Changeset 1456


Ignore:
Timestamp:
Jan 31, 2011, 1:27:30 PM (7 years ago)
Author:
business@…
Message:

moved gdt package to org.dbnp, moved tests for RelTime?, TemplateEntity?, Template etc. to gdt plugin

Location:
trunk
Files:
8 deleted
45 edited

Legend:

Unmodified
Added
Removed
  • trunk/application.properties

    r1443 r1456  
    11#Grails Metadata file
    2 #Wed Jan 26 21:41:18 CET 2011
     2#Mon Jan 31 13:18:07 CET 2011
    33app.build.display.info=0
    44app.build.svn.revision=1079
     
    1313plugins.db-util=0.4
    1414plugins.famfamfam=1.0.1
    15 plugins.gdt=0.0.5
     15plugins.gdt=0.0.6
    1616plugins.grom=0.2.2
    1717plugins.hibernate=1.3.6
  • trunk/grails-app/conf/BootStrap.groovy

    r1430 r1456  
    22import dbnp.authentication.SecUser
    33import org.codehaus.groovy.grails.commons.GrailsApplication
    4 import nl.grails.plugins.gdt.*
     4import org.dbnp.gdt.*
    55import dbnp.studycapturing.Study
    66import dbnp.studycapturing.Subject
  • trunk/grails-app/conf/BootStrapStudies.groovy

    r1430 r1456  
    1010
    1111import dbnp.studycapturing.*
    12 import nl.grails.plugins.gdt.*
     12import org.dbnp.gdt.*
    1313import org.codehaus.groovy.grails.commons.GrailsApplication
    1414import grails.util.GrailsUtil
  • trunk/grails-app/conf/BootStrapTemplates.groovy

    r1430 r1456  
    1010
    1111import dbnp.studycapturing.*
    12 import nl.grails.plugins.gdt.*
     12import org.dbnp.gdt.*
    1313import org.codehaus.groovy.grails.commons.GrailsApplication
    1414
  • trunk/grails-app/controllers/dbnp/exporter/ExporterController.groovy

    r1430 r1456  
    1616
    1717import dbnp.studycapturing.*
     18import org.dbnp.gdt.*
    1819
    1920import org.apache.poi.hssf.util.HSSFColor
     
    210211        println "----- SUBJECT -----"
    211212        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)
    213214            println tf.name
    214215            row.createCell((short)9+u).setCellValue(tf.name)
     
    221222        println "----- SAMPLING EVENT -----"
    222223        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)
    224225            println tf.name
    225226            row.createCell((short)9+sample.parentSubject.giveFields().unique().size()+t).setCellValue("samplingEvent-"+tf.name)
     
    237238        println "----- SAMPLE -----"
    238239        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)
    240241            println tf.name
    241242            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  
    22
    33import dbnp.studycapturing.*
    4 import nl.grails.plugins.gdt.*
    5 import org.apache.poi.ss.usermodel.Workbook
     4
    65import grails.converters.JSON
    76//import cr.co.arquetipos.crypto.Blowfish
    87import org.codehaus.groovy.grails.plugins.web.taglib.ValidationTagLib
    98import grails.plugins.springsecurity.Secured
    10 import org.hibernate.SessionFactory
    119
    1210/**
     
    415413                                entity.giveFields().each { field ->
    416414                                        // 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 &&
    418416                                                params["entity_" + entity.getIdentifier() + "_" + field.escapedName()] == "#invalidterm"
    419417                                        ) {
    420418                                                invalidontologies++
    421419                                        } else
    422                                         if (field.type == nl.grails.plugins.gdt.TemplateFieldType.ONTOLOGYTERM &&
     420                                        if (field.type == org.dbnp.gdt.TemplateFieldType.ONTOLOGYTERM &&
    423421                                                params["entity_" + entity.getIdentifier() + "_" + field.escapedName()] != "#invalidterm") {
    424422                                                removeFailedCell(flow.importer_failedcells, entity)
  • trunk/grails-app/controllers/dbnp/query/AdvancedQueryController.groovy

