Changes between Initial Version and Version 1 of CreatingNewAnnotationEntry

Timestamp:

07/16/2018 10:07:37 PM (4 years ago)

Author:

sena

Comment:

--

CreatingNewAnnotationEntry

@@ +1 @@
+== Creating an annotation entry ==
+
+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:
+    
+   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();
+
+String msEntryDisplayName = msEntry.getDisplayName();
+String msAnnotName = wizard.getInitial().getListEntries().get(msEntryDisplayName);
+msAnnotationEntry.setDisplayName(msAnnotName);
+}}}
+
+    2. Creating the property: We need to know the annotation folder to be able to assign a unique annotation id to the metadata in the property. "createRandomId" does the following: randomly generate an id and check to make sure it does not exist in the folder already.
+
+{{{
+        // getting the annotation folder
+        File msAnnFile = getAnnotationFolder(msEntry);  
+        String msAnnotationFolder = msAnnFile.getAbsolutePath();
+
+        MSGlycanAnnotationProperty t_property = new MSGlycanAnnotationProperty();
+        MSGlycanAnnotationMetaData metaData = new MSGlycanAnnotationMetaData();         
+        t_property.setMSAnnotationMetaData(metaData);
+        metaData.setAnnotationId(this.createRandomId(msAnnotationFolder));
+        metaData.setDescription(somedescripton);
+        metaData.setVersion(MSGlycanAnnotationMetaData.CURRENT_VERSION);
+        metaData.setName(t_property.getMetaDataFileName());
+
+}}}
+
+Getting the annotation folder for the given ms entry:
+
+{{{
+        protected File getAnnotationFolder( Entry msEntry ) {
+
+                String workspaceLocation = PropertyHandler.getVariable("workspace_location");
+                MSGlycanAnnotationProperty t_property = new MSGlycanAnnotationProperty();
+                Entry projectEntry = DataModelSearch.findParentByType(msEntry, ProjectProperty.TYPE);
+                String projectName = projectEntry.getDisplayName();
+
+                String msAnnotationFolder = workspaceLocation + projectName + File.separator + t_property.getArchiveFolder();   
+                File msAnnotationFolderFile = new File(msAnnotationFolder);
+                msAnnotationFolderFile.mkdirs();
+
+                return msAnnotationFolderFile;
+        }
+}}}
+
+   3. Creating the data files and link them to the metadata created in the previous step:
+
+{{{
+
+}}}
+
+{{{
+ 
+final MassSpecProperty prop = (MassSpecProperty) msEntry.getProperty();
+Entry msAnnotationEntry = new Entry();          
+String sWorkspaceFolder = fWorkspaceFolderFile.getAbsolutePath();
+
+File msAnnFile = getAnnotationFolder(msEntry);  
+String msAnnotationFolder = msAnnFile.getAbsolutePath();
+MSGlycanAnnotationProperty msAnnotProperty = (MSGlycanAnnotationProperty) getMSAnnotationProperty(shell, wizard, msAnnotationFolder);
+
+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();
+
+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();
+
+// 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);
+
+        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());
+
+        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());
+}
+
+}}}
+
+
+{{{
+
+
+        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);
+                }
+        }
+
+}}}