taverna-biomart-martservice/
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/9e08cac0 Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/tree/9e08cac0 Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/diff/9e08cac0 Branch: refs/heads/master Commit: 9e08cac01487f85a399c6534b1a0b1f93f729b8a Parents: 0de1f90 Author: Stian Soiland-Reyes <st...@apache.org> Authored: Mon Feb 2 09:50:17 2015 +0000 Committer: Stian Soiland-Reyes <st...@apache.org> Committed: Mon Feb 2 09:55:09 2015 +0000 ---------------------------------------------------------------------- .gitignore | 24 - .travis.yml | 1 - README.md | 3 - 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-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 0 -> 90 bytes .../biomart/martservice/config/ui/expand.gif | Bin 0 -> 93 bytes .../martservice/config/ui/gene_schematic.gif | Bin 0 -> 734 bytes .../config/ui/gene_schematic_3utr.gif | Bin 0 -> 717 bytes .../config/ui/gene_schematic_5utr.gif | Bin 0 -> 722 bytes .../config/ui/gene_schematic_cdna.gif | Bin 0 -> 743 bytes .../config/ui/gene_schematic_coding.gif | Bin 0 -> 760 bytes .../ui/gene_schematic_coding_gene_flank.gif | Bin 0 -> 715 bytes .../gene_schematic_coding_transcript_flank.gif | Bin 0 -> 765 bytes .../config/ui/gene_schematic_gene_exon.gif | Bin 0 -> 504 bytes .../ui/gene_schematic_gene_exon_intron.gif | Bin 0 -> 710 bytes .../config/ui/gene_schematic_gene_flank.gif | Bin 0 -> 710 bytes .../config/ui/gene_schematic_peptide.gif | Bin 0 -> 760 bytes .../ui/gene_schematic_transcript_exon.gif | Bin 0 -> 920 bytes .../gene_schematic_transcript_exon_intron.gif | Bin 0 -> 716 bytes .../ui/gene_schematic_transcript_flank.gif | Bin 0 -> 751 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 ++ 119 files changed, 13954 insertions(+), 13982 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/9e08cac0/.gitignore ---------------------------------------------------------------------- diff --git a/.gitignore b/.gitignore deleted file mode 100644 index ebe0e5b..0000000 --- a/.gitignore +++ /dev/null @@ -1,24 +0,0 @@ -# ignore project files # -.classpath -.project -.settings/ -catalog-v001.xml - -# ignore target files # -target/ -bin/ -build/ -dist/ -apidoc/ -*.swp - -# ignore svn files if there -.svn - -# ignore log files # -*.log -/logs/* -*/logs/* - - - http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/9e08cac0/.travis.yml ---------------------------------------------------------------------- diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index dff5f3a..0000000 --- a/.travis.yml +++ /dev/null @@ -1 +0,0 @@ -language: java http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/9e08cac0/README.md ---------------------------------------------------------------------- diff --git a/README.md b/README.md deleted file mode 100644 index 801cc7d..0000000 --- a/README.md +++ /dev/null @@ -1,3 +0,0 @@ -Biomart webservice API - -This code was previously hosted at http://taverna.googlecode.com/svn/taverna/utils/org.biomart.martservice/ \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/9e08cac0/pom.xml ---------------------------------------------------------------------- diff --git a/pom.xml b/pom.xml deleted file mode 100644 index 582a601..0000000 --- a/pom.xml +++ /dev/null @@ -1,105 +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>org.biomart</groupId> - <artifactId>martservice</artifactId> - <packaging>bundle</packaging> - <name>MartService</name> - <version>2.0.1-SNAPSHOT</version> - <description>Biomart webservice API</description> - - <build> - <plugins> - <plugin> - <groupId>org.apache.felix</groupId> - <artifactId>maven-bundle-plugin</artifactId> - <version>2.3.7</version> - <extensions>true</extensions> - <configuration> - <instructions> - <Private-Package>org.ensembl.mart.lib,org.ensembl.mart.lib.config,org.ensembl.mart.util</Private-Package> - <Import-Package>!org.ensembl.util,!org.ensembl.mart.editor,!oracle.sql,!gnu.getopt,!org.ewin.*,*</Import-Package> - </instructions> - </configuration> - </plugin> - </plugins> - </build> - - <dependencies> - <dependency> - <groupId>org.biomart</groupId> - <artifactId>martj</artifactId> - <version>0.6</version> - <scope>provided</scope> - </dependency> - <dependency> - <groupId>org.jdom</groupId> - <artifactId>com.springsource.org.jdom</artifactId> - <version>1.1.0</version> - </dependency> - <dependency> - <groupId>org.apache.commons</groupId> - <artifactId>com.springsource.org.apache.commons.httpclient</artifactId> - <version>3.1.0</version> - </dependency> - <dependency> - <groupId>org.apache.commons</groupId> - <artifactId>com.springsource.org.apache.commons.io</artifactId> - <version>1.4.0</version> - </dependency> - <dependency> - <groupId>org.apache.log4j</groupId> - <artifactId>com.springsource.org.apache.log4j</artifactId> - <version>${log4j.version}</version> - </dependency> - <dependency> - <groupId>junit</groupId> - <artifactId>junit</artifactId> - <version>${junit.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> - <repository> - <id>com.springsource.repository.bundles.release</id> - <name>SpringSource Enterprise Bundle Repository - SpringSource Bundle Releases</name> - <url>http://repository.springsource.com/maven/bundles/release</url> - </repository> - <repository> - <id>com.springsource.repository.bundles.external</id> - <name>SpringSource Enterprise Bundle Repository - External Bundle Releases</name> - <url>http://repository.springsource.com/maven/bundles/external</url> - </repository> - </repositories> - <scm> - <connection>scm:git:https://github.com/taverna/taverna-biomart-martservice.git</connection> - <developerConnection>scm:git:ssh://g...@github.com:taverna/taverna-biomart-martservice.git</developerConnection> - <url>https://github.com/taverna/taverna-biomart-martservice/</url> - <tag>HEAD</tag> - </scm> -</project> http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/9e08cac0/src/main/java/org/biomart/martservice/DatasetLink.