    r1432 r1456  
    11package dbnp.query
    2 
    3 import dbnp.studycapturing.*
    4 import nl.grails.plugins.gdt.*
    52
    63// TODO: Make use of the searchable-plugin possibilities instead of querying the database directly
  • trunk/grails-app/controllers/dbnp/studycapturing/AssayModuleController.groovy

    r1430 r1456  
    1515package dbnp.studycapturing
    1616
    17 import nl.grails.plugins.gdt.*
    18 
    1917class AssayModuleController {
    2018        // Scaffold this class to circumvent not being able to add assays (0.4)
    21         def scaffold = nl.grails.plugins.gdt.AssayModule
     19        def scaffold = org.dbnp.gdt.AssayModule
    2220}
  • trunk/grails-app/controllers/dbnp/studycapturing/StudyController.groovy

    r1440 r1456  
    33import grails.converters.*
    44import grails.plugins.springsecurity.Secured
    5 import nl.grails.plugins.gdt.TemplateFieldType
     5import org.dbnp.gdt.TemplateFieldType
     6import org.dbnp.gdt.RelTime
     7
    68
    79/**
     
    314316                                if( value ) {
    315317                                        if( templateField.type == TemplateFieldType.RELTIME )
    316                                                 value = new nl.grails.plugins.gdt.RelTime( value ).toString();
     318                                                value = new RelTime( value ).toString();
    317319
    318320                        def param = templateField.name + " = " + value;
  • trunk/grails-app/controllers/dbnp/studycapturing/StudyWizardController.groovy

    r1430 r1456  
    11package dbnp.studycapturing
    22
    3 import dbnp.data.*
    4 import grails.converters.*
    53import grails.plugins.springsecurity.Secured
    6 import dbnp.authentication.AuthenticationService
     4
    75import dbnp.authentication.SecUser
    86import org.codehaus.groovy.grails.plugins.web.taglib.ValidationTagLib
    9 import nl.grails.plugins.gdt.*
     7import org.dbnp.gdt.RelTime
    108
    119/**
     
    15531551                                                                def samplingEventName = ucwords(event.template.name)
    15541552                                                                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,})", "")
    15561554                                                                def tempSampleIterator = 0
    15571555                                                                def tempSampleName = sampleName
     
    16491647                                                        def samplingEventName = ucwords(samplingEvent.template.name)
    16501648                                                        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,})", "")
    16521650                                                        def tempSampleIterator = 0
    16531651                                                        def tempSampleName = sampleName
  • trunk/grails-app/controllers/dbnp/studycapturing/TermEditorController.groovy

    r1430 r1456  
    1414 */
    1515package dbnp.studycapturing
    16 
    17 import nl.grails.plugins.gdt.*
    1816
    1917class TermEditorController {
  • trunk/grails-app/domain/dbnp/importer/ImportCell.groovy

    r1452 r1456  
    11package dbnp.importer
    2 import nl.grails.plugins.gdt.*
    32
    43/**
  • trunk/grails-app/domain/dbnp/importer/ImportRecord.groovy

    r1452 r1456  
    1414 */
    1515package dbnp.importer
    16 import nl.grails.plugins.gdt.*
    1716
    1817class ImportRecord extends Identity {
  • trunk/grails-app/domain/dbnp/importer/MappingColumn.groovy

    r1430 r1456  
    11package dbnp.importer
    22
    3 import nl.grails.plugins.gdt.*
     3import org.dbnp.gdt.TemplateFieldType
    44
    55/**
     
    1515
    1616        String name
    17         nl.grails.plugins.gdt.TemplateFieldType templatefieldtype
     17        TemplateFieldType templatefieldtype
    1818        Class entity
    1919        String property
  • trunk/grails-app/domain/dbnp/studycapturing/Assay.groovy

    r1454 r1456  
    11package dbnp.studycapturing
    2 import nl.grails.plugins.gdt.*
    3 import java.util.UUID;
    42
    53/**
  • trunk/grails-app/domain/dbnp/studycapturing/Event.groovy

    r1452 r1456  
    11package dbnp.studycapturing
    2 
    3 import nl.grails.plugins.gdt.*
    42
    53/**
  • trunk/grails-app/domain/dbnp/studycapturing/EventGroup.groovy

