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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 21:44:36 UTC
[16/16] incubator-taverna-plugin-bioinformatics git commit:
temporarily empty repository
temporarily empty repository
... as Software Grant is not yet formally on gfile
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/e13e3b74
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/tree/e13e3b74
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/diff/e13e3b74
Branch: refs/heads/master
Commit: e13e3b7419f7c67ddf3c3e4184a59686639484cd
Parents: 7936285
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Feb 17 20:44:04 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Feb 17 20:44:04 2015 +0000
----------------------------------------------------------------------
pom.xml | 41 -
taverna-biomart-activity-ui/pom.xml | 94 -
.../BiomartActivityConfigurationAction.java | 74 -
.../actions/BiomartConfigurationPanel.java | 134 -
.../menu/BiomartConfigurationMenuAction.java | 68 -
.../BiomartActivityIcon.java | 59 -
.../BiomartServiceDescription.java | 146 -
.../BiomartServiceProvider.java | 147 -
.../BiomartServiceProviderConfig.java | 36 -
.../views/BiomartActivityContextualView.java | 117 -
.../views/BiomartActivityViewFactory.java | 86 -
...rvicedescriptions.ServiceDescriptionProvider | 1 -
.../net.sf.taverna.t2.ui.menu.MenuComponent | 1 -
...a.t2.workbench.activityicons.ActivityIconSPI | 1 -
...ntextualviews.activity.ContextualViewFactory | 1 -
.../spring/biomart-activity-ui-context-osgi.xml | 30 -
.../spring/biomart-activity-ui-context.xml | 29 -
.../src/main/resources/biomart.png | Bin 3175 -> 0 bytes
.../TestBiomartActivityContextualView.java | 94 -
.../src/test/resources/biomart-query.xml | 24 -
taverna-biomart-activity/pom.xml | 77 -
.../t2/activities/biomart/BiomartActivity.java | 351 --
.../BiomartActivityConfigurationBean.java | 47 -
.../biomart/BiomartActivityFactory.java | 144 -
.../biomart/BiomartActivityHealthChecker.java | 76 -
...averna.t2.workflowmodel.health.HealthChecker | 1 -
.../spring/biomart-activity-context-osgi.xml | 15 -
.../spring/biomart-activity-context.xml | 13 -
.../src/main/resources/schema.json | 19 -
.../biomart/BiomartActivityFactoryTest.java | 65 -
.../src/test/resources/biomart-query.xml | 17 -
taverna-biomart-martservice/pom.xml | 105 -
.../org/biomart/martservice/DatasetLink.java | 220 --
.../org/biomart/martservice/MartDataset.java | 342 --
.../java/org/biomart/martservice/MartQuery.java | 436 ---
.../org/biomart/martservice/MartRegistry.java | 96 -
.../org/biomart/martservice/MartService.java | 709 ----
.../martservice/MartServiceException.java | 86 -
.../biomart/martservice/MartServiceUtils.java | 725 ----
.../martservice/MartServiceXMLHandler.java | 390 --
.../biomart/martservice/MartURLLocation.java | 422 ---
.../org/biomart/martservice/ResultReceiver.java | 61 -
.../martservice/ResultReceiverException.java | 85 -
.../config/QueryConfigController.java | 388 --
.../martservice/config/QueryConfigUtils.java | 598 ---
.../config/event/QueryComponentAdapter.java | 109 -
.../config/event/QueryComponentEvent.java | 120 -
.../config/event/QueryComponentListener.java | 104 -
.../config/ui/ConfigDisplayObject.java | 125 -
.../martservice/config/ui/ExpandableBox.java | 204 -
.../martservice/config/ui/MartServiceIcons.java | 104 -
.../ui/MartServiceQueryConfigUIFactory.java | 3543 ------------------
.../martservice/config/ui/MinimalLayout.java | 158 -
.../martservice/config/ui/QueryComponent.java | 342 --
.../config/ui/QueryConfigUIFactory.java | 345 --
.../biomart/martservice/query/Attribute.java | 198 -
.../org/biomart/martservice/query/Dataset.java | 309 --
.../org/biomart/martservice/query/Filter.java | 243 --
.../org/biomart/martservice/query/Link.java | 181 -
.../org/biomart/martservice/query/Query.java | 555 ---
.../martservice/query/QueryListener.java | 108 -
.../martservice/query/QueryXMLHandler.java | 332 --
.../biomart/martservice/config/ui/contract.gif | Bin 90 -> 0 bytes
.../biomart/martservice/config/ui/expand.gif | Bin 93 -> 0 bytes
.../martservice/config/ui/gene_schematic.gif | Bin 734 -> 0 bytes
.../config/ui/gene_schematic_3utr.gif | Bin 717 -> 0 bytes
.../config/ui/gene_schematic_5utr.gif | Bin 722 -> 0 bytes
.../config/ui/gene_schematic_cdna.gif | Bin 743 -> 0 bytes
.../config/ui/gene_schematic_coding.gif | Bin 760 -> 0 bytes
.../ui/gene_schematic_coding_gene_flank.gif | Bin 715 -> 0 bytes
.../gene_schematic_coding_transcript_flank.gif | Bin 765 -> 0 bytes
.../config/ui/gene_schematic_gene_exon.gif | Bin 504 -> 0 bytes
.../ui/gene_schematic_gene_exon_intron.gif | Bin 710 -> 0 bytes
.../config/ui/gene_schematic_gene_flank.gif | Bin 710 -> 0 bytes
.../config/ui/gene_schematic_peptide.gif | Bin 760 -> 0 bytes
.../ui/gene_schematic_transcript_exon.gif | Bin 920 -> 0 bytes
.../gene_schematic_transcript_exon_intron.gif | Bin 716 -> 0 bytes
.../ui/gene_schematic_transcript_flank.gif | Bin 751 -> 0 bytes
.../biomart/martservice/MartDatasetTest.java | 335 --
.../biomart/martservice/MartRegistryTest.java | 113 -
.../martservice/MartServiceUtilsTest.java | 65 -
.../martservice/MartServiceXMLHandlerTest.java | 218 --
.../martservice/MartURLLocationTest.java | 255 --
.../config/event/QueryComponentEventTest.java | 131 -
.../config/ui/MartServiceIconsTest.java | 77 -
.../martservice/query/AttributeTest.java | 164 -
.../biomart/martservice/query/DatasetTest.java | 308 --
.../biomart/martservice/query/FilterTest.java | 242 --
.../biomart/martservice/query/QueryTest.java | 303 --
taverna-biomoby-activity-ui/pom.xml | 86 -
.../biomoby/actions/AddParserActionHelper.java | 280 --
.../BioMobyObjectTreeCustomRenderer.java | 97 -
.../BioMobyServiceTreeCustomRenderer.java | 86 -
.../biomoby/actions/BiomobyActionHelper.java | 852 -----
.../BiomobyActivityConfigurationAction.java | 60 -
.../actions/BiomobyObjectActionHelper.java | 787 ----
.../biomoby/actions/BiomobyScavengerDialog.java | 136 -
.../actions/MobyObjectDetailsAction.java | 83 -
.../biomoby/actions/MobyObjectTreeNode.java | 50 -
.../activities/biomoby/actions/MobyPanel.java | 136 -
.../biomoby/actions/MobyParserAction.java | 70 -
.../actions/MobyServiceDetailsAction.java | 65 -
.../biomoby/actions/MobyServiceTreeNode.java | 42 -
.../activities/biomoby/actions/PopupThread.java | 34 -
.../biomoby/actions/SimpleActionFrame.java | 46 -
.../BiomobyDatatypeDescription.java | 143 -
.../edits/AddBiomobyCollectionDataTypeEdit.java | 60 -
.../edits/AddBiomobyConsumingServiceEdit.java | 236 --
.../biomoby/edits/AddBiomobyDataTypeEdit.java | 207 -
.../biomoby/edits/AddMobyParseDatatypeEdit.java | 220 --
.../biomoby/edits/AddUpstreamObjectEdit.java | 216 --
