Export as GPAD is not working....

[cooperl09]

Export as GPAD is not working, I have tried various models Get the following Error:

Proxy Error The proxy server received an invalid response from an upstream server. The proxy server could not handle the request GET /download/gomodel:592dd65c00000001/gpad. Reason: Error reading from remote server

Seems to be working fine on GO Noctua....

[kltm]

Besides something going on specific to your end, there are a couple things that could be going wrong. Is this change in behavior at all related to updates in the client or server version? As well, it might be good to give a time for this error and check the minerva logs.

[elserj]

The error isn't consistent. Sometimes it returns without error, although the gpad header is the only line. Noctua log complains of a timeout error on the times it does fail: [proxy_http:error] [pid 9365] (70007)The timeout specified has expired: [client 208.81.152.5:44494] AH01102: error reading status line from remote server 192.168.0.52:8910, referer: http://noctua-dev.planteome.org/ Can't see anything different in the Minerva logs between ones that work and when it errors.

[kltm]

For me, currently, curl http://noctua-dev.planteome.org/download/gomodel:592dd65c00000001/gpad gives no error, only an empty GPAD. Are GPAD rows expected in this case? A quick look at the models seems to show that evidence is not often used, meaning that GPAD rows will not be generated.

Anyways, with that proxy error, this sounds like either a minerva issue or minerva/apache interaction issue then. My guess is the former. How is minerva running here? Is it trying to look up labels in external servers? Is it attempting validation?

It might be worth trying to upgrade to the most recent versions of noctua and minerva and seeing if that helps. Recent versions of noctua no longer work particularly well with the "embedded" minerva, so minerva needs to be downloaded build separately (./build.sh), with a new variable in noctua's startup.yaml to override the use of the "embedded" one:

## Minerva operations preferences.
MINERVA_JAR:
  comment: The JAR to use for Minerva.
  type: string
  value: '../minerva/minerva-cli/bin/minerva-cli.jar'

[elserj]

I'm already using the newer minerva with the external jar, with your help while we were in Corvallis. I can do some updates though to see if that fixes it.

[elserj]

I updated to latest for both minerva and noctua. I saw the error the first time after I got it restarted, but not since after trying several times.

What exactly do we need to add to one of the test files to make a line actually show up in the gpad?

[kltm]

My wild and unsupported guess is that this error has to do with the lookup and/or validation of IDs: once a failing ID has been attempted, and the error thrown back to the client, it is cached within minerva and no longer causes a problem.

Critically, you need to add evidence to the model if you want to produce content with the GPAD export tools.

[kltm]

As an addendum to the above, it may be happening less frequently now as the restart of minerva has allowed it to possibly get newer versions of the ontologies, causing less "misses", whatever those actually are.

[cooperl09]

I am getting the following error when I try to add an evidence code:

Error (error): Could not successfully handle batch request. Exception: org.geneontology.minerva.MolecularModelManager$UnknownIdentifierException. Could not validate the id: ECO:0000006; your operation was likely not performed.

[kltm]

@cooperl09 It's possible that these are related. Is that for just the one evidence class, or is this a general issue? I'd wonder if you are importing the ontologies needed. Also tagging @cmungall .

[cmungall]

looks like old versions. Not sure how to tell the version of noctua/minerva, but I note the screen goes grey with reasoner on - it's been green for a long time now