示例#1
0
  /** getXml. */
  @Get
  public void getXml() {
    authenticate();
    WorkflowService ss = BeanFactory.getWorkflowServiceBean();
    Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
    JaxbObject<Workflow> jaxbTool = new JaxbObject<Workflow>();
    Workflow workflow = (Workflow) testIfNull(ss.findBySWAccession(Integer.parseInt(getId())));
    Workflow dto = copier.hibernate2dto(Workflow.class, workflow);

    if (fields.contains("params")) {
      SortedSet<WorkflowParam> wps = workflow.getWorkflowParams();
      if (wps != null) {
        SortedSet<WorkflowParam> copiedParams = new TreeSet<WorkflowParam>();
        for (WorkflowParam param : workflow.getWorkflowParams()) {
          copiedParams.add(copier.hibernate2dto(WorkflowParam.class, param));
        }
        dto.setWorkflowParams(copiedParams);
      } else {
        Log.info("Could not be found: workflow params");
      }
    }
    if (fields.contains("attributes")) {
      Set<WorkflowAttribute> was = workflow.getWorkflowAttributes();
      if (was != null && !was.isEmpty()) {
        Set<WorkflowAttribute> newwas = new TreeSet<WorkflowAttribute>();
        for (WorkflowAttribute wa : was) {
          newwas.add(copier.hibernate2dto(WorkflowAttribute.class, wa));
        }
        dto.setWorkflowAttributes(newwas);
      }
    }

    Document line = XmlTools.marshalToDocument(jaxbTool, dto);
    getResponse().setEntity(XmlTools.getRepresentation(line));
  }
示例#2
0
  /** getXml. */
  @Get
  public void getXml() {
    JaxbObject<Lane> jaxbTool = new JaxbObject<>();
    Hibernate3DtoCopier copier = new Hibernate3DtoCopier();

    Lane dto;
    authenticate();

    LaneService ss = BeanFactory.getLaneServiceBean();
    Lane lane = testIfNull(ss.findBySWAccession(getId()));
    CollectionPropertyName<Lane>[] createCollectionPropertyNames =
        CollectionPropertyName.createCollectionPropertyNames(
            Lane.class, new String[] {"laneAttributes"});
    dto =
        copier.hibernate2dto(
            Lane.class,
            lane,
            new Class<?>[] {LibraryStrategy.class, LibrarySource.class, LibrarySelection.class},
            createCollectionPropertyNames);

    if (fields.contains("sequencerRun")) {
      SequencerRun sr = lane.getSequencerRun();
      if (sr != null) {
        SequencerRun copySR = copier.hibernate2dto(SequencerRun.class, sr);
        dto.setSequencerRun(copySR);
      } else {
        Log.info("Could not be found sequencer run");
      }
    }

    Document line = XmlTools.marshalToDocument(jaxbTool, dto);
    getResponse().setEntity(XmlTools.getRepresentation(line));
  }
示例#3
0
 @Test
 public void testMonitoring() throws IOException {
   String listCommand =
       "-p net.sourceforge.seqware.pipeline.plugins.WorkflowStatusChecker -- --tp 1000";
   String listOutput = ITUtility.runSeqWareJar(listCommand, ReturnValue.SUCCESS);
   Log.info(listOutput);
 }
示例#4
0
 /**
  * getHtml.
  *
  * @param obj a {@link java.lang.Object} object.
  * @param registration a {@link net.sourceforge.seqware.common.model.Registration} object.
  * @param listSeqencerRunNodeId a {@link java.util.List} object.
  * @param treeType a {@link java.lang.String} object.
  * @return a {@link java.lang.String} object.
  */
 public static String getHtml(
     Object obj, Registration registration, List<String> listSeqencerRunNodeId, String treeType) {
   String html = "";
   if (obj instanceof SequencerRun) {
     html = getAllHtml((SequencerRun) obj, registration, null, treeType);
   }
   if (obj instanceof Lane) {
     html = getAllHtml((Lane) obj, registration, null, treeType);
   }
   if (obj instanceof IUS) {
     Log.info("ius call");
     html = getAllHtml((IUS) obj, registration, null, false, false, treeType);
   }
   if (obj instanceof Processing) {
     html =
         getAllHtml(
             (Processing) obj,
             registration,
             null,
             0,
             listSeqencerRunNodeId,
             true,
             false,
             treeType);
   }
   return html;
 }
示例#5
0
 @Test
 public void testLaunchScheduled() throws IOException {
   // launch-scheduled
   String schedCommand =
       "-p net.sourceforge.seqware.pipeline.plugins.WorkflowLauncher -- --launch-scheduled";
   String schedOutput = ITUtility.runSeqWareJar(schedCommand, ReturnValue.SUCCESS);
   Log.info(schedOutput);
 }
  private String getNameNode(Integer id, String typeNode) {
    String name = "";