.../menu/BiomobyActivityDetailsMenuAction.java | 40 -
.../menu/BiomobyActivityParserMenuAction.java | 41 -
.../menu/ConfigureBiomobyMenuAction.java | 52 -
.../biomoby/query/BiomobyActivityIcon.java | 36 -
.../biomoby/query/BiomobyActivityItem.java | 94 -
.../query/BiomobyObjectActivityIcon.java | 32 -
.../query/BiomobyObjectActivityItem.java | 76 -
.../biomoby/query/BiomobyQueryHelper.java | 270 --
.../t2/activities/biomoby/query/CacheImpl.java | 568 ---
.../BiomobyServiceDescription.java | 137 -
.../BiomobyServiceProvider.java | 121 -
.../BiomobyServiceProviderConfig.java | 37 -
.../biomoby/ui/AddBiomobyDialogue.java | 94 -
.../biomoby/ui/BiomobyObjectTree.java | 635 ----
.../activities/biomoby/ui/DatatypeMenuItem.java | 196 -
.../view/BiomobyActivityContextualView.java | 106 -
.../BiomobyActivityContextualViewFactory.java | 50 -
.../biomoby/view/BiomobyConfigView.java | 108 -
.../BiomobyObjectActivityContextualView.java | 95 -
...mobyObjectActivityContextualViewFactory.java | 67 -
.../view/MobyParseDatatypeContextualView.java | 62 -
.../MobyParseDatatypeContextualViewFactory.java | 69 -
.../src/main/resources/Add24.gif | Bin 470 -> 0 bytes
.../src/main/resources/Cut24.gif | Bin 1193 -> 0 bytes
.../src/main/resources/Information24.gif | Bin 1328 -> 0 bytes
...averna.t2.partition.PartitionAlgorithmSetSPI | 1 -
...sf.taverna.t2.partition.PropertyExtractorSPI | 1 -
.../net.sf.taverna.t2.partition.QueryFactory | 1 -
...rvicedescriptions.ServiceDescriptionProvider | 1 -
.../net.sf.taverna.t2.ui.menu.MenuComponent | 5 -
...a.t2.workbench.activityicons.ActivityIconSPI | 2 -
...ntextualviews.activity.ContextualViewFactory | 3 -
.../spring/biomoby-activity-ui-context-osgi.xml | 28 -
.../spring/biomoby-activity-ui-context.xml | 42 -
.../src/main/resources/Search24.gif | Bin 820 -> 0 bytes
.../src/main/resources/authority.png | Bin 481 -> 0 bytes
.../src/main/resources/biomoby_object.png | Bin 981 -> 0 bytes
.../src/main/resources/collection.png | Bin 628 -> 0 bytes
.../src/main/resources/input.png | Bin 489 -> 0 bytes
.../src/main/resources/moby.png | Bin 981 -> 0 bytes
.../src/main/resources/moby_small.gif | Bin 787 -> 0 bytes
.../src/main/resources/output.png | Bin 511 -> 0 bytes
.../src/main/resources/parse.png | Bin 227 -> 0 bytes
.../src/main/resources/registry.gif | Bin 935 -> 0 bytes
.../src/main/resources/service.png | Bin 441 -> 0 bytes
.../view/BiomobyContextualViewFactoryTest.java | 49 -
taverna-biomoby-activity/pom.xml | 142 -
.../t2/activities/biomoby/BiomobyActivity.java | 1319 -------
.../BiomobyActivityConfigurationBean.java | 142 -
.../biomoby/BiomobyActivityFactory.java | 49 -
.../biomoby/BiomobyActivityHealthChecker.java | 45 -
.../t2/activities/biomoby/BiomobyCache.java | 78 -
.../biomoby/BiomobyObjectActivity.java | 545 ---
.../BiomobyObjectActivityConfigurationBean.java | 81 -
.../biomoby/BiomobyObjectActivityFactory.java | 49 -
.../BiomobyObjectActivityHealthChecker.java | 57 -
.../biomoby/ExecuteAsyncCgiService.java | 517 ---
.../biomoby/ExecuteAsyncMobyService.java | 695 ----
.../activities/biomoby/ExecuteCgiService.java | 70 -
.../activities/biomoby/ExecuteMobyService.java | 38 -
.../activities/biomoby/GetOntologyThread.java | 59 -
.../biomoby/MobyParseDatatypeActivity.java | 417 ---
...yParseDatatypeActivityConfigurationBean.java | 81 -
.../MobyParseDatatypeActivityFactory.java | 49 -
.../MobyParseDatatypeActivityHealthChecker.java | 58 -
.../t2/activities/biomoby/ParseMobyXML.java | 192 -
.../activities/biomoby/RetrieveWsdlThread.java | 57 -
.../t2/activities/biomoby/XMLUtilities.java | 1927 ----------
...averna.t2.workflowmodel.health.HealthChecker | 3 -
.../spring/biomoby-activity-context-osgi.xml | 17 -
.../spring/biomoby-activity-context.xml | 14 -
.../BiomobyActivityHealthCheckerTest.java | 45 -
.../BiomobyObjectActivityHealthCheckerTest.java | 45 -
...yParseDatatypeActivityHealthCheckerTest.java | 45 -
taverna-ncbi-activity-ui/pom.xml | 49 -
.../spring/ncbi-activity-ui-context-osgi.xml | 9 -
.../spring/ncbi-activity-ui-context.xml | 6 -
.../src/main/resources/ncbi_services | 0
.../src/main/resources/wsdl.png | Bin 748 -> 0 bytes
taverna-soaplab-activity-ui/pom.xml | 103 -
.../SoaplabActivityConfigurationAction.java | 68 -
.../actions/SoaplabConfigurationPanel.java | 183 -
.../ConfigureSoaplabActivityMenuAction.java | 54 -
.../MissingSoaplabException.java | 63 -
.../SoaplabActivityIcon.java | 60 -
.../servicedescriptions/SoaplabCategory.java | 80 -
.../SoaplabScavengerAgent.java | 144 -
.../SoaplabServiceDescription.java | 131 -
.../SoaplabServiceProvider.java | 183 -
.../SoaplabServiceProviderConfig.java | 38 -
.../views/SoaplabActivityContextualView.java | 156 -
.../views/SoaplabActivityViewFactory.java | 73 -
...rvicedescriptions.ServiceDescriptionProvider | 1 -
.../net.sf.taverna.t2.ui.menu.MenuComponent | 1 -
...a.t2.workbench.activityicons.ActivityIconSPI | 1 -
...ntextualviews.activity.ContextualViewFactory | 1 -
.../spring/soaplab-activity-ui-context-osgi.xml | 28 -
.../spring/soaplab-activity-ui-context.xml | 27 -
.../main/resources/analysis_metadata_2_html.xsl | 96 -
.../src/main/resources/soaplab.png | Bin 701 -> 0 bytes
.../TestSoaplabActivityContextualView.java | 61 -
taverna-soaplab-activity/pom.xml | 80 -
.../sf/taverna/t2/activities/soaplab/Soap.java | 82 -
.../t2/activities/soaplab/SoaplabActivity.java | 413 --
.../SoaplabActivityConfigurationBean.java | 119 -
.../soaplab/SoaplabActivityFactory.java | 216 --
.../soaplab/SoaplabActivityHealthChecker.java | 66 -
...averna.t2.workflowmodel.health.HealthChecker | 1 -
.../spring/soaplab-activity-context-osgi.xml | 15 -
.../spring/soaplab-activity-context.xml | 12 -
.../src/main/resources/schema.json | 40 -
.../SoaplabActivityConfigurationBeanTest.java | 92 -
.../activities/soaplab/SoaplabActivityTest.java | 127 -
224 files changed, 32788 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
deleted file mode 100644
index 5102f18..0000000
--- a/pom.xml
+++ /dev/null
@@ -1,41 +0,0 @@
-<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>taverna-parent</artifactId>
- <version>1-incubating-SNAPSHOT</version>
- </parent>
- <groupId>org.apache.taverna.bioinformatics</groupId>
- <artifactId>taverna-plugin-bioinformatics</artifactId>
- <version>3.1.0-incubating-SNAPSHOT</version>
- <packaging>pom</packaging>
- <name>Apache Taverna Plugin for Bioinformatics</name>
- <properties>
- <taverna.language.version>0.15.0-incubating-SNAPSHOT</taverna.language.version>
- <taverna.osgi.version>0.2.0-incubating-SNAPSHOT</taverna.osgi.version>
- <taverna.engine.version>3.1.0-incubating-SNAPSHOT</taverna.engine.version>
