Merge pull request #1385 from alliance-genome/release/v0.28.0-rc2

Release/v0.28.0 rc2
alliance-genome · Jan 8, 2024 · 681368a · 681368a
2 parents 8b5b27c + 467b38c
commit 681368a
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Showing 31 changed files with 91 additions and 69 deletions.
diff --git a/src/main/java/org/alliancegenome/curation_api/controllers/base/BaseEntityCrudController.java b/src/main/java/org/alliancegenome/curation_api/controllers/base/BaseEntityCrudController.java
@@ -61,6 +61,10 @@ public SearchResponse<E> find(Integer page, Integer limit, HashMap<String, Objec
  Pagination pagination = new Pagination(page, limit);
  return service.findByParams(pagination, params);
  }
+
+ public SearchResponse<E> findForPublic(Integer page, Integer limit, HashMap<String, Object> params) {
+ return find(page, limit, params);
+ }
 
  public SearchResponse<E> search(Integer page, Integer limit, HashMap<String, Object> params) {
  if (params == null)

diff --git a/src/main/java/org/alliancegenome/curation_api/interfaces/base/BaseIdCrudInterface.java b/src/main/java/org/alliancegenome/curation_api/interfaces/base/BaseIdCrudInterface.java
@@ -60,6 +60,12 @@ public interface BaseIdCrudInterface<E extends BaseEntity> {
  @JsonView(View.FieldsAndLists.class)
  public SearchResponse<E> find(@DefaultValue("0") @QueryParam("page") Integer page, @DefaultValue("10") @QueryParam("limit") Integer limit, @RequestBody HashMap<String, Object> params);
 
+ @POST
+ @Path("/findForPublic")
+ @Tag(name = "Public Web API Database Searching Endpoints")
+ @JsonView(View.ForPublic.class)
+ public SearchResponse<E> findForPublic(@DefaultValue("0") @QueryParam("page") Integer page, @DefaultValue("10") @QueryParam("limit") Integer limit, @RequestBody HashMap<String, Object> params);
+
  @POST
  @Path("/search")
  @Tag(name = "Search Database Browsing Endpoints")

diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/AGMDiseaseAnnotation.java b/src/main/java/org/alliancegenome/curation_api/model/entities/AGMDiseaseAnnotation.java
@@ -48,36 +48,36 @@ public class AGMDiseaseAnnotation extends DiseaseAnnotation {
  @Fetch(FetchMode.SELECT)
  @org.hibernate.annotations.OnDelete(action = org.hibernate.annotations.OnDeleteAction.CASCADE)
  @JoinColumn(foreignKey = @ForeignKey(name = "fk_agmdasubject"))
- @JsonView({ View.FieldsOnly.class })
+ @JsonView({ View.FieldsOnly.class, View.ForPublic.class })
  private AffectedGenomicModel subject;
 
  @IndexedEmbedded(includeDepth = 2)
  @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
  @ManyToOne
  @Fetch(FetchMode.SELECT)
- @JsonView({ View.FieldsOnly.class })
+ @JsonView({ View.FieldsOnly.class, View.ForPublic.class })
  private Gene inferredGene;
 
  @IndexedEmbedded(includeDepth = 2)
  @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
  @ManyToOne
  @Fetch(FetchMode.SELECT)
- @JsonView({ View.FieldsOnly.class })
+ @JsonView({ View.FieldsOnly.class, View.ForPublic.class })
  private Allele inferredAllele;
 
  @IndexedEmbedded(includeDepth = 2)
  @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
  @ManyToMany
  @Fetch(FetchMode.SELECT)
  @JoinTable(indexes = @Index(columnList = "agmdiseaseannotation_id"))
- @JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class })
+ @JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class })
  private List<Gene> assertedGenes;
 
  @IndexedEmbedded(includeDepth = 2)
  @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
  @ManyToOne
  @Fetch(FetchMode.SELECT)
- @JsonView({ View.FieldsOnly.class })
+ @JsonView({ View.FieldsOnly.class, View.ForPublic.class })
  private Allele assertedAllele;
 
  @Transient

diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/AffectedGenomicModel.java b/src/main/java/org/alliancegenome/curation_api/model/entities/AffectedGenomicModel.java
@@ -34,7 +34,7 @@
 public class AffectedGenomicModel extends GenomicEntity {
 
  @Column(columnDefinition = "TEXT")
- @JsonView({ View.FieldsOnly.class })
+ @JsonView({ View.FieldsOnly.class, View.ForPublic.class })
  private String name;
 