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/biomart/martservice/DatasetLink.java b/src/main/java/org/biomart/martservice/DatasetLink.java deleted file mode 100644 index e5dccd4..0000000 --- a/src/main/java/org/biomart/martservice/DatasetLink.java +++ /dev/null @@ -1,220 +0,0 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * 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 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: DatasetLink.java,v $ - * Revision $Revision: 1.2 $ - * Release status $State: Exp $ - * Last modified on $Date: 2007/12/13 11:38:55 $ - * by $Author: davidwithers $ - * Created on 12-Apr-2006 - *****************************************************************/ -package org.biomart.martservice; - -import java.util.Comparator; -import java.util.HashSet; -import java.util.Set; - -/** - * The link between two MartDatasets and the list of possible the link IDs that - * could join the source and target MartDataset. - * - * @author David Withers - */ -public class DatasetLink { - private static final Comparator<DatasetLink> displayComparator = new DatasetLinkComparator(); - - private MartDataset sourceDataset; - - private MartDataset targetDataset; - - private Set<String> links = new HashSet<String>(); - - /** - * Constructs an instance of an <code>DatasetLink</code> with the - * specified source and target. - * - * @param sourceDataset - * the link source - * @param targetDataset - * the link target - */ - public DatasetLink(MartDataset sourceDataset, MartDataset targetDataset) { - this.sourceDataset = sourceDataset; - this.targetDataset = targetDataset; - } - - /** - * Returns the source Dataset. - * - * @return the source Dataset - */ - public MartDataset getSourceDataset() { - return sourceDataset; - } - - /** - * Sets the source Dataset. - * - * @param sourceDataset - * the sourceDataset to set - */ - public void setSourceDataset(MartDataset sourceDataset) { - this.sourceDataset = sourceDataset; - } - - /** - * Returns the target Dataset. - * - * @return the target Dataset - */ - public MartDataset getTargetDataset() { - return targetDataset; - } - - /** - * Sets the target Dataset. - * - * @param targetDataset - * the target Dataset to set - */ - public void setTargetDataset(MartDataset targetDataset) { - this.targetDataset = targetDataset; - } - - /** - * Returns the link IDs that could join the source and target MartDatasets. - * - * @return the link IDs that could join the source and target MartDatasets - */ - public String[] getLinks() { - return links.toArray(new String[links.size()]); - } - - /** - * Adds a link ID. - * - * @param link - * the link ID to add. - */ - public void addLink(String link) { - links.add(link); - } - - /** - * Returns true if this DatasetLink has link IDs. - * - * @return true if this DatasetLink has link IDs - */ - public boolean hasLinks() { - return !links.isEmpty(); - } - - public String toString() { - return "[" + sourceDataset.getMartURLLocation().getDisplayName() + "] " - + sourceDataset.getDisplayName(); - } - - /* (non-Javadoc) - * @see java.lang.Object#hashCode() - */ - public int hashCode() { - final int PRIME = 31; - int result = 1; - result = PRIME * result + ((sourceDataset == null) ? 0 : sourceDataset.hashCode()); - result = PRIME * result + ((targetDataset == null) ? 0 : targetDataset.hashCode()); - return result; - } - - /* (non-Javadoc) - * @see java.lang.Object#equals(java.lang.Object) - */ - public boolean equals(Object obj) { - if (this == obj) - return true; - if (obj == null) - return false; - if (getClass() != obj.getClass()) - return false; - final DatasetLink other = (DatasetLink) obj; - if (sourceDataset == null) { - if (other.sourceDataset != null) - return false; - } else if (!sourceDataset.equals(other.sourceDataset)) - return false; - if (targetDataset == null) { - if (other.targetDataset != null) - return false; - } else if (!targetDataset.equals(other.targetDataset)) - return false; - return true; - } - - /** - * Returns a Comparator that compares DatasetLinks based on the display name - * of the source dataset and the display name of the MartURLLocation - * containing the source dataset. - * - * @return the display comparator - */ - public static Comparator<DatasetLink> getDisplayComparator() { - return displayComparator; - } - -} - -/** - * Comparator that compares DatasetLinks based on the display name of the source - * MartDataset and the display name of the MartURLLocation containing the source - * MartDataset. - * - * @author David Withers - */ -class DatasetLinkComparator implements Comparator<DatasetLink> { - - /** - * Compares two DatasetLinks based on the display name of the source dataset - * and the display name of the MartURLLocation containing the source - * dataset. - * - * @param o1 - * the first DatasetLink to be compared - * @param o2 - * the second DatasetLink to be compared - * @return a negative integer, zero, or a positive integer as the first - * argument is less than, equal to, or greater than the second - */ - public int compare(DatasetLink o1, DatasetLink o2) { - MartDataset ds1 = o1.getSourceDataset(); - MartDataset ds2 = o2.getSourceDataset(); - int result = ds1.getDisplayName().compareTo(ds2.getDisplayName()); - if (result == 0) { - result = ds1.getMartURLLocation().getDisplayName().compareTo( - ds2.getMartURLLocation().getDisplayName()); - } - return result; - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/9e08cac0/src/main/java/org/biomart/martservice/MartDataset.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/biomart/martservice/MartDataset.java b/src/main/java/org/biomart/martservice/MartDataset.java deleted file mode 100644 index 8c0f584..0000000 --- a/src/main/java/org/biomart/martservice/MartDataset.java +++ /dev/null @@ -1,342 +0,0 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * 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 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: MartDataset.java,v $ - * Revision $Revision: 1.2 $ - * Release status $State: Exp $ - * Last modified on $Date: 2007/10/04 14:17:19 $ - * by $Author: davidwithers $ - * Created on 17-Mar-2006 - *****************************************************************/ -package org.biomart.martservice; - -import java.util.Comparator; - -/** - * The dataset returned by a BioMart web service. - * - * @author David Withers - */ -public class MartDataset { - private static final Comparator<MartDataset> displayComparator = new MartDatasetComparator(); - - private String type; - - private String name; - - private String displayName; - - private boolean visible; - - private long initialBatchSize; - - private long maximumBatchSize; - - private String interfaceValue; - - private String modified; - - private MartURLLocation martURLLocation; - - /** - * Returns the displayName. - * - * @return the displayName. - */ - public String getDisplayName() { - return displayName; - } - - /** - * Sets the displayName. - * - * @param displayName - * the displayName to set. - */ - public void setDisplayName(String displayName) { - this.displayName = displayName; - } - - /** - * Returns the initialBatchSize. - * - * @return the initialBatchSize. - */ - public long getInitialBatchSize() { - return initialBatchSize; - } - - /** - * Sets the initialBatchSize. - * - * @param initialBatchSize - * the initialBatchSize to set. - */ - public void setInitialBatchSize(long initialBatchSize) { - this.initialBatchSize = initialBatchSize; - } - - /** - * Returns the maximumBatchSize. - * - * @return the maximumBatchSize. - */ - public long getMaximumBatchSize() { - return maximumBatchSize; - } - - /** - * Sets the maximumBatchSize. - * - * @param maximumBatchSize - * the maximumBatchSize to set. - */ - public void setMaximumBatchSize(long