text2fhir: add new submodule for converting NLP to FHIR #32
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mikix
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- Adds some new methods in ctakesclient.text2fhir like nlp_condition or nlp_observation that take a ctakes MatchText and return a fhirclient resource for it. - These returned resources include extensions for defining polarity, derivation span, and what source algorithm generated the NLP.
comorbidity
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Oct 24, 2022
| self.conceptAttributes = [] | ||
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| # sort list of concepts ensuring same ordering | ||
| unsorted = list(UmlsConcept(c) for c in source.get('conceptAttributes')) |
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OK. Curious when is conceptAttributes missing? Is this only when using "Identified" custom dictionary annotations that are from the 3 column BSV? Either way, seems like a good check.
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Ah yeah this was an unrelated change I just had sitting on my laptop from earlier testing. I had manually constructed a MatchText I think in a test file and hit an exception because it didn't have a conceptAttributes defined. Easy enough to fix in the test file (I just added the field). But I had also removed the requirement here and am just now committing it.
It should always be defined anyway, but I figured no harm in being a bit graceful when its not.
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This only includes five new public methods:
Each will take a
MatchTextand some other parameters and return afhirclientresource. The id will be randomly generated.