Changeset 70


Ignore:
Timestamp:
Jan 4, 2010, 12:13:36 PM (9 years ago)
Author:
keesvb
Message:

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

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
     3app.grails.version=1.2.0
     4app.name=gscf
     5app.servlet.version=2.4
     6app.version=0.1
     7plugins.db-util=0.4
     8plugins.hibernate=1.2.0
     9plugins.jquery=1.3.2.4
     10plugins.mail=0.9
     11plugins.nimble=0.3-SNAPSHOT
    312plugins.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
     13plugins.tomcat=1.2.0

  • trunk/grails-app/controllers/BaseController.groovy

    r39 r70  
    2828     * @visibility public
    2929     */
    30     def scaffold = false;
     30    //def scaffold = false;
    3131
    3232    /**
    … …  
    4343
    4444        // 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');
    4646    }
    4747

  • trunk/grails-app/controllers/HomeController.groovy

    r53 r70  
     1import dbnp.studycapturing.Study
     2
    13class HomeController {
    24
    35    def index = {
    4        [ studyCount: Study.count() ]
     6       [ studyCount: dbnp.studycapturing.Study.count() ]
    57    }
    68}

  • trunk/grails-app/controllers/LoadController.groovy

    r65 r70  
    1818    def load = {
    1919
    20         static ArrayList attributs = new ArrayList();
     20        //ArrayList attributes = new ArrayList();
    2121
    2222        render("Loading ...\n");
    … …  
    2525        BufferedReader fileReader = new BufferedReader(new InputStreamReader(inputStream));
    2626
    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();
    3737
    3838        for (i in fileReader.readLines()){
    … …  
    162162                }
    163163                else if (tmp_list[0]=="Publication Status") {
    164                     def status = new magetab.idf.OntologyTerm();
     164                    def status = new dbnp.transcriptomics.magetab.idf.OntologyTerm();
    165165                    status.text = tmp_list[1];
    166166                    status.save();
    … …  
    177177                }
    178178                else if (tmp_list[0]=="Protocol Type") {
    179                     def type = new magetab.idf.OntologyTerm();
     179                    def type = new dbnp.transcriptomics.magetab.idf.OntologyTerm();
    180180                    for (j in 1..tmp_list.size()){
    181181                        type.text = tmp_list[j];

  • trunk/grails-app/controllers/StudyController.groovy

    r53 r70  
    11class StudyController extends BaseController {
    22
    3     def scaffold = true
     3    def scaffold = dbnp.studycapturing.Study
    44}

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

    r69 r70  
    1 package magetab.adf
     1package dbnp.transcriptomics.magetab.adf
    22
    33class ArrayDesign {
    … …  
    88        String provider
    99        String printingProtocol
    10         magetab.idf.OntologyTerm arrayDesignRef
    11         magetab.idf.OntologyTerm surfaceType
    12         magetab.idf.OntologyTerm sequencePolymerType
    13         magetab.idf.OntologyTerm technologyType
    14         magetab.idf.OntologyTerm substrateType
     10        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
    1515
    1616        static hasMany = [
    1717                designElements:DesignElement,
    18                 userDefinedAttributes:magetab.idf.UserDefinedAttribute
     18                userDefinedAttributes:dbnp.transcriptomics.magetab.idf.UserDefinedAttribute
    1919        ]
    2020

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

    r69 r70  
    1 package magetab.adf
     1package dbnp.transcriptomics.magetab.adf
    22
    33class CompositeElement {
    … …  
    55        String name
    66        String comment
    7         magetab.idf.OntologyTerm dataBaseEntry
     7        dbnp.transcriptomics.magetab.idf.OntologyTerm dataBaseEntry
    88
    99        static constraints = {

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

    r69 r70  
    1 package magetab.adf
     1package dbnp.transcriptomics.magetab.adf
    22
    33class DesignElement {

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

    r69 r70  
    1 package magetab.adf
     1package dbnp.transcriptomics.magetab.adf
    22
    33class MatrixColumn {
    … …  
    55    int columnNumber
    66    String columnData
    7     magetab.sdrf.Node columnHeader
    8     magetab.idf.OntologyTerm quantitationType
     7    dbnp.transcriptomics.magetab.sdrf.Node columnHeader
     8    dbnp.transcriptomics.magetab.idf.OntologyTerm quantitationType
    99
    1010    static constraints = {

