Changes between Version 1 and Version 2 of CreatingNewAnnotationEntry

Timestamp:

07/16/2018 10:51:05 PM (4 years ago)

Author:

sena

Comment:

--

CreatingNewAnnotationEntry

@@ -3 +3 @@
 At the end of the annotation, we need to create a new MS Annotation Entry and add that as a child entry for the corresponding MS Entry and save the project (that contains the MS Entry) to make changes permanent.
 
-* Creation of a MS Annotation Entry and its corresponding Property
-
-   Several steps are included in this process:
+Several steps are included in this process (see org.grits.toolbox.importer.ms.annotation.glycan.simiansearch.handler.GelatoWorker):
     
    1. Create a new Entry and set its display name: In the example below, we are getting the name from the wizard where a user enters a name for the annotation for each MS entry that is annotated.
 
 {{{
-Entry msAnnotationEntry = new Entry();
+        Entry msAnnotationEntry = new Entry();
 
-String msEntryDisplayName = msEntry.getDisplayName();
-String msAnnotName = wizard.getInitial().getListEntries().get(msEntryDisplayName);
-msAnnotationEntry.setDisplayName(msAnnotName);
+        String msEntryDisplayName = msEntry.getDisplayName();
+        String msAnnotName = wizard.getInitial().getListEntries().get(msEntryDisplayName);
+        msAnnotationEntry.setDisplayName(msAnnotName);
 }}}
 
@@ -31 +29 @@
         metaData.setVersion(MSGlycanAnnotationMetaData.CURRENT_VERSION);
         metaData.setName(t_property.getMetaDataFileName());
+        msAnnotationEntry.setProperty (t_property);        
 
 }}}
@@ -52 +51 @@
 }}}
 
-   3. Creating the data files and link them to the metadata created in the previous step:
+   3. Creating the data files and linking them to the metadata created in the previous step:
 
 {{{
+
+        Data data = new Data();
+        DataHeader dHeader = new DataHeader();
+        data.setDataHeader(dHeader);
+        data.getDataHeader().setMethod(somemethod);     // somemethod is the Method object initialized in the wizard with all the different annotation settings
+}}}
+
+During annotation this data file is populated with annotation information and written to the file (see 
+
+   4. Saving the metadata and annotation files
+{{{
+
+        // if everything worked, save to workspace all of the appropriate files for Annotation
+        msAnnotProperty.getMSAnnotationMetaData().addAnnotationFile(dataFile);      // dataFile is the file we have used for annotation (a handle (MSPropertyDataFile) to the mzxml file for example)
+
+        PropertyDataFile msMetaData = MSAnnotationProperty.getNewSettingsFile(msAnnotProperty.getMetaDataFileName(), msAnnotProperty.getMSAnnotationMetaData());
+        msAnnotProperty.getDataFiles().add(msMetaData);
+        addResultFileToMetaData(dHeader.getMethod().getMsType(), msAnnotProperty);
+        MSAnnotationProperty.marshallSettingsFile(msAnnotProperty.getAnnotationFolder(msEntry) + File.separator + msAnnotProperty.getMetaDataFileName(), msAnnotProperty.getMSAnnotationMetaData());
 
 }}}
 
 {{{
- 
-final MassSpecProperty prop = (MassSpecProperty) msEntry.getProperty();
-Entry msAnnotationEntry = new Entry();          
-String sWorkspaceFolder = fWorkspaceFolderFile.getAbsolutePath();
+        protected void addResultFileToMetaData(String sMSType, MSAnnotationProperty msAnnotProperty) {
+                if( sMSType.equals(Method.MS_TYPE_LC) ) {
+                        NewGelatoHandlerLCMSMS.addResultFileToMetaData(gsa, (MSGlycanAnnotationProperty) msAnnotProperty);
+                } else {
+                        NewGelatoHandler.addResultFileToMetaData(gsa, msAnnotProperty);
+                }               
+        }
 
