Tm 690 fix slowness

application.properties

@@ -3,4 +3,4 @@
 app.grails.version=2.3.11
 app.name=transmart
 app.servlet.version=2.5
-app.version=tranSMART 16.2 CI
+app.version=16.2.1.UMich.1

grails-app/conf/BootStrap.groovy

@@ -78,7 +78,7 @@ class BootStrap {
         }
 
         if (!tsAppRScriptsDir || !tsAppRScriptsDir.isDirectory()) {
-            throw new RuntimeException('Could not determine proper for ' +
+            throw new RuntimeException('Could not determine proper value for ' +
                     'com.recomdata.transmart.data.export.rScriptDirectory')
         }
         c.com.recomdata.transmart.data.export.rScriptDirectory = tsAppRScriptsDir.canonicalPath

grails-app/conf/BuildConfig.groovy

@@ -18,6 +18,8 @@ grails.project.fork = [
         console: forkSettingsOther]
 
 grails.project.war.file = "target/${appName}.war"
+grails.plugin.location.'rdc-rmodules' = '../Rmodules-kretzlerLab'
+grails.plugin.location.'transmart-core' = '../transmart-core-db-kretzlerLab'
 
 /* we need at least servlet-api 2.4 because of HttpServletResponse::setCharacterEncoding */
 grails.servlet.version = "2.5"
@@ -58,7 +60,7 @@ grails.project.dependency.resolution = {
 
         runtime 'org.javassist:javassist:3.16.1-GA'
 
-        compile 'org.transmartproject:transmart-core-api:16.2-SNAPSHOT'
+        compile 'org.transmartproject:transmart-core-api:16.2'
 
         compile 'antlr:antlr:2.7.7'
         compile 'net.sf.opencsv:opencsv:2.3'
@@ -71,6 +73,7 @@ grails.project.dependency.resolution = {
             excludes 'groovy', 'nekohtml', 'httpclient', 'httpcore'
         }
         compile 'org.rosuda:Rserve:1.7.3'
+	compile 'org.rosuda:REngine:1.7.3'
         compile 'com.google.guava:guava:18.0'
         compile 'net.sf.ehcache:ehcache:2.9.0'
         compile 'org.apache.httpcomponents:httpclient:4.4.1'
@@ -134,30 +137,33 @@ grails.project.dependency.resolution = {
         compile ":codenarc:0.21"
 
         if (!dm) {
-            runtime ':smart-r:1.1-STABLE-SNAPSHOT'
-            compile ':rdc-rmodules:16.2-SNAPSHOT'
-            runtime ':transmart-core:16.2-SNAPSHOT'
-            compile ':transmart-gwas:16.2-SNAPSHOT'
+            runtime ':smart-r:16.2-STABLE'
+            compile ':rdc-rmodules:16.2'
+            runtime ':transmart-core:16.2'
+            compile ':transmart-gwas:16.2'
+            compile ':transmart-gwas-plink:16.2'
             //// already included in transmart-gwas
-            //compile ':transmart-legacy-db:16.2-SNAPSHOT'
+            //compile ':transmart-legacy-db:16.2'
             //// already included in transmart-gwas
-            //compile ':folder-management:16.2-SNAPSHOT'
+            //compile ':folder-management:16.2'
             //// already included in transmart-gwas, folder-management
-            //compile ':search-domain:16.2-SNAPSHOT'
+            //compile ':search-domain:16.2'
             //// already included in search-domain, transmart-gwas,
             //                       folder-management
-            //compile ':biomart-domain:16.2-SNAPSHOT'
+            //compile ':biomart-domain:16.2'
             //// already included in biomart-domain
-            //compile ':transmart-java:16.2-SNAPSHOT'
-            runtime ':dalliance-plugin:16.2-SNAPSHOT'
-            runtime ':transmart-mydas:16.2-SNAPSHOT'
-            runtime ':transmart-rest-api:16.2-SNAPSHOT'
-            runtime ':blend4j-plugin:16.2-SNAPSHOT'
-            runtime ':transmart-metacore-plugin:16.2-SNAPSHOT'
-            runtime ':transmart-xnat-importer:16.2-SNAPSHOT'
-            runtime ':xnat-viewer:16.2-SNAPSHOT'
-
-            test ':transmart-core-db-tests:16.2-SNAPSHOT'
+            //compile ':transmart-java:16.2'
+            // -- Genome Browser plugin --
+            //   to include the plugin, uncomment the following two lines
+            //runtime ':dalliance-plugin:16.2'
+            //runtime ':transmart-mydas:16.2'
+            runtime ':transmart-rest-api:16.2'
+            runtime ':blend4j-plugin:16.2'
+            runtime ':transmart-metacore-plugin:16.2'
+            runtime ':transmart-xnat-importer:16.2'
+            runtime ':xnat-viewer:16.2'
+
+            //test ':transmart-core-db-tests:16.2'
         } else {
             dm.internalDependencies delegate
         }
@@ -170,15 +176,18 @@ grails.project.dependency.resolution = {
 dm?.with {
     configureInternalPlugin 'compile', 'rdc-rmodules'
     configureInternalPlugin 'runtime', 'transmart-core'
-    configureInternalPlugin 'test', 'transmart-core-db-tests'
+    //configureInternalPlugin 'test', 'transmart-core-db-tests'
     configureInternalPlugin 'compile', 'transmart-gwas'
+    configureInternalPlugin 'compile', 'transmart-gwas-plink'
     configureInternalPlugin 'compile', 'transmart-java'
     configureInternalPlugin 'compile', 'biomart-domain'
     configureInternalPlugin 'compile', 'search-domain'
     configureInternalPlugin 'compile', 'folder-management'
     configureInternalPlugin 'compile', 'transmart-legacy-db'
-    configureInternalPlugin 'runtime', 'dalliance-plugin'
-    configureInternalPlugin 'runtime', 'transmart-mydas'
+    // -- Genome Browser plugin --
+    //   to include the plugin, uncomment the following two lines
+    //configureInternalPlugin 'runtime', 'dalliance-plugin'
+    //configureInternalPlugin 'runtime', 'transmart-mydas'
     configureInternalPlugin 'runtime', 'transmart-rest-api'
     configureInternalPlugin 'runtime', 'blend4j-plugin'
     configureInternalPlugin 'runtime', 'transmart-metacore-plugin'

