test data failing

[stebo85]

Dear @rhancockn, @neurosutton, @bpinsard

@Remi-Gau and I are trying to get the HCPPipelines bids-app updated and tested again :)

We are currently running into the problem that the test data is not working, that's what we tried:

          wget https://raw.githubusercontent.com/bids-apps/maintenance-tools/main/utils/get_data_from_osf.sh
          bash get_data_from_osf.sh hcp_example_bids_v3
  
          docker run -ti --rm --read-only \
            -v ~/data/hcp_example_bids_v3:/bids_dataset \
              bids/${CIRCLE_PROJECT_REPONAME,,} \
                /bids_dataset \
                /outputs \
                participant --participant_label 100307 \
                --stages PreFreeSurfer \
                --processing_mode legacy \
                --license_key="*CxjskRdd7" \
                --n_cpus 2

Unfortunately this results in:

Traceback (most recent call last):
  File "/run.py", line 274, in <module>
    t1_spacing = layout.get_metadata(t1ws[0])["DwellTime"]
KeyError: 'DwellTime'

Exited with code exit status 1

Do you by any chance have an idea what this could be?

I also saw a couple of open pull requests. Would anyone of you be able to help us merge these pull requests and get this bidsapp updated and nicely working?

Thank you
Steffen

[neurosutton]

Would changing run.py L274 to t1_spacing = layout.get_metadata(t1ws[0]).get("DwellTime", 0) get most users past the error appropriately? If I understand the comments from #65 correctly, setting 0 as the default here in the get call would skip distortion correction. t1_spacing = layout.get_metadata(t1ws[0]).get("DwellTime", None) might be the better change, if the following comment is the preferred way forward.

@rhancockn Add error handling around t1_spacing = layout.get_metadata(t1ws[0])["DwellTime"] (and maybe t2_spacing = layout.get_metadata(t2ws[0])["DwellTime"]). If distortion correction is to be done, throw a descriptive error message about why this field is required. Otherwise, set t1_spacing = 'NONE'.

[Remi-Gau]

that would probably do it but that would require to rebuild the image which at the moment fails: https://app.circleci.com/pipelines/github/bids-apps/HCPPipelines/30/workflows/f2cad6b5-6f46-4c19-b2a0-71cc32c37b95/jobs/212

so the approach for now was at least make sure that when people pull the latest image from docker hub that it "runs properly" and hence trying to just make sure that original tests pass which apparently is not the case.

I can edit the data on OSF but just want to be sure that this is the right thing to do: I would have assumed that the latest image should work on the dataset that was present when it was first built.