Interface database-details nearly finished (other Remedy Compositions…

… to finish) Need some fix on the model before (add Remedy entity, a set of plant ingredients)
acheype · May 16, 2017 · 7b75759 · 7b75759
1 parent ba09755
commit 7b75759
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Showing 41 changed files with 148 additions and 125 deletions.
diff --git a/src/main/java/nc/ird/malariaplantdb/repository/InVitroPharmacoRepository.java b/src/main/java/nc/ird/malariaplantdb/repository/InVitroPharmacoRepository.java
@@ -23,7 +23,7 @@ public interface InVitroPharmacoRepository extends JpaRepository<InVitroPharmaco
     //    ".plantIngredients where inVitroPharmaco.id =:id")
     //InVitroPharmaco findOneWithEagerRelationships(@Param("id") Long id);
 
-    @Query("select iv from InVitroPharmaco iv join iv.plantIngredients pi where iv.publication.id = :pubId and pi.id in :piIds")
+    @Query("select distinct iv from InVitroPharmaco iv join iv.plantIngredients pi where iv.publication.id = :pubId and pi.id in :piIds")
     List<InVitroPharmaco> findByPublicationIdAndPlantIngredients(@Param("pubId") Long pubId, @Param("piIds") List<Long>
         piIds);
 

diff --git a/src/main/java/nc/ird/malariaplantdb/repository/InVivoPharmacoRepository.java b/src/main/java/nc/ird/malariaplantdb/repository/InVivoPharmacoRepository.java
@@ -24,7 +24,7 @@ public interface InVivoPharmacoRepository extends JpaRepository<InVivoPharmaco,L
     //    ".plantIngredients where inVivoPharmaco.id =:id")
     //InVivoPharmaco findOneWithEagerRelationships(@Param("id") Long id);
 
-    @Query("select iv from InVivoPharmaco iv join iv.plantIngredients pi where iv.publication.id = :pubId and pi.id in :piIds")
+    @Query("select distinct iv from InVivoPharmaco iv join iv.plantIngredients pi where iv.publication.id = :pubId and pi.id in :piIds")
     List<InVivoPharmaco> findByPublicationIdAndPlantIngredients(@Param("pubId") Long pubId, @Param("piIds") List<Long>
         piIds);
 

diff --git a/src/main/java/nc/ird/malariaplantdb/web/rest/PubSpeciesResource.java b/src/main/java/nc/ird/malariaplantdb/web/rest/PubSpeciesResource.java
@@ -124,7 +124,7 @@ public ResponseEntity<List<PubSpecies>> getPubSpeciesByPublicationId(@PathVariab
     }
 
     /**
-     * GET  /publications/:pubId/pi/:piIds/ethnologies -> get all the pubSpecies with the "id" publication and the
+     * GET  /publications/:pubId/pi/:piIds/pubSpecies -> get all the pubSpecies with the "id" publication and the
      * list of plant ingredient ids
      */
     @RequestMapping(value = "/publications/{pubId}/pi/{piIds}/pubSpecies",

diff --git a/src/main/resources/.h2.server.properties b/src/main/resources/.h2.server.properties
@@ -1,5 +1,5 @@
 #H2 Server Properties
-#Mon Jan 11 10:45:16 NCT 2016
+#Tue May 16 17:44:33 NCT 2017
 0=JHipster H2 (Memory)|org.h2.Driver|jdbc\:h2\:mem\:jhipster|
 webAllowOthers=true
 webPort=8082

diff --git a/src/main/resources/config/liquibase/test_data/201601080000_test_data_insertions.xml b/src/main/resources/config/liquibase/test_data/201601080000_test_data_insertions.xml
@@ -61,6 +61,16 @@
                   separator=","
                   tableName="in_vivo_pharmaco_plant_ingredient"/>
 
