Changeset 1103 for trunk/grails-app

Timestamp:

Nov 9, 2010, 10:14:23 AM (10 years ago)

Author:

t.w.abma@…

Message:

• added error page for importer
• empty ontologies detected in Excel still should be shown as "unknown" fields in the failed ontology-mapping step

Location:

trunk/grails-app

Files:

• controllers/dbnp/importer/ImporterController.groovy (modified) (5 diffs)
• domain/dbnp/importer/MappingColumn.groovy (modified) (1 diff)
• services/dbnp/importer/ImporterService.groovy (modified) (6 diffs)
• views/importer/common/_error.gsp (added)
• views/importer/common/_failedcells.gsp (modified) (1 diff)
• views/importer/common/_missingproperties.gsp (modified) (1 diff)
• views/importer/index_simple.gsp (modified) (1 diff)
• views/importer/step1_simple.gsp (modified) (1 diff)
• views/importer/step3_simple.gsp (modified) (1 diff)

trunk/grails-app/controllers/dbnp/importer/ImporterController.groovy

@@ -41 +41 @@
         //session.import_referer = request.forwardURI
         // should do a check what is in the url, strip it?
-        session.import_referer = params.redirectTo        
+        session.import_referer = params.redirectTo
+        render(view:"index_simple",
+               model:[studies:Study.findAllWhere(owner:AuthenticationService.getLoggedInUser()),
+               entities: grailsApplication.config.gscf.domain.importableEntities])
     }
 
     def simpleWizard = {
-        render(view:"index_simple", model:[studies:Study.findAllWhere(owner:AuthenticationService.getLoggedInUser()), entities: grailsApplication.config.gscf.domain.importableEntities])
+        //render(view:"index_simple", model:[studies:Study.findAllWhere(owner:AuthenticationService.getLoggedInUser()), entities: grailsApplication.config.gscf.domain.importableEntities])
     }
 
     def advancedWizard = {
-        render(view:"index_advanced", model:[templates:Template.list()])
+        //render(view:"index_advanced", model:[templates:Template.list()])
     }
 
@@ -85 +88 @@
         session.importer_workbook = wb
         session.importer_study = Study.get(params.study.id.toInteger())
-        session.importer_template_id = params.template_id
-        session.importer_sheetindex = params.sheetindex.toInteger() -1 // 0 == first sheet
-        session.importer_datamatrix_start = params.datamatrix_start.toInteger() -1 // 0 == first row
-        session.importer_headerrow = params.headerrow.toInteger()
-
-        // Get the header from the Excel file using the arguments given in the first step of the wizard
-        session.importer_header = ImporterService.getHeader(wb,
-                                                            session.importer_sheetindex,
-                                                            session.importer_headerrow,
-                                                            session.importer_datamatrix_start,
-                                                            entityClass)
+        
+        if (session.importer_study.canWrite(AuthenticationService.getLoggedInUser())) {
+            session.importer_template_id = params.template_id
+            session.importer_sheetindex = params.sheetindex.toInteger() -1 // 0 == first sheet
+            session.importer_datamatrix_start = params.datamatrix_start.toInteger() -1 // 0 == first row
+            session.importer_headerrow = params.headerrow.toInteger()
+
+            // Get the header from the Excel file using the arguments given in the first step of the wizard
+            session.importer_header = ImporterService.getHeader(wb,
+                                                                session.importer_sheetindex,
+                                                                session.importer_headerrow,
+                                                                session.importer_datamatrix_start,
+                                                                entityClass)
         
-        // Initialize 'selected entities', used to show entities above the columns
-        session.importer_header.each {
-            selectedentities.add([name:params.entity, columnindex:it.key.toInteger()])
-        }
-
-        def templates = Template.get(session.importer_template_id)
+            // Initialize 'selected entities', used to show entities above the columns
+            session.importer_header.each {
+                selectedentities.add([name:params.entity, columnindex:it.key.toInteger()])
+            }
+
+            def templates = Template.get(session.importer_template_id)
         
-        render(view:"step2_simple", model:[entities: selectedentities,
-                                           header:session.importer_header,
-                                           datamatrix:ImporterService.getDatamatrix(
-                                               wb, session.importer_header,
-                                               session.importer_sheetindex,
-                                               session.importer_datamatrix_start,
-                                               5),
-                                           templates:templates])
+            render(view:"step2_simple", model:[entities: selectedentities,
+                                        header:session.importer_header,
+                                        datamatrix:ImporterService.getDatamatrix(
+                                        wb, session.importer_header,
+                                        session.importer_sheetindex,
+                                        session.importer_datamatrix_start,
+                                        5),
+                                        templates:templates])
+        } // end of if
+        else {
+            render (template:"common/error", 
+                    model:[error:"Wrong permissions: you are not allowed to write to the study you selected (${session.importer_study})."])
+        }
     }
 
@@ -139 +149 @@
         session.importer_importeddata.each { table ->
             table.each { entity ->
-                entity.giveFields().each { field ->
-                    //print ":" + params["entity_" + entity.hashCode() + "_" + field.escapedName()]
+                entity.giveFields().each { field ->                 
                     entity.setFieldValue (field.toString(), params["entity_" + entity.hashCode() + "_" + field.escapedName()])
                 }               
@@ -171 +180 @@
                     correctedcells)
 
