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Handle explain type of query #112
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This is not working as-expected. For example, we would expect KCNMA1 -(e0)-> biolink:NamedThing <-(e1)- TAAR1 to do the following:
Instead, something seems to be going on that makes the query (TRAPI, listed in the next comment) take a long time (like >30 minutes). Andrew tried separately running the one-hops (1 and 2) above (also listed in the next comment), and both were quick (<6 seconds each). I think these logs from my console are relevant. I used a JSON viewer to help me read the path parts. This is my interpretation of the logs:
LOGS:
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TRAPI query for KCNMA1 -(e0)-> biolink:NamedThing <-(e1)- TAAR1
Fast One Hop 1: KCNMA1-(e0)-> biolink:NamedThing
Fast One Hop 2: TAAR1-(e1)-> biolink:NamedThing
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This is a special kind of Explain-query we also want to support (see TRAPI query below): ChemicalSubstance celecoxib (PUBCHEM.COMPOUND:2662) -> PTGS1 (HGNC:9604). It's from a Translator standup meeting. The minimal expected behavior is:
Currently, BTE is only doing 1 and ID-resolving the gene ID in the query. Expected edges in the answer: For the example query, I would expect only the following edges to exist in the Response:
The TRAPI query:
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This functionality is high priority since it's come up in standup queries and the demo (Workflow D, maybe Workflow C). |
Note that @ericz1803 found this repo https://github.com/kevinxin90/explain.js from Kevin that handles the special case of explain queries with one intermediate node (used at https://biothings.io/explorer/explain). It is based on |
one-hop explain query:
two-hop explain query (version 1):
two-hop explain query (version 2):
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#112 (comment) |
This is the new result for this two hop query above, new logs will explain the process hopefully. |
For Workflow D:
Note:
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some queries with 2 intermediates:Note: This test query should have this path as a result:
This path should exist: Pathway REACT:R-HSA-1368082 <-> Gene NCBIGene:1374 <-> ChemicalSubstance CHEBI:35553 - Disease MONDO:0009287
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What the results object should look like:
For this query:
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Note: Kevin's opening query, reformatted now has results that look as expected. The query:
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The new query-handler handles these cases, this was checked during my testing process for the code. |
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