- add the docker folder to deploy in production

- fix a lazy not initialized publication field in the listing of authors

Gruntfile.js

@@ -152,8 +152,8 @@ module.exports = function (grunt) {
                     src: [
                         '<%= yeoman.dist %>/scripts/**/*.js',
                         '<%= yeoman.dist %>/assets/styles/**/*.css',
-                        '<%= yeoman.dist %>/assets/images/**/*.{png,jpg,jpeg,gif,webp,svg}'//,
-                        //'<%= yeoman.dist %>/assets/fonts/*'
+                        '<%= yeoman.dist %>/assets/images/**/*.{png,jpg,jpeg,gif,webp,svg}',
+                        '<%= yeoman.dist %>/assets/fonts/*'
                     ]
                 }
             }
@@ -166,7 +166,8 @@ module.exports = function (grunt) {
                     html: {
                         steps: {
                             js: ['concat', 'uglifyjs'],
-                            css: ['cssmin', useminAutoprefixer] // Let cssmin concat files so it corrects relative paths to fonts and images
+                            css: ['cssmin']//, useminAutoprefixer] // Let cssmin concat files so it corrects
+                            // relative paths to fonts and images
                         },
                         post: {}
                     }
@@ -268,8 +269,8 @@ module.exports = function (grunt) {
                     src: [
                         '*.html',
                         'scripts/**/*.html',
-                        'assets/images/**/*.{png,gif,webp,jpg,jpeg,svg}'
-                        //'assets/fonts/*'
+                        'assets/images/**/*.{png,gif,webp,jpg,jpeg,svg}',
+                        'assets/fonts/*'
                     ]
                 }, {
                     expand: true,

README.md

@@ -55,8 +55,9 @@ Then navigate to [http://localhost:8080](http://localhost:8080) in your browser.
    cd docker/test
    docker-compose build
 
+   mkdir /data
    mkdir /data/postgres -R
    mkdir /data/es-data
-   sudo chown 999:999 es-data/
+   sudo chown 999:999 /data/es-data/
 
 

docker/prod/docker-compose.yml

@@ -15,6 +15,8 @@ services:
             - MAIL_HOST= smtp.ird.nc
             - MAIL_PORT= 25
         env_file: ./malariaplantdb-web.env
+        # please define the variables POSTGRES_USER, POSTGRES_PASSWORD, MAIL_USERNAME and MAIL_PASSWORD in the
+        # malariaplantdb-web.env file.
         # example of the environment file content :
         # POSTGRES_USER=malariaplantdb
         # POSTGRES_PASSWORD=mpdb
@@ -28,9 +30,6 @@ services:
             - /data/postgresql:/var/lib/postgresql/data
         ports:
             - "5432:5432"
-        environment:
-            - POSTGRES_USER=malariaplantdb
-            - POSTGRES_PASSWORD=mpdb
         env_file: ./malariaplantdb-db.env
         # please define the variables POSTGRES_USER and POSTGRES_PASSWORD in the malariaplantdb-db.env file.
         # example of the environment file content :
@@ -39,12 +38,11 @@ services:
 
     elasticsearch:
         container_name: malariaplantdb-es
-        image: elasticsearch:5.6.5
+        image: itzg/elasticsearch:1.3
         volumes:
-            - /data/es-data:/usr/share/elasticsearch/data
+            - /data/es-data:/data
         ports:
             - "9200:9200"
             - "9300:9300"
         environment:
-            - cluster.name=malariaplantdb-cluster
-            - ES_JAVA_OPTS=-Xms1g -Xmx1g
+            - CLUSTER=malariaplantdb-cluster

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

@@ -16,7 +16,7 @@ public interface InVitroPharmacoRepository extends JpaRepository<InVitroPharmaco
 
     List<InVitroPharmaco> findByPublicationId(Long id);
 
-    // Other method to fetch the authors and compilers relationships, but as it's by a join, the firsResult and
+    // Other method to fetch the authors and compilers relationships, but as it's by a join, the firstResult and
     // maxResults are applied in memory
     //@Query("select distinct inVitroPharmaco from InVitroPharmaco inVitroPharmaco  left join fetch inVitroPharmaco" +
     //    ".plantIngredients")

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

@@ -14,6 +14,7 @@
 import org.springframework.http.HttpStatus;
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
+import org.springframework.transaction.annotation.Transactional;
 import org.springframework.web.bind.annotation.*;
 
 import javax.inject.Inject;
@@ -87,9 +88,12 @@ public ResponseEntity<Author> updateAuthor(@Valid @RequestBody Author author) th
             method = RequestMethod.GET,
             produces = MediaType.APPLICATION_JSON_VALUE)
     @Timed
+    @Transactional(readOnly = true)
     public ResponseEntity<List<Author>> getAllAuthors(Pageable pageable)
         throws URISyntaxException {
         Page<Author> page = authorRepository.findAll(pageable);
+        // eagerly load the association
+        page.getContent().stream().forEach(author -> author.getPublication().getTitle());
         HttpHeaders headers = PaginationUtil.generatePaginationHttpHeaders(page, "/api/authors");
         return new ResponseEntity<>(page.getContent(), headers, HttpStatus.OK);
     }
@@ -101,11 +105,15 @@ public ResponseEntity<List<Author>> getAllAuthors(Pageable pageable)
             method = RequestMethod.GET,
             produces = MediaType.APPLICATION_JSON_VALUE)
     @Timed
+    @Transactional(readOnly = true)
     public ResponseEntity<Author> getAuthor(@PathVariable Long id) {
         log.debug("REST request to get Author : {}", id);
-        return Optional.ofNullable(authorRepository.findOne(id))
-            .map(author -> new ResponseEntity<>(
-                author,
+        Author author = authorRepository.findOne(id);
+        // eagerly load the association
+        author.getPublication().getTitle();
+        return Optional.ofNullable(author)
+            .map(aut -> new ResponseEntity<>(
+                aut,
                 HttpStatus.OK))
             .orElse(new ResponseEntity<>(HttpStatus.NOT_FOUND));
     }

src/main/resources/config/application-prod.yml

@@ -35,7 +35,8 @@ spring:
             hibernate.cache.region.factory_class: org.hibernate.cache.ehcache.SingletonEhCacheRegionFactory
     data:
         elasticsearch:
-            cluster-nodes: {ELASTICSEARCH_HOST}:9300
+            cluster-name: ${ELASTICSEARCH_CLUSTER}
+            cluster-nodes: ${ELASTICSEARCH_HOST}:9300
     mail:
         host: ${MAIL_HOST}
         port: ${MAIL_PORT}