  @OneToMany(mappedBy = "subject", cascade = CascadeType.ALL, orphanRemoval = true)
@@ -43,6 +43,6 @@ public class AffectedGenomicModel extends GenomicEntity {
  @IndexedEmbedded(includeDepth = 1)
  @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
  @ManyToOne
- @JsonView({ View.FieldsOnly.class })
+ @JsonView({ View.FieldsOnly.class, View.ForPublic.class })
  private VocabularyTerm subtype;
 }
diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/Allele.java b/src/main/java/org/alliancegenome/curation_api/model/entities/Allele.java
@@ -94,7 +94,7 @@ public class Allele extends GenomicEntity {
  @IndexedEmbedded(includePaths = { "displayText", "formatText", "nameType.name", "synonymScope.name", "evidence.curie", "displayText_keyword", "formatText_keyword", "nameType.name_keyword", "synonymScope.name_keyword", "evidence.curie_keyword"})
  @OneToOne(mappedBy = "singleAllele", cascade = CascadeType.ALL, orphanRemoval=true)
  @JsonManagedReference
- @JsonView({ View.FieldsOnly.class })
+ @JsonView({ View.FieldsOnly.class, View.ForPublic.class })
  private AlleleSymbolSlotAnnotation alleleSymbol;
 
  @IndexedEmbedded(includePaths = { "displayText", "formatText", "nameType.name", "synonymScope.name", "evidence.curie", "displayText_keyword", "formatText_keyword", "nameType.name_keyword", "synonymScope.name_keyword", "evidence.curie_keyword"})

diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/AlleleDiseaseAnnotation.java b/src/main/java/org/alliancegenome/curation_api/model/entities/AlleleDiseaseAnnotation.java
@@ -50,22 +50,22 @@ public class AlleleDiseaseAnnotation extends DiseaseAnnotation {
  @Fetch(FetchMode.SELECT)
  @org.hibernate.annotations.OnDelete(action = org.hibernate.annotations.OnDeleteAction.CASCADE)
  @JoinColumn(foreignKey = @ForeignKey(name = "fk_alleledasubject"))
- @JsonView({ View.FieldsOnly.class })
+ @JsonView({ View.FieldsOnly.class, View.ForPublic.class })
  private Allele subject;
 
  @IndexedEmbedded(includeDepth = 2)
  @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
  @ManyToOne
  @Fetch(FetchMode.SELECT)
- @JsonView({ View.FieldsOnly.class })
+ @JsonView({ View.FieldsOnly.class, View.ForPublic.class })
  private Gene inferredGene;
 
  @IndexedEmbedded(includeDepth = 2)
  @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
  @ManyToMany
  @Fetch(FetchMode.SELECT)
  @JoinTable(indexes = { @Index(columnList = "allelediseaseannotation_id"), @Index(columnList = "assertedgenes_curie")})
- @JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class })
+ @JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class })
  private List<Gene> assertedGenes;
 
  @Transient

diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/Annotation.java b/src/main/java/org/alliancegenome/curation_api/model/entities/Annotation.java
@@ -87,22 +87,22 @@ public class Annotation extends SingleReferenceAssociation {
  @IndexedEmbedded(includeDepth = 2)
  @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
  @ManyToMany
- @JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class })
+ @JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class })
  @JoinTable(indexes = { @Index(name = "annotation_conditionrelation_annotation_id_index", columnList = "annotation_id"), @Index(name = "annotation_conditionrelation_conditionrelations_id_index", columnList = "conditionrelations_id")})
  private List<ConditionRelation> conditionRelations;
 
  @IndexedEmbedded(includeDepth = 1)
  @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
  @OneToMany(cascade = CascadeType.ALL, orphanRemoval=true)
- @JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class })
+ @JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class })
  @JoinTable(indexes = { @Index(name = "annotation_note_annotation_id_index", columnList = "annotation_id"), @Index(name = "annotation_note_relatednotes_id_index",columnList = "relatednotes_id")})
  private List<Note> relatedNotes;
 
  @IndexedEmbedded(includeDepth = 2)
  @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
  @ManyToOne
  @Fetch(FetchMode.SELECT)
- @JsonView({ View.FieldsOnly.class })
+ @JsonView({ View.FieldsOnly.class, View.ForPublic.class })
  protected DataProvider dataProvider;
 
 }
diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/BiologicalEntity.java b/src/main/java/org/alliancegenome/curation_api/model/entities/BiologicalEntity.java
@@ -48,7 +48,7 @@ public class BiologicalEntity extends CurieAuditedObject {
  @IndexedEmbedded(includePaths = {"name", "curie", "name_keyword", "curie_keyword"})
  @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
  @ManyToOne
- @JsonView({ View.FieldsOnly.class })
+ @JsonView({ View.FieldsOnly.class, View.ForPublic.class })
  private NCBITaxonTerm taxon;
 