    if ("st".equals(typeNode)) {
      Log.info("find Study");
      name = getStudyService().findByID(id).getTitle();
    }
    if ("exp".equals(typeNode)) {
      Log.info("find Experiment");
      name = getExperimentService().findByID(id).getTitle();
    }
    if ("sam".equals(typeNode)) {
      Log.info("find Sample");
      name = getSampleService().findByID(id).getTitle();
    }
    if ("seq".equals(typeNode)) {
      Log.info("find Lane");
      name = getLaneService().findByID(id).getName();
    }
    if ("ius".equals(typeNode)) {
      Log.info("find IUS");
      name = getIUSService().findByID(id).getName();
    }
    if ("ae".equals(typeNode)) {
      Log.info("find Study");
      name = "SWID " + getProcessingService().findByID(id).getSwAccession().toString();
    }
    if ("sr".equals(typeNode)) {
      Log.info("find Seq Run");
      name = getSequencerRunService().findByID(id).getName();
    }

    return name;
  }
  /** getXml. */
  @Get
  public void getXml() {
    authenticate();

    JaxbObject<Lane> jaxbTool = new JaxbObject<>();
    Hibernate3DtoCopier copier = new Hibernate3DtoCopier();

    SampleService ss = BeanFactory.getSampleServiceBean();
    Sample sample = testIfNull(ss.findBySWAccession(getId()));
    CollectionPropertyName<Sample>[] createCollectionPropertyNames =
        CollectionPropertyName.createCollectionPropertyNames(
            Sample.class, new String[] {"sampleAttributes"});
    Sample dto =
        copier.hibernate2dto(
            Sample.class, sample, new Class<?>[] {}, createCollectionPropertyNames);

    if (fields.contains("lanes")) {
      SortedSet<Lane> lanes = sample.getLanes();
      if (lanes != null) {
        SortedSet<Lane> copiedLanes = new TreeSet<>();
        for (Lane lane : lanes) {
          copiedLanes.add(copier.hibernate2dto(Lane.class, lane));
        }
        dto.setLanes(copiedLanes);
      } else {
        Log.info("Could not be found: lanes");
      }
    }
    if (fields.contains("ius")) {
      SortedSet<IUS> ius = sample.getIUS();
      if (ius != null) {
        SortedSet<IUS> copiedIUS = new TreeSet<>();
        for (IUS i : ius) {
          copiedIUS.add(copier.hibernate2dto(IUS.class, i));
        }
        dto.setIUS(copiedIUS);
      }
      {
        Log.info("Could not be found : ius");
      }
    }

    Document line = XmlTools.marshalToDocument(jaxbTool, dto);
    getResponse().setEntity(XmlTools.getRepresentation(line));
  }
示例#8
0
 /**
  * getInstance.
  *
  * @return a {@link net.sourceforge.seqware.common.ContextImpl} object.
  */
 public static synchronized ContextImpl getInstance() {
   if (ctx == null) {
     ApplicationContext c = ContextLoader.getCurrentWebApplicationContext();
     if (c == null) {
       Log.info("ContextImpl: Could not find web context. Switching to XML context.");
       c = new ClassPathXmlApplicationContext("applicationContext.xml");
     }
     ctx = (ContextImpl) c.getBean("contextImpl");
   }
   return ctx;
 }
 @Test
 public void runDatabaseCheck() throws IOException {
   String listCommand = "-p net.sourceforge.seqware.pipeline.plugins.checkdb.CheckDB";
   String listOutput = ITUtility.runSeqWareJar(listCommand, ReturnValue.SUCCESS, null);
   Log.info(listOutput);
   String[] split = listOutput.split("Printed report to ");
   File report = new File(split[split.length - 1].trim());
   String readFileToString = FileUtils.readFileToString(report, (Charset) null);
   Assert.assertTrue("report empty", readFileToString.length() > 0);
   Assert.assertTrue(
       "report does not contain report", readFileToString.contains("CheckDB Report"));
   Assert.assertTrue("report contains exceptions", !readFileToString.contains("Exception"));
   FileUtils.deleteQuietly(report);
 }
示例#10
0
  /**
   * {@inheritDoc}
   *
   * @return
   */
  @Override
  @Put
  public Representation put(Representation entity) {
    authenticate();
    Representation representation = null;
    Lane newLane = null;
    JaxbObject<Lane> jo = new JaxbObject<>();
    try {