+        <loadData encoding="UTF-8"
+                  file="config/liquibase/test_data/in_vitro_pharmaco.csv"
+                  separator=","
+                  tableName="in_vitro_pharmaco"/>
+
+        <loadData encoding="UTF-8"
+                  file="config/liquibase/test_data/in_vitro_pharmaco_plant_ingredient.csv"
+                  separator=","
+                  tableName="in_vitro_pharmaco_plant_ingredient"/>
+
     </changeSet>
 
 </databaseChangeLog>
diff --git a/src/main/resources/config/liquibase/test_data/in_vitro_pharmaco.csv b/src/main/resources/config/liquibase/test_data/in_vitro_pharmaco.csv
@@ -0,0 +1,3 @@
+"PUBLICATION_ID","ID","TESTED_ENTITY","EXTRACTION_SOLVENT","ADDITIVE_PRODUCT","COMPOUND_NAME","SCREENING_TEST","MEASURE_METHOD","CONCENTRATION","MOL_CONCENTRATION","INHIBITION","IC50","MOL_IC50","SELECTIVITY_INDEX","COMPILERS_OBSERVATIONS"
+"2","1","Fraction",null,null,null,"Erythrocyt","Enzymatic",null,null,null,null,"4.4700",null,null
+"2","2","Extract","Methanol",null,null,"Toxicity","Enzymatic",null,null,null,null,null,"1.80","A compiler observation example ! Done."
diff --git a/src/main/resources/config/liquibase/test_data/in_vitro_pharmaco_plant_ingredient.csv b/src/main/resources/config/liquibase/test_data/in_vitro_pharmaco_plant_ingredient.csv
@@ -0,0 +1,5 @@
+"PLANT_INGREDIENTS_ID","IN_VITRO_PHARMACOS_ID"
+"1","1"
+"2","1"
+"1","2"
+"2","2"
diff --git a/src/main/scss/main.scss b/src/main/scss/main.scss
@@ -109,11 +109,7 @@ $citation-font: 'EB Garamond';
     margin: 10px auto 10px auto;
 }
 
-.colored-background {
-    background-color: $gray-lighter;
-}
-
-.colored-background .table-striped > tbody > tr:nth-of-type(odd) {
+.table-striped > tbody > tr:nth-of-type(odd) {
     background-color: #fff;
 }
 
@@ -236,6 +232,7 @@ ul#strength {
 .alerts .alert{
     text-overflow: ellipsis;
 }
+
 .alert pre{
     background: none;
     border: none;

diff --git a/src/main/webapp/scripts/app/admin/health/health.controller.js b/src/main/webapp/scripts/app/admin/health/health.controller.js
@@ -1,7 +1,7 @@
 'use strict';
 
 angular.module('malariaplantdbApp')
-    .controller('HealthController', function ($scope, MonitoringService, $modal) {
+    .controller('HealthController', function ($scope, MonitoringService, $uibModal) {
         $scope.updatingHealth = true;
         $scope.separator = '.';
 
@@ -62,7 +62,7 @@ angular.module('malariaplantdbApp')
 
 
         $scope.showHealth = function(health) {
-            var modalInstance = $modal.open({
+            var modalInstance = $uibModal.open({
                 templateUrl: 'scripts/app/admin/health/health.modal.html',
                 controller: 'HealthModalController',
                 size: 'lg',

diff --git a/src/main/webapp/scripts/app/admin/health/health.modal.controller.js b/src/main/webapp/scripts/app/admin/health/health.modal.controller.js
@@ -1,12 +1,12 @@
 'use strict';
 
 angular.module('malariaplantdbApp')
-    .controller('HealthModalController', function($scope, $modalInstance, currentHealth, baseName, subSystemName) {
+    .controller('HealthModalController', function($scope, $uibModalInstance, currentHealth, baseName, subSystemName) {
 
         $scope.currentHealth = currentHealth;
         $scope.baseName = baseName, $scope.subSystemName = subSystemName;
 
