Java tutorial
/* * Copyright (C) 2011 SeqWare * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 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 General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package net.sourceforge.seqware.webservice.resources.tables; import java.sql.ResultSet; import java.sql.SQLException; import java.util.ArrayList; import java.util.HashSet; import java.util.List; import java.util.Set; import net.sf.beanlib.CollectionPropertyName; import net.sf.beanlib.hibernate3.Hibernate3DtoCopier; import net.sourceforge.seqware.common.business.FileService; import net.sourceforge.seqware.common.business.WorkflowRunService; import net.sourceforge.seqware.common.factory.BeanFactory; import net.sourceforge.seqware.common.factory.DBAccess; import net.sourceforge.seqware.common.metadata.MetadataDB; import net.sourceforge.seqware.common.model.File; import net.sourceforge.seqware.common.model.IUS; import net.sourceforge.seqware.common.model.Lane; import net.sourceforge.seqware.common.model.Processing; import net.sourceforge.seqware.common.model.WorkflowRun; import net.sourceforge.seqware.common.model.lists.WorkflowRunList; import net.sourceforge.seqware.common.model.lists.WorkflowRunList2; import net.sourceforge.seqware.common.util.Log; import net.sourceforge.seqware.common.util.xmltools.JaxbObject; import net.sourceforge.seqware.common.util.xmltools.XmlTools; import static net.sourceforge.seqware.webservice.resources.BasicResource.testIfNull; import org.apache.commons.dbutils.DbUtils; import org.apache.commons.dbutils.ResultSetHandler; import org.apache.commons.lang.ArrayUtils; import org.restlet.data.Status; import org.restlet.resource.Get; import org.restlet.resource.ResourceException; import org.w3c.dom.Document; /** * This resource will pull back the workflow runs that are generated from a * particular file. * * In order: a) Workflow runs found via processing, processing_relationship, * workflow_run b) Workflow runs found via the IUS, ius_workflow_runs c) * Workflow runs found via the lane, lane_workflow_runs * * @author dyuen * @version $Id: $Id */ public class FileChildWorkflowRunsResource extends DatabaseResource { /** * A direct search uses the workflow_run_input_files table rather than * attempting a search via the ius_workflow_run and lane_workflow_run and processing hierarchy */ public static final String DIRECT_SEARCH = "DIRECT_SEARCH"; /** * <p>Constructor for FileChildWorkflowRunsResource.</p> */ public FileChildWorkflowRunsResource() { super("file"); } /** * <p>getXml.</p> * @throws java.sql.SQLException */ @Get public void getXml() throws SQLException { authenticate(); final Hibernate3DtoCopier copier = new Hibernate3DtoCopier(); JaxbObject jaxbTool; Log.debug("Dealing with FileChildWorkflowRunsResource"); if (queryValues.keySet().contains(DIRECT_SEARCH) && queryValues.get(DIRECT_SEARCH).equalsIgnoreCase("true")) { handleDirectGetXML(); return; } FileService fs = BeanFactory.getFileServiceBean(); Set<File> files = new HashSet<>(); SEARCH_TYPE searchType = SEARCH_TYPE.CHILDREN_VIA_PROCESSING_RELATIONSHIP; Log.debug("File service started"); for (String key : queryValues.keySet()) { Log.debug("key: " + key + " -> " + queryValues.get(key)); if (key.equals("files")) { String value = queryValues.get(key); String[] filesSWIDs = value.split(","); for (String swid : filesSWIDs) { File findByID = (File) testIfNull(fs.findBySWAccession(Integer.valueOf(swid))); files.add(findByID); } } if (key.equals("search")) { String value = queryValues.get(key); try { searchType = SEARCH_TYPE.valueOf(value); } catch (IllegalArgumentException e) { throw new ResourceException(Status.CLIENT_ERROR_NOT_FOUND, "Object cannot be found"); } } } Log.debug("Working with " + files.size() + " files and doing a search of type: " + searchType.toString()); // these variables will be used to return information jaxbTool = new JaxbObject<>(); WorkflowRunList2 eList = new WorkflowRunList2(); eList.setList(new ArrayList()); Log.debug("JaxbObjects started"); assert eList.getList().isEmpty(); // the logic here is, we consider