  @IndexedEmbedded(includePaths = {"sourceOrganization.abbreviation", "sourceOrganization.fullName", "sourceOrganization.shortName", "crossReference.displayName", "crossReference.referencedCurie",

diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/ConditionRelation.java b/src/main/java/org/alliancegenome/curation_api/model/entities/ConditionRelation.java
@@ -42,7 +42,7 @@ public class ConditionRelation extends UniqueIdAuditedObject {
  @IndexedEmbedded(includeDepth = 1)
  @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
  @ManyToOne
- @JsonView({ View.FieldsOnly.class })
+ @JsonView({ View.FieldsOnly.class, View.ForPublic.class })
  private VocabularyTerm conditionRelationType;
 
  @FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer")
@@ -60,7 +60,7 @@ public class ConditionRelation extends UniqueIdAuditedObject {
  @IndexedEmbedded(includeDepth = 1)
  @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
  @ManyToMany
- @JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ConditionRelationView.class })
+ @JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ConditionRelationView.class, View.ForPublic.class })
  private List<ExperimentalCondition> conditions;
 
  public void addExperimentCondition(ExperimentalCondition experimentalCondition) {

diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/CrossReference.java b/src/main/java/org/alliancegenome/curation_api/model/entities/CrossReference.java
@@ -41,7 +41,7 @@ public class CrossReference extends GeneratedAuditedObject {
 
  @FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer")
  @KeywordField(name = "referencedCurie_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES, normalizer = "sortNormalizer")
- @JsonView({ View.FieldsOnly.class })
+ @JsonView({ View.FieldsOnly.class, View.ForPublic.class })
  @EqualsAndHashCode.Include
  private String referencedCurie;
 
@@ -55,7 +55,7 @@ public class CrossReference extends GeneratedAuditedObject {
  @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
  @ManyToOne
  @Fetch(FetchMode.SELECT)
- @JsonView({ View.FieldsOnly.class })
+ @JsonView({ View.FieldsOnly.class, View.ForPublic.class })
  private ResourceDescriptorPage resourceDescriptorPage;
 
  public String getPrefix() {

diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/DataProvider.java b/src/main/java/org/alliancegenome/curation_api/model/entities/DataProvider.java
@@ -35,13 +35,13 @@ public class DataProvider extends GeneratedAuditedObject {
  @IndexedEmbedded(includeDepth = 1)
  @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
  @OneToOne
- @JsonView({ View.FieldsOnly.class })
+ @JsonView({ View.FieldsOnly.class, View.ForPublic.class })
  private Organization sourceOrganization;
 
  @IndexedEmbedded(includeDepth = 1)
  @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
  @OneToOne
- @JsonView({ View.FieldsOnly.class })
+ @JsonView({ View.FieldsOnly.class, View.ForPublic.class })
  private CrossReference crossReference;
 
 }
diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/DiseaseAnnotation.java b/src/main/java/org/alliancegenome/curation_api/model/entities/DiseaseAnnotation.java
@@ -67,25 +67,25 @@ public abstract class DiseaseAnnotation extends Annotation {
  @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
  @ManyToOne
  @Fetch(FetchMode.SELECT)
- @JsonView({ View.FieldsOnly.class })
+ @JsonView({ View.FieldsOnly.class, View.ForPublic.class })
  private DOTerm object;
 
  @FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer", valueBridge = @ValueBridgeRef(type = BooleanValueBridge.class))
  @KeywordField(name = "negated_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES, valueBridge = @ValueBridgeRef(type = BooleanValueBridge.class))
- @JsonView({ View.FieldsOnly.class })
+ @JsonView({ View.FieldsOnly.class, View.ForPublic.class })
  @Column(columnDefinition = "boolean default false", nullable = false)
  private Boolean negated = false;
 
  @IndexedEmbedded(includeDepth = 1)
  @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
  @ManyToOne
- @JsonView({ View.FieldsOnly.class })
+ @JsonView({ View.FieldsOnly.class, View.ForPublic.class })
  private VocabularyTerm relation;
 
  @IndexedEmbedded(includeDepth = 1)
  @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
  @ManyToMany
- @JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class })
+ @JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class })
  @JoinTable(indexes = { @Index(columnList = "diseaseannotation_id"), @Index(columnList = "evidencecodes_curie")})
  private List<ECOTerm> evidenceCodes;
 
