Remodeling of range for analyte_cateogry #2249
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…m) that inherit from AnalyteCategoryEnum minus certain invalid PVs (ex NucleotideSequencingEnum has no PV metaproteome). assigned NucleotideSequencing and MassSpectrometry subclasses these enums in analyte_category. added two new tests to invalid folder (NucleotideSequencing-working.yaml and MassSpectrometry-working.yaml) which should allow test to pass because they use nonpermissible values (metaproteome and metagenome respectively) in analyte_category. BUT test is failing when these are in the invalid folder and passing when they're in the valid folder. need to figure out why
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…into-types-allowable-for-nucleotidesequencing-and-massspectrometry
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@aclum and @turbomam FYI, neither @samobermiller or I could actually get the inheritance on the "sub Enums" to result in properly validating or invalidating examples (see this example src/data/invalid/MassSpectrometry-working.yaml in this branch validates but it should not). We tried a few different things to no avail. We only opened this PR to see if the documentation would render appropriately (it doesn't). Just to give you a heads up about this branch and PR. I don't think @samobermiller or I plan to pick it back up anytime soon (we were using it as a training example for how to write and test example yaml data). |
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This does not appear to be working properly based on the passing invalid data MassSpectrometry-working.yaml, it should fail b/c of an invalid analyte_category PV. |
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@kheal yes, I see that now. |
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cc @pkalita-lbl in case you have any linkml insights |
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The JSON Schema generator only handles explicitly defined permissible values at the moment: https://github.com/linkml/linkml/blob/5cc5a16e345d3ee5233a193eba4909a8999b43db/linkml/generators/jsonschemagen.py#L426-L457 So, in particular, it doesn't have any logic yet to deal with |
aclum
changed the title
NucleotideSequencing and MassSpectrometry, post berkeley
aclum
changed the title
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I will wait until the 12/16 release to merge this in but @turbomam @sierra-moxon @kheal @mslarae13 I need at least one reviewer on this |
| @@ -413,7 +413,7 @@ slots: | |||
| description: > | |||
| The type of analyte(s) that were measured in the data generation process and analyzed | |||
| in the Workflow Chain | |||
| range: AnalyteCategoryEnum | |||
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👍 - so for now, we fall back to "string" for the range of analyte_category if not otherwise defined in slot_usage.
aclum
deleted the
2154-berkeley-breakdown-analytecategoryenum-into-types-allowable-for-nucleotidesequencing-and-massspectrometry
branch
This PR replaces AnalyteCategoryEnum with NucelotideSequencingEnum and MassSpectrometryEnum and adds titles to the corresponding permissible values
fixes #2154