Changeset 267


Ignore:
Timestamp:
Mar 30, 2012, 2:35:19 PM (8 years ago)
Author:
work@…
Message:

transcriptomics changes

Location:
branches/dbxp-transcriptomics
Files:
2 added
11 edited

Legend:

Unmodified
Added
Removed
  • branches/dbxp-transcriptomics

    • Property svn:ignore
      •  

        old new  
        1111
        1212*.iml
         13[:]
         14[:]
  • branches/dbxp-transcriptomics/application.properties

    r260 r267  
    66app.build.type=dev
    77app.grails.version=1.3.7
    8 app.name=metabolomicsModule
     8app.name=transcriptomicsModule
    99app.servlet.version=2.4
    1010app.version=0.2.1
     
    2323plugins.resources=1.1.6
    2424plugins.tomcat=1.3.7
    25 plugins.trackr=0.6.2
     25#plugins.trackr=0.6.2
    2626plugins.uploadr=0.5.9
  • branches/dbxp-transcriptomics/grails-app/conf/BootStrap.groovy

    r4 r267  
     1import org.dbxp.metabolomicsModule.identity.FeatureProperty
     2
    13class BootStrap {
     4    def init = { servletContext ->
     5        if (FeatureProperty.count() == 0) {
     6            // add default feature properties
     7            if (!FeatureProperty.findByLabel('ratio')) { new FeatureProperty(label: 'ratio', synonyms: '').save() }
     8            if (!FeatureProperty.findByLabel('intensity')) { new FeatureProperty(label: 'intensity', synonyms: '').save() }
     9            if (!FeatureProperty.findByLabel('EntrezID')) { new FeatureProperty(label: 'EntrezID', synonyms: 'entrez_id,entrez,eID').save() }
     10            if (!FeatureProperty.findByLabel('symbol')) { new FeatureProperty(label: 'symbol', synonyms: '').save() }
     11            if (!FeatureProperty.findByLabel('probeID')) { new FeatureProperty(label: 'probeID', synonyms: 'probe id,probe_id,probe').save() }
     12        }
     13    }
    214
    3     def init = { servletContext ->
    4     }
    515    def destroy = {
    616    }
  • branches/dbxp-transcriptomics/grails-app/conf/Config.groovy

    r259 r267  
    8888
    8989// set default properties here in case default.properties in not placed in classpath and no external config
    90 grails.serverURL='http://localhost:8083/metabolomicsModule'
     90grails.serverURL='http://localhost:8083/transcriptomicsModule'
    9191gscf.baseURL='http://localhost:8080/gscf'
    92 module.consumerId='http://localhost:8083/metabolomicsModule' //replace @runtime by resource(dir: '/', absolute: true)
    93 module.name='Metabolomics Module'
     92module.consumerId='http://localhost:8083/transcriptomicsModule' //replace @runtime by resource(dir: '/', absolute: true)
     93module.name='Transcriptomics Module'
    9494module.synchronization.classes.assay = 'org.dbxp.metabolomicsModule.MetabolomicsAssay'
    9595
    9696// ****** trackR Config ******
    9797trackr.path = "/tmp/"
    98 trackr.prefix = "nmcdsp.${grails.util.GrailsUtil.environment}."
     98trackr.prefix = "transcriptomics.${grails.util.GrailsUtil.environment}."
  • branches/dbxp-transcriptomics/grails-app/conf/MetabolomicsModuleResources.groovy

    r137 r267  
    22
    33modules = {
    4         metabolomicsModule {
     4    transcriptomicsModule {
    55                dependsOn 'moduleBase, uploadr'
    66
  • branches/dbxp-transcriptomics/grails-app/conf/default.properties

    r141 r267  
    66
    77# server URL
    8 grails.serverURL=http://localhost:8083/metabolomicsModule
     8grails.serverURL=http://localhost:8083/transcriptomicsModule
    99# change the server port in BuildConfig.groovy
    1010# as it does not work in here, e.g.:
     