maximumBatchSize) { - this.maximumBatchSize = maximumBatchSize; - } - - /** - * Returns the name. - * - * @return the name. - */ - public String getName() { - return name; - } - - /** - * Sets the name. - * - * @param name - * the name to set. - */ - public void setName(String name) { - this.name = name; - } - - /** - * Returns the type. - * - * @return the type. - */ - public String getType() { - return type; - } - - /** - * Sets the type. - * - * @param type - * the type to set. - */ - public void setType(String type) { - this.type = type; - } - - /** - * Returns the visible flag. - * - * @return the visible flag - */ - public boolean isVisible() { - return visible; - } - - /** - * Sets the visible flag. - * - * @param visible - * the visible flag - */ - public void setVisible(boolean visible) { - this.visible = visible; - } - - /** - * Returns the modified date. - * - * @return the modified date - */ - public String getModified() { - return modified; - } - - /** - * Sets the modified date. - * - * @param modified the new modified date - */ - public void setModified(String modified) { - this.modified = modified; - } - - /** - * Returns the interface. - * - * @return the interface - */ - public String getInterface() { - return interfaceValue; - } - - /** - * Sets the interface. - * - * @param interfaceValue the new interface - */ - public void setInterface(String interfaceValue) { - this.interfaceValue = interfaceValue; - } - - /** - * Returns the martURLLocation. - * - * @return the martURLLocation - */ - public MartURLLocation getMartURLLocation() { - return martURLLocation; - } - - /** - * Sets the martURLLocation. - * - * @param martURLLocation - * the martURLLocation to set. - */ - public void setMartURLLocation(MartURLLocation martURLLocation) { - this.martURLLocation = martURLLocation; - } - - /** - * Returns the virtualSchema of the martURLLocation. If the martURLLocation - * is null, null is returned. - * - * @return the virtualSchema of the martURLLocation - */ - public String getVirtualSchema() { - MartURLLocation martURLLocation = getMartURLLocation(); - if (martURLLocation != null) { - return martURLLocation.getVirtualSchema(); - } else { - return null; - } - } - - /** - * Returns the qualified name of this dataset in the format - * 'virtualSchemaName.datasetName'. If there is no virtualSchema the - * datasetName is returned. - * - * @return the qualified name of this dataset - */ - public String getQualifiedName() { - String schema = getVirtualSchema(); - if (schema != null) { - return schema + "." + getName(); - } else { - return getName(); - } - } - - /** - * Returns the display name. - * - * @return the display name - */ - public String toString() { - return getDisplayName(); - } - - /* - * (non-Javadoc) - * - * @see java.lang.Object#hashCode() - */ - public int hashCode() { - final int PRIME = 31; - int result = 1; - result = PRIME - * result - + ((getQualifiedName() == null) ? 0 : getQualifiedName() - .hashCode()); - return result; - } - - /** - * Tests equality based on the qualified name. - * - * @return true if the objects are equal based on the qualified name - */ - public boolean equals(Object obj) { - if (this == obj) - return true; - if (obj == null) - return false; - if (getClass() != obj.getClass()) - return false; - final MartDataset other = (MartDataset) obj; - if (getQualifiedName() == null) { - if (other.getQualifiedName() != null) - return false; - } else if (!getQualifiedName().equals(other.getQualifiedName())) - return false; - return true; - } - - /** - * Returns a Comparator that compares MartDatasets based on their display - * names. - * - * @return the display comparator - */ - public static Comparator<MartDataset> getDisplayComparator() { - return displayComparator; - } - -} - -/** - * Comparator that compares MartDatasets based on their display names. - * - * @author David Withers - */ -class MartDatasetComparator implements Comparator<MartDataset> { - - /** - * Compares two MartDatasets based on their display names. - * - * @param martDataset1 - * the first MartDataset to be compared - * @param martDataset2 - * the second MartDataset to be compared - * @return a negative integer, zero, or a positive integer as the first - * argument is less than, equal to, or greater than the second - */ - public int compare(MartDataset martDataset1, MartDataset martDataset2) { - return martDataset1.getDisplayName().compareTo(martDataset2.getDisplayName()); - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/9e08cac0/src/main/java/org/biomart/martservice/MartQuery.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/biomart/martservice/MartQuery.java b/src/main/java/org/biomart/martservice/MartQuery.java deleted file mode 100644 index 9f75566..0000000 --- a/src/main/java/org/biomart/martservice/MartQuery.java +++ /dev/null @@ -1,436 +0,0 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * 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 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: MartQuery.java,v $ - * Revision $Revision: 1.2 $ - * Release status $State: Exp $ - * Last modified on $Date: 2007/12/13 11:38:55 $ - * by $Author: davidwithers $ - * Created on 08-May-2006 - *****************************************************************/ -package org.biomart.martservice; - -import java.util.ArrayList; -import java.util.HashMap; -import java.util.Iterator; -import java.util.List; -import java.util.Map; -import java.util.Set; - -import org.biomart.martservice.query.Attribute; -import org.biomart.martservice.query.Dataset; -import org.biomart.martservice.query.Filter; -import org.biomart.martservice.query.Link; -import org.biomart.martservice.query.Query; -import org.ensembl.mart.lib.config.AttributeDescription; -import org.ensembl.mart.lib.config.DatasetConfig; - -/** - * Class for creating queries to send to a BioMart web service. - * - * @author David Withers - */ -public class MartQuery { - private MartService martService; - - private MartDataset martDataset; - - private Query query; - - private Map<String, String> linkedDatasets = new HashMap<String, String>(); - - private String softwareVersion; - - public MartQuery() { - - } - - public MartQuery(MartService martService, MartDataset martDataset, String requestId) { - String version = null; - try { - version = martService.getVersion(martDataset.getMartURLLocation()); - } catch (MartServiceException e) { - //assume it's a pre 0.5 mart service - } - setMartService(martService); - setMartDataset(martDataset); - if (version == null || version.equals("0.4")) { - setQuery(new Query(martDataset.getVirtualSchema(), null, requestId)); - } else { - setQuery(new Query(martDataset.getVirtualSchema(), version, requestId)); - } - } - - /** - * @param martService - * @param martDataset - * @param query - */ - public MartQuery(MartService martService, MartDataset