    r1452 r1456  
    11package dbnp.studycapturing
    2 import nl.grails.plugins.gdt.*
    32
    43/**
  • trunk/grails-app/domain/dbnp/studycapturing/Person.groovy

    r1452 r1456  
    11package dbnp.studycapturing
    2 import nl.grails.plugins.gdt.*
    32
    43/**
  • trunk/grails-app/domain/dbnp/studycapturing/PersonAffiliation.groovy

    r1452 r1456  
    11package dbnp.studycapturing
    2 import nl.grails.plugins.gdt.*
    32
    43/**
  • trunk/grails-app/domain/dbnp/studycapturing/PersonRole.groovy

    r1452 r1456  
    11package dbnp.studycapturing
    2 import nl.grails.plugins.gdt.*
    32
    43/**
  • trunk/grails-app/domain/dbnp/studycapturing/Publication.groovy

    r1452 r1456  
    11package dbnp.studycapturing
    2 import nl.grails.plugins.gdt.*
    32
    43/**
  • trunk/grails-app/domain/dbnp/studycapturing/Sample.groovy

    r1454 r1456  
    11package dbnp.studycapturing
    2 
    3 import nl.grails.plugins.gdt.*
    4 import java.util.UUID;
    52
    63/**
  • trunk/grails-app/domain/dbnp/studycapturing/SamplingEvent.groovy

    r1452 r1456  
    11package dbnp.studycapturing
    2 import nl.grails.plugins.gdt.*
    32
    43/**
  • trunk/grails-app/domain/dbnp/studycapturing/Study.groovy

    r1454 r1456  
    22
    33import dbnp.authentication.SecUser
    4 import nl.grails.plugins.gdt.*
    5 import java.util.UUID;
    6 import dbnp.modules.*;
    74
    85/**
  • trunk/grails-app/domain/dbnp/studycapturing/StudyPerson.groovy

    r1452 r1456  
    11package dbnp.studycapturing
    2 import nl.grails.plugins.gdt.*
    32
    43/**
  • trunk/grails-app/domain/dbnp/studycapturing/Subject.groovy

    r1452 r1456  
    11package dbnp.studycapturing
    2 
    3 import nl.grails.plugins.gdt.*
    42
    53/**
  • trunk/grails-app/services/dbnp/importer/ImporterService.groovy

    r1430 r1456  
    1818
    1919import org.apache.poi.ss.usermodel.*
    20 import org.apache.poi.xssf.usermodel.XSSFCell
    21 
    22 import nl.grails.plugins.gdt.*
     20
    2321import dbnp.studycapturing.*
    24 import org.apache.commons.lang.RandomStringUtils
    2522
    2623class ImporterService {
  • trunk/grails-app/services/dbnp/modules/ModuleNotificationService.groovy

    r1446 r1456  
    1515package dbnp.modules
    1616
    17 import nl.grails.plugins.gdt.*
    1817import dbnp.studycapturing.*
    1918
  • trunk/grails-app/taglib/dbnp/importer/ImporterTagLib.groovy

    r1443 r1456  
    1616package dbnp.importer
    1717
    18 import dbnp.studycapturing.*
    19 import nl.grails.plugins.gdt.*
    2018import org.apache.poi.ss.usermodel.Cell
    2119import org.apache.poi.ss.usermodel.DataFormatter
     
    159157         * @return HTML select object
    160158         *
    161          * @see nl.grails.plugins.gdt.TemplateFieldType
     159         * @see org.dbnp.gdt.TemplateFieldType
    162160         */
    163161
     
    186184         * @return HTML select object
    187185         *
    188          * @see nl.grails.plugins.gdt.TemplateFieldType
     186         * @see org.dbnp.gdt.TemplateFieldType
    189187         */
    190188        def templatefieldtypeSelect = { attrs ->
  • trunk/grails-app/taglib/dbnp/studycapturing/WizardTagLib.groovy

    r1447 r1456  
    11package dbnp.studycapturing
    22
    3 import dbnp.studycapturing.*
    4 import nl.grails.plugins.gdt.*
    53import dbnp.authentication.SecUser
    64import 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" %>
    22<%
    33        /**
  • 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" %>
    22<%
    33/**
  • trunk/grails-app/views/study/show.gsp