-        //render("failed cells saved")
-     
         render(view:"step3_simple", model:[datamatrix:session.importer_importeddata])
 
@@ -296 +303 @@
         session.importer_failedcells = failedcells
 
-        render(view:"step2a_simple", model:[failedcells:session.importer_failedcells])
-
-        /*if (params.layout=="horizontal")
-            render(view:"step3_simple", model:[datamatrix:session.importer_importeddata])
-        else if (params.layout=="vertical")
-            render(view:"step3", model:[datamatrix:session.importer_importeddata])*/
+        if (failedcells.size()!=0)
+            render(view:"step2a_simple", model:[failedcells:session.importer_failedcells])
+        else {
+            if (params.layout=="horizontal")
+                render(view:"step3_simple", model:[datamatrix:session.importer_importeddata])
+            else if (params.layout=="vertical")
+                render(view:"step3", model:[datamatrix:session.importer_importeddata])
+        }
     }
 

trunk/grails-app/domain/dbnp/importer/MappingColumn.groovy

@@ -22 +22 @@
         Boolean dontimport
 
+    static transients = [ "templatefieldtype", "entity" ]
+
     static constraints = {
             name(unique: true)

trunk/grails-app/services/dbnp/importer/ImporterService.groovy

@@ -258 +258 @@
     def saveCorrectedCells(datamatrix, failedcells, correctedcells) {       
         // Loop through all failed cells
+
         failedcells.each { mcrecord ->
             mcrecord.each { mappingcolumn ->
@@ -265 +266 @@
                   // Find the record in the table which the mappingcolumn belongs to
                   def tablerecord = datamatrix.find { it.hashCode() == mcrecord.key }
-                  
+
                   // Loop through all entities in the record
                   tablerecord.each { rec ->
-                      rec.each { entity ->                          
+                      rec.each { entity ->
                             try {
                                 // Update the entity field
@@ -280 +281 @@
                   } // end of table record
             } // end of mapping record
-        } // end of failed cells loop
+        } // end of failed cells loop     
     }
    
@@ -425 +426 @@
                 def df = new DataFormatter()
                 def template = Template.get(template_id)
+                def tft = TemplateFieldType
                 def record = [] // list of entities and the read values
                 def failed = [] // list of failed columns [mappingcolumn] with the value which couldn't be mapped into the entity
@@ -449 +451 @@
                                 }
 
+
+                                //println "temateplfedielfdtype=" + mc.templatefieldtype
+                                // Are we trying to map an ontology term which is empty? Then it is a failed cell
+                                /*if (value=="") {
+                                    println "empty term"
+                                    def temp = new MappingColumn()
+                                    //temp.properties = mc.properties
+                                    temp.value = "undefined"
+                                    failed.add(temp)
+                                }*/
+                              
+
                                 try {
+                                    /*if ((mc.templatefieldtype == TemplateFieldType.ONTOLOGYTERM) && (value == ""))
+                                        {
+                                            def temp = new MappingColumn()
+                                            temp.properties = mc.properties
+                                            temp.value="unknown"
+                                            failed.add(temp)
+                                        }*/
 
                                 // which entity does the current cell (field) belong to?
@@ -476 +497 @@
                                     def temp = new MappingColumn()
                                     temp.properties = mc.properties
-                                    temp.value = value                                    
+                                    temp.value = value
                                     failed.add(temp)
                                 }

trunk/grails-app/views/importer/common/_failedcells.gsp

@@ -50 +50 @@
   <tr>
     <td colspan="4">
-        <input type="submit" value="Accept changes">
+        <input type="submit" value="Next">
     </td>
   </tr>

trunk/grails-app/views/importer/common/_missingproperties.gsp

@@ -25 +25 @@
         <g:set var="showHeader" value="${true}"/>
             <g:each status="index" var="table" in="${datamatrix}">
-                <g:each status="i" var="entity" in="${table}">
+                <g:each status="i" var="entity" in="${table}">                  
                     <g:if test="${showHeader}">
                         <g:set var="showHeader" value="${false}"/>

trunk/grails-app/views/importer/index_simple.gsp

@@ -75 +75 @@
 </head>
   <body>
-    <h1>Importer wizard (simple)</h1>
+    <h1>Importer wizard</h1>
     <p>You can import your Excel data to the server by choosing a file from your local harddisk in the form below.</p>
         <form id="simplewizardform" controller="importer" method="post" action="upload_simple" enctype="multipart/form-data">

trunk/grails-app/views/importer/step1_simple.gsp

@@ -20 +20 @@
     <meta name="layout" content="main"/>
     <link rel="stylesheet" href="${resource(dir: 'css', file: 'importer.css')}"/>
-    <title>Step 1: import wizard preview (simple)</title>
+    <title>Step 1: import wizard preview</title>
   </head>
   <body>
-    <h1>Step 1: import wizard preview (simple)</h1>
+    <h1>Step 1: import wizard preview</h1>
     <p>Below you see a preview of your imported file, please correct the automatically detected types.</p>
   <importer:preview header="${header}" datamatrix="${datamatrix}"/>  

trunk/grails-app/views/importer/step3_simple.gsp

@@ -1 +1 @@
 <%
         /**
-         * Thirds step in the importer, showing the imported data
+         * Third step in the importer, showing the imported data
          *
          * @author Tjeerd Abma