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[ALS-5656] Make TimeSeriesProcessor handle missing concept paths #97

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merged 1 commit into from
Jan 10, 2024
Merged

[ALS-5656] Make TimeSeriesProcessor handle missing concept paths #97

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13 changes: 13 additions & 0 deletions ...essing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/AbstractProcessor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -667,6 +667,19 @@ protected PhenoCube getCube(String path) {
}
}

/**
* Get a cube without throwing an error if not found.
* Useful for federated pic-sure's where there are fewer
* guarantees about concept paths.
*/
protected Optional<PhenoCube<?>> nullableGetCube(String path) {
try {
return Optional.ofNullable(store.get(path));
} catch (InvalidCacheLoadException | ExecutionException e) {
return Optional.empty();
}
}

public TreeMap<String, ColumnMeta> getDictionary() {
return phenotypeMetaStore.getMetaStore();
}
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7 changes: 4 additions & 3 deletions ...sing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/TimeseriesProcessor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -103,11 +103,12 @@ private void addDataForConcepts(Collection<String> pathList, Set<String> exporte
continue;
}
ArrayList<String[]> dataEntries = new ArrayList<String[]>();
PhenoCube<?> cube = abstractProcessor.getCube(conceptPath);
if(cube == null) {
log.warn("Attempting export of non-existant concept: " + conceptPath);
Optional<PhenoCube<?>> maybeCube = abstractProcessor.nullableGetCube(conceptPath);
if(maybeCube.isEmpty()) {
log.warn("Attempting export of non-existant concept: {}", conceptPath);
continue;
}
PhenoCube<?> cube = maybeCube.get();
log.debug("Exporting " + conceptPath);
List<?> valuesForKeys = cube.getValuesForKeys(idList);
for (Object kvObj : valuesForKeys) {
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