Changeset 2156 for trunk/grails-app/services/dbnp

Timestamp:

Jan 30, 2012, 3:41:51 PM (10 years ago)

Author:

m.s.vanvliet@…

Message:

Added support for exporting meta-data from a module.
When meta-data is present it will restructure the export format to include the measurement meta-data (including the properties)

File:

• trunk/grails-app/services/dbnp/studycapturing/AssayService.groovy (modified) (15 diffs)

trunk/grails-app/services/dbnp/studycapturing/AssayService.groovy

@@ -63 +63 @@
                                         'Sampling Event Data' :     getUsedTemplateFields( samples*."parentEvent".unique() ),
                                         'Sample Data' :             getUsedTemplateFields( samples ),
-                                        'Event Group' :             [[name: 'name', comment: 'Name of Event Group', displayName: 'name']],
+                                        'Event Group' :             [
+                                                [name: 'name', comment: 'Name of Event Group', displayName: 'name']
+                                        ],
                                         'Module Measurement Data':  moduleMeasurements,
                                         'Module Error':             moduleError
@@ -186 +188 @@
                 }
 
-                def moduleError = '', moduleMeasurementData = [:]
+                def moduleError = '', moduleMeasurementData = [:], moduleMeasurementMetaData = [:]
 
                 if (measurementTokens) {
 
                         try {
-                                moduleMeasurementData = requestModuleMeasurements(assay, measurementTokens, samples, remoteUser)
+                                moduleMeasurementData           = requestModuleMeasurements(assay, measurementTokens, samples, remoteUser)
                         } catch (e) {
-                                moduleMeasurementData = ['error' : ['Module error, module not available or unknown assay'] * samples.size() ]
+                                moduleMeasurementData = ['error' : [
+                                                'Module error, module not available or unknown assay']
+                                        * samples.size() ]
                                 e.printStackTrace()
                                 moduleError =  e.message
                         }
-
-                }
-
-                [   'Subject Data' :            getFieldValues(samples, fieldMap['Subject Data'], 'parentSubject'),
-                        'Sampling Event Data' :     getFieldValues(samples, fieldMap['Sampling Event Data'], 'parentEvent'),
-                        'Sample Data' :             getFieldValues(samples, fieldMap['Sample Data']),
-                        'Event Group' :             eventFieldMap,
-                        'Module Measurement Data' : moduleMeasurementData,
-                        'Module Error' :            moduleError
-                ]
+                }
+
+                [   'Subject Data' :                            getFieldValues(samples, fieldMap['Subject Data'], 'parentSubject'),
+                                        'Sampling Event Data' :                 getFieldValues(samples, fieldMap['Sampling Event Data'], 'parentEvent'),
+                                        'Sample Data' :                         getFieldValues(samples, fieldMap['Sample Data']),
+                                        'Event Group' :                         eventFieldMap,
+                                        'Module Measurement Data' :             moduleMeasurementData,
+                                        'Module Error' :                        moduleError
+                                ]
         }
 
@@ -225 +228 @@
                         def value = assay.parent.getFieldValue( it.name )
                         if( value )
-                                studyData[ it.name ] = [value] * numValues
+                                studyData[ it.name ] = [value]* numValues
                 }
 
@@ -249 +252 @@
                         def value = assay.getFieldValue( it.name )
                         if( value )
-                                assayData[ it.name ] = [value] * numValues
+                                assayData[ it.name ] = [value]* numValues
                 }
 
@@ -304 +307 @@
                 def tokenString = ''
 
-                inputMeasurementTokens.each{
-                        tokenString+="&measurementToken=${it.encodeAsURL()}"
-                }
-
+                inputMeasurementTokens.each{ tokenString+="&measurementToken=${it.encodeAsURL()}" }
+
+                /* Contact module to fetch measurement data */
                 def path = moduleUrl + "/rest/getMeasurementData/query"
-
                 def query = "assayToken=$assay.assayUUID$tokenString"
 
                 if (samples) {
-                         query += '&' + samples*.sampleUUID.collect { "sampleToken=$it" }.join('&')
+                        query += '&' + samples*.sampleUUID.collect { "sampleToken=$it" }.join('&')
                 }
 