    r1430 r1456  
    11<%@ page import="dbnp.studycapturing.*" %>
    2 <%@ page import="nl.grails.plugins.gdt.*" %>
     2<%@ page import="org.dbnp.gdt.*" %>
    33<html>
    44<head>
  • trunk/grails-app/views/study/show_events_table.gsp

    r1430 r1456  
    11<%@ page import="dbnp.studycapturing.*" %>
    2 <%@ page import="nl.grails.plugins.gdt.*" %>
     2<%@ page import="org.dbnp.gdt.*" %>
    33<g:if test="${studyList*.eventGroups?.flatten()?.size()==0}">
    44  No event groups in this study
  • trunk/src/groovy/dbnp/query/Criterion.groovy

    r1436 r1456  
    11package dbnp.query
    22
    3 import java.util.Date;
    4 import java.util.List;
    53import java.text.SimpleDateFormat;
    6 
    7 import nl.grails.plugins.gdt.*
    84
    95/**
  • trunk/src/groovy/dbnp/query/SampleSearch.groovy

    r1436 r1456  
    1515package dbnp.query
    1616
    17 import java.util.List
    1817import dbnp.studycapturing.*
    19 import nl.grails.plugins.gdt.*
    2018
    2119class SampleSearch extends Search {
  • trunk/src/groovy/dbnp/query/Search.groovy

    r1430 r1456  
    1616package dbnp.query
    1717
    18 import nl.grails.plugins.gdt.*
    19 import java.util.List;
    20 import java.text.DateFormat;
    2118import java.text.SimpleDateFormat
    2219
  • trunk/src/groovy/dbnp/query/StudySearch.groovy

    r1430 r1456  
    1616
    1717import dbnp.studycapturing.*
    18 import nl.grails.plugins.gdt.*
    1918
    2019class StudySearch extends Search {
  • trunk/test/integration/dbnp/query/SampleSearchTests.groovy

    r1436 r1456  
    22
    33import dbnp.studycapturing.*
    4 import dbnp.data.*
    5 import dbnp.authentication.*;
    6 import grails.test.*
    7 import nl.grails.plugins.gdt.*
    84
    95/**
  • trunk/test/integration/gscf/OntologyTests.groovy

    r1432 r1456  
    22
    33import grails.test.*
    4 import dbnp.data.*
    5 import nl.grails.plugins.gdt.*
    6 import uk.ac.ebi.ontocat.*
    74
    85/**
  • trunk/test/integration/gscf/SampleTests.groovy

    r1432 r1456  
    22
    33import dbnp.studycapturing.*
    4 import grails.test.GrailsUnitTestCase
    5 import nl.grails.plugins.gdt.*
    64
    75/**
  • trunk/test/integration/gscf/SubjectTests.groovy

    r1436 r1456  
    11package gscf
    22
    3 import grails.test.*
    43import dbnp.studycapturing.*
    5 import dbnp.data.*
    6 import nl.grails.plugins.gdt.*
    74
    85/**
  • trunk/test/unit/dbnp/query/CriterionTests.groovy

    r1433 r1456  
    11package dbnp.query
    22
    3 import nl.grails.plugins.gdt.*
    43import grails.test.*
    5 import java.util.Date;
    6 import java.text.DateFormat;
    74
    85/**
  • trunk/test/unit/dbnp/query/SearchTests.groovy

    r1433 r1456  
    11package dbnp.query
    22
    3 import nl.grails.plugins.gdt.*
    43import grails.test.*
    54
  • trunk/test/unit/dbnp/studycapturing/AssayServiceTests.groovy

    r1455 r1456  
    66import org.apache.poi.ss.usermodel.Cell
    77import grails.converters.JSON
    8 import nl.grails.plugins.gdt.Term
    9 import nl.grails.plugins.gdt.TemplateField
    10 import nl.grails.plugins.gdt.Template
    11 import nl.grails.plugins.gdt.TemplateFieldType
     8import org.dbnp.gdt.Term
     9import org.dbnp.gdt.TemplateField
     10import org.dbnp.gdt.Template
     11import org.dbnp.gdt.TemplateFieldType
    1212
    1313/**
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