Changeset 70
- Timestamp:
- Jan 4, 2010, 12:13:36 PM (13 years ago)
- Location:
- trunk
- Files:
-
- 3 added
- 39 deleted
- 51 edited
- 2 moved
Legend:
- Unmodified
- Added
- Removed
-
trunk/application.properties
r67 r70 1 #utf-8 2 #Wed Dec 16 17:23:46 CET 2009 1 #Grails Metadata file 2 #Tue Dec 29 14:59:12 CET 2009 3 app.grails.version=1.2.0 4 app.name=gscf 5 app.servlet.version=2.4 6 app.version=0.1 7 plugins.db-util=0.4 8 plugins.hibernate=1.2.0 9 plugins.jquery=1.3.2.4 10 plugins.mail=0.9 11 plugins.nimble=0.3-SNAPSHOT 3 12 plugins.shiro=1.0.1 4 plugins.mail=0.9 5 app.version=0.1 6 plugins.jquery=1.3.2.4 7 app.servlet.version=2.4 8 plugins.hibernate=1.1.2 9 app.name=gscf 10 plugins.nimble=0.3-SNAPSHOT 11 app.grails.version=1.1.2 13 plugins.tomcat=1.2.0 -
trunk/grails-app/controllers/BaseController.groovy
r39 r70 28 28 * @visibility public 29 29 */ 30 def scaffold = false;30 //def scaffold = false; 31 31 32 32 /** … … 43 43 44 44 // dynamically set scaffolding 45 this.scaffold = (GrailsUtil.environment == GrailsApplication.ENV_DEVELOPMENT && this.class.name != 'BaseController');45 //this.scaffold = (GrailsUtil.environment == GrailsApplication.ENV_DEVELOPMENT && this.class.name != 'BaseController'); 46 46 } 47 47 -
trunk/grails-app/controllers/HomeController.groovy
r53 r70 1 import dbnp.studycapturing.Study 2 1 3 class HomeController { 2 4 3 5 def index = { 4 [ studyCount: Study.count() ]6 [ studyCount: dbnp.studycapturing.Study.count() ] 5 7 } 6 8 } -
trunk/grails-app/controllers/LoadController.groovy
r65 r70 18 18 def load = { 19 19 20 static ArrayList attributs = new ArrayList();20 //ArrayList attributes = new ArrayList(); 21 21 22 22 render("Loading ...\n"); … … 25 25 BufferedReader fileReader = new BufferedReader(new InputStreamReader(inputStream)); 26 26 27 def investigationDesign = new magetab.idf.InvestigationDesign();28 def person = new magetab.idf.Person();29 def protocol = new magetab.idf.Protocol();30 def publication = new magetab.idf.Publication();31 def normalization = new magetab.sdrf.Normalization();32 //def termSource = new magetab.adf.Termsource();33 def comment = new magetab.idf.Comment();34 def experimentalInfo = new magetab.idf.ExperimentalInfo();35 36 ArrayList rows = new ArrayList();27 def investigationDesign = new dbnp.transcriptomics.magetab.idf.InvestigationDesign(); 28 def person = new dbnp.transcriptomics.magetab.idf.Person(); 29 def protocol = new dbnp.transcriptomics.magetab.idf.MAGEProtocol(); 30 def publication = new dbnp.transcriptomics.magetab.idf.Publication(); 31 def normalization = new dbnp.transcriptomics.magetab.sdrf.Normalization(); 32 //def termSource = new dbnp.transcriptomics.magetab.adf.Termsource(); 33 def comment = new dbnp.transcriptomics.magetab.idf.Comment(); 34 def experimentalInfo = new dbnp.transcriptomics.magetab.idf.ExperimentalInfo(); 35 36 //ArrayList rows = new ArrayList(); 37 37 38 38 for (i in fileReader.readLines()){ … … 162 162 } 163 163 else if (tmp_list[0]=="Publication Status") { 164 def status = new magetab.idf.OntologyTerm();164 def status = new dbnp.transcriptomics.magetab.idf.OntologyTerm(); 165 165 status.text = tmp_list[1]; 166 166 status.save(); … … 177 177 } 178 178 else if (tmp_list[0]=="Protocol Type") { 179 def type = new magetab.idf.OntologyTerm();179 def type = new dbnp.transcriptomics.magetab.idf.OntologyTerm(); 180 180 for (j in 1..tmp_list.size()){ 181 181 type.text = tmp_list[j]; -
trunk/grails-app/controllers/StudyController.groovy
r53 r70 1 1 class StudyController extends BaseController { 2 2 3 def scaffold = true3 def scaffold = dbnp.studycapturing.Study 4 4 } -
trunk/grails-app/domain/dbnp/transcriptomics/magetab/adf/ArrayDesign.groovy