    1414gscf.baseURL=http://localhost:8080/gscf
    1515# consumer ID of this module that is used in communication with GSCF
    16 module.consumerId=http://localhost:8083/metabolomicsModule
     16module.consumerId=http://localhost:8083/transcriptomicsModule
    1717# module name in GSCF
    18 module.name=Metabolomics Module
     18module.name=Transcriptomics Module
    1919
    2020# mongo DB configuration
    2121grails.mongo.host=127.0.0.1
    2222grails.mongo.port=27017
    23 grails.mongo.databaseName=metabolomicsModuleDev
     23grails.mongo.databaseName=transcriptomicsModuleDev
    2424
    2525# datasource
  • branches/dbxp-transcriptomics/grails-app/controllers/org/dbxp/metabolomicsModule/BootStrapController.groovy

    r255 r267  
    3636               
    3737                //add default feature property mappings
    38                 if (!FeatureProperty.findByLabel('m/z')) { new FeatureProperty(label: 'm/z', synonyms: 'mz,m z,m over z,Mass Quan#').save() }
    39                 if (!FeatureProperty.findByLabel('InChI')) { new FeatureProperty(label: 'InChI', synonyms: 'inchi,Inchi,inchie').save() }
    40                 if (!FeatureProperty.findByLabel('PubChem')) { new FeatureProperty(label: 'PubChem', synonyms: 'pubchem').save() }
    41                 if (!FeatureProperty.findByLabel('ChEBI ID')) { new FeatureProperty(label: 'ChEBI ID', synonyms: 'chebi,Chebi,chebi_id,ChEBI_ID').save() }
    42                
     38//              if (!FeatureProperty.findByLabel('m/z')) { new FeatureProperty(label: 'm/z', synonyms: 'mz,m z,m over z,Mass Quan#').save() }
     39//              if (!FeatureProperty.findByLabel('InChI')) { new FeatureProperty(label: 'InChI', synonyms: 'inchi,Inchi,inchie').save() }
     40//              if (!FeatureProperty.findByLabel('PubChem')) { new FeatureProperty(label: 'PubChem', synonyms: 'pubchem').save() }
     41//              if (!FeatureProperty.findByLabel('ChEBI ID')) { new FeatureProperty(label: 'ChEBI ID', synonyms: 'chebi,Chebi,chebi_id,ChEBI_ID').save() }
     42
    4343                if (assay != null) {
    4444                       
  • branches/dbxp-transcriptomics/grails-app/services/org/dbxp/metabolomicsModule/measurements/MeasurementService.groovy

    r253 r267  
    55import org.dbxp.moduleBase.Assay
    66import org.dbxp.metabolomicsModule.MetabolomicsAssay
     7import org.dbxp.metabolomicsModule.identity.FeatureProperty
    78
    89class MeasurementService {
     
    7879
    7980        def createHeaderSuggestions(columns) {
    80                
    8181                def featureHeaderSuggestions = [:]
    82                 FeatureProperty.list().collect { featureHeaderSuggestions[it.label] = it.synonyms.split(",") }
     82                FeatureProperty.list().collect { featureHeaderSuggestions[it.label] = it.synonyms?.split(",") }
    8383
    8484                columns.collect { column ->
  • branches/dbxp-transcriptomics/grails-app/views/layouts/main.gsp

    r243 r267  
    66                <meta app-version="${meta(name: 'app.version')} "/>
    77                <meta app-revision="${meta(name: 'app.build.svn.revision')}"/>
    8                 <title><g:layoutTitle default="Metabolomics Module"/></title>
     8                <title><g:layoutTitle default="Transcriptomics Module"/></title>
    99                <g:layoutHead/>
    10                 <r:require modules="metabolomicsModule"/>
     10                <r:require modules="transcriptomicsModule"/>
    1111        </head>
    1212
  • branches/dbxp-transcriptomics/grails-app/views/parseConfiguration/index.gsp

    r236 r267  
    66        <div class="dataTypeOptionText">
    77                <b>Clean Data</b><br />
    8                 Metabolomics data without quality control samples.
     8        Transcriptomics data without quality control samples.
    99        </div>
    1010        <img class="dataTypeImage" src="images/filetype_clean.png" alt="Clean Data Files">
     
