Changeset 650

Timestamp:

Jul 13, 2010, 6:26:50 PM (13 years ago)

Author:

vinlud

Message:

Multiple changes in structure/view/logic

Location:

trunk

Files:

• grails-app/controllers/dbnp/query/SimpleQueryController.groovy (modified) (6 diffs)
• grails-app/views/simpleQuery/common/_query.gsp (modified) (7 diffs)
• test/unit/dbnp/studycapturing/SimpleQueryControllerTests.groovy (added)
• web-app/css/simpleQuery.css (modified) (2 diffs)
• web-app/js/simpleQuery.js (modified) (1 diff)

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

@@ -36 +36 @@
             println "Starting webflow simpleQuery"
             flow.search_term            = null
+            flow.search_sa_compounds    = []
+            flow.search_sa_operators    = []
+            flow.search_sa_values       = []
             flow.page                   = 0
                         flow.pages = [
@@ -50 +53 @@
               println "Rendering mainPage"
               flow.operators              = ['>', '=', '<']
-              flow.showFirstRowCompounds  = true
+
+              if (flow.search_sa_compounds.size() == 0) {
+                flow.showFirstRowCompounds  = true
+                println "showRow true"
+              } else {
+                flow.showFirstRowCompounds  = false
+                println "showRow false"
+              }
+
               flow.species = Term.findAll()
               flow.page = 1
@@ -69 +80 @@
         searching {
            action {
-              println "Starting search..."
+              println "Starting simpleQuery search..."
               def searchResult
               def searchGscfResult
-              def searchSamResult
+              def searchSamResult   = []
 
               // TODO: walk parameters, remove empty entries
 
-              // Map parameters
-              flow.search_term            = params.search_term
-              flow.search_sa_compounds    = params.sa_compound
-              flow.search_sa_operators    = params.sa_operator
-              flow.search_sa_values       = params.sa_value
-              flow.search_tt_genepaths    = params.sa_genepath
-              flow.search_tt_regulations  = params.sa_regulation
-
-              // Check to see how parameters are being handled
-              if (flow.search_sa_compounds.class.getName() == "java.lang.String") {
-                println "string"
+              // Map GSCF parameters
+              flow.search_term            = params.search_term        // String
+
+              // Map SAM parameters
+              if (params.sa_compound instanceof String) {
+                //flow.search_sam = [:]
+                flow.search_sa_compounds = []
+                flow.search_sa_operators = []
+                flow.search_sa_values    = []
+
+                flow.search_sa_compounds.add(params.sa_compound)
+                flow.search_sa_operators.add(params.sa_operator)
+                flow.search_sa_values.add(params.sa_value)
               } else {
-                println "array of size " + flow.search_sa_compounds.length
+                flow.search_sa_compounds  = params.sa_compound as List
+                flow.search_sa_operators  = params.sa_operator as List
+                flow.search_sa_values     = params.sa_value as List
               }
 
@@ -102 +117 @@
               // ... todo when the plugin works and I can see the output
 
-              // Search in the SAM module
-              println "checking compounds"
-              if (flow.search_sa_compounds) {
-                objComs = new CommunicationManager()
-
-                if (flow.search_sa_compounds.class.getName() == "java.lang.String") {
-                  searchSamResult = objComs.getSAMStudies(flow.search_sa_compounds, flow.search_sa_values, flow.search_sa_operators)
-                } else {
-                  def tmpSamResult
-                  flow.search_sa_compounds.each {
-                    obj, i -> println " ${i}: ${obj}" // objComs.getSAMStudies()
-                    tmpSamResult = objComs.getSAMStudies(flow.search_sa_compounds[i], flow.search_sa_values[i], flow.search_sa_operators[i])
-
-                    // Combine each search
-                    // searchSamResult = Merge(searchSamResult, tmpSamResult)
-                    searchSamResult = tmpSamResult
-                  };
-                }
-              }
-
+              // Search in the SAM module when a compound is entered
+              // Todo: check whether the module is active and to be used
+              // ...
+              if (flow.search_sa_compounds.size() > 0) {
+                def resultSAM = []
+                resultSAM = this.searchSAM(flow.search_sa_compounds)
+                println "Sam result: " + resultSAM
+              }
+                                         
              // Merge the results of all searches
-             /*
              if (searchGscfResult.size() > 0) {
-                searchResult = Merge(searchSamResult, searchGscfResult)
+               
+                searchResult = searchSamResult + searchGscfResult
              }             
-             */
 