      String text = entity.getText();
      newLane = (Lane) XmlTools.unMarshal(jo, new Lane(), text);
    } catch (SAXException | IOException ex) {
      ex.printStackTrace();
      throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, ex);
    }
    try {
      LaneService fs = BeanFactory.getLaneServiceBean();
      Lane lane = testIfNull(fs.findByID(newLane.getLaneId()));
      lane.givesPermission(registration);
      // simple types
      String name = newLane.getName();
      String desc = newLane.getDescription();
      Integer laneIndex = newLane.getLaneIndex();
      String cycleDescriptor = newLane.getCycleDescriptor();
      Boolean skip = newLane.getSkip();
      String tags = newLane.getTags();
      String regions = newLane.getRegions();
      // foreign keys
      Sample sample = newLane.getSample();
      Registration owner = newLane.getOwner();

      Set<LaneAttribute> newAttributes = newLane.getLaneAttributes();

      if (name != null) {
        lane.setName(name);
      }
      if (desc != null) {
        lane.setDescription(desc);
      }
      if (laneIndex != null) {
        lane.setLaneIndex(laneIndex);
      }
      if (cycleDescriptor != null) {
        lane.setCycleDescriptor(cycleDescriptor);
      }
      if (skip != null) {
        lane.setSkip(skip);
      }
      if (tags != null) {
        lane.setTags(tags);
      }
      if (regions != null) {
        lane.setRegions(regions);
      }

      if (sample != null) {
        SampleService ss = BeanFactory.getSampleServiceBean();
        Sample newSample = ss.findByID(sample.getSampleId());
        if (newSample != null && newSample.givesPermission(registration)) {
          lane.setSample(newSample);
        } else if (newSample == null) {
          Log.info("Could not be found " + sample);
        }
      }

      if (owner != null) {
        RegistrationService rs = BeanFactory.getRegistrationServiceBean();
        Registration newReg = rs.findByEmailAddress(owner.getEmailAddress());
        if (newReg != null) {
          lane.setOwner(newReg);
        } else {
          Log.info("Could not be found " + owner);
        }
      } else if (lane.getOwner() == null) {
        lane.setOwner(registration);
      }
      if (newAttributes != null) {
        // SEQWARE-1577 - AttributeAnnotator cascades deletes when annotating
        LaneIDResource.mergeAttributes(lane.getLaneAttributes(), newAttributes, lane);
      }

      fs.update(registration, lane);

      Hibernate3DtoCopier copier = new Hibernate3DtoCopier();

      Lane detachedLane =
          copier.hibernate2dto(
              Lane.class,
              lane,
              new Class<?>[] {LibraryStrategy.class, LibrarySource.class, LibrarySelection.class},
              new CollectionPropertyName<?>[] {});

      Document line = XmlTools.marshalToDocument(jo, detachedLane);
      representation = XmlTools.getRepresentation(line);
      getResponse().setEntity(representation);
      getResponse()
          .setLocationRef(getRequest().getRootRef() + "/lanes/" + detachedLane.getSwAccession());
      getResponse().setStatus(Status.SUCCESS_CREATED);
    } catch (SecurityException e) {
      getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN, e.getMessage());
    } catch (Exception e) {
      e.printStackTrace();
      getResponse().setStatus(Status.SERVER_ERROR_INTERNAL, e.getMessage());
    }

