Changeset 36 for trunk


Ignore:
Timestamp:
Apr 5, 2011, 4:08:13 PM (8 years ago)
Author:
robert@…
Message:

Renamed Metagenomics module to MassSequencing? module

Location:
trunk/grails-app/conf
Files:
6 edited

Legend:

Unmodified
Added
Removed

  • trunk/grails-app/conf/BaseFilters.groovy

    r26 r36  
    2020import org.codehaus.groovy.grails.commons.ConfigurationHolder
    2121
    22 import nl.tno.metagenomics.auth.User;
    23 import nl.tno.metagenomics.integration.*;
     22import nl.tno.massSequencing.auth.User;
     23import nl.tno.massSequencing.integration.*;
    2424 
    2525class BaseFilters {
    … …  
    116116                                               
    117117                                                // First check if the user is authenticated. If he isn't, he should provide credentials at GSCF
    118                                                 def authentication = JSON.parse("${ConfigurationHolder.config.gscf.baseURL}/rest/isUser?consumer=${ConfigurationHolder.config.metagenomics.consumerID}&token=${session.sessionToken}".toURL().text)
     118                                                def authentication = JSON.parse("${ConfigurationHolder.config.gscf.baseURL}/rest/isUser?consumer=${ConfigurationHolder.config.massSequencing.consumerID}&token=${session.sessionToken}".toURL().text)
    119119                                               
    120120                                                if( !authentication.authenticated ) {
    … …  
    125125                                               
    126126                                                // Now find the user data
    127                                                 JSON.parse("${ConfigurationHolder.config.gscf.baseURL}/rest/getUser?consumer=${ConfigurationHolder.config.metagenomics.consumerID}&token=${session.sessionToken}".toURL().text).each { userProperty ->
     127                                                JSON.parse("${ConfigurationHolder.config.gscf.baseURL}/rest/getUser?consumer=${ConfigurationHolder.config.massSequencing.consumerID}&token=${session.sessionToken}".toURL().text).each { userProperty ->
    128128                                                        user["${userProperty.key}"] = "${userProperty.value}"
    129129                                                }

  • trunk/grails-app/conf/BootStrap.groovy

    r22 r36  
    1 import nl.tno.metagenomics.auth.*;
     1import nl.tno.massSequencing.auth.*;
    22
    33class BootStrap {       

  • trunk/grails-app/conf/Config.groovy

    r24 r36  
    2626
    2727// Whether to synchronize with gscf or not. By default, synchronization is turned on
    28 metagenomics.synchronization = true
     28massSequencing.synchronization = true
    2929
    3030// By default, Metagenomics only fetches studies that have been changed by GSCF. GSCF sends
    … …  
    3535// between two consecutive full synchronizations. Setting it to zero disables full synchronization, but
    3636// is strongly discouraged.
    37 metagenomics.fullSynchronization = 24 * 3600 // 1 day
     37massSequencing.fullSynchronization = 24 * 3600 // 1 day
    3838
    3939// Temporary directory to upload files to.
    … …  
    4141// Otherwise, it should be given as an absolute path (e.g. '/home/user/sequences')
    4242// The directory should be writable by the webserver user
    43 metagenomics.fileUploadDir = "fileuploads/temp"
     43massSequencing.fileUploadDir = "fileuploads/temp"
    4444
    4545// Maximum age that uploaded files should be kept on the server before deleting them. When a user uploads a file,
    … …  
    4747// remain in the upload directory. This mechanism ensures that the upload directory is cleaned after some time.
    4848// The time is given in seconds.
    49 metagenomics.fileUploadMaxAge = 2 * 24 * 3600 // 2 days
     49massSequencing.fileUploadMaxAge = 2 * 24 * 3600 // 2 days
    5050
    5151// Directory to save the uploaded files permanently
    … …  
    5353// Otherwise, it should be given as an absolute path (e.g. '/home/user/sequences')
    5454// The directory should be writable by the webserver user
    55 metagenomics.fileDir = "fileuploads/permanent"
     55massSequencing.fileDir = "fileuploads/permanent"
    5656
    5757// Filename of the (.fna, .qual and .oligos) files that are exported
    5858// Only the part before the extension is mentioned. If you enter "sequences", the exported files will be
    5959// sequences.fna, sequences.qual and sequences.oligos
    60 metagenomics.exportFilename = "1.TCA.454Reads"
     60massSequencing.exportFilename = "1.TCA.454Reads"
    6161
    6262// Path in GSCF that is used after baseURL for adding a new study

  • trunk/grails-app/conf/config-dbnptest.properties

    r24 r36  
    66
    77# server URL
    8 grails.serverURL=http://test.metagenomics.dbnp.org
     8grails.serverURL=http://test.massSequencing.dbnp.org
    99
    1010# DATABASE
    … …  
    1919# GSCF configuration - in order to synchronize correctly
    2020gscf.baseURL=http://test.dbnp.org
    21 metagenomics.consumerID=http://test.metagenomics.dbnp.org
    22 metagenomics.synchronization = true
     21massSequencing.consumerID=http://test.massSequencing.dbnp.org
     22massSequencing.synchronization = true
    2323
    2424# File uploads
    25 metagenomics.fileUploadDir=/tmp/metagenomics/temp
    26 metagenomics.fileDir=/tmp/metagenomics/permanent
     25massSequencing.fileUploadDir=/tmp/metagenomics/temp
     26massSequencing.fileDir=/tmp/metagenomics/permanent
    2727
    2828# Filename of the (.fna, .qual and .oligos) files that are exported
    29 metagenomics.exportFilename=1.TCA.454Reads
     29massSequencing.exportFilename=1.TCA.454Reads

  • trunk/grails-app/conf/config-development.properties

    r24 r36  
    66
    77# server URL
    8 grails.serverURL=http://localhost:8184/metagenomics
     8grails.serverURL=http://localhost:8184/massSequencing
    99grails.server.port.http=8184
    1010
    … …  
    1919# GSCF configuration - in order to synchronize correctly
    2020gscf.baseURL=http://localhost:8080/gscf
    21 metagenomics.consumerID=http://localhost:8184/metagenomics
    22 metagenomics.synchronization = true
     21massSequencing.consumerID=http://localhost:8184/massSequencing
     22massSequencing.synchronization = true
    2323
    2424# File uploads
    25 metagenomics.fileUploadDir=fileuploads/temp
    26 metagenomics.fileDir=fileuploads/permanent
     25massSequencing.fileUploadDir=fileuploads/temp
     26massSequencing.fileDir=fileuploads/permanent
    2727
    2828# Filename of the (.fna, .qual and .oligos) files that are exported
    29 metagenomics.exportFilename=1.TCA.454Reads
     29massSequencing.exportFilename=1.TCA.454Reads

  • trunk/grails-app/conf/config-test.properties

    r7 r36  
    66
    77# server URL
    8 grails.serverURL=http://localhost:9431/metagenomics
     8grails.serverURL=http://localhost:9431/massSequencing
    99
    1010# DATABASE
    … …  
    1818# GSCF configuration - in order to synchronize correctly
    1919gscf.baseURL=http://localhost:9432
    20 metagenomics.consumerID=http://localhost:9431/metagenomics
    21 metagenomics.synchronization = true
     20massSequencing.consumerID=http://localhost:9431/massSequencing
     21massSequencing.synchronization = true
    2222
    2323# File uploads
    24 metagenomics.fileUploadDir=/tmp/temp
    25 metagenomics.fileDir=/tmp/permanent
     24massSequencing.fileUploadDir=/tmp/temp
     25massSequencing.fileDir=/tmp/permanent
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