Interface database and database-details finalized (still need some te…

…sts)

bower.json

@@ -4,32 +4,31 @@
   "appPath": "src/main/webapp",
   "testPath": "src/test/javascript/spec",
   "dependencies": {
-    "angular": "1.4.5",
-    "angular-animate": "~1.4.8",
-    "angular-aria": "1.4.5",
-    "angular-bootstrap": "0.13.3",
+    "angular": "1.6.4",
+    "angular-animate": "1.6.4",
+    "angular-aria": "1.6.4",
+    "angular-bootstrap": "2.5.0",
     "angular-cache-buster": "0.4.3",
-    "angular-cookies": "1.4.5",
-    "angular-jqcloud": "1.0.2",
+    "angular-cookies": "1.6.4",
+    "angular-jqcloud": "1.0.3",
     "angular-local-storage": "0.2.2",
-    "angular-resource": "1.4.5",
-    "angular-sanitize": "1.4.5",
-    "angular-ui-router": "0.2.15",
-    "bootstrap-sass": "3.3.5",
-    "bootswatch": "3.3.5",
-    "jquery": "2.1.4",
+    "angular-resource": "1.6.4",
+    "angular-sanitize": "1.6.4",
+    "angular-ui-router": "0.4.2",
+    "angular-touch": "1.6.4",
+    "bootstrap-sass": "3.3.7",
+    "bootswatch": "3.3.7",
     "json3": "3.3.2",
     "modernizr": "2.8.3",
     "ng-file-upload": "7.0.17",
     "swagger-ui": "2.1.2"
   },
   "devDependencies": {
-    "angular-mocks": "1.4.5",
-    "angular-scenario": "1.4.5"
+    "angular-mocks": "1.6.4",
+    "angular-scenario": "1.6.4"
   },
   "resolutions": {
-    "angular": "1.4.5",
-    "angular-cookies": "1.4.5",
-    "jquery": "2.1.4"
+    "angular": "1.6.4",
+    "angular-cookies": "1.6.4"
   }
 }

src/main/java/nc/ird/malariaplantdb/repository/EthnologyRepository.java

@@ -23,7 +23,7 @@ public interface EthnologyRepository extends JpaRepository<Ethnology,Long> {
     //Ethnology findOneWithEagerRelationships(@Param("id") Long id);
 
     @Query("select e from Ethnology e join e.plantIngredients pi where e.publication.id = :pubId and pi.id in :piIds")
-    List<Ethnology> findByPublicationIdAndPlantIngredients(@Param("pubId") Long pubId, @Param("piIds") List<Long>
+    Ethnology findByPublicationIdAndPlantIngredients(@Param("pubId") Long pubId, @Param("piIds") List<Long>
         piIds);
 
 }

src/main/java/nc/ird/malariaplantdb/repository/InVitroPharmacoRepository.java

@@ -2,6 +2,8 @@
 
 import nc.ird.malariaplantdb.domain.InVitroPharmaco;
 import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.jpa.repository.Query;
+import org.springframework.data.repository.query.Param;
 
 import java.util.List;
 
@@ -21,4 +23,8 @@ 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")
+    List<InVitroPharmaco> findByPublicationIdAndPlantIngredients(@Param("pubId") Long pubId, @Param("piIds") List<Long>
+        piIds);
+
 }

src/main/java/nc/ird/malariaplantdb/repository/InVivoPharmacoRepository.java

@@ -27,4 +27,5 @@ public interface InVivoPharmacoRepository extends JpaRepository<InVivoPharmaco,L
     @Query("select 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);
+
 }

src/main/java/nc/ird/malariaplantdb/web/rest/EthnologyResource.java

@@ -124,19 +124,23 @@ public ResponseEntity<List<Ethnology>> getEthnologiesByPublicationId(@PathVariab
     }
 