- <taverna.commonactivities.version>2.1.0-incubating-SNAPSHOT</taverna.commonactivities.version>
- </properties>
- <modules>
- <module>taverna-biomart-activity</module>
- <module>taverna-biomart-activity-ui</module>
- <module>taverna-biomart-martservice</module>
- <module>taverna-biomoby-activity</module>
- <module>taverna-biomoby-activity-ui</module>
- <module>taverna-ncbi-activity-ui</module>
- <module>taverna-soaplab-activity</module>
- <module>taverna-soaplab-activity-ui</module>
- </modules>
- <repositories>
- <repository>
- <id>taverna-incubating</id>
- <name>Apache Taverna incubating Repository</name>
- <url>http://repository.mygrid.org.uk/artifactory/incubator-snapshot-local/</url>
- <releases>
- <enabled>false</enabled>
- </releases>
- <snapshots />
- </repository>
- </repositories>
-</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/pom.xml b/taverna-biomart-activity-ui/pom.xml
deleted file mode 100644
index 8465101..0000000
--- a/taverna-biomart-activity-ui/pom.xml
+++ /dev/null
@@ -1,94 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<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>
- <artifactId>biomart-activity-ui</artifactId>
- <version>2.0-SNAPSHOT</version>
- <packaging>bundle</packaging>
- <name>Taverna 2 Biomart Activity UI</name>
- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.felix</groupId>
- <artifactId>maven-bundle-plugin</artifactId>
- <configuration>
- <instructions>
- <Import-Package>net.sf.taverna.t2.ui.menu,*</Import-Package>
- </instructions>
- </configuration>
- </plugin>
- </plugins>
- </build>
- <dependencies>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>biomart-activity</artifactId>
- <version>${t2.activities.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-api</groupId>
- <artifactId>activity-icons-api</artifactId>
- <version>${t2.ui.api.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-api</groupId>
- <artifactId>activity-palette-api</artifactId>
- <version>${t2.ui.api.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-api</groupId>
- <artifactId>contextual-views-api</artifactId>
- <version>${t2.ui.api.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-api</groupId>
- <artifactId>activity-tools</artifactId>
- <version>${t2.ui.api.version}</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.configuration</groupId>
- <artifactId>taverna-app-configuration-api</artifactId>
- <version>${taverna.configuration.version}</version>
- </dependency>
-
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>${junit.version}</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-impl</groupId>
- <artifactId>configuration-impl</artifactId>
- <version>${t2.ui.impl.version}</version>
- <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/e13e3b74/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartActivityConfigurationAction.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartActivityConfigurationAction.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartActivityConfigurationAction.java
deleted file mode 100644
index a0b51e7..0000000
--- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartActivityConfigurationAction.java
+++ /dev/null
@@ -1,74 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomart.actions;
-
-import java.awt.Frame;
-import java.awt.event.ActionEvent;
-
-import javax.swing.Action;
-
-import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workbench.ui.actions.activity.ActivityConfigurationAction;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityConfigurationDialog;
-import uk.org.taverna.commons.services.ServiceRegistry;
-import uk.org.taverna.configuration.app.ApplicationConfiguration;
-import uk.org.taverna.scufl2.api.activity.Activity;
-
-@SuppressWarnings("serial")
-public class BiomartActivityConfigurationAction extends ActivityConfigurationAction {
-
- public static final String CONFIGURE_BIOMART = "Configure Biomart query";
- private final EditManager editManager;
- private final FileManager fileManager;
- private final ApplicationConfiguration applicationConfiguration;
- private final ServiceRegistry serviceRegistry;
-
- public BiomartActivityConfigurationAction(Activity activity, Frame owner,
- EditManager editManager, FileManager fileManager, ActivityIconManager activityIconManager,
- ApplicationConfiguration applicationConfiguration, ServiceDescriptionRegistry serviceDescriptionRegistry,
- ServiceRegistry serviceRegistry) {
- super(activity, activityIconManager, serviceDescriptionRegistry);
- this.editManager = editManager;
- this.fileManager = fileManager;
- this.applicationConfiguration = applicationConfiguration;
- this.serviceRegistry = serviceRegistry;
- putValue(Action.NAME, CONFIGURE_BIOMART);
- }
-
- public void actionPerformed(ActionEvent action) {
- ActivityConfigurationDialog currentDialog = ActivityConfigurationAction.getDialog(getActivity());
- if (currentDialog != null) {
- currentDialog.toFront();
- return;
- }
-
- final BiomartConfigurationPanel configurationPanel = new BiomartConfigurationPanel(
- getActivity(), applicationConfiguration, serviceRegistry);
- final ActivityConfigurationDialog dialog = new ActivityConfigurationDialog(
- getActivity(), configurationPanel, editManager);
-
- ActivityConfigurationAction.setDialog(getActivity(), dialog, fileManager);
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartConfigurationPanel.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartConfigurationPanel.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartConfigurationPanel.java
deleted file mode 100644
index 2b6f662..0000000
--- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartConfigurationPanel.java
+++ /dev/null
@@ -1,134 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomart.actions;
-
-import java.awt.Dimension;
-import java.io.File;
-import java.io.IOException;
-import java.io.StringReader;
-import java.net.URI;
-
-import javax.swing.Box;
-import javax.swing.BoxLayout;
-import javax.swing.JLabel;
-
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityConfigurationPanel;
-
-import org.apache.log4j.Logger;
-import org.biomart.martservice.MartQuery;
-import org.biomart.martservice.MartService;
-import org.biomart.martservice.MartServiceException;
-import org.biomart.martservice.MartServiceXMLHandler;
-import org.biomart.martservice.config.QueryConfigController;
-import org.biomart.martservice.config.ui.MartServiceQueryConfigUIFactory;
-import org.biomart.martservice.config.ui.QueryConfigUIFactory;
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.input.SAXBuilder;
-import org.jdom.output.XMLOutputter;
-
-import uk.org.taverna.commons.services.ServiceRegistry;
-import uk.org.taverna.configuration.app.ApplicationConfiguration;
