- Add the search functionnality on the database (to fix : nested obje…

…cts are not indexed) - Add the How to participate menu and two explicative web pages
acheype · Feb 27, 2018 · af9309a · af9309a
1 parent bb6e6df
commit af9309a
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Showing 39 changed files with 735 additions and 78 deletions.
diff --git a/package-lock.json b/package-lock.json
diff --git a/src/main/java/nc/ird/malariaplantdb/domain/Ethnology.java b/src/main/java/nc/ird/malariaplantdb/domain/Ethnology.java
@@ -6,6 +6,8 @@
 import org.hibernate.annotations.CacheConcurrencyStrategy;
 import org.hibernate.annotations.Type;
 import org.springframework.data.elasticsearch.annotations.Document;
+import org.springframework.data.elasticsearch.annotations.Field;
+import org.springframework.data.elasticsearch.annotations.FieldType;
 
 import javax.persistence.*;
 import javax.validation.constraints.NotNull;
@@ -41,30 +43,36 @@ public class Ethnology implements Serializable, Comparable<Ethnology> {
 
     @NotNull
     @ManyToOne(fetch = FetchType.EAGER)
+//    @Field(type = FieldType.Nested)
     private Remedy remedy;
 
     @NotNull
     @Lob
     @Type(type = "org.hibernate.type.StringClobType")
     @Column(name = "ethno_relevancy", nullable = false)
+    @Field(type = FieldType.String)
     private String ethnoRelevancy;
 
     @NotNull
     @Size(max = 255)
     @Column(name = "treatment_type", length = 255, nullable = false)
+    @Field(type = FieldType.String)
     private String treatmentType;
 
     @Lob
     @Type(type = "org.hibernate.type.StringClobType")
     @Column(name = "traditional_recipe_details")
+    @Field(type = FieldType.String)
     private String traditionalRecipeDetails;
 
     @Size(max = 255)
     @Column(name = "preparation_mode", length = 255)
+    @Field(type = FieldType.String)
     private String preparationMode;
 
     @Size(max = 255)
     @Column(name = "administration_route", length = 255)
+    @Field(type = FieldType.String)
     private String administrationRoute;
 
     public Long getId() {

diff --git a/src/main/java/nc/ird/malariaplantdb/domain/InVitroPharmaco.java b/src/main/java/nc/ird/malariaplantdb/domain/InVitroPharmaco.java
@@ -6,6 +6,8 @@
 import org.hibernate.annotations.CacheConcurrencyStrategy;
 import org.hibernate.annotations.Type;
 import org.springframework.data.elasticsearch.annotations.Document;
+import org.springframework.data.elasticsearch.annotations.Field;
+import org.springframework.data.elasticsearch.annotations.FieldType;
 
 import javax.persistence.*;
 import javax.validation.constraints.*;
@@ -42,6 +44,7 @@ public class InVitroPharmaco implements Serializable, Comparable<InVitroPharmaco
 
     @NotNull
     @ManyToOne(fetch = FetchType.EAGER)
+    @Field(type = FieldType.Nested)
     private Remedy remedy;
 
     @NotNull

diff --git a/src/main/java/nc/ird/malariaplantdb/domain/InVivoPharmaco.java b/src/main/java/nc/ird/malariaplantdb/domain/InVivoPharmaco.java
@@ -6,6 +6,8 @@
 import org.hibernate.annotations.CacheConcurrencyStrategy;
 import org.hibernate.annotations.Type;
 import org.springframework.data.elasticsearch.annotations.Document;
+import org.springframework.data.elasticsearch.annotations.Field;
+import org.springframework.data.elasticsearch.annotations.FieldType;
 
 import javax.persistence.*;
 import javax.validation.constraints.*;
@@ -42,6 +44,7 @@ public class InVivoPharmaco implements Serializable, Comparable<InVivoPharmaco>
 
     @NotNull
     @ManyToOne(fetch = FetchType.EAGER)
+    @Field(type = FieldType.Nested)
     private Remedy remedy;
 
     @NotNull

diff --git a/src/main/java/nc/ird/malariaplantdb/domain/PlantIngredient.java b/src/main/java/nc/ird/malariaplantdb/domain/PlantIngredient.java
@@ -6,6 +6,8 @@
 import org.hibernate.annotations.Cache;
 import org.hibernate.annotations.CacheConcurrencyStrategy;
 import org.springframework.data.elasticsearch.annotations.Document;
+import org.springframework.data.elasticsearch.annotations.Field;
+import org.springframework.data.elasticsearch.annotations.FieldType;
 
 import javax.persistence.*;
 import javax.validation.constraints.NotNull;
@@ -40,6 +42,7 @@ public class PlantIngredient implements Serializable, Comparable<PlantIngredient
 
