Changeset 1456
- Timestamp:
- Jan 31, 2011, 1:27:30 PM (12 years ago)
- Location:
- trunk
- Files:
-
- 8 deleted
- 45 edited
Legend:
- Unmodified
- Added
- Removed
-
trunk/application.properties
r1443 r1456 1 1 #Grails Metadata file 2 # Wed Jan 26 21:41:18CET 20112 #Mon Jan 31 13:18:07 CET 2011 3 3 app.build.display.info=0 4 4 app.build.svn.revision=1079 … … 13 13 plugins.db-util=0.4 14 14 plugins.famfamfam=1.0.1 15 plugins.gdt=0.0. 515 plugins.gdt=0.0.6 16 16 plugins.grom=0.2.2 17 17 plugins.hibernate=1.3.6 -
trunk/grails-app/conf/BootStrap.groovy
r1430 r1456 2 2 import dbnp.authentication.SecUser 3 3 import org.codehaus.groovy.grails.commons.GrailsApplication 4 import nl.grails.plugins.gdt.*4 import org.dbnp.gdt.* 5 5 import dbnp.studycapturing.Study 6 6 import dbnp.studycapturing.Subject -
trunk/grails-app/conf/BootStrapStudies.groovy
r1430 r1456 10 10 11 11 import dbnp.studycapturing.* 12 import nl.grails.plugins.gdt.*12 import org.dbnp.gdt.* 13 13 import org.codehaus.groovy.grails.commons.GrailsApplication 14 14 import grails.util.GrailsUtil -
trunk/grails-app/conf/BootStrapTemplates.groovy
r1430 r1456 10 10 11 11 import dbnp.studycapturing.* 12 import nl.grails.plugins.gdt.*12 import org.dbnp.gdt.* 13 13 import org.codehaus.groovy.grails.commons.GrailsApplication 14 14 -
trunk/grails-app/controllers/dbnp/exporter/ExporterController.groovy
r1430 r1456 16 16 17 17 import dbnp.studycapturing.* 18 import org.dbnp.gdt.* 18 19 19 20 import org.apache.poi.hssf.util.HSSFColor … … 210 211 println "----- SUBJECT -----" 211 212 for (u in 0..sample.parentSubject.giveFields().unique().size()-1){ 212 nl.grails.plugins.gdt.TemplateField tf = sample.parentSubject.giveFields().getAt(u)213 TemplateField tf = sample.parentSubject.giveFields().getAt(u) 213 214 println tf.name 214 215 row.createCell((short)9+u).setCellValue(tf.name) … … 221 222 println "----- SAMPLING EVENT -----" 222 223 for (t in 0..sample.parentEvent.giveFields().unique().size()-1){ 223 nl.grails.plugins.gdt.TemplateField tf =sample.parentEvent.giveFields().getAt(t)224 TemplateField tf =sample.parentEvent.giveFields().getAt(t) 224 225 println tf.name 225 226 row.createCell((short)9+sample.parentSubject.giveFields().unique().size()+t).setCellValue("samplingEvent-"+tf.name) … … 237 238 println "----- SAMPLE -----" 238 239 for (v in 0..sample.giveFields().unique().size()-1){ 239 nl.grails.plugins.gdt.TemplateField tf =sample.giveFields().getAt(v)240 TemplateField tf =sample.giveFields().getAt(v) 240 241 println tf.name 241 242 row.createCell((short)9+sample.parentSubject.giveFields().unique().size()+v+sample.parentEvent.giveFields().unique().size()).setCellValue("sample-"+tf.name) -
trunk/grails-app/controllers/dbnp/importer/ImporterController.groovy
r1444 r1456 2 2 3 3 import dbnp.studycapturing.* 4 import nl.grails.plugins.gdt.* 5 import org.apache.poi.ss.usermodel.Workbook 4 6 5 import grails.converters.JSON 7 6 //import cr.co.arquetipos.crypto.Blowfish 8 7 import org.codehaus.groovy.grails.plugins.web.taglib.ValidationTagLib 9 8 import grails.plugins.springsecurity.Secured 10 import org.hibernate.SessionFactory11 9 12 10 /** … … 415 413 entity.giveFields().each { field -> 416 414 // field of type ontology and value "#invalidterm"? 417 if (field.type == nl.grails.plugins.gdt.TemplateFieldType.ONTOLOGYTERM &&415 if (field.type == org.dbnp.gdt.TemplateFieldType.ONTOLOGYTERM && 418 416 params["entity_" + entity.getIdentifier() + "_" + field.escapedName()] == "#invalidterm" 419 417 ) { 420 418 invalidontologies++ 421 419 } else 422 if (field.type == nl.grails.plugins.gdt.TemplateFieldType.ONTOLOGYTERM &&420 if (field.type == org.dbnp.gdt.TemplateFieldType.ONTOLOGYTERM && 423 421 params["entity_" + entity.getIdentifier() + "_" + field.escapedName()] != "#invalidterm") { 424 422 removeFailedCell(flow.importer_failedcells, entity) -