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

    r69 r70  
    1 package magetab.adf
     1package dbnp.transcriptomics.magetab.adf
    22
    33class MatrixRow {

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

    r69 r70  
    1 package magetab.adf
     1package dbnp.transcriptomics.magetab.adf
    22
    33class MatrixRowId {

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

    r69 r70  
    1 package magetab.adf
     1package dbnp.transcriptomics.magetab.adf
    22
    33class Reporter {
    … …  
    55    String name
    66    String sequence
    7     magetab.idf.OntologyTerm group
    8     magetab.idf.OntologyTerm controlType
    9     magetab.idf.OntologyTerm databaseEntry
     7    dbnp.transcriptomics.magetab.idf.OntologyTerm group
     8    dbnp.transcriptomics.magetab.idf.OntologyTerm controlType
     9    dbnp.transcriptomics.magetab.idf.OntologyTerm databaseEntry
    1010
    1111    static constraints ={

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

    r69 r70  
    1 package magetab.idf
     1package dbnp.transcriptomics.magetab.idf
    22
    33class Comment {

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

    r69 r70  
    1 package magetab.idf
     1package dbnp.transcriptomics.magetab.idf
    22
    33class ExperimentalInfo {
    … …  
    99    String design_term_source_ref
    1010
    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     ]
     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    ]*/
    1818
    1919    static constraints = {

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

    r69 r70  
    1 package magetab.idf
     1package dbnp.transcriptomics.magetab.idf
    22
    33class Factor {

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

    r69 r70  
    1 package magetab.idf
     1package dbnp.transcriptomics.magetab.idf
    22
    33class InvestigationDesign {
    … …  
    1010    static hasMany = [
    1111        experimentalFactors: Factor,
    12         protocols: Protocol,
     12        protocols: MAGEProtocol,
    1313        publications: Publication,
    14         //sdrfs: magetab.sdrf.SampleAndDataRelationship,
     14        //sdrfs: dbnp.transcriptomics.magetab.sdrf.SampleAndDataRelationship,
    1515        userDefinedAttributes: UserDefinedAttribute,
    1616        contacts: Person,
    … …  
    1919        replicateTypes: OntologyTerm,
    2020        experimentalDesigns: OntologyTerm
    21 //        termSources: magetab.adf.TermSource
     21//        termSources: dbnp.transcriptomics.magetab.adf.TermSource
    2222    ]
    2323

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

    r69 r70  
    1 package magetab.idf
     1package dbnp.transcriptomics.magetab.idf
    22
    3 class Protocol {
     3class MAGEProtocol {
    44
    55    String name

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

    r69 r70  
    1 package magetab.idf
     1package dbnp.transcriptomics.magetab.idf
    22
    33class OntologyTerm {
    … …  
    66    String category
    77    String accessionNumber
    8 //    magetab.adf.TermSource termSource
     8//    dbnp.transcriptomics.magetab.adf.TermSource termSource
    99
    1010

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

    r69 r70  
    1 package magetab.idf
     1package dbnp.transcriptomics.magetab.idf
    22
    33class Parameter {

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

    r69 r70  
    1 package magetab.idf
     1package dbnp.transcriptomics.magetab.idf
    22
    33class Person {

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

    r69 r70  
    1 package magetab.idf
     1package dbnp.transcriptomics.magetab.idf
    22
    33class Publication {

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

    r69 r70  
    1 package magetab.idf
     1package dbnp.transcriptomics.magetab.idf
    22
    33class UserDefinedAttribute {

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

    r69 r70  
    1 package magetab.sdrf
     1package dbnp.transcriptomics.magetab.sdrf
    22
    33class ArrayData {

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

    r69 r70  
    1 package magetab.sdrf
     1package dbnp.transcriptomics.magetab.sdrf
    22
    33class ArrayDataMatrix {

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

    r69 r70  
    1 package magetab.sdrf
     1package dbnp.transcriptomics.magetab.sdrf
    22
    33class Assay {

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

    r69 r70  
    1 package magetab.sdrf
     1package dbnp.transcriptomics.magetab.sdrf
    22
    33class DataObject {