    return representation;
  }
示例#11
0
  /** {@inheritDoc} */
  @Override
  @Put
  public Representation put(Representation entity) {
    authenticate();
    Representation representation = null;
    Experiment newObj = null;
    JaxbObject<Experiment> jo = new JaxbObject<Experiment>();
    try {
      String text = entity.getText();
      newObj = (Experiment) XmlTools.unMarshal(jo, new Experiment(), text);
    } catch (SAXException ex) {
      ex.printStackTrace();
      throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, ex);
    } catch (IOException e) {
      e.printStackTrace();
      throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, e);
    }
    try {
      ExperimentService service = BeanFactory.getExperimentServiceBean();
      Experiment exp = (Experiment) testIfNull(service.findByID(newObj.getExperimentId()));
      exp.givesPermission(registration);

      // simple types
      String title = newObj.getTitle();
      String name = newObj.getName();
      String desc = newObj.getDescription();
      String alias = newObj.getAlias();
      String accession = newObj.getAccession();
      String status = newObj.getStatus();
      String centerName = newObj.getCenterName();
      String sequencerSpace = newObj.getSequenceSpace();
      String baseCaller = newObj.getBaseCaller();
      String qualityScorer = newObj.getQualityScorer();
      Integer qualityNumberLevels = newObj.getQualityNumberOfLevels();
      Integer qualityMultiplier = newObj.getQualityMultiplier();
      Long expectedNumberSpots = newObj.getExpectedNumberSpots();
      Long expectedNumberReads = newObj.getExpectedNumberReads();

      // foreign keys
      Study study = newObj.getStudy();
      Registration owner = newObj.getOwner();

      // sets
      Set<ExperimentAttribute> expAttributes = newObj.getExperimentAttributes();

      if (title != null) {
        exp.setTitle(title);
      }
      if (name != null) {
        exp.setName(name);
      }
      if (desc != null) {
        exp.setDescription(desc);
      }
      if (alias != null) {
        exp.setAlias(alias);
      }
      if (accession != null) {
        exp.setAccession(accession);
      }
      if (status != null) {
        exp.setStatus(status);
      }
      if (centerName != null) {
        exp.setCenterName(centerName);
      }
      if (sequencerSpace != null) {
        exp.setSequenceSpace(sequencerSpace);
      }
      if (baseCaller != null) {
        exp.setBaseCaller(baseCaller);
      }
      if (qualityScorer != null) {
        exp.setQualityScorer(qualityScorer);
      }
      if (qualityNumberLevels != null) {
        exp.setQualityNumberOfLevels(qualityNumberLevels);
      }
      if (qualityMultiplier != null) {
        exp.setQualityMultiplier(qualityMultiplier);
      }
      if (expectedNumberSpots != null) {
        exp.setExpectedNumberSpots(expectedNumberSpots);
      }
      if (expectedNumberReads != null) {
        exp.setExpectedNumberReads(expectedNumberReads);
      }

      if (study != null) {
        StudyService ss = BeanFactory.getStudyServiceBean();
        Study newStudy = ss.findByID(study.getStudyId());
        if (newStudy != null && newStudy.givesPermission(registration)) {
          exp.setStudy(newStudy);
        } else if (newStudy == null) {
          Log.info("Could not be found " + study);
        }
      }

      if (owner != null) {
        RegistrationService rs = BeanFactory.getRegistrationServiceBean();
        Registration newReg = rs.findByEmailAddress(owner.getEmailAddress());
        if (newReg != null) {
          exp.setOwner(newReg);
        } else {
          Log.info("Could not be found " + owner);
        }
      } else if (exp.getOwner() == null) {
        exp.setOwner(registration);
      }

      if (null != expAttributes) {
        exp.getExperimentAttributes().clear();
        for (ExperimentAttribute ea : expAttributes) {
          ea.setExperiment(exp);
          exp.getExperimentAttributes().add(ea);
        }
      }

      service.update(registration, exp);

      Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
      Experiment detachedLane = copier.hibernate2dto(Experiment.class, exp);

