- http://github.com/jai-imageio/ -->
+ <javahelp.version>2.0.02</javahelp.version>
+ <javax.el.version>1.0.0</javax.el.version>
+ <javax.servlet.jsp.version>2.1.0</javax.servlet.jsp.version>
+ <javax.servlet.version>2.5.0</javax.servlet.version>
+ <javax.transaction.version>1.1.0</javax.transaction.version>
+ <jaxb.version>2.2.11</jaxb.version>
+ <jaxen.version>1.1.6</jaxen.version>
+ <jaxp.ri.version>1.4</jaxp.ri.version>
+ <jaxws.api.version>2.1</jaxws.api.version>
+ <jdom.version>1.1.0</jdom.version> <!-- com.springsource.org.jdom -->
+ <jedit.syntax.version>2.2.5</jedit.syntax.version>
+ <jena.version>3.6.0</jena.version><!-- See also jsonld-java and httpcomponents -->
+ <jersey.client.version>1.19.1</jersey.client.version>
+ <jetty.version>6.1.24</jetty.version>
+ <jmimemagic.version>0.1.2</jmimemagic.version>
+ <jmoby.version>1.1.5-taverna</jmoby.version>
+ <joda-time.version>2.9.9</joda-time.version>
+ <json.lib.version>2.3</json.lib.version>
+ <jsonldjava.version>0.11.1</jsonldjava.version> <!-- upgrade from jena, sync with jackson and httpcomponents -->
+ <junit.version>4.11</junit.version>
+ <log4j.version>1.2.17</log4j.version>
+ <mail.version>1.4.1</mail.version>
+ <macify.version>1.6</macify.version>
+ <martj.version>0.6</martj.version>
+ <mimeutil.version>2.1.2-6</mimeutil.version>
+ <mockito.version>1.9.5</mockito.version>
+ <opm.version>1.1.8</opm.version>
+ <org.fife.ui.hexeditor.version>1.0.2011-07-04</org.fife.ui.hexeditor.version>
+ <org.icepdf.version>4.1.1-taverna</org.icepdf.version>
+ <org.xhtmlrenderer.core-renderer.version>R8</org.xhtmlrenderer.core-renderer.version>
+ <osgi.core.version>4.3.1</osgi.core.version>
+ <osgi.enterprise.version>4.2.0</osgi.enterprise.version>
+ <osgi.equinox.version>3.8.0.v20120529-1548</osgi.equinox.version>
+ <osgi.compendium.version>4.3.1</osgi.compendium.version>
+ <poi.ooxml.version>3.6</poi.ooxml.version>
+ <poi.version>3.6</poi.version>
+ <saxpath.version>1.0-FCS</saxpath.version>
+ <servletapi.version>2.5</servletapi.version>
+ <sesame.version>2.7.0</sesame.version>
+ <simple-jndi.version>0.11.1</simple-jndi.version>
+ <slf4j.version>1.7.20</slf4j.version>
+ <spring.dm.version>2.0.0.M1</spring.dm.version>
+ <spring.version>3.0.5.RELEASE</spring.version>
+ <stax.version>1.0</stax.version>
+ <tupelo.version>2.6</tupelo.version>
+ <xalan.version>2.7.1</xalan.version>
+ <servicemix.xerces.version>2.11.0_1</servicemix.xerces.version>
+ <xmlbeans.version>2.4.0</xmlbeans.version>
+ <xml.rpc.version>1.1.0</xml.rpc.version>
+ <xstream.version>1.4.1</xstream.version>
+
+
+
</properties>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.felix</groupId>
+ <artifactId>maven-bundle-plugin</artifactId>
+ <extensions>true</extensions>
+ </plugin>
+ </plugins>
+ </build>
<modules>
<module>taverna-biomart-activity</module>
<module>taverna-biomart-activity-ui</module>
@@ -62,6 +157,28 @@
<enabled>false</enabled>
</releases>
</repository>
+ <repository>
+ <releases />
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <id>mygrid-repository</id>
+ <name>myGrid Repository</name>
+ <url>http://www.mygrid.org.uk/maven/repository
+ </url>
+ </repository>
+ <repository>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <snapshots />
+ <id>mygrid-snapshot-repository</id>
+ <name>myGrid Snapshot Repository</name>
+ <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
+ </repository>
+ </repositories>
+
+
</repositories>
</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/c3d73263/taverna-biomart-activity-ui/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/pom.xml b/taverna-biomart-activity-ui/pom.xml
index b09936c..df1962d 100644
--- a/taverna-biomart-activity-ui/pom.xml
+++ b/taverna-biomart-activity-ui/pom.xml