martDataset, - Query query) { - setMartService(martService); - setMartDataset(martDataset); - setQuery(query); - } - - /** - * Returns the martDataset. - * - * @return the martDataset. - */ - public MartDataset getMartDataset() { - return martDataset; - } - - /** - * Sets the martDataset. - * - * @param martDataset - * the martDataset to set. - */ - public void setMartDataset(MartDataset martDataset) { - this.martDataset = martDataset; - } - - /** - * Returns the martService. - * - * @return the martService. - */ - public MartService getMartService() { - return martService; - } - - /** - * Sets the martService. - * - * @param martService - * the martService to set. - */ - public void setMartService(MartService martService) { - this.martService = martService; - } - - /** - * Returns the query. - * - * @return the query. - */ - public Query getQuery() { - return query; - } - - /** - * Sets the query. - * - * @param query - * the query to set. - */ - public void setQuery(Query query) { - this.query = query; - softwareVersion = query.getSoftwareVersion(); - } - - /** - * Adds the ID that links the specified dataset to the initial dataset. - * - * @param datasetName - * the dataset - * @param linkId - * the link ID - */ - public void addLinkedDataset(String datasetName, String linkId) { - linkedDatasets.put(datasetName, linkId); - } - - /** - * Removes a dataset and any datasets linked to it. - * - * @param datasetName - * the dataset to remove - */ - public void removeLinkedDataset(String datasetName) { - linkedDatasets.remove(datasetName); - if (query.containsDataset(datasetName)) { - Dataset dataset = query.getDataset(datasetName); - dataset.removeAllAttributes(); - dataset.removeAllFilters(); - query.removeDataset(dataset); - for (Link link : query.getLinks(datasetName)) { - removeLinkedDataset(link.getTarget()); - } - - } - if (query.containsLink(datasetName)) { - query.removeLink(query.getLink(datasetName)); - } - } - - /** - * Changes the ID that links a dataset. This method performs no function, - * nor does it throw an exception, if the specified dataset does not exist. - * - * @param datasetName - * the dataset - * @param linkId - * the link ID - */ - public void changeLinkedDataset(String datasetName, String linkId) { - if (linkedDatasets.containsKey(datasetName)) { - linkedDatasets.put(datasetName, linkId); - if (query.containsLink(datasetName)) { - query.getLink(datasetName).setDefaultLink(linkId); - } - } - } - - public Set<String> getLinkedDatasets() { - return linkedDatasets.keySet(); - } - - public String getLink(String datasetName) { - return (String) linkedDatasets.get(datasetName); - } - - /** - * Returns the Datasets that this Query contains in the order specified by - * the links. - * - * @return the Datasets that this Query contains in the order specified by - * the links - */ - public List<Dataset> getDatasetsInLinkOrder() { - if (query.getLinks().size() > 0) { - List<Dataset> datasets = new ArrayList<Dataset>(); - datasets.addAll(getLinkedDatasets(martDataset.getName())); - // add other datasets - for (Dataset dataset : query.getDatasets()) { - if (!datasets.contains(dataset)) { - datasets.add(dataset); - } - } - return datasets; - } else { - return query.getDatasets(); - } - } - - /** - * @param dataset - * @return - */ - private List<Dataset> getLinkedDatasets(String dataset) { - List<Dataset> datasets = new ArrayList<Dataset>(); - datasets.add(query.getDataset(dataset)); - if (query.containsLink(dataset)) { - Link link = query.getLink(dataset); - if (!link.getTarget().equals(martDataset.getName())) { - datasets.addAll(getLinkedDatasets(link.getTarget())); - } - } - return datasets; - } - - /** - * Returns all the Attributes from all the Datasets in this Query in the - * order specified by the links. - * - * @return all the Attributes from all the Datasets in this Query in the - * order specified by the links - */ - public List<Attribute> getAttributesInLinkOrder() { - List<Attribute> attributes = new ArrayList<Attribute>(); - List<Dataset> datasets; - if (softwareVersion == null) { - datasets = getDatasetsInLinkOrder(); - } else { - datasets = query.getDatasets(); - } - for (Dataset dataset : datasets) { - attributes.addAll(dataset.getAttributes()); - } - return attributes; - } - - /** - * Adds an Attribute to the Dataset with the given datasetName. If the Query - * has no Dataset with the given datasetName then a new Dataset is created. - * - * @param datasetName - * the name of the Dataset to add the Attribute to - * @param attribute - * the Attribute to add - * @throws MartServiceException - */ - public void addAttribute(String datasetName, Attribute attribute) { - if (!query.containsDataset(datasetName)) { - Dataset dataset = new Dataset(datasetName); - if (datasetName.equals(martDataset.getName())) { - query.addDataset(0, dataset); - } else { - query.addDataset(dataset); - } - } - Dataset dataset = query.getDataset(datasetName); - dataset.addAttribute(attribute); - } - - /** - * Removes an Attribute from its containing Dataset. - * - * @param attribute - */ - public void removeAttribute(Attribute attribute) { - Dataset dataset = attribute.getContainingDataset(); - if (dataset != null) { - if (dataset.removeAttribute(attribute)) { - if (!dataset.hasAttributes() && !dataset.hasFilters()) { - Query query = dataset.getContainingQuery(); - if (query != null) { - query.removeDataset(dataset); - } - } - } - } - } - - /** - * Adds a Filter to the Dataset with the given datasetName. If the Query has - * no Dataset with the given datasetName then a new Dataset is created. - * - * @param datasetName - * the name of the Dataset to add the Filter to - * @param filter - * the Filter to add - * @throws MartServiceException - */ - public void addFilter(String datasetName, Filter filter) { - if (!query.containsDataset(datasetName)) { - Dataset dataset = new Dataset(datasetName); - if (datasetName.equals(martDataset.getName())) { - query.addDataset(0, dataset); - } else { - query.addDataset(dataset); - } - } - Dataset dataset = query.getDataset(datasetName); - dataset.addFilter(filter); - } - - /** - * Removes a Filter from its containing Dataset. - * - * @param filter - */ - public void removeFilter(Filter filter) { - Dataset dataset = filter.getContainingDataset(); - if (dataset != null) { - if (dataset.removeFilter(filter)) { - if (!dataset.hasAttributes() && !dataset.hasFilters()) { - Query query = dataset.getContainingQuery(); - if (query != null) { - query.removeDataset(dataset); - } - } - } - } - } - - /** - * @throws MartServiceException - */ - public void calculateLinks() throws MartServiceException { - if (softwareVersion == null) { - if (!martService.linksCalculated()) { - martService.calculateLinks(); - } - for (Link link : query.getLinks()) { - query.removeLink(link); - } - for (Dataset dataset : query.getDatasets()) { - if (!martDataset.getName().equals(dataset.getName())) { - addLinks(dataset.getName()); - } - } - } - } - - /** - * @param source - * @throws MartServiceException - */ - public void addLinks(String source) throws MartServiceException { - MartDataset sourceDataset = martService.getDataset(martDataset - .getVirtualSchema(), source); - MartDataset targetDataset = martDataset; - List<MartDataset> path = martService.getPath(sourceDataset, targetDataset); - if (path == null) { - path = martService.getPath(targetDataset, sourceDataset); - } - if (path == null) { - throw new MartServiceException("No link between " + source - + " and " + targetDataset.getName()); - } - Iterator<MartDataset> iter = path.iterator(); - if (iter.hasNext()) { - MartDataset lastDataset = (MartDataset) iter.next(); - while (iter.hasNext()) { - MartDataset dataset = (MartDataset) iter.next(); - DatasetLink link = martService.getLinkBetween(lastDataset, - dataset); - String linkId = link.getLinks()[0]; - if (link.getLinks().length > 1) { - if (getLink(source) != null) { - linkId = getLink(source); - } else { - List<Attribute> attributes = query.getDataset(source) - .getAttributes(); - if (attributes.size() > 0) { - Attribute attribute = (Attribute) attributes.get(0); - DatasetConfig config = martService - .getDatasetConfig(sourceDataset); - if (config.containsAttributeDescription(attribute - .getName())) { - AttributeDescription description = config - .getAttributeDescriptionByInternalName(attribute - .getName()); - String datasetLink = description - .getDatasetLink(); - if (datasetLink != null) { - linkId = datasetLink; - } - } - } - } - } - query.addLink(new Link(lastDataset.getName(), - dataset.getName(), linkId)); - lastDataset = dataset; - } - } - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/9e08cac0/src/main/java/org/biomart/martservice/MartRegistry.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/biomart/martservice/MartRegistry.java b/src/main/java/org/biomart/martservice/MartRegistry.java deleted file mode 100644 index 93bf04d..0000000 --- a/src/main/java/org/biomart/martservice/MartRegistry.java +++ /dev/null @@ -1,96 +0,0 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * 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 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: MartRegistry.java,v $ - * Revision $Revision: 1.2 $ - * Release status $State: Exp $ - * Last modified on $Date: 2007/12/13 11:38:55 $ - * by $Author: davidwithers $ - * Created on 17-Mar-2006 - *****************************************************************/ -package org.biomart.martservice; - -import java.util.ArrayList; -import java.util.List; - -/** - * The MartRegistry returned by a BioMart web service. - * - * @author David Withers - */ -public class MartRegistry { - private List<MartURLLocation> martURLLocations = new ArrayList<MartURLLocation>(); - - /** - * Returns the martURLLocations. - * - * @return the martURLLocations. - */ - public MartURLLocation[] getMartURLLocations() { - return martURLLocations - .toArray(new MartURLLocation[martURLLocations.size()]); - } - - /** - * Adds a martURLLocation to the registry. - * - * @param martURLLocations - * the martURLLocations to add. - */ - public void addMartURLLocation(MartURLLocation martURLLocation) { - martURLLocations.add(martURLLocation); - } - - /* (non-Javadoc) - * @see java.lang.Object#hashCode() - */ - public int hashCode() { - final int PRIME = 31; - int result = 1; - result = PRIME * result + ((martURLLocations == null) ? 0 : martURLLocations.hashCode()); - return result; - } - - /* (non-Javadoc) - * @see java.lang.Object#equals(java.lang.Object) - */ - public boolean equals(Object obj) { - if (this == obj) - return true; - if (obj == null) - return false; - if (getClass() != obj.getClass()) - return false; - final MartRegistry other = (MartRegistry) obj; - if (martURLLocations == null) { - if (other.martURLLocations != null) - return false; - } else if (!martURLLocations.equals(other.martURLLocations)) - return false; - return true; - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/9e08cac0/src/main/java/org/biomart/martservice/MartService.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/biomart/martservice/MartService.java b/src/main/java/org/biomart/martservice/MartService.java deleted file mode 100644 index c02bbb5..0000000 --- a/src/main/java/org/biomart/martservice/MartService.java +++ /dev/null @@ -1,709 +0,0 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * 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 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: MartService.java,v $errors/failure.html - * Revision $Revision: 1.7 $ - * Release status $State: Exp $ - * Last modified on $Date: 2008/08/11 12:48:29 $ - * by $Author: davidwithers $ - * Created on 17-Mar-2006 - *****************************************************************/ -package org.biomart.martservice; - -import java.io.File; -import java.io.FileInputStream; -import java.io.FileOutputStream; -import java.io.IOException; -import java.lang.ref.SoftReference; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.HashMap; -import java.util.HashSet; -import java.util.LinkedList; -import java.util.List; -import java.util.Map; -import java.util.Set; -import java.util.zip.GZIPInputStream; -import java.util.zip.GZIPOutputStream; - -import org.apache.log4j.Logger; -import org.biomart.martservice.query.Query; -import org.ensembl.mart.lib.config.ConfigurationException; -import org.ensembl.mart.lib.config.DatasetConfig; -import org.ensembl.mart.lib.config.DatasetConfigXMLUtils; -import org.ensembl.mart.lib.config.Exportable; -import org.ensembl.mart.lib.config.Importable; -import org.jdom.Document; -import org.jdom.JDOMException; -import org.jdom.input.SAXBuilder; -import org.xml.sax.InputSource; - -/** - * A class for interacting with a BioMart web service. - * - * @author David Withers - */ -public class MartService { - private static Logger logger = Logger.getLogger(MartServiceUtils.class); - - private String location; - - private String requestId; - - private File cacheDirectory; - - private MartRegistry registry; - - private Map<MartURLLocation, String> versionMap = new HashMap<MartURLLocation, String>(); - - private Map<String, MartDataset[]> datasetsMap = new HashMap<String, MartDataset[]>(); - - private Map<String, SoftReference<DatasetConfig>> datasetConfigMap = new HashMap<String, SoftReference<DatasetConfig>>(); - - private Map<String, Importable[]> importablesMap = new HashMap<String, Importable[]>(); - - private Map<String, Exportable[]> exportablesMap = new HashMap<String, Exportable[]>(); - - private Map<MartDataset, List<DatasetLink>> linkableDatasetsMap = new HashMap<MartDataset, List<DatasetLink>>(); - - private Map<MartDataset, Set<DatasetLink>> datasetToLinkSetMap = new HashMap<MartDataset, Set<DatasetLink>>(); - - private