@@ -94,47 +94,47 @@ public abstract class DiseaseAnnotation extends Annotation {
  @ManyToMany
  @Fetch(FetchMode.SELECT)
  @JoinTable(indexes = { @Index(columnList = "diseaseannotation_id"), @Index(columnList = "with_curie") })
- @JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class })
+ @JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class })
  private List<Gene> with;
 
  @IndexedEmbedded(includeDepth = 1)
  @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
  @ManyToOne
- @JsonView({ View.FieldsOnly.class })
+ @JsonView({ View.FieldsOnly.class, View.ForPublic.class })
  private VocabularyTerm annotationType;
 
  @IndexedEmbedded(includeDepth = 1)
  @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
  @ManyToMany
- @JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class })
+ @JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class })
  @JoinTable(indexes = { @Index(columnList = "diseaseannotation_id"), @Index(columnList = "diseasequalifiers_id")})
  private List<VocabularyTerm> diseaseQualifiers;
 
  @IndexedEmbedded(includeDepth = 1)
  @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
  @ManyToOne
- @JsonView({ View.FieldsOnly.class })
+ @JsonView({ View.FieldsOnly.class, View.ForPublic.class })
  private VocabularyTerm geneticSex;
 
  @IndexedEmbedded(includeDepth = 2)
  @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
  @ManyToOne
  @Fetch(FetchMode.SELECT)
- @JsonView({ View.FieldsOnly.class })
+ @JsonView({ View.FieldsOnly.class, View.ForPublic.class })
  private DataProvider secondaryDataProvider;
 
  @IndexedEmbedded(includeDepth = 1)
  @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
  @ManyToMany
  @Fetch(FetchMode.SELECT)
- @JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class })
+ @JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class })
  @JoinTable(indexes = { @Index(columnList = "diseaseannotation_id"), @Index(columnList = "diseasegeneticmodifiers_curie")})
  private List<BiologicalEntity> diseaseGeneticModifiers;
 
  @IndexedEmbedded(includeDepth = 1)
  @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
  @ManyToOne
- @JsonView({ View.FieldsOnly.class })
+ @JsonView({ View.FieldsOnly.class, View.ForPublic.class })
  private VocabularyTerm diseaseGeneticModifierRelation;
 
  @Transient

diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/ExperimentalCondition.java b/src/main/java/org/alliancegenome/curation_api/model/entities/ExperimentalCondition.java
@@ -48,7 +48,7 @@ public class ExperimentalCondition extends UniqueIdAuditedObject {
 
  @FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer")
  @KeywordField(name = "conditionSummary_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES, normalizer = "sortNormalizer")
- @JsonView({ View.FieldsOnly.class })
+ @JsonView({ View.FieldsOnly.class, View.ForPublic.class })
  private String conditionSummary;
 
  @IndexedEmbedded(includeDepth = 1)

diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/Gene.java b/src/main/java/org/alliancegenome/curation_api/model/entities/Gene.java
@@ -52,13 +52,13 @@ public class Gene extends GenomicEntity {
  @IndexedEmbedded(includePaths = { "displayText", "formatText", "nameType.name", "synonymScope.name", "evidence.curie", "displayText_keyword", "formatText_keyword", "nameType.name_keyword", "synonymScope.name_keyword", "evidence.curie_keyword"})
  @OneToOne(mappedBy = "singleGene", cascade = CascadeType.ALL, orphanRemoval = true)
  @JsonManagedReference
- @JsonView({ View.FieldsOnly.class })
+ @JsonView({ View.FieldsOnly.class, View.ForPublic.class })
  private GeneSymbolSlotAnnotation geneSymbol;
 
  @IndexedEmbedded(includePaths = { "displayText", "formatText", "nameType.name", "synonymScope.name", "evidence.curie", "displayText_keyword", "formatText_keyword", "nameType.name_keyword", "synonymScope.name_keyword", "evidence.curie_keyword"})
  @OneToOne(mappedBy = "singleGene", cascade = CascadeType.ALL, orphanRemoval = true)
  @JsonManagedReference
- @JsonView({ View.FieldsOnly.class })
+ @JsonView({ View.FieldsOnly.class, View.ForPublic.class })
  private GeneFullNameSlotAnnotation geneFullName;
 
