http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartService.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartService.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartService.java deleted file mode 100644 index c02bbb5..0000000 --- a/taverna-biomart-martservice/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/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceException.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceException.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceException.java deleted file mode 100644 index f1f0639..0000000 --- a/taverna-biomart-martservice/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); - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceUtils.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceUtils.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceUtils.java deleted file mode 100644 index cdcb400..0000000 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceUtils.java +++ /dev/null @@ -1,725 +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: MartServiceUtils.java,v $ - * Revision $Revision: 1.12 $ - * Release status $State: Exp $ - * Last modified on $Date: 2008/07/31 15:06:49 $ - * by $Author: davidwithers $ - * Created on 17-Mar-2006 - *****************************************************************/ -package org.biomart.martservice; - -import java.io.BufferedReader; -import java.io.IOException; -import java.io.InputStream; -import java.io.InputStreamReader; -import java.io.Reader; -import java.net.MalformedURLException; -import java.net.URL; -import java.util.ArrayList; -import java.util.List; - -import org.apache.commons.httpclient.DefaultHttpMethodRetryHandler; -import org.apache.commons.httpclient.HttpClient; -import org.apache.commons.httpclient.HttpMethod; -import org.apache.commons.httpclient.HttpStatus; -import org.apache.commons.httpclient.NameValuePair; -import org.apache.commons.httpclient.UsernamePasswordCredentials; -import org.apache.commons.httpclient.auth.AuthScope; -import org.apache.commons.httpclient.methods.GetMethod; -import org.apache.commons.httpclient.methods.PostMethod; -import org.apache.commons.httpclient.params.HttpMethodParams; -import org.apache.commons.io.IOUtils; -import org.apache.log4j.Logger; -import org.biomart.martservice.query.Attribute; -import org.biomart.martservice.query.Dataset; -import org.biomart.martservice.query.Query; -import org.biomart.martservice.query.QueryXMLHandler; -import org.ensembl.mart.lib.config.ConfigurationException; -import org.ensembl.mart.lib.config.DatasetConfig; -import org.ensembl.mart.lib.config.DatasetConfigXMLUtils; -import org.jdom.DocType; -import org.jdom.Document; -import org.jdom.Element; -import org.jdom.JDOMException; -import org.jdom.Namespace; -import org.jdom.input.SAXBuilder; -import org.jdom.output.XMLOutputter; -import org.xml.sax.InputSource; - -/** - * Utility class for interacting with a BioMart web service. - * - * @author David Withers - */ -public class MartServiceUtils { - private static Logger logger = Logger.getLogger(MartServiceUtils.class); - - private static String lineSeparator = System.getProperty("line.separator"); - - public static final String QUERY_ATTRIBUTE = "query"; - - public static final String DATASET_ATTRIBUTE = "dataset"; - - public static final String MART_ATTRIBUTE = "mart"; - - public static final String SCHEMA_ATTRIBUTE = "virtualschema"; - - public static final String TYPE_ATTRIBUTE = "type"; - - public static final String MART_USER_ATTRIBUTE = "martuser"; - - public static final String INTERFACE_ATTRIBUTE = "interface"; - - public static final String REQUEST_ID_ATTRIBUTE = "requestid"; - - public static final String REGISTRY_VALUE = "registry"; - - public static final String VERSION_VALUE = "version"; - - public static final String DATASETS_VALUE = "datasets"; - - public static final String DATASET_VALUE = "dataset"; - - public static final String CONFIGURATION_VALUE = "configuration"; - - /** - * Sends a registry request to the Biomart webservice and constructs a - * MartRegistry from the XML returned by the webservice. - * - * @param martServiceLocation - * the URL of the Biomart webservice - * @return a MartRegistry - * @throws MartServiceException - * if the Biomart webservice returns an error or is unavailable - */ - public static MartRegistry getRegistry(String martServiceLocation, - String requestId) throws MartServiceException { - List<NameValuePair> data = new ArrayList<NameValuePair>(); - data.add(new NameValuePair(TYPE_ATTRIBUTE, REGISTRY_VALUE)); - if (requestId != null) { - data.add(new NameValuePair(REQUEST_ID_ATTRIBUTE, requestId)); - } - HttpMethod method = new GetMethod(martServiceLocation); - method.setQueryString(data - .toArray(new NameValuePair[data.size()])); - try { - InputStream in = executeMethod(method, martServiceLocation); - Document document = new SAXBuilder().build(in); - Element root = document.getRootElement(); - return MartServiceXMLHandler.elementToRegistry(root, - Namespace.NO_NAMESPACE); - } catch (IOException e) { - String errorMessage = "Error getting registry from " - + martServiceLocation; - throw new MartServiceException(errorMessage, e); - } catch (JDOMException e) { - String errorMessage = "Error getting registry from " - + martServiceLocation; - throw new MartServiceException(errorMessage, e); - } finally { - method.releaseConnection(); - } - - } - - public static String getVersion(String martServiceLocation, - String requestId, MartURLLocation mart) throws MartServiceException { - String errorMessage = "Error getting version from " + martServiceLocation; - - List<NameValuePair> data = new ArrayList<NameValuePair>(); - data.add(new NameValuePair(TYPE_ATTRIBUTE, VERSION_VALUE)); - if (mart.getVirtualSchema() != null) { - data.add(new NameValuePair(SCHEMA_ATTRIBUTE, mart - .getVirtualSchema())); - } - data.add(new NameValuePair(MART_ATTRIBUTE, mart.getName())); - if (requestId != null) { - data.add(new