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NCATSTranslator / testing

Materials and tools for testing Translator components
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Workflow - Gene - related_to - ChemicalSubstance (CHEBI:45783) #113

Open sstemann opened 3 years ago

sstemann commented 3 years ago

Query: workflow.json PK: Updated 9/7 - 8f60efd6-d125-4f95-8271-487928f61c28 (67356825-8425-4f50-bd5c-f3a1b5dc643d) Control: looking for results to be capped at 50 (via the workflow parameters) Results Tracking Sheet

image

cbizon commented 3 years ago

The link to the query is giving a 404?

andrewsu commented 3 years ago

I noticed the typo in the URL -- fixed it (though @sstemann should probably still confirm...)

cbizon commented 3 years ago

Aragorn shouldn't be returning a 500, but it doesn't implement these operations. From our smartapi registration:

"operations":["lookup","enrich_results","connect_knodes","score"]}
dkoslicki commented 3 years ago

@sstemann This may actually be a problem with the ARS, since POSTing the query directly to ARAX returns results as expected: https://arax.ncats.io/api/arax/v1.1/response/24144 (you can view the results here: https://arax.ncats.io/?r=24144) Perhaps @edeutsch or @MarkDWilliams can decipher the error message in the PK for ARAX (about a bad gateway):

undefined INFO:    ARS info: <html>
 <head><title>502 Bad Gateway</title></head>
 <body bgcolor="white">
 <center><h1>502 Bad Gateway</h1></center>
 <hr><center>nginx</center>
 </body>
 </html>
   undefined INFO:    ARS info: tr_ars.Server: nginx
   undefined INFO:    ARS info: tr_ars.Date: Fri, 03 Sep 2021 19:06:36 GMT
   undefined INFO:    ARS info: tr_ars.Content-Type: text/html
   undefined INFO:    ARS info: tr_ars.Content-Length: 166
   undefined INFO:    ARS info: tr_ars.Connection: keep-alive
   undefined INFO:    ARS info: tr_ars.reason: Bad Gateway
   undefined INFO:    ARS info: tr_ars.url: https://arax.ncats.io/api/arax/v1.1/query
edeutsch commented 3 years ago

This is the sort of error error you see when nginx can't reach the ARAX process. The time stamp here is last Friday midday when ARAX was known to be dead and waiting for Trung to reset the instance. So the 502 Bad Gateway means that ARAX was unreachable last Friday. Was fixed later in the day.

webyrd commented 3 years ago

Looks like Unsecret is getting answers from MolePro.

I won't be able to make it to today's standup, unfortunately. I'll be working on improving the plumbing of our TRAPI server this week and next.

Cheers,

--Will

On Tue, Sep 7, 2021 at 1:43 AM Eric Deutsch @.***> wrote:

This is the sort of error error you see when nginx can't reach the ARAX process. The time stamp here is last Friday midday when ARAX was known to be dead and waiting for Trung to reset the instance. So the 502 Bad Gateway means that ARAX was unreachable last Friday. Was fixed later in the day.

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sstemann commented 3 years ago

@dkoslicki @edeutsch thanks for the feedback - updated the PK and screenshots in the ticket

andrewsu commented 3 years ago

Also a note that ChemicalSubstance should probably be changed to SmallMolecule or another Biolink 2.2 class?

GregHydeDartmouth commented 2 years ago

CHP Now returns that it doesn't handle the workflow for overlay_compute_ngd operations and returns a 400 as expected.

https://arax.ncats.io/?source=ARS&id=04bcd6a4-bfe2-4f31-a35b-dceec12b4cdc