Changeset 27 for trunk


Ignore:
Timestamp:
Apr 5, 2011, 3:58:18 PM (8 years ago)
Author:
robert@…
Message:

Renamed module to massSequencing

Location:
trunk/grails-app/controllers/nl/tno/metagenomics
Files:
12 edited

Legend:

Unmodified
Added
Removed
  • trunk/grails-app/controllers/nl/tno/metagenomics/AssayController.groovy

    r24 r27  
    1 package nl.tno.metagenomics
     1package nl.tno.massSequencing
    22
    33import java.util.List;
     
    3131                synchronizationService.synchronizeAssay( assay );
    3232
     33                if( !assay.study || !assay.study.canRead( session.user ) ) {
     34                        flash.error = "You don't have sufficient privileges to access assay " + assay.name
     35                        redirect( action: "index" );
     36                        return;
     37                }
     38               
    3339                // Determine runs not used in this assay
    3440                def otherRuns = Run.list( sort: "name" ).findAll { !it.assays.contains( assay ) }
  • trunk/grails-app/controllers/nl/tno/metagenomics/AssaySampleController.groovy

    r7 r27  
    1 package nl.tno.metagenomics
     1package nl.tno.massSequencing
    22
    33class AssaySampleController {
  • trunk/grails-app/controllers/nl/tno/metagenomics/FastaController.groovy

    r14 r27  
    1 package nl.tno.metagenomics
     1package nl.tno.massSequencing
    22
    33import org.codehaus.groovy.grails.commons.ConfigurationHolder
     
    222222                }
    223223
    224                 File permanentDir = fileService.absolutePath( ConfigurationHolder.config.metagenomics.fileDir )
     224                File permanentDir = fileService.absolutePath( ConfigurationHolder.config.massSequencing.fileDir )
    225225                int numSuccesful = 0;
    226226                def errors = [];
  • trunk/grails-app/controllers/nl/tno/metagenomics/RunController.groovy

    r26 r27  
    1 package nl.tno.metagenomics
     1package nl.tno.massSequencing
    22
    33import java.util.Date;
  • trunk/grails-app/controllers/nl/tno/metagenomics/SampleController.groovy

    r24 r27  
    1 package nl.tno.metagenomics
     1package nl.tno.massSequencing
    22
    33import java.util.List;
  • trunk/grails-app/controllers/nl/tno/metagenomics/StudyController.groovy

    r24 r27  
    1 package nl.tno.metagenomics
     1package nl.tno.massSequencing
    22
    33import java.util.List;
  • trunk/grails-app/controllers/nl/tno/metagenomics/auth/LogoutController.groovy

    r3 r27  
    1 package nl.tno.metagenomics.auth
     1package nl.tno.massSequencing.auth
    22
    33
     
    1515               
    1616                //logout on GSCF side, and do not redirect back to metagenomics (&spring-security-redirect=${ConfigurationHolder.config.grails.serverURL}/study/list)
    17                 def redirectURL = "${ConfigurationHolder.config.gscf.baseURL}/logout/remote?consumer=${ConfigurationHolder.config.metagenomics.ConsumerID}&token=${session.sessionToken}"
     17                def redirectURL = "${ConfigurationHolder.config.gscf.baseURL}/logout/remote?consumer=${ConfigurationHolder.config.massSequencing.ConsumerID}&token=${session.sessionToken}"
    1818                log.info("Redirecting to: ${redirectURL}")
    1919               
  • trunk/grails-app/controllers/nl/tno/metagenomics/files/FileController.groovy

    r25 r27  
    1313 * $Date: 2010-11-22 17:27:23 +0100 (Mon, 22 Nov 2010) $
    1414 */
    15 package nl.tno.metagenomics.files
    16 
    17 import nl.tno.metagenomics.*;
     15package nl.tno.massSequencing.files
     16
     17import nl.tno.massSequencing.*;
    1818
    1919import org.codehaus.groovy.grails.commons.ConfigurationHolder
     
    6262         */
    6363        def getPermanent  = {
    64                 if( checkPermissions( params, fileService.absolutePath( ConfigurationHolder.config.metagenomics.fileDir ) ) ) {
    65                         retrieveFile( params, fileService.absolutePath( ConfigurationHolder.config.metagenomics.fileDir ) );
     64                if( checkPermissions( params, fileService.absolutePath( ConfigurationHolder.config.massSequencing.fileDir ) ) ) {
     65                        retrieveFile( params, fileService.absolutePath( ConfigurationHolder.config.massSequencing.fileDir ) );
    6666                } else {
    6767                        render 'No access';
  • trunk/grails-app/controllers/nl/tno/metagenomics/integration/ActionController.groovy

    r13 r27  
    1 package nl.tno.metagenomics.integration
    2 import nl.tno.metagenomics.*;
     1package nl.tno.massSequencing.integration
     2import nl.tno.massSequencing.*;
    33
    44class ActionController {
  • trunk/grails-app/controllers/nl/tno/metagenomics/integration/RestController.groovy

    r18 r27  
    1 package nl.tno.metagenomics.integration
     1package nl.tno.massSequencing.integration
    22
    33import grails.converters.*
    4 import nl.tno.metagenomics.*
     4import nl.tno.massSequencing.*
    55
    66import org.apache.catalina.connector.Response;
     
    6060                // update it immediately when asked for
    6161                if( !study ) {
    62                         log.info( "METAGENOMICS: GSCF notification for new study " + studyToken );
     62                        log.info( "MassSequencing: GSCF notification for new study " + studyToken );
    6363                        study = new Study(
    6464                                        name: "",
     
    6767                                        )
    6868                } else {
    69                         log.info( "METAGENOMICS: GSCF notification for existing study " + studyToken );
     69                        log.info( "MassSequencing: GSCF notification for existing study " + studyToken );
    7070                        study.isDirty = true;
    7171                }
  • trunk/grails-app/controllers/nl/tno/metagenomics/integration/SynchronizeController.groovy

    r18 r27  
    1 package nl.tno.metagenomics.integration
     1package nl.tno.massSequencing.integration
    22
    33
  • trunk/grails-app/controllers/nl/tno/metagenomics/integration/TrashController.groovy

    r12 r27  
    1 package nl.tno.metagenomics.integration
     1package nl.tno.massSequencing.integration
    22
    3 import nl.tno.metagenomics.*;
     3import nl.tno.massSequencing.*;
    44
    55class TrashController {
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