 
              // Save the results in the flow
              flow.listStudies = searchGscfResult.results
+             println flow.listStudies
 
            }
@@ -148 +152 @@
               flow.page = 2
 
-              // TODO: Fix the showing of entered data, broke with plugin develeopment
-              if (flow.search_sa_compounds) {
-                if (flow.search_sa_compounds.class.getName() == "java.lang.String") {
-                  flow.resultString = true
-                } else {
-                  flow.resultString = false
-                }
-              }
+              flow.showFirstRowCompounds  = false
             }
 
@@ -173 +170 @@
 
     }
+
+
+   static List searchSAM (List compounds) {
+     if (compounds.size() == 1) {
+       println "Single SAM call"
+       def mapSamResult
+       mapSamResult = CommunicationManager.getQueryResult(compounds.get(0))
+       
+       return mapSamResult.studies
+
+     } else {
+       println "Multiple SAM calls"
+       def tmpSamResult
+       def i = 0
+
+       compounds.each() {
+         println compounds.get(i)
+
+         println "set tmpSamResult"
+
+         // Combine each search
+         // searchSamResult = Merge(searchSamResult, tmpSamResult)
+         // searchSamResult += tmpSamResult
+         i++
+       };
+     }
+
+   }
+
+
+
+   static List merge (List list1, List list2) {
+
+     def resultList = []
+     resultList = list1.intersect(list2)
+
+     return resultList
+   }
+
 }

trunk/grails-app/views/simpleQuery/common/_query.gsp

@@ -30 +30 @@
       </div>
 
-      <h3><a href="#">Simple Assays</a></h3>
+      <h3><a href="#">Simple Assays (optional)</a></h3>
       <div class="element">
         <div id="compoundGroup">
@@ -36 +36 @@
           <g:if test="${showFirstRowCompounds}">
           <div id="compoundRow1">
-            <div class="descriptionSA">Compound</div>
-            <div class="input"><g:textField name="sa_compound" value="${search_sa_compounds}"/></div>
-            <div class="descriptionSA">Operator</div>
-            <div class="input" id="operatorInput"><g:select name="operator" from="${operators}" value="="/></div>
-            <div class="descriptionSA">Value</div>
-            <div class="input"><g:textField name="sa_value" value="${search_sa_values}"/></div>
+            <div class="descriptionSA">Compound</div><div class="input"><g:textField name="sa_compound" value=""/></div><div class="descriptionSA">Operator</div><div class="input" id="operatorInput"><g:select name="operator" from="${operators}" value="="/></div><div class="descriptionSA">Value</div><div class="input"><g:textField name="sa_value" value=""/></div>
           </div>
           </g:if>
@@ -48 +43 @@
             <g:each status="i" in="${search_sa_compounds}" var="compound">
             <div id="compoundRow${i}">
-              <div class="descriptionSA">Compound (e.g. 'glucose')</div>
-              <div class="input"><g:textField name="sa_compound" value="${compound}"/></div>
-              <div class="descriptionSA">Type of regulations</div>
-              <div class="input"><g:select name="operator" from="${operators}" value="="/></div>
-              <div class="descriptionSA">Value</div>
-              <div class="input"><g:textField name="sa_value" value="${search_sa_values[i]}"/></div>
+              <div class="descriptionSA">Compound (e.g. 'glucose')</div><div class="input"><g:textField name="sa_compound" value="${search_sa_compounds.get(i)}"/></div><div class="descriptionSA">Type of regulations</div><div class="input"><g:select name="operator" from="${operators}" value="="/></div><div class="descriptionSA">Value</div><div class="input"><g:textField name="sa_value" value="${search_sa_values.get(i)}"/></div>
             </div>
             </g:each>
@@ -61 +51 @@
       </div>
 
