Exemplo n.º 1
0
  public static GridPanel getSamplePairsByAnalysisPanel(
      List<FileGroup> analysisFileGroupList,
      Map<FileGroup, Sample> fileGroupHpa2SampleMap,
      Map<FileGroup, Sample> fileGroupMsp1SampleMap) {
    GridPanel panel = new GridPanel();
    panel.setTitle("Sample Pairs");
    panel.setResizable(true);
    panel.setMaximizable(true);
    panel.setOrder(1);

    GridContent content = new GridContent();
    content.addDataFields(new GridDataField("Analysis", "String")); // dataIndex, datatype
    content.addDataFields(
        new GridDataField("Hpa2/Beta-GT Sample", "String")); // dataIndex, datatype
    content.addDataFields(new GridDataField("Msp1 Sample", "String")); // dataIndex, datatype

    content.addColumn(
        new GridColumn("Analysis", "Analysis", 500, 0)); // header,dataIndex	     width=250; flex=0
    content.addColumn(
        new GridColumn(
            "Hpa2/Beta-GT Sample",
            "Hpa2/Beta-GT Sample",
            250,
            0)); // header,dataIndex width=250; flex=0
    content.addColumn(
        new GridColumn("Msp1 Sample", "Msp1 Sample", 1)); // header,dataIndex width=250; flex=0

    // create rows with  information
    for (FileGroup fileGroup : analysisFileGroupList) {

      if (fileGroupHpa2SampleMap.isEmpty()) {
        logger.debug("fileGroupHpa2SampleMap is empty ");
      }
      List<String> row = new ArrayList<String>();
      row.add(fileGroup.getDescription());
      Sample hpa2Sample = fileGroupHpa2SampleMap.get(fileGroup);
      String hpa2SampleName = "Unexpected Error";
      if (hpa2Sample != null) {
        hpa2SampleName = hpa2Sample.getName();

      } else {
        logger.debug("hpa2Sample is null");
      }
      Sample msp1Sample = fileGroupMsp1SampleMap.get(fileGroup);
      String msp1SampleName = "Standard Reference";
      if (msp1Sample != null && msp1Sample.getId().intValue() > 0) {
        msp1SampleName = msp1Sample.getName();
      }
      logger.debug("hpa2SampleName = " + hpa2SampleName);
      logger.debug("msp1SampleName = " + msp1SampleName);
      row.add(hpa2SampleName);
      row.add(msp1SampleName);
      content.addDataRow(row);
    }

    panel.setContent(content);
    return panel;
  }
Exemplo n.º 2
0
  public static GridPanel getPluginSpecificFileDefinitionsPanel(List<String> fileDescriptionList) {
    GridPanel panel = new GridPanel();
    panel.setTitle("HAM for HELPtagging File Descriptions");
    panel.setResizable(true);
    panel.setMaximizable(true);
    panel.setOrder(1);

    GridContent content = new GridContent();
    content.addDataFields(new GridDataField("Description", "String")); // dataIndex, datatype
    content.addColumn(new GridColumn("Description", "Description", 1)); // header,dataIndex flex=1

    for (String description : fileDescriptionList) {
      List<String> row = new ArrayList<String>();
      row.add(description);
      content.addDataRow(row);
    }
    panel.setContent(content);
    return panel;
  }
Exemplo n.º 3
0
  public static GridPanel getFilesByAnalysisPanel(
      WaspPluginRegistry pluginRegistry,
      FileUrlResolver fileUrlResolver,
      FileService fileService,
      List<FileGroup> analysisFileGroupList,
      Map<FileGroup, List<FileGroup>> outerCollectionFileGroupInnerFileGroupListMap) {
    // create the panel
    GridPanel panel = new GridPanel();
    panel.setTitle("Files By Analysis");
    panel.setResizable(true);
    panel.setMaximizable(true);
    panel.setOrder(1);
    panel.setGrouping(true);
    panel.setGroupField("Analysis");

    // create content (think of it as the table)
    GridContent content = new GridContent();
    // create the data model
    content.addDataFields(
        new GridDataField(
            "Analysis", "String")); // THIS WILL BE THE UNIQUE GROUPING FIELD //dataIndex, datatype
    content.addDataFields(new GridDataField("File", "String")); // dataIndex, datatype
    content.addDataFields(new GridDataField("Size", "String")); // dataIndex, datatype
    content.addDataFields(new GridDataField("MD5", "String")); // dataIndex, datatype

