Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

SCRUM-3649 ensure to set phylogeneticOrderIndex to gene of DA and not… #1168

Merged
merged 1 commit into from
Mar 14, 2024
Merged

SCRUM-3649 ensure to set phylogeneticOrderIndex to gene of DA and not… #1168

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
11 changes: 6 additions & 5 deletions ...n/java/org/alliancegenome/indexer/indexers/curation/DiseaseAnnotationCurationIndexer.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -197,13 +197,14 @@ private List<GeneDiseaseAnnotationDocument> createGeneDiseaseAnnotationDocuments
HashMap<String, GeneDiseaseAnnotationDocument> lookup = new HashMap<>();

for (DiseaseAnnotation da : entry.getValue().getRight()) {
Gene gene = entry.getValue().getLeft();
VocabularyTerm relation = relationIsImplicatedIn;

if (da instanceof GeneDiseaseAnnotation gda) {
if (da instanceof GeneDiseaseAnnotation) {
relation = da.getRelation();
} else {
DiseaseAnnotation generatedAnnotation = createImplicatedDA(da);
addCreatedDiseaseAnnotationsImplicatedToMap(generatedAnnotation, entry.getValue().getKey());
addCreatedDiseaseAnnotationsImplicatedToMap(generatedAnnotation, gene);
}

String key = relation.getName() + "_" + da.getObject().getName() + "_" + da.getNegated();
Expand All @@ -220,8 +221,8 @@ private List<GeneDiseaseAnnotationDocument> createGeneDiseaseAnnotationDocuments

if (gdad == null) {
gdad = new GeneDiseaseAnnotationDocument();
gdad.setSubject(entry.getValue().getLeft());
HashMap<String, Integer> order = SpeciesType.getSpeciesOrderByTaxonID(entry.getValue().getLeft().getTaxon().getCurie());
gdad.setSubject(gene);
HashMap<String, Integer> order = SpeciesType.getSpeciesOrderByTaxonID(gene.getTaxon().getCurie());
gdad.setSpeciesOrder(order);
gdad.setRelation(relation);
String generatedRelationString = getGeneratedRelationString(gdad.getRelation().getName(), da.getNegated());
Expand All @@ -248,7 +249,7 @@ private List<GeneDiseaseAnnotationDocument> createGeneDiseaseAnnotationDocuments
gdad.addPubMedPubModID(getPubmedPubModID(da.getSingleReference()));
gdad.addPrimaryAnnotation(da);
gdad.addBasedOnGenes(da.getWith());
gdad.setPhylogeneticSortingIndex(getPhylogeneticSortOrder(da.getSubjectTaxonCurie()));
gdad.setPhylogeneticSortingIndex(getPhylogeneticSortOrder(gene.getTaxon().getCurie()));
}
ph.progressProcess();
ret.addAll(lookup.values());
Expand Down
Loading