Update vocabulary path to parse and return `nb:Diagnosis` options

alyssadai commented 1 year ago

Add workflow for the path /attributes/nb:Diagnosis/vocab that:

[x] Reads in a file of SNOMED diagnosis term-label mappings (downloaded from Athena) on startup + creates a lookup file
- a copy should probably be stored in the repo for now, under https://github.com/neurobagel/api/tree/main/vocab/backup_external
- The diagnosis term-label mappings can be found here https://github.com/neurobagel/annotation_tool/blob/main/static/diagnosisTerms.json
[x] Processes the mappings into a VocabLabelsResponse object
[x] append the missing terms (see below) to the SNOMED-CT .json dump
- already done in .json used by annotation tool
[x] update the code snippet in https://github.com/neurobagel/planning/issues/52 to also include the appended terms that are missing, so it is re-executable
~Allows only password-authenticated users to access that endpoint~

Other TODO:

[x] wrap requests to external vocab APIs in a try-except for httpx network errors (currently, if the network connection cannot be established if, e.g. the internet is down, an exception is raised and the app cannot start)
- [x] if catch is hit, raise informative warning and use local copy of vocab file

surchs commented 12 months ago

do we have a list of diagnoses that we would need for OpenNeuro but that aren't in our SNOMED-CT dump? Check https://github.com/neurobagel/annotation_tool/issues/591

@rmanaem could you dump the diff (ideally with labels) here

rmanaem commented 12 months ago

6 terms that are present in the open_neuro but not in this newly curated list:

neurobagel / api