@@ -20,11 +20,10 @@
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
- <groupId>net.sf.taverna</groupId>
- <artifactId>taverna-parent</artifactId>
- <version>3.0.1-SNAPSHOT</version>
+ <groupId>io.github.taverna-extras.bioinformatics</groupId>
+ <artifactId>taverna-plugin-bioinformatics</artifactId>
+ <version>3.1.0-SNAPSHOT</version>
</parent>
- <groupId>net.sf.taverna.t2.ui-activities</groupId>
<artifactId>biomart-activity-ui</artifactId>
<version>2.0-SNAPSHOT</version>
<packaging>bundle</packaging>
@@ -87,26 +86,5 @@
<scope>test</scope>
</dependency>
</dependencies>
- <repositories>
- <repository>
- <releases />
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- <id>mygrid-repository</id>
- <name>myGrid Repository</name>
- <url>http://www.mygrid.org.uk/maven/repository
- </url>
- </repository>
- <repository>
- <releases>
- <enabled>false</enabled>
- </releases>
- <snapshots />
- <id>mygrid-snapshot-repository</id>
- <name>myGrid Snapshot Repository</name>
- <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
- </repository>
- </repositories>
</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/c3d73263/taverna-biomart-activity/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity/pom.xml b/taverna-biomart-activity/pom.xml
index 5240520..4dd54d8 100644
--- a/taverna-biomart-activity/pom.xml
+++ b/taverna-biomart-activity/pom.xml
@@ -21,13 +21,12 @@
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
- <groupId>net.sf.taverna</groupId>
- <artifactId>taverna-parent</artifactId>
- <version>3.0.1-SNAPSHOT</version>
+ <groupId>io.github.taverna-extras.bioinformatics</groupId>
+ <artifactId>taverna-plugin-bioinformatics</artifactId>
+ <version>3.1.0-SNAPSHOT</version>
</parent>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <version>2.0.1-SNAPSHOT</version>
<artifactId>biomart-activity</artifactId>
+ <version>2.0.1-SNAPSHOT</version>
<packaging>bundle</packaging>
<name>Taverna 2 Biomart Activity.</name>
<dependencies>
@@ -85,11 +84,5 @@
<url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
</repository>
</repositories>
- <scm>
- <connection>scm:git:https://github.com/taverna/taverna-biomart-activity.git</connection>
- <developerConnection>scm:git:ssh://git@github.com/taverna/taverna-biomart-activity.git</developerConnection>
- <url>https://github.com/taverna/taverna-biomart-activity/</url>
- <tag>HEAD</tag>
- </scm>
</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/c3d73263/taverna-biomart-martservice/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/pom.xml b/taverna-biomart-martservice/pom.xml
index 7c8ae8f..8e2b0dd 100644
--- a/taverna-biomart-martservice/pom.xml
+++ b/taverna-biomart-martservice/pom.xml
@@ -21,11 +21,10 @@
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
- <groupId>net.sf.taverna</groupId>
- <artifactId>taverna-parent</artifactId>
- <version>3.0.1-SNAPSHOT</version>
+ <groupId>io.github.taverna-extras.bioinformatics</groupId>
+ <artifactId>taverna-plugin-bioinformatics</artifactId>
+ <version>3.1.0-SNAPSHOT</version>
</parent>
- <groupId>org.biomart</groupId>
<artifactId>martservice</artifactId>
<packaging>bundle</packaging>
<name>MartService</name>
@@ -86,24 +85,6 @@
<repositories>
<repository>
- <releases />
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- <id>mygrid-repository</id>
- <name>myGrid Repository</name>
- <url>http://www.mygrid.org.uk/maven/repository</url>
- </repository>
- <repository>
- <releases>
- <enabled>false</enabled>
- </releases>
- <snapshots />
- <id>mygrid-snapshot-repository</id>
- <name>myGrid Snapshot Repository</name>
- <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
- </repository>
- <repository>
<id>com.springsource.repository.bundles.release</id>
