Support Location, Organization, Practitioner, and PractitionerRole #447
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| class BaseCovidCtakesTask(tasks.BaseNlpTask): | ||
| """Covid Symptom study task, to generate symptom lists from ED notes using cTAKES + a polarity check""" | ||
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| tags: ClassVar = {"covid_symptom", "gpu"} |
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This tags cleanup is unrelated - I just noticed it while adding new tasks.
I had made these tags obsolete when I added the nlp subtask and took out the no-longer-needed --task-filter support. So this is just some cleanup around that.
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| ARG ETL_VERSION | ||
| RUN [ -z "$ETL_VERSION" ] || sed -i "s/0\.0\.0/$ETL_VERSION/" /app/cumulus_etl/__init__.py | ||
| RUN [ -z "$ETL_VERSION" ] || sed -i "s/1\!0\.0\.0/$ETL_VERSION/" /app/cumulus_etl/__init__.py |
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The 1! prefix was slipping into the Docker releases, so this just updates the regex to chop that off.
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| // ** Location: https://www.hl7.org/fhir/R4/location.html ** | ||
| // This is not a patient-linked resource, so we aren't as worried about PHI here. | ||
| {"path": "Location.identifier.where(system='http://hl7.org/fhir/sid/us-npi')", "method": "keep"}, |
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One interesting thing to call out here - normally, we don't include identifier at all in resources, since it can have business-identifiers that could be PHI. Famously MRNs would qualify, but we do it for all patient-linked resources out of an abundance of caution.
But for these new resources, there's less risk of that. But still, in my sample Epic export, there are tax IDs in there and other Epic-internal IDs. While I guess that's not exactly secret intel either, I figured the standard NPI identifiers would be (should be?) good enough. And even that is a big deal, privacy wise - because for Practitioners below, you can get name etc from that. But practitioners have a different level of privacy expectation here. And matching by NPI could be useful for a study / internal QA / is sometimes the only useful identifier left after we strip out name, telephone, and address.
Open to tweak this, but that's my initial pitch 🤷
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i think we should kick this conversation up the chain - i buy it, but who knows about edge cases
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For posterity, our team talked about this internally - we figured this approach is fine. 👍
| // keep just the year for privacy (note: 90+ HIPAA grouping is done downstream in SQL | ||
| "cases": {"true": "$this.toString().replaceMatches('^(?<year>\\\\d+).*', '${year}')"}}, | ||
| // Skip Practitioner.photo | ||
| {"path": "Practitioner.qualification.identifier", "method": "keep"}, |
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Another identifier callout - this is identifying the qualification, not a human. So I figured, just allow all identifiers, no filtering here.
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Same thought - i buy it, let's check.
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| // ** Location: https://www.hl7.org/fhir/R4/location.html ** | ||
| // This is not a patient-linked resource, so we aren't as worried about PHI here. | ||
| {"path": "Location.identifier.where(system='http://hl7.org/fhir/sid/us-npi')", "method": "keep"}, |
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i think we should kick this conversation up the chain - i buy it, but who knows about edge cases
| // keep just the year for privacy (note: 90+ HIPAA grouping is done downstream in SQL | ||
| "cases": {"true": "$this.toString().replaceMatches('^(?<year>\\\\d+).*', '${year}')"}}, | ||
| // Skip Practitioner.photo | ||
| {"path": "Practitioner.qualification.identifier", "method": "keep"}, |
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Same thought - i buy it, let's check.
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