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datalad / datalad-xnat

Track XNAT projects with DataLad
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Verify and implement CI test for NITRC IR #29

Closed mih closed 3 years ago

mih commented 3 years ago

This is a modified XNAT instance that ships other data types than DICOM.

Here is a possible public dataset to test against:

https://www.nitrc.org/ir/app/action/DisplayItemAction/search_element/xnat%3AprojectData/search_field/xnat%3AprojectData.ID/search_value/fcon_1000

jhuguetn commented 3 years ago

FYI, Any XNAT instance (no modification required) can coarsely handle imaging data types other than DICOM (eg. see CENTRAL05_E03795).
That's actually one of the reasons why pyxnat requires browsing Resources for each Scan entity before moving down and track scan Files (multiple formats of the imaging data may co-exist as resources).

Hope it helps. Good luck with the project, such an interesting initiative.

mih commented 3 years ago

Thanks for the feedback!

mih commented 3 years ago

With #48 I can query a NITRC IR project, but the download fails:

addurls(error): /tmp/nitrc/xnat_S01288/xnat_E01288/anat_mprage_anonymized/scan_mprage_anonymized.nii.gz (file) [AnnexBatchCommandError(AnnexBatchCommandError: 'addurl' [Error, annex reported failure for addurl (url='https://www.nitrc.org/data/experiments/xnat_E01288/scans/anat_mprage_anonymized/resources/7900/files/scan_mprage_anonymized.nii.gz'): {'command': 'addurl', 'success': False, 'input': ['https://www.nitrc.org/data/experiments/xnat_E01288/scans/anat_mprage_anonymized/resources/7900/files/scan_mprage_anonymized.nii.gz xnat_S01288/xnat_E01288/anat_mprage_anonymized/scan_mprage_anonymized.nii.gz'], 'error-messages': ['  download failed: Not Found'], 'file': 'xnat_S01288/xnat_E01288/anat_mprage_anonymized/scan_mprage_anonymized.nii.gz'}])]

Seems to be the same issue as #47, but in the table generation.