Look for human-readable names for conditions #3112
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #3112 +/- ##
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+ Coverage 87.03% 91.53% +4.50%
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Files 221 118 -103
Lines 13664 7074 -6590
Branches 708 738 +30
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- Hits 11892 6475 -5417
+ Misses 1763 590 -1173
Partials 9 9
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JNygaard-Skylight
requested review from
akasper,
angelathe,
austin-hall-skylight,
BobanL,
gordonfarrell,
lina-roth,
mcmcgrath13 and
robertmitchellv
as code owners
… look up human-readable name. Also add fallbacks to text
…ncept, and clean up text logic
…jnygaard-skylight:CDCgov/phdi into josh/message-parser-readable-conditions
mcmcgrath13
reviewed
Jan 17, 2025
| @@ -349,7 +349,7 @@ | |||
| } | |||
| }, | |||
| "condition": { | |||
| "fhir_path": "Observation.valueCodeableConcept.coding.display", | |||
| "fhir_path": "iif(Observation.valueCodeableConcept.text.exists(), Observation.valueCodeableConcept.text, Observation.valueCodeableConcept.coding.display)", | |||
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does the display need a first since there can be multiple?
mcmcgrath13
reviewed
Jan 17, 2025
| None, | ||
| ) | ||
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| if condition_code: |
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Suggested change
| if condition_code: | |
| if condition_code is not None: |
mcmcgrath13
reviewed
Jan 17, 2025
Comment on lines
+266
to
+267
| elif "display" in condition_code: | ||
| resource["valueCodeableConcept"]["text"] = condition_code["display"] |
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what's the thinking around including the display as a fallback? the display would be in the resulting fhir bundle either way, right? so it's not stamping new/outside info
mcmcgrath13
reviewed
Jan 17, 2025
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| Example: | ||
| $ python seed_rckms_database.py <archive.zip> <database.db> | ||
| A significantly paired down version of the original script to seed the RCKMS database. This script will extract the conditions from the RCKMS CSV in assets (downloaded from https://www.rckms.org/content-repository) files and load them into the SQLite database. |
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Suggested change
| A significantly paired down version of the original script to seed the RCKMS database. This script will extract the conditions from the RCKMS CSV in assets (downloaded from https://www.rckms.org/content-repository) files and load them into the SQLite database. | |
| A significantly pared down version of the original script to seed the RCKMS database. This script will extract the conditions from the RCKMS CSV in assets (downloaded from https://www.rckms.org/content-repository) files and load them into the SQLite database. |
mcmcgrath13
reviewed
Jan 17, 2025
| "VALUES (:snomed, 'http://snomed.info/sct', :name) " | ||
| "ON CONFLICT DO NOTHING", | ||
| condition.__dict__, | ||
| "INSERT INTO conditions (id, system, name, description) VALUES (?, ?, ?, ?)", |
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do we ever get conflicts in practice?
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PULL REQUEST
Summary
The message-parser config the seed script uses is not getting human readable names.
Related Issue
Fixes # n/a
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