-import uk.org.taverna.scufl2.api.activity.Activity;
-
-public class BiomartConfigurationPanel extends ActivityConfigurationPanel {
- private static Logger logger = Logger.getLogger(BiomartConfigurationPanel.class);
-
- private static final long serialVersionUID = 1884045346293327621L;
-
- public static final URI ACTIVITY_TYPE = URI.create("http://ns.taverna.org.uk/2010/activity/biomart");
-
- private String configurationString;
-
- private MartQuery biomartQuery;
-
- private static XMLOutputter outputter = new XMLOutputter();
-
- private final ApplicationConfiguration applicationConfiguration;
-
- private final ServiceRegistry serviceRegistry;
-
- public BiomartConfigurationPanel(Activity activity, ApplicationConfiguration applicationConfiguration,
- ServiceRegistry serviceRegistry) {
- super(activity);
- this.applicationConfiguration = applicationConfiguration;
- this.serviceRegistry = serviceRegistry;
- initialise();
- }
-
- protected void initialise() {
- super.initialise();
- removeAll();
-
- configurationString = getProperty("martQuery");
- Element martQuery = null;
- try {
- martQuery = new SAXBuilder().build(new StringReader(configurationString)).getRootElement();
- } catch (JDOMException | IOException e) {
- logger.warn(e);
- }
- setLayout(new BoxLayout(this,BoxLayout.Y_AXIS));
-
- biomartQuery = MartServiceXMLHandler.elementToMartQuery(martQuery, null);
- MartService service = biomartQuery.getMartService();
-
- File homeRoot=applicationConfiguration.getApplicationHomeDir();
- if (homeRoot==null) {
- logger.error("unable to determine application home for biomart cache");
- homeRoot=new File(System.getProperty("java.io.tmpdir"));
- }
- File cache=new File(homeRoot,"t2-biomart-activity");
- service.setCacheDirectory(new File(cache,"cache"));
- logger.info("Biomart is using cache directory:"+cache.getAbsolutePath());
-
- QueryConfigController controller = new QueryConfigController(biomartQuery);
- try {
- QueryConfigUIFactory queryConfigUIFactory = new MartServiceQueryConfigUIFactory(
- service, controller, biomartQuery.getMartDataset());
- add(queryConfigUIFactory.getDatasetConfigUI());
- add(Box.createGlue());
- } catch (MartServiceException e) {
- add(new JLabel("Error reading configuration properties"));
- add(new JLabel(e.getMessage()));
- add(Box.createGlue());
- }
- this.setPreferredSize(new Dimension(900,500));
- this.validate();
- }
-
- public Element getQuery() {
- return MartServiceXMLHandler.martQueryToElement(biomartQuery, null);
- }
-
- @Override
- public void noteConfiguration() {
- setProperty("martQuery", outputter.outputString(new Document(getQuery())));
- configureInputPorts(serviceRegistry);
- configureOutputPorts(serviceRegistry);
- }
-
- @Override
- public boolean checkValues() {
- // TODO Not yet done
- return true;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/menu/BiomartConfigurationMenuAction.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/menu/BiomartConfigurationMenuAction.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/menu/BiomartConfigurationMenuAction.java
deleted file mode 100644
index 775ce95..0000000
--- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/menu/BiomartConfigurationMenuAction.java
+++ /dev/null
@@ -1,68 +0,0 @@
-package net.sf.taverna.t2.activities.biomart.menu;
-
-import java.net.URI;
-
-import javax.swing.Action;
-
-import net.sf.taverna.t2.activities.biomart.actions.BiomartActivityConfigurationAction;
-import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
-import net.sf.taverna.t2.ui.menu.ContextualMenuComponent;
-import net.sf.taverna.t2.ui.menu.MenuComponent;
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
-import net.sf.taverna.t2.workbench.activitytools.AbstractConfigureActivityMenuAction;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import uk.org.taverna.commons.services.ServiceRegistry;
-import uk.org.taverna.configuration.app.ApplicationConfiguration;
-
-public class BiomartConfigurationMenuAction extends AbstractConfigureActivityMenuAction implements
- MenuComponent, ContextualMenuComponent {
-
- private static final URI BIOMART_ACTIVITY = URI
- .create("http://ns.taverna.org.uk/2010/activity/biomart");
- private EditManager editManager;
- private FileManager fileManager;
- private ActivityIconManager activityIconManager;
- private ApplicationConfiguration applicationConfiguration;
- private ServiceDescriptionRegistry serviceDescriptionRegistry;
- private ServiceRegistry serviceRegistry;
-
- public BiomartConfigurationMenuAction() {
- super(BIOMART_ACTIVITY);
- }
-
- @Override
- protected Action createAction() {
- BiomartActivityConfigurationAction configAction = new BiomartActivityConfigurationAction(
- findActivity(), getParentFrame(), editManager, fileManager, activityIconManager,
- applicationConfiguration, serviceDescriptionRegistry, serviceRegistry);
- configAction.putValue(Action.NAME, BiomartActivityConfigurationAction.CONFIGURE_BIOMART);
- addMenuDots(configAction);
- return configAction;
- }
-
- public void setEditManager(EditManager editManager) {
- this.editManager = editManager;
- }
-
- public void setFileManager(FileManager fileManager) {
- this.fileManager = fileManager;
- }
-
- public void setActivityIconManager(ActivityIconManager activityIconManager) {
- this.activityIconManager = activityIconManager;
- }
-
- public void setApplicationConfiguration(ApplicationConfiguration applicationConfiguration) {
- this.applicationConfiguration = applicationConfiguration;
- }
-
- public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
- this.serviceDescriptionRegistry = serviceDescriptionRegistry;
- }
-
- public void setServiceRegistry(ServiceRegistry serviceRegistry) {
- this.serviceRegistry = serviceRegistry;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartActivityIcon.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartActivityIcon.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartActivityIcon.java
deleted file mode 100644
index 845665e..0000000
--- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartActivityIcon.java
+++ /dev/null
@@ -1,59 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomart.servicedescriptions;
-
-import java.net.URI;
-
-import javax.swing.Icon;
-import javax.swing.ImageIcon;
-
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI;
-
-/**
- *
- * @author Alex Nenadic
- * @author Alan R Williams
- *
- */
-public class BiomartActivityIcon implements ActivityIconSPI {
-
- private static final URI BIOMART_ACTIVITY = URI.create("http://ns.taverna.org.uk/2010/activity/biomart");
-
- static Icon icon = null;
-
- public int canProvideIconScore(URI activityType) {