-      <h3><a href="#">Transcriptomics</a></h3>
+      <h3><a href="#">Transcriptomics (optional)</a></h3>
 
       <div class="element">
         <div id="transcriptomeGroup">
           <div id="transcriptomeRow1">
-            <div class="description">List of Gene IDs or pathway IDs</div>
-            <div class="input"><g:textField name="genepath" value="" /></div>
-            <div class="description">Type of regulations</div>
-            <div class="input" id="regulationInput"><g:select name="regulation" from="" value="${regulation}" noSelection="['':'--- select regulation ---']"/></div>
+            <div class="description">List of Gene IDs or pathway IDs</div><div class="input"><g:textField name="genepath" value="" /></div><div class="description">Type of regulations</div><div class="input" id="regulationInput"><g:select name="regulation" from="" value="${regulation}" noSelection="['':'--- select regulation ---']"/></div>
           </div>
         </div>
-        <div id="addTranscriptome">Add transciptome</div>
+        <div id="addTranscriptome" class="submit">Add transciptome</div>
       </div>
     </div>
@@ -81 +68 @@
 
     <g:if test="${search_term}">
-        <h1><g:message code="Search results for term ${search_term}"/></h1>
+        <h1><g:message code="Search results for term '${search_term}'"/></h1>
 
         <g:if test="${listStudies}">
@@ -88 +75 @@
                 <thead>
                     <tr>
+                        <g:sortableColumn property="id" title="${message(code: 'study.id', default: 'ID')}" />
                         <g:sortableColumn property="title" title="${message(code: 'study.title.label', default: 'Study')}" />
+                        <g:sortableColumn property="samples" title="${message(code: 'study.sample', default: 'Samples')}" />
                     </tr>
                 </thead>
@@ -94 +83 @@
                 <g:each in="${listStudies}" var="Study" status="i" >
                   <tr class="${(i % 2) == 0 ? 'odd' : 'even'}">
+                    <td><g:link url="[action:'show',controller:'study']" id="${Study.id}">${fieldValue(bean: Study, field: "id")}</g:link></td>
                     <td><g:link url="[action:'show',controller:'study']" id="${Study.id}">${fieldValue(bean: Study, field: "title")}</g:link></td>
+                    <td><g:link url="[action:'show',controller:'study']" id="${Study.id}">${fieldValue(bean: Study, field: "samples")}</g:link></td>
                   </tr>
                 </g:each>

trunk/web-app/css/simpleQuery.css

@@ -26 +26 @@
 
 .simplequery .submit {
-    padding: 5px;
-    display: inline;
+    margin-top: 15px;
+    padding: 2px;
     font-size: 11px;
-    word-wrap: break-word;
+    border: 3px outset lightblue;
+    width: 100px;
+    text-align: center;
 }
 
 .simplequery .element .input {
     display: inline;
-    margin-right: 10px;
     font-size: 11px;
-    word-wrap: break-word;
 }
 
@@ -42 +42 @@
     vertical-align: top;
     border: 1px solid #CCC;
-    margin: 2px 0;
-    padding: 2px 4px;
 }
 

trunk/web-app/js/simpleQuery.js

@@ -56 +56 @@
         newCompoundRowDiv6.innerHTML = "<input type='text' name='sa_value' value=''>";
         newCompoundDiv.appendChild(newCompoundRowDiv6); 
+
+        //var newCompoundRowDiv7 = document.createElement('div');
+        //newCompoundRowDiv7.setAttribute('class', 'delete');
+        //newCompoundRowDiv7.innerHTML = "delete";
+        //newCompoundDiv.appendChild(newCompoundRowDiv7);
         compoundGroup.appendChild(newCompoundDiv);