     @NotNull
     @ManyToOne
+    @Field(type = FieldType.Nested)
     private Species species;
 
     @NotNull

diff --git a/src/main/java/nc/ird/malariaplantdb/domain/PubSpecies.java b/src/main/java/nc/ird/malariaplantdb/domain/PubSpecies.java
@@ -5,6 +5,8 @@
 import org.hibernate.annotations.Cache;
 import org.hibernate.annotations.CacheConcurrencyStrategy;
 import org.springframework.data.elasticsearch.annotations.Document;
+import org.springframework.data.elasticsearch.annotations.Field;
+import org.springframework.data.elasticsearch.annotations.FieldType;
 
 import javax.persistence.*;
 import javax.validation.constraints.NotNull;
@@ -40,6 +42,7 @@ public class PubSpecies implements Serializable, Comparable<PubSpecies> {
 
     @NotNull
     @ManyToOne
+    @Field(type = FieldType.Nested)
     private Species species = new Species();
 
     @NotNull

diff --git a/src/main/java/nc/ird/malariaplantdb/domain/Publication.java b/src/main/java/nc/ird/malariaplantdb/domain/Publication.java
@@ -1,11 +1,12 @@
 package nc.ird.malariaplantdb.domain;
 
-import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonPropertyOrder;
 import org.hibernate.annotations.*;
 import org.hibernate.annotations.Cache;
 import org.springframework.data.elasticsearch.annotations.Document;
+import org.springframework.data.elasticsearch.annotations.Field;
+import org.springframework.data.elasticsearch.annotations.FieldType;
 
 import javax.persistence.*;
 import javax.persistence.Entity;
@@ -52,6 +53,7 @@ public class Publication implements Serializable {
     @BatchSize(size = 100)
     @Cache(usage = CacheConcurrencyStrategy.NONSTRICT_READ_WRITE)
     @SortNatural
+    @Field(type = FieldType.Nested)
     private SortedSet<Author> authors = new TreeSet<>();
 
     @NotNull
@@ -63,70 +65,87 @@ public class Publication implements Serializable {
     @NotNull
     @Size(max = 255)
     @Column(name = "title", length = 255, nullable = false)
+    @Field(type = FieldType.String)
     private String title;
 
     @Size(max = 255)
     @Column(name = "journal", length = 255)
+    @Field(type = FieldType.String)
     private String journal;
 
     @Size(max = 255)
     @Column(name = "pages", length = 255)
+    @Field(type = FieldType.String)
     private String pages;
 
     @Size(max = 255)
     @Column(name = "volume", length = 255)
+    @Field(type = FieldType.String)
     private String volume;
 
     @Size(max = 255)
     @Column(name = "nb_of_volumes", length = 255)
+    @Field(type = FieldType.String)
     private String nbOfVolumes;
 
     @Size(max = 255)
     @Column(name = "number", length = 255)
+    @Field(type = FieldType.String)
     private String number;
 
     @Size(max = 255)
     @Column(name = "book_title", length = 255)
+    @Field(type = FieldType.String)
     private String bookTitle;
 
     @Size(max = 255)
     @Column(name = "publisher", length = 255)
+    @Field(type = FieldType.String)
     private String publisher;
 
     @Size(max = 255)
     @Column(name = "edition", length = 255)
+    @Field(type = FieldType.String)
     private String edition;
 
     @Size(max = 255)
     @Column(name = "conference_name", length = 255)
+    @Field(type = FieldType.String)
     private String conferenceName;
 
     @Size(max = 255)
     @Column(name = "conference_place", length = 255)
+    @Field(type = FieldType.String)
     private String conferencePlace;
 
     @Size(max = 255)
     @Column(name = "university", length = 255)
+    @Field(type = FieldType.String)
     private String university;
 
     @Size(max = 255)
     @Column(name = "institution", length = 255)
+    @Field(type = FieldType.String)
     private String institution;
 
     @Size(max = 255)
     @Column(name = "doi", length = 255)
+    @Field(type = FieldType.String)
     private String doi;
 