         $scope.cancel = function() {
-            $modalInstance.dismiss('cancel');
+            $uibModalInstance.dismiss('cancel');
         };
     });
diff --git a/src/main/webapp/scripts/app/admin/metrics/metrics.controller.js b/src/main/webapp/scripts/app/admin/metrics/metrics.controller.js
@@ -1,7 +1,7 @@
 'use strict';
 
 angular.module('malariaplantdbApp')
-    .controller('MetricsController', function ($scope, MonitoringService, $modal) {
+    .controller('MetricsController', function ($scope, MonitoringService, $uibModal) {
         $scope.metrics = {};
         $scope.updatingMetrics = true;
 
@@ -43,7 +43,7 @@ angular.module('malariaplantdbApp')
         $scope.refreshThreadDumpData = function() {
             MonitoringService.threadDump().then(function(data) {
 
-                var modalInstance = $modal.open({
+                var modalInstance = $uibModal.open({
                     templateUrl: 'scripts/app/admin/metrics/metrics.modal.html',
                     controller: 'MetricsModalController',
                     size: 'lg',

diff --git a/src/main/webapp/scripts/app/admin/metrics/metrics.modal.controller.js b/src/main/webapp/scripts/app/admin/metrics/metrics.modal.controller.js
@@ -1,7 +1,7 @@
 'use strict';
 
 angular.module('malariaplantdbApp')
-    .controller('MetricsModalController', function($scope, $modalInstance, threadDump) {
+    .controller('MetricsModalController', function($scope, $uibModalInstance, threadDump) {
 
         $scope.threadDump = threadDump;
         $scope.threadDumpRunnable = 0;
@@ -25,7 +25,7 @@ angular.module('malariaplantdbApp')
             $scope.threadDumpTimedWaiting + $scope.threadDumpBlocked;
 
         $scope.cancel = function() {
-            $modalInstance.dismiss('cancel');
+            $uibModalInstance.dismiss('cancel');
         };
 
         $scope.getLabelClass = function (threadState) {

diff --git a/src/main/webapp/scripts/app/database/database-detail.controller.js b/src/main/webapp/scripts/app/database/database-detail.controller.js
@@ -8,21 +8,15 @@ angular.module('malariaplantdbApp')
         $scope.ethnology = ethnology;
         $scope.inVivoPharmacos = inVivoPharmacos;
         $scope.inVitroPharmacos = inVitroPharmacos;
+        $scope.otherRemedies = {};
 
