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frostyfan109 / tranql

A Translator Query Language
https://researchsoftwareinstitute.github.io/data-translator/apps/tranql
MIT License
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Indigo endpoint does not return a knowledge map #37

Open frostyfan109 opened 5 years ago

frostyfan109 commented 5 years ago

Currently, any queries that involve the Indigo endpoint will fail if any statements querying Indigo are not the very last transition. This is because they have no knowledge_map, and therefore, it cannot continue because it lacks the mappings from Indigo. We should probably add the functionality to disable querying endpoints that don't have knowledge_maps unless it is the last transition, or else a large amount of complex queries from /schema will fail. Also, we could ask if they plan on adding a knowledge_map to their /query endpoint, which would allow us to utilize it for such queries.

On a semi-related note, Indigo's chemical_substance->targets->gene transition does not seem to work at all?

frostyfan109 commented 5 years ago

Due to the way that it has been built, it seems very complicated to accomplish what was suggested in this issue about allowing it only for the last transition. For now, Indigo is being removed from the schema until it is updated to contain a knowledge_map.

frostyfan109 commented 5 years ago

Perhaps we can construct a knowledge map on our end somehow? No

frostyfan109 commented 5 years ago

Indigo also returns strange type names which should be normalized. Things like "Disease" are returned instead of "disease". As one could imagine, this would be quite easy to fix. It would just check if the type was equal to any other types when case-insensitive, and, if so, it would adjust accordingly.