r69 r70 1 package magetab.adf1 package dbnp.transcriptomics.magetab.adf 2 2 3 3 class ArrayDesign { … … 8 8 String provider 9 9 String printingProtocol 10 magetab.idf.OntologyTerm arrayDesignRef11 magetab.idf.OntologyTerm surfaceType12 magetab.idf.OntologyTerm sequencePolymerType13 magetab.idf.OntologyTerm technologyType14 magetab.idf.OntologyTerm substrateType10 dbnp.transcriptomics.magetab.idf.OntologyTerm arrayDesignRef 11 dbnp.transcriptomics.magetab.idf.OntologyTerm surfaceType 12 dbnp.transcriptomics.magetab.idf.OntologyTerm sequencePolymerType 13 dbnp.transcriptomics.magetab.idf.OntologyTerm technologyType 14 dbnp.transcriptomics.magetab.idf.OntologyTerm substrateType 15 15 16 16 static hasMany = [ 17 17 designElements:DesignElement, 18 userDefinedAttributes: magetab.idf.UserDefinedAttribute18 userDefinedAttributes:dbnp.transcriptomics.magetab.idf.UserDefinedAttribute 19 19 ] 20 20 -
trunk/grails-app/domain/dbnp/transcriptomics/magetab/adf/CompositeElement.groovy
r69 r70 1 package magetab.adf1 package dbnp.transcriptomics.magetab.adf 2 2 3 3 class CompositeElement { … … 5 5 String name 6 6 String comment 7 magetab.idf.OntologyTerm dataBaseEntry7 dbnp.transcriptomics.magetab.idf.OntologyTerm dataBaseEntry 8 8 9 9 static constraints = { -
trunk/grails-app/domain/dbnp/transcriptomics/magetab/adf/DesignElement.groovy
r69 r70 1 package magetab.adf1 package dbnp.transcriptomics.magetab.adf 2 2 3 3 class DesignElement { -
trunk/grails-app/domain/dbnp/transcriptomics/magetab/adf/MatrixColumn.groovy
r69 r70 1 package magetab.adf1 package dbnp.transcriptomics.magetab.adf 2 2 3 3 class MatrixColumn { … … 5 5 int columnNumber 6 6 String columnData 7 magetab.sdrf.Node columnHeader8 magetab.idf.OntologyTerm quantitationType7 dbnp.transcriptomics.magetab.sdrf.Node columnHeader 8 dbnp.transcriptomics.magetab.idf.OntologyTerm quantitationType 9 9 10 10 static constraints = { -
trunk/grails-app/domain/dbnp/transcriptomics/magetab/adf/MatrixRow.groovy
r69 r70 1 package magetab.adf1 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.adf1 package dbnp.transcriptomics.magetab.adf 2 2 3 3 class MatrixRowId { -
trunk/grails-app/domain/dbnp/transcriptomics/magetab/adf/Reporter.groovy
r69 r70 1 package magetab.adf1 package dbnp.transcriptomics.magetab.adf 2 2 3 3 class Reporter { … … 5 5 String name 6 6 String sequence 7 magetab.idf.OntologyTerm group8 magetab.idf.OntologyTerm controlType9 magetab.idf.OntologyTerm databaseEntry7 dbnp.transcriptomics.magetab.idf.OntologyTerm group 8 dbnp.transcriptomics.magetab.idf.OntologyTerm controlType 9 dbnp.transcriptomics.magetab.idf.OntologyTerm databaseEntry 10 10 11 11 static constraints ={ -
trunk/grails-app/domain/dbnp/transcriptomics/magetab/idf/Comment.groovy
r69 r70 1 package magetab.idf1 package dbnp.transcriptomics.magetab.idf 2 2 3 3 class Comment { -
trunk/grails-app/domain/dbnp/transcriptomics/magetab/idf/ExperimentalInfo.groovy
r69 r70 1 package magetab.idf1 package dbnp.transcriptomics.magetab.idf 2 2 3 3 class ExperimentalInfo { … … 9 9 String design_term_source_ref 10 10 11 static hasMany = [12 //factor_name:String,13 //factor_type:String,14 //design:String15 //design_term_source_ref:String,16 //factor_term_source_ref:String17 ] 11 /*static hasMany = [ 12 factor_name:String, 13 factor_type:String, 14 design:String 15 design_term_source_ref:String, 16 factor_term_source_ref:String 17 ]*/ 18 18 19 19 static constraints = { -
trunk/grails-app/domain/dbnp/transcriptomics/magetab/idf/Factor.groovy
r69 r70 1 package magetab.idf1 package dbnp.transcriptomics.magetab.idf 2 2 3 3 class Factor { -
trunk/grails-app/domain/dbnp/transcriptomics/magetab/idf/InvestigationDesign.groovy
r69 r70 1 package magetab.idf1 package dbnp.transcriptomics.magetab.idf 2 2 3 3 class InvestigationDesign { … … 10 10 static hasMany = [ 11 11 experimentalFactors: Factor, 12 protocols: Protocol,12 protocols: MAGEProtocol, 13 13 publications: Publication, 14 //sdrfs: magetab.sdrf.SampleAndDataRelationship,14 //sdrfs: dbnp.transcriptomics.magetab.sdrf.SampleAndDataRelationship, 15 15 userDefinedAttributes: UserDefinedAttribute, 16 16 contacts: Person, … … 19 19 replicateTypes: OntologyTerm, 20 20 experimentalDesigns: OntologyTerm 21 // termSources: magetab.adf.TermSource21 // termSources: dbnp.transcriptomics.magetab.adf.TermSource 22 22 ] 23 23 -