-        angular.forEach(pubSummary.plantIngredients, function(key, value){
-            if (angular.equals(value.plantIngredientsIds, $stateParams.piIds)) {
-               delete pubSummary.plantIngredients[key];
+        var paramPiIds = $stateParams.piIds.split(",").map(Number);
+
+        angular.forEach(pubSummary.plantIngredients, function(value, key){
+            if (angular.equals(value.plantIngredientsIds, paramPiIds)) {
+                $scope.plantIngredientsStr = key;
+            } else {
+                $scope.otherRemedies[key] = value;
             }
         });
-        $scope.pubSummary = pubSummary.plantIngredients;
-
-        var plantIngredients = ethnology ? ethnology.plantIngredients :
-            (inVivoPharmacos.length > 0 ? inVivoPharmacos[0].plantIngredients :
-                (inVitroPharmacos.length > 0 ? inVitroPharmacos[0].plantIngredients : null));
-
-        $scope.plantIngredientsStr = plantIngredients && plantIngredients.length > 0 ?
-            plantIngredients.map(
-                function(o) {return o.species.family + ' ' + o.species.species + ', ' + o.partUsed}
-            ).join(" / ") :
-            pubSpecies[0].species.family + " " + pubSpecies[0].species.species;
     });
diff --git a/src/main/webapp/scripts/app/database/database-detail.html b/src/main/webapp/scripts/app/database/database-detail.html
@@ -345,32 +345,34 @@ <h3>Details for <small>&laquo;	{{plantIngredientsStr}} &raquo;</small></h3><br/>
                                                 </div>
                                                 <div class="col-xs-6 col-sm-6 col-md-2 property-label properties-col">
                                                     Measure method
+                                                </div>
                                                 <div class="col-xs-6 col-sm-6 col-md-2 properties-col">
                                                     {{ivt.measureMethod | placeholder}}
                                                 </div>
-                                                <div ng-if="ivt.screeningTest != 'Toxicity && ivt.concentration'"
+                                                <div ng-if="ivt.screeningTest != 'Toxicity' && ivt.concentration"
                                                      class="col-xs-6 col-sm-6 col-md-2 property-label properties-col">
                                                     Concentration for selected result <small>(&micro;g/kg)</small>
                                                 </div>
-                                                <div ng-if="ivt.screeningTest != 'Toxicity && ivt.concentration'"
+                                                <div ng-if="ivt.screeningTest != 'Toxicity' && ivt.concentration"
                                                      class="col-xs-6 col-sm-6 col-md-2 properties-col">
                                                     {{ivt.concentration | placeholder}}
                                                 </div>
-                                                <div ng-if="ivt.screeningTest != 'Toxicity && ivt.molConcentration'"
+                                                <div ng-if="ivt.screeningTest != 'Toxicity' && ivt.molConcentration"
                                                      class="col-xs-6 col-sm-6 col-md-2 property-label properties-col">
                                                     Concentration for selected result <small>(&micro;mol/kg)</small>
                                                 </div>
-                                                <div ng-if="ivt.screeningTest != 'Toxicity && ivt.molConcentration'"
+                                                <div ng-if="ivt.screeningTest != 'Toxicity' && ivt.molConcentration"
                                                      class="col-xs-6 col-sm-6 col-md-2 properties-col">
                                                     {{ivt.concentration | placeholder}}
                                                 </div>
                                                 <div
-                                                    ng-if="ivt.screeningTest != 'Toxicity && !ivt.concentration &&
+                                                    ng-if="ivt.screeningTest != 'Toxicity' && !ivt.concentration &&
                                                     !ivt.molConcentration"
                                                      class="col-xs-6 col-sm-6 col-md-2 property-label properties-col">
                                                     Concentration for selected result
                                                 </div>
-                                                <div ng-if="ivt.screeningTest != 'Toxicity && ivt.molConcentration'"
+                                                <div ng-if="ivt.screeningTest != 'Toxicity' && !ivt.concentration &&
+                                                    !ivt.molConcentration"
                                                      class="col-xs-6 col-sm-6 col-md-2 properties-col">
                                                     {{null | placeholder}}
                                                 </div>
@@ -445,11 +447,11 @@ <h3>Details for <small>&laquo;	{{plantIngredientsStr}} &raquo;</small></h3><br/>
         <!-- OTHER INGREDIENTS -->
         <div ng-if="pubSummary.plantIngredients.length" class="row">
             <div class="col-xs-12 col-sm-12 col-md-12 review-label">
-                Other ingredients
+                Other remedy compositions
             </div>
         </div>
-        <div class="row ingredients-item" ng-repeat="(pi, piTests) in pubSummary.plantIngredients">
-            <summary publication="pub" plant-ingredient-str="pi" pi-summary="piTests"></summary>
+        <div class="row ingredients-item" ng-repeat="(pi, piTests) in otherRemedies">
+            <summary publication="publication" plant-ingredient-str="pi" pi-summary="piTests"></summary>
         </div>
     </div>
 </div>
diff --git a/src/main/webapp/scripts/app/entities/author/author-dialog.controller.js b/src/main/webapp/scripts/app/entities/author/author-dialog.controller.js
@@ -1,8 +1,8 @@
 'use strict';
 
 angular.module('malariaplantdbApp').controller('AuthorDialogController',
-    ['$scope', '$stateParams', '$modalInstance', 'entity', 'Author', 'Publication',
-        function ($scope, $stateParams, $modalInstance, entity, Author, Publication) {
+    ['$scope', '$stateParams', '$uibModalInstance', 'entity', 'Author', 'Publication',
+        function ($scope, $stateParams, $uibModalInstance, entity, Author, Publication) {
 
