@Override
public FileHandle createAndSaveInnerFileHandle(String fileName, FileType fileType) {
FileHandle fileHandle = new FileHandle();
fileHandle.setFileName(fileName);
fileHandle.setFileType(fileType);
fileHandle = fileService.addFile(fileHandle);
return fileHandle;
}
@Override
public FileGroup createAndSaveInnerFileGroup(
FileHandle fileHandle, Software software, String description) {
FileGroup fileGroup = new FileGroup();
fileGroup.setDescription(description);
fileGroup.setFileType(fileHandle.getFileType());
fileGroup.setSoftwareGeneratedById(software.getId());
fileGroup.setIsActive(0);
Set<FileHandle> fileHandleSet = new HashSet<FileHandle>();
fileHandleSet.add(fileHandle);
fileGroup.setFileHandles(fileHandleSet);
fileGroup = fileService.addFileGroup(fileGroup);
return fileGroup;
}
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;
}
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;
}