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domain

Timestamp:

Jan 4, 2010, 12:13:36 PM (13 years ago)

Author:

keesvb

Message:

updated to Grails 1.2, restructured packages, added some domain classes, removed obsolete code

Location:

trunk/grails-app/domain

Files:

: 3 added
: 22 deleted
: 40 edited
: 2 moved

Chip.groovy (deleted)
ChipAnnotation.groovy (deleted)
Data.groovy (deleted)
DataType.groovy (deleted)
Experiment.groovy (deleted)
ExperimentSample.groovy (deleted)
Expression.groovy (deleted)
MetaData.groovy (deleted)
MetaField.groovy (deleted)
MetaFieldGroup.groovy (deleted)
MetaFieldOption.groovy (deleted)
MetaFieldType.groovy (deleted)
MetaObject.groovy (deleted)
MetaTemplate.groovy (deleted)
MetaTemplateMetaField.groovy (deleted)
Sample.groovy (deleted)
SampleType.groovy (deleted)
Source.groovy (deleted)
Species.groovy (deleted)
Strain.groovy (deleted)
Study.groovy (deleted)
StudyTypeMetaTemplate.groovy (deleted)
dbnp (added)
dbnp/studycapturing (added)
dbnp/transcriptomics (added)
dbnp/transcriptomics/magetab (moved) (moved from trunk/grails-app/domain/magetab)
dbnp/transcriptomics/magetab/adf/ArrayDesign.groovy (modified) (2 diffs)
dbnp/transcriptomics/magetab/adf/CompositeElement.groovy (modified) (2 diffs)
dbnp/transcriptomics/magetab/adf/DesignElement.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/adf/MatrixColumn.groovy (modified) (2 diffs)
dbnp/transcriptomics/magetab/adf/MatrixRow.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/adf/MatrixRowId.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/adf/Reporter.groovy (modified) (2 diffs)
dbnp/transcriptomics/magetab/idf/Comment.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/idf/ExperimentalInfo.groovy (modified) (2 diffs)
dbnp/transcriptomics/magetab/idf/Factor.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/idf/InvestigationDesign.groovy (modified) (3 diffs)
dbnp/transcriptomics/magetab/idf/MAGEProtocol.groovy (moved) (moved from trunk/grails-app/domain/magetab/idf/Protocol.groovy) (1 diff)
dbnp/transcriptomics/magetab/idf/OntologyTerm.groovy (modified) (2 diffs)
dbnp/transcriptomics/magetab/idf/Parameter.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/idf/Person.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/idf/Publication.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/idf/UserDefinedAttribute.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/sdrf/ArrayData.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/sdrf/ArrayDataMatrix.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/sdrf/Assay.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/sdrf/DataObject.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/sdrf/DerivedArrayData.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/sdrf/DerivedArrayDataMatrix.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/sdrf/Edge.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/sdrf/ExtractObj.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/sdrf/FactorValue.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/sdrf/Hybridization.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/sdrf/Image.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/sdrf/LabeledExtract.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/sdrf/Material.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/sdrf/Node.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/sdrf/NodeList.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/sdrf/Normalization.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/sdrf/ParameterValue.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/sdrf/ProtocolApplication.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/sdrf/Provider.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/sdrf/SampleAndDataRelationship.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/sdrf/Scan.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/sdrf/URIValue.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/sdrf/UserDefinedValue.groovy (modified) (1 diff)
dbnp/transcriptomics/magetab/sdrf/Value.groovy (modified) (1 diff)

Legend:

: Unmodified
: Added
: Removed

trunk/grails-app/domain/dbnp/transcriptomics/magetab/adf/ArrayDesign.groovy

-                      r69
+                      r70
 package magetab.adf
+package dbnp.transcriptomics.magetab.adf
 class ArrayDesign {
 …
         String provider
         String printingProtocol
         magetab.idf.OntologyTerm arrayDesignRef
         magetab.idf.OntologyTerm surfaceType
         magetab.idf.OntologyTerm sequencePolymerType
         magetab.idf.OntologyTerm technologyType
         magetab.idf.OntologyTerm substrateType
+        dbnp.transcriptomics.magetab.idf.OntologyTerm arrayDesignRef
+        dbnp.transcriptomics.magetab.idf.OntologyTerm surfaceType
+        dbnp.transcriptomics.magetab.idf.OntologyTerm sequencePolymerType
+        dbnp.transcriptomics.magetab.idf.OntologyTerm technologyType
+        dbnp.transcriptomics.magetab.idf.OntologyTerm substrateType
         static hasMany = [
                 designElements:DesignElement,
                 userDefinedAttributes:magetab.idf.UserDefinedAttribute
+                userDefinedAttributes:dbnp.transcriptomics.magetab.idf.UserDefinedAttribute
+        ]

trunk/grails-app/domain/dbnp/transcriptomics/magetab/adf/CompositeElement.groovy

-                      r69
+                      r70
 package magetab.adf
+package dbnp.transcriptomics.magetab.adf
 class CompositeElement {
 …
         String name
         String comment
         magetab.idf.OntologyTerm dataBaseEntry
+        dbnp.transcriptomics.magetab.idf.OntologyTerm dataBaseEntry
         static constraints = {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/adf/DesignElement.groovy

r69	r70
1		package magetab.adf
	1	package dbnp.transcriptomics.magetab.adf
2	2
3	3	class DesignElement {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/adf/MatrixColumn.groovy

