Changeset 268


Ignore:
Timestamp:
Mar 30, 2012, 2:41:11 PM (8 years ago)
Author:
work@…
Message:
  • added transcriptomics bugfixes to metabolomics module (it was broken for about a month... is anybody using this???)
Location:
trunk
Files:
4 edited

Legend:

Unmodified
Added
Removed
  • trunk

    • Property svn:ignore
      •  

        old new  
        99dbxpModuleStorage-inplacePlugin.iml
        1010.settings
        11 
        1211*.iml
         12stacktrace.log
  • trunk/grails-app/conf/BootStrap.groovy

    r4 r268  
     1import org.dbxp.metabolomicsModule.identity.FeatureProperty
     2
    13class BootStrap {
     4    def init = { servletContext ->
     5        // add default feature properties if we don't have any
     6        if (FeatureProperty.count() == 0) {
     7            if (!FeatureProperty.findByLabel('m/z')) { new FeatureProperty(label: 'm/z', synonyms: 'mz,m z,m over z,Mass Quan#').save() }
     8            if (!FeatureProperty.findByLabel('InChI')) { new FeatureProperty(label: 'InChI', synonyms: 'inchi,Inchi,inchie').save() }
     9            if (!FeatureProperty.findByLabel('PubChem')) { new FeatureProperty(label: 'PubChem', synonyms: 'pubchem').save() }
     10            if (!FeatureProperty.findByLabel('ChEBI ID')) { new FeatureProperty(label: 'ChEBI ID', synonyms: 'chebi,Chebi,chebi_id,ChEBI_ID').save() }
     11        }
     12    }
    213
    3     def init = { servletContext ->
    4     }
    514    def destroy = {
    615    }
  • trunk/grails-app/controllers/org/dbxp/metabolomicsModule/BootStrapController.groovy

    r255 r268  
    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() }
     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() }
    4242               
    4343                if (assay != null) {
  • trunk/grails-app/services/org/dbxp/metabolomicsModule/measurements/MeasurementService.groovy

    r253 r268  
    55import org.dbxp.moduleBase.Assay
    66import org.dbxp.metabolomicsModule.MetabolomicsAssay
     7import org.dbxp.metabolomicsModule.identity.FeatureProperty
    78
    89class MeasurementService {
     
    8081               
    8182                def featureHeaderSuggestions = [:]
    82                 FeatureProperty.list().collect { featureHeaderSuggestions[it.label] = it.synonyms.split(",") }
     83                FeatureProperty.list().collect { featureHeaderSuggestions[it.label] = it.synonyms?.split(",") }
    8384
    8485                columns.collect { column ->
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