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SCRUM-4667 make AgmAgmAssociation live under the general AgmAssociati… #1816

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SCRUM-4667 make AgmAgmAssociation live under the general AgmAssociati… #1816

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81f645d
SCRUM-4667 make AgmAgmAssociation live under the general AgmAssociati…
cmpich Jan 22, 2025
5c820c3
SCRUM-4667 fix renaming fallout
cmpich Jan 23, 2025
fed7118
SCRUM-4667 removing individual bulkload tables entries
cmpich Jan 23, 2025
a6769dc
SCRUM-4667 fix sql query ordering
cmpich Jan 23, 2025
c831a30
SCRUM-4667 fix review suggestions
cmpich Jan 24, 2025
d4456f1
SCRUM-4667 fix checkstyle
cmpich Jan 25, 2025
0370e53
SCRUM-4667 fix test errors
cmpich Jan 27, 2025
abeec4c
SCRUM-4667 rename indexes and FK constraints
cmpich Jan 30, 2025
46b9151
Merge branch 'alpha' into SCRUM-4667
cmpich Jan 30, 2025
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2 changes: 0 additions & 2 deletions src/main/java/org/alliancegenome/curation_api/jobs/executors/BulkLoadJobExecutor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -107,8 +107,6 @@ public void process(BulkLoadFileHistory bulkLoadFileHistory, Boolean cleanUp) th
if (loadType == AGM_ASSOCIATION || loadType == FULL_INGEST) {
agmStrAssociationExecutor.execLoad(bulkLoadFileHistory, cleanUp);
agmAlleleAssociationExecutor.execLoad(bulkLoadFileHistory, cleanUp);
}
if (loadType == AGM_AGM_ASSOCIATION || loadType == FULL_INGEST) {
agmAgmAssociationExecutor.execLoad(bulkLoadFileHistory, cleanUp);
}

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2 changes: 1 addition & 1 deletion src/main/java/org/alliancegenome/curation_api/model/entities/AffectedGenomicModel.java
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Expand Up @@ -113,7 +113,7 @@ public class AffectedGenomicModel extends GenomicEntity {
"agmAssociationObject.secondaryIdentifiers",
"agmAssociationObject.secondaryIdentifiers_keyword"
})
@OneToMany(mappedBy = "agmAssociationObject", cascade = CascadeType.ALL, orphanRemoval = true)
@OneToMany(mappedBy = "agmAgmAssociationObject", cascade = CascadeType.ALL, orphanRemoval = true)
@JsonView({View.FieldsAndLists.class, View.AffectedGenomicModelDetailView.class})
private List<AgmAgmAssociation> agmAgmObjectAssociations;
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2 changes: 1 addition & 1 deletion ...ncegenome/curation_api/model/entities/associations/agmAssociations/AgmAgmAssociation.java
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Expand Up @@ -61,5 +61,5 @@ public class AgmAgmAssociation extends Association {
@ManyToOne
@JsonView({View.FieldsOnly.class})
@JsonIgnoreProperties({"agmAgmAssociations", "agmAgmObjectAssociations", "agmSequenceTargetingReagentAssociations"})
private AffectedGenomicModel agmAssociationObject;
private AffectedGenomicModel agmAgmAssociationObject;
}
2 changes: 1 addition & 1 deletion ...cegenome/curation_api/services/associations/agmAssociations/AgmAgmAssociationService.java
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Expand Up @@ -144,7 +144,7 @@ private void addAssociationToAgm(AgmAgmAssociation association) {
}

private void addAssociationToStr(AgmAgmAssociation association) {
AffectedGenomicModel str = association.getAgmAssociationObject();
AffectedGenomicModel str = association.getAgmAgmAssociationObject();
List<AgmAgmAssociation> currentAssociations = str.getAgmAgmAssociations();
if (currentAssociations == null) {
currentAssociations = new ArrayList<>();
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4 changes: 2 additions & 2 deletions ...i/services/validation/dto/associations/agmAssociations/AgmAgmAssociationDTOValidator.java
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Expand Up @@ -84,15 +84,15 @@ public AgmAgmAssociation validateAgmAgmAssociationDTO(AgmAgmAssociationDTO dto,
}
}

if (association.getAgmAssociationObject() == null && !StringUtils.isBlank(dto.getAgmObjectIdentifier())) {
if (association.getAgmAgmAssociationObject() == null && !StringUtils.isBlank(dto.getAgmObjectIdentifier())) {

AffectedGenomicModel object = agmService.findByIdentifierString(dto.getAgmObjectIdentifier());
if (object == null) {
response.addErrorMessage("agm_object_identifier", ValidationConstants.INVALID_MESSAGE + " (" + dto.getAgmObjectIdentifier() + ")");
} else if (beDataProvider != null && !object.getDataProvider().getAbbreviation().equals(beDataProvider.sourceOrganization)) {
response.addErrorMessage("agm_object_identifier", ValidationConstants.INVALID_MESSAGE + " for " + beDataProvider.name() + " load (" + dto.getAgmObjectIdentifier() + ")");
} else {
association.setAgmAssociationObject(object);
association.setAgmAgmAssociationObject(object);
}
}
association = validateAuditedObjectDTO(association, dto);
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