This is based on #3321 and includes those changes, they should be merged in first.
The focus of this PR is to support migrating from the XML API to JSON.
Changes how we pull in metadata from ENA to use the new JSON API
Completely reworks the Surveyor for SRA to handle either a sample or an experiment accession code.
Adds recursive dict flattening utility function for handling deeply nested JSON responses.
Adds tests with updated values from the API because some of them have changed since the migration.
Methods
Science:
Most of the attributes look very similar and are mapped according to common sense. I think it would be nice to have a one over specifically in _apply_metadata_to_experiment in surveyor/sra.py.
Types of changes
Bugfix (non-breaking change which fixes an issue)
New feature (non-breaking change which adds functionality)
Functional tests
n/a local tests
Checklist
[X] Lint and unit tests pass locally with my changes
[X] I have added tests that prove my fix is effective or that my feature works
Issue Number
3320
Purpose/Implementation Notes
This is based on #3321 and includes those changes, they should be merged in first.
The focus of this PR is to support migrating from the XML API to JSON.
Methods
Science:
_apply_metadata_to_experimentinsurveyor/sra.py.Types of changes
Functional tests
n/a local tests
Checklist
Screenshots
n/a