    1414        <div class="dataTypeOptionText">
    1515                <b>Raw Data</b><br />
    16                 Metabolomics data including quality control samples.
     16        Transcriptomics data including quality control samples.
    1717        </div>
    1818        <img class="dataTypeImage" src="images/filetype_raw.png" alt="Raw Data Files">
  • branches/dbxp-transcriptomics/scripts/gscfMock.groovy

    r197 r267  
    4949                                                                case 'aaa':
    5050                                                                        strResponse = '''[
    51 {"assayToken":"yyy","name":"Assay Y","module":{"class":"org.dbnp.gdt.AssayModule","id":2,"name":"Metabolomics module","notify":false,"openInFrame":true,"url":"http://localhost:8083/metabolomicsModule"},"Description":null,"Spectrometry technique":{"class":"org.dbnp.gdt.TemplateFieldListItem","id":25,"name":"LC/MS","parent":{"class":"TemplateField","id":88}},"parentStudyToken":"aaa"},
    52 {"assayToken":"zzz","name":"Assay Z","module":{"class":"org.dbnp.gdt.AssayModule","id":2,"name":"Metabolomics module","notify":false,"openInFrame":true,"url":"http://localhost:8083/metabolomicsModule"},"Description":null,"Spectrometry technique":{"class":"org.dbnp.gdt.TemplateFieldListItem","id":25,"name":"GC/MS","parent":{"class":"TemplateField","id":88}},"parentStudyToken":"aaa"}]'''
     51{"assayToken":"yyy","name":"Assay Y","module":{"class":"org.dbnp.gdt.AssayModule","id":2,"name":"Transcriptomics module","notify":false,"openInFrame":true,"url":"http://localhost:8083/transcriptomicsModule"},"Description":null,"Spectrometry technique":{"class":"org.dbnp.gdt.TemplateFieldListItem","id":25,"name":"LC/MS","parent":{"class":"TemplateField","id":88}},"parentStudyToken":"aaa"},
     52{"assayToken":"zzz","name":"Assay Z","module":{"class":"org.dbnp.gdt.AssayModule","id":2,"name":"Transcriptomics module","notify":false,"openInFrame":true,"url":"http://localhost:8083/transcriptomicsModule"},"Description":null,"Spectrometry technique":{"class":"org.dbnp.gdt.TemplateFieldListItem","id":25,"name":"GC/MS","parent":{"class":"TemplateField","id":88}},"parentStudyToken":"aaa"}]'''
    5353                                                                        break
    5454                                                                case 'bbb':
    5555                                                                        strResponse = '''[
    56 {"assayToken":"xxx","name":"Assay X","module":{"class":"org.dbnp.gdt.AssayModule","id":2,"name":"Metabolomics module","notify":false,"openInFrame":true,"url":"http://localhost:8083/metabolomicsModule"},"Description":null,"Spectrometry technique":{"class":"org.dbnp.gdt.TemplateFieldListItem","id":26,"name":"MS/MS","parent":{"class":"TemplateField","id":88}},"parentStudyToken":"bbb"}]'''
     56{"assayToken":"xxx","name":"Assay X","module":{"class":"org.dbnp.gdt.AssayModule","id":2,"name":"Transcriptomics module","notify":false,"openInFrame":true,"url":"http://localhost:8083/transcriptomicsModule"},"Description":null,"Spectrometry technique":{"class":"org.dbnp.gdt.TemplateFieldListItem","id":26,"name":"MS/MS","parent":{"class":"TemplateField","id":88}},"parentStudyToken":"bbb"}]'''
    5757                                                                        break
    5858                                                                case 'f79a2713-c9bb-4f1c-93a9-ddfcb125930a':
    5959                                                                        strResponse = '''[
    60 {"module":{"id":54,"openInFrame":false,"notify":true,"name":"Metabolomics module","class":"org.dbnp.gdt.AssayModule","url":"http://localhost:8083/metabolomicsModule"},"parentStudyToken":"f79a2713-c9bb-4f1c-93a9-ddfcb125930a","assayToken":"32012ce2-ec1e-4e21-9852-a7f527757aaf","name":"NMR Urine Samples"}]'''
