Changeset 106

Timestamp:

Jan 22, 2010, 1:02:40 PM (13 years ago)

Author:

keesvb

Message:

added first version of clean data layer specification and clinical data module

Location:

trunk

Files:

• grails-app/conf/BootStrap.groovy (modified) (1 diff)
• grails-app/controllers/LoadController.groovy (modified) (1 diff)
• grails-app/controllers/OntologyController.groovy (modified) (1 diff)
• grails-app/controllers/TermController.groovy (modified) (1 diff)
• grails-app/controllers/dbnp/clinicaldata (added)
• grails-app/controllers/dbnp/clinicaldata/ClinicalAssayController.groovy (added)
• grails-app/controllers/dbnp/clinicaldata/ClinicalMeasurementController.groovy (added)
• grails-app/domain/dbnp/clinicaldata (added)
• grails-app/domain/dbnp/clinicaldata/ClinicalAssay.groovy (added)
• grails-app/domain/dbnp/clinicaldata/ClinicalAssayInstance.groovy (added)
• grails-app/domain/dbnp/clinicaldata/ClinicalFloatData.groovy (added)
• grails-app/domain/dbnp/clinicaldata/ClinicalMeasurement.groovy (added)
• grails-app/domain/dbnp/clinicaldata/ClinicalMeasurementType.groovy (added)
• grails-app/domain/dbnp/clinicaldata/ClinicalStringData.groovy (added)
• grails-app/domain/dbnp/data (added)
• grails-app/domain/dbnp/data/FeatureBase.groovy (added)
• grails-app/domain/dbnp/data/Ontology.groovy (moved) (moved from trunk/grails-app/domain/dbnp/studycapturing/Ontology.groovy) (1 diff)
• grails-app/domain/dbnp/data/Term.groovy (moved) (moved from trunk/grails-app/domain/dbnp/studycapturing/Term.groovy) (1 diff)
• grails-app/domain/dbnp/studycapturing/EventDescription.groovy (modified) (1 diff)
• grails-app/domain/dbnp/studycapturing/Protocol.groovy (modified) (1 diff)
• grails-app/domain/dbnp/studycapturing/ProtocolParameter.groovy (modified) (1 diff)
• grails-app/domain/dbnp/studycapturing/Sample.groovy (modified) (1 diff)
• grails-app/domain/dbnp/studycapturing/Study.groovy (modified) (1 diff)
• grails-app/domain/dbnp/studycapturing/Subject.groovy (modified) (1 diff)
• grails-app/services/dbnp (added)
• grails-app/services/dbnp/clinicaldata (added)
• grails-app/services/dbnp/clinicaldata/ClinicalDataLayerService.groovy (added)
• grails-app/views/clinicalAssay (added)
• grails-app/views/clinicalData (added)
• src/java/dbnp (added)
• src/java/dbnp/data (added)
• src/java/dbnp/data/CleanDataLayer.java (added)
• test/unit/dbnp/clinicaldata (added)
• test/unit/dbnp/clinicaldata/ClinicalAssayControllerTests.groovy (added)
• test/unit/dbnp/clinicaldata/ClinicalAssayInstanceTests.groovy (added)
• test/unit/dbnp/clinicaldata/ClinicalAssayTests.groovy (added)
• test/unit/dbnp/clinicaldata/ClinicalDataLayerServiceTests.groovy (added)
• test/unit/dbnp/clinicaldata/ClinicalFloatDataTests.groovy (added)
• test/unit/dbnp/clinicaldata/ClinicalMeasurementControllerTests.groovy (added)
• test/unit/dbnp/clinicaldata/ClinicalMeasurementTests.groovy (added)
• test/unit/dbnp/clinicaldata/ClinicalStringDataTests.groovy (added)
• test/unit/dbnp/data (added)
• test/unit/dbnp/data/FeatureBaseTests.groovy (added)

trunk/grails-app/conf/BootStrap.groovy

@@ -2 +2 @@
 import grails.util.GrailsUtil
 import dbnp.studycapturing.*
-import intient.nimble.InstanceGenerator
+
+import dbnp.data.Ontology
+import dbnp.data.Term
 
 /**

trunk/grails-app/controllers/LoadController.groovy

@@ -35 +35 @@
         def investigationDesign = new dbnp.transcriptomics.magetab.idf.InvestigationDesign();
         def person = new dbnp.transcriptomics.magetab.idf.Person();
-        def protocol = new dbnp.transcriptomics.magetab.idf.MAGEProtocol();l
+        def protocol = new dbnp.transcriptomics.magetab.idf.MAGEProtocol();
         def publication = new dbnp.transcriptomics.magetab.idf.Publication();
         def normalization = new dbnp.transcriptomics.magetab.sdrf.Normalization();

trunk/grails-app/controllers/OntologyController.groovy

@@ +1 @@
+import dbnp.data.Ontology
+
 class OntologyController {
 
-    def scaffold = dbnp.studycapturing.Ontology
+    def scaffold = Ontology
 }

trunk/grails-app/controllers/TermController.groovy

@@ +1 @@
+import dbnp.data.Term
+
 class TermController {
 
-    def scaffold = dbnp.studycapturing.Term
+    def scaffold = Term
 }

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

@@ -1 @@
-package dbnp.studycapturing
+package dbnp.data
 
 /**

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

@@ -1 @@
-package dbnp.studycapturing
+package dbnp.data
+
+import dbnp.data.Ontology
 
 /**

trunk/grails-app/domain/dbnp/studycapturing/EventDescription.groovy

@@ -1 +1 @@
 package dbnp.studycapturing
+
+import dbnp.data.Term
 
 /**

trunk/grails-app/domain/dbnp/studycapturing/Protocol.groovy

@@ -1 +1 @@
 package dbnp.studycapturing
+
+import dbnp.data.Term
 
 /**

trunk/grails-app/domain/dbnp/studycapturing/ProtocolParameter.groovy

@@ -1 +1 @@
 package dbnp.studycapturing
+
+import dbnp.data.Term
 
 /**

trunk/grails-app/domain/dbnp/studycapturing/Sample.groovy

@@ -1 +1 @@
 package dbnp.studycapturing
+
+import dbnp.data.Term
 
 /**

trunk/grails-app/domain/dbnp/studycapturing/Study.groovy

@@ -22 +22 @@
 
         static hasMany = [      editors:                nimble.User,
-                                                readers:                nimble.User,
-                                                subjects:               Subject,
-                                                groups:                 SubjectGroup,
-                                                events:                 Event,
-                                                samplingEvents: SamplingEvent
+                                readers:                nimble.User,
+                                subjects:               Subject,
+                                groups:                 SubjectGroup,
+                                events:                 Event,
+                                samplingEvents: SamplingEvent
         ]
 

trunk/grails-app/domain/dbnp/studycapturing/Subject.groovy

@@ -1 +1 @@
 package dbnp.studycapturing
+
+import dbnp.data.Term
 
 /**