     @Size(max = 255)
     @Column(name = "pmid", length = 255)
+    @Field(type = FieldType.String)
     private String pmid;
 
     @Size(max = 255)
     @Column(name = "isbn", length = 255)
+    @Field(type = FieldType.String)
     private String isbn;
 
     @Size(max = 255)
     @Column(name = "url", length = 255)
+    @Field(type = FieldType.String)
     private String url;
 
     @ManyToMany(fetch = FetchType.EAGER)
@@ -136,40 +155,46 @@ public class Publication implements Serializable {
         joinColumns = @JoinColumn(name = "publications_id", referencedColumnName = "ID"),
         inverseJoinColumns = @JoinColumn(name = "compilers_id", referencedColumnName = "ID"))
     @SortNatural
+//    @Field(type = FieldType.Nested)
     private SortedSet<Compiler> compilers = new TreeSet<>();
 
     @Lob
     @Type(type = "org.hibernate.type.StringClobType")
     @Column(name = "compilers_notes")
+    @Field(type = FieldType.String)
     private String compilersNotes;
 
     @Lob
     @Type(type = "org.hibernate.type.StringClobType")
     @Column(name = "citation")
     private String citation;
 
-    @JsonIgnore
+    //@JsonIgnore
     @OneToMany(mappedBy = "publication")
     @Cache(usage = CacheConcurrencyStrategy.NONSTRICT_READ_WRITE)
     @SortNatural
+//    @Field(type = FieldType.Nested)
     private SortedSet<PubSpecies> pubSpecies = new TreeSet<>();
 
-    @JsonIgnore
+    //@JsonIgnore
     @OneToMany(mappedBy = "publication")
     @Cache(usage = CacheConcurrencyStrategy.NONSTRICT_READ_WRITE)
     @SortNatural
+    @Field(type = FieldType.Nested)
     private SortedSet<Ethnology> ethnologies = new TreeSet<>();
 
-    @JsonIgnore
+    //@JsonIgnore
     @OneToMany(mappedBy = "publication")
     @Cache(usage = CacheConcurrencyStrategy.NONSTRICT_READ_WRITE)
     @SortNatural
+//    @Field(type = FieldType.Nested)
     private SortedSet<InVivoPharmaco> inVivoPharmacos = new TreeSet<>();
 
-    @JsonIgnore
+    //@JsonIgnore
     @OneToMany(mappedBy = "publication")
     @Cache(usage = CacheConcurrencyStrategy.NONSTRICT_READ_WRITE)
     @SortNatural
+//    @Field(type = FieldType.Nested)
     private SortedSet<InVitroPharmaco> inVitroPharmacos = new TreeSet<>();
 
     public Long getId() {

diff --git a/src/main/java/nc/ird/malariaplantdb/domain/Remedy.java b/src/main/java/nc/ird/malariaplantdb/domain/Remedy.java
@@ -9,6 +9,8 @@
 import org.hibernate.annotations.CacheConcurrencyStrategy;
 import org.hibernate.annotations.SortNatural;
 import org.springframework.data.elasticsearch.annotations.Document;
+import org.springframework.data.elasticsearch.annotations.Field;
+import org.springframework.data.elasticsearch.annotations.FieldType;
 
 import javax.persistence.*;
 import javax.validation.constraints.NotNull;
@@ -43,6 +45,7 @@ public class Remedy implements Serializable, Comparable<Remedy> {
     @BatchSize(size = 100)
     @Cache(usage = CacheConcurrencyStrategy.NONSTRICT_READ_WRITE)
     @SortNatural
+    @Field(type = FieldType.Nested)
     private SortedSet<PlantIngredient> plantIngredients = new TreeSet<>();
 
     public Long getId() {

diff --git a/src/main/java/nc/ird/malariaplantdb/service/IndexerService.java b/src/main/java/nc/ird/malariaplantdb/service/IndexerService.java
@@ -1,5 +1,8 @@
 package nc.ird.malariaplantdb.service;
 
+import nc.ird.malariaplantdb.domain.*;
+import nc.ird.malariaplantdb.domain.Compiler;
+import nc.ird.malariaplantdb.repository.CompilerRepository;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.elasticsearch.core.ElasticsearchTemplate;
 import org.springframework.data.elasticsearch.core.query.IndexQuery;
@@ -10,38 +13,47 @@
 