@@ -373 +374 @@
 
                 return map;
+        }
+
+        /**
+         * Retrieves module measurement meta data through a rest call to the module
+         *
+         * @param assay                         Assay for which the module measurements should be retrieved
+         * @param measurementTokens     List with the names of the fields to be retrieved. Format: [ 'measurementName1', 'measurementName2' ]
+         * @return
+         */
+        def requestModuleMeasurementMetaDatas(assay, inputMeasurementTokens, SecUser remoteUser = null) {
+
+                def measurementTokenMetaData = [:]
+
+                def moduleUrl = assay.module.url
+
+                def tokenString = ''
+                inputMeasurementTokens.each{ tokenString+="&measurementToken=${it.encodeAsURL()}" }
+
+                def pathMeasurementMetaData = moduleUrl + "/rest/getMeasurementMetaData/"
+                def queryMeasurementMetaData = "assayToken=$assay.assayUUID$tokenString"
+
+                try {
+                        moduleCommunicationService.callModuleMethod(moduleUrl, pathMeasurementMetaData, queryMeasurementMetaData, "POST", remoteUser).each { metaDataArray ->
+                                if (metaDataArray['name']){
+                                        measurementTokenMetaData[metaDataArray['name']] = metaDataArray //convert list to an associative array
+                                }
+                        }
+                } catch (e) {
+                        e.printStackTrace()
+                        throw new Exception("An error occured while trying to get the measurement meta data from the $assay.module.name. \
+                        This means the module containing the measurement data is not available right now. Please try again \
+                        later or notify the system administrator if the problem persists. URL: $path?$query.")
+                }
+
+                return measurementTokenMetaData
+        }
+
+        /**
+         * Injects meta-data(s) into rowData before creating a CSV or tab
+         */
+        def mergeModuleDataWithMetadata(data, metadata = null){
+
+                if (metadata == null){
+                        return data
+                }
+
+                //check if there is meta-data available for the features in the data
+                if (!(data[1].intersect(metadata.keySet()))){
+                        return data
+                }
+                
+                //find out where the measurements start in the data
+                def addLabelsAtColumnPosition = null
+                data[0].eachWithIndex { cat, i ->
+                        if (cat == 'Module Measurement Data'){
+                                addLabelsAtColumnPosition = i
+                        }
+                }
+
+                //check if we have a position to inject the labels
+                if (addLabelsAtColumnPosition == null){
+                        return data //returning data as we were unable to find any measurements. Or at least where the start.
+                }
+
+                //find out all (unique) feature properties
+                def featureProperties = []
+                metadata.values().each { featureProperties += it.keySet() }
+                featureProperties = featureProperties.unique()
+
+                //prepare the additional rows with meta-data
+                def additionalRows = []
+                featureProperties.each { mdfp ->
+                        def addRow = []
+                        (1..addLabelsAtColumnPosition).each {
+                                //add some empty fields before the labels of the meta-data properties
+                                addRow.add(null)
+                        }
+                        addRow.add(mdfp)
+                        data[1].eachWithIndex { feature, i ->
+                                if (i >= addLabelsAtColumnPosition) { addRow.add(metadata[feature][mdfp]) }
+                        }
+                        additionalRows.add(addRow)
+                }
+
+                //add the additional row and add a null to the feature label column in the data rows
+                if (additionalRows){
+                        def tempData = []
+                        data.eachWithIndex { row, iRow ->
+                                
+                                //this is an existing row (not meta-data), so we add a null under the feature label column
+                                def tempR = []
+                                row.eachWithIndex { rowElement, iRowElement ->
+                                        if ((iRow != 0) && (iRowElement == addLabelsAtColumnPosition)){
+                                                tempR.add(null) //add an empty element under the meta-data label
+                                        }
+                                        tempR.add(rowElement)
+                                }
+                                tempData.add(tempR)
+
+                                //as the additional rows have already been formatted in the correct way we only have to add them under the row that holds the categories
+                                if (iRow == 1){
+                                        additionalRows.each { additionalRow ->
+                                                tempData.add(additionalRow)
+                                        }
+                                }
+                        }
+                        //overwrite data with the tempRowData
+                        data = tempData
+                }
+
+                return data
         }
 
@@ -457 +569 @@
                                         } else {
                                                 // Append empty string for each entity if the field doesn't exist
-                                                categoryValues[ field ] += [""] * numValues[ idx ]
+                                                categoryValues[ field ] += [""]* numValues[ idx ]
                                         }
                                 }
@@ -519 +631 @@
                 // A map with keys being the sampleIds, and the values are the indices of that sample in the values list
                 def idMap = [:]
-                
+
                 // A map with the key being an index in the value list, and the value is the index the values should be copied to
                 def convertMap = [:]
@@ -534 +646 @@
                         }
                 }
-                
+
                 /*
                  * Example output: 
@@ -544 +656 @@
                  * loop through the values and remove the row that has been merged.
                  */
-                
-                convertMap.sort { a, b -> b.key <=> a.key }.each { 
+
+                convertMap.sort { a, b -> b.key <=> a.key }.each {
                         def row = it.key;
                         def mergeWith = it.value;
-                        
+
                         if( row != mergeWith ) {
                                 // Combine the data on row [row] with the data on row [mergeWith]
-                                
-                                mergedData.each { 
+
+                                mergedData.each {
                                         def cat = it.key; def fields = it.value;
                                         fields.each { fieldData ->
-                                                def fieldName = fieldData.key; 
+                                                def fieldName = fieldData.key;
                                                 def fieldValues = fieldData.value;
-                                                
+
                                                 // If one of the fields to merge is empty, use the other one
                                                 // Otherwise the values should be the same (e.g. study, subject, sample data)
                                                 fieldValues[ mergeWith ] = ( fieldValues[ mergeWith ] == null || fieldValues[ mergeWith ] == "" ) ? fieldValues[ row ] : fieldValues[ mergeWith ]
-                                                
+
                                                 // Remove the row from this list
                                                 fieldValues.remove( row );
@@ -568 +680 @@
                         }
                 }
-                
+
                 // Remove sample id if required
                 if( removeIdColumn )
                         mergedData[ "Sample Data" ].remove( "id" );
-                
+
                 return mergedData
         }
@@ -605 +717 @@
                 if (columnData.every { it.value.every { it.value instanceof ArrayList } }) {
 
-                        def headers = [[],[]]
+                        def headers = [[], []]
 
                         columnData.each { category ->
@@ -613 +725 @@
                                         // put category keys into first row separated by null values
                                         // wherever there are > 1 columns per category
-                                        headers[0] += [category.key] + [null] * (category.value.size() - 1)
+                                        headers[0] += [category.key]+ [null]* (category.value.size() - 1)
 
                                         // put non-category column headers into 2nd row
@@ -691 +803 @@
 
                 outputStream << rowData.collect { row ->
+
                         row.collect{
 
@@ -761 +874 @@
                                         def value = rowData[ri][ci]
 
-                                        value = (value instanceof Number | value?.class in [boolean.class, String.class, Date.class]) ? value : value?.toString()
+                                        value = (value instanceof Number | value?.class in [
+                                                boolean.class,
+                                                String.class,
+                                                Date.class
+                                        ]) ? value : value?.toString()
 
                                         // write the value (or an empty String if null) to the cell