      Document line = XmlTools.marshalToDocument(jo, detachedLane);
      representation = XmlTools.getRepresentation(line);
      getResponse().setEntity(representation);
      getResponse()
          .setLocationRef(
              getRequest().getRootRef() + "/experiments/" + detachedLane.getSwAccession());
      getResponse().setStatus(Status.SUCCESS_CREATED);
    } catch (SecurityException e) {
      getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN, e.getMessage());
    } catch (Exception e) {
      e.printStackTrace();
      getResponse().setStatus(Status.SERVER_ERROR_INTERNAL, e.getMessage());
    }

    return representation;
  }
  /**
   * {@inheritDoc}
   *
   * @return
   */
  @Override
  public ReturnValue do_run() {
    ReturnValue ret = new ReturnValue();
    ResultSet rs = null;
    MetadataDB mdb = null;
    PreparedStatement prepareStatement = null;
    try {
      String query =
          new StringBuilder()
              .append(
                  "select w.sw_accession, w.workflow_run_id, w.status, f.* FROM workflow_run w LEFT OUTER JOIN workflow_run_input_files f ")
              .append(
                  "ON w.workflow_run_id = f.workflow_run_id WHERE (status = 'completed' OR status= 'failed') AND ")
              .append("f.workflow_run_id IS NULL ORDER BY w.sw_accession;")
              .toString();

      Log.info("Executing query: " + query);
      mdb = DBAccess.get();

      List<int[]> ids =
          mdb.executeQuery(
              query,
              new ResultSetHandler<List<int[]>>() {
                @Override
                public List<int[]> handle(ResultSet rs) throws SQLException {
                  List<int[]> ids = new ArrayList<>();
                  while (rs.next()) {
                    ids.add(new int[] {rs.getInt("sw_accession"), rs.getInt("workflow_run_id")});
                  }
                  return ids;
                }
              });

      mdb.getDb().setAutoCommit(false);
      prepareStatement =
          mdb.getDb()
              .prepareStatement(
                  "INSERT INTO workflow_run_input_files (workflow_run_id, file_id) VALUES(?,?)");
      for (int[] i : ids) {
        int workflowSWID = i[0];
        int workflowRunID = i[1];
        Log.stdout("Working on workflow_run " + workflowSWID);

        // populate input files
        List<Integer> listOfFiles = this.getListOfFiles(workflowSWID);
        Log.stdout("Found " + listOfFiles.size() + " input files for workflow_run " + workflowSWID);
        // insert into new workflow_run_input_files table
        for (Integer fSWID : listOfFiles) {
          Integer fileID = this.metadata.getFile(fSWID).getFileId();
          prepareStatement.setInt(1, workflowRunID);
          prepareStatement.setInt(2, fileID);
          prepareStatement.executeUpdate();
        }
      }
      Log.stdout("Success!");
      mdb.getDb().commit();
      return ret;
    } catch (SQLException ex) {
      Log.fatal("Population failed, aborting.");
      Logger.getLogger(WorkflowRunFilesInitialPopulationPlugin.class.getName())
          .log(Level.SEVERE, null, ex);
      ret.setExitStatus(ReturnValue.FAILURE);
    } finally {
      if (mdb != null) {
        DbUtils.closeQuietly(mdb.getDb(), mdb.getSql(), rs);
      }
      DBAccess.close();
      DbUtils.closeQuietly(prepareStatement);
    }
    ret.setExitStatus(ReturnValue.FAILURE);
    return ret;
  }
示例#13
0
  @Test
  public void testPackageBundleAndInstallSeparately() throws IOException {

    separateTempDir = Files.createTempDir();
    Log.info("Trying to package archetype at: " + separateTempDir.getAbsolutePath());
    PluginRunner it = new PluginRunner();
    String SEQWARE_VERSION = it.getClass().getPackage().getImplementationVersion();
    Assert.assertTrue("unable to detect seqware version", SEQWARE_VERSION != null);
    Log.info("SeqWare version detected as: " + SEQWARE_VERSION);

    File packageDir = Files.createTempDir();