     /**
-     * GET  /publications/:pubId/pi/:piIds/ethnologies -> get all the ethnologies with the "id" publication and the
+     * GET  /publications/:pubId/pi/:piIds/ethnology -> get the ethnology with the "id" publication and the
      * list of plant ingredient ids
      */
-    @RequestMapping(value = "/publications/{pubId}/pi/{piIds}/ethnologies",
+    @RequestMapping(value = "/publications/{pubId}/pi/{piIds}/ethnology",
         method = RequestMethod.GET,
         produces = MediaType.APPLICATION_JSON_VALUE)
     @Timed
-    public ResponseEntity<List<Ethnology>> getEthnologiesByPubIdAndPiIds(@PathVariable Long pubId, @PathVariable
+    public ResponseEntity<Ethnology> getEthnologyByPubIdAndPiIds(@PathVariable Long pubId, @PathVariable
     List<Long> piIds) {
-        log.debug("REST request to get the Ethnologies of the Publication : {}, and the PlantIngredient(s) : {}",
+        log.debug("REST request to get the Ethnologiy of the Publication : {}, and the PlantIngredient(s) : {}",
             pubId, piIds.stream().map(id -> id.toString()).collect(Collectors.joining(",")));
-        List<Ethnology> ethnologies = ethnologyRepository.findByPublicationIdAndPlantIngredients(pubId, piIds);
-        return new ResponseEntity<>(ethnologies,  HttpStatus.OK);
+
+        return Optional.ofNullable(ethnologyRepository.findByPublicationIdAndPlantIngredients(pubId, piIds))
+            .map(ethnology -> new ResponseEntity<>(
+                ethnology,
+                HttpStatus.OK))
+            .orElse(new ResponseEntity<>(HttpStatus.NOT_FOUND));
     }
 
     /**

src/main/java/nc/ird/malariaplantdb/web/rest/InVitroPharmacoResource.java

@@ -123,6 +123,24 @@ public ResponseEntity<List<InVitroPharmaco>> getInVitroPharmacosByPublicationId(
         return new ResponseEntity<>(invitropharmacos, HttpStatus.OK);
     }
 
+    /**
+     * GET  /publications/:pubId/pi/:piIds/inVitroPharmacos -> get all the inVitroPharmacos with the "id" publication
+     * and the list of plant ingredient ids
+     */
+    @RequestMapping(value = "/publications/{pubId}/pi/{piIds}/inVitroPharmacos",
+        method = RequestMethod.GET,
+        produces = MediaType.APPLICATION_JSON_VALUE)
+    @Timed
+    public ResponseEntity<List<InVitroPharmaco>> getInVitroPharmacosByPubIdAndPiIds(@PathVariable Long pubId,
+                                                                                  @PathVariable
+    List<Long> piIds) {
+        log.debug("REST request to get the InVitroPharmaco of the Publication : {}, and the PlantIngredient(s) : {}",
+            pubId, piIds.stream().map(id -> id.toString()).collect(Collectors.joining(",")));
+        List<InVitroPharmaco> inVitroPharmacos = inVitroPharmacoRepository.findByPublicationIdAndPlantIngredients
+            (pubId, piIds);
+        return new ResponseEntity<>(inVitroPharmacos,  HttpStatus.OK);
+    }
+
     /**
      * DELETE  /inVitroPharmacos/:id -> delete the "id" inVitroPharmaco.
      */

src/main/java/nc/ird/malariaplantdb/web/rest/InVivoPharmacoResource.java

@@ -131,15 +131,14 @@ public ResponseEntity<List<InVivoPharmaco>> getInVivoPharmacosByPublicationId(@P
         method = RequestMethod.GET,
         produces = MediaType.APPLICATION_JSON_VALUE)
     @Timed
-    public ResponseEntity<List<InVivoPharmaco>> getEthnologiesByPubIdAndPiIds(@PathVariable Long pubId, @PathVariable
+    public ResponseEntity<List<InVivoPharmaco>> getInVivoByPubIdAndPiIds(@PathVariable Long pubId, @PathVariable
     List<Long> piIds) {
         log.debug("REST request to get the InVivoPharmaco of the Publication : {}, and the PlantIngredient(s) : {}",
             pubId, piIds.stream().map(id -> id.toString()).collect(Collectors.joining(",")));
         List<InVivoPharmaco> inVivoPharmacos = inVivoPharmacoRepository.findByPublicationIdAndPlantIngredients(pubId, piIds);
         return new ResponseEntity<>(inVivoPharmacos,  HttpStatus.OK);
     }
 
-
     /**
      * DELETE  /inVivoPharmacos/:id -> delete the "id" inVivoPharmaco.
      */

src/main/java/nc/ird/malariaplantdb/web/rest/PublicationResource.java

@@ -132,6 +132,24 @@ public ResponseEntity<Publication> getPublication(@PathVariable Long id) {
             .orElse(new ResponseEntity<>(HttpStatus.NOT_FOUND));
     }
 