-                      r69
+                      r70
 package magetab.adf
+package dbnp.transcriptomics.magetab.adf
 class MatrixColumn {
 …
     int columnNumber
     String columnData
     magetab.sdrf.Node columnHeader
     magetab.idf.OntologyTerm quantitationType
+    dbnp.transcriptomics.magetab.sdrf.Node columnHeader
+    dbnp.transcriptomics.magetab.idf.OntologyTerm quantitationType
     static constraints = {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/adf/MatrixRow.groovy

r69	r70
1		package magetab.adf
	1	package dbnp.transcriptomics.magetab.adf
2	2
3	3	class MatrixRow {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/adf/MatrixRowId.groovy

r69	r70
1		package magetab.adf
	1	package dbnp.transcriptomics.magetab.adf
2	2
3	3	class MatrixRowId {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/adf/Reporter.groovy

-                      r69
+                      r70
 package magetab.adf
+package dbnp.transcriptomics.magetab.adf
 class Reporter {
 …
     String name
     String sequence
     magetab.idf.OntologyTerm group
     magetab.idf.OntologyTerm controlType
     magetab.idf.OntologyTerm databaseEntry
+    dbnp.transcriptomics.magetab.idf.OntologyTerm group
+    dbnp.transcriptomics.magetab.idf.OntologyTerm controlType
+    dbnp.transcriptomics.magetab.idf.OntologyTerm databaseEntry
     static constraints ={

trunk/grails-app/domain/dbnp/transcriptomics/magetab/idf/Comment.groovy

r69	r70
1		package magetab.idf
	1	package dbnp.transcriptomics.magetab.idf
2	2
3	3	class Comment {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/idf/ExperimentalInfo.groovy

-                      r69
+                      r70
 package magetab.idf
+package dbnp.transcriptomics.magetab.idf
 class ExperimentalInfo {
 …
     String design_term_source_ref
     static hasMany = [
         //factor_name:String,
         //factor_type:String,
         //design:String
         //design_term_source_ref:String,
         //factor_term_source_ref:String
+    ]
+    /*static hasMany = [
+        factor_name:String,
+        factor_type:String,
+        design:String
+        design_term_source_ref:String,
+        factor_term_source_ref:String
+    ]*/
     static constraints = {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/idf/Factor.groovy

r69	r70
1		package magetab.idf
	1	package dbnp.transcriptomics.magetab.idf
2	2
3	3	class Factor {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/idf/InvestigationDesign.groovy

-                      r69
+                      r70
 package magetab.idf
+package dbnp.transcriptomics.magetab.idf
 class InvestigationDesign {
 …
     static hasMany = [
         experimentalFactors: Factor,
         protocols: Protocol,
+        protocols: MAGEProtocol,
         publications: Publication,
         //sdrfs: magetab.sdrf.SampleAndDataRelationship,
+        //sdrfs: dbnp.transcriptomics.magetab.sdrf.SampleAndDataRelationship,
         userDefinedAttributes: UserDefinedAttribute,
         contacts: Person,
 …
         replicateTypes: OntologyTerm,
         experimentalDesigns: OntologyTerm
 //        termSources: magetab.adf.TermSource
+//        termSources: dbnp.transcriptomics.magetab.adf.TermSource
+    ]

trunk/grails-app/domain/dbnp/transcriptomics/magetab/idf/MAGEProtocol.groovy

-                      r69
+                      r70
 package magetab.idf
+package dbnp.transcriptomics.magetab.idf
 class Protocol {
+class MAGEProtocol {
     String name

trunk/grails-app/domain/dbnp/transcriptomics/magetab/idf/OntologyTerm.groovy

-                      r69
+                      r70
 package magetab.idf
+package dbnp.transcriptomics.magetab.idf
 class OntologyTerm {
 …
     String category
     String accessionNumber
 //    magetab.adf.TermSource termSource
+//    dbnp.transcriptomics.magetab.adf.TermSource termSource

trunk/grails-app/domain/dbnp/transcriptomics/magetab/idf/Parameter.groovy

r69	r70
1		package magetab.idf
	1	package dbnp.transcriptomics.magetab.idf
2	2
3	3	class Parameter {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/idf/Person.groovy

r69	r70
1		package magetab.idf
	1	package dbnp.transcriptomics.magetab.idf
2	2
3	3	class Person {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/idf/Publication.groovy

r69	r70
1		package magetab.idf
	1	package dbnp.transcriptomics.magetab.idf
2	2
3	3	class Publication {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/idf/UserDefinedAttribute.groovy