trunk/grails-app/domain/dbnp/transcriptomics/magetab/idf/MAGEProtocol.groovy
r69 r70 1 package magetab.idf1 package dbnp.transcriptomics.magetab.idf 2 2 3 class Protocol {3 class MAGEProtocol { 4 4 5 5 String name -
trunk/grails-app/domain/dbnp/transcriptomics/magetab/idf/OntologyTerm.groovy
r69 r70 1 package magetab.idf1 package dbnp.transcriptomics.magetab.idf 2 2 3 3 class OntologyTerm { … … 6 6 String category 7 7 String accessionNumber 8 // magetab.adf.TermSource termSource8 // dbnp.transcriptomics.magetab.adf.TermSource termSource 9 9 10 10 -
trunk/grails-app/domain/dbnp/transcriptomics/magetab/idf/Parameter.groovy
r69 r70 1 package magetab.idf1 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.idf1 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.idf1 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.idf1 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.sdrf1 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.sdrf1 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.sdrf1 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.sdrf1 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.sdrf1 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.sdrf1 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.sdrf1 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.sdrf1 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.sdrf1 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.sdrf1 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.sdrf1 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.sdrf1 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.sdrf1 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.sdrf1 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.sdrf1 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.sdrf1 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.sdrf1 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.sdrf1 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.sdrf1 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.sdrf1 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.sdrf1 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.sdrf1 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.sdrf1 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.sdrf1 package dbnp.transcriptomics.magetab.sdrf 2 2 3 3 class Value { -
trunk/grails-app/i18n/messages.properties
r4 r70 23 23 default.number.format=0 24 24 25 default.created.message={0} {1} created 26 default.updated.message={0} {1} updated 27 default.deleted.message={0} {1} deleted 28 default.not.deleted.message={0} {1} could not be deleted 29 default.not.found.message={0} not found with id {1} 30 default.optimistic.locking.failure=Another user has updated this {0} while you were editing 31 32 default.home.label=Home 33 default.list.label={0} List 34 default.add.label=Add {0} 35 default.new.label=New {0} 36 default.create.label=Create {0} 37 default.show.label=Show {0} 38 default.edit.label=Edit {0} 39 40 default.button.create.label=Create 41 default.button.edit.label=Edit 42 default.button.update.label=Update 43 default.button.delete.label=Delete 44 default.button.delete.confirm.message=Are you sure? 45 25 46 # Data binding errors. Use "typeMismatch.$className.$propertyName to customize (eg typeMismatch.Book.author) 26 47 typeMismatch.java.net.URL=Property {0} must be a valid URL -
trunk/grails-app/i18n/messages_de.properties