-File msAnnFile = getAnnotationFolder(msEntry);  
-String msAnnotationFolder = msAnnFile.getAbsolutePath();
-MSGlycanAnnotationProperty msAnnotProperty = (MSGlycanAnnotationProperty) getMSAnnotationProperty(shell, wizard, msAnnotationFolder);
+        /**
+         * Determines the annotation file name and folder name (if applicable), creates MSPropertyDataFile objects for them, and adds
+         * them to the meta data for the result files.
+         * 
+         * @param gsa, the GlycanStructureAnnotation specific for the MS Type other than LC-MS/MS
+         * @param msAnnotProperty, the Property to add the results file to
+         */
+        private static void addResultFileToMetaData(GlycanStructureAnnotation gsa, MSAnnotationProperty msAnnotProperty) {
+                String sAnnotationFile = gsa.getFinalArchiveName();
+                File annotationFile = new File( sAnnotationFile );
+                MSPropertyDataFile pdfFolder = new MSPropertyDataFile(annotationFile.getName(), 
+                                MSAnnotationFileInfo.MS_ANNOTATION_CURRENT_VERSION, 
+                                MSAnnotationFileInfo.MS_ANNOTATION_TYPE_FILE,
+                                FileCategory.ANNOTATION_CATEGORY, 
+                                GeneralInformationMulti.FILE_TYPE_GELATO,
+                                annotationFile.getPath(), new ArrayList<String>() );
+                msAnnotProperty.getMSAnnotationMetaData().addFile(pdfFolder);
 
-String msEntryDisplayName = msEntry.getDisplayName();
-String msAnnotName = wizard.getInitial().getListEntries().get(msEntryDisplayName);
-msAnnotationEntry.setDisplayName(msAnnotName);
-msAnnotationEntry.setProperty(msAnnotProperty);
+        }
+}}}
 
-Data data = getNewDataObject(wizard);
-DataHeader dHeader = data.getDataHeader();
+     5. Saving the entries. (see org.grits.toolbox.importer.ms.annotation.glycan.simiansearch.handler.OpenGelatoWizard)
 
-MSPropertyDataFile dataFile = wizard.getInitial().getFileMap().get(msEntry.getDisplayName());
-String workspaceLocation = PropertyHandler.getVariable("workspace_location");
-String projectName = DataModelSearch.findParentByType(msEntry, ProjectProperty.TYPE).getDisplayName();
-String pathToFile = workspaceLocation + projectName + File.separator + MassSpecProperty.getFoldername();
+{{{
+              gritsDataModelService.addEntry (msEntry, msAnnotationEntry);
+              // parent of MS Entry is Sample, parent of Sample is the Project
+              ProjectFileHandler.saveProject(msEntry.getParent().getParent());
+}}}
 
-// call performAnnotation - does all the work. 
-iStatus = performAnnotation( gpd, data, sWorkspaceFolder, msAnnotationFolder, msAnnotProperty, 
-                dataFile.getMSFileWithReader(pathToFile, prop.getMassSpecMetaData().getMsExperimentType()));
-if( iStatus == GRITSProcessStatus.OK ) {
-        // if everything worked, save to workspace all of the appropriate files for Annotation
-        msAnnotProperty.getMSAnnotationMetaData().addAnnotationFile(dataFile);
+      6. Locking the annotation files since they are now used in an annotation. This allows us to mark (annotation) files as "in use" in MS entry display. (see org.grits.toolbox.importer.ms.annotation.glycan.simiansearch.handler.OpenGelatoWizard)
 