     60{"module":{"id":54,"openInFrame":false,"notify":true,"name":"Transcriptomics module","class":"org.dbnp.gdt.AssayModule","url":"http://localhost:8083/transcriptomicsModule"},"parentStudyToken":"f79a2713-c9bb-4f1c-93a9-ddfcb125930a","assayToken":"32012ce2-ec1e-4e21-9852-a7f527757aaf","name":"NMR Urine Samples"}]'''
    6161                                                                        break
    6262                                                                case '1962f9d0-77b3-415f-9857-81f00e6395b3':
    6363                                                                        strResponse = '''[
    64 {"Description":null,"module":{"id":2,"openInFrame":true,"notify":false,"name":"Metabolomics module","class":"org.dbnp.gdt.AssayModule","url":"http://localhost:8083/metabolomicsModule"},"parentStudyToken":"1962f9d0-77b3-415f-9857-81f00e6395b3","assayToken":"bc117e31-f66e-474a-9b55-26ca94add48b","Spectrometry technique":{"id":25,"name":"GC/MS","parent":{"id":88,"class":"TemplateField"},"class":"org.dbnp.gdt.TemplateFieldListItem"},"name":"Lipidomics profile after"},
    65 {"Description":null,"module":{"id":2,"openInFrame":true,"notify":false,"name":"Metabolomics module","class":"org.dbnp.gdt.AssayModule","url":"http://localhost:8083/metabolomicsModule"},"parentStudyToken":"1962f9d0-77b3-415f-9857-81f00e6395b3","assayToken":"f80878f9-791a-4045-af01-c160bfdc7795","Spectrometry technique":{"id":25,"name":"GC/MS","parent":{"id":88,"class":"TemplateField"},"class":"org.dbnp.gdt.TemplateFieldListItem"},"name":"Lipidomics profile before"}]'''
     64{"Description":null,"module":{"id":2,"openInFrame":true,"notify":false,"name":"Transcriptomics module","class":"org.dbnp.gdt.AssayModule","url":"http://localhost:8083/transcriptomicsModule"},"parentStudyToken":"1962f9d0-77b3-415f-9857-81f00e6395b3","assayToken":"bc117e31-f66e-474a-9b55-26ca94add48b","Spectrometry technique":{"id":25,"name":"GC/MS","parent":{"id":88,"class":"TemplateField"},"class":"org.dbnp.gdt.TemplateFieldListItem"},"name":"Lipidomics profile after"},
     65{"Description":null,"module":{"id":2,"openInFrame":true,"notify":false,"name":"Transcriptomics module","class":"org.dbnp.gdt.AssayModule","url":"http://localhost:8083/transcriptomicsModule"},"parentStudyToken":"1962f9d0-77b3-415f-9857-81f00e6395b3","assayToken":"f80878f9-791a-4045-af01-c160bfdc7795","Spectrometry technique":{"id":25,"name":"GC/MS","parent":{"id":88,"class":"TemplateField"},"class":"org.dbnp.gdt.TemplateFieldListItem"},"name":"Lipidomics profile before"}]'''
    6666                                                                        break
    6767                                                                case 'cba83175-89dc-4a92-8680-99c90a6dd0b4':
    6868                                                                        strResponse = '''[
    69 {"Description":null,"module":{"id":2,"openInFrame":true,"notify":false,"name":"Metabolomics module","class":"org.dbnp.gdt.AssayModule","url":"http://localhost:8083/metabolomicsModule"},"parentStudyToken":"cba83175-89dc-4a92-8680-99c90a6dd0b4","assayToken":"65798013-7b6e-4ba7-96a1-d827a02dc509","Spectrometry technique":{"id":26,"name":"LC/MS","parent":{"id":88,"class":"TemplateField"},"class":"org.dbnp.gdt.TemplateFieldListItem"},"name":"Lipidomics profile"}]'''
     69{"Description":null,"module":{"id":2,"openInFrame":true,"notify":false,"name":"Transcriptomics module","class":"org.dbnp.gdt.AssayModule","url":"http://localhost:8083/transcriptomicsModule"},"parentStudyToken":"cba83175-89dc-4a92-8680-99c90a6dd0b4","assayToken":"65798013-7b6e-4ba7-96a1-d827a02dc509","Spectrometry technique":{"id":26,"name":"LC/MS","parent":{"id":88,"class":"TemplateField"},"class":"org.dbnp.gdt.TemplateFieldListItem"},"name":"Lipidomics profile"}]'''
    7070                                                                        break
    7171                                                        }
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