database interface ok

begin of database-detail interface (request the data, no good display for the moment)
acheype · Apr 11, 2017 · 94b657e · 94b657e
1 parent ac6338e
commit 94b657e
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diff --git a/src/main/java/nc/ird/malariaplantdb/repository/EthnologyRepository.java b/src/main/java/nc/ird/malariaplantdb/repository/EthnologyRepository.java
@@ -2,6 +2,8 @@
 
 import nc.ird.malariaplantdb.domain.Ethnology;
 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;
 
@@ -20,4 +22,8 @@ public interface EthnologyRepository extends JpaRepository<Ethnology,Long> {
     // .id =:id")
     //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>
+        piIds);
+
 }
diff --git a/src/main/java/nc/ird/malariaplantdb/repository/InVivoPharmacoRepository.java b/src/main/java/nc/ird/malariaplantdb/repository/InVivoPharmacoRepository.java
@@ -2,6 +2,8 @@
 
 import nc.ird.malariaplantdb.domain.InVivoPharmaco;
 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;
 
@@ -22,4 +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")
+    List<InVivoPharmaco> findByPublicationIdAndPlantIngredients(@Param("pubId") Long pubId, @Param("piIds") List<Long>
+        piIds);
 }
diff --git a/src/main/java/nc/ird/malariaplantdb/repository/PubSpeciesRepository.java b/src/main/java/nc/ird/malariaplantdb/repository/PubSpeciesRepository.java
@@ -2,6 +2,8 @@
 
 import nc.ird.malariaplantdb.domain.PubSpecies;
 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;
 
@@ -12,4 +14,8 @@ public interface PubSpeciesRepository extends JpaRepository<PubSpecies,Long> {
 
     List<PubSpecies> findByPublicationId(Long id);
 
+    @Query("select ps from PubSpecies ps, PlantIngredient pi join ps.species s join pi.species s2 where ps.publication.id = :pubId and s.id = s2.id and pi.id in :piIds")
+    List<PubSpecies> findByPublicationIdAndPlantIngredients(@Param("pubId") Long pubId, @Param("piIds") List<Long>
+        piIds);
+
 }
diff --git a/src/main/java/nc/ird/malariaplantdb/repository/SpeciesRepository.java b/src/main/java/nc/ird/malariaplantdb/repository/SpeciesRepository.java
@@ -1,9 +1,7 @@
 package nc.ird.malariaplantdb.repository;
 
 import nc.ird.malariaplantdb.domain.Species;
-import org.springframework.data.jpa.repository.*;
-
-import java.util.List;
+import org.springframework.data.jpa.repository.JpaRepository;
 
 /**
  * Spring Data JPA repository for the Species entity.

diff --git a/src/main/java/nc/ird/malariaplantdb/service/PublicationService.java b/src/main/java/nc/ird/malariaplantdb/service/PublicationService.java
@@ -0,0 +1,38 @@
+package nc.ird.malariaplantdb.service;
+
+import nc.ird.malariaplantdb.domain.Publication;
+import nc.ird.malariaplantdb.domain.util.CitationConverter;
+import nc.ird.malariaplantdb.repository.PublicationRepository;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.stereotype.Service;
+import org.springframework.transaction.annotation.Transactional;
+
+import javax.inject.Inject;
+
+/**
+ * Service for the Publication entity
+ */
+@Service
+@Transactional
+public class PublicationService {
+
+    private final Logger log = LoggerFactory.getLogger(PublicationService.class);
+
+    @Inject
+    private PublicationRepository publicationRepository;
+
+    /**
+     * Save a publication entity which the citation has been set
+     *
+     * @param publication the publication to save
+     * @return the saved publication
+     */
+    public Publication save(Publication publication){
+
+        CitationConverter converter = new CitationConverter();
+        publication.setCitation(converter.convert(publication));
+
+        return publicationRepository.save(publication);
+    }
+}
diff --git a/src/main/java/nc/ird/malariaplantdb/web/rest/EthnologyResource.java b/src/main/java/nc/ird/malariaplantdb/web/rest/EthnologyResource.java
@@ -123,6 +123,22 @@ public ResponseEntity<List<Ethnology>> getEthnologiesByPublicationId(@PathVariab
         return new ResponseEntity<>(ethnologies,  HttpStatus.OK);
     }
 
