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UMLS data generator utility #1214

Merged
merged 1 commit into from
Dec 7, 2022
Merged

UMLS data generator utility #1214

merged 1 commit into from
Dec 7, 2022

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codyebberson
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@codyebberson codyebberson commented Dec 5, 2022

Checkpoint for a utility that generates bite sized files out of the 30 GB UMLS data set.

There is separate future work to ingest these files by the server. The terminologies are too big to be stored in the naive default "JSON string in a TEXT column" method.

Options for consideration:

  • Completely separate super admin endpoint to ingest the files directly - path of least resistance, allows for fine grained control over behavior
  • Accept huge ValueSet resources, but strip out all "concept" properties - more semantically correct, allows for end users to submit their own large terminologies

Reference: HAPI FHIR docs on importing terminologies: https://hapifhir.io/hapi-fhir/docs/tools/hapi_fhir_cli.html#upload-terminology

@codyebberson codyebberson requested a review from a team as a code owner December 5, 2022 15:48
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Coverage Status

Coverage remained the same at 94.071% when pulling ad00313 on cody-umls-data-generator into 6dbdb7f on main.

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sonarcloud bot commented Dec 5, 2022

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
No Duplication information No Duplication information

@reshmakh
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reshmakh commented Dec 6, 2022

Related to #992

@reshmakh reshmakh added fhir-datastore Related to the FHIR datastore, includes API and FHIR operations analytics Features and fixes related to analytics labels Dec 6, 2022
@codyebberson codyebberson merged commit 4ce5112 into main Dec 7, 2022
@codyebberson codyebberson deleted the cody-umls-data-generator branch December 7, 2022 20:18
@reshmakh reshmakh added the medications Features and fixes related to medications label Dec 11, 2022
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3 participants