Adding HTPexpressiondatasetannotation entities

src/main/cliapp/src/service/DataLoadService.js

@@ -81,6 +81,7 @@ export class DataLoadService extends BaseAuthService {
 		const bulkLoadTypes = {
 			BulkFMSLoad: [
 				'GFF',
+				'HTP EXPRESSION DATASET ANNOTATION',
 				'INTERACTION-GEN',
 				'INTERACTION-MOL',
 				'MOLECULE',

src/main/java/org/alliancegenome/curation_api/enums/BackendBulkLoadType.java

@@ -23,7 +23,8 @@ public enum BackendBulkLoadType {
 	INTERACTION_GEN("tsv"),
 	PARALOGY("json"),
 	SEQUENCE_TARGETING_REAGENT("json"),
-	EXPRESSION("json");
+	EXPRESSION("json"),
+	HTP_EXPRESSION_DATASET_ANNOTATION("json");
 
 	public String fileExtension;
 

src/main/java/org/alliancegenome/curation_api/model/entities/HighThroughputExpressionDatasetAnnotation.java

@@ -0,0 +1,60 @@
+package org.alliancegenome.curation_api.model.entities;
+
+import java.util.List;
+
+import org.alliancegenome.curation_api.model.entities.base.SubmittedObject;
+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.search.mapper.pojo.automaticindexing.ReindexOnUpdate;
+import org.hibernate.search.mapper.pojo.mapping.definition.annotation.Indexed;
+import org.hibernate.search.mapper.pojo.mapping.definition.annotation.IndexedEmbedded;
+import org.hibernate.search.mapper.pojo.mapping.definition.annotation.IndexingDependency;
+
+import com.fasterxml.jackson.annotation.JsonView;
+
+import jakarta.persistence.Entity;
+import jakarta.persistence.Index;
+import jakarta.persistence.JoinTable;
+import jakarta.persistence.ManyToMany;
+import lombok.Data;
+import lombok.EqualsAndHashCode;
+import lombok.ToString;
+
+@Indexed
+@Entity
+@Data
+@EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
+@ToString(callSuper = true)
+@Schema(name = "HighThroughputExpressionDatasetAnnotation", description = "POJO that represents the HighThroughputExpressionDatasetAnnotation")
+public class HighThroughputExpressionDatasetAnnotation extends SubmittedObject{
+
+	@JsonView({ View.FieldsOnly.class })
+	private String name;   
+
+    @IndexedEmbedded(includePaths = {"curie", "primaryCrossReferenceCurie", "crossReferences.referencedCurie", "curie_keyword", "primaryCrossReferenceCurie_keyword", "crossReferences.referencedCurie_keyword"})
+	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
+	@ManyToMany
+	@Fetch(FetchMode.JOIN)
+	@JoinTable(indexes = {
+		@Index(name = "htpdatasetannotation_reference_htpdataset_index", columnList = "highthroughputexpressiondatasetannotation_id"),
+		@Index(name = "htpdatasetannotation_reference_references_index", columnList = "references_id")
+	})
+	@JsonView({ View.FieldsAndLists.class })
+	private List<Reference> references;
+
+    @JsonView({ View.FieldsOnly.class })
+    private String realtedNote;
+
+    @JsonView({ View.FieldsOnly.class })
+    private Integer numberOfChannels;
+
+    @IndexedEmbedded(includePaths = {"name", "name_keyword"})
+	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
+    @ManyToMany
+    @JsonView({ View.FieldsAndLists.class })
+	@JoinTable(name = "htpexpressiondatasetannotation_categorytags", indexes = { @Index(name = "htpdatasetannotation_htpdatasetid_index", columnList = "highthroughputexpressiondatasetannotation_id"), @Index(name = "htpdatasetannotation_categorytags_index", columnList = "categorytags_id")})
+    List<VocabularyTerm> categoryTags;
+
+}