NameValuePair(REQUEST_ID_ATTRIBUTE, requestId)); - } - if (requestId != null) { - data.add(new NameValuePair(REQUEST_ID_ATTRIBUTE, requestId)); - } - HttpMethod method = new GetMethod(martServiceLocation); - method.setQueryString(data - .toArray(new NameValuePair[data.size()])); - try { - InputStream in = executeMethod(method, martServiceLocation); - BufferedReader bufferedReader = new BufferedReader( - new InputStreamReader(in)); - String version = bufferedReader.readLine(); - if (version == null) { - throw new MartServiceException(errorMessage + ": No version returned"); - } - version = version.trim(); - // fix for biomart's 'let's add a blank line' thing - if ("".equals(version)) { - version = bufferedReader.readLine(); - if (version == null) { - throw new MartServiceException(errorMessage + ": No version returned"); - } - version = version.trim(); - } - bufferedReader.close(); - return version; - } catch (IOException e) { - throw new MartServiceException(errorMessage, e); - } finally { - method.releaseConnection(); - } - } - - /** - * Sends a datasets request to the Biomart webservice and constructs an - * array of MartDataset from the tab separated rows of data returned by the - * webservice. - * - * @param martServiceLocation - * the URL of the Biomart webservice - * @param mart - * the mart to get datasets from - * @return an array of MartDataset - * @throws MartServiceException - * if the Biomart webservice returns an error or is unavailable - */ - public static MartDataset[] getDatasets(String martServiceLocation, - String requestId, MartURLLocation mart) throws MartServiceException { - List<NameValuePair> data = new ArrayList<NameValuePair>(); - data.add(new NameValuePair(TYPE_ATTRIBUTE, DATASETS_VALUE)); - if (mart.getVirtualSchema() != null) { - data.add(new NameValuePair(SCHEMA_ATTRIBUTE, mart - .getVirtualSchema())); - } - data.add(new NameValuePair(MART_ATTRIBUTE, mart.getName())); - if (mart.getMartUser() != null) { - data - .add(new NameValuePair(MART_USER_ATTRIBUTE, mart - .getMartUser())); - } - if (requestId != null) { - data.add(new NameValuePair(REQUEST_ID_ATTRIBUTE, requestId)); - } - HttpMethod method = new GetMethod(martServiceLocation); - method.setQueryString(data - .toArray(new NameValuePair[data.size()])); - try { - InputStream in = executeMethod(method, martServiceLocation); - - MartDataset[] datasets = tabSeparatedReaderToDatasets( - new InputStreamReader(in), mart); - in.close(); - return datasets; - } catch (IOException e) { - String errorMessage = "Error getting datasets from " - + martServiceLocation; - throw new MartServiceException(errorMessage, e); - } finally { - method.releaseConnection(); - } - } - - /** - * Sends a configuration request to the Biomart webservice and constructs a - * DatasetConfig from the XML returned by the webservice. - * - * @param martServiceLocation - * the URL of the Biomart webservice - * @param dataset - * the dataset to get the configuration for - * @return a DatasetConfig - * @throws MartServiceException - * if the Biomart webservice returns an error or is unavailable - */ - public static DatasetConfig getDatasetConfig(String martServiceLocation, - String requestId, MartDataset dataset) throws MartServiceException { - List<NameValuePair> data = new ArrayList<NameValuePair>(); - data.add(new NameValuePair(TYPE_ATTRIBUTE, CONFIGURATION_VALUE)); - MartURLLocation mart = dataset.getMartURLLocation(); - // if the dataset has a location specify the virtual schema to uniquely - // identify the dataset - if (mart != null && mart.getVirtualSchema() != null) { - data.add(new NameValuePair(SCHEMA_ATTRIBUTE, mart - .getVirtualSchema())); - } - data.add(new NameValuePair(DATASET_VALUE, dataset.getName())); -// if (dataset.getInterface() != null) { -// data.add(new NameValuePair(INTERFACE_ATTRIBUTE, dataset -// .getInterface())); -// } - if (mart != null && mart.getMartUser() != null) { - data - .add(new NameValuePair(MART_USER_ATTRIBUTE, mart - .getMartUser())); - } - if (requestId != null) { - data.add(new NameValuePair(REQUEST_ID_ATTRIBUTE, requestId)); - } - HttpMethod method = new GetMethod(martServiceLocation); - method.setQueryString(data - .toArray(new NameValuePair[data.size()])); - - try { - InputStream in = executeMethod(method, martServiceLocation); - - DatasetConfigXMLUtils datasetConfigXMLUtils = new DatasetConfigXMLUtils( - true); - SAXBuilder builder = new SAXBuilder(); - Document doc = builder.build(new InputSource(in)); - // Document doc = datasetConfigXMLUtils.getDocumentForXMLStream(in); - - DatasetConfig datasetConfig = datasetConfigXMLUtils - .getDatasetConfigForDocument(doc); - datasetConfigXMLUtils.loadDatasetConfigWithDocument(datasetConfig, - doc); - return datasetConfig; - } catch (ConfigurationException e) { - String errorMessage = "Error parsing configuration from " - + martServiceLocation; - logger.debug(errorMessage, e); - throw new MartServiceException(errorMessage, e); - } catch (JDOMException e) { - String errorMessage = "Error parsing configuration from " - + martServiceLocation; - logger.debug(errorMessage, e); - throw new MartServiceException(errorMessage, e); - } catch (IOException e) { - String errorMessage = "Error getting configuration from " - + martServiceLocation; - logger.debug(errorMessage, e); - throw new MartServiceException(errorMessage, e); - } finally { - method.releaseConnection(); - } - } - - /** - * Sends a query to the Biomart webservice and constructs an array of List - * of String results from the tab separated rows of data returned by the - * webservice. - * - * @param martServiceLocation - * the URL of the Biomart webservice - * @param query - * the query to send to the webservice - * @return an array of List of String - * @throws MartServiceException - * if the Biomart webservice returns an error or is unavailable - */ - public static Object[] getResults(String martServiceLocation, - String requestId, Query query) throws MartServiceException { - Object[] results = new Object[0]; - // int attributes = query.getAttributes().size(); - int attributes = getAttributeCount(query.getAttributes()); - boolean count = query.getCount() == 1; - // if there are no attributes and we're not doing a count there's no - // point in doing the query - if (attributes > 0 || count) { - // The 'new' 0.5 server now resolves the attribute lists so there's - // no need to do the split here any more - // String queryXml = queryToXML(splitAttributeLists(query)); - String queryXml = queryToXML(query); - logger.info(queryXml); - NameValuePair[] data = { new NameValuePair(QUERY_ATTRIBUTE, - queryXml) }; - PostMethod method = new PostMethod(martServiceLocation); - method.setRequestBody(data); - - try { - InputStream in = executeMethod(method, martServiceLocation); - if (query.getFormatter() == null) { - results = tabSeparatedReaderToResults( - new InputStreamReader(in), count ? 