Changeset 1196 for trunk/grails-app/controllers

Timestamp:

Nov 24, 2010, 11:47:41 AM (10 years ago)

Author:

j.saito@…

Message:

Streamlined CommunicationManager? and adjusted it to suit CommunicationManager? in SAM.
Removed horrible debugoutputs from SimpleQueryController?. (Is this used any longer at all??)

File:

• trunk/grails-app/controllers/dbnp/query/SimpleQueryController.groovy (modified) (15 diffs)

trunk/grails-app/controllers/dbnp/query/SimpleQueryController.groovy

@@ -35 +35 @@
         // Starting simpleQuery flow, initialize variables
         onStart {
-            println "Starting webflow simpleQuery"
             flow.search_term            = null
             flow.search_sa_compounds    = []
@@ -51 +50 @@
                         render(view: "/simpleQuery/mainPage")
 
+
             onRender {
-              println "Rendering mainPage"
               flow.operators              = ['>', '=', '<']
 
               if (!flow.search_sa_compounds) {
                 flow.showFirstRowCompounds  = true
-                println "showRow true"
               } else {
                 flow.showFirstRowCompounds  = false
-                println "showRow false"
               }
 
@@ -68 +65 @@
 
             on("search") {
-              println "Search!"
               if (!params.search_term.trim()) {
                 return [:]
@@ -81 +77 @@
         searching {
            action {
-              println "Starting simpleQuery search..."
               def searchResult
               def searchGscfResult
               def searchSamResult   = []
 
-              // TODO: walk parameters, remove empty entries
-
               // Map GSCF parameters
               flow.search_term            = params.search_term        // String
@@ -93 +86 @@
               // Map SAM parameters
               if (params.sa_compound instanceof String) {
-                println "Compounds as String"
-                //flow.search_sam = [:]
                 flow.search_sa_compounds = []
                 flow.search_sa_operators = []
@@ -105 +96 @@
                 }
               } else {
-                println "Compounds as List"
                 flow.search_sa_compounds  = params.sa_compound as List
                 flow.search_sa_operators  = params.sa_operator as List
@@ -114 +104 @@
               try {
                 searchGscfResult = searchableService.search(flow.search_term)
-                println "RESULT: " + searchGscfResult
               } catch (SearchEngineQueryParseException ex) {
                 println ex
@@ -124 +113 @@
 
               // Search in the SAM module when a compound is entered
-              // Todo: check whether the module is active and to be used
-              // ...
               def listSamStudies = []
               def listGscfStudies = []
@@ -133 +120 @@
                 def resultSAM = [:]
                 resultSAM = this.searchSAM(flow.search_sa_compounds, flow.search_sa_operators, flow.search_sa_values)
-                println "Sam result: " + resultSAM
                 listSamStudies = resultSAM.get('studies')
               }
 
              for (i in searchGscfResult.results) {
-               //def x = i.id
                def objStudy = Study.get(i.id)
-               println objStudy
                listGscfStudies.add(objStudy.id)
              }
 
 
-             println "GSCF studies: " + listGscfStudies
-             println "Sam studies " + listSamStudies
                                          
              // Merge the results of all searches
              if (listSamStudies.size() > 0) {
                listStudies = listGscfStudies.intersect(listSamStudies)
-               println "Combined: " + listStudies
              } else {
                if (!flow.search_sa_compounds) {
@@ -168 +149 @@
              // Save the results in the flow
              flow.listStudies = listObjStudies
-             println flow.listStudies
 
            }
@@ -182 +162 @@
 
             onRender {
-              println "Rendering resultPage"
               flow.page = 2
 
@@ -196 +175 @@
               flow.search_tt_genepaths    = null
               flow.search_tt_regulations  = null
-              println "Resetting query flow"
             }.to "query"
 
@@ -207 +185 @@
   
    static Map searchSAM (List compounds, List operators, List values) {
+
+
      if (compounds.size() == 1) {
-       println "Single SAM call"
-       def mapSamResult = [:]
-
-       //def listAssays = [3, 1]
-       //mapSamResult.put("assays", listAssays)
-       //println "CommMngr result: " + mapSamResult
-
-       CommunicationManager.addRestWrapper( 'http://localhost:8182/sam/rest', 'getQueryResult', ['query'] )
-       mapSamResult = CommunicationManager.getQueryResult( compounds.get(0) )
-       println "SAM REST query: " + compounds.get(0)
-       println "SAM REST result: " + mapSamResult
-
-       // mapSamResult = CommunicationManager.getQueryResult(compounds.get(0), operators.get(0), values.get(0))
-
-       //objAssay = objAssay.get(i)
-       //println "Assay: " + objAssay
-
-       /*
-       for (i in mapSamResult.assays) {
-         //def listStudies = Study.findAll("from Study as s where s.assays.id = " + i)
-         def listStudies = Study.findAll("from Study as s where exists (from Assay as a where a.id = s.assays and a.id = ${i})")
-         println "Studies found: " + listStudies
-       }
-       */
+       def tmpResult = CommunicationManager.getQueryResult( compounds.get(0) )
+       def studies = tmpResult.studiesIds.collect{ Study.findByCode(it) }
+       def assays  = tmpResult.assays.collect { [it, Assay.findByExternalAssayID( it.externalAssayID ) ] } 
+           def mapSamResult = [studies:studies, assays:assays] 
+
 
        def listStudies = []
@@ -245 +206 @@
 
      } else {
-       println "Multiple SAM calls"
-       def tmpSamResult = [:]
-       def mapSamResult = [assays:[]]
+       def tmpResult = CommunicationManager.getQueryResult( compounds.get(0) )
+       def studies = tmpResult.studiesIds.collect{ Study.findByCode(it) }
+           def mapSamResult = [studies:studies, assays:[]] 
+
        def i = 0
-
        compounds.each { compound ->
-         println "SAM Search with " + compound
-         CommunicationManager.addRestWrapper( 'http://localhost:8182/sam/rest', 'getQueryResult', ['query'] )
          tmpSamResult = CommunicationManager.getQueryResult(compound)
-         println "tmpsamres: " + tmpSamResult
 
          if (i == 0) {
@@ -263 +221 @@
            }
          }
-
          i++
        }