- if (BIOMART_ACTIVITY.equals(activityType))
- return DEFAULT_ICON + 1;
- else
- return NO_ICON;
- }
-
- public Icon getIcon(URI activityType) {
- return getBiomartIcon();
- }
-
- public static Icon getBiomartIcon() {
- if (icon == null) {
- icon = new ImageIcon(BiomartActivityIcon.class.getResource("/biomart.png"));
- }
- return icon;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceDescription.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceDescription.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceDescription.java
deleted file mode 100644
index ca50019..0000000
--- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceDescription.java
+++ /dev/null
@@ -1,146 +0,0 @@
-/* Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomart.servicedescriptions;
-
-import java.net.URI;
-import java.util.Arrays;
-import java.util.List;
-
-import javax.swing.Icon;
-
-import net.sf.taverna.t2.servicedescriptions.ServiceDescription;
-
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.output.XMLOutputter;
-
-import uk.org.taverna.scufl2.api.configurations.Configuration;
-
-import com.fasterxml.jackson.databind.node.ObjectNode;
-
-/**
- * @author alanrw
- * @author David Withers
- */
-public class BiomartServiceDescription extends ServiceDescription {
-
- public static final URI ACTIVITY_TYPE = URI.create("http://ns.taverna.org.uk/2010/activity/biomart");
-
- private String url;
- private String dataset;
- private String location;
-
- private static final String BIOMART = "Biomart @ ";
- private Element martQuery;
-
- public Element getMartQuery() {
- return martQuery;
- }
-
- /**
- * @return the url
- */
- public String getUrl() {
- return url;
- }
-
- /**
- * @param url
- * the url to set
- */
- public void setUrl(String url) {
- this.url = url;
- }
-
- /**
- * @return the dataset
- */
- public String getDataset() {
- return dataset;
- }
-
- /**
- * @param dataset
- * the dataset to set
- */
- public void setDataset(String dataset) {
- this.dataset = dataset;
- }
-
- /**
- * @return the location
- */
- public String getLocation() {
- return location;
- }
-
- /**
- * @param location
- * the location to set
- */
- public void setLocation(String location) {
- this.location = location;
- }
-
- public void setMartQuery(Element martQuery) {
- this.martQuery = martQuery;
- }
-
- @Override
- public URI getActivityType() {
- return ACTIVITY_TYPE;
- }
-
- @Override
- public Configuration getActivityConfiguration() {
- Configuration configuration = new Configuration();
- configuration.setType(ACTIVITY_TYPE.resolve("#Config"));
- String queryText = new XMLOutputter().outputString(new Document(martQuery));
- ((ObjectNode) configuration.getJson()).put("martQuery", queryText);
- return configuration;
- }
-
- @Override
- public Icon getIcon() {
- return BiomartActivityIcon.getBiomartIcon();
- }
-
- @Override
- public String getName() {
- return dataset;
- }
-
- @Override
- public List<? extends Comparable<?>> getPath() {
- List<String> result;
- result = Arrays.asList(BIOMART + url, location);
- return result;
- }
-
- @Override
- protected List<Object> getIdentifyingData() {
- return Arrays.<Object> asList(getUrl(), getLocation(), getDataset());
- }
-
- @Override
- public boolean isTemplateService() {
- return true;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceProvider.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceProvider.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceProvider.java
deleted file mode 100644
index 712e8d8..0000000
--- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceProvider.java
+++ /dev/null
@@ -1,147 +0,0 @@
-/**
- *
- */
-package net.sf.taverna.t2.activities.biomart.servicedescriptions;
-
-import java.net.URI;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-import javax.swing.Icon;
-
-import net.sf.taverna.t2.servicedescriptions.AbstractConfigurableServiceProvider;
-import net.sf.taverna.t2.servicedescriptions.ServiceDescription;
-import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
-
-import org.biomart.martservice.MartDataset;
-import org.biomart.martservice.MartQuery;
-import org.biomart.martservice.MartRegistry;
-import org.biomart.martservice.MartService;
-import org.biomart.martservice.MartServiceException;
-import org.biomart.martservice.MartServiceXMLHandler;
-import org.biomart.martservice.MartURLLocation;
-
-/**
- * @author alanrw
- * @author David Withers
- */
-public class BiomartServiceProvider extends AbstractConfigurableServiceProvider<BiomartServiceProviderConfig> {
-
- private static final String TAVERNA = "taverna";
- private static final String BIOMART_SERVICE = "Biomart service";
-
- private static final URI providerId = URI
- .create("http://taverna.sf.net/2010/service-provider/biomart");
-
- private ServiceDescriptionRegistry serviceDescriptionRegistry;
-
- public BiomartServiceProvider() {
- super(new BiomartServiceProviderConfig("http://somehost/biomart"));
- }
-
- public void findServiceDescriptionsAsync(
- FindServiceDescriptionsCallBack callBack) {
- List<ServiceDescription> descriptions = new ArrayList<ServiceDescription>();
- String url = serviceProviderConfig.getUrl();
- callBack.status("About to parse biomart:" + url);
- try {
- MartService martService = MartService
- .getMartService(getBiomartServiceLocation(url));
- martService.setRequestId(TAVERNA);
- MartRegistry registry = martService.getRegistry();
- MartURLLocation[] martURLLocations = registry.getMartURLLocations();
- for (MartURLLocation martURLLocation : martURLLocations) {
- if (martURLLocation.isVisible()) {
-
- MartDataset[] datasets = martService
- .getDatasets(martURLLocation);
- Arrays.sort(datasets, MartDataset.getDisplayComparator());
- for (MartDataset dataset : datasets) {
- if (dataset.isVisible()) {
- BiomartServiceDescription item = new BiomartServiceDescription();
- item.setUrl(martService.getLocation());
- item.setLocation(martURLLocation.getDisplayName());
- item.setDataset(dataset.getName());
- item.setDescription(dataset.getDisplayName());
- MartQuery biomartQuery = new MartQuery(martService,
- dataset, TAVERNA);
- item.setMartQuery(MartServiceXMLHandler.martQueryToElement(biomartQuery, null));
- descriptions.add(item);
- }
- }
- if (descriptions.size() > 0) {
- callBack.partialResults(descriptions);
- descriptions.clear();
- }
- }
- }
- callBack.finished();
- }
- catch (MartServiceException e) {
- callBack.fail("Failed to load Biomart from " + url, e);
- }
- }
-
- public Icon getIcon() {
- return BiomartActivityIcon.getBiomartIcon();
- }
-
- public String getName() {
- return BIOMART_SERVICE;
- }
-
- /**
- * Attempts to construct a valid MartService URL from the location given.
