- possibility to delete in the web interface a publication, a pubspec…

…ies, an ethnlogy, an in vivo or an in vitro with the cascade of the associated entities

- fix the mailto in the community page

src/main/java/nc/ird/malariaplantdb/domain/Author.java

@@ -37,7 +37,7 @@ public class Author implements Serializable, Comparable<Author> {
     private Long id;
 
     @NotNull
-    @ManyToOne
+    @ManyToOne(fetch=FetchType.LAZY)
     private Publication publication;
 
     @NotNull

src/main/java/nc/ird/malariaplantdb/domain/Ethnology.java

@@ -40,7 +40,7 @@ public class Ethnology implements Serializable, Comparable<Ethnology> {
     private Publication publication;
 
     @NotNull
-    @OneToOne(fetch = FetchType.EAGER, cascade = CascadeType.ALL, orphanRemoval = true)
+    @ManyToOne(fetch = FetchType.EAGER)
     private Remedy remedy;
 
     @NotNull

src/main/java/nc/ird/malariaplantdb/domain/InVitroPharmaco.java

@@ -41,7 +41,7 @@ public class InVitroPharmaco implements Serializable, Comparable<InVitroPharmaco
     private Publication publication;
 
     @NotNull
-    @OneToOne(fetch = FetchType.EAGER, cascade = CascadeType.ALL, orphanRemoval = true)
+    @ManyToOne(fetch = FetchType.EAGER)
     private Remedy remedy;
 
     @NotNull

src/main/java/nc/ird/malariaplantdb/domain/InVivoPharmaco.java

@@ -41,7 +41,7 @@ public class InVivoPharmaco implements Serializable, Comparable<InVivoPharmaco>
     private Publication publication;
 
     @NotNull
-    @OneToOne(fetch = FetchType.EAGER, cascade = CascadeType.ALL, orphanRemoval = true)
+    @ManyToOne(fetch = FetchType.EAGER)
     private Remedy remedy;
 
     @NotNull

src/main/java/nc/ird/malariaplantdb/domain/Remedy.java

@@ -39,7 +39,7 @@ public class Remedy implements Serializable, Comparable<Remedy> {
     private Long id;
 
     @JsonIgnoreProperties(value = {"remedy"})
-    @OneToMany(mappedBy = "remedy", fetch = FetchType.EAGER, cascade = CascadeType.ALL, orphanRemoval = true)
+    @OneToMany(mappedBy = "remedy", fetch = FetchType.EAGER, cascade = CascadeType.ALL)
     @BatchSize(size = 100)
     @Cache(usage = CacheConcurrencyStrategy.NONSTRICT_READ_WRITE)
     @SortNatural

src/main/java/nc/ird/malariaplantdb/domain/util/comparator/AuthorComparator.java

@@ -1,6 +1,7 @@
 package nc.ird.malariaplantdb.domain.util.comparator;
 
 import nc.ird.malariaplantdb.domain.Author;
+import org.apache.commons.lang.ObjectUtils;
 
 import java.util.Comparator;
 
@@ -19,6 +20,12 @@ public class AuthorComparator implements Comparator<Author> {
 
     @Override
     public int compare(Author a1, Author a2) {
-        return a1.equals(a2) ? 0 : BY_POSITION_AND_ID.compare(a1, a2);
+        if (a1 == null && a2 == null || ObjectUtils.equals(a1, a2))
+            return 0;
+        else if (a1 == null)
+            return -1;
+        else if (a2 == null)
+            return 1;
+        return BY_POSITION_AND_ID.compare(a1, a2);
     }
 }

src/main/java/nc/ird/malariaplantdb/domain/util/comparator/CompilerComparator.java

@@ -1,6 +1,7 @@
 package nc.ird.malariaplantdb.domain.util.comparator;
 
 import nc.ird.malariaplantdb.domain.Compiler;
+import org.apache.commons.lang.ObjectUtils;
 
 import java.util.Comparator;
 
@@ -16,7 +17,13 @@ public class CompilerComparator implements Comparator<Compiler> {
 
     @Override
     public int compare(Compiler c1, Compiler c2) {
-        return c1.equals(c2) ? 0 : BY_NAME_AND_ID.compare(c1, c2);
+        if (c1 == null && c2 == null || ObjectUtils.equals(c1, c2))
+            return 0;
+        else if (c1 == null)
+            return -1;
+        else if (c2 == null)
+            return 1;
+        return BY_NAME_AND_ID.compare(c1, c2);
     }
 
 }

src/main/java/nc/ird/malariaplantdb/domain/util/comparator/EthnologyComparator.java

@@ -1,6 +1,7 @@
 package nc.ird.malariaplantdb.domain.util.comparator;
 
 import nc.ird.malariaplantdb.domain.Ethnology;
+import org.apache.commons.lang.ObjectUtils;
 
 import java.util.Comparator;
 
@@ -15,7 +16,13 @@ public class EthnologyComparator implements Comparator<Ethnology> {
         .thenComparing(Ethnology::getId);
 