1 : attributes); - if (!count) { - results = reassembleAttributeLists(results, query); - } - } else { - results = readResult(in, query.getFormatter()); - } - in.close(); - } catch (IOException e) { - String errorMessage = "Error reading data from " - + martServiceLocation; - throw new MartServiceException(errorMessage, e); - } finally { - method.releaseConnection(); - } - - } - - return results; - } - - public static void putResults(String martServiceLocation, String requestId, - Query query, ResultReceiver resultReceiver) throws MartServiceException, ResultReceiverException { - int attributeCount = getAttributeCount(query.getAttributes()); - boolean count = query.getCount() == 1; - // if there are no attributes and we're not doing a count there's no - // point in doing the query - if (attributeCount > 0 || count) { - String queryXml = queryToXML(query); - logger.info(queryXml); - NameValuePair[] data = { new NameValuePair(QUERY_ATTRIBUTE, - queryXml) }; - PostMethod method = new PostMethod(martServiceLocation); - method.setRequestBody(data); - - try { - InputStream in = executeMethod(method, martServiceLocation); - if (query.getFormatter() == null) { - if (count) { - resultReceiver.receiveResult(tabSeparatedReaderToResults(new InputStreamReader(in), 1), 0); - } else { - List<Attribute> attributes = query.getAttributes(); - Object[] result = new Object[attributes.size()]; - BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(in)); - String line = bufferedReader.readLine(); - for (long i = 0; line != null; line = bufferedReader.readLine(), i++) { - String[] tokens = line.split("\t", -1); - if (attributeCount == tokens.length) { - for (int ri = 0, ti = 0; ri < result.length && ti < tokens.length; ri++) { - Attribute attribute = attributes.get(ri); - if (attribute.getAttributes() == null) { - result[ri] = tokens[ti]; - ti++; - } else { - int nestedAttributeCount = attribute.getAttributesCount(); - List<Object> list = new ArrayList<Object>(); - for (int j = 0; j < nestedAttributeCount; j++) { - list.add(tokens[ti]); - ti++; - } - result[ri] = list; - } - } - resultReceiver.receiveResult(result, i); - } else { - resultReceiver.receiveError(line, i); - } - } - } - } else { - resultReceiver.receiveResult(readResult(in, query.getFormatter()), 0); - } - in.close(); - } catch (IOException e) { - String errorMessage = "Error reading data from " - + martServiceLocation; - throw new MartServiceException(errorMessage, e); - } finally { - method.releaseConnection(); - } - - } - } - -// private static String getLocation(MartURLLocation martUrlLocation) { -// StringBuffer location = new StringBuffer("http://";); -// location.append(martUrlLocation.getHost()); -// location.append(":" + martUrlLocation.getPort()); -// location.append(martUrlLocation.getPath()); -// return location.toString(); -// } - - private static int getAttributeCount(List<Attribute> attributeList) { - int result = 0; - for (Attribute attribute : attributeList) { - if (attribute.getAttributes() == null) { - result++; - } else { - result += attribute.getAttributesCount(); - } - } - return result; - } - - private static Object[] reassembleAttributeLists(Object[] lists, Query query) { - int index = 0; - List<Object> result = new ArrayList<Object>(); - for (Attribute attribute : query.getAttributes()) { - if (attribute.getAttributes() == null) { - result.add(lists[index]); - index++; - } else { - int attributesCount = attribute.getAttributesCount(); - List<Object> list = new ArrayList<Object>(); - for (int i = 0; i < attributesCount; i++) { - list.add(lists[index]); - index++; - } - result.add(list); - } - } - return result.toArray(); - } - - public static Query splitAttributeLists(Query query) { - Query result = new Query(query); - for (Dataset dataset : result.getDatasets()) { - List<Attribute> attributeList = dataset.getAttributes(); - dataset.removeAllAttributes(); - for (Attribute attribute : attributeList) { - if (attribute.getAttributes() == null) { - dataset.addAttribute(attribute); - } else { - String[] attributes = attribute.getAttributes().split(","); - for (int i = 0; i < attributes.length; i++) { - dataset.addAttribute(new Attribute(attributes[i])); - } - } - } - } - return result; - } - - public static String getMimeTypeForFormatter(String formatter) { - String mimeType = "'text/plain'"; - if ("ADF".equals(formatter)) { - mimeType = "'text/plain'"; - } else if ("AXT".equals(formatter)) { - mimeType = "'text/plain'"; - } else if ("AXTPLUS".equals(formatter)) { - mimeType = "'text/plain'"; - } else if ("CSV".equals(formatter)) { - mimeType = "'text/plain'"; - } else if ("FASTA".equals(formatter)) { - mimeType = "'text/plain'"; - } else if ("FASTACDNA".equals(formatter)) { - mimeType = "'text/plain'"; - } else if ("GFF".equals(formatter)) { - mimeType = "'text/plain'"; - } else if ("HTML".equals(formatter)) { - mimeType = "'text/html'"; - } else if ("MAF".equals(formatter)) { - mimeType = "'text/plain'"; - } else if ("MFA".equals(formatter)) { - mimeType = "'text/plain'"; - } else if ("MFASTA".equals(formatter)) { - mimeType = "'text/plain'"; - } else if ("TSV".equals(formatter)) { - mimeType = "'text/tab-separeted-values'"; - } else if ("TXT".equals(formatter)) { - mimeType = "'text/plain'"; - } else if ("XLS".equals(formatter)) { - mimeType = "'application/excel'"; - } - - return mimeType; - } - - private static List<String>[] tabSeparatedReaderToResults(Reader reader, - int resultsCount) throws IOException { - List<String>[] results = new List[resultsCount]; - for (int i = 0; i < results.length; i++) { - results[i] = new ArrayList<String>(); - } - BufferedReader bufferedReader = new BufferedReader(reader); - String line = bufferedReader.readLine(); - while (line != null) { - String[] tokens = line.split("\t", -1); - for (int i = 0; i < results.length && i < tokens.length; i++) { - results[i].add(tokens[i]); - } - line = bufferedReader.readLine(); - } - return results; - } - - private static Object[] readResult(InputStream inputStream, String formatter) throws IOException { - Object[] result = new Object[1]; - - if (getMimeTypeForFormatter(formatter).contains("application/")) { - result[0] = IOUtils.toByteArray(inputStream); - } else { - result[0] = IOUtils.toString(inputStream); - } - return result; - } - - private static MartDataset[] tabSeparatedReaderToDatasets(Reader reader, - MartURLLocation martURLLocation) throws IOException { - List<MartDataset> datasetList = new ArrayList<MartDataset>(); - BufferedReader bufferedReader = new BufferedReader(reader); - String line = bufferedReader.readLine(); - while (line != null) { - String[] tokens = line.split("\t"); - - if (tokens.length >= 7) { - MartDataset dataset = new MartDataset(); - - dataset.setType(tokens[0]); - dataset.setName(tokens[1]); - dataset.setDisplayName(tokens[2]); - if (tokens[3].equals("1")) { - dataset.setVisible(true); - } else { - dataset.setVisible(false); - } - // value at position 4 is not documented so it's skipped - try { - dataset.setInitialBatchSize(Long.parseLong(tokens[5])); - } catch (NumberFormatException e) { - dataset.setInitialBatchSize(0); - } - try { - dataset.setMaximumBatchSize(Long.parseLong(tokens[6])); - } catch (NumberFormatException e) { - dataset.setMaximumBatchSize(0); - } - - if (tokens.length > 7) { - dataset.setInterface(tokens[7]); - dataset.setModified(tokens[8]); - } - - dataset.setMartURLLocation(martURLLocation); - - datasetList.add(dataset); - } - line = bufferedReader.readLine(); - } - return datasetList.toArray(new MartDataset[datasetList.size()]); - } - - /** - * Creates an XML string from a query - * - * @param query - * @return an XML string - */ - public static String queryToXML(Query query) { - Document document = new Document(QueryXMLHandler.queryToElement(query, - Namespace.NO_NAMESPACE), new DocType("Query")); - return new XMLOutputter().outputString(document); - } - - /** - * @param martServiceLocation - * @param data - * @return - * @throws MartServiceException - */ - private static InputStream executeMethod(HttpMethod method, - String martServiceLocation) throws MartServiceException { - HttpClient client = new HttpClient(); - if (isProxyHost(martServiceLocation)) { - setProxy(client); - } - - method.getParams().setParameter(HttpMethodParams.RETRY_HANDLER, - new DefaultHttpMethodRetryHandler(3, false)); -// method.getParams().setSoTimeout(60000); - try { - int statusCode = client.executeMethod(method); - if (statusCode != HttpStatus.SC_OK) { - throw constructException(method, martServiceLocation, null); - } - return method.getResponseBodyAsStream(); - } catch (IOException e) { - throw constructException(method, martServiceLocation, e); - } - } - - /** - * - * @param client - */ - public static void setProxy(HttpClient client) { - String host = System.getProperty("http.proxyHost"); - String port = System.getProperty("http.proxyPort"); - String user = System.getProperty("http.proxyUser"); - String password = System.getProperty("http.proxyPassword"); - - if (host != null && port != null) { - try { - int portInteger = Integer.parseInt(port); - client.getHostConfiguration().setProxy(host, portInteger); - if (user != null && password != null) { - client.getState().setProxyCredentials( - new AuthScope(host, portInteger), - new UsernamePasswordCredentials(user, password)); - } - } catch (NumberFormatException e) { - logger.error("Proxy port not an integer", e); - } - } - } - - public static boolean isProxyHost(String location) { - String httpNonProxyHosts = System.getProperty("http.nonProxyHosts"); - if (httpNonProxyHosts != null) { - try { - String host = new URL(location).getHost(); - String[] nonProxyHosts = httpNonProxyHosts.split("\\|"); - for (int i = 0; i < nonProxyHosts.length; i++) { - if (nonProxyHosts[i].startsWith("*")) { - if (host.endsWith(nonProxyHosts[i].substring(1))) { - return false; - } - } else if (nonProxyHosts[i].endsWith("*")) { - if (host.startsWith(nonProxyHosts[i].substring(0, - nonProxyHosts[i].length() - 1))) { - return false; - } - } else { - if (host.equals(nonProxyHosts[i])) { - return false; - } - } - } - } catch (MalformedURLException e) { - logger.warn("'" + location + "' is not a valid URL. " - + "Cannot compare host with http.nonProxyHosts", e); - } - } - return true; - } - - private static MartServiceException constructException(HttpMethod method, - String martServiceLocation, Exception cause) { - StringBuffer errorMessage = new StringBuffer(); - errorMessage.append("Error posting to " + martServiceLocation - + lineSeparator); - if (cause == null) { - errorMessage.append(" " + method.getStatusLine() - + lineSeparator); - } - if (method instanceof PostMethod) { - PostMethod postMethod = (PostMethod) method; - NameValuePair[] data = postMethod.getParameters(); - for (int i = 0; i < data.length; i++) { - errorMessage.append(" " + data[i].getName() + " = " - + data[i].getValue() - + lineSeparator); - } - - } else { - errorMessage.append(method.getQueryString()); - } - return new MartServiceException(errorMessage.toString(), cause); - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceXMLHandler.