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IHEC / ihec-ecosystems

This repo is for code and documentation associated with the ihec-ecosystems working group
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Refatoring, busgfixes. Donor not working yet #85

Closed juettemann closed 4 years ago

juettemann commented 4 years ago

Testrun with missing DONOR attributes pass, seems like allof is not recognised in combination with required.

ilsley commented 4 years ago

The problem with donor is addressed in pull request #88. This should be reviewed first.

dzerbino commented 4 years ago

In that case, could we just delete this PR (ie. #85)?

juettemann commented 4 years ago

It is easier to keep this request and add the relevant changes from #88. As far as I can see I addressed everything except the biomaterial_type and change curie to uri, which are only 6 lines. This request contains the same adjustments to donor, the issue that it is not working is, as far as I can see, the way it is implemented, not the array issue addressed here. In addition to correcting several required sections, ordering them to make checking the easier, adding descriptions, the code is now also much more readable. Redoing all this will take a while, whereby changing the 6 lines should be relatively fast.

sitag commented 4 years ago

@juettemann can we get donor to work in this request before merging? it's also time we hook in a proper testbench so we can reference what bugs are fixed.

sitag commented 4 years ago

@juettemann we can always replicate donor inside each biomaterial type for now and come back to it once we have 1.0 validated.

juettemann commented 4 years ago

@sitag The donor is corrected in the sample. Either the issue is within the validator code, or the structure of the sample is incorrect. Replicating the donor is also what I will try today, should be done in the next 4-5 hours.

juettemann commented 4 years ago

Created new branch from master, tj_json_schema_update, deleting this one