- *
- * @param biomartLocation
- * @return a (hopefully) valid MartService URL
- */
- private String getBiomartServiceLocation(String biomartLocation) {
- StringBuffer sb = new StringBuffer();
- if (biomartLocation.endsWith("martservice")) {
- sb.append(biomartLocation);
- } else if (biomartLocation.endsWith("martview")) {
- sb.append(biomartLocation.substring(0, biomartLocation
- .lastIndexOf("martview")));
- sb.append("martservice");
- } else if (biomartLocation.endsWith("/")) {
- sb.append(biomartLocation);
- sb.append("martservice");
- } else {
- sb.append(biomartLocation);
- sb.append("/martservice");
- }
- return sb.toString();
- }
-
- public List<BiomartServiceProviderConfig> getDefaultConfigurations() {
-
- List<BiomartServiceProviderConfig> defaults = new ArrayList<BiomartServiceProviderConfig>();
-
- // If defaults have failed to load from a configuration file then load them here.
- if (!serviceDescriptionRegistry.isDefaultSystemConfigurableProvidersLoaded()){
- defaults.add(new BiomartServiceProviderConfig(
- "http://www.biomart.org/biomart/martservice"));
- } // else return an empty list
-
- return defaults;
-
- }
-
- @Override
- protected List<? extends Object> getIdentifyingData() {
- List<String> result;
- result = Arrays.asList(getConfiguration().getUrl());
- return result;
- }
-
- public String getId() {
- return providerId.toString();
- }
-
- public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
- this.serviceDescriptionRegistry = serviceDescriptionRegistry;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceProviderConfig.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceProviderConfig.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceProviderConfig.java
deleted file mode 100644
index 9891fae..0000000
--- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceProviderConfig.java
+++ /dev/null
@@ -1,36 +0,0 @@
-/**
- *
- */
-package net.sf.taverna.t2.activities.biomart.servicedescriptions;
-
-import net.sf.taverna.t2.lang.beans.PropertyAnnotated;
-import net.sf.taverna.t2.lang.beans.PropertyAnnotation;
-
-/**
- * @author alanrw
- *
- */
-public class BiomartServiceProviderConfig extends PropertyAnnotated {
-
- private String url;
-
- public BiomartServiceProviderConfig() {
- }
-
- public BiomartServiceProviderConfig(String url) {
- this.url = url.trim();
- }
-
- @PropertyAnnotation(displayName = "Biomart location", preferred = true)
- public String getUrl() {
- return url;
- }
-
- public void setUrl(String url) {
- this.url = url.trim();
- }
-
- public String toString() {
- return getUrl();
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityContextualView.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityContextualView.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityContextualView.java
deleted file mode 100644
index 87a2294..0000000
--- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityContextualView.java
+++ /dev/null
@@ -1,117 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomart.views;
-
-import java.awt.Frame;
-import java.io.IOException;
-import java.io.StringReader;
-
-import javax.swing.Action;
-
-import net.sf.taverna.t2.activities.biomart.actions.BiomartActivityConfigurationAction;
-import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
-import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workbench.ui.actions.activity.HTMLBasedActivityContextualView;
-
-import org.biomart.martservice.MartQuery;
-import org.biomart.martservice.MartServiceXMLHandler;
-import org.biomart.martservice.query.Attribute;
-import org.biomart.martservice.query.Filter;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.input.SAXBuilder;
-
-import uk.org.taverna.commons.services.ServiceRegistry;
-import uk.org.taverna.configuration.app.ApplicationConfiguration;
-import uk.org.taverna.scufl2.api.activity.Activity;
-
-@SuppressWarnings("serial")
-public class BiomartActivityContextualView extends HTMLBasedActivityContextualView {
-
- private final EditManager editManager;
- private final FileManager fileManager;
- private final ActivityIconManager activityIconManager;
- private final ApplicationConfiguration applicationConfiguration;
- private final ServiceDescriptionRegistry serviceDescriptionRegistry;
- private final ServiceRegistry serviceRegistry;
-
- public BiomartActivityContextualView(Activity activity, EditManager editManager,
- FileManager fileManager, ActivityIconManager activityIconManager,
- ColourManager colourManager, ApplicationConfiguration applicationConfiguration,
- ServiceDescriptionRegistry serviceDescriptionRegistry, ServiceRegistry serviceRegistry) {
- super(activity, colourManager);
- this.editManager = editManager;
- this.fileManager = fileManager;
- this.activityIconManager = activityIconManager;
- this.applicationConfiguration = applicationConfiguration;
- this.serviceDescriptionRegistry = serviceDescriptionRegistry;
- this.serviceRegistry = serviceRegistry;
- }
-
- @Override
- protected String getRawTableRowsHtml() {
- String queryText = getConfigBean().getJson().get("martQuery").textValue();
- Element martQuery = null;
- try {
- martQuery = new SAXBuilder().build(new StringReader(queryText)).getRootElement();
- } catch (JDOMException | IOException e) {
- }
- MartQuery q = MartServiceXMLHandler.elementToMartQuery(martQuery, null);
- String html = "<tr><td>URL</td><td>" + q.getMartService().getLocation() + "</td></tr>";
- html += "<tr><td>Location</td><td>"
- + q.getMartDataset().getMartURLLocation().getDisplayName() + "</td></tr>";
- boolean firstFilter = true;
- for (Filter filter : q.getQuery().getFilters()) {
- html += firstFilter ? "<tr><td>Filter</td><td>" : "<tr><td></td></td>";
- firstFilter = false;
- html += filter.getName() + "</td></tr>";
- }
- boolean firstAttribute = true;
- for (Attribute attribute : q.getQuery().getAttributes()) {
- html += firstAttribute ? "<tr><td>Attribute</td><td>" : "<tr><td></td><td>";
- firstAttribute = false;
- html += attribute.getName() + "</td></tr>";
- }
- html += "<tr><td>Dataset</td><td>" + q.getMartDataset().getDisplayName() + "</td></tr>";
- return html;
- }
-
- @Override
- public String getViewTitle() {
- return "Biomart service";
- }
-
- @Override
- public Action getConfigureAction(Frame owner) {
- return new BiomartActivityConfigurationAction(getActivity(), owner, editManager,
- fileManager, activityIconManager, applicationConfiguration,
- serviceDescriptionRegistry, serviceRegistry);
- }
-
- @Override
- public int getPreferredPosition() {
- return 100;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityViewFactory.java
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diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityViewFactory.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityViewFactory.java
deleted file mode 100644
index ad8321a..0000000
--- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityViewFactory.java
+++ /dev/null
@@ -1,86 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomart.views;
-
-import java.util.Arrays;
-import java.util.List;
-