     @Override
-    public int compare(Ethnology s1, Ethnology s2) {
-        return s1.equals(s2) ? 0 : BY_REMEDY_AND_ID.compare(s1, s2);
+    public int compare(Ethnology i1, Ethnology i2) {
+        if (i1 == null && i2 == null || ObjectUtils.equals(i1, i2))
+            return 0;
+        else if (i1 == null)
+            return -1;
+        else if (i2 == null)
+            return 1;
+        return BY_REMEDY_AND_ID.compare(i1, i2);
     }
 }

src/main/java/nc/ird/malariaplantdb/domain/util/comparator/InVitroPharmacoComparator.java

@@ -1,6 +1,7 @@
 package nc.ird.malariaplantdb.domain.util.comparator;
 
 import nc.ird.malariaplantdb.domain.InVitroPharmaco;
+import org.apache.commons.lang.ObjectUtils;
 
 import java.util.Comparator;
 
@@ -15,7 +16,13 @@ public class InVitroPharmacoComparator implements Comparator<InVitroPharmaco> {
         .thenComparing(InVitroPharmaco::getId);
 
     @Override
-    public int compare(InVitroPharmaco s1, InVitroPharmaco s2) {
-        return s1.equals(s2) ? 0 : BY_REMEDY_AND_ID.compare(s1, s2);
+    public int compare(InVitroPharmaco i1, InVitroPharmaco i2) {
+        if (i1 == null && i2 == null || ObjectUtils.equals(i1, i2))
+            return 0;
+        else if (i1 == null)
+            return -1;
+        else if (i2 == null)
+            return 1;
+        return BY_REMEDY_AND_ID.compare(i1, i2);
     }
 }

src/main/java/nc/ird/malariaplantdb/domain/util/comparator/InVivoPharmacoComparator.java

@@ -1,6 +1,7 @@
 package nc.ird.malariaplantdb.domain.util.comparator;
 
 import nc.ird.malariaplantdb.domain.InVivoPharmaco;
+import org.apache.commons.lang.ObjectUtils;
 
 import java.util.Comparator;
 
@@ -15,7 +16,13 @@ public class InVivoPharmacoComparator implements Comparator<InVivoPharmaco> {
         .thenComparing(InVivoPharmaco::getId);
 
     @Override
-    public int compare(InVivoPharmaco s1, InVivoPharmaco s2) {
-        return s1.equals(s2) ? 0 : BY_REMEDY_AND_ID.compare(s1, s2);
+    public int compare(InVivoPharmaco i1, InVivoPharmaco i2) {
+        if (i1 == null && i2 == null || ObjectUtils.equals(i1, i2))
+            return 0;
+        else if (i1 == null)
+            return -1;
+        else if (i2 == null)
+            return 1;
+        return BY_REMEDY_AND_ID.compare(i1, i2);
     }
 }

src/main/java/nc/ird/malariaplantdb/domain/util/comparator/PlantIngredientComparator.java

@@ -1,6 +1,7 @@
 package nc.ird.malariaplantdb.domain.util.comparator;
 
 import nc.ird.malariaplantdb.domain.PlantIngredient;
+import org.apache.commons.lang.ObjectUtils;
 
 import java.util.Comparator;
 
@@ -19,7 +20,13 @@ public class PlantIngredientComparator implements Comparator<PlantIngredient> {
 
     @Override
     public int compare(PlantIngredient pi1, PlantIngredient pi2) {
-        return pi1.equals(pi2) ? 0 : BY_SPECIES_AND_PART.compare(pi1, pi2);
+        if (pi1 == null && pi2 == null || ObjectUtils.equals(pi1, pi2))
+            return 0;
+        else if (pi1 == null)
+            return -1;
+        else if (pi2 == null)
+            return 1;
+        return BY_SPECIES_AND_PART.compare(pi1, pi2);
     }
 
 }

src/main/java/nc/ird/malariaplantdb/domain/util/comparator/PubSpeciesComparator.java

@@ -1,6 +1,7 @@
 package nc.ird.malariaplantdb.domain.util.comparator;
 
 import nc.ird.malariaplantdb.domain.PubSpecies;
+import org.apache.commons.lang.ObjectUtils;
 
 import java.util.Comparator;
 
@@ -18,6 +19,12 @@ public class PubSpeciesComparator implements Comparator<PubSpecies> {
 
     @Override
     public int compare(PubSpecies ps1, PubSpecies ps2) {
-        return ps1.equals(ps2) ? 0 : BY_SPECIES_AND_ID.compare(ps1, ps2);
+        if (ps1 == null && ps2 == null || ObjectUtils.equals(ps1, ps2))
+            return 0;
+        else if (ps1 == null)
+            return -1;
+        else if (ps2 == null)
+            return 1;
+        return BY_SPECIES_AND_ID.compare(ps1, ps2);
     }
 }

src/main/java/nc/ird/malariaplantdb/domain/util/comparator/RemedyComparator.java

@@ -2,6 +2,7 @@
 
 import nc.ird.malariaplantdb.domain.PlantIngredient;
 import nc.ird.malariaplantdb.domain.Remedy;
+import org.apache.commons.lang.ObjectUtils;
 
 import java.util.Comparator;
 
