[BI-1647] View Experiments: Observation Dataset Table#280
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mlm483
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Aug 7, 2023
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- One change requested for performance, I tested my suggested code change it was an order of magnitude faster locally for a large experiment (16731 Observations).
- Probably out of scope for this story, but if you see an easy way to tackle this performance story I just created, please do!
src/main/java/org/breedinginsight/brapps/importer/daos/BrAPIObservationUnitDAO.java
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| for (BrAPIObservationUnit observationUnit: observationUnits) { | ||
| String germplasmDbId = observationUnit.getGermplasmDbId(); | ||
| BrAPIGermplasm germplasm = this.germplasmService.getGermplasmByDBID(program.getId(), germplasmDbId).get() ; | ||
| observationUnit.putAdditionalInfoItem("gid", germplasm.getAccessionNumber()); | ||
| } |
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| for (BrAPIObservationUnit observationUnit: observationUnits) { | |
| String germplasmDbId = observationUnit.getGermplasmDbId(); | |
| BrAPIGermplasm germplasm = this.germplasmService.getGermplasmByDBID(program.getId(), germplasmDbId).get() ; | |
| observationUnit.putAdditionalInfoItem("gid", germplasm.getAccessionNumber()); | |
| } | |
| // Load germplasm for program into map. | |
| // TODO: if we use redis search, that may be more efficient than loading all germplasm for the program. | |
| HashMap<String, BrAPIGermplasm> germplasmByDbId = new HashMap<>(); | |
| this.germplasmService.getGermplasm(programId).forEach((germplasm -> germplasmByDbId.put(germplasm.getGermplasmDbId(), germplasm))); | |
| for (BrAPIObservationUnit observationUnit: observationUnits) { | |
| BrAPIGermplasm germplasm = germplasmByDbId.get(observationUnit.getGermplasmDbId()); | |
| observationUnit.putAdditionalInfoItem("gid", germplasm.getAccessionNumber()); | |
| } |
This is loading all Germplasm in the program from the cache for each observationUnit, which really hurts performance for large datasets. I would load all germplasm for the program into a HashMap (key: germplasmDbId => value: Germplasm object) outside of the for loop and then access by key inside the loop.
I think there's an eventual desire to use something like https://redis.io/docs/interact/search-and-query/ to make more fine-grained cache retrievals, but for now, just use a HashMap.
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Excellent! Thank you.
Done.
nickpalladino
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Aug 14, 2023
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| for (BrAPIObservationUnit observationUnit: observationUnits) { | ||
| String germplasmDbId = observationUnit.getGermplasmDbId(); | ||
| BrAPIGermplasm germplasm = this.germplasmService.getGermplasmByDBID(program.getId(), germplasmDbId).get() ; | ||
| observationUnit.putAdditionalInfoItem("gid", germplasm.getAccessionNumber()); | ||
| } |
| for (BrAPIObservationUnit observationUnit: observationUnits) { | ||
| String germplasmDbId = observationUnit.getGermplasmDbId(); | ||
| BrAPIGermplasm germplasm = this.germplasmService.getGermplasmByDBID(program.getId(), germplasmDbId).get() ; | ||
| observationUnit.putAdditionalInfoItem("gid", germplasm.getAccessionNumber()); |
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Can we add gid to BrAPIAdditionalInfoFields constants and use that here?
nickpalladino
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Aug 22, 2023
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Description
BI-1647 (View Experiments: Observation Dataset Table)
Added the ability to retrieve the GID in the additional information element of the Observation Unit.
Dependencies
bi-web: branch feature/BI-1647
Testing
see bi-web PR.
Checklist: