Changeset 80

Timestamp:

Jan 7, 2010, 1:38:25 PM (13 years ago)

Author:

keesvb

Message:

added Event and ProtocolInstance? classes, updated DataSource? to work with 1.2, added packages to dbnp.transcriptomics.data classes, added a number of scaffold controllers, added Selenium tests

Location:

trunk

Files:

• grails-app/conf/DataSource.groovy (modified) (1 diff)
• grails-app/controllers/OntologyController.groovy (added)
• grails-app/controllers/ProtocolController.groovy (added)
• grails-app/controllers/ProtocolParameterController.groovy (added)
• grails-app/controllers/TermController.groovy (added)
• grails-app/domain/dbnp/studycapturing/Event.groovy (added)
• grails-app/domain/dbnp/studycapturing/Ontology.groovy (modified) (1 diff)
• grails-app/domain/dbnp/studycapturing/Protocol.groovy (modified) (1 diff)
• grails-app/domain/dbnp/studycapturing/ProtocolInstance.groovy (added)
• grails-app/domain/dbnp/studycapturing/ProtocolParameter.groovy (modified) (1 diff)
• grails-app/domain/dbnp/studycapturing/ProtocolParameterType.groovy (added)
• grails-app/domain/dbnp/studycapturing/Template.groovy (modified) (1 diff)
• grails-app/domain/dbnp/studycapturing/Term.groovy (modified) (1 diff)
• grails-app/domain/dbnp/transcriptomics/data/Chip.groovy (modified) (1 diff)
• grails-app/domain/dbnp/transcriptomics/data/ChipAnnotation.groovy (modified) (1 diff)
• grails-app/domain/dbnp/transcriptomics/data/Expression.groovy (modified) (1 diff)
• grails-app/domain/nimble/User.groovy (modified) (2 diffs)
• test/unit/OntologyControllerTests.groovy (added)
• test/unit/ProtocolControllerTests.groovy (added)
• test/unit/ProtocolParameterControllerTests.groovy (added)
• test/unit/TermControllerTests.groovy (added)
• test/unit/dbnp/studycapturing/EventTests.groovy (added)
• test/unit/dbnp/studycapturing/ProtocolInstanceTests.groovy (added)
• tests (added)
• tests/create_protocol_parameter (added)
• tests/create_template_study (added)

trunk/grails-app/conf/DataSource.groovy

@@ -8 +8 @@
     cache.use_second_level_cache=true
     cache.use_query_cache=true
-    cache.provider_class='com.opensymphony.oscache.hibernate.OSCacheProvider'
+    cache.provider_class='net.sf.ehcache.hibernate.EhCacheProvider'
 }
 // environment specific settings

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

@@ -5 +5 @@
     String name
     String shortName
-    URI url
+    String url
 
-    static constraints = {
-    }
 }

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

@@ -1 +1 @@
 package dbnp.studycapturing
 
+/**
+ * Class describing the available protocols in the database, and their respective protocol parameters
+ * Concrete instances of protocol application (and parameter values) should be stored as ProtocolInstance
+ */
 class Protocol {
+
+    String name
+    Term reference
+    
+    static hasMany = [parameters : ProtocolParameter]
 
     static constraints = {

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

@@ -3 +3 @@
 class ProtocolParameter {
 
-    enum ParameterType { STRING, NUMBER, LIST }
+    String name
+    ProtocolParameterType type
+    String unit
+    String description
+    Term reference
 
-    String name
-    ParameterType type
-    
+    static hasMany = [listEntries : String]
+
     static constraints = {
     }

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

@@ -7 +7 @@
   
     static constraints = {
+        name(unique:true)
+    }
+
+    def String toString() {
+        return this.name;
     }
 }

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

@@ -5 +5 @@
     String name
     Ontology ontology
-    long accessionNumber
+    String accession
 
     static constraints = {

trunk/grails-app/domain/dbnp/transcriptomics/data/Chip.groovy

@@ +1 @@
+package dbnp.transcriptomics.data
 /**
  * The Chip entity.

trunk/grails-app/domain/dbnp/transcriptomics/data/ChipAnnotation.groovy

@@ +1 @@
+package dbnp.transcriptomics.data
 /**
  * The Chip entity.

trunk/grails-app/domain/dbnp/transcriptomics/data/Expression.groovy

@@ +1 @@
+package dbnp.transcriptomics.data
 /**
  * The Chip entity.

trunk/grails-app/domain/nimble/User.groovy

@@ -1 @@
-
 package nimble
 
@@ -6 +5 @@
         // Extend UserBase with your custom values here
 
+    def String toString() {
+        return this.username;
+    }
+
+
 }