    // for this test, we're going to create, install and package just one archetype. Doing more
    // seems redundant for this test
    String[] archetypes = {
      "java-workflow" /*, "simplified-ftl-workflow", "legacy-ftl-workflow", "simple-legacy-ftl-workflow"*/
    };
    for (String archetype : archetypes) {
      String workflow = "seqware-archetype-" + archetype;
      // generate and install archetypes to local maven repo
      String command =
          "mvn archetype:generate -DarchetypeCatalog=local -Dpackage=com.seqware.github -DgroupId=com.github.seqware -DarchetypeArtifactId="
              + workflow
              + " -Dversion=1.0-SNAPSHOT -DarchetypeGroupId=com.github.seqware -DartifactId="
              + workflow
              + " -DworkflowDirectoryName="
              + workflow
              + " -DworkflowName="
              + workflow
              + " -DworkflowVersion=1.0-SNAPSHOT -B -Dgoals=install";
      String genOutput = ITUtility.runArbitraryCommand(command, 0, separateTempDir);
      Log.info(genOutput);
      // install the workflows to the database and record their information
      File workflowDir = new File(separateTempDir, workflow);
      File targetDir = new File(workflowDir, "target");
      File bundleDir =
          new File(
              targetDir,
              "Workflow_Bundle_" + workflow + "_1.0-SNAPSHOT_SeqWare_" + SEQWARE_VERSION);

      String packageCommand =
          "-p net.sourceforge.seqware.pipeline.plugins.BundleManager -verbose -- -b "
              + packageDir
              + " -p "
              + bundleDir.getAbsolutePath();
      String packageOutput = ITUtility.runSeqWareJar(packageCommand, ReturnValue.SUCCESS);
      Log.info(packageOutput);

      // locate the zip bundle and then install it
      File zippedBundle = new File(packageDir, bundleDir.getName() + ".zip");
      Assert.assertTrue(
          "zipped bundle " + zippedBundle.getAbsolutePath() + ".zip", zippedBundle.exists());

      String installCommand =
          "-p net.sourceforge.seqware.pipeline.plugins.BundleManager -verbose -- -b "
              + zippedBundle
              + " -i";
      String installOutput = ITUtility.runSeqWareJar(installCommand, ReturnValue.SUCCESS);
      Log.info(installOutput);
    }

    FileUtils.deleteDirectory(packageDir);
  }
  /**
   * Handles the user's request to submit a new study.
   *
   * @param request HttpServletRequest
   * @param response HttpServletResponse
   * @param command Study command object
   * @return ModelAndView
   * @throws java.lang.Exception if any.
   */
  public ModelAndView handleSubmit(
      HttpServletRequest request, HttpServletResponse response, UploadFile command)
      throws Exception {

    Registration registration = Security.getRegistration(request);
    if (registration == null) return new ModelAndView("redirect:/login.htm");

    ServletContext context = this.getServletContext();
    command.setFolderStore(context.getInitParameter("path.to.upload.directory"));
    command.setStrStartURL(context.getInitParameter("true.protocols"));

    ModelAndView modelAndView = null;
    BindingResult errors = this.validate(request, command);
    if (errors.hasErrors()) {
      Map model = errors.getModel();
      Integer id = getRequestedId(request);
      String typeNode = getRequestedTypeNode(request);
      String nameNode = getNameNode(id, typeNode);
      List<FileType> listFileType = getFileTypeService().list();

      model.put("id", id);
      model.put("tn", typeNode);
      model.put("nameNode", nameNode);
      model.put("listFileType", listFileType);

      modelAndView = new ModelAndView("UploadFile", model);
    } else {
      String folderStore = context.getInitParameter("path.to.upload.directory");

      // MultipartFile file = command.getFile();

      // MultipartFile file = command.getFileFromURL();

      Log.info("URL = " + command.getFileURL());
      Log.info("USE URL ? = " + command.getUseURL());

      FileType fileType = getFileTypeService().findByID(command.getFileTypeId());

      Integer id = getRequestedId(request);
      String typeNode = getRequestedTypeNode(request);

      Log.info("ID = " + id);
      Log.info("typeNode = " + typeNode);

      if ("st".equals(typeNode)) {
        Study study = getStudyService().findByID(id);
        getFileUploadService().uploadFile(study, command, fileType, registration);
      }