  @IndexedEmbedded(includePaths = { "displayText", "formatText", "nameType.name", "synonymScope.name", "evidence.curie", "displayText_keyword", "formatText_keyword", "nameType.name_keyword", "synonymScope.name_keyword", "evidence.curie_keyword"})

diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/GeneDiseaseAnnotation.java b/src/main/java/org/alliancegenome/curation_api/model/entities/GeneDiseaseAnnotation.java
@@ -40,7 +40,7 @@ public class GeneDiseaseAnnotation extends DiseaseAnnotation {
  @ManyToOne
  @org.hibernate.annotations.OnDelete(action = org.hibernate.annotations.OnDeleteAction.CASCADE)
  @JoinColumn(foreignKey = @ForeignKey(name = "fk_genedasubject"))
- @JsonView({ View.FieldsOnly.class })
+ @JsonView({ View.FieldsOnly.class, View.ForPublic.class })
  private Gene subject;
 
  @IndexedEmbedded(includeDepth = 1)

diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/GenomicEntity.java b/src/main/java/org/alliancegenome/curation_api/model/entities/GenomicEntity.java
@@ -42,7 +42,7 @@ public class GenomicEntity extends BiologicalEntity {
  @Index(columnList = "genomicentity_curie", name = "genomicentity_crossreference_genomicentity_curie_index"),
  @Index(columnList = "crossreferences_id", name = "genomicentity_crossreference_crossreferences_id_index")
  })
- @JsonView({ View.FieldsAndLists.class })
+ @JsonView({ View.FieldsAndLists.class, View.ForPublic.class })
  private List<CrossReference> crossReferences;
 
  @IndexedEmbedded(includePaths = {"constructSubject.curie", "constructSubject.constructSymbol.displayText", "constructSubject.constructSymbol.formatText",

diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/Note.java b/src/main/java/org/alliancegenome/curation_api/model/entities/Note.java
@@ -9,6 +9,8 @@
 import org.alliancegenome.curation_api.model.entities.base.GeneratedAuditedObject;
 import org.alliancegenome.curation_api.view.View;
 import org.eclipse.microprofile.openapi.annotations.media.Schema;
+import org.hibernate.annotations.Fetch;
+import org.hibernate.annotations.FetchMode;
 import org.hibernate.envers.Audited;
 import org.hibernate.search.engine.backend.types.Aggregable;
 import org.hibernate.search.engine.backend.types.Searchable;
@@ -47,14 +49,15 @@ public class Note extends GeneratedAuditedObject {
 
  @FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer", valueBridge = @ValueBridgeRef(type = FreeTextValueBridge.class))
  @KeywordField(name = "freeText_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES, normalizer = "sortNormalizer", valueBridge = @ValueBridgeRef(type = FreeTextValueBridge.class))
- @JsonView({ View.FieldsOnly.class })
+ @JsonView({ View.FieldsOnly.class, View.ForPublic.class })
  @Column(columnDefinition = "TEXT")
  private String freeText;
 
  @IndexedEmbedded(includeDepth = 1)
  @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
  @ManyToOne
- @JsonView({ View.FieldsOnly.class })
+ @Fetch(FetchMode.SELECT)
+ @JsonView({ View.FieldsOnly.class, View.ForPublic.class })
  private VocabularyTerm noteType;
 
  @IndexedEmbedded(includeDepth = 1)

diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/Organization.java b/src/main/java/org/alliancegenome/curation_api/model/entities/Organization.java
@@ -42,7 +42,7 @@ public class Organization extends Agent {
 
  @FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer")
  @KeywordField(name = "abbreviation_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES, normalizer = "sortNormalizer")
- @JsonView({ View.FieldsOnly.class, View.PersonSettingView.class })
+ @JsonView({ View.FieldsOnly.class, View.PersonSettingView.class, View.ForPublic.class })
  @Column(unique = true)
  private String abbreviation;
 
@@ -59,6 +59,6 @@ public class Organization extends Agent {
  @IndexedEmbedded(includeDepth = 1)
  @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
  @OneToOne
- @JsonView({ View.FieldsOnly.class })
+ @JsonView({ View.FieldsOnly.class, View.ForPublic.class })
  private ResourceDescriptorPage homepageResourceDescriptorPage;
 }
diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/Reference.java b/src/main/java/org/alliancegenome/curation_api/model/entities/Reference.java
@@ -50,7 +50,7 @@ public class Reference extends InformationContentEntity {
  @IndexedEmbedded(includeDepth = 1)
  @IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
  @ManyToMany
- @JsonView({View.FieldsOnly.class})
+ @JsonView({ View.FieldsOnly.class, View.ForPublic.class })
  @JoinTable(indexes = {@Index(columnList = "Reference_curie"), @Index(columnList = "crossReferences_id")})
  @EqualsAndHashCode.Include
  private List<CrossReference> crossReferences;