Changeset 1689

Timestamp:

Apr 4, 2011, 11:54:25 AM (12 years ago)

Author:

robert@…

Message:

Removed assayModule platform field (#387)

Location:

trunk/grails-app

Files:

• conf/DatabaseUpgrade.groovy (modified) (2 diffs)
• conf/dbnp/configuration/ExampleStudies.groovy (modified) (6 diffs)
• views/advancedQuery/studyresults.gsp (modified) (1 diff)
• views/exporter/index.gsp (modified) (1 diff)
• views/pilot/list.gsp (modified) (1 diff)
• views/study/list.gsp (modified) (1 diff)
• views/study/show_assays.gsp (modified) (2 diffs)

trunk/grails-app/conf/DatabaseUpgrade.groovy

@@ -37 +37 @@
                 alterStudyAndAssay(sql, db)                                     // r1594
                 fixDateCreatedAndLastUpdated(sql, db)
+                dropAssayModulePlatform(sql, db)                        // r1689
         }
 
@@ -283 +284 @@
                 }
         }
+        
+        
+        /**
+         * drops the field platform from assay modules
+         * @param sql
+         * @param db
+         */
+        public static void dropAssayModulePlatform(sql, db) {
+                // are we running postgreSQL?
+                if (db == "org.postgresql.Driver") {
+                        // do we need to perform this update?
+                        if (sql.firstRow("SELECT * FROM information_schema.columns WHERE columns.table_name='assay_module' AND columns.column_name='platform'")) {
+                                if (String.metaClass.getMetaMethod("grom")) "performing database upgrade: removing assayModule platform".grom()
+
+                                try {
+                                        sql.execute("ALTER TABLE assay_module DROP COLUMN platform")
+                                } catch (Exception e) {
+                                        println "dropAssayModulePlatform database upgrade failed: " + e.getMessage()
+                                }
+                        }
+                }
+        }
 }

trunk/grails-app/conf/dbnp/configuration/ExampleStudies.groovy

@@ -43 +43 @@
                 def clinicalModule = new AssayModule(
                         name: 'SAM module for clinical data',
-                        platform: 'clinical measurements',
                         url: config.modules.sam.url.toString()
                 ).save(failOnError:true)
@@ -50 +49 @@
                 def metabolomicsModule = new AssayModule(
                         name: 'Metabolomics module',
-                        platform: 'GCMS/LCMS',
                         url: config.modules.metabolomics.url.toString()
                 ).save(failOnError:true)
@@ -57 +55 @@
                 def metagenomicsModule = new AssayModule(
                         name: 'Metagenomics module',
-                        platform: 'High throughput sequencing',
                         url: config.modules.metagenomics.url.toString()
                 ).save(failOnError:true)
@@ -400 +397 @@
                 def clinicalModule = new AssayModule(
                         name: 'SAM module for clinical data',
-                        platform: 'clinical measurements',
                         url: config.modules.sam.url.toString()
                 ).save(failOnError:true)
@@ -407 +403 @@
                 def metabolomicsModule = new AssayModule(
                         name: 'Metabolomics module',
-                        platform: 'GCMS/LCMS',
                         url: config.modules.metabolomics.url.toString()
                 ).save(failOnError:true)
@@ -414 +409 @@
                 def metagenomicsModule = new AssayModule(
                         name: 'Metagenomics module',
-                        platform: 'High throughput sequencing',
                         url: config.modules.metagenomics.url.toString()
                 ).save(failOnError:true)

trunk/grails-app/views/advancedQuery/studyresults.gsp

@@ -78 +78 @@
                                         </g:if>
                                         <g:else>
-                                                ${studyInstance.assays.module.platform.unique().join(', ')}
+                                                ${studyInstance.assays.module.name.unique().join(', ')}
                                         </g:else>
                                 </td>

trunk/grails-app/views/exporter/index.gsp

@@ -71 +71 @@
                     </g:if>
                     <g:else>
-                      ${studyInstance.assays.module.platform.unique().join( ', ' )}
+                      ${studyInstance.assays.module.name.unique().join( ', ' )}
                     </g:else>
                   </td>

trunk/grails-app/views/pilot/list.gsp

@@ -44 +44 @@
                     </g:if>
                     <g:else>
-                      ${studyInstance.assays.module.platform.unique().join( ', ' )}
+                      ${studyInstance.assays.module.name.unique().join( ', ' )}
                     </g:else>
                   </td>

trunk/grails-app/views/study/list.gsp

@@ -75 +75 @@
                                                         </g:if>
                                                         <g:else>
-                                                                ${studyInstance.assays.module.platform.unique().join(', ')}
+                                                                ${studyInstance.assays.module.name.unique().join(', ')}
                                                         </g:else>
                                                 </td>

trunk/grails-app/views/study/show_assays.gsp

@@ -11 +11 @@
                 <th width="100">Assay Name</th>
                 <th width="100">Module</th>
-                <th width="150">Platform</th>
                 <th>Link</th>
                 <th>Samples</th>
@@ -28 +27 @@
                   <td>${assay?.name}</td>
                   <td>${assay?.module?.name}</td>
-                  <td>${assay?.module?.platform}</td>
                   <td>
                         <g:if test="${assay?.module.openInFrame == null || assay?.module.openInFrame == Boolean.TRUE}">
                   <jumpbar:link frameSource="${assay?.module.url}/assay/showByToken/${assay?.giveUUID()}" pageTitle="${assay?.module.name}">
-                                view
+                                details
                           </jumpbar:link>
                          </g:if>
                          <g:else>
-                                <g:link url="${assay?.module.url}/assay/showByToken/${assay?.giveUUID()}">view</g:link>
+                                <g:link url="${assay?.module.url}/assay/showByToken/${assay?.giveUUID()}">details</g:link>
                          </g:else>
                 </td>