<name>SpringSource Enterprise Bundle Repository - SpringSource Bundle Releases</name>
<url>http://repository.springsource.com/maven/bundles/release</url>
@@ -114,10 +95,4 @@
<url>http://repository.springsource.com/maven/bundles/external</url>
</repository>
</repositories>
- <scm>
- <connection>scm:git:https://github.com/taverna/taverna-biomart-martservice.git</connection>
- <developerConnection>scm:git:ssh://git@github.com:taverna/taverna-biomart-martservice.git</developerConnection>
- <url>https://github.com/taverna/taverna-biomart-martservice/</url>
- <tag>HEAD</tag>
- </scm>
</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/c3d73263/taverna-biomoby-activity-ui/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/pom.xml b/taverna-biomoby-activity-ui/pom.xml
index 1b3fc4e..babcbb5 100644
--- a/taverna-biomoby-activity-ui/pom.xml
+++ b/taverna-biomoby-activity-ui/pom.xml
@@ -20,11 +20,10 @@
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
- <groupId>net.sf.taverna</groupId>
- <artifactId>taverna-parent</artifactId>
- <version>3.0.1-SNAPSHOT</version>
+ <groupId>io.github.taverna-extras.bioinformatics</groupId>
+ <artifactId>taverna-plugin-bioinformatics</artifactId>
+ <version>3.1.0-SNAPSHOT</version>
</parent>
- <groupId>net.sf.taverna.t2.ui-activities</groupId>
<artifactId>biomoby-activity-ui</artifactId>
<version>2.0.1-SNAPSHOT</version>
<name>Taverna 2 Biomoby Activity UI</name>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/c3d73263/taverna-biomoby-activity/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/pom.xml b/taverna-biomoby-activity/pom.xml
index 456f1a2..bd92ee3 100644
--- a/taverna-biomoby-activity/pom.xml
+++ b/taverna-biomoby-activity/pom.xml
@@ -20,12 +20,11 @@
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>net.sf.taverna</groupId>
- <artifactId>taverna-parent</artifactId>
- <version>3.0.1-SNAPSHOT</version>
- </parent>
- <groupId>net.sf.taverna.t2.activities</groupId>
+ <parent>
+ <groupId>io.github.taverna-extras.bioinformatics</groupId>
+ <artifactId>taverna-plugin-bioinformatics</artifactId>
+ <version>3.1.0-SNAPSHOT</version>
+ </parent>
<artifactId>biomoby-activity</artifactId>
<version>2.0.1-SNAPSHOT</version>
<packaging>bundle</packaging>
@@ -150,11 +149,4 @@
<url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
</repository>
</repositories>
- <scm>
- <connection>scm:git:https://github.com/taverna/taverna-biomoby-activity.git</connection>
- <developerConnection>scm:git:ssh://git@github.com/taverna/taverna-biomoby-activity.git</developerConnection>
- <url>https://github.com/taverna/taverna-biomoby-activity/</url>
- <tag>HEAD</tag>
- </scm>
-
</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/c3d73263/taverna-ncbi-activity-ui/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-ncbi-activity-ui/pom.xml b/taverna-ncbi-activity-ui/pom.xml
index 32fdb8b..0009b59 100644
--- a/taverna-ncbi-activity-ui/pom.xml
+++ b/taverna-ncbi-activity-ui/pom.xml
@@ -19,12 +19,11 @@
-->
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>net.sf.taverna</groupId>
- <artifactId>taverna-parent</artifactId>
- <version>3.0.1-SNAPSHOT</version>
- </parent>
- <groupId>net.sf.taverna.t2.ui-activities</groupId>
+ <parent>
+ <groupId>io.github.taverna-extras.bioinformatics</groupId>
+ <artifactId>taverna-plugin-bioinformatics</artifactId>
+ <version>3.1.0-SNAPSHOT</version>
+ </parent>
<artifactId>ncbi-activity-ui</artifactId>
<name>Taverna 2 NCBI web service Activity UI</name>
<dependencies>
@@ -42,26 +41,6 @@
<!-- testing dependencies -->
</dependencies>
- <repositories>
- <repository>
- <releases />
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- <id>mygrid-repository</id>
- <name>myGrid Repository</name>