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

    r69 r70  
    1 package magetab.sdrf
     1package dbnp.transcriptomics.magetab.sdrf
    22
    33class DerivedArrayData {

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

    r69 r70  
    1 package magetab.sdrf
     1package dbnp.transcriptomics.magetab.sdrf
    22
    33class DerivedArrayDataMatrix {

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

    r69 r70  
    1 package magetab.sdrf
     1package dbnp.transcriptomics.magetab.sdrf
    22
    33class Edge {

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

    r69 r70  
    1 package magetab.sdrf
     1package dbnp.transcriptomics.magetab.sdrf
    22
    33// 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
     1package dbnp.transcriptomics.magetab.sdrf
    22
    33class FactorValue {

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

    r69 r70  
    1 package magetab.sdrf
     1package dbnp.transcriptomics.magetab.sdrf
    22
    33class Hybridization {

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

    r69 r70  
    1 package magetab.sdrf
     1package dbnp.transcriptomics.magetab.sdrf
    22
    33class Image {

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

    r69 r70  
    1 package magetab.sdrf
     1package dbnp.transcriptomics.magetab.sdrf
    22
    33class LabeledExtract {

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

    r69 r70  
    1 package magetab.sdrf
     1package dbnp.transcriptomics.magetab.sdrf
    22
    33class Material {

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

    r69 r70  
    1 package magetab.sdrf
     1package dbnp.transcriptomics.magetab.sdrf
    22
    33class Node {

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

    r69 r70  
    1 package magetab.sdrf
     1package dbnp.transcriptomics.magetab.sdrf
    22
    33class NodeList {

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

    r69 r70  
    1 package magetab.sdrf
     1package dbnp.transcriptomics.magetab.sdrf
    22
    33class Normalization {

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

    r69 r70  
    1 package magetab.sdrf
     1package dbnp.transcriptomics.magetab.sdrf
    22
    33class ParameterValue {

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

    r69 r70  
    1 package magetab.sdrf
     1package dbnp.transcriptomics.magetab.sdrf
    22
    33class ProtocolApplication {

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

    r69 r70  
    1 package magetab.sdrf
     1package dbnp.transcriptomics.magetab.sdrf
    22
    33class Provider {

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

    r69 r70  
    1 package magetab.sdrf
     1package dbnp.transcriptomics.magetab.sdrf
    22
    33class SampleAndDataRelationship {

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

    r69 r70  
    1 package magetab.sdrf
     1package dbnp.transcriptomics.magetab.sdrf
    22
    33class Scan {

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

    r69 r70  
    1 package magetab.sdrf
     1package dbnp.transcriptomics.magetab.sdrf
    22
    33class URIValue {

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

    r69 r70  
    1 package magetab.sdrf
     1package dbnp.transcriptomics.magetab.sdrf
    22
    33class UserDefinedValue {

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

    r69 r70  
    1 package magetab.sdrf
     1package dbnp.transcriptomics.magetab.sdrf
    22
    33class Value {

  • trunk/grails-app/i18n/messages.properties

    r4 r70  
    2323default.number.format=0
    2424
     25default.created.message={0} {1} created
     26default.updated.message={0} {1} updated
     27default.deleted.message={0} {1} deleted
     28default.not.deleted.message={0} {1} could not be deleted
     29default.not.found.message={0} not found with id {1}
     30default.optimistic.locking.failure=Another user has updated this {0} while you were editing
     31
     32default.home.label=Home
     33default.list.label={0} List
     34default.add.label=Add {0}
     35default.new.label=New {0}
     36default.create.label=Create {0}
     37default.show.label=Show {0}
     38default.edit.label=Edit {0}
     39
     40default.button.create.label=Create
     41default.button.edit.label=Edit
     42default.button.update.label=Update
     43default.button.delete.label=Delete
     44default.button.delete.confirm.message=Are you sure?
     45
    2546# Data binding errors. Use "typeMismatch.$className.$propertyName to customize (eg typeMismatch.Book.author)
    2647typeMismatch.java.net.URL=Property {0} must be a valid URL

