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hubmapconsortium / portal-visualization

Given HuBMAP Dataset JSON, creates a Vitessce configuration
MIT License
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NickAkhmetov/HMP-540/Update `get_view_config_builder` to use `get_assaytype` instead of `get_assay` #82

Closed NickAkhmetov closed 9 months ago

NickAkhmetov commented 9 months ago

This PR adds support for the assaytype endpoint instead of get_assay. This is a breaking change which requires revisions to support, so it is accompanied by a minor version change (to v0.1.0)

I validated the functionality of each builder using a local portal instance (using the branch https://github.com/hubmapconsortium/portal-ui/pull/3361); each visualization appeared to work as expected when pointed at prod data. I have also updated the tests and fixtures accordingly to reflect the new interface.

TODOs from December 14

- Image pyramid visualizations are functional - I have identified UUID's for datasets that trigger each of the given assaytype builders and created assaytype fixtures corresponding to those UUID's - I updated the other "good" test fixtures' UUIDs to match the identified entities - still need to debug the "good entity" tests and get them to actually pass - still need to come up with a strategy to handle the "bad entity" tests

TODOs from December 12

- Troubleshoot seqfish image pyramid display - update current uses of `get_assay` within portal-visualization