-        PropertyDataFile msMetaData = MSAnnotationProperty.getNewSettingsFile(msAnnotProperty.getMetaDataFileName(), msAnnotProperty.getMSAnnotationMetaData());
-        msAnnotProperty.getDataFiles().add(msMetaData);
-        addResultFileToMetaData(dHeader.getMethod().getMsType(), msAnnotProperty);
-        MSAnnotationProperty.marshallSettingsFile(msAnnotProperty.getAnnotationFolder(msEntry) + File.separator +
-                        msAnnotProperty.getMetaDataFileName(), msAnnotProperty.getMSAnnotationMetaData());
+{{{
+        private void lockFiles(MSGlycanAnnotationWizard wizard, Entry msEntry, Entry msAnnotationEntry) {
+                MassSpecProperty prop = (MassSpecProperty) msEntry.getProperty();
+                FileLockManager mng;
+                try {
+                        String lockFileLocation = prop.getLockFilePath(msEntry);
+                        mng = FileLockingUtils.readLockFile(lockFileLocation);
+                        MSPropertyDataFile file = wizard.getInitial().getFileMap().get(msEntry.getDisplayName());
+                        if (file != null) {
+                                mng.lockFile(file.getName(), msAnnotationEntry);
+                                FileLockingUtils.writeLockFile(mng, lockFileLocation);
+                        }
+                } catch (IOException e) {
+                        logger.error("Could not lock the file", e);
+                } catch (JAXBException e) {
+                        logger.error("Could not lock the file", e);
+                }       
+        }
 
-        Entry[] entries = new Entry[2];
-        entries[0] = msEntry; // entry for the source MS
-        entries[1] = msAnnotationEntry; // the new entry for the MS Annotation
+}}}
 
-        // return list is a List<Entry[]>. 
-        returnList.add(entries);
-} else if (iStatus == GRITSProcessStatus.CANCEL) {
-        deleteResultFiles(dHeader.getMethod().getMsType());
+    7. Opening the editor to display the annotation results (see org.grits.toolbox.importer.ms.annotation.glycan.simiansearch.handler.OpenGelatoWizard):
+
+{{{
+
+try {
+        // need to set the partService to refresh gritsUIServices' stale partService, see ticket #799
+        gritsUIService.setPartService(partService);
+        gritsUIService.openEntryInPart(msAnnotationEntry);
+} catch (Exception e) {
+        logger.debug("Could not open the part", e);
 }
 
 }}}
 
-
-{{{
-
-
-        List<Entry[]> resultEntries = handler.process(shell2);                  
-        if( resultEntries != null ) {
-                for( int i = 0; i < resultEntries.size(); i++ ) {
-                        Entry[] curEntries = resultEntries.get(i);
-                        gritsDataModelService.addEntry(curEntries[0], curEntries[1]);
-                }
-        }
-
-        if( resultEntries != null && ! resultEntries.isEmpty() && resultEntries.get(resultEntries.size()-1)[1] != null ) {
-                // save the project first
-                try
-                {
-                        // parent of MS Entry is Sample, parent of Sample is the Project
-                        ProjectFileHandler.saveProject(resultEntries.get(resultEntries.size()-1)[0].getParent().getParent());
-                } catch (IOException e)
-                {
-                        logger.error("Something went wrong while saving project entry \n" + e.getMessage(),e);
-                        logger.fatal("Closing project entry \""
-                                        + resultEntries.get(resultEntries.size()-1)[0].getParent().getParent().getDisplayName() + "\"");
-                        gritsDataModelService.closeProject(resultEntries.get(resultEntries.size()-1)[0].getParent().getParent());
-                        throw e;
-                }
-                for( int i = 0; i < resultEntries.size(); i++ ) {
-                        Entry[] curEntries = resultEntries.get(i);
-                        lockFiles (wizard, curEntries[0], curEntries[1]);
-                }
-                final Entry lastMSEntry = (Entry) resultEntries.get(resultEntries.size()-1)[1] ;
-                eventBroker.send(IGritsDataModelService.EVENT_SELECT_ENTRY, lastMSEntry);
-                
-                try {
-                    // need to set the partService to refresh gritsUIServices' stale partService, see ticket #799
-                        gritsUIService.setPartService(partService);
-                        gritsUIService.openEntryInPart(lastMSEntry);
-                } catch (Exception e) {
-                        logger.debug("Could not open the part", e);
-                }
-        }
-
-}}}