Changeset 184


Ignore:
Timestamp:
Feb 9, 2010, 5:01:03 PM (9 years ago)
Author:
keesvb
Message:

Deleted transcriptomics data model: moved some classes to study capture, the rest goes to the transcriptomics submodule. Added module location description for assays. Added Compound entity.

Location:
trunk/grails-app
Files:
7 added
1 deleted
4 edited

Legend:

Unmodified
Added
Removed
  • trunk/grails-app/controllers/LoadController.groovy

    r162 r184  
    1 /*
    2  * To change this template, choose Tools | Templates
    3  * and open the template in the editor.
    4  */
    5 
    61/**
    72 *
    83 * @author ademcan
    94 */
     5
     6import dbnp.studycapturing.*
     7import dbnp.data.Term
     8
    109class LoadController {
    1110
     
    3332        BufferedReader fileReader = new BufferedReader(new InputStreamReader(inputStream));
    3433
    35         def investigationDesign = new dbnp.transcriptomics.magetab.idf.InvestigationDesign();
    36         def person = new dbnp.transcriptomics.magetab.idf.Person();
    37         def protocol = new dbnp.transcriptomics.magetab.idf.MAGEProtocol();
    38         def publication = new dbnp.transcriptomics.magetab.idf.Publication();
    39         def normalization = new dbnp.transcriptomics.magetab.sdrf.Normalization();
     34        def study = new Study();
     35        def person = new Person();
     36        //def protocol = new dbnp.transcriptomics.magetab.idf.MAGEProtocol();
     37        def publication = Publication();
     38        //def normalization = new dbnp.transcriptomics.magetab.sdrf.Normalization();
    4039        //def termSource = new dbnp.transcriptomics.magetab.adf.Termsource();
    41         def comment = new dbnp.transcriptomics.magetab.idf.Comment();
    42         def experimentalInfo = new dbnp.transcriptomics.magetab.idf.ExperimentalInfo();
    43         def factor = new dbnp.transcriptomics.magetab.idf.Factor();
     40        //def comment = new dbnp.transcriptomics.magetab.idf.Comment();
     41        //def experimentalInfo = new dbnp.transcriptomics.magetab.idf.ExperimentalInfo();
     42        //def factor = new dbnp.transcriptomics.magetab.idf.Factor();
    4443
    4544        //ArrayList rows = new ArrayList();
     45
     46        // TODO: remap to dbnp studycapturing data model + extra template fields for MIAMI studies
    4647
    4748        for (i in fileReader.readLines()){
     
    219220                }
    220221                else if (tmp_list[0]=="Publication Status") {
    221                     def status = new dbnp.transcriptomics.magetab.idf.OntologyTerm();
     222                    def status = new Term();
    222223                    status.text = tmp_list[1];
    223224                    status.save();
     
    239240                //todo list of type
    240241                else if (tmp_list[0]=="Protocol Type") {
    241                     def type = new dbnp.transcriptomics.magetab.idf.OntologyTerm();
     242                    def type = new Term();
    242243                    for (j in 1..tmp_list.size()){
    243244                        type.text = tmp_list[j];
  • trunk/grails-app/domain/dbnp/studycapturing/Assay.groovy

    r162 r184  
    99
    1010    String name
    11     AssayType type
    12     String platform
     11    AssayModule module
     12    long externalAssayId
    1313
    1414    static hasMany = [samples : Sample]
  • trunk/grails-app/domain/dbnp/studycapturing/Protocol.groovy

    r162 r184  
    1414    Term   reference
    1515   
    16     static hasMany = [parameters : ProtocolParameter]
     16    static hasMany = [parameters : ProtocolParameter, compounds: Compound]
    1717    static constraints = { }
    1818
  • trunk/grails-app/domain/dbnp/studycapturing/Study.groovy

    r177 r184  
    2727                                                groups: SubjectGroup,
    2828                                                events: Event,
    29                                                 samplingEvents: SamplingEvent
     29                                                samplingEvents: SamplingEvent,
     30                        persons: StudyPerson,
     31                        publications: Publication
    3032        ]
    3133
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