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TASK-5571 Autocomplete with ontologies not working for CMH #686

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merged 2 commits into from
Feb 5, 2024
Merged

TASK-5571 Autocomplete with ontologies not working for CMH #686

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0218f40
lib: ignore the query parameter apiKey when building the BSON object …
jtarraga Feb 1, 2024
ed83935
lib: use ParamConstants to the parameters name (dataRelease and apiKe…
jtarraga Feb 2, 2024
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14 changes: 11 additions & 3 deletions cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/OntologyMongoDBAdaptor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -64,6 +64,8 @@ public CellBaseIterator<OntologyTerm> iterator(OntologyQuery query) throws CellB
QueryOptions queryOptions = query.toQueryOptions();

MongoDBCollection mongoDBCollection = getCollectionByRelease(mongoDBCollectionByRelease, query.getDataRelease());
System.out.println("ontology mongodb adaptor: mongoDBCollection = " + mongoDBCollection.toString() + ", data release = "
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+ query.getDataRelease());
MongoDBIterator<OntologyTerm> iterator = mongoDBCollection.iterator(null, bson, projection, CONVERTER, queryOptions);
return new CellBaseMongoDBIterator<>(iterator);
}
Expand Down Expand Up @@ -114,9 +116,15 @@ public Bson parseQuery(OntologyQuery query) {
try {
for (Map.Entry<String, Object> entry : query.toObjectMap().entrySet()) {
String dotNotationName = entry.getKey();
if (!"dataRelease".equals(dotNotationName)) {
Object value = entry.getValue();
createAndOrQuery(value, dotNotationName, QueryParam.Type.STRING, andBsonList);
switch (dotNotationName) {
case "dataRelease":
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case "apiKey":
// Nothing to do
break;
default: {
Object value = entry.getValue();
createAndOrQuery(value, dotNotationName, QueryParam.Type.STRING, andBsonList);
}
}
}
} catch (IllegalAccessException e) {
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