Map<MartDataset, Map<MartDataset, MartDataset>> datasetsToPathMap = new HashMap<MartDataset, Map<MartDataset, MartDataset>>(); - - private static final Map<String, MartService> martServiceMap = new HashMap<String, MartService>(); - - private static final String fs = System.getProperty("file.separator"); - - private boolean linksCalculated = false; - - /** - * Constructs an instance of a <code>MartService</code> with the specified - * location. - * - * The location must be the URL of a valid BioMart MartService, e.g. - * http://www.biomart.org/biomart/martservice - * - * @param location - * the URL of the MartService - */ - private MartService(String location) { - this.location = location; - } - - /** - * Returns a <code>MartService</code> for the specified location. If a - * <code>MartService</code> does not exist for the location a new one is - * constructed. - * - * The location must be the URL of a valid BioMart MartService, e.g. - * http://www.biomart.org/biomart/martservice - * - * @param location - * the URL of the MartService - */ - public static MartService getMartService(String location) { - if (!martServiceMap.containsKey(location)) { - martServiceMap.put(location, new MartService(location)); - } - return martServiceMap.get(location); - } - - /** - * Returns the requestId. - * - * @return the requestId - */ - public String getRequestId() { - return requestId; - } - - /** - * Sets the requestId. - * - * @param requestId - * the new requestId - */ - public void setRequestId(String requestId) { - this.requestId = requestId; - } - - /** - * Returns the cacheDirectory. - * - * @return the cacheDirectory - */ - public File getCacheDirectory() { - return cacheDirectory; - } - - /** - * Sets the cacheDirectory. - * - * @param cacheDirectory - * the new cacheDirectory - */ - public void setCacheDirectory(File cacheDirectory) { - this.cacheDirectory = cacheDirectory; - } - - /** - * Returns the URL of the MartService. - * - * @return the URL of the MartService - */ - public String getLocation() { - return location; - } - - /** - * Removes any cached items. - */ - public void clearCache() { - registry = null; - datasetsMap.clear(); - datasetConfigMap.clear(); - importablesMap.clear(); - exportablesMap.clear(); - } - - /** - * Returns the MartRegistry for this MartService. - * - * @return the MartRegistry for this MartService - * @throws MartServiceException - * if the MartService returns an error or is unavailable - */ - public MartRegistry getRegistry() throws MartServiceException { - if (registry == null) { - registry = MartServiceUtils.getRegistry(location, requestId); - } - return registry; - } - - public String getVersion(MartURLLocation martURLLocation) - throws MartServiceException { - if (!versionMap.containsKey(martURLLocation)) { - versionMap.put(martURLLocation, MartServiceUtils.getVersion( - location, requestId, martURLLocation)); - } - return versionMap.get(martURLLocation); - } - - /** - * Returns all the datasets available from this MartService. - * - * @return all the datasets available from this MartService. - * @throws MartServiceException - * if the MartService returns an error or is unavailable - */ - public MartDataset[] getDatasets() throws MartServiceException { - List<MartDataset> datasets = new ArrayList<MartDataset>(); - MartURLLocation[] locations = getRegistry().getMartURLLocations(); - for (int i = 0; i < locations.length; i++) { - datasets.addAll(Arrays.asList(getDatasets(locations[i]))); - } - return datasets.toArray(new MartDataset[datasets.size()]); - } - - /** - * Returns the datasets belonging to the virtualSchema. - * - * @param virtualSchema - * the virtual schema to include datasets from. - * @return the datasets belonging to the virtualSchema. - * @throws MartServiceException - * if the MartService returns an error or is unavailable - */ - public MartDataset[] getDatasets(String virtualSchema) - throws MartServiceException { - List<MartDataset> datasets = new ArrayList<MartDataset>(); - MartURLLocation[] locations = getRegistry().getMartURLLocations(); - for (int i = 0; i < locations.length; i++) { - if (virtualSchema == null - || virtualSchema.equals(locations[i].getVirtualSchema())) { - datasets.addAll(Arrays.asList(getDatasets(locations[i]))); - } - } - return datasets.toArray(new MartDataset[datasets.size()]); - } - - /** - * Returns the datasets specified by martURLLocation. - * - * @param martURLLocation - * where to find the datasets. - * @return the datasets specified by martURLLocation. - * @throws MartServiceException - * if the MartService returns an error or is unavailable - */ - public MartDataset[] getDatasets(MartURLLocation martURLLocation) - throws MartServiceException { - String name = martURLLocation.getName(); - if (!datasetsMap.containsKey(name)) { - datasetsMap.put(name, MartServiceUtils.getDatasets(location, - requestId, martURLLocation)); - } - return datasetsMap.get(name); - } - - /** - * Returns the dataset specified by a virtualSchema and a dataset name. - * - * @param virtualSchema - * the virtualSchema containing the dataset - * @param datasetName - * the name of the dataset to return - * @return a dataset - * @throws MartServiceException - * if the MartService returns an error or is unavailable - */ - public MartDataset getDataset(String virtualSchema, String datasetName) - throws MartServiceException { - MartDataset result = null; - MartDataset[] datasets = getDatasets(virtualSchema); - for (int i = 0; i < datasets.length; i++) { - if (datasetName.equals(datasets[i].getName())) { - result = datasets[i]; - break; - } - } - return result; - } - - /** - * Returns the configuration for a dataset. - * - * @param dataset - * the dataset to get the configuration for - * @return the configuration for a dataset - * @throws MartServiceException - * if the MartService returns an error or is unavailable - */ - public DatasetConfig getDatasetConfig(MartDataset dataset) - throws MartServiceException { - String qualifiedName = dataset.getQualifiedName(); - DatasetConfig datasetConfig; - if (!datasetConfigMap.containsKey(qualifiedName)) { - if (dataset.getModified() != null && cacheDirectory != null) { - datasetConfig = getDatasetConfigFromCache(dataset); - } else { - datasetConfig = MartServiceUtils.getDatasetConfig(location, - requestId, dataset); - } - datasetConfigMap.put(qualifiedName, - new SoftReference<DatasetConfig>(datasetConfig)); - } else { - datasetConfig = datasetConfigMap.get(qualifiedName).get(); - if (datasetConfig == null) { - if (dataset.getModified() != null && cacheDirectory != null) { - datasetConfig = getDatasetConfigFromCache(dataset); - } else { - datasetConfig = MartServiceUtils.getDatasetConfig(location, - requestId, dataset); - } - datasetConfigMap.put(qualifiedName, - new SoftReference<DatasetConfig>(datasetConfig)); - } - - } - return