+    /**
+     * GET  /publications/:pubId/pi/:piIds/ethnologies -> get all the ethnologies with the "id" publication and the
+     * list of plant ingredient ids
+     */
+    @RequestMapping(value = "/publications/{pubId}/pi/{piIds}/ethnologies",
+        method = RequestMethod.GET,
+        produces = MediaType.APPLICATION_JSON_VALUE)
+    @Timed
+    public ResponseEntity<List<Ethnology>> getEthnologiesByPubIdAndPiIds(@PathVariable Long pubId, @PathVariable
+    List<Long> piIds) {
+        log.debug("REST request to get the Ethnologies 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);
+    }
+
     /**
      * DELETE  /ethnologies/:id -> delete the "id" ethnology.
      */

diff --git a/src/main/java/nc/ird/malariaplantdb/web/rest/InVitroPharmacoResource.java b/src/main/java/nc/ird/malariaplantdb/web/rest/InVitroPharmacoResource.java
@@ -113,7 +113,7 @@ public ResponseEntity<InVitroPharmaco> getInVitroPharmaco(@PathVariable Long id)
     /**
      * GET  /publications/:id/invitropharmacos -> get all the inVitroPharmacos of the "id" publication.
      */
-    @RequestMapping(value = "/publications/{id}/invitropharmacos",
+    @RequestMapping(value = "/publ/{id}/invitropharmacos",
         method = RequestMethod.GET,
         produces = MediaType.APPLICATION_JSON_VALUE)
     @Timed

diff --git a/src/main/java/nc/ird/malariaplantdb/web/rest/InVivoPharmacoResource.java b/src/main/java/nc/ird/malariaplantdb/web/rest/InVivoPharmacoResource.java
@@ -111,18 +111,35 @@ public ResponseEntity<InVivoPharmaco> getInVivoPharmaco(@PathVariable Long id) {
     }
 
     /**
-     * GET  /publications/:id/invivopharmacos -> get all the inVivoPharmacos of the "id" publication.
+     * GET  /publications/:id/inVivoPharmacos -> get all the inVivoPharmacos of the "id" publication.
      */
-    @RequestMapping(value = "/publications/{id}/invivopharmacos",
+    @RequestMapping(value = "/pub/{id}/inVivoPharmacos",
         method = RequestMethod.GET,
         produces = MediaType.APPLICATION_JSON_VALUE)
     @Timed
     public ResponseEntity<List<InVivoPharmaco>> getInVivoPharmacosByPublicationId(@PathVariable Long id) {
-        log.debug("REST request to get the inVivoPharmacos of the Publication : {}", id);
-        List<InVivoPharmaco> invivopharmacos = inVivoPharmacoRepository.findByPublicationId(id);
-        return new ResponseEntity<>(invivopharmacos, HttpStatus.OK);
+        log.debug("REST request to get the InVivoPharmacos of the Publication : {}", id);
+        List<InVivoPharmaco> inVivoPharmacos = inVivoPharmacoRepository.findByPublicationId(id);
+        return new ResponseEntity<>(inVivoPharmacos, HttpStatus.OK);
     }
 
+    /**
+     * GET  /publications/:pubId/pi/:piIds/inVivoPharmacos -> get all the inVivoPharmacos with the "id" publication and the
+     * list of plant ingredient ids
+     */
+    @RequestMapping(value = "/publications/{pubId}/pi/{piIds}/inVivoPharmacos",
+        method = RequestMethod.GET,
+        produces = MediaType.APPLICATION_JSON_VALUE)
+    @Timed
+    public ResponseEntity<List<InVivoPharmaco>> getEthnologiesByPubIdAndPiIds(@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.
      */

diff --git a/src/main/java/nc/ird/malariaplantdb/web/rest/PubSpeciesResource.java b/src/main/java/nc/ird/malariaplantdb/web/rest/PubSpeciesResource.java
@@ -123,6 +123,22 @@ public ResponseEntity<List<PubSpecies>> getPubSpeciesByPublicationId(@PathVariab
         return new ResponseEntity<>(pubSpecies,  HttpStatus.OK);
     }
 