trunk/grails-app/controllers/dbnp/query/AdvancedQueryController.groovy
r1432 r1456 1 1 package dbnp.query 2 3 import dbnp.studycapturing.*4 import nl.grails.plugins.gdt.*5 2 6 3 // TODO: Make use of the searchable-plugin possibilities instead of querying the database directly -
trunk/grails-app/controllers/dbnp/studycapturing/AssayModuleController.groovy
r1430 r1456 15 15 package dbnp.studycapturing 16 16 17 import nl.grails.plugins.gdt.*18 19 17 class AssayModuleController { 20 18 // Scaffold this class to circumvent not being able to add assays (0.4) 21 def scaffold = nl.grails.plugins.gdt.AssayModule19 def scaffold = org.dbnp.gdt.AssayModule 22 20 } -
trunk/grails-app/controllers/dbnp/studycapturing/StudyController.groovy
r1440 r1456 3 3 import grails.converters.* 4 4 import grails.plugins.springsecurity.Secured 5 import nl.grails.plugins.gdt.TemplateFieldType 5 import org.dbnp.gdt.TemplateFieldType 6 import org.dbnp.gdt.RelTime 7 6 8 7 9 /** … … 314 316 if( value ) { 315 317 if( templateField.type == TemplateFieldType.RELTIME ) 316 value = new nl.grails.plugins.gdt.RelTime( value ).toString();318 value = new RelTime( value ).toString(); 317 319 318 320 def param = templateField.name + " = " + value; -
trunk/grails-app/controllers/dbnp/studycapturing/StudyWizardController.groovy
r1430 r1456 1 1 package dbnp.studycapturing 2 2 3 import dbnp.data.*4 import grails.converters.*5 3 import grails.plugins.springsecurity.Secured 6 import dbnp.authentication.AuthenticationService 4 7 5 import dbnp.authentication.SecUser 8 6 import org.codehaus.groovy.grails.plugins.web.taglib.ValidationTagLib 9 import nl.grails.plugins.gdt.*7 import org.dbnp.gdt.RelTime 10 8 11 9 /** … … 1553 1551 def samplingEventName = ucwords(event.template.name) 1554 1552 def eventGroupName = ucwords(eventGroup.name).replaceAll("([ ]{1,})", "") 1555 def sampleName = (ucwords(subject.name) + '_' + samplingEventName + '_' + eventGroupName + '_' + new nl.grails.plugins.gdt.RelTime(event.startTime).toString()).replaceAll("([ ]{1,})", "")1553 def sampleName = (ucwords(subject.name) + '_' + samplingEventName + '_' + eventGroupName + '_' + new RelTime(event.startTime).toString()).replaceAll("([ ]{1,})", "") 1556 1554 def tempSampleIterator = 0 1557 1555 def tempSampleName = sampleName … … 1649 1647 def samplingEventName = ucwords(samplingEvent.template.name) 1650 1648 def eventGroupName = ucwords(eventGroup.name) 1651 def sampleName = (ucwords(subject.name) + '_' + samplingEventName + '_' + eventGroupName + '_' + new nl.grails.plugins.gdt.RelTime(samplingEvent.startTime).toString()).replaceAll("([ ]{1,})", "")1649 def sampleName = (ucwords(subject.name) + '_' + samplingEventName + '_' + eventGroupName + '_' + new RelTime(samplingEvent.startTime).toString()).replaceAll("([ ]{1,})", "") 1652 1650 def tempSampleIterator = 0 1653 1651 def tempSampleName = sampleName -
trunk/grails-app/controllers/dbnp/studycapturing/TermEditorController.groovy
r1430 r1456 14 14 */ 15 15 package dbnp.studycapturing 16 17 import nl.grails.plugins.gdt.*18 16 19 17 class TermEditorController { -
trunk/grails-app/domain/dbnp/importer/ImportCell.groovy
r1452 r1456 1 1 package dbnp.importer 2 import nl.grails.plugins.gdt.*3 2 4 3 /** -
trunk/grails-app/domain/dbnp/importer/ImportRecord.groovy