first workflow_run children found via the children of the processing // if that is empty, then we consider workflow_run found via the IUS (ius_workflow_run table) // if that is empty, then we consider workflow_run found via the lane (lane_workflow_run table) if (searchType == SEARCH_TYPE.CHILDREN_VIA_PROCESSING_RELATIONSHIP) { eList = handleWorkflowRunsViaChild(files, copier); } else if (searchType == SEARCH_TYPE.CHILDREN_VIA_IUS_WORKFLOW_RUN) { eList = handleWorkflowRunsViaIUS(files, copier); } else if (searchType == SEARCH_TYPE.CHILDREN_VIA_LANE_WORKFLOW_RUN) { eList = handleWorkflowRunsViaLane(files, copier); } final Document line = XmlTools.marshalToDocument(jaxbTool, eList); getResponse().setEntity(XmlTools.getRepresentation(line)); getResponse().setStatus(Status.SUCCESS_CREATED); } protected WorkflowRunList2 handleWorkflowRunsViaChild(final Set<File> files, final Hibernate3DtoCopier copier) { final WorkflowRunList2 results = new WorkflowRunList2(); for (File file : files) { //1) check if we have children in the processing tree that are relevant for (Processing p : file.getProcessings()) { for (Processing c : p.getChildren()) { if (c.getWorkflowRun() == null) { continue; } WorkflowRun dto = copier.hibernate2dto(WorkflowRun.class, c.getWorkflowRun()); results.add(dto); } } } if (results.getList().size() > 0) { Log.debug("Found " + results.getList().size() + " workflow runs via Processing children"); } else { Log.debug("Did not find any workflow runs via Processing children"); } return results; } protected WorkflowRunList2 handleWorkflowRunsViaIUS(Set<File> files, final Hibernate3DtoCopier copier) { WorkflowRunList2 result = new WorkflowRunList2(); Set<WorkflowRun> parentWorkflowRuns = new HashSet<>(); for (File file : files) { //2) check if we have children in the ius_workflow_runs that are relevant for (Processing p : file.getProcessings()) { WorkflowRun parentRun = p.getWorkflowRun(); if (parentRun == null) { parentRun = p.getWorkflowRunByAncestorWorkflowRunId(); } if (parentRun == null) { continue; } parentWorkflowRuns.add(parentRun); for (IUS ius : parentRun.getIus()) { for (WorkflowRun anyRun : ius.getWorkflowRuns()) { isWorkflowRunAttached(parentWorkflowRuns, anyRun); WorkflowRun dto = copier.hibernate2dto(WorkflowRun.class, anyRun); result.add(dto); } } } } if (result.getList().size() > 0) { Log.debug("Found " + result.getList().size() + " workflow runs via ius"); } else { Log.debug("Did not find any workflow runs via ius"); } return result; } protected WorkflowRunList2 handleWorkflowRunsViaLane(final Set<File> files, final Hibernate3DtoCopier copier) { final WorkflowRunList2 result = new WorkflowRunList2(); Set<WorkflowRun> parentWorkflowRuns = new HashSet<>(); for (File file : files) { //3) check if we have children in the lane_workflow_runs that are relevant for (Processing p : file.getProcessings()) { WorkflowRun parentRun = p.getWorkflowRun(); if (parentRun == null) { parentRun = p.getWorkflowRunByAncestorWorkflowRunId(); } if (parentRun == null) { continue; } parentWorkflowRuns.add(parentRun); for (Lane lane : parentRun.getLanes()) { for (WorkflowRun anyRun : lane.getWorkflowRuns()) { if (isWorkflowRunAttached(parentWorkflowRuns, anyRun)) continue; final WorkflowRun dto = copier.hibernate2dto(WorkflowRun.class, anyRun); result.add(dto); } } } } if (result.getList().size() > 0) { Log.debug("Found " + result.getList().size() + " workflow runs via lane"); } else { Log.debug("Did not find any workflow runs via lane"); } return result; } /** * Disallows a workflow run if it should not be considered since it is properly attached to the processing hierarchy * @param parentWorkflowRuns * @param anyRun * @return */ private boolean isWorkflowRunAttached(Set<WorkflowRun> parentWorkflowRuns, WorkflowRun anyRun) { if (parentWorkflowRuns.contains(anyRun)) { Log.debug("Disallowed " + anyRun.getSwAccession() + " because we have seen it on the same level as a file"); return true; } // check that this workflow run has not actually been linked up into the Processing hierarchy if (anyRun.getProcessings() != null && anyRun.getProcessings().size() > 0) { Log.debug("Disallowed " + anyRun.getSwAccession() + " because it is already attached via Processing.workflow_run_id"); return true; } if (anyRun.getOffspringProcessings() != null && anyRun.getOffspringProcessings().size() > 0) { Log.debug("Disallowed " + anyRun.getSwAccession() + " because it is already attached via Processing.ancestor_workflow_run_id"); return true; } return false; } /** * Use SQL to directly retrieve relevant workflows runs (defined as any workflow runs that * include one or more files in the set we were given) * @param files * @param interestingWorkflows * @return * @throws SQLException */ protected static WorkflowRunList2 directRetrieveWorkflowRuns(List<Integer> files, List<Integer> interestingWorkflows) throws SQLException { final Hibernate3DtoCopier copier = new Hibernate3DtoCopier(); final WorkflowRunList2 runs = new WorkflowRunList2(); runs.setList(new ArrayList()); if (files.size() > 0) { ResultSet rs = null; MetadataDB mdb = null; try { WorkflowRunService ss = BeanFactory.getWorkflowRunServiceBean(); StringBuilder query = new StringBuilder(); query.append("select distinct r.sw_accession from workflow_run r, workflow w, "); query.append("workflow_run_input_files rf, file f WHERE r.workflow_run_id = rf.workflow_run_id " + "AND rf.file_id = f.file_id " + "AND w.workflow_id = r.workflow_id " + "AND ("); // handle file accessions for (int i = 0; i < files.size() - 1; i++) { Integer fInt = files.get(i); query.append(" f.sw_accession = ").append(fInt).append(" OR"); } Integer fInt = files.get(files.size() - 1); query.append(" f.sw_accession = ").append(fInt).append(")"); // handle interesting workflow accessions if (interestingWorkflows.size() > 0) { query.append(" AND ("); for (int i = 0; i < interestingWorkflows.size() - 1; i++) { Integer wInt = interestingWorkflows.get(i); query.append(" w.sw_accession = ").append(wInt).append(" OR"); } Integer wInt = interestingWorkflows.get(interestingWorkflows.size() - 1); query.append(" w.sw_accession = ").append(wInt).append(")"); } query.append(" ORDER BY sw_accession"); Log.info("Executing query: " + query); mdb = DBAccess.get(); List<Integer> workflowSWIDs = mdb.executeQuery(query.toString(), new ResultSetHandler<List<Integer>>() { @Override public List<Integer> handle(ResultSet rs) throws SQLException { List<Integer> ids = new ArrayList<>(); while (rs.next()) { ids.add(rs.getInt("sw_accession")); } return ids; } }); for (int workflowSWID : workflowSWIDs) { WorkflowRun workflowRun = (WorkflowRun) testIfNull(ss.findBySWAccession(workflowSWID)); CollectionPropertyName<WorkflowRun>[] createCollectionPropertyNames = CollectionPropertyName .createCollectionPropertyNames(WorkflowRun.class, new String[] { "inputFileAccessions" }); WorkflowRun dto = copier.hibernate2dto(WorkflowRun.class, workflowRun, ArrayUtils.EMPTY_CLASS_ARRAY, createCollectionPropertyNames); runs.add(dto); } } finally { if (mdb != null) { DbUtils.closeQuietly(mdb.getDb(), mdb.getSql(), rs); } DBAccess.close(); } } return runs; } private void handleDirectGetXML() throws SQLException, NumberFormatException { JaxbObject jaxbTool; Log.info("Using direct search"); List<Integer> files = new ArrayList<>(); for (String key : queryValues.keySet()) { Log.debug("key: " + key + " -> " + queryValues.get(key)); if (key.equals("files")) { String value = queryValues.get(key); String[] filesSWIDs = value.split(","); for (String swid : filesSWIDs) { files.add(Integer.valueOf(swid)); } } } Log.debug("Working with " + files.size() + " files"); WorkflowRunList2 runs = directRetrieveWorkflowRuns(files, new ArrayList<Integer>()); // these variables will be used to return information jaxbTool = new JaxbObject<>(); Log.debug("JaxbObjects started"); assert runs.getList().isEmpty(); final Document line = XmlTools.marshalToDocument(jaxbTool, runs); getResponse().setEntity(XmlTools.getRepresentation(line)); getResponse().setStatus(Status.SUCCESS_CREATED); } public enum SEARCH_TYPE { CHILDREN_VIA_PROCESSING_RELATIONSHIP, CHILDREN_VIA_IUS_WORKFLOW_RUN, CHILDREN_VIA_LANE_WORKFLOW_RUN } }