+    /**
+     * GET  /publications/:pubId/pi/:piIds/ethnologies -> get all the pubSpecies with the "id" publication and the
+     * list of plant ingredient ids
+     */
+    @RequestMapping(value = "/publications/{pubId}/pi/{piIds}/pubSpecies",
+        method = RequestMethod.GET,
+        produces = MediaType.APPLICATION_JSON_VALUE)
+    @Timed
+    public ResponseEntity<List<PubSpecies>> getPubSpeciesByPubIdAndPiIds(@PathVariable Long pubId, @PathVariable
+    List<Long> piIds) {
+        log.debug("REST request to get the PubSpecies of the Publication : {}, and the PlantIngredient(s) : {}",
+            pubId, piIds.stream().map(id -> id.toString()).collect(Collectors.joining(",")));
+        List<PubSpecies> pubSpecies = pubSpeciesRepository.findByPublicationIdAndPlantIngredients(pubId, piIds);
+        return new ResponseEntity<>(pubSpecies,  HttpStatus.OK);
+    }
+
     /**
      * DELETE  /pubSpecies/:id -> delete the "id" pubSpecies.
      */

diff --git a/src/main/java/nc/ird/malariaplantdb/web/rest/dto/PISummaryDTO.java b/src/main/java/nc/ird/malariaplantdb/web/rest/dto/PISummaryDTO.java
@@ -1,6 +1,7 @@
 package nc.ird.malariaplantdb.web.rest.dto;
 
 import java.math.BigDecimal;
+import java.util.List;
 
 /**
  * Plant Ingredient summary used to display the publications list
@@ -31,6 +32,8 @@ public enum TestType {
 
     public final static String ERYTHROCYT_TXT = "erythrocyt";
 
+    private List<Long> plantIngredientsIds;
+
     private boolean isInVivo = false;
 
     private boolean isInVivoPeters = false;
@@ -71,6 +74,10 @@ public enum TestType {
 
     private boolean isInVitroToxicity = false;
 
+    public PISummaryDTO(List<Long> plantIngredientsIds) {
+        this.plantIngredientsIds = plantIngredientsIds;
+    }
+
     public void setTestedEntity(TestType testType, String screeningTest, BigDecimal inVivoInhibition, BigDecimal
         inVivoEd50, BigDecimal inVitroInhibition, BigDecimal inVitroIC50, BigDecimal inVitroMolIc50){
         if (TestType.IN_VIVO.equals(testType))
@@ -135,6 +142,14 @@ public void setTestedEntity(TestType testType, String screeningTest, BigDecimal
         }
     }
 
+    public List<Long> getPlantIngredientsIds() {
+        return plantIngredientsIds;
+    }
+
+    public void setPlantIngredientsIds(List<Long> plantIngredientsIds) {
+        this.plantIngredientsIds = plantIngredientsIds;
+    }
+
     public boolean isInVivo() {
         return isInVivo;
     }

diff --git a/src/main/java/nc/ird/malariaplantdb/web/rest/dto/PubSummaryDTO.java b/src/main/java/nc/ird/malariaplantdb/web/rest/dto/PubSummaryDTO.java
@@ -2,10 +2,7 @@
 
 import nc.ird.malariaplantdb.domain.*;
 
-import java.util.SortedMap;
-import java.util.SortedSet;
-import java.util.TreeMap;
-import java.util.TreeSet;
+import java.util.*;
 import java.util.stream.Collectors;
 