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceXMLHandler.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceXMLHandler.java deleted file mode 100644 index e8a5189..0000000 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceXMLHandler.java +++ /dev/null @@ -1,390 +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: MartServiceXMLHandler.java,v $ - * Revision $Revision: 1.4 $ - * Release status $State: Exp $ - * Last modified on $Date: 2007/12/13 11:38:55 $ - * by $Author: davidwithers $ - * Created on 28-Apr-2006 - *****************************************************************/ -package org.biomart.martservice; - -import java.util.Iterator; -import java.util.List; -import java.util.Set; - -import org.biomart.martservice.query.QueryXMLHandler; -import org.jdom.Element; -import org.jdom.Namespace; - -/** - * Utility class for serializing mart service classes to XML. - * - * @author David Withers - */ -public class MartServiceXMLHandler { - public static final String MART_SERVICE_ELEMENT = "MartService"; - - public static final String MART_URL_LOCATION_ELEMENT = "MartURLLocation"; - - public static final String MART_DATASET_ELEMENT = "MartDataset"; - - public static final String MART_QUERY_ELEMENT = "MartQuery"; - - public static final String LINKED_DATASETS_ELEMENT = "LinkedDatasets"; - - public static final String LINKED_DATASET_ELEMENT = "LinkedDataset"; - - public static final String VIRTUAL_SCHEMA_ELEMENT = "virtualSchema"; - - public static final String LOCATION_ATTRIBUTE = "location"; - - public static final String DATABASE_ATTRIBUTE = "database"; - - public static final String DEFAULT_ATTRIBUTE = "default"; - - public static final String DEFAULT_VALUE_ATTRIBUTE = "defaultValue"; - - public static final String DISPLAY_NAME_ATTRIBUTE = "displayName"; - - public static final String HOST_ATTRIBUTE = "host"; - - public static final String INCLUDE_DATASETS_ATTRIBUTE = "includeDatasets"; - - public static final String LINK_ATTRIBUTE = "LINK"; - - public static final String MART_USER_ATTRIBUTE = "martUser"; - - public static final String NAME_ATTRIBUTE = "name"; - - public static final String PATH_ATTRIBUTE = "path"; - - public static final String PORT_ATTRIBUTE = "port"; - - public static final String TYPE_ATTRIBUTE = "type"; - - public static final String INITIAL_BATCH_SIZE_ATTRIBUTE = "initialBatchSize"; - - public static final String MAXIMUM_BATCH_SIZE_ATTRIBUTE = "maximumBatchSize"; - - public static final String VIRTUAL_SCHEMA_ATTRIBUTE = "virtualSchema"; - - public static final String SERVER_VIRTUAL_SCHEMA_ATTRIBUTE = "serverVirtualSchema"; - - public static final String VISIBLE_ATTRIBUTE = "visible"; - - public static final String REDIRECT_ATTRIBUTE = "redirect"; - - public static final String INTERFACE_ATTRIBUTE = "interface"; - - public static final String MODIFIED_ATTRIBUTE = "modified"; - - /** - * Converts a <code>MartService</code> to an XML element. - * - * @param martService - * the <code>MartService</code> to serialize - * @param namespace - * the <code>Namespace</code> to use when constructing the - * <code>Element</code> - * @return an XML serialization of the <code>MartService</code> - */ - public static Element martServiceToElement(MartService martService, - Namespace namespace) { - Element element = new Element(MART_SERVICE_ELEMENT, namespace); - element.setAttribute(LOCATION_ATTRIBUTE, martService.getLocation()); - return element; - } - - /** - * Creates a <code>MartService</code> from an XML element. - * - * @param element - * the <code>Element</code> to deserialize - * @return a deserialized <code>MartService</code> - */ - public static MartService elementToMartService(Element element) { - return MartService.getMartService(element - .getAttributeValue(LOCATION_ATTRIBUTE)); - } - - /** - * Converts a <code>MartDataset</code> to an XML element. - * - * @param dataset - * the <code>MartDataset</code> to serialize - * @param namespace - * the <code>Namespace</code> to use when constructing the - * <code>Element</code> - * @return an XML serialization of the <code>MartDataset</code> - */ - public static Element datasetToElement(MartDataset dataset, - Namespace namespace) { - Element element = new Element(MART_DATASET_ELEMENT, namespace); - element.setAttribute(DISPLAY_NAME_ATTRIBUTE, dataset.getDisplayName()); - element.setAttribute(NAME_ATTRIBUTE, dataset.getName()); - element.setAttribute(TYPE_ATTRIBUTE, dataset.getType()); - element.setAttribute(INITIAL_BATCH_SIZE_ATTRIBUTE, String - .valueOf(dataset.getInitialBatchSize())); - element.setAttribute(MAXIMUM_BATCH_SIZE_ATTRIBUTE, String - .valueOf(dataset.getMaximumBatchSize())); - element.setAttribute(VISIBLE_ATTRIBUTE, String.valueOf(dataset - .isVisible())); - if (dataset.getInterface() != null) { - element.setAttribute(INTERFACE_ATTRIBUTE, dataset.getInterface()); - } - if (dataset.getModified() != null) { - element.setAttribute(MODIFIED_ATTRIBUTE, dataset.getModified()); - } - element.addContent(locationToElement(dataset.getMartURLLocation(), - namespace)); - return element; - } - - /** - * Creates a <code>MartDataset</code> from an XML element. - * - * @param element - * the <code>Element</code> to deserialize - * @param namespace - * the <code>Namespace</code> containing the - * <code>Element</code> - * @return a deserialized <code>MartDataset</code> - */ - public static MartDataset elementToDataset(Element element, - Namespace namespace) { - MartDataset dataset = new MartDataset(); - dataset.setDisplayName(element - .getAttributeValue(DISPLAY_NAME_ATTRIBUTE)); - dataset.setName(element.getAttributeValue(NAME_ATTRIBUTE)); - dataset.setType(element.getAttributeValue(TYPE_ATTRIBUTE)); - dataset.setInitialBatchSize(Long.parseLong(element - .getAttributeValue(INITIAL_BATCH_SIZE_ATTRIBUTE))); - dataset.setMaximumBatchSize(Long.parseLong(element - .getAttributeValue(MAXIMUM_BATCH_SIZE_ATTRIBUTE))); - dataset.setVisible(Boolean.getBoolean(element - .getAttributeValue(VISIBLE_ATTRIBUTE))); - dataset.setInterface(element.getAttributeValue(INTERFACE_ATTRIBUTE)); - dataset.setModified(element.getAttributeValue(MODIFIED_ATTRIBUTE)); - dataset.setMartURLLocation(elementToLocation(element.getChild( - MART_URL_LOCATION_ELEMENT, namespace))); - return dataset; - } - - /** - * Creates a <code>MartRegistry</code> from an XML element. - * - * @param element - * the <code>Element</code> to deserialize - * @param namespace - * the <code>Namespace</code> containing the - * <code>Element</code> - * @return a deserialized <code>MartRegistry</code> - */ - public static MartRegistry elementToRegistry(Element root, - Namespace namespace) { - MartRegistry registry = new MartRegistry(); - List<Element> children = root.getChildren(); - for (Element childElement : children) { - if (childElement.getNamespace().equals(namespace)) { - if (childElement.getName().equals(MART_URL_LOCATION_ELEMENT)) { - MartURLLocation martURLLocation = MartServiceXMLHandler - .elementToLocation(childElement); - martURLLocation.setVirtualSchema("default"); - registry.addMartURLLocation(martURLLocation); - } else if (childElement.getName() - .equals(VIRTUAL_SCHEMA_ELEMENT)) { - String virtualSchema = childElement - .getAttributeValue(NAME_ATTRIBUTE); - List<Element> locations = childElement.getChildren( - MART_URL_LOCATION_ELEMENT, namespace); - for (Element location : locations) { - MartURLLocation martURLLocation = MartServiceXMLHandler - .elementToLocation(location); - martURLLocation.setVirtualSchema(virtualSchema); - registry.addMartURLLocation(martURLLocation); - } - } - } - } - return registry; - } - - /** - * Converts a <code>MartURLLocation</code> to an XML element. - * - * @param location - * the <code>MartURLLocation</code> to serialize - * @param namespace - * the <code>Namespace</code> to use when constructing the - * <code>Element</code> - * @return an XML serialization of the <code>MartURLLocation</code> - */ - public static Element locationToElement(MartURLLocation location, - Namespace namespace) { - Element element = new Element(MART_URL_LOCATION_ELEMENT, namespace); - if (location.getDatabase() != null) { - element.setAttribute(DATABASE_ATTRIBUTE, location.getDatabase()); - } - element.setAttribute(DEFAULT_ATTRIBUTE, location.isDefault() ? "1" - : "0"); - element.setAttribute(DISPLAY_NAME_ATTRIBUTE, location.getDisplayName()); - element.setAttribute(HOST_ATTRIBUTE, location.getHost()); - if (location.getIncludeDatasets() != null) { - element.setAttribute(INCLUDE_DATASETS_ATTRIBUTE, location - .getIncludeDatasets()); - } - if (location.getMartUser() != null) { - element.setAttribute(MART_USER_ATTRIBUTE, location.getMartUser()); - } - element.setAttribute(NAME_ATTRIBUTE, location.getName()); - if (location.getPath() != null) { - element.setAttribute(PATH_ATTRIBUTE, location.getPath()); - } - element - .setAttribute(PORT_ATTRIBUTE, String - .valueOf(location.getPort())); - element.setAttribute(SERVER_VIRTUAL_SCHEMA_ATTRIBUTE, location - .getServerVirtualSchema()); - if (location.getVirtualSchema() != null) { - element.setAttribute(VIRTUAL_SCHEMA_ATTRIBUTE, location - .getVirtualSchema()); - } - element.setAttribute(VISIBLE_ATTRIBUTE, location.isVisible() ? "1" - : "0"); - element.setAttribute(REDIRECT_ATTRIBUTE, location.isRedirect() ? "1" - : "0"); - return element; - } - - /** - * Creates a <code>MartURLLocation</code> from an XML element. - * - * @param element - * the <code>Element</code> to deserialize - * @return a deserialized <code>MartURLLocation</code> - */ - public static MartURLLocation elementToLocation(Element element) { - MartURLLocation location = new MartURLLocation(); - location.setDatabase(element.getAttributeValue(DATABASE_ATTRIBUTE)); - location.setDefault("1".equals(element - .getAttributeValue(DEFAULT_ATTRIBUTE))); - location.setDisplayName(element - .getAttributeValue(DISPLAY_NAME_ATTRIBUTE)); - location.setHost(element.getAttributeValue(HOST_ATTRIBUTE)); - location.setIncludeDatasets(element - .getAttributeValue(INCLUDE_DATASETS_ATTRIBUTE)); - location.setMartUser(element.getAttributeValue(MART_USER_ATTRIBUTE)); - location.setName(element.getAttributeValue(NAME_ATTRIBUTE)); - location.setPath(element.getAttributeValue(PATH_ATTRIBUTE)); - try { - location.setPort(Integer.parseInt(element - .getAttributeValue(PORT_ATTRIBUTE))); - } catch (NumberFormatException e) { - location.setPort(80); - } - location.setServerVirtualSchema(element - .getAttributeValue(SERVER_VIRTUAL_SCHEMA_ATTRIBUTE)); - location.setVirtualSchema(element - .getAttributeValue(VIRTUAL_SCHEMA_ATTRIBUTE)); - location.setVisible("1".equals(element - .getAttributeValue(VISIBLE_ATTRIBUTE))); - location.setRedirect("1".equals(element - .getAttributeValue(REDIRECT_ATTRIBUTE))); - return location; - } - - /** - * Creates a <code>MartQuery</code> from an XML element. - * - * @param element - * the <code>Element</code> to deserialize - * @param namespace - * the <code>Namespace</code> containing the - * <code>Element</code> - * @return a deserialized <code>MartQuery</code> - */ - public static MartQuery elementToMartQuery(Element element, - Namespace namespace) { - MartQuery martQuery = new MartQuery(); - martQuery.setMartService(MartServiceXMLHandler - .elementToMartService(element.getChild(MART_SERVICE_ELEMENT, - namespace))); - martQuery.setMartDataset(elementToDataset(element.getChild( - MART_DATASET_ELEMENT, namespace), namespace)); - martQuery.setQuery(QueryXMLHandler.elementToQuery(element.getChild( - QueryXMLHandler.QUERY_ELEMENT, namespace), namespace)); - Element linksElement = element.getChild(LINKED_DATASETS_ELEMENT, namespace); - if (linksElement != null) { - List linkedDatasets = linksElement.getChildren(LINKED_DATASETS_ELEMENT, - namespace); - for (Iterator iter = linkedDatasets.iterator(); iter.hasNext();) { - Element datasetElement = (Element) iter.next(); - String datasetName = datasetElement.getAttributeValue(NAME_ATTRIBUTE); - String linkId = datasetElement.getAttributeValue(LINK_ATTRIBUTE); - martQuery.addLinkedDataset(datasetName, linkId); - } - } - return