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Adding new indexes for htpdatasample #1689

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Oct 15, 2024
Merged

Adding new indexes for htpdatasample #1689

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42368f7
Adding new indexes for htpdatasample
VarunReddy1111 Oct 14, 2024
aea2179
Added _index to biosamplegenomicinfo indexes
VarunReddy1111 Oct 15, 2024
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5 changes: 5 additions & 0 deletions ...main/java/org/alliancegenome/curation_api/model/entities/BioSampleGenomicInformation.java
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Expand Up @@ -29,6 +29,11 @@
@Schema(name = "BioSampleGenomicInformation", description = "POJO that represents the BioSampleGenomicInformation")
@AGRCurationSchemaVersion(min = "2.7.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = { AuditedObject.class })
@Indexed
@Table(indexes = {
@Index(name = "biosamplegenomicinfo_bioSampleAllele", columnList = "bioSampleAllele_id"),
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@Index(name = "biosamplegenomicinfo_bioSampleAgm", columnList = "bioSampleAgm_id"),
@Index(name = "biosamplegenomicinfo_bioSampleAgmType", columnList = "bioSampleAgmType_id")
})
public class BioSampleGenomicInformation extends AuditedObject {

@IndexedEmbedded(includePaths = {
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16 changes: 12 additions & 4 deletions .../org/alliancegenome/curation_api/model/entities/HTPExpressionDatasetSampleAnnotation.java
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Expand Up @@ -36,10 +36,18 @@
@Schema(name = "HTPExpressionDatasetSampleAnnotation", description = "POJO that represents the HighThroughputExpressionDatasetSampleAnnotation")
@AGRCurationSchemaVersion(min = "2.7.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = { AuditedObject.class })
@Table(indexes = {
@Index(name = "htpdatasetsampleannotation_htpExpressionSample_index", columnList = "htpExpressionSample_id"),
@Index(name = "htpdatasetsampleannotation_dataprovider_index", columnList = "dataprovider_id"),
@Index(name = "htpdatasetsampleannotation_createdby_index", columnList = "createdby_id"),
@Index(name = "htpdatasetsampleannotation_updatedby_index", columnList = "updatedby_id")
@Index(name = "htpdatasample_htpExpressionSample_index", columnList = "htpExpressionSample_id"),
@Index(name = "htpdatasample_htpExpressionSampleType_index", columnList = "htpExpressionSampleType_id"),
@Index(name = "htpdatasample_expressionAssayUsed_index", columnList = "expressionAssayUsed_id"),
@Index(name = "htpdatasample_htpExpressionSampleAge_index", columnList = "htpExpressionSampleAge_id"),
@Index(name = "htpdatasample_genomicInformation_index", columnList = "genomicInformation_id"),
@Index(name = "htpdatasample_microarraySampleDetails_index", columnList = "microarraySampleDetails_id"),
@Index(name = "htpdatasample_geneticSex_index", columnList = "geneticSex_id"),
@Index(name = "htpdatasample_sequencingFormat_index", columnList = "sequencingFormat_id"),
@Index(name = "htpdatasample_taxon_index", columnList = "taxon_id"),
@Index(name = "htpdatasample_dataprovider_index", columnList = "dataprovider_id"),
@Index(name = "htpdatasample_createdby_index", columnList = "createdby_id"),
@Index(name = "htpdatasample_updatedby_index", columnList = "updatedby_id")
})
public class HTPExpressionDatasetSampleAnnotation extends AuditedObject {

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24 changes: 24 additions & 0 deletions src/main/resources/db/migration/v0.37.0.60__htpdatasample_adding_new_indexes.sql
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@@ -0,0 +1,24 @@
--Renaming existing indexes
ALTER INDEX htpdatasetsampleannotation_createdby_index RENAME TO htpdatasample_createdby_index;
ALTER INDEX htpdatasetsampleannotation_updatedby_index RENAME TO htpdatasample_updatedby_index;
ALTER INDEX htpdatasetsampleannotation_dataprovider_index RENAME TO htpdatasample_dataprovider_index;
ALTER INDEX htpdatasetsampleannotation_htpexpressionsample_index RENAME TO htpdatasample_htpexpressionsample_index;

--Creating new indexes
CREATE INDEX htpdatasample_htpExpressionSampleType_index ON htpexpressiondatasetsampleannotation USING btree (htpExpressionSampleType_id);
CREATE INDEX htpdatasample_expressionAssayUsed_index ON htpexpressiondatasetsampleannotation USING btree (expressionAssayUsed_id);
CREATE INDEX htpdatasample_htpExpressionSampleAge_index ON htpexpressiondatasetsampleannotation USING btree (htpExpressionSampleAge_id);
CREATE INDEX htpdatasample_genomicInformation_index ON htpexpressiondatasetsampleannotation USING btree (genomicInformation_id);
CREATE INDEX htpdatasample_microarraySampleDetails_index ON htpexpressiondatasetsampleannotation USING btree (microarraySampleDetails_id);
CREATE INDEX htpdatasample_geneticSex_index ON htpexpressiondatasetsampleannotation USING btree (geneticSex_id);
CREATE INDEX htpdatasample_sequencingFormat_index ON htpexpressiondatasetsampleannotation USING btree (sequencingFormat_id);
CREATE INDEX htpdatasample_taxon_index ON htpexpressiondatasetsampleannotation USING btree (taxon_id);

CREATE INDEX biosamplegenomicinfo_bioSampleAllele ON biosamplegenomicinformation USING btree (bioSampleAllele_id);
CREATE INDEX biosamplegenomicinfo_bioSampleAgm ON biosamplegenomicinformation USING btree (bioSampleAgm_id);
CREATE INDEX biosamplegenomicinfo_bioSampleAgmType ON biosamplegenomicinformation USING btree (bioSampleAgmType_id);

--Adding 3 new htp category tags
INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'bulk RNA-seq', id FROM vocabulary WHERE vocabularylabel = 'data_set_category_tags';
INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'single cell RNA-seq', id FROM vocabulary WHERE vocabularylabel = 'data_set_category_tags';
INSERT INTO vocabularyterm (id, name, vocabulary_id) SELECT nextval('vocabularyterm_seq'), 'spatial RNA-seq', id FROM vocabulary WHERE vocabularylabel = 'data_set_category_tags';
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