- <url>http://www.mygrid.org.uk/maven/repository</url>
- </repository>
- <repository>
- <releases>
- <enabled>false</enabled>
- </releases>
- <snapshots />
- <id>mygrid-snapshot-repository</id>
- <name>myGrid Snapshot Repository</name>
- <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
- </repository>
- </repositories>
</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/c3d73263/taverna-soaplab-activity-ui/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity-ui/pom.xml b/taverna-soaplab-activity-ui/pom.xml
index cedc438..f3097de 100644
--- a/taverna-soaplab-activity-ui/pom.xml
+++ b/taverna-soaplab-activity-ui/pom.xml
@@ -20,11 +20,10 @@
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
- <groupId>net.sf.taverna</groupId>
- <artifactId>taverna-parent</artifactId>
- <version>3.0.1-SNAPSHOT</version>
+ <groupId>io.github.taverna-extras.bioinformatics</groupId>
+ <artifactId>taverna-plugin-bioinformatics</artifactId>
+ <version>3.1.0-SNAPSHOT</version>
</parent>
- <groupId>net.sf.taverna.t2.ui-activities</groupId>
<artifactId>soaplab-activity-ui</artifactId>
<version>2.0-SNAPSHOT</version>
<packaging>bundle</packaging>
@@ -89,33 +88,6 @@
<scope>test</scope>
</dependency>
</dependencies>
- <repositories>
- <repository>
- <releases />
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- <id>mygrid-repository</id>
- <name>myGrid Repository</name>
- <url>http://www.mygrid.org.uk/maven/repository
- </url>
- </repository>
- <repository>
- <releases>
- <enabled>false</enabled>
- </releases>
- <snapshots />
- <id>mygrid-snapshot-repository</id>
- <name>myGrid Snapshot Repository</name>
- <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
- </repository>
- </repositories>
- <scm>
- <connection>scm:git:https://github.com/taverna/taverna-soaplab-activity-ui.git</connection>
- <developerConnection>scm:git:ssh://git@github.com/taverna/taverna-soaplab-activity-ui.git</developerConnection>
- <url>https://github.com/taverna/taverna-soaplab-activity-ui/</url>
- <tag>HEAD</tag>
- </scm>
</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/c3d73263/taverna-soaplab-activity/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity/pom.xml b/taverna-soaplab-activity/pom.xml
index 1a6194e..2a517da 100644
--- a/taverna-soaplab-activity/pom.xml
+++ b/taverna-soaplab-activity/pom.xml
@@ -20,11 +20,10 @@
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
- <groupId>net.sf.taverna</groupId>
- <artifactId>taverna-parent</artifactId>
- <version>3.0.1-SNAPSHOT</version>
+ <groupId>io.github.taverna-extras.bioinformatics</groupId>
+ <artifactId>taverna-plugin-bioinformatics</artifactId>
+ <version>3.1.0-SNAPSHOT</version>
</parent>
- <groupId>net.sf.taverna.t2.activities</groupId>
<artifactId>soaplab-activity</artifactId>
<packaging>bundle</packaging>
<name>Taverna 2 Soaplab Activity</name>
@@ -67,32 +66,6 @@
<scope>test</scope>
</dependency>
</dependencies>
- <repositories>
- <repository>
- <releases />
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- <id>mygrid-repository</id>
- <name>myGrid Repository</name>
- <url>http://www.mygrid.org.uk/maven/repository</url>
- </repository>
- <repository>
- <releases>
- <enabled>false</enabled>
- </releases>
- <snapshots />
- <id>mygrid-snapshot-repository</id>
- <name>myGrid Snapshot Repository</name>
- <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
- </repository>
- </repositories>
- <scm>
- <connection>scm:git:https://github.com/taverna/taverna-soaplab-activity.git</connection>
- <developerConnection>scm:git:ssh://git@github.com:taverna/taverna-soaplab-activity.git</developerConnection>
- <url>https://github.com/taverna/taverna-soaplab-activity</url>
- <tag>HEAD</tag>
- </scm>
</project>