r4 r70 18 18 default.paginate.prev=Vorherige 19 19 default.paginate.next=NÀchste 20 default.boolean.true=Wahr 21 default.boolean.false=Falsch 22 default.date.format=dd.MM.yyyy HH:mm:ss z 23 default.number.format=0 24 25 default.created.message={0} {1} wurde angelegt 26 default.updated.message={0} {1} wurde geÀndert 27 default.deleted.message={0} {1} wurde gelöscht 28 default.not.deleted.message={0} {1} konnte nicht gelöscht werden 29 default.not.found.message={0} mit der id {1} wurde nicht gefunden 30 default.optimistic.locking.failure=Ein anderer Benutzer hat das {0} Object geÀndert wÀhrend Sie es bearbeitet haben 31 32 default.home.label=Home 33 default.list.label={0} Liste 34 default.add.label={0} hinzufÌgen 35 default.new.label={0} anlegen 36 default.create.label={0} anlegen 37 default.show.label={0} anzeigen 38 default.edit.label={0} bearbeiten 39 40 default.button.create.label=Anlegen 41 default.button.edit.label=Bearbeiten 42 default.button.update.label=Aktualisieren 43 default.button.delete.label=Löschen 44 default.button.delete.confirm.message=Sind Sie sicher? 20 45 21 46 # Data binding errors. Use "typeMismatch.$className.$propertyName to customize (eg typeMismatch.Book.author) -
trunk/grails-app/i18n/messages_nl.properties
r4 r70 8 8 default.invalid.min.message=Attribuut [{0}] van entiteit [{1}] met waarde [{2}] is minder dan de minimumwaarde [{3}] 9 9 default.invalid.max.size.message=Attribuut [{0}] van entiteit [{1}] met waarde [{2}] overschrijdt de maximumgrootte van [{3}] 10 default.invalid.min.size.message=Attribuut [{0}] van entiteit [{1}] met waarde [{2}] is minder dan m ainimumgrootte van [{3}]10 default.invalid.min.size.message=Attribuut [{0}] van entiteit [{1}] met waarde [{2}] is minder dan minimumgrootte van [{3}] 11 11 default.invalid.validator.message=Attribuut [{0}] van entiteit [{1}] met waarde [{2}] is niet geldig 12 12 default.not.inlist.message=Attribuut [{0}] van entiteit [{1}] met waarde [{2}] komt niet voor in de lijst [{3}] … … 23 23 default.number.format=0 24 24 25 default.created.message={0} {1} ingevoerd 26 default.updated.message={0} {1} gewijzigd 27 default.deleted.message={0} {1} verwijderd 28 default.not.deleted.message={0} {1} kon niet worden verwijderd 29 default.not.found.message={0} met id {1} kon niet worden gevonden 30 default.optimistic.locking.failure=Een andere gebruiker heeft deze {0} al gewijzigd 31 32 default.home.label=Home 33 default.list.label={0} Overzicht 34 default.add.label=Toevoegen {0} 35 default.new.label=Invoeren {0} 36 default.create.label=Invoeren {0} 37 default.show.label=Details {0} 38 default.edit.label=Wijzigen {0} 39 40 default.button.create.label=Invoeren 41 default.button.edit.label=Wijzigen 42 default.button.update.label=Opslaan 43 default.button.delete.label=Verwijderen 44 default.button.delete.confirm.message=Weet je het zeker? 45 25 46 # Data binding errors. Use "typeMismatch.$className.$propertyName to customize (eg typeMismatch.Book.author) 26 47 typeMismatch.java.net.URL=Attribuut {0} is geen geldige URL -
trunk/web-app/WEB-INF/applicationContext.xml
r4 r70 16 16 <property name="application" ref="grailsApplication" /> 17 17 </bean> 18 19 <bean id="pluginMetaManager" class="org.codehaus.groovy.grails.plugins.DefaultPluginMetaManager">20 <property name="grailsApplication" ref="grailsApplication" />21 <property name="resourcePattern" value="/WEB-INF/plugins/*/plugin.xml" />22 </bean>23 18 24 19 <bean id="grailsConfigurator" class="org.codehaus.groovy.grails.commons.spring.GrailsRuntimeConfigurator"> -
trunk/web-app/WEB-INF/sitemesh.xml
r4 r70 2 2 <page-parsers> 3 3 <parser content-type="text/html" 4 class=" com.opensymphony.module.sitemesh.parser.HTMLPageParser" />4 class="org.codehaus.groovy.grails.web.sitemesh.GrailsHTMLPageParser" /> 5 5 <parser content-type="text/html;charset=ISO-8859-1" 6 class=" com.opensymphony.module.sitemesh.parser.HTMLPageParser" />6 class="org.codehaus.groovy.grails.web.sitemesh.GrailsHTMLPageParser" /> 7 7 <parser content-type="text/html;charset=UTF-8" 8 class=" com.opensymphony.module.sitemesh.parser.HTMLPageParser" />8 class="org.codehaus.groovy.grails.web.sitemesh.GrailsHTMLPageParser" /> 9 9 </page-parsers> 10 10 -
trunk/web-app/WEB-INF/tld/grails.tld
r4 r70 542 542 </variable> 543 543 <attribute> 544 <name> name</name>544 <name>tagName</name> 545 545 <required>true</required> 546 546 <rtexprvalue>true</rtexprvalue>
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