r1452 r1456 14 14 */ 15 15 package dbnp.importer 16 import nl.grails.plugins.gdt.*17 16 18 17 class ImportRecord extends Identity { -
trunk/grails-app/domain/dbnp/importer/MappingColumn.groovy
r1430 r1456 1 1 package dbnp.importer 2 2 3 import nl.grails.plugins.gdt.*3 import org.dbnp.gdt.TemplateFieldType 4 4 5 5 /** … … 15 15 16 16 String name 17 nl.grails.plugins.gdt.TemplateFieldType templatefieldtype17 TemplateFieldType templatefieldtype 18 18 Class entity 19 19 String property -
trunk/grails-app/domain/dbnp/studycapturing/Assay.groovy
r1454 r1456 1 1 package dbnp.studycapturing 2 import nl.grails.plugins.gdt.*3 import java.util.UUID;4 2 5 3 /** -
trunk/grails-app/domain/dbnp/studycapturing/Event.groovy
r1452 r1456 1 1 package dbnp.studycapturing 2 3 import nl.grails.plugins.gdt.*4 2 5 3 /** -
trunk/grails-app/domain/dbnp/studycapturing/EventGroup.groovy
r1452 r1456 1 1 package dbnp.studycapturing 2 import nl.grails.plugins.gdt.*3 2 4 3 /** -
trunk/grails-app/domain/dbnp/studycapturing/Person.groovy
r1452 r1456 1 1 package dbnp.studycapturing 2 import nl.grails.plugins.gdt.*3 2 4 3 /** -
trunk/grails-app/domain/dbnp/studycapturing/PersonAffiliation.groovy
r1452 r1456 1 1 package dbnp.studycapturing 2 import nl.grails.plugins.gdt.*3 2 4 3 /** -
trunk/grails-app/domain/dbnp/studycapturing/PersonRole.groovy
r1452 r1456 1 1 package dbnp.studycapturing 2 import nl.grails.plugins.gdt.*3 2 4 3 /** -
trunk/grails-app/domain/dbnp/studycapturing/Publication.groovy
r1452 r1456 1 1 package dbnp.studycapturing 2 import nl.grails.plugins.gdt.*3 2 4 3 /** -
trunk/grails-app/domain/dbnp/studycapturing/Sample.groovy
r1454 r1456 1 1 package dbnp.studycapturing 2 3 import nl.grails.plugins.gdt.*4 import java.util.UUID;5 2 6 3 /** -
trunk/grails-app/domain/dbnp/studycapturing/SamplingEvent.groovy
r1452 r1456 1 1 package dbnp.studycapturing 2 import nl.grails.plugins.gdt.*3 2 4 3 /** -
trunk/grails-app/domain/dbnp/studycapturing/Study.groovy
r1454 r1456 2 2 3 3 import dbnp.authentication.SecUser 4 import nl.grails.plugins.gdt.*5 import java.util.UUID;6 import dbnp.modules.*;7 4 8 5 /** -
trunk/grails-app/domain/dbnp/studycapturing/StudyPerson.groovy
r1452 r1456 1 1 package dbnp.studycapturing 2 import nl.grails.plugins.gdt.*3 2 4 3 /** -
trunk/grails-app/domain/dbnp/studycapturing/Subject.groovy
r1452 r1456 1 1 package dbnp.studycapturing 2 3 import nl.grails.plugins.gdt.*4 2 5 3 /** -
trunk/grails-app/services/dbnp/importer/ImporterService.groovy
r1430 r1456 18 18 19 19 import org.apache.poi.ss.usermodel.* 20 import org.apache.poi.xssf.usermodel.XSSFCell 21 22 import nl.grails.plugins.gdt.* 20 23 21 import dbnp.studycapturing.* 24 import org.apache.commons.lang.RandomStringUtils25 22 26 23 class ImporterService { -
trunk/grails-app/services/dbnp/modules/ModuleNotificationService.groovy
r1446 r1456 15 15 package dbnp.modules 16 16 17 import nl.grails.plugins.gdt.*18 17 import dbnp.studycapturing.* 19 18 -
trunk/grails-app/taglib/dbnp/importer/ImporterTagLib.groovy
r1443 r1456 16 16 package dbnp.importer 17 17 18 import dbnp.studycapturing.*19 import nl.grails.plugins.gdt.*20 18 import org.apache.poi.ss.usermodel.Cell 21 19 import org.apache.poi.ss.usermodel.DataFormatter … … 159 157 * @return HTML select object 160 158 * 161 * @see nl.grails.plugins.gdt.TemplateFieldType159 * @see org.dbnp.gdt.TemplateFieldType 162 160 */ 163 161 … … 186 184 * @return HTML select object 187 185 * 188 * @see nl.grails.plugins.gdt.TemplateFieldType186 * @see org.dbnp.gdt.TemplateFieldType 189 187 */ 190 188 def templatefieldtypeSelect = { attrs -> -
trunk/grails-app/taglib/dbnp/studycapturing/WizardTagLib.groovy