src/main/resources/db/migration/v0.36.0.4__highthroughputexpressiondataset.sql

@@ -0,0 +1,103 @@
+-- To create bulk loads
+
+INSERT INTO bulkloadgroup (id, name) VALUES (nextval('bulkloadgroup_seq'), 'HTP Expression Dataset Annotation Bulk Loads');
+
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+SELECT nextval('bulkload_seq'), 'HTP_EXPRESSION_DATASET_ANNOTATION', 'FB HTP Expression Dataset Annotation Load', 'STOPPED', id FROM bulkloadgroup WHERE name = 'HTP Expression Dataset Annotation Bulk Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+SELECT nextval('bulkload_seq'), 'HTP_EXPRESSION_DATASET_ANNOTATION', 'ZFIN HTP Expression Dataset Annotation Load', 'STOPPED', id FROM bulkloadgroup WHERE name = 'HTP Expression Dataset Annotation Bulk Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+SELECT nextval('bulkload_seq'), 'HTP_EXPRESSION_DATASET_ANNOTATION', 'MGI HTP Expression Dataset Annotation Load', 'STOPPED', id FROM bulkloadgroup WHERE name = 'HTP Expression Dataset Annotation Bulk Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+SELECT nextval('bulkload_seq'), 'HTP_EXPRESSION_DATASET_ANNOTATION', 'RGD HTP Expression Dataset Annotation Load', 'STOPPED', id FROM bulkloadgroup WHERE name = 'HTP Expression Dataset Annotation Bulk Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+SELECT nextval('bulkload_seq'), 'HTP_EXPRESSION_DATASET_ANNOTATION', 'SGD HTP Expression Dataset Annotation Load', 'STOPPED', id FROM bulkloadgroup WHERE name = 'HTP Expression Dataset Annotation Bulk Loads';
+INSERT INTO bulkload (id, backendbulkloadtype, name, bulkloadstatus, group_id)
+SELECT nextval('bulkload_seq'), 'HTP_EXPRESSION_DATASET_ANNOTATION', 'WB HTP Expression Dataset Annotation Load', 'STOPPED', id FROM bulkloadgroup WHERE name = 'HTP Expression Dataset Annotation Bulk Loads';
+
+INSERT INTO bulkscheduledload (id, cronschedule, scheduleactive)
+SELECT id, '0 0 22 ? * SUN-THU', false FROM bulkload WHERE backendbulkloadtype = 'HTP_EXPRESSION_DATASET_ANNOTATION';
+
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+SELECT id, 'HTP_EXPRESSION_DATASET_ANNOTATION', 'FB' FROM bulkload WHERE name = 'FB HTP Expression Dataset Annotation Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+SELECT id, 'HTP_EXPRESSION_DATASET_ANNOTATION', 'MGI' FROM bulkload WHERE name = 'MGI HTP Expression Dataset Annotation Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+SELECT id, 'HTP_EXPRESSION_DATASET_ANNOTATION', 'RGD' FROM bulkload WHERE name = 'RGD HTP Expression Dataset Annotation Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+SELECT id, 'HTP_EXPRESSION_DATASET_ANNOTATION', 'SGD' FROM bulkload WHERE name = 'SGD HTP Expression Dataset Annotation Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+SELECT id, 'HTP_EXPRESSION_DATASET_ANNOTATION', 'WB' FROM bulkload WHERE name = 'WB HTP Expression Dataset Annotation Load';
+INSERT INTO bulkfmsload (id, fmsdatatype, fmsdatasubtype)
+SELECT id, 'HTP_EXPRESSION_DATASET_ANNOTATION', 'ZFIN' FROM bulkload WHERE name = 'ZFIN HTP Expression Dataset Annotation Load';
+
+
+--Adding 3 extra vocabulary terms for HTPTags
+
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'epigenome', id FROM vocabulary WHERE vocabularylabel = 'data_set_category_tags';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'functional genomics and proteomics', id FROM vocabulary WHERE vocabularylabel = 'data_set_category_tags';
+INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'karyotyping', id FROM vocabulary WHERE vocabularylabel = 'data_set_category_tags';