@@ -21,7 +22,13 @@ public class RemedyComparator implements Comparator<Remedy> {
 
     @Override
     public int compare(Remedy r1, Remedy r2) {
-        return r1.equals(r2) ? 0 : BY_PLANT_INGREDIENTS_SET_AND_ID.compare(r1, r2);
+        if (r1 == null && r2 == null || ObjectUtils.equals(r1, r2))
+            return 0;
+        else if (r1 == null)
+            return -1;
+        else if (r2 == null)
+            return 1;
+        return BY_PLANT_INGREDIENTS_SET_AND_ID.compare(r1, r2);
     }
 
 }

src/main/java/nc/ird/malariaplantdb/domain/util/comparator/SpeciesComparator.java

@@ -1,6 +1,7 @@
 package nc.ird.malariaplantdb.domain.util.comparator;
 
 import nc.ird.malariaplantdb.domain.Species;
+import org.apache.commons.lang.ObjectUtils;
 
 import java.util.Comparator;
 
@@ -15,6 +16,12 @@ public class SpeciesComparator implements Comparator<Species> {
 
     @Override
     public int compare(Species s1, Species s2) {
-        return s1.equals(s2) ? 0 : BY_SPECIES.compare(s1, s2);
+        if (s1 == null && s2 == null || ObjectUtils.equals(s1, s2))
+            return 0;
+        else if (s1 == null)
+            return -1;
+        else if (s2 == null)
+            return 1;
+        else return BY_SPECIES.compare(s1, s2);
     }
 }

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

@@ -25,5 +25,8 @@ public interface EthnologyRepository extends JpaRepository<Ethnology,Long> {
     //Ethnology findOneWithEagerRelationships(@Param("id") Long id);
 
     @Query("select e from Ethnology e join e.remedy r where e.publication.id = :pubId and r.id = :remId")
-    Ethnology findByPublicationIdAndAndRemedy(@Param("pubId") Long pubId, @Param("remId") Long remId);
+    Ethnology findByPublicationIdAndAndRemedyId(@Param("pubId") Long pubId, @Param("remId") Long remId);
+
+    List<Ethnology> findByRemedyId(Long remedyId);
+
 }

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

@@ -27,6 +27,8 @@ public interface InVitroPharmacoRepository extends JpaRepository<InVitroPharmaco
 
     @Query("select iv from InVitroPharmaco iv join iv.remedy r where iv.publication.id = :pubId " +
         "and r.id = :remId")
-    List<InVitroPharmaco> findByPublicationIdAndRemedy(@Param("pubId") Long pubId, @Param("remId") Long remId);
+    List<InVitroPharmaco> findByPublicationIdAndRemedyId(@Param("pubId") Long pubId, @Param("remId") Long remId);
+
+    List<InVitroPharmaco> findByRemedyId(Long remedyId);
 
 }

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

@@ -28,6 +28,8 @@ public interface InVivoPharmacoRepository extends JpaRepository<InVivoPharmaco,L
 
     @Query("select iv from InVivoPharmaco iv join iv.remedy r where iv.publication.id = :pubId " +
         "and r.id = :remId")
-    List<InVivoPharmaco> findByPublicationIdAndRemedy(@Param("pubId") Long pubId, @Param("remId") Long remId);
+    List<InVivoPharmaco> findByPublicationIdAndRemedyId(@Param("pubId") Long pubId, @Param("remId") Long remId);
+
+    List<InVivoPharmaco> findByRemedyId(Long remedyId);
 
 }

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

@@ -4,10 +4,14 @@
 import org.springframework.data.jpa.repository.JpaRepository;
 import org.springframework.stereotype.Repository;
 
+import java.util.List;
+
 /**
  * Spring Data JPA repository for the PlantIngredient entity.
  */
 @Repository
 public interface PlantIngredientRepository extends JpaRepository<PlantIngredient,Long> {
 
+    List<PlantIngredient> findBySpeciesId(Long speciesId);
+
 }

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

@@ -20,4 +20,6 @@ public interface PubSpeciesRepository extends JpaRepository<PubSpecies,Long> {
         "where ps.publication.id = :pubId and s.id = s2.id and r.id = :remId")
     List<PubSpecies> findByPublicationIdAndRemedy(@Param("pubId") Long pubId, @Param("remId") Long remId);
 
+    List<PubSpecies> findBySpeciesId(Long speciesId);
+
 }

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

@@ -10,4 +10,5 @@
 @Repository
 public interface RemedyRepository extends JpaRepository<Remedy,Long> {
 
+//    List<Remedy> findByPlantIngredientId()
 }