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 ---------------------------------------------------------------------- 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 ---------------------------------------------------------------------- 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 ---------------------------------------------------------------------- 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 ---------------------------------------------------------------------- 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 ---------------------------------------------------------------------- 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 ---------------------------------------------------------------------- diff --git a/taverna-biomart-activity-ui/src/main/resources/biomart.png b/taverna-biomart-activity-ui/src/main/resources/biomart.png deleted file mode 100644 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 ---------------------------------------------------------------------- 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 ---------------------------------------------------------------------- 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://g...@github.com/taverna/taverna-biomart-activity.git</developerConnection> - <url>https://github.com/taverna/taverna-biomart-activity/</url> - <tag>HEAD</tag> - </scm> -</project> -
