Changeset 1945 for trunk/grails-app/services/dbnp

Timestamp:

Jun 29, 2011, 10:10:48 AM (11 years ago)

Author:

robert@…

Message:

• Updated the import algorithm in the simpleWizard, so it won't be too slow with > 200 samples
• Changed the warning added in r1944 so the user knows why the import will be slow

File:

• trunk/grails-app/services/dbnp/importer/ImporterService.groovy (modified) (6 diffs)

trunk/grails-app/services/dbnp/importer/ImporterService.groovy

@@ -22 +22 @@
 class ImporterService {
         def authenticationService
+        def sessionFactory
 
         static transactional = false
@@ -258 +259 @@
                 if( !mcmap )
                         return;
+                        
+                def hibernateSession = sessionFactory.getCurrentSession() 
 
                 // Check whether the rows should be imported in one or more entities
@@ -269 +272 @@
                 def sheet = wb.getSheetAt(sheetindex)
                 def table = []
+                def samples = []
                 def failedcells = [] // list of cells that have failed to import
                 
@@ -287 +291 @@
                         if( row && !rowIsEmpty( row ) ) {
                                 // Create an entity record based on a row read from Excel and store the cells which failed to be mapped
-                                def (record, failed) = importOrUpdateRecord( templates, entities, row, mcmap, parent, table, existingEntities[i] );
-        
+                                def (record, failed) = importOrUpdateRecord( templates, entities, row, mcmap, parent, samples, existingEntities[i] );
+
                                 // Setup the relationships between the imported entities
                                 relateEntities( record );
-        
+
                                 // Add record with entities and its values to the table
                                 table.add(record)
-        
+
                                 // If failed cells have been found, add them to the failed cells list
                                 if (failed?.importcells?.size() > 0) failedcells.add(failed)
+                                
+                                // Add a sample to the list of samples if possible
+                                def sample = record.find { it instanceof dbnp.studycapturing.Sample }
+                                if( sample && !samples.contains( sample ) )
+                                        samples << sample
                         }
                 }
@@ -357 +366 @@
          * @param       mcmap           Hashmap of mappingcolumns, with the first entry in the hashmap containing information about the first column, etc.
          * @param       parent          Study to import all data into. Is used for determining which sample/event/subject/assay to update
-         * @param       importedRows    Rows that have been imported before this row. These rows might contain the same entities as are
-         *                                                      imported in this row. These entities should be used again, to avoid importing duplicates.
+         * @param       importedSamples Samples that have been imported before this row. These entities should be used again if possible, 
+         *                                                      to avoid importing duplicates.
          * @return      List            List with two entries:
          *                      0                       List with ImportRecords, one for each row in the excelsheet
@@ -364 +373 @@
          *                                              (because the value in the excelsheet can't be entered into the template field)
          */
-        def importOrUpdateRecord(def templates, def entities, Row excelRow, mcmap, Study parent = null, List importedRows, Map existingEntities ) {
+        def importOrUpdateRecord(def templates, def entities, Row excelRow, mcmap, Study parent = null, List importedSamples, Map existingEntities ) {
                 DataFormatter df = new DataFormatter();
                 def record = [] // list of entities and the read values
                 def failed = new ImportRecord() // map with entity identifier and failed mappingcolumn
 
+                def currentTime = System.currentTimeMillis();
+                
                 // Check whether this record mentions a sample that has been imported before. In that case,
                 // we update that record, in order to prevent importing the same sample multiple times
                 def importedEntities = [];
-                if( importedRows )
-                        importedEntities = importedRows.flatten().findAll { it.class == dbnp.studycapturing.Sample }.unique();
+                if( importedSamples )
+                        importedEntities = importedSamples
 
                 def importedSample = findEntityInImportedEntities( dbnp.studycapturing.Sample, excelRow, mcmap, importedEntities, df )