datasetConfig; - } - - private DatasetConfig getDatasetConfigFromCache(MartDataset dataset) - throws MartServiceException { - DatasetConfig datasetConfig = null; - MartURLLocation mart = dataset.getMartURLLocation(); - String path = mart.getHost() + fs + mart.getName() + fs - + mart.getVirtualSchema(); - File martCacheDir = new File(cacheDirectory, path); - martCacheDir.mkdirs(); - File cache = new File(martCacheDir, dataset.getName() + ".cfg"); - DatasetConfigXMLUtils datasetConfigXMLUtils = new DatasetConfigXMLUtils( - true); - if (cache.exists()) { - try { - SAXBuilder builder = new SAXBuilder(); - Document doc = builder.build(new InputSource( - new GZIPInputStream(new FileInputStream(cache)))); - - // Document doc = - // datasetConfigXMLUtils.getDocumentForXMLStream(new - // FileInputStream(cache)); - - datasetConfig = datasetConfigXMLUtils - .getDatasetConfigForDocument(doc); - datasetConfigXMLUtils.loadDatasetConfigWithDocument( - datasetConfig, doc); - if (!datasetConfig.getModified().trim().equals( - dataset.getModified().trim())) { - logger.info(" " + datasetConfig.getModified().trim() - + " != " + dataset.getModified().trim()); - logger.info(" Database: " - + dataset.getMartURLLocation().getDatabase() - + ", Dataset: " + dataset.getName()); - datasetConfig = null; - } - } catch (IOException e) { - logger.debug("error reading cache from " + cache.getPath(), e); - datasetConfig = null; - } catch (ConfigurationException e) { - logger.debug("error parsing from " + cache.getPath(), e); - datasetConfig = null; - } catch (JDOMException e) { - logger.debug("error parsing from " + cache.getPath(), e); - datasetConfig = null; - } - } - if (datasetConfig == null) { - datasetConfig = MartServiceUtils.getDatasetConfig(location, - requestId, dataset); - try { - GZIPOutputStream zipOutputStream = new GZIPOutputStream( - new FileOutputStream(cache)); - datasetConfigXMLUtils.writeDatasetConfigToOutputStream( - datasetConfig, zipOutputStream); - zipOutputStream.flush(); - zipOutputStream.close(); - } catch (IOException e) { - logger.debug("error writing cache to " + cache.getPath(), e); - } catch (ConfigurationException e) { - logger.debug("error writing cache to " + cache.getPath(), e); - } - } - return datasetConfig; - } - - /** - * Returns the importables for a dataset. - * - * @param dataset - * @return the importables for a dataset - * @throws MartServiceException - * if the MartService returns an error or is unavailable - */ - public Importable[] getImportables(MartDataset dataset) - throws MartServiceException { - String qualifiedName = dataset.getQualifiedName(); - if (!importablesMap.containsKey(qualifiedName)) { - try { - importablesMap.put(qualifiedName, getDatasetConfig(dataset) - .getImportables()); - } catch (MartServiceException e) { - return new Importable[0]; - } - } - return importablesMap.get(qualifiedName); - } - - /** - * Returns the exportables for a dataset. - * - * @param dataset - * @return the exportables for a dataset - * @throws MartServiceException - * if the MartService returns an error or is unavailable - */ - public Exportable[] getExportables(MartDataset dataset) - throws MartServiceException { - String qualifiedName = dataset.getQualifiedName(); - if (!exportablesMap.containsKey(qualifiedName)) { - try { - exportablesMap.put(qualifiedName, getDatasetConfig(dataset) - .getExportables()); - } catch (MartServiceException e) { - return new Exportable[0]; - } - } - return exportablesMap.get(qualifiedName); - } - - /** - * Sends a <code>Query</code> to the MartService and returns the results - * of executing the query. - * - * The results are returned as an array of lists; one list for each - * attribute specified in the query. - * - * @param query - * the query to execute - * @return the results of executing the query - * @throws MartServiceException - * if the MartService returns an error or is unavailable - */ - public Object[] executeQuery(Query query) throws MartServiceException { - // logger.info(MartServiceUtils.queryToXML(query)); - return MartServiceUtils.getResults(location, requestId, query); - } - - /** - * Sends a <code>Query</code> to the MartService and writes the results to - * the <code>ResultReceiver</code> as each line of the result stream is - * read. - * - * @param query - * @param resultReceiver - * @throws MartServiceException - * if the MartService returns an error or is unavailable - * @throws ResultReceiverException - * if the ResultReceiver cannot receive the result - * @see ResultReceiver - */ - public void executeQuery(Query query, ResultReceiver resultReceiver) - throws MartServiceException, ResultReceiverException { - MartServiceUtils.putResults(location, requestId, query, resultReceiver); - } - - /** - * Returns a list of datasets that can be linked to the specified dataset. - * - * @param martDataset - * @return datasets that can be linked to the specified dataset - * @throws MartServiceException - */ - public List<DatasetLink> getLinkableDatasets(MartDataset martDataset) - throws MartServiceException { - if (!linkableDatasetsMap.containsKey(martDataset)) { - List<DatasetLink> linkableDatasets = new ArrayList<DatasetLink>(); - - Set<String> importableSet = new HashSet<String>(); - Importable[] importables = getImportables(martDataset); - for (int i = 0; i < importables.length; i++) { - importableSet.add(importables[i].getLinkName()); - } - - MartDataset[] datasets = getDatasets(martDataset.getVirtualSchema()); - for (int j = 0; j < datasets.length; j++) { - if (datasets[j].isVisible() - && !datasets[j].getName().equals(martDataset.getName())) { - DatasetLink datasetLink = new DatasetLink(datasets[j], - martDataset); - Exportable[] exportables = getExportables(datasets[j]); - for (int k = 0; k < exportables.length; k++) { - String link = exportables[k].getLinkName(); - if (importableSet.contains(link)) { - datasetLink.addLink(link); - } - } - if (datasetLink.hasLinks()) { - linkableDatasets.add(datasetLink); - } - } - } - linkableDatasetsMap.put(martDataset, linkableDatasets); - } - - return linkableDatasetsMap.get(martDataset); - } - - /* - * (non-Javadoc) - * - * @see java.lang.Object#equals(java.lang.Object) - */ - public boolean equals(Object obj) { - boolean result = false; - if (obj != null) { - MartService other = (MartService) obj; - if (location == null) { - result = other.location == null; - } else { - result = location.equals(other.location); - } - } - return result; - } - - /* - * (non-Javadoc) - * - * @see java.lang.Object#hashCode() - */ - public int hashCode() { - return location.hashCode(); - } - - public boolean linksCalculated() { - return linksCalculated; - } - - // java implementation of the perl stuff that calculates links. - // all this should go for the next version of biomart. - - public void calculateLinks() throws MartServiceException { - synchronized (location) { - if (!linksCalculated) { - datasetToLinkSetMap.clear(); - datasetsToPathMap.clear(); - - MartDataset[] allDatasets = getDatasets(); - for (int i = 0; i < allDatasets.length; i++) { - MartDataset[] datasets = getDatasets(allDatasets[i] - .getVirtualSchema()); - for (int j = 0; j < datasets.length; j++) { - if (!allDatasets[i].getName().equals( - datasets[j].getName())) { - linkDatasets(allDatasets[i], datasets[j]); - } - } - } - for (int i = 0; i < allDatasets.length; i++) { - datasetsToPathMap.put(allDatasets[i], - dijkstra(allDatasets[i])); - } - linksCalculated = true; - } - } - } - - public List<MartDataset> getPath(MartDataset source, MartDataset target) { - List<MartDataset> path = new ArrayList<MartDataset>(); - - Map<MartDataset, MartDataset> pathMap = datasetsToPathMap.get(source); - - MartDataset currentDataset = target; - - while (currentDataset != null) { - path.add(0, currentDataset); - currentDataset = (MartDataset) pathMap.get(currentDataset); - } - - if (path.size() < 2 || !path.get(0).equals(source) - || !path.get(path.size() - 1).equals(target)) { - return null; - } - - return path; - } - - public DatasetLink getLinkBetween(MartDataset exportingDataset, - MartDataset importingDataset) { - Set<DatasetLink> links = datasetToLinkSetMap.get(exportingDataset); - for (DatasetLink link : links) { - MartDataset targetDataset = link.getTargetDataset(); - if (importingDataset.equals(targetDataset)) { - return link; - } - } - - return null; - } - - public List<DatasetLink> getLinksFrom(MartDataset dataset) { - List<DatasetLink> linksFrom = new ArrayList<DatasetLink>(); - Set<DatasetLink> links = datasetToLinkSetMap.get(dataset); - if (links != null) { - for (DatasetLink link : links) { - if (link.getSourceDataset().equals(dataset)) { - linksFrom.add(link); - } - } - } - return linksFrom; - } - - public void linkDatasets(MartDataset source, MartDataset target) - throws MartServiceException { - DatasetLink datasetLink = new DatasetLink(source, target); - Importable[] importables = getImportables(target); - for (int i = 0; i < importables.length; i++) { - Exportable[] exportables = getExportables(source); - for (int j = 0; j < exportables.length; j++) { - if (importables[i].getLinkName().equals( - exportables[j].getLinkName())) { - String importVersion = importables[i].getLinkVersion(); - String exportVersion = exportables[j].getLinkVersion(); - if (importVersion != null && exportVersion != null) { - if (importVersion.equals(exportVersion)) { - datasetLink.addLink(importables[i].getLinkName()); - } - } else { - datasetLink.addLink(importables[i].getLinkName()); - } - } - } - } - if (datasetLink.hasLinks()) { - if (!datasetToLinkSetMap.containsKey(source)) { - datasetToLinkSetMap.put(source, new HashSet<DatasetLink>()); - } - if (!datasetToLinkSetMap.containsKey(target)) { - datasetToLinkSetMap.put(target, new HashSet<DatasetLink>()); - } - datasetToLinkSetMap.get(source).add(datasetLink); - datasetToLinkSetMap.get(target).add(datasetLink); - } - } - - public Map<MartDataset, MartDataset> dijkstra(MartDataset dataset) - throws MartServiceException { - Map<MartDataset, MartDataset> path = new HashMap<MartDataset, MartDataset>(); - LinkedList<MartDataset> vertices = new LinkedList<MartDataset>(Arrays - .asList(getDatasets(dataset.getVirtualSchema()))); - Map<MartDataset, Integer> dist = new HashMap<MartDataset, Integer>(); - for (MartDataset vertex : vertices) { - dist.put(vertex, new Integer(10000)); - } - - dist.put(dataset, new Integer(0)); - - while (vertices.size() > 0) { - int min_vert_idx = 0; - MartDataset min_vert = (MartDataset) vertices.get(min_vert_idx); - int min_dist = ((Integer) dist.get(min_vert)).intValue(); - - for (int vertex_idx = 0; vertex_idx < vertices.size(); vertex_idx++) { - MartDataset vertex = (MartDataset) vertices.get(vertex_idx); - if (((Integer) dist.get(vertex)).intValue() < min_dist) { - min_vert_idx = vertex_idx; - min_vert = vertex; - min_dist = ((Integer) dist.get(vertex)).intValue(); - } - } - - if (min_dist == 10000) { - // Exhausted a disjoint set of datasets. - break; - } - - vertices.remove(min_vert_idx); - - List<DatasetLink> edges = getLinksFrom(min_vert); - for (DatasetLink edge : edges) { - MartDataset vertex = edge.getTargetDataset(); - - if (((Integer) dist.get(vertex)).intValue() > ((Integer) dist - .get(min_vert)).intValue() + 1) { - dist.put(vertex, new Integer(((Integer) dist.get(min_vert)) - .intValue() + 1)); - path.put(vertex, min_vert); - } - } - } - - return path; - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/9e08cac0/src/main/java/org/biomart/martservice/MartServiceException.java ---------------------------------------------------------------------- diff --git a/src/main/java/org/biomart/martservice/MartServiceException.java b/src/main/java/org/biomart/martservice/MartServiceException.java deleted file mode 100644 index f1f0639..0000000 --- a/src/main/java/org/biomart/martservice/MartServiceException.java +++ /dev/null @@ -1,86 +0,0 @@ -/* - * Copyright (C) 2003 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. Authorship - * of the modifications may be determined from the ChangeLog placed at - * the end of this file. - * - * 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 - * USA. - * - **************************************************************** - * Source code information - * ----------------------- - * Filename $RCSfile: MartServiceException.java,v $ - * Revision $Revision: 1.1 $ - * Release status $State: Exp $ - * Last modified on $Date: 2007/01/31 14:12:05 $ - * by $Author: davidwithers $ - * Created on 05-May-2006 - *****************************************************************/ -package org.biomart.martservice; - -/** - * Thrown when a MartService is inaccessable or returns an error. - * - * @author David Withers - */ -public class MartServiceException extends Exception { - private static final long serialVersionUID = 5535008907746588537L; - - /** - * Constructs a new exception with no detail message. - * - */ - public MartServiceException() { - super(); - } - - /** - * Constructs a new exception with the specified detail message. - * - * @param message - * the detail message - * @param cause - * the cause (a null value is permitted, and indicates that the - * cause is nonexistent or unknown) - */ - public MartServiceException(String message, Throwable cause) { - super(message, cause); - } - - /** - * Constructs a new exception with the specified detail message and cause. - * - * @param message - * the detail message - */ - public MartServiceException(String message) { - super(message); - } - - /** - * Constructs a new exception with the specified cause. - * - * @param cause - * the cause (a null value is permitted, and indicates that the - * cause is nonexistent or unknown) - */ - public MartServiceException(Throwable cause) { - super(cause); - } - -}