  • trunk/grails-app/i18n/messages_de.properties

    r4 r70  
    1818default.paginate.prev=Vorherige
    1919default.paginate.next=NÀchste
     20default.boolean.true=Wahr
     21default.boolean.false=Falsch
     22default.date.format=dd.MM.yyyy HH:mm:ss z
     23default.number.format=0
     24
     25default.created.message={0} {1} wurde angelegt
     26default.updated.message={0} {1} wurde geÀndert
     27default.deleted.message={0} {1} wurde gelöscht
     28default.not.deleted.message={0} {1} konnte nicht gelöscht werden
     29default.not.found.message={0} mit der id {1} wurde nicht gefunden
     30default.optimistic.locking.failure=Ein anderer Benutzer hat das {0} Object geÀndert wÀhrend Sie es bearbeitet haben
     31
     32default.home.label=Home
     33default.list.label={0} Liste
     34default.add.label={0} hinzufÃŒgen
     35default.new.label={0} anlegen
     36default.create.label={0} anlegen
     37default.show.label={0} anzeigen
     38default.edit.label={0} bearbeiten
     39
     40default.button.create.label=Anlegen
     41default.button.edit.label=Bearbeiten
     42default.button.update.label=Aktualisieren
     43default.button.delete.label=Löschen
     44default.button.delete.confirm.message=Sind Sie sicher?
    2045
    2146# Data binding errors. Use "typeMismatch.$className.$propertyName to customize (eg typeMismatch.Book.author)

  • trunk/grails-app/i18n/messages_nl.properties

    r4 r70  
    88default.invalid.min.message=Attribuut [{0}] van entiteit [{1}] met waarde [{2}] is minder dan de minimumwaarde [{3}]
    99default.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 mainimumgrootte van [{3}]
     10default.invalid.min.size.message=Attribuut [{0}] van entiteit [{1}] met waarde [{2}] is minder dan minimumgrootte van [{3}]
    1111default.invalid.validator.message=Attribuut [{0}] van entiteit [{1}] met waarde [{2}] is niet geldig
    1212default.not.inlist.message=Attribuut [{0}] van entiteit [{1}] met waarde [{2}] komt niet voor in de lijst [{3}]
    … …  
    2323default.number.format=0
    2424
     25default.created.message={0} {1} ingevoerd
     26default.updated.message={0} {1} gewijzigd
     27default.deleted.message={0} {1} verwijderd
     28default.not.deleted.message={0} {1} kon niet worden verwijderd
     29default.not.found.message={0} met id {1} kon niet worden gevonden
     30default.optimistic.locking.failure=Een andere gebruiker heeft deze {0} al gewijzigd
     31
     32default.home.label=Home
     33default.list.label={0} Overzicht
     34default.add.label=Toevoegen {0}
     35default.new.label=Invoeren {0}
     36default.create.label=Invoeren {0}
     37default.show.label=Details {0}
     38default.edit.label=Wijzigen {0}
     39
     40default.button.create.label=Invoeren
     41default.button.edit.label=Wijzigen
     42default.button.update.label=Opslaan
     43default.button.delete.label=Verwijderen
     44default.button.delete.confirm.message=Weet je het zeker?
     45
    2546# Data binding errors. Use "typeMismatch.$className.$propertyName to customize (eg typeMismatch.Book.author)
    2647typeMismatch.java.net.URL=Attribuut {0} is geen geldige URL

  • trunk/web-app/WEB-INF/applicationContext.xml

    r4 r70  
    1616        <property name="application" ref="grailsApplication" />
    1717        </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>
    2318
    2419    <bean id="grailsConfigurator" class="org.codehaus.groovy.grails.commons.spring.GrailsRuntimeConfigurator">

  • trunk/web-app/WEB-INF/sitemesh.xml

    r4 r70  
    22    <page-parsers>
    33        <parser content-type="text/html"
    4             class="com.opensymphony.module.sitemesh.parser.HTMLPageParser" />
     4            class="org.codehaus.groovy.grails.web.sitemesh.GrailsHTMLPageParser" />
    55        <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" />
    77        <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" />           
    99    </page-parsers>
    1010

  • trunk/web-app/WEB-INF/tld/grails.tld

    r4 r70  
    542542        </variable>
    543543        <attribute>
    544             <name>name</name>
     544            <name>tagName</name>
    545545            <required>true</required>
    546546            <rtexprvalue>true</rtexprvalue>
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