martQuery; - } - - /** - * Converts a <code>MartQuery</code> to an XML element. - * - * @param martQuery - * the <code>MartQuery</code> to serialize - * @param namespace - * the <code>Namespace</code> to use when constructing the - * <code>Element</code> - * @return an XML serialization of the <code>MartQuery</code> - */ - public static Element martQueryToElement(MartQuery martQuery, - Namespace namespace) { - Element element = new Element(MART_QUERY_ELEMENT, namespace); - element.addContent(martServiceToElement(martQuery.getMartService(), - namespace)); - element.addContent(datasetToElement(martQuery.getMartDataset(), - namespace)); - element.addContent(QueryXMLHandler.queryToElement(martQuery.getQuery(), - namespace)); - Set linkedDatasets = martQuery.getLinkedDatasets(); - if (linkedDatasets.size() > 0) { - Element linksElement = new Element(LINKED_DATASETS_ELEMENT, namespace); - for (Iterator iter = linkedDatasets.iterator(); iter.hasNext();) { - String datasetName = (String) iter.next(); - Element datasetElement = new Element(LINKED_DATASETS_ELEMENT, namespace); - datasetElement.setAttribute(NAME_ATTRIBUTE, datasetName); - datasetElement.setAttribute(LINK_ATTRIBUTE, martQuery - .getLink(datasetName)); - linksElement.addContent(datasetElement); - } - element.addContent(linksElement); - } - return element; - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartURLLocation.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartURLLocation.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartURLLocation.java deleted file mode 100644 index 476956d..0000000 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartURLLocation.java +++ /dev/null @@ -1,422 +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: MartURLLocation.java,v $ - * Revision $Revision: 1.2 $ - * Release status $State: Exp $ - * Last modified on $Date: 2007/10/04 14:15:59 $ - * by $Author: davidwithers $ - * Created on 17-Mar-2006 - *****************************************************************/ -package org.biomart.martservice; - -import org.ensembl.mart.lib.config.MartLocation; - -/** - * The MartURLLocation contained by the MartRegistry returned by a BioMart web - * service. - * - * @author David Withers - */ -public class MartURLLocation implements MartLocation { - private static final String URL_TYPE = "URL"; - - private String database; - - private boolean defaultValue; - - private String displayName; - - private String host; - - private String includeDatasets; - - private String martUser; - - private String name; - - private String path; - - private int port; - - private String serverVirtualSchema; - - private String virtualSchema; - - private boolean visible; - - private boolean redirect; - - /** - * Returns the database. - * - * @return the database - */ - public String getDatabase() { - return database; - } - - /** - * Sets the database. - * - * @param database the new database - */ - public void setDatabase(String database) { - this.database = database; - } - - /** - * Returns true if the default flag is set. - * - * @return true if the default flag is set - */ - public boolean isDefault() { - return defaultValue; - } - - /** - * Sets the default flag. - * - * @param defaultValue - * the value of the default flag - */ - public void setDefault(boolean defaultValue) { - this.defaultValue = defaultValue; - } - - /** - * 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 host. - * - * @return the host. - */ - public String getHost() { - return host; - } - - /** - * Sets the host. - * - * @param host - * the host to set. - */ - public void setHost(String host) { - this.host = host; - } - - /** - * Returns the includeDatasets. - * - * @return the includeDatasets - */ - public String getIncludeDatasets() { - return includeDatasets; - } - - /** - * Sets the includeDatasets. - * - * @param includeDatasets the new includeDatasets - */ - public void setIncludeDatasets(String includeDatasets) { - this.includeDatasets = includeDatasets; - } - - /** - * Returns the martUser. - * - * @return the martUser - */ - public String getMartUser() { - return martUser; - } - - /** - * Sets the martUser. - * - * @param martUser the new martUser - */ - public void setMartUser(String martUser) { - this.martUser = martUser; - } - - /** - * 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 path. - * - * @return the path - */ - public String getPath() { - return path; - } - - /** - * Sets the path. - * - * @param path the new path - */ - public void setPath(String path) { - this.path = path; - } - - /** - * Returns the port. - * - * @return the port. - */ - public int getPort() { - return port; - } - - /** - * Sets the port. - * - * @param port - * the port to set. - */ - public void setPort(int port) { - this.port = port; - } - - /** - * Returns the serverVirtualSchema. - * - * @return the serverVirtualSchema. - */ - public String getServerVirtualSchema() { - return serverVirtualSchema; - } - - /** - * Sets the serverVirtualSchema. - * - * @param serverVirtualSchema - * the serverVirtualSchema to set. - */ - public void setServerVirtualSchema(String serverVirtualSchema) { - this.serverVirtualSchema = serverVirtualSchema; - } - - /** - * Returns the virtualSchema. - * - * @return the virtualSchema. - */ - public String getVirtualSchema() { - return virtualSchema; - } - - /** - * Sets the virtualSchema. - * - * @param virtualSchema - * the virtualSchema to set. - */ - public void setVirtualSchema(String virtualSchema) { - this.virtualSchema = virtualSchema; - } - - /** - * Returns true if the location is visible. - * - * @return Returns the visible. - */ - public boolean isVisible() { - return visible; - } - - /** - * @param visible - * The visible to set. - */ - public void setVisible(boolean visible) { - this.visible = visible; - } - - /** - * Returns true if this location is redirected. - * - * @return the redirect - */ - public boolean isRedirect() { - return redirect; - } - - /** - * @param redirect the redirect to set - */ - public void setRedirect(boolean redirect) { - this.redirect = redirect; - } - - /* - * (non-Javadoc) - * - * @see org.ensembl.mart.lib.config.MartLocation#getType() - */ - public String getType() { - return URL_TYPE; - } - - /** - * Returns the display name. - * - * @return the display name - */ - public String toString() { - return getDisplayName(); - } - - @Override - public int hashCode() { - final int prime = 31; - int result = 1; - result = prime * result - + ((database == null) ? 