    // create columns and associate each column with its displayed header and a data model attribute
    // (dataIndex)
    /////// unique grouping field is NOT displayed: content.addColumn(new GridColumn("Analysis",
    // "Analysis"));//header,dataIndex
    content.addColumn(
        new GridColumn("File", "File", 1, true)); // header,dataIndex					flex=1, shown in tooltip
    content.addColumn(
        new GridColumn("Size", "Size", 100, 0)); // header,dataIndex					width=270; flex=0
    content.addColumn(
        new GridColumn("MD5", "MD5", 170, 0)); // header,dataIndex					width=270; flex=0

    for (FileGroup outerCollectionFileGroup : analysisFileGroupList) {
      String headerForGroup = outerCollectionFileGroup.getDescription();
      for (FileGroup innerFileGroup :
          outerCollectionFileGroupInnerFileGroupListMap.get(outerCollectionFileGroup)) {
        List<String> row = new ArrayList<String>();
        row.add(headerForGroup); // won't be displayed on each row, but will be the header for each
        // section (but must be part of the row)

        FileHandle fileHandle = new ArrayList<FileHandle>(innerFileGroup.getFileHandles()).get(0);
        row.add(fileHandle.getFileName());
        Integer sizeK = fileHandle.getSizek();
        if (sizeK != null) {
          row.add(fileHandle.getSizek().toString());
        } else {
          row.add("");
        }
        row.add(fileHandle.getMd5hash());
        content.addDataRow(row); // add the new row to the content				
        List<Action> actionList = new ArrayList<Action>();
        // add download action to the list
        String resolvedURL = "";
        try {
          resolvedURL = fileUrlResolver.getURL(fileHandle).toString();
        } catch (Exception e) {
          logger.debug("UNABLE TO RESOLVE URL for file: " + fileHandle.getFileName());
        }
        actionList.add(
            new Action("icon-download", "Download", CallbackFunctionType.DOWNLOAD, resolvedURL));

        if (!fileService.getTabViewProvidingPluginsByFileGroup(innerFileGroup).isEmpty())
          actionList.add(
              new Action(
                  "icon-view-file",
                  "View",
                  CallbackFunctionType.OPEN_IN_CSS_WIN,
                  innerFileGroup.getId().toString()));

        List<GenomeBrowserProviding> plugins = new ArrayList<>();
        plugins.addAll(pluginRegistry.getPlugins(GenomeBrowserProviding.class));
        for (GenomeBrowserProviding plugin : plugins) {
          Action action = plugin.getAction(innerFileGroup);
          if (action != null) {
            actionList.add(action);
          }
        }
        content.addActions(actionList);
      }
    }

    panel.setContent(content);
    return panel;
  }
Exemplo n.º 4
0
  public static GridPanel getLibrariesAndHcountFilesUsedByAnalysisPanel(
      List<FileGroup> analysisFileGroupList,
      Map<FileGroup, List<Sample>> fileGroupLibrariesUsedMap,
      Map<FileGroup, List<FileHandle>> fileGroupHcountFilesUsedMap) {

    GridPanel panel = new GridPanel();
    panel.setTitle("Libraries & Hcount Files Used");
    panel.setResizable(true);
    panel.setMaximizable(true);
    panel.setOrder(1);

    GridContent content = new GridContent();
    content.addDataFields(new GridDataField("Analysis", "String")); // dataIndex, datatype
    content.addDataFields(new GridDataField("Libraries Used", "String")); // dataIndex, datatype
    content.addDataFields(new GridDataField("Hcount Files Used", "String")); // dataIndex, datatype

    content.addColumn(
        new GridColumn("Analysis", "Analysis", 500, 0)); // header,dataIndex	     width=500; flex=0
    content.addColumn(
        new GridColumn(
            "Libraries Used", "Libraries Used", 150, 0)); // header,dataIndex	width=300;      flex=0
    content.addColumn(
        new GridColumn("Hcount Files Used", "Hcount Files Used", 1)); // header,dataIndex flex=1

    // create rows with  information
    for (FileGroup fileGroup : analysisFileGroupList) {

      List<String> row = new ArrayList<String>();
      row.add(fileGroup.getDescription());

      List<Sample> libraries = fileGroupLibrariesUsedMap.get(fileGroup);
      if (libraries.isEmpty()) {
        row.add("Error");
      } else {
        StringBuilder libraryNamesAsStringBuilder = new StringBuilder();
        for (Sample library : libraries) {
          if (libraryNamesAsStringBuilder.length() > 0) {
            libraryNamesAsStringBuilder.append("<br />");
          }
          libraryNamesAsStringBuilder.append(library.getName());
        }
        row.add(new String(libraryNamesAsStringBuilder));
      }

      List<FileHandle> bamFiles = fileGroupHcountFilesUsedMap.get(fileGroup);
      if (bamFiles.isEmpty()) {
        row.add("Error");
      } else {
        StringBuilder fileNamesAsStringBuilder = new StringBuilder();
        for (FileHandle fh : bamFiles) {
          if (fileNamesAsStringBuilder.length() > 0) {
            fileNamesAsStringBuilder.append("<br />");
          }
          fileNamesAsStringBuilder.append(fh.getFileName());
        }
        row.add(new String(fileNamesAsStringBuilder));
      }

      content.addDataRow(row);
    }

    panel.setContent(content);
    return panel;
  }