Changeset 187

Timestamp:

Feb 10, 2010, 4:09:52 PM (13 years ago)

Author:

keesvb

Message:

changed definition of clean data layer, implemented it for the clinical data module, added demonstration to the sandbox

Location:

trunk

Files:

• grails-app/conf/BootStrap.groovy (modified) (2 diffs)
• grails-app/controllers/SandboxController.groovy (modified) (3 diffs)
• grails-app/domain/dbnp/clinicaldata/ClinicalMeasurement.groovy (modified) (2 diffs)
• grails-app/domain/dbnp/clinicaldata/ClinicalMeasurementType.groovy (deleted)
• grails-app/domain/dbnp/data/FeatureBase.groovy (modified) (1 diff)
• grails-app/domain/dbnp/data/FeatureType.groovy (copied) (copied from trunk/grails-app/domain/dbnp/studycapturing/AssayType.groovy) (1 diff)
• grails-app/services/dbnp/clinicaldata/ClinicalDataLayerService.groovy (modified) (1 diff)
• src/java/dbnp/data/CleanDataLayer.java (modified) (1 diff)

trunk/grails-app/conf/BootStrap.groovy

@@ -295 +295 @@
                                 name: 'LDL',
                                 unit: 'mg/dL',
-                                type: dbnp.clinicaldata.ClinicalMeasurementType.NUMBER,
+                                type: dbnp.data.FeatureType.QUANTITATIVE,
                                 referenceValues: '100 mg/dL',
                                 detectableLimit: 250,
@@ -304 +304 @@
                                 name: 'HDL',
                                 unit: 'mg/dL',
-                                type: dbnp.clinicaldata.ClinicalMeasurementType.NUMBER,
+                                type: dbnp.data.FeatureType.QUANTITATIVE,
                                 referenceValues: '50 mg/dL',
                                 detectableLimit: 100,

trunk/grails-app/controllers/SandboxController.groovy

@@ -1 +1 @@
 import dbnp.studycapturing.*
+import dbnp.clinicaldata.ClinicalFloatData
+import dbnp.clinicaldata.ClinicalMeasurement
 
 // The sandbox is meant for internal communication over code examples etc.
 
 class SandboxController {
+
+        def clinicalDataLayerService
 
         def index = {
@@ -22 +26 @@
 
                 //Let's get a certain field for a certain subject
-                def subject = Subject.findByName('A1')
+                /*def subject = st.subjects.get(1)
+
+                if (subject) {
                 println st.template.getSubjectFieldType('Age')
                 println subject.getFieldValue('Genotype')
@@ -28 +34 @@
                 println subject.getFieldValue('Genotype')
                 subject.setFieldValue('name','hallo')
-                println subject.name
+                println subject.name }*/
 
-                println Study.get(2).giveSamples()*.name
-        
+
+                // Demonstration of querying mechanism
+                println clinicalDataLayerService.getFeaturesQuantitative(1)
+                clinicalDataLayerService.getDataQuantitative('LDL',1,['A1_B','A3_B'] as String[])
 
                 // Specify which variables we want to be available in the controller (implicit return statement)
                 [fields: f, subjects: st.subjects]
+        }
 }
-}

trunk/grails-app/domain/dbnp/clinicaldata/ClinicalMeasurement.groovy

@@ -1 +1 @@
 package dbnp.clinicaldata
+
+import dbnp.data.FeatureType
 
 class ClinicalMeasurement
  extends dbnp.data.FeatureBase {
 
-        ClinicalMeasurementType type
+        // For now, let's assume that quantitative values are stored as float,
+        // and qualitative values as string
+        // We can always add an additional ClinicalMeasurementType datatype (FLOAT, INTEGER etc.) later (as was here until rev 186)
+
         String referenceValues
         float detectableLimit
@@ -13 +18 @@
 
         static constraints = {
+                name(unique:true)
                 referenceValues(nullable: true, blank: true)
                 detectableLimit(nullable: true)
                 correctionMethod(nullable: true, blank: true)
         }
+
+        Map getValues(long assayID, String[] sampleIDs) {
+                FeatureType featureType = type
+                switch(featureType) {
+                        case FeatureType.QUANTITATIVE:
+                                def values = ClinicalFloatData.withCriteria {
+                                        assay { eq("id",assayID) }
+                                        eq("measurement",this)
+                                        'in'("sample",sampleIDs)
+                                }
+                                def result = new HashMap<String,Float>();
+                                values.each {
+                                        result.put(it.sample,it.value)
+                                }
+                                return result
+                        default:
+                                throw new NoSuchFieldException("Feature type ${featureType} not supported")
+                }
+        }
 }

trunk/grails-app/domain/dbnp/data/FeatureBase.groovy

@@ -5 +5 @@
         String name
         String unit
+        FeatureType type
 
         static hasMany = [

trunk/grails-app/domain/dbnp/data/FeatureType.groovy

@@ -1 @@
-package dbnp.studycapturing
+package dbnp.data
 
 /**
  * Enum describing the different assay types (aka omics submodules).
  */
-public enum AssayType {
-    TRANSCRIPTOMICS('Transcriptomics'),
-    METABOLOMICS('Metabolomics'),
-    CLINICAL_DATA('Clinical data')
+public enum FeatureType {
+    QUANTITATIVE('Quantitative'),
+    QUALITATIVE('Qualitative'),
+    PAIRED('Paired'),
+    DIFFERENTIAL('Differential')
 
     String name
 
-    AssayType(String name) {
+    FeatureType(String name) {
      this.name = name
     }
 
     static list() {
-     [TRANSCRIPTOMICS, METABOLOMICS, CLINICAL_DATA]
+     [QUANTITATIVE, QUALITATIVE, PAIRED, DIFFERENTIAL]
     }
 

trunk/grails-app/services/dbnp/clinicaldata/ClinicalDataLayerService.groovy

@@ -5 +5 @@
         boolean transactional = false
 
-        String getAssayDescription(long assayID) {
-                return "";
+        Map getDataQuantitative(String feature, long assayID, String[] sampleIDs) {
+                def measurement = ClinicalMeasurement.findByName(feature)
+                if (!measurement) throw new NoSuchFieldException("Feature ${feature} not found")
+                measurement.getValues(assayID,sampleIDs)
         }
 
-        String[] getFeatureNames(long assayID) {
-                return new String[0];
-        }
-
-        Map getFeatureData(long assayID, long[] sampleIDs) {
-                return null;
-        }
-
-        Map getFeatureDataDifferential(long assayID, long[] sampleIDs1, long[] sampleIDs2) {
-                return null;
+        String[] getFeaturesQuantitative(long assayID) {
+                return ClinicalAssayInstance.get(assayID).assay.measurements*.name;
         }
 }

trunk/src/java/dbnp/data/CleanDataLayer.java

@@ -8 +8 @@
 public interface CleanDataLayer {
 
-        public String getAssayDescription(long assayID);
-        public String[] getFeatureNames(long assayID);
-        public Map getFeatureData(long assayID, long[] sampleIDs);
-        public Map getFeatureDataDifferential(long assayID, long[] sampleIDs1, long[] sampleIDs2);
+        /**
+         * Get the names of all quantitative features that are available for a certain assay
+         * @param assayID the module internal ID for the assay
+         * @return
+         */
+        public String[] getFeaturesQuantitative(long assayID);
+
+        /**
+         * Get the data for a quantitative feature for a certain assay for a certain set of samples
+         * @param feature
+         * @param assayID
+         * @param sampleIDs
+         * @return
+         */
+        public Map getDataQuantitative(String feature, long assayID, String[] sampleIDs);
 
 }