      if ("exp".equals(typeNode)) {
        Experiment experiment = getExperimentService().findByID(id);
        getFileUploadService().uploadFile(experiment, command, fileType, registration);
      }
      if ("sam".equals(typeNode)) {
        Sample sample = getSampleService().findByID(id);
        getFileUploadService().uploadFile(sample, command, fileType, registration);
      }
      if ("seq".equals(typeNode)) {
        Lane lane = getLaneService().findByID(id);
        getFileUploadService().uploadFile(lane, command, fileType, registration);
      }
      if ("ius".equals(typeNode)) {
        IUS ius = getIUSService().findByID(id);
        getFileUploadService().uploadFile(ius, command, fileType, registration);
      }
      if ("ae".equals(typeNode)) {
        Processing processing = getProcessingService().findByID(id);
        getFileUploadService().uploadFile(processing, command, fileType, registration);
      }
      if ("sr".equals(typeNode)) {
        SequencerRun sequencerRun = getSequencerRunService().findByID(id);
        getFileUploadService().uploadFile(sequencerRun, command, fileType, registration);
      }
      modelAndView = new ModelAndView(getViewName(request));
    }

    return modelAndView;
  }
示例#15
0
  /**
   * getAllHtml.
   *
   * @param processing a {@link net.sourceforge.seqware.common.model.Processing} object.
   * @param registration a {@link net.sourceforge.seqware.common.model.Registration} object.
   * @param openingNodeId a {@link java.lang.String} object.
   * @param currPosId a {@link java.lang.Integer} object.
   * @param listNodeId a {@link java.util.List} object.
   * @param isFirstCall a boolean.
   * @param isViewCurrentNode a boolean.
   * @param treeType a {@link java.lang.String} object.
   * @return a {@link java.lang.String} object.
   */
  public static String getAllHtml(
      Processing processing,
      Registration registration,
      String openingNodeId,
      Integer currPosId,
      List<String> listNodeId,
      boolean isFirstCall,
      boolean isViewCurrentNode,
      String treeType) {
    currPosId++;
    String id = getParentId(currPosId, listNodeId);

    if (id.indexOf("wfr_") != -1) {
      currPosId++;
      id = getParentId(currPosId, listNodeId);
    }

    if (id.indexOf("sr_") != -1 && !isViewCurrentNode) {
      SequencerRun sequencerRun = getParentSequencerRun(processing, Constant.getId(id));
      if (sequencerRun == null) {
        return "";
      }
      Log.info("openingNodeId = " + openingNodeId);
      return getAllHtml(
          sequencerRun, registration, openingNodeId /*processing.getProcessingId()*/, treeType);
    } else if (id.indexOf("seq_") != -1 && !isViewCurrentNode) {
      Lane lane = getParentLane(processing, Constant.getId(id));
      if (lane == null) {
        return "";
      }
      return getAllHtml(lane, registration, openingNodeId, treeType);
      // 1	return getAllHtml(lane, registration, processing.getProcessingId());
      // 2	return getAllHtml(lane, registration, processing.getProcessingId(), isOpenProc, true);
    } else if (id.indexOf("ius_") != -1 && !isViewCurrentNode) {
      Log.info("Proc IUS HTML");
      IUS ius = getParentIUS(processing, Constant.getId(id));
      if (ius == null) {
        return "";
      }
      return getAllHtml(ius, registration, openingNodeId, !isFirstCall, true, treeType);
    } else {
      Processing currProc;
      if (isFirstCall) {
        currProc = processing;
      } else {
        currProc = getParentProcessing(processing, Constant.getId(id));
        if (currProc == null) {
          return "";
        }
        openingNodeId = getParentId(currPosId - 1, listNodeId);
        if (openingNodeId.indexOf("wfr_") != -1) {
          openingNodeId = getParentId(currPosId - 2, listNodeId);
        }
      }

      Log.info("  -> openingNodeId Proc = " + openingNodeId);

      String childHtml =
          NodeHtmlUtil.getProcessingHtml(
              currProc, registration, TYPE_TREE, openingNodeId, treeType);

      String parentHtml =
          getAllHtml(currProc, registration, id, currPosId, listNodeId, false, false, treeType);
      String parentId = Constant.PROCESSING_PREFIX + currProc.getProcessingId();
      return NodeHtmlUtil.pasteHtmlIntoParentNode(childHtml, parentHtml, parentId, true);

      //			Log.info("currProcId = " + currProc.getProcessingId());

      //			String childHtml = NodeHtmlUtil.getProcessingHtml(currProc, registration, TYPE_TREE,
      // openingNodeId);