         $scope.author = entity;
         $scope.publications = Publication.sortedQuery();
@@ -14,7 +14,7 @@ angular.module('malariaplantdbApp').controller('AuthorDialogController',
 
         var onSaveFinished = function (result) {
             $scope.$emit('malariaplantdbApp:authorUpdate', result);
-            $modalInstance.close(result);
+            $uibModalInstance.close(result);
         };
 
         $scope.save = function () {
@@ -26,6 +26,6 @@ angular.module('malariaplantdbApp').controller('AuthorDialogController',
         };
 
         $scope.clear = function() {
-            $modalInstance.dismiss('cancel');
+            $uibModalInstance.dismiss('cancel');
         };
 }]);
diff --git a/src/main/webapp/scripts/app/entities/author/author.js b/src/main/webapp/scripts/app/entities/author/author.js
@@ -44,8 +44,8 @@ angular.module('malariaplantdbApp')
                 data: {
                     authorities: ['ROLE_USER'],
                 },
-                onEnter: ['$stateParams', '$state', '$modal', function($stateParams, $state, $modal) {
-                    $modal.open({
+                onEnter: ['$stateParams', '$state', '$uibModal', function($stateParams, $state, $uibModal) {
+                    $uibModal.open({
                         templateUrl: 'scripts/app/entities/author/author-dialog.html',
                         controller: 'AuthorDialogController',
                         size: 'lg',
@@ -67,8 +67,8 @@ angular.module('malariaplantdbApp')
                 data: {
                     authorities: ['ROLE_USER'],
                 },
-                onEnter: ['$stateParams', '$state', '$modal', function($stateParams, $state, $modal) {
-                    $modal.open({
+                onEnter: ['$stateParams', '$state', '$uibModal', function($stateParams, $state, $uibModal) {
+                    $uibModal.open({
                         templateUrl: 'scripts/app/entities/author/author-dialog.html',
                         controller: 'AuthorDialogController',
                         size: 'lg',

diff --git a/src/main/webapp/scripts/app/entities/compiler/compiler-dialog.controller.js b/src/main/webapp/scripts/app/entities/compiler/compiler-dialog.controller.js
@@ -1,8 +1,8 @@
 'use strict';
 
 angular.module('malariaplantdbApp').controller('CompilerDialogController',
-    ['$scope', '$stateParams', '$modalInstance', 'entity', 'Compiler',
-        function($scope, $stateParams, $modalInstance, entity, Compiler) {
+    ['$scope', '$stateParams', '$uibModalInstance', 'entity', 'Compiler',
+        function($scope, $stateParams, $uibModalInstance, entity, Compiler) {
 
         $scope.compiler = entity;
         $scope.load = function(id) {
@@ -13,7 +13,7 @@ angular.module('malariaplantdbApp').controller('CompilerDialogController',
 
         var onSaveFinished = function (result) {
             $scope.$emit('malariaplantdbApp:compilerUpdate', result);
-            $modalInstance.close(result);
+            $uibModalInstance.close(result);
         };
 
         $scope.save = function () {
@@ -25,6 +25,6 @@ angular.module('malariaplantdbApp').controller('CompilerDialogController',
         };
 
