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bridgedb / create-bridgedb-metabolites

Create BridgeDb identity mapping files from HMDB, ChEBI, and Wikidata
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Jenkins build failure for names.rq #25

Open DeniseSl22 opened 3 years ago

DeniseSl22 commented 3 years ago

image

I think the build "fails" due to this item in the build options: image

(I've had a similar issue with the disease mapping db). I've removed the last build option for now, to check if the build will succeed (the .bridge file is being created).

DeniseSl22 commented 3 years ago

Mhh, now I'm getting the following failure:

curl: (18) transfer closed with outstanding read data remaining Build step 'Execute shell' marked build as failure Archiving artifacts Finished: FAILURE

DeniseSl22 commented 3 years ago

Seems to be related to names.rq (either timing out due to wikidata endpoint timeout, or Jenkins not receiving data anymore....).

Suggestion: limit query....

egonw commented 3 years ago

It happens now and then. Next tun often works again.

egonw commented 3 years ago

Can we conclude this just happens now and then and depends on the WDQS?

DeniseSl22 commented 3 years ago

I think so.... I ran the names.rq manually on the WD endpoint 2 hours ago, and also got a timeout But tried half an hour later, and then it worked..... so when the traffic on the WD endpoint is high, most likely we will get a timeout, and manually need to restart the job at a later stage. Or we should split up the names.rq query in two sections, and combine the results later in groovy..... @egonw ?

egonw commented 3 years ago

We should start using the regular API for things like this, i think

egonw commented 2 years ago

I discussed this today in the Telegram Wikidata group. The problem is the download timing out.