0 : database.hashCode()); - result = prime * result + (defaultValue ? 1231 : 1237); - result = prime * result - + ((displayName == null) ? 0 : displayName.hashCode()); - result = prime * result + ((host == null) ? 0 : host.hashCode()); - result = prime * result - + ((includeDatasets == null) ? 0 : includeDatasets.hashCode()); - result = prime * result - + ((martUser == null) ? 0 : martUser.hashCode()); - result = prime * result + ((name == null) ? 0 : name.hashCode()); - result = prime * result + ((path == null) ? 0 : path.hashCode()); - result = prime * result + port; - result = prime * result + (redirect ? 1231 : 1237); - result = prime - * result - + ((serverVirtualSchema == null) ? 0 : serverVirtualSchema - .hashCode()); - result = prime * result - + ((virtualSchema == null) ? 0 : virtualSchema.hashCode()); - result = prime * result + (visible ? 1231 : 1237); - return result; - } - - @Override - public boolean equals(Object obj) { - if (this == obj) - return true; - if (obj == null) - return false; - if (getClass() != obj.getClass()) - return false; - final MartURLLocation other = (MartURLLocation) obj; - if (database == null) { - if (other.database != null) - return false; - } else if (!database.equals(other.database)) - return false; - if (defaultValue != other.defaultValue) - return false; - if (displayName == null) { - if (other.displayName != null) - return false; - } else if (!displayName.equals(other.displayName)) - return false; - if (host == null) { - if (other.host != null) - return false; - } else if (!host.equals(other.host)) - return false; - if (includeDatasets == null) { - if (other.includeDatasets != null) - return false; - } else if (!includeDatasets.equals(other.includeDatasets)) - return false; - if (martUser == null) { - if (other.martUser != null) - return false; - } else if (!martUser.equals(other.martUser)) - return false; - if (name == null) { - if (other.name != null) - return false; - } else if (!name.equals(other.name)) - return false; - if (path == null) { - if (other.path != null) - return false; - } else if (!path.equals(other.path)) - return false; - if (port != other.port) - return false; - if (redirect != other.redirect) - return false; - if (serverVirtualSchema == null) { - if (other.serverVirtualSchema != null) - return false; - } else if (!serverVirtualSchema.equals(other.serverVirtualSchema)) - return false; - if (virtualSchema == null) { - if (other.virtualSchema != null) - return false; - } else if (!virtualSchema.equals(other.virtualSchema)) - return false; - if (visible != other.visible) - return false; - return true; - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiver.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiver.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiver.java deleted file mode 100644 index cc1d062..0000000 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiver.java +++ /dev/null @@ -1,61 +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: ResultReceiver.java,v $ - * Revision $Revision: 1.2 $ - * Release status $State: Exp $ - * Last modified on $Date: 2008/07/31 15:06:49 $ - * by $Author: davidwithers $ - * Created on Jan 18, 2008 - *****************************************************************/ -package org.biomart.martservice; - -/** - * An interface for receiving results of a Query. - * - * @author David Withers - */ -public interface ResultReceiver { - - /** - * Receives a single row from the results of executing a Query. - * - * This method will be called frequently and should not block. - * - * @param resultRow - */ - public void receiveResult(Object[] resultRow, long index) throws ResultReceiverException; - - /** - * Receives an error for a single row from the results of executing a Query. - * - * This method will be called frequently and should not block. - * - * @param resultRow - */ - public void receiveError(String errorMessage, long index) throws ResultReceiverException; - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiverException.java ---------------------------------------------------------------------- diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiverException.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiverException.java deleted file mode 100644 index c3498e6..0000000 --- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiverException.java +++ /dev/null @@ -1,85 +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: ResultReceiverException.java,v $ - * Revision $Revision: 1.1 $ - * Release status $State: Exp $ - * Last modified on $Date: 2008/03/04 16:47:57 $ - * by $Author: davidwithers $ - * Created on 05-May-2006 - *****************************************************************/ -package org.biomart.martservice; - -/** - * - * @author David Withers - */ -public class ResultReceiverException extends Exception { - private static final long serialVersionUID = 7151337259555845771L; - - /** - * Constructs a new exception with no detail message. - * - */ - public ResultReceiverException() { - 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 ResultReceiverException(String message, Throwable cause) { - super(message, cause); - } - - /** - * Constructs a new exception with the specified detail message and cause. - * - * @param message - * the detail message - */ - public ResultReceiverException(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 ResultReceiverException(Throwable cause) { - super(cause); - } - -}