-import net.sf.taverna.t2.activities.biomart.servicedescriptions.BiomartServiceDescription;
-import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
-import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
-import uk.org.taverna.commons.services.ServiceRegistry;
-import uk.org.taverna.configuration.app.ApplicationConfiguration;
-import uk.org.taverna.scufl2.api.activity.Activity;
-
-public class BiomartActivityViewFactory implements ContextualViewFactory<Activity> {
-
- private EditManager editManager;
- private FileManager fileManager;
- private ActivityIconManager activityIconManager;
- private ColourManager colourManager;
- private ApplicationConfiguration applicationConfiguration;
- private ServiceDescriptionRegistry serviceDescriptionRegistry;
- private ServiceRegistry serviceRegistry;
-
- public boolean canHandle(Object object) {
- return object instanceof Activity && ((Activity) object).getType().equals(BiomartServiceDescription.ACTIVITY_TYPE);
- }
-
- public List<ContextualView> getViews(Activity activity) {
- return Arrays.asList(new ContextualView[] { new BiomartActivityContextualView(activity,
- editManager, fileManager, activityIconManager, colourManager,
- applicationConfiguration, serviceDescriptionRegistry, serviceRegistry) });
- }
-
- public void setEditManager(EditManager editManager) {
- this.editManager = editManager;
- }
-
- public void setFileManager(FileManager fileManager) {
- this.fileManager = fileManager;
- }
-
- public void setActivityIconManager(ActivityIconManager activityIconManager) {
- this.activityIconManager = activityIconManager;
- }
-
- public void setColourManager(ColourManager colourManager) {
- this.colourManager = colourManager;
- }
-
- public void setApplicationConfiguration(ApplicationConfiguration applicationConfiguration) {
- this.applicationConfiguration = applicationConfiguration;
- }
-
- public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
- this.serviceDescriptionRegistry = serviceDescriptionRegistry;
- }
-
- public void setServiceRegistry(ServiceRegistry serviceRegistry) {
- this.serviceRegistry = serviceRegistry;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider b/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
deleted file mode 100644
index 637d76a..0000000
--- a/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
+++ /dev/null
@@ -1 +0,0 @@
-net.sf.taverna.t2.activities.biomart.servicedescriptions.BiomartServiceProvider
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
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diff --git a/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent b/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
deleted file mode 100644
index dbff4b7..0000000
--- a/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
+++ /dev/null
@@ -1 +0,0 @@
-net.sf.taverna.t2.activities.biomart.menu.BiomartConfigurationMenuAction
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI b/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
deleted file mode 100644
index e8506ef..0000000
--- a/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
+++ /dev/null
@@ -1 +0,0 @@
-net.sf.taverna.t2.activities.biomart.servicedescriptions.BiomartActivityIcon
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
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diff --git a/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory b/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
deleted file mode 100644
index 355b9ef..0000000
--- a/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
+++ /dev/null
@@ -1 +0,0 @@
-net.sf.taverna.t2.activities.biomart.views.BiomartActivityViewFactory
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/main/resources/META-INF/spring/biomart-activity-ui-context-osgi.xml
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diff --git a/taverna-biomart-activity-ui/src/main/resources/META-INF/spring/biomart-activity-ui-context-osgi.xml b/taverna-biomart-activity-ui/src/main/resources/META-INF/spring/biomart-activity-ui-context-osgi.xml
deleted file mode 100644
index e5ea96b..0000000
--- a/taverna-biomart-activity-ui/src/main/resources/META-INF/spring/biomart-activity-ui-context-osgi.xml
+++ /dev/null
@@ -1,30 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:beans="http://www.springframework.org/schema/beans"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd
- http://www.springframework.org/schema/osgi
- http://www.springframework.org/schema/osgi/spring-osgi.xsd">
-
- <service ref="BiomartActivityIcon" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI" />
-
- <service ref="BiomartServiceProvider">
- <interfaces>
- <beans:value>net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider</beans:value>
- <beans:value>net.sf.taverna.t2.servicedescriptions.ConfigurableServiceProvider</beans:value>
- </interfaces>
- </service>
-
- <service ref="BiomartConfigurationMenuAction" auto-export="interfaces" />
-
- <service ref="BiomartActivityViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" />
-
- <reference id="editManager" interface="net.sf.taverna.t2.workbench.edits.EditManager" />
- <reference id="fileManager" interface="net.sf.taverna.t2.workbench.file.FileManager" />
- <reference id="activityIconManager" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconManager" />
- <reference id="colourManager" interface="net.sf.taverna.t2.workbench.configuration.colour.ColourManager" />
- <reference id="serviceDescriptionRegistry" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry"/>
- <reference id="applicationConfiguration" interface="uk.org.taverna.configuration.app.ApplicationConfiguration" />
- <reference id="serviceRegistry" interface="uk.org.taverna.commons.services.ServiceRegistry" />
-
-</beans:beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/main/resources/META-INF/spring/biomart-activity-ui-context.xml
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diff --git a/taverna-biomart-activity-ui/src/main/resources/META-INF/spring/biomart-activity-ui-context.xml b/taverna-biomart-activity-ui/src/main/resources/META-INF/spring/biomart-activity-ui-context.xml
deleted file mode 100644
index 21b43b2..0000000
--- a/taverna-biomart-activity-ui/src/main/resources/META-INF/spring/biomart-activity-ui-context.xml
+++ /dev/null
@@ -1,29 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd">
-
- <bean id="BiomartActivityIcon" class="net.sf.taverna.t2.activities.biomart.servicedescriptions.BiomartActivityIcon" />
-
- <bean id="BiomartServiceProvider" class="net.sf.taverna.t2.activities.biomart.servicedescriptions.BiomartServiceProvider">
- <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
- </bean>
-
- <bean id="BiomartConfigurationMenuAction" class="net.sf.taverna.t2.activities.biomart.menu.BiomartConfigurationMenuAction">
- <property name="editManager" ref="editManager" />
- <property name="fileManager" ref="fileManager" />
- <property name="activityIconManager" ref="activityIconManager" />
- <property name="applicationConfiguration" ref="applicationConfiguration" />