      //			String parentHtml = getAllHtml(currProc, registration, currProc.getProcessingId(),
      // currPosId, listNodeId, false, false);
      //			String parentId = Constant.PROCESSING_PREFIX + currProc.getProcessingId();
      //			return NodeHtmlUtil.pasteHtmlIntoParentNode(childHtml, parentHtml, parentId, true);
    }
  }
示例#16
0
  /** {@inheritDoc} */
  @Override
  public Representation put(Representation entity) {
    authenticate();
    Representation representation = null;
    Workflow newWorkflow = null;
    JaxbObject<Workflow> jo = new JaxbObject<Workflow>();
    try {
      String text = entity.getText();
      newWorkflow = (Workflow) XmlTools.unMarshal(jo, new Workflow(), text);
    } catch (SAXException ex) {
      ex.printStackTrace();
      throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, ex.getMessage());
    } catch (IOException e) {
      e.printStackTrace();
      throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, e.getMessage());
    }
    try {
      WorkflowService fs = BeanFactory.getWorkflowServiceBean();
      Workflow workflow = (Workflow) testIfNull(fs.findByID(newWorkflow.getWorkflowId()));
      workflow.givesPermission(registration);
      // simple types
      String name = newWorkflow.getName();
      String desc = newWorkflow.getDescription();
      String baseIniFile = newWorkflow.getBaseIniFile();
      String command = newWorkflow.getCommand();
      String cwd = newWorkflow.getCwd();
      String host = newWorkflow.getHost();
      String inputAlgorithm = newWorkflow.getInputAlgorithm();
      String permanentBundleLocation = newWorkflow.getPermanentBundleLocation();
      String seqwareVersion = newWorkflow.getSeqwareVersion();
      String template = newWorkflow.getTemplate();
      String username = newWorkflow.getUsername();
      String version = newWorkflow.getVersion();
      // foreign keys
      Registration owner = newWorkflow.getOwner();

      workflow.setName(name);
      workflow.setDescription(desc);
      workflow.setBaseIniFile(baseIniFile);
      workflow.setCommand(command);
      workflow.setCwd(cwd);
      workflow.setHost(host);
      workflow.setInputAlgorithm(inputAlgorithm);
      workflow.setPermanentBundleLocation(permanentBundleLocation);
      workflow.setSeqwareVersion(seqwareVersion);
      workflow.setTemplate(template);
      workflow.setUsername(username);
      workflow.setVersion(version);
      workflow.setUpdateTimestamp(new Date());
      workflow.setWorkflowClass(newWorkflow.getWorkflowClass());
      workflow.setWorkflowType(newWorkflow.getWorkflowType());
      workflow.setWorkflowEngine(newWorkflow.getWorkflowEngine());

      if (owner != null) {
        RegistrationService rs = BeanFactory.getRegistrationServiceBean();
        Registration newReg = rs.findByEmailAddress(owner.getEmailAddress());
        if (newReg != null) {
          workflow.setOwner(newReg);
        } else {
          Log.info("Could not be found: " + owner);
        }
      } else if (workflow.getOwner() == null) {
        workflow.setOwner(registration);
      }

      if (newWorkflow.getWorkflowAttributes() != null) {
        workflow.getWorkflowAttributes().clear();
        for (WorkflowAttribute wfa : newWorkflow.getWorkflowAttributes()) {
          wfa.setWorkflow(workflow);
          workflow.getWorkflowAttributes().add(wfa);
        }
      }
      fs.update(registration, workflow);
      Hibernate3DtoCopier copier = new Hibernate3DtoCopier();
      Workflow detachedWorkflow = copier.hibernate2dto(Workflow.class, workflow);

      Document line = XmlTools.marshalToDocument(jo, detachedWorkflow);
      representation = XmlTools.getRepresentation(line);
      getResponse().setEntity(representation);
      getResponse()
          .setLocationRef(
              getRequest().getRootRef() + "/workflows/" + detachedWorkflow.getSwAccession());
      getResponse().setStatus(Status.SUCCESS_CREATED);
    } catch (SecurityException e) {
      getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN, e.getMessage());
    } catch (Exception e) {
      e.printStackTrace();
      getResponse().setStatus(Status.SERVER_ERROR_INTERNAL, e.getMessage());
    }

    return representation;
  }