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nadeemlab / SPT

Spatial profiling toolbox for spatial characterization of tumor immune microenvironment in multiplex images (https://oncopathtk.org)
https://oncopathtk.org
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Make GNN plots available as an SPT CLI command and API endpoint #320

Closed CarlinLiao closed 3 months ago

CarlinLiao commented 4 months ago

To close #319.

CarlinLiao commented 4 months ago

Although I wanted to change the database query to be direct instead of through the API server, for expediency's sake + don't-fix-what-ain't-broke, I'll stick with the API server counts implementation and commit a thinner version of DataAccessor for now.

CarlinLiao commented 3 months ago

test/apiserver/unit_tests/record_counts1.txt and build/build_scripts/expected_table_counts.txt are identical. Is this redundancy necessary?

jimmymathews commented 3 months ago

This work entails updating the documentation in spt-data: https://github.mskcc.org/mathewj2/spt-data/tree/main/findings

Also, I suppose, committing the plot specification artifacts to spt-data for now. Similar to findings.

CarlinLiao commented 3 months ago

All tests pass except for workflow tests, which complain about default_study_lookup not being present. Not sure if it's unrelated or if the change to the first test database broke something.

jimmymathews commented 3 months ago

I would check that the new system of data-preloaded-images is getting used (in a recent update I moved these images to docker hub, so development doesn't require building them locally).

jimmymathews commented 3 months ago

test/apiserver/unit_tests/record_counts1.txt and build/build_scripts/expected_table_counts.txt are identical. Is this redundancy necessary?

We will have to check usage, probably the idea was that the test and build scripts would not need to reach into each other's directory contents.

CarlinLiao commented 3 months ago

If the data loaded images live remotely, and I've modified one of the data loaded images to have two importance score studies so the plotting has something to compare, would that cause an issue?

jimmymathews commented 3 months ago

Yes, this is the scenario where, when this PR is complete, we would update the docker hub images. I suppose for now you would need to make sure that your development setup is using your locally-built images. I'm not sure what docker does when both remote and local are available, I think it depends on the pull policy.

jimmymathews commented 3 months ago

Tests passed.