+
+-- Adding highthroughputexpressiondatasetannotation
+
+CREATE SEQUENCE highthroughputexpressiondatasetannotation_seq START WITH 1 INCREMENT BY 50 NO MINVALUE NO MAXVALUE CACHE 1;
+
+CREATE TABLE highthroughputexpressiondatasetannotation (
+     id bigint NOT NULL,
+     datecreated timestamp(6) with time zone,
+     dateupdated timestamp(6) with time zone,
+     dbdatecreated timestamp(6) with time zone,
+     dbdateupdated timestamp(6) with time zone,
+     internal boolean DEFAULT false NOT NULL,
+     obsolete boolean DEFAULT false NOT NULL,
+     curie character varying(255),
+     modentityid character varying(255),
+     modinternalid character varying(255),
+     name character varying(255),
+     numberofchannels integer,
+     realtednote character varying(255),
+     createdby_id bigint,
+     updatedby_id bigint,
+     dataprovider_id bigint
+);
+
+CREATE TABLE highthroughputexpressiondatasetannotation_categorytags (
+     highthroughputexpressiondatasetannotation_id bigint NOT NULL,
+     categorytags_id bigint NOT NULL
+ );
+
+CREATE TABLE highthroughputexpressiondatasetannotation_reference (
+     highthroughputexpressiondatasetannotation_id bigint NOT NULL,
+     references_id bigint NOT NULL
+ );
+
+ALTER TABLE highthroughputexpressiondatasetannotation ADD CONSTRAINT highthroughputexpressiondatasetannotation_pkey PRIMARY KEY (id);
+
+CREATE INDEX htpdatasetannotation_reference_htpdataset_index ON highthroughputexpressiondatasetannotation_reference USING btree (highthroughputexpressiondatasetannotation_id);
+
+CREATE INDEX htpdatasetannotation_reference_references_index ON highthroughputexpressiondatasetannotation_reference USING btree (references_id);
+
+CREATE INDEX htpdatasetannotation_categorytags_index ON highthroughputexpressiondatasetannotation_categorytags USING btree (categorytags_id);
+
+CREATE INDEX htpdatasetannotation_htpdatasetid_index ON highthroughputexpressiondatasetannotation_categorytags USING btree (highthroughputexpressiondatasetannotation_id);
+
+ALTER TABLE highthroughputexpressiondatasetannotation_categorytags
+    ADD CONSTRAINT highthroughputexpressiondatasetannotation_categorytags_highthroughputexpressiondatasetannotation_id_fk FOREIGN KEY (highthroughputexpressiondatasetannotation_id) REFERENCES highthroughputexpressiondatasetannotation(id);
+
+ALTER TABLE highthroughputexpressiondatasetannotation
+    ADD CONSTRAINT highthroughputexpressiondatasetannotation_dataprovider_id_fk FOREIGN KEY (dataprovider_id) REFERENCES dataprovider(id);
+
+ALTER TABLE highthroughputexpressiondatasetannotation_categorytags
+    ADD CONSTRAINT htpdatasetannotation_categorytags_categorytags_id_fk FOREIGN KEY (categorytags_id) REFERENCES vocabularyterm(id);
+
+ALTER TABLE highthroughputexpressiondatasetannotation_reference
+    ADD CONSTRAINT htpdatasetannotation_reference_htpdatasetannotation_id_fk FOREIGN KEY (highthroughputexpressiondatasetannotation_id) REFERENCES highthroughputexpressiondatasetannotation(id);
+
+ALTER TABLE highthroughputexpressiondatasetannotation_reference
+    ADD CONSTRAINT htpdatasetannotation_reference_references_id_fk FOREIGN KEY (references_id) REFERENCES reference(id);
+
+ALTER TABLE highthroughputexpressiondatasetannotation
+    ADD CONSTRAINT htpdatasetannotation_updatedby_id_fk FOREIGN KEY (updatedby_id) REFERENCES person(id);
+
+ALTER TABLE highthroughputexpressiondatasetannotation
+    ADD CONSTRAINT htpdatasetannotation_createdby_id_fk FOREIGN KEY (createdby_id) REFERENCES person(id);