Jerome Kelleher

Update protocol errors tests.

1

Update `tests/unit/test_protocol_errors.py``to test all search endpoints. Run the tests using``nosetests -vs tests/unit/test_protocol_errors.py``. - Remove the TODO comment, and the check requestClass being in the set of supported methods. (Ignore comment...

In ga4gh/frontend.py we have no test coverage on the MethodNotAllowedException branch of the handleFlaskGetRequest, handleFlaskListRequest and handleFlaskPostRequest functions. This module handles all the HTTP transactions. We need to add test...

Data driven tests allow us to run a set of tests against a range of input files. This is very useful for ...quirky... bioinformatics file formats, so we can verify...

OIDC documentation insufficient

1

The documentation for setting up OIDC authentication is fragmentary and insufficient. We should have a top-level page dedicated to authentication, where we clearly explain how it all works, as well...

Release tarball contains tests and test data

2

The release tarball currently contains all of our test cases and test data. This seems like a bad thing, since in the nominal case of a `pip install` these will...

Authorisation by datasets

1

Now that we have authentication via OIC, it's time to start thinking about authorisation of users to access data. A simple model is as follows: 1. All authenticated users can...

CRAM support feasibility

10

An initial quick hack seems to imply that CRAM support might be quite easy to add. The only difficult bit is probably ensuring that the required references are present, and...

prevProgramId broken in readGroup.program

4

The output for the prevProgramId field is not working as intended. Right now we get ``` json { "commandLine": "bwa aln -q 15 -f $sai_file $reference_fasta $fastq_file\tPP:bwa_index", "prevProgramId": null, "id":...

Assumes #1166 has been merged. The `SimulatedDataset` and `SimulatedDataRepository` class now do very little. We should remove these classes, and consolidate the functionality into a factory function (`simulated_repository_factory`?), which takes...

It would be very useful to get some insight into how a full installation of the server with auth behaves. For example, it would be very useful to record how...