         $scope.clear = function() {
-            $modalInstance.dismiss('cancel');
+            $uibModalInstance.dismiss('cancel');
         };
 }]);
diff --git a/src/main/webapp/scripts/app/entities/compiler/compiler.js b/src/main/webapp/scripts/app/entities/compiler/compiler.js
@@ -44,8 +44,8 @@ angular.module('malariaplantdbApp')
                 data: {
                     authorities: ['ROLE_USER'],
                 },
-                onEnter: ['$stateParams', '$state', '$modal', function($stateParams, $state, $modal) {
-                    $modal.open({
+                onEnter: ['$stateParams', '$state', '$uibModal', function($stateParams, $state, $uibModal) {
+                    $uibModal.open({
                         templateUrl: 'scripts/app/entities/compiler/compiler-dialog.html',
                         controller: 'CompilerDialogController',
                         size: 'lg',
@@ -67,8 +67,8 @@ angular.module('malariaplantdbApp')
                 data: {
                     authorities: ['ROLE_USER'],
                 },
-                onEnter: ['$stateParams', '$state', '$modal', function($stateParams, $state, $modal) {
-                    $modal.open({
+                onEnter: ['$stateParams', '$state', '$uibModal', function($stateParams, $state, $uibModal) {
+                    $uibModal.open({
                         templateUrl: 'scripts/app/entities/compiler/compiler-dialog.html',
                         controller: 'CompilerDialogController',
                         size: 'lg',

diff --git a/src/main/webapp/scripts/app/entities/ethnology/ethnology-dialog.controller.js b/src/main/webapp/scripts/app/entities/ethnology/ethnology-dialog.controller.js
@@ -1,8 +1,8 @@
 'use strict';
 
 angular.module('malariaplantdbApp').controller('EthnologyDialogController',
-    ['$scope', '$stateParams', '$modalInstance', 'entity', 'Ethnology', 'Publication', 'PlantIngredient',
-        function($scope, $stateParams, $modalInstance, entity, Ethnology, Publication, PlantIngredient) {
+    ['$scope', '$stateParams', '$uibModalInstance', 'entity', 'Ethnology', 'Publication', 'PlantIngredient',
+        function($scope, $stateParams, $uibModalInstance, entity, Ethnology, Publication, PlantIngredient) {
 
         $scope.ethnology = entity;
         $scope.publications = Publication.sortedQuery();
@@ -15,7 +15,7 @@ angular.module('malariaplantdbApp').controller('EthnologyDialogController',
 
         var onSaveFinished = function (result) {
             $scope.$emit('malariaplantdbApp:ethnologyUpdate', result);
-            $modalInstance.close(result);
+            $uibModalInstance.close(result);
         };
 
         $scope.save = function () {
@@ -27,6 +27,6 @@ angular.module('malariaplantdbApp').controller('EthnologyDialogController',
         };
 
         $scope.clear = function() {
-            $modalInstance.dismiss('cancel');
+            $uibModalInstance.dismiss('cancel');
         };
 }]);
diff --git a/src/main/webapp/scripts/app/entities/ethnology/ethnology.js b/src/main/webapp/scripts/app/entities/ethnology/ethnology.js
@@ -44,8 +44,8 @@ angular.module('malariaplantdbApp')
                 data: {
                     authorities: ['ROLE_USER'],
                 },
-                onEnter: ['$stateParams', '$state', '$modal', function($stateParams, $state, $modal) {
-                    $modal.open({
+                onEnter: ['$stateParams', '$state', '$uibModal', function($stateParams, $state, $uibModal) {
+                    $uibModal.open({
                         templateUrl: 'scripts/app/entities/ethnology/ethnology-dialog.html',
                         controller: 'EthnologyDialogController',
                         size: 'lg',
@@ -67,8 +67,8 @@ angular.module('malariaplantdbApp')
                 data: {
                     authorities: ['ROLE_USER'],
                 },
-                onEnter: ['$stateParams', '$state', '$modal', function($stateParams, $state, $modal) {
-                    $modal.open({
+                onEnter: ['$stateParams', '$state', '$uibModal', function($stateParams, $state, $uibModal) {
+                    $uibModal.open({
                         templateUrl: 'scripts/app/entities/ethnology/ethnology-dialog.html',
                         controller: 'EthnologyDialogController',
                         size: 'lg',