 /**
@@ -15,6 +12,8 @@
  */
 public class PubSummaryDTO {
 
+    private Long id;
+
     private String citation;
 
     private String doi;
@@ -30,6 +29,7 @@ public class PubSummaryDTO {
     private SortedMap<String, PISummaryDTO> plantIngredients = new TreeMap<>();
 
     public PubSummaryDTO(Publication pub) {
+        id = pub.getId();
         citation = pub.getCitation();
         doi = pub.getDoi();
         pmid = pub.getPmid();
@@ -43,8 +43,11 @@ public PubSummaryDTO(Publication pub) {
         for (InVivoPharmaco inVivoPharmaco : pub.getInVivoPharmacos()){
             String plantIngredientStr = buildPlantIngredientsKey(inVivoPharmaco.getPlantIngredients());
 
-            if (!plantIngredients.containsKey(plantIngredientStr))
-                plantIngredients.put(plantIngredientStr, new PISummaryDTO());
+            if (!plantIngredients.containsKey(plantIngredientStr)) {
+                List<Long> plantIngredientsIds = inVivoPharmaco.getPlantIngredients().stream().map(pi -> pi.getId())
+                    .collect(Collectors.toList());
+                plantIngredients.put(plantIngredientStr, new PISummaryDTO(plantIngredientsIds));
+            }
 
             plantIngredients.get(plantIngredientStr).setTestedEntity(PISummaryDTO.TestType.IN_VIVO,
                 inVivoPharmaco.getScreeningTest(), inVivoPharmaco.getInhibition(), inVivoPharmaco.getEd50(), null,
@@ -54,8 +57,11 @@ public PubSummaryDTO(Publication pub) {
         for (InVitroPharmaco inVitroPharmaco : pub.getInVitroPharmacos()){
             String plantIngredientStr = buildPlantIngredientsKey(inVitroPharmaco.getPlantIngredients());
 
-            if (!plantIngredients.containsKey(plantIngredientStr))
-                plantIngredients.put(plantIngredientStr, new PISummaryDTO());
+            if (!plantIngredients.containsKey(plantIngredientStr)) {
+                List<Long> plantIngredientsIds = inVitroPharmaco.getPlantIngredients().stream().map(pi -> pi.getId())
+                    .collect(Collectors.toList());
+                plantIngredients.put(plantIngredientStr, new PISummaryDTO(plantIngredientsIds));
+            }
 
             plantIngredients.get(plantIngredientStr).setTestedEntity(PISummaryDTO.TestType.IN_VITRO,
                 inVitroPharmaco.getScreeningTest(), null, null, inVitroPharmaco.getInhibition(),
@@ -69,6 +75,14 @@ private String buildPlantIngredientsKey(SortedSet<PlantIngredient> plantIngredie
                     .collect(Collectors.joining(" / "));
     }
 
+    public Long getId() {
+        return id;
+    }
+
+    public void setId(Long id) {
+        this.id = id;
+    }
+
     public String getCitation() {
         return citation;
     }

diff --git a/src/main/resources/hibernate.cfg.xml b/src/main/resources/hibernate.cfg.xml
@@ -0,0 +1,14 @@
+<?xml version='1.0' encoding='utf-8'?>
+<!DOCTYPE hibernate-configuration PUBLIC
+    "-//Hibernate/Hibernate Configuration DTD//EN"
+    "http://www.hibernate.org/dtd/hibernate-configuration-3.0.dtd">
+<hibernate-configuration>
+  <session-factory>
+    <property name="connection.url"/>
+    <property name="connection.driver_class"/>
+    <property name="connection.username"/>
+    <property name="connection.password"/>
+    <!-- DB schema will be updated if needed -->
+    <!-- <property name="hbm2ddl.auto">update</property> -->
+  </session-factory>
+</hibernate-configuration>
diff --git a/src/main/scss/_variables.scss b/src/main/scss/_variables.scss
@@ -65,6 +65,7 @@ $font-family-base:        $font-family-sans-serif !default;
 $font-size-base:          15px !default;
 $font-size-large:         ceil(($font-size-base * 1.25)) !default; // ~18px
 $font-size-small:         ceil(($font-size-base * 0.85)) !default; // ~12px
+$font-size-smaller:       ceil(($font-size-base * 0.75)) !default;
 
 $font-size-h1:            floor(($font-size-base * 2.6)) !default; // ~36px
 $font-size-h2:            floor(($font-size-base * 2.15)) !default; // ~30px