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Annotations missing from noctua.mgi.gpad on snapshot #335
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@ukemi Can you confirm that the correct (latest) version of you model is at: https:/geneontology/noctua-models/blob/master/models/5ee8120100001244.ttl ? According to GH and the model metadata, no changes since 2020-07-06. (I just want to make sure we're at least starting from the issues is in minerva and not in saving, model push, etc.) |
Hi @kltm, Yes, this is the model. |
@ukemi when you look at the model in noctua, are the annotations missing - e.g. http://noctua.geneontology.org/workbench/annpreview/?model_id=gomodel:5ee8120100001244 |
The annotations are there. |
Alka-Selzer moment 6/18 NOCTUA Annotations: |
TL;DR: So, what we seem to have here is the Any ideas @balhoff or @goodb ? To spell out how to reproduce this:
From @ukemi 's comment #335 (comment) , we know that these have gotten at least into GH. This would seem to leave to error points: 1) pipeline mechanics (in feeding or handling) or 2) minerva error. Grabbing the log from the last successful
Poking around the stage logs a bit, this seems mechanically what I'd expect. Trying to simulate locally:
Which, I believe, means that our annotation have gotten this far. The final step is:
and there is no further output...which I think is a problem? In the script the following seems to be triggered: if (!grep {$_ eq 'model-state=production'} @props) { Ah!
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There is a method in the GPAD sparql export that gathers model annotations such as state. This was getting confused because, at that point in the code, the RDF for the model also contains the RDF for all the Arachne rules. See comment in CoreMMM .
@kltm I think it would be straightforward to add a parameter to the minerva client that would apply the 'production-only' filter at the time the GPAD was generated. Do you want me to do that? Having that perl script that you discovered in the middle of the gpad assembly process for the pipeline seems maybe not so good from the standpoint of testing and stability. LMK. |
Just wondering: we are still missing about 50% in the download. Any progress? |
In the release candidate we are missing several annotations coming from SynGO via Noctua:
I think this is blocking for the Sept 2020 release. |
We Did get ours back last week (we were missing 50%, mix of both SynGO and MGI |
@kltm could the files we loaded be out of date ? |
The current snapshot file appears to have 6916 lines attributed to SynGO. File header is date is 8/30/2020 |
Thanks @hdrabkin |
@pgaudet I think that if this is an issue, it would be a new issue, not related to the "production" tag issue we had here. Are you looking at the output GPAD products from like noctua_mgi.gpad.gz? |
Talking to @pgaudet earlier, this may just be an "echo" of this issue as it passes through various external pipelines that are on different schedules. |
The mgi gpad file on snapshot appears to be missing annotations:
http://snapshot.geneontology.org/products/annotations/noctua_mgi.gpad.gz
This model checks out but I can't find any of the annotations in snapshot from 7/19/2020.
http://noctua.geneontology.org/editor/graph/gomodel:5ee8120100001244?model_id=gomodel:5ee8120100001244
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