r69	r70
1		package magetab.idf
	1	package dbnp.transcriptomics.magetab.idf
2	2
3	3	class UserDefinedAttribute {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/sdrf/ArrayData.groovy

r69	r70
1		package magetab.sdrf
	1	package dbnp.transcriptomics.magetab.sdrf
2	2
3	3	class ArrayData {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/sdrf/ArrayDataMatrix.groovy

r69	r70
1		package magetab.sdrf
	1	package dbnp.transcriptomics.magetab.sdrf
2	2
3	3	class ArrayDataMatrix {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/sdrf/Assay.groovy

r69	r70
1		package magetab.sdrf
	1	package dbnp.transcriptomics.magetab.sdrf
2	2
3	3	class Assay {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/sdrf/DataObject.groovy

r69	r70
1		package magetab.sdrf
	1	package dbnp.transcriptomics.magetab.sdrf
2	2
3	3	class DataObject {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/sdrf/DerivedArrayData.groovy

r69	r70
1		package magetab.sdrf
	1	package dbnp.transcriptomics.magetab.sdrf
2	2
3	3	class DerivedArrayData {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/sdrf/DerivedArrayDataMatrix.groovy

r69	r70
1		package magetab.sdrf
	1	package dbnp.transcriptomics.magetab.sdrf
2	2
3	3	class DerivedArrayDataMatrix {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/sdrf/Edge.groovy

r69	r70
1		package magetab.sdrf
	1	package dbnp.transcriptomics.magetab.sdrf
2	2
3	3	class Edge {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/sdrf/ExtractObj.groovy

r69	r70
1		package magetab.sdrf
	1	package dbnp.transcriptomics.magetab.sdrf
2	2
3	3	// Renamed from Extract to ExtractObj to circumvent problems with Hibernate / SQL EXTRACT keyword

trunk/grails-app/domain/dbnp/transcriptomics/magetab/sdrf/FactorValue.groovy

r69	r70
1		package magetab.sdrf
	1	package dbnp.transcriptomics.magetab.sdrf
2	2
3	3	class FactorValue {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/sdrf/Hybridization.groovy

r69	r70
1		package magetab.sdrf
	1	package dbnp.transcriptomics.magetab.sdrf
2	2
3	3	class Hybridization {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/sdrf/Image.groovy

r69	r70
1		package magetab.sdrf
	1	package dbnp.transcriptomics.magetab.sdrf
2	2
3	3	class Image {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/sdrf/LabeledExtract.groovy

r69	r70
1		package magetab.sdrf
	1	package dbnp.transcriptomics.magetab.sdrf
2	2
3	3	class LabeledExtract {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/sdrf/Material.groovy

r69	r70
1		package magetab.sdrf
	1	package dbnp.transcriptomics.magetab.sdrf
2	2
3	3	class Material {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/sdrf/Node.groovy

r69	r70
1		package magetab.sdrf
	1	package dbnp.transcriptomics.magetab.sdrf
2	2
3	3	class Node {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/sdrf/NodeList.groovy

r69	r70
1		package magetab.sdrf
	1	package dbnp.transcriptomics.magetab.sdrf
2	2
3	3	class NodeList {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/sdrf/Normalization.groovy

r69	r70
1		package magetab.sdrf
	1	package dbnp.transcriptomics.magetab.sdrf
2	2
3	3	class Normalization {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/sdrf/ParameterValue.groovy

r69	r70
1		package magetab.sdrf
	1	package dbnp.transcriptomics.magetab.sdrf
2	2
3	3	class ParameterValue {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/sdrf/ProtocolApplication.groovy

r69	r70
1		package magetab.sdrf
	1	package dbnp.transcriptomics.magetab.sdrf
2	2
3	3	class ProtocolApplication {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/sdrf/Provider.groovy

r69	r70
1		package magetab.sdrf
	1	package dbnp.transcriptomics.magetab.sdrf
2	2
3	3	class Provider {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/sdrf/SampleAndDataRelationship.groovy

r69	r70
1		package magetab.sdrf
	1	package dbnp.transcriptomics.magetab.sdrf
2	2
3	3	class SampleAndDataRelationship {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/sdrf/Scan.groovy

r69	r70
1		package magetab.sdrf
	1	package dbnp.transcriptomics.magetab.sdrf
2	2
3	3	class Scan {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/sdrf/URIValue.groovy

r69	r70
1		package magetab.sdrf
	1	package dbnp.transcriptomics.magetab.sdrf
2	2
3	3	class URIValue {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/sdrf/UserDefinedValue.groovy

r69	r70
1		package magetab.sdrf
	1	package dbnp.transcriptomics.magetab.sdrf
2	2
3	3	class UserDefinedValue {

trunk/grails-app/domain/dbnp/transcriptomics/magetab/sdrf/Value.groovy

r69	r70
1		package magetab.sdrf
	1	package dbnp.transcriptomics.magetab.sdrf
2	2
3	3	class Value {

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