+    /**
+     * GET  /pubSummaries/:id -> get the "id" pubSummaries.
+     */
+    @RequestMapping(value = "/pubSummaries/{id}",
+        method = RequestMethod.GET,
+        produces = MediaType.APPLICATION_JSON_VALUE)
+    @Transactional(readOnly = true)
+    @Timed
+    public ResponseEntity<PubSummaryDTO> getPubSummary(@PathVariable Long id) {
+        log.debug("REST request to get Publication : {}", id);
+        return Optional.ofNullable(publicationRepository.findOne(id))
+            .map(publication -> new ResponseEntity<>(
+                new PubSummaryDTO(publication),
+                HttpStatus.OK))
+            .orElse(new ResponseEntity<>(HttpStatus.NOT_FOUND));
+    }
+
+
     /**
      * DELETE  /publications/:id -> delete the "id" publication.
      */

src/main/java/nc/ird/malariaplantdb/web/rest/dto/PubSummaryDTO.java

@@ -71,7 +71,7 @@ public PubSummaryDTO(Publication pub) {
 
     private String buildPlantIngredientsKey(SortedSet<PlantIngredient> plantIngredients) {
         return plantIngredients.stream()
-                    .map(pi -> pi.getSpecies().getFamily() + " " + pi.getSpecies().getSpecies() + ", " + pi.getPartUsed())
+                    .map(pi -> pi.getSpecies().getSpecies() + ", " + pi.getPartUsed())
                     .collect(Collectors.joining(" / "));
     }
 

src/main/scss/main.scss

@@ -402,7 +402,7 @@ ul#strength {
 }
 
 .pub-item {
-    padding: 10px 0px;
+    padding: 10px 10px;
     margin: 0 10px 20px;
     border-left: 5px solid $blue2;
     background-color: #fff;
@@ -419,6 +419,10 @@ ul#strength {
     margin-top: 5px;
 }
 
+.pub-url {
+    margin-right: 10px;
+}
+
 .ingredients-item {
     padding: 5px 5px 0 5px;
     margin: 2px 10px 8px 20px;
@@ -501,7 +505,6 @@ ul#strength {
     .cat-test-tag-block{
         display: block;
     }
-
 }
 
 .cat1-test-tag {
@@ -524,10 +527,79 @@ ul#strength {
     background-color: $red2;
 }
 
+h3 small {
+    font-size: 75%;
+    color: $gray-base;
+}
+
+.publication-label{
+    font-weight: bolder;
+    font-size: $font-size-small;
+    color : $blue2;
+}
+
+.review-label{
+    font-weight: bolder;
+    color: $blue2;
+    margin-top: 20px;
+    margin-bottom: 5px;
+    font-size: $font-size-large;
+}
+
+.btn-review-item{
+    padding: 5px 2px;
+}
+.nav-pills > li.btn-review-item > a {
+    padding: 5px 10px;
+}
+.nav-pills > .active.btn-review-item > a,
+.nav-pills > .active.btn-review-item > a:hover,
+.nav-pills > .active.btn-review-item > a:focus{
+    background-color: $green-super-lighter;
+    color: $green;
+    font-weight: bold;
+}
+
+.pub-item .nav-tabs > li > a {
+    padding: 5px 10px;
+    font-size: $font-size-small;
+}
+
+.cat-properties-label {
+    font-weight: bolder;
+    font-size: $font-size-small;
+    color: $green;
+    margin-top: 5px;
+}
+
+.cat-properties-item {
+    padding: 2px 5px 0 5px;
+    margin: 2px 10px 8px 20px;
+}
+
+.properties-col {
+    border-top: 2px solid $green-super-lighter;
+}
+
+.property-label {
+    font-weight: bolder;
+    font-size: $font-size-small;
+    text-align: right;
+}
+
+.nav-tabs {
+    border-bottom: 4px solid $green-super-lighter;
+}
+
 .top-buffer {
     margin-top: 10px;
 }
+
 .top-little-buffer {
     margin-top: 5px;
 }
+
+.right-buffer {
+    margin-right : 10px;
+}
 /* End of database part */

src/main/webapp/bower_components/angular-animate/.bower.json

@@ -1,19 +1,20 @@
 {
   "name": "angular-animate",
-  "version": "1.4.8",
+  "version": "1.6.4",
+  "license": "MIT",
   "main": "./angular-animate.js",
   "ignore": [],
   "dependencies": {
-    "angular": "1.4.8"
+    "angular": "1.6.4"
   },
   "homepage": "https://github.com/angular/bower-angular-animate",
-  "_release": "1.4.8",
+  "_release": "1.6.4",
   "_resolution": {
     "type": "version",
-    "tag": "v1.4.8",
-    "commit": "cc1d9740059f5e8fd43abf0e2e80695d43b3b6b1"
+    "tag": "v1.6.4",
+    "commit": "a6c7e14a23096348e55a342a8f671466239ed3ab"
   },
-  "_source": "git://github.com/angular/bower-angular-animate.git",
-  "_target": "~1.4.8",
+  "_source": "https://github.com/angular/bower-angular-animate.git",
+  "_target": "1.6.4",
   "_originalSource": "angular-animate"
 }