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nadeemlab / SPT

Spatial profiling toolbox for spatial characterization of tumor immune microenvironment in multiplex images
https://oncopathtk.org
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Add support for graph-transformer plugin #292

Closed CarlinLiao closed 9 months ago

CarlinLiao commented 10 months ago

Will close #268.

Per the tests, something seems to have broken with the apiserver initialization that could use a second look over before merging.

CarlinLiao commented 10 months ago

Removing that stray import fixed the major apiserver issue, but the test verifying the change to the way importance scores are indexed is still failing.

jimmymathews commented 9 months ago

Can you report the logs from the tests that failed?

CarlinLiao commented 9 months ago

I don't have them on this computer, it'll have to wait until the evening or tomorrow. It was just the apiserver importance module test though. If I recall correctly the issue was that the data object parsed from the JSON returned from the API query was empty.

I force rebuilt my data loaded images so I don't think that was the issue.

CarlinLiao commented 9 months ago

Upon inspection, the current implementation of GraphsAccess could potentially return multiple feature specifications. We decided that we should break out getting one feature specification as a helper function to ensure that it only comes back with one feature specification.

CarlinLiao commented 9 months ago

I separated the feature specification fetch in GraphsAccess so it'd always only return one or zero specifications, but I can't figure out why the test fails now.

CarlinLiao commented 9 months ago

All tests pass. It took like 10 or 20 minutes, but the total time at the end showed 219393s or 2.5 days, which I can assure you is a slight overestimate. This isn't the first time either.

jimmymathews commented 9 months ago

Tests pass for me.