 @Service
 public class IndexerService {
+
+    private static final Class[] CLASSES_TO_INDEX = {Author.class, Compiler.class, Ethnology.class,
+        InVivoPharmaco.class, InVitroPharmaco.class, PlantIngredient.class, Publication.class, PubSpecies.class,
+        Remedy.class, Species.class, User.class};
+
+    @Autowired
+    CompilerRepository compilerRepository;
+
     private  static  final  String INDEX_NAME = "compiler";
     public static final double INDEX_COMMIT_SIZE = 100;
 
     // https://stackoverflow.com/questions/37312415/batch-indexing-spring-data-jpa-entries-to-elastic-through-spring-data-elasticsea
 
     @Autowired
     ElasticsearchTemplate elasticsearchTemplate;
+
     public long bulkIndex() throws Exception {
         int counter = 0;
         try {
-            if (!elasticsearchTemplate.indexExists(INDEX_NAME)) {
-
-            } else {
-                elasticsearchTemplate.deleteIndex(INDEX_NAME);
+            if (elasticsearchTemplate.indexExists("compiler")) {
+                elasticsearchTemplate.deleteIndex("compiler");
             }
-            elasticsearchTemplate.createIndex(INDEX_NAME);
 
+            elasticsearchTemplate.createIndex("compiler");
+
+            List<Compiler> compilers = compilerRepository.findAll();
             List<IndexQuery> queries = new ArrayList<IndexQuery>();
 
-//            for (Car car : cars) {
+            for (Compiler compiler : compilers) {
                 IndexQuery indexQuery = new IndexQuery();
 //                indexQuery.setId(car.getId().toString());
 //                indexQuery.setSource(gson.toJson(car));
-                indexQuery.setIndexName(INDEX_NAME);
+                indexQuery.setIndexName("compiler");
                 queries.add(indexQuery);
                 if (counter % INDEX_COMMIT_SIZE == 0) {
                     elasticsearchTemplate.bulkIndex(queries);
                     queries.clear();
                     System.out.println("bulkIndex counter : " + counter);
                 }
                 counter++;
-//            }
+            }
             if (queries.size() > 0) {
                 elasticsearchTemplate.bulkIndex(queries);
             }

diff --git a/src/main/java/nc/ird/malariaplantdb/web/rest/AuthorResource.java b/src/main/java/nc/ird/malariaplantdb/web/rest/AuthorResource.java
@@ -94,7 +94,7 @@ public ResponseEntity<List<Author>> getAllAuthors(Pageable pageable)
         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");
+        HttpHeaders headers = PaginationUtil.generatePaginationHttpHeaders(page, "/authors");
         return new ResponseEntity<>(page.getContent(), headers, HttpStatus.OK);
     }
 

diff --git a/src/main/java/nc/ird/malariaplantdb/web/rest/CompilerResource.java b/src/main/java/nc/ird/malariaplantdb/web/rest/CompilerResource.java
@@ -95,7 +95,7 @@ public ResponseEntity<Compiler> updateCompiler(@Valid @RequestBody Compiler comp
     public ResponseEntity<List<Compiler>> getAllCompilers(Pageable pageable)
         throws URISyntaxException {
         Page<Compiler> page = compilerRepository.findAll(pageable);
-        HttpHeaders headers = PaginationUtil.generatePaginationHttpHeaders(page, "/api/compilers");
+        HttpHeaders headers = PaginationUtil.generatePaginationHttpHeaders(page, "/compilers");
         return new ResponseEntity<>(page.getContent(), headers, HttpStatus.OK);
     }
 

diff --git a/src/main/java/nc/ird/malariaplantdb/web/rest/EthnologyResource.java b/src/main/java/nc/ird/malariaplantdb/web/rest/EthnologyResource.java
@@ -100,7 +100,7 @@ public ResponseEntity<Ethnology> updateEthnology(@Valid @RequestBody Ethnology e
     public ResponseEntity<List<Ethnology>> getAllEthnologies(Pageable pageable)
         throws URISyntaxException {
         Page<Ethnology> page = ethnologyRepository.findAll(pageable);
-        HttpHeaders headers = PaginationUtil.generatePaginationHttpHeaders(page, "/api/ethnologies");
+        HttpHeaders headers = PaginationUtil.generatePaginationHttpHeaders(page, "/ethnologies");
         return new ResponseEntity<>(page.getContent(), headers, HttpStatus.OK);
     }