r1447 r1456 1 1 package dbnp.studycapturing 2 2 3 import dbnp.studycapturing.*4 import nl.grails.plugins.gdt.*5 3 import dbnp.authentication.SecUser 6 4 import cr.co.arquetipos.crypto.Blowfish -
trunk/grails-app/views/importer/common/_properties_horizontal.gsp
r1444 r1456 1 <%@ page import=" nl.grails.plugins.gdt.GdtService" %>1 <%@ page import="org.dbnp.gdt.GdtService" %> 2 2 <% 3 3 /** -
trunk/grails-app/views/importer/pages/_page_one.gsp
r1443 r1456 1 <%@ page import=" nl.grails.plugins.gdt.GdtService" %>1 <%@ page import="org.dbnp.gdt.GdtService" %> 2 2 <% 3 3 /** -
trunk/grails-app/views/study/show.gsp
r1430 r1456 1 1 <%@ page import="dbnp.studycapturing.*" %> 2 <%@ page import=" nl.grails.plugins.gdt.*" %>2 <%@ page import="org.dbnp.gdt.*" %> 3 3 <html> 4 4 <head> -
trunk/grails-app/views/study/show_events_table.gsp
r1430 r1456 1 1 <%@ page import="dbnp.studycapturing.*" %> 2 <%@ page import=" nl.grails.plugins.gdt.*" %>2 <%@ page import="org.dbnp.gdt.*" %> 3 3 <g:if test="${studyList*.eventGroups?.flatten()?.size()==0}"> 4 4 No event groups in this study -
trunk/src/groovy/dbnp/query/Criterion.groovy
r1436 r1456 1 1 package dbnp.query 2 2 3 import java.util.Date;4 import java.util.List;5 3 import java.text.SimpleDateFormat; 6 7 import nl.grails.plugins.gdt.*8 4 9 5 /** -
trunk/src/groovy/dbnp/query/SampleSearch.groovy
r1436 r1456 15 15 package dbnp.query 16 16 17 import java.util.List18 17 import dbnp.studycapturing.* 19 import nl.grails.plugins.gdt.*20 18 21 19 class SampleSearch extends Search { -
trunk/src/groovy/dbnp/query/Search.groovy
r1430 r1456 16 16 package dbnp.query 17 17 18 import nl.grails.plugins.gdt.*19 import java.util.List;20 import java.text.DateFormat;21 18 import java.text.SimpleDateFormat 22 19 -
trunk/src/groovy/dbnp/query/StudySearch.groovy
r1430 r1456 16 16 17 17 import dbnp.studycapturing.* 18 import nl.grails.plugins.gdt.*19 18 20 19 class StudySearch extends Search { -
trunk/test/integration/dbnp/query/SampleSearchTests.groovy
r1436 r1456 2 2 3 3 import dbnp.studycapturing.* 4 import dbnp.data.*5 import dbnp.authentication.*;6 import grails.test.*7 import nl.grails.plugins.gdt.*8 4 9 5 /** -
trunk/test/integration/gscf/OntologyTests.groovy
r1432 r1456 2 2 3 3 import grails.test.* 4 import dbnp.data.*5 import nl.grails.plugins.gdt.*6 import uk.ac.ebi.ontocat.*7 4 8 5 /** -
trunk/test/integration/gscf/SampleTests.groovy
r1432 r1456 2 2 3 3 import dbnp.studycapturing.* 4 import grails.test.GrailsUnitTestCase5 import nl.grails.plugins.gdt.*6 4 7 5 /** -
trunk/test/integration/gscf/SubjectTests.groovy
r1436 r1456 1 1 package gscf 2 2 3 import grails.test.*4 3 import dbnp.studycapturing.* 5 import dbnp.data.*6 import nl.grails.plugins.gdt.*7 4 8 5 /** -
trunk/test/unit/dbnp/query/CriterionTests.groovy
r1433 r1456 1 1 package dbnp.query 2 2 3 import nl.grails.plugins.gdt.*4 3 import grails.test.* 5 import java.util.Date;6 import java.text.DateFormat;7 4 8 5 /** -
trunk/test/unit/dbnp/query/SearchTests.groovy
r1433 r1456 1 1 package dbnp.query 2 2 3 import nl.grails.plugins.gdt.*4 3 import grails.test.* 5 4 -
trunk/test/unit/dbnp/studycapturing/AssayServiceTests.groovy
r1455 r1456 6 6 import org.apache.poi.ss.usermodel.Cell 7 7 import grails.converters.JSON 8 import nl.grails.plugins.gdt.Term9 import nl.grails.plugins.gdt.TemplateField10 import nl.grails.plugins.gdt.Template11 import nl.grails.plugins.gdt.TemplateFieldType8 import org.dbnp.gdt.Term 9 import org.dbnp.gdt.TemplateField 10 import org.dbnp.gdt.Template 11 import org.dbnp.gdt.TemplateFieldType 12 12 13 13 /**
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