- <property name="serviceRegistry" ref="serviceRegistry" />
- </bean>
-
- <bean id="BiomartActivityViewFactory" class="net.sf.taverna.t2.activities.biomart.views.BiomartActivityViewFactory">
- <property name="editManager" ref="editManager" />
- <property name="fileManager" ref="fileManager" />
- <property name="activityIconManager" ref="activityIconManager" />
- <property name="colourManager" ref="colourManager" />
- <property name="applicationConfiguration" ref="applicationConfiguration" />
- <property name="serviceRegistry" ref="serviceRegistry" />
- </bean>
-
-</beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/main/resources/biomart.png
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diff --git a/taverna-biomart-activity-ui/src/main/resources/biomart.png b/taverna-biomart-activity-ui/src/main/resources/biomart.png
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index a969908..0000000
Binary files a/taverna-biomart-activity-ui/src/main/resources/biomart.png and /dev/null differ
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/test/java/net/sf/taverna/t2/biomart/views/TestBiomartActivityContextualView.java
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diff --git a/taverna-biomart-activity-ui/src/test/java/net/sf/taverna/t2/biomart/views/TestBiomartActivityContextualView.java b/taverna-biomart-activity-ui/src/test/java/net/sf/taverna/t2/biomart/views/TestBiomartActivityContextualView.java
deleted file mode 100644
index 04ad076..0000000
--- a/taverna-biomart-activity-ui/src/test/java/net/sf/taverna/t2/biomart/views/TestBiomartActivityContextualView.java
+++ /dev/null
@@ -1,94 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.biomart.views;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.URI;
-
-import net.sf.taverna.t2.activities.biomart.actions.BiomartActivityConfigurationAction;
-import net.sf.taverna.t2.activities.biomart.views.BiomartActivityContextualView;
-
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.input.SAXBuilder;
-import org.jdom.output.XMLOutputter;
-import org.junit.Before;
-import org.junit.Ignore;
-import org.junit.Test;
-
-import uk.org.taverna.scufl2.api.activity.Activity;
-import uk.org.taverna.scufl2.api.configurations.Configuration;
-import uk.org.taverna.scufl2.api.profiles.Profile;
-
-import com.fasterxml.jackson.databind.node.ObjectNode;
-
-public class TestBiomartActivityContextualView {
- Activity activity;
-
- @Before
- public void setup() throws Exception {
- activity = new Activity();
- activity.setParent(new Profile());
-
- Element el = getQueryElement("biomart-query.xml");
-
- Configuration configuration = new Configuration();
- configuration.setType(URI.create("http://ns.taverna.org.uk/2010/activity/biomart").resolve("#Config"));
- String queryText = new XMLOutputter().outputString(new Document(el));
- ((ObjectNode) configuration.getJson()).put("martQuery", queryText);
-
- configuration.setConfigures(activity);
- }
-
- @Test @Ignore
- public void testConfigurationAction() throws Exception {
- BiomartActivityContextualView view = new BiomartActivityContextualView(activity, null, null, null, null, null, null, null);
- assertNotNull("The view should provide a configuration action",view.getConfigureAction(null));
- assertTrue("The configuration action should be an instance of BiomartActivityConfigurationAction",view.getConfigureAction(null) instanceof BiomartActivityConfigurationAction);
- }
-
- private Element getQueryElement(String resourceName) throws Exception {
- InputStream inStream = TestBiomartActivityContextualView.class
- .getResourceAsStream("/"+resourceName);
-
- if (inStream == null)
- throw new IOException(
- "Unable to find resource for:"
- + resourceName);
- SAXBuilder builder = new SAXBuilder();
- return builder.build(inStream).detachRootElement();
- }
-
- private void run() throws Exception {
- setup();
- BiomartActivityContextualView view = new BiomartActivityContextualView(activity, null, null, null, null, null, null, null);
- view.setVisible(true);
- }
-
- public static void main(String[] args) throws Exception {
- new TestBiomartActivityContextualView().run();
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/test/resources/biomart-query.xml
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diff --git a/taverna-biomart-activity-ui/src/test/resources/biomart-query.xml b/taverna-biomart-activity-ui/src/test/resources/biomart-query.xml
deleted file mode 100644
index 0e52a23..0000000
--- a/taverna-biomart-activity-ui/src/test/resources/biomart-query.xml
+++ /dev/null
@@ -1,24 +0,0 @@
-<biomart:MartQuery
- xmlns:biomart="http://org.embl.ebi.escience/xscufl-biomart/0.1alpha">
- <biomart:MartService
- location="http://www.biomart.org/biomart/martservice" />
- <biomart:MartDataset displayName="Homo sapiens genes (NCBI36)"
- name="hsapiens_gene_ensembl" type="TableSet" initialBatchSize="10"
- maximumBatchSize="50000" visible="false" interface="default"
- modified="2006-11-27 12:49:27">
- <biomart:MartURLLocation database="ensembl_mart_41" default="1"
- displayName="ENSEMBL 41 (SANGER)" host="www.biomart.org"
- includeDatasets="" martUser="" name="ensembl"
- path="/biomart/martservice" port="80" serverVirtualSchema="default"
- virtualSchema="default" visible="1" />
- </biomart:MartDataset>
- <biomart:Query virtualSchemaName="default" count="0" uniqueRows="0"
- softwareVersion="0.5" requestId="taverna">
- <biomart:Dataset name="hsapiens_gene_ensembl">
- <biomart:Attribute name="coding_gene_flank" />
- <biomart:Attribute name="gene_stable_id" />
- <biomart:Filter name="ensembl_gene_id" value="" list="true" />
- <biomart:Filter name="upstream_flank" value="100" />
- </biomart:Dataset>
- </biomart:Query>
-</biomart:MartQuery>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity/pom.xml b/taverna-biomart-activity/pom.xml
deleted file mode 100644
index 2662e59..0000000
--- a/taverna-biomart-activity/pom.xml
+++ /dev/null
@@ -1,77 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<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>
- <version>2.0.1-SNAPSHOT</version>
- <artifactId>biomart-activity</artifactId>
- <packaging>bundle</packaging>
- <name>Taverna 2 Biomart Activity.</name>
- <dependencies>
- <dependency>
- <groupId>org.biomart</groupId>
- <artifactId>martservice</artifactId>
- <version>2.0.1-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>workflowmodel-api</artifactId>
- <version>${t2.core.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>reference-api</artifactId>
- <version>${t2.core.version}</version>
- </dependency>
- <dependency>
- <groupId>com.fasterxml.jackson.core</groupId>
- <artifactId>jackson-databind</artifactId>
- <version>${jackson-databind.version}</version>
- </dependency>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>${junit.version}</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>activity-test-utils</artifactId>
- <version>${t2.activities.version}</version>
- <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-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>
-