May 30, 2013, 4:13:48 PM (10 years ago)

Refs #805. Support for simplifying ProteomeXchange submission by creating a ProteomeXchange Submission Summary *.px file updated by adding option for automatic file selection via associations:

  1. Class/file action/file/ProteomeXchangeExport.java in client/servlet/ updated with new check box getIncludeFilesFromAssociationsCB coupled to new valid parameter VBoolean CreateProteomeXchangeExportJob.VGETINCLUDEFILESFROMASSOCIATIONS.
  2. Class/file action/file/SelectProteomeXchangeIncludeFilesStep1a.java in client/servlet/ updated to obtain value of valid parameter VBoolean CreateProteomeXchangeExportJob.VGETINCLUDEFILESFROMASSOCIATIONS from request and save it to session. If the parameter has value true, all file types will be marked for inclusion, but the user will only be able to select files of ProteomeXchange file type "other", to which automatically found feature files will later be added.
  3. Class/file action/file/CreateProteomeXchangeExportJob.java in client/servlet/ updated with new valid parameter VBoolean VGETINCLUDEFILESFROMASSOCIATIONS, whose value is obtained from session. If the parameter has value true, include files will be selected using associations and annotations. New private convenience method String fetchBaseFilename(File file) added. It returns the base filename of a file (filename without file extension).
  4. Class/file core/Feature.java in api/core/ updated with new public static method List<File> getUniqueFeatureFilesForMsFile(Project project, File msFile, DbControl dc). It uses new pre-defined query GET_UNIQUE_FEATUREFILES_IN_FEATURES_FOR_MSFILE_IN_PROJECT to find unique feature files for a peaklist file in project.
  5. SQL query XML file conf/common-queries.xml in api/core/ is updated with new query with id "GET_UNIQUE_FEATUREFILES_IN_FEATURES_FOR_MSFILE_IN_PROJECT".
  6. English dictionary file locale/en/dictionary in client/servlet/ updated with new string key entry.
1 edited


  • trunk/api/core/conf/common-queries.xml

    r4472 r4475  
    360360  </query>
     363    <sql>
     364      SELECT DISTINCT h.featureFile
     365      FROM FeatureData h
     366      WHERE h.project = :project AND h.msFile = :msFile
     367    </sql>
     368    <description>
     369      Load all distinct (unique) feature files for an ms file in the Feature table for a project
     370    </description>
     371  </query>
    362373  <query id="DELETE_FEATURES_FOR_MSFILE_IN_PROJECT" type="HQL">
    363374    <sql>
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