Changeset 184

Timestamp:

Feb 9, 2010, 5:01:03 PM (14 years ago)

Author:

keesvb

Message:

Deleted transcriptomics data model: moved some classes to study capture, the rest goes to the transcriptomics submodule. Added module location description for assays. Added Compound entity.

Location:

trunk/grails-app

Files:

• controllers/LoadController.groovy (modified) (4 diffs)
• domain/dbnp/studycapturing/Assay.groovy (modified) (1 diff)
• domain/dbnp/studycapturing/AssayModule.groovy (added)
• domain/dbnp/studycapturing/Compound.groovy (added)
• domain/dbnp/studycapturing/Person.groovy (added)
• domain/dbnp/studycapturing/PersonAffiliation.groovy (added)
• domain/dbnp/studycapturing/PersonRole.groovy (added)
• domain/dbnp/studycapturing/Protocol.groovy (modified) (1 diff)
• domain/dbnp/studycapturing/Publication.groovy (added)
• domain/dbnp/studycapturing/Study.groovy (modified) (1 diff)
• domain/dbnp/studycapturing/StudyPerson.groovy (added)
• domain/dbnp/transcriptomics (deleted)

trunk/grails-app/controllers/LoadController.groovy

@@ -1 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
-
 /**
  *
  * @author ademcan
  */
+
+import dbnp.studycapturing.*
+import dbnp.data.Term
+
 class LoadController {
 
@@ -33 +32 @@
         BufferedReader fileReader = new BufferedReader(new InputStreamReader(inputStream));
 
-        def investigationDesign = new dbnp.transcriptomics.magetab.idf.InvestigationDesign();
-        def person = new dbnp.transcriptomics.magetab.idf.Person();
-        def protocol = new dbnp.transcriptomics.magetab.idf.MAGEProtocol();
-        def publication = new dbnp.transcriptomics.magetab.idf.Publication();
-        def normalization = new dbnp.transcriptomics.magetab.sdrf.Normalization();
+        def study = new Study();
+        def person = new Person();
+        //def protocol = new dbnp.transcriptomics.magetab.idf.MAGEProtocol();
+        def publication = Publication();
+        //def normalization = new dbnp.transcriptomics.magetab.sdrf.Normalization();
         //def termSource = new dbnp.transcriptomics.magetab.adf.Termsource();
-        def comment = new dbnp.transcriptomics.magetab.idf.Comment();
-        def experimentalInfo = new dbnp.transcriptomics.magetab.idf.ExperimentalInfo();
-        def factor = new dbnp.transcriptomics.magetab.idf.Factor();
+        //def comment = new dbnp.transcriptomics.magetab.idf.Comment();
+        //def experimentalInfo = new dbnp.transcriptomics.magetab.idf.ExperimentalInfo();
+        //def factor = new dbnp.transcriptomics.magetab.idf.Factor();
 
         //ArrayList rows = new ArrayList();
+
+        // TODO: remap to dbnp studycapturing data model + extra template fields for MIAMI studies
 
         for (i in fileReader.readLines()){
@@ -219 +220 @@
                 }
                 else if (tmp_list[0]=="Publication Status") {
-                    def status = new dbnp.transcriptomics.magetab.idf.OntologyTerm();
+                    def status = new Term();
                     status.text = tmp_list[1];
                     status.save();
@@ -239 +240 @@
                 //todo list of type
                 else if (tmp_list[0]=="Protocol Type") {
-                    def type = new dbnp.transcriptomics.magetab.idf.OntologyTerm();
+                    def type = new Term();
                     for (j in 1..tmp_list.size()){
                         type.text = tmp_list[j];

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

@@ -9 +9 @@
 
     String name
-    AssayType type
-    String platform
+    AssayModule module
+    long externalAssayId
 
     static hasMany = [samples : Sample]

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

@@ -14 +14 @@
     Term   reference
     
-    static hasMany = [parameters : ProtocolParameter]
+    static hasMany = [parameters : ProtocolParameter, compounds: Compound]
     static constraints = { }
 

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

@@ -27 +27 @@
                                                 groups: SubjectGroup,
                                                 events: Event,
-                                                samplingEvents: SamplingEvent
+                                                samplingEvents: SamplingEvent,
+                        persons: StudyPerson,
+                        publications: Publication
         ]