grails-app/conf/GlobalResources.groovy

@@ -116,6 +116,7 @@ modules = {
         resource url: 'css/datasetExplorer.css'
         resource url: 'css/querypanels.css'
         resource url: 'css/sanofi.css'
+        resource url: 'css/font-awesome-4.7.0/css/font-awesome.min.css'
     }
 
     uploadDataTab {

grails-app/controllers/ChartController.groovy

@@ -83,7 +83,7 @@ class ChartController {
         log.trace(user.toString());
         def concept_key = params.concept_key;
         log.trace("Requested counts for parent_concept_path=" + concept_key);
-        def counts = i2b2HelperService.getChildrenWithPatientCountsForConcept(concept_key)
+        def counts = i2b2HelperService.getChildrenWithPatientCountsForConcept(concept_key,user)
         def access = i2b2HelperService.getChildrenWithAccessForUserNew(concept_key, user)
         log.trace("access:" + (access as JSON));
         log.trace("counts = " + (counts as JSON))
@@ -222,7 +222,6 @@ class ChartController {
         def subsets = chartService.computeChartsForSubsets(chartService.getSubsetsFromRequest(params))
         def concepts = chartService.getConceptsForSubsets(subsets)
         concepts.putAll(chartService.getHighDimensionalConceptsForSubsets(subsets))
-
         // Time to delivery !
         render(template: "summaryStatistics", model: [subsets: subsets, concepts: concepts])
     }
@@ -232,6 +231,7 @@ class ChartController {
         String concept_key = params.concept_key;
         def result_instance_id1 = params.result_instance_id1;
         def result_instance_id2 = params.result_instance_id2;
+        def user = AuthUser.findByUsername(springSecurityService.getPrincipal().username)
 
         /*which subsets are present? */
         boolean s1 = (result_instance_id1 == "" || result_instance_id1 == null) ? false : true;
@@ -245,8 +245,8 @@ class ChartController {
         if (table == null) {
 
             table = new ExportTableNew();
-            if (s1) i2b2HelperService.addAllPatientDemographicDataForSubsetToTable(table, result_instance_id1, "subset1");
-            if (s2) i2b2HelperService.addAllPatientDemographicDataForSubsetToTable(table, result_instance_id2, "subset2");
+            if (s1) i2b2HelperService.addAllPatientDemographicDataForSubsetToTable(table, result_instance_id1, "subset1", user);
+            if (s2) i2b2HelperService.addAllPatientDemographicDataForSubsetToTable(table, result_instance_id2, "subset2", user);
 
