Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Adds client #3

Open
wants to merge 8 commits into
base: development
Choose a base branch
from
Open

Adds client #3

wants to merge 8 commits into from

Conversation

bwalsh
Copy link
Collaborator

@bwalsh bwalsh commented Aug 13, 2024 •
edited
Loading

Use Case:

As a fhir-aggregator user, I need a way to connect to FHIR servers, determine their contents and run queries.

This PR:

  • Adds a client with plugin authorization modules
  • Adds convenience methods to interrogate servers' CapabilityStatement and ResearchStudy objects
  • Harvests test fixtures to be used for unit tests see here
  • Simplifies and aggregates ResearchStudy into a tsv

Decision log:

Installation:

pip install fhir-aggregator==0.2rc2

To install development dependencies
pip install -r requirements-dev.txt

Testing:

Unit tests:

  • run pytest tests/unit

Integration tests:

  • Please see tests/fixtures/README.md about getting a dbgap token
  • run pytest tests/integration

@bwalsh bwalsh requested review from kellrott and teslajoy August 13, 2024 01:47
@teslajoy
Copy link
Member

Unit test passes after installing inflection module 👍 LGTM

For integration test - not sure about the syntax of dbgap-task-specific-token.json or where the last sentence "Consult the API documentation for how to include the token in your request to the API" is referring to.

@bwalsh
Copy link
Collaborator Author

bwalsh commented Aug 14, 2024 •
edited
Loading

@teslajoy

For integration test - not sure about the syntax of dbgap-task-specific-token.json or where the last sentence "Consult the API documentation for how to include the token in your request to the API" is referring to.

I've updated instructions. See 94f6931

image

@bwalsh
Copy link
Collaborator Author

bwalsh commented Aug 14, 2024

@teslajoy

fhir_aggregator.client.smart_auth.FHIRAuthError: Failed to get gcloud_access_token [Errno 2] No such file or directory: 'gcloud'

I've added code to skip that test if gcloud or anvil access not available

teslajoy
teslajoy approved these changes Aug 15, 2024
View reviewed changes
Copy link
Member

@teslajoy teslajoy left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

LGTM 👍

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@teslajoy teslajoy teslajoy approved these changes

@kellrott kellrott Awaiting requested review from kellrott

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@bwalsh @teslajoy