fix: make i2b2 transforms faster by skipping fhirclient #158
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Much like the recent change to drop fhirclient objects from our core ETL loop, this drops them from the i2b2 conversion code. Speeds are improved by 50-70%. The only remaining use of fhirclient is for its oauth bits in our bulk export code. There are also two tiny i2b2 changes, while I was there: - For Condition, mark ICD10PROC/ICD9PROC as icd-10-pcs/icd-9-pcs systems, rather than our custom i2b2 system. - For Observation, if the tval_char isn't one of the known covid test results (Positive/Negative/Absent), stop converting it to Absent, and just leave them as-is, marked with our custom i2b2 system url.
mikix
commented
Jan 26, 2023
Comment on lines
-176
to
+146
| lab_result = "Absent" | ||
| observation.valueCodeableConcept = make_concept( | ||
| external_mappings.SNOMED_LAB_RESULT[lab_result], "http://snomed.info/sct", display=lab_result | ||
| ) | ||
| lab_result = obsfact.tval_char | ||
| lab_result_system = "http://cumulus.smarthealthit.org/i2b2" | ||
| observation["valueCodeableConcept"] = make_concept(lab_result, lab_result_system, display=obsfact.tval_char) |
There was a problem hiding this comment.
This is one of the two actual i2b2 changes: don't massage unknown things to Absent
Comment on lines
+180
to
+185
| elif i2b2_sys in ["ICD10PROC"]: | ||
| i2b2_sys = "http://hl7.org/fhir/sid/icd-10-pcs" | ||
| elif i2b2_sys in ["ICD9", "ICD-9"]: | ||
| i2b2_sys = "http://hl7.org/fhir/sid/icd-9-cm" | ||
| elif i2b2_sys in ["ICD9PROC"]: | ||
| i2b2_sys = "http://hl7.org/fhir/sid/icd-9-pcs" |
There was a problem hiding this comment.
This is the other change: a couple new recognized systems.
dogversioning
approved these changes
Jan 26, 2023
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Description
Much like the recent change to drop fhirclient objects from our core ETL loop, this drops them from the i2b2 conversion code.
Speeds are improved by 50-70%.
The only remaining use of fhirclient is for its oauth bits in our bulk export code.
There are also two tiny i2b2 changes, while I was there:
Checklist
docs/) needs to be updated