             List<String> keys = i2b2HelperService.getConceptKeysInSubsets(result_instance_id1, result_instance_id2);
             Set<String> uniqueConcepts = i2b2HelperService.getDistinctConceptSet(result_instance_id1, result_instance_id2);
@@ -258,8 +258,8 @@ class ChartController {
 
                 if (!i2b2HelperService.isHighDimensionalConceptKey(keys.get(i))) {
                     log.trace("adding concept data for " + keys.get(i));
-                    if (s1) i2b2HelperService.addConceptDataToTable(table, keys.get(i), result_instance_id1);
-                    if (s2) i2b2HelperService.addConceptDataToTable(table, keys.get(i), result_instance_id2);
+                    if (s1) i2b2HelperService.addConceptDataToTable(table, keys.get(i), result_instance_id1, user);
+                    if (s2) i2b2HelperService.addConceptDataToTable(table, keys.get(i), result_instance_id2, user);
                 }
             }
 
@@ -272,16 +272,14 @@ class ChartController {
         PrintWriter pw = new PrintWriter(response.getOutputStream());
 
         if (concept_key && !concept_key.isEmpty()) {
-
-
             // We retrieve the highdimension parameters from the client, if they were passed
             def omics_params = [:]
             params.findAll { k, v ->
                 k.startsWith("omics_")
             }.each { k, v ->
                 omics_params[k] = v
             }
-            if (omics_params) {  // empty maps are coerced to false by groovy
+            if (omics_params) {
                 omics_params.concept_key = concept_key
                 if (s1) highDimensionQueryService.addHighDimConceptDataToTable(table, omics_params, result_instance_id1)
                 if (s2) highDimensionQueryService.addHighDimConceptDataToTable(table, omics_params, result_instance_id2)
@@ -302,8 +300,8 @@ class ChartController {
                     conceptKeys.add(concept_key);
 
                 for (ck in conceptKeys) {
-                    if (s1) i2b2HelperService.addConceptDataToTable(table, ck, result_instance_id1);
-                    if (s2) i2b2HelperService.addConceptDataToTable(table, ck, result_instance_id2);
+                    if (s1) i2b2HelperService.addConceptDataToTable(table, ck, result_instance_id1, user);
+                    if (s2) i2b2HelperService.addConceptDataToTable(table, ck, result_instance_id2, user);
                 }
             }
 
@@ -326,8 +324,8 @@ class ChartController {
 
         accessLogService.report(currentUserBean, 'Grid View Data Export',
                 eventMessage: "User (IP: ${request.getHeader('X-FORWARDED-FOR') ?: request.remoteAddr}) just exported" +
-                        " data for tieal(s) (${trialsCsv}): variables (${exportedVariablesCsv}) measurements for the" +
-                        " folowing patients set(s): " +
+                        " data for trial(s) (${trialsCsv}): variables (${exportedVariablesCsv}) measurements for the" +
+                        " following patient set(s): " +
                         [params.result_instance_id1, params.result_instance_id2].findAll().join(', '),
                 requestURL: request.forwardURI)
 

grails-app/controllers/DataAttestationController.groovy

@@ -0,0 +1,45 @@
+import DataAttestation
+import org.springframework.web.servlet.support.RequestContextUtils
+import org.transmart.searchapp.AuthUser
+
+class DataAttestationController {
+
+    def springSecurityService
+    def messageSource
+
+    def index = {
+        def user = AuthUser.findByUsername(springSecurityService.getPrincipal().username)
+    	if (DataAttestation.needsDataAttestation(user))
+            render(view:"attestation")
+        else
+            redirect(uri:'/datasetExplorer/index');
+    }
+    def agree = {
+        def user = AuthUser.findByUsername(springSecurityService.getPrincipal().username)
+        DataAttestation.updateOrAddNewAgreementDate(user)
+        if (springSecurityService.currentUser.changePassword) {
+            flash.message = messageSource.getMessage('changePassword', new Objects[0], RequestContextUtils.getLocale(request))
+            redirect(controller: 'changeMyPassword')
+        } else {
+            redirect(uri: '/datasetExplorer/index')
+        }
+    }
+
+    def disagree = {
+        redirect(uri: '/logout')
+    }
+
+	def clear = {
+	    def user = AuthUser.findByUsername(springSecurityService.getPrincipal().username)
+    	def da = DataAttestation.findByAuthUserId(user.id)
+    	if (da != null) {
+            try {
+                da.delete(flush: true)
+            }
+		    catch (org.springframework.dao.DataIntegrityViolationException e) {
+                flash.message = "Could not delete user ${user}"
+            }
+        }
+        redirect(uri: '/logout')		
+	}    
+}