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geneontology / noctua

Graph-based modeling environment for biology, including prototype editor and services
http://noctua.geneontology.org/
BSD 3-Clause "New" or "Revised" License
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zebrafish genes unavailable in Noctua #595

Closed sabrinatoro closed 4 years ago

sabrinatoro commented 5 years ago

I am unable to find zebrafish gene in both the form and in the graph view. The genes I am trying to annotate (and are not found in the interface) are:

These genes are in our GPI file.

thanks!

kltm commented 5 years ago

All three in upstream: https://zfin.org/downloads/zfin.gpi.gz Note loader failure https://build.berkeleybop.org/job/load-golr-noctua-neo/161/ Trying refresh.

cmungall commented 5 years ago

Confirming ZDB-GENE-030519-2 made it into http://purl.obolibrary.org/obo/go/noctua/neo.owl, so the solr loader failure seems most likely explanation

kltm commented 5 years ago

I've been unable to get the job to run in Jenkins or manually. @cmungall Has anything significant changed in the load/NEO that you know of? We've had little problem with it until the 22nd. Also, is there anything in the command that could be peeled out? It always seems to run for a while, then chokes on a 

Exception in thread "main" org.apache.solr.client.solrj.SolrServerException: java.net.SocketException: Broken pipe (Write failed)
        at org.apache.solr.client.solrj.impl.CommonsHttpSolrServer.request(CommonsHttpSolrServer.java:475)

after a half to two and a half hours.

java -Xms1024M -DentityExpansionLimit=4086000 -Djava.awt.headless=true -Xmx192G -jar ./java/lib/owltools-runner-all.jar http://purl.obolibrary.org/obo/go/extensions/go-lego.owl http://purl.obolibrary.org/obo/eco.owl http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl http://purl.obolibrary.org/obo/cl/cl-basic.owl http://purl.obolibrary.org/obo/go/extensions/gorel.owl http://purl.obolibrary.org/obo/pato.owl http://purl.obolibrary.org/obo/po.owl http://purl.obolibrary.org/obo/chebi.owl http://purl.obolibrary.org/obo/uberon/basic.owl http://purl.obolibrary.org/obo/wbbt.owl http://purl.obolibrary.org/obo/go/extensions/go-modules-annotations.owl http://purl.obolibrary.org/obo/go/extensions/go-taxon-subsets.owl --log-info --merge-support-ontologies --merge-imports-closure --remove-subset-entities upperlevel --remove-disjoints --silence-elk --reasoner elk --solr-taxon-subset-name amigo_grouping_subset --solr-eco-subset-name go_groupings --ontology-pre-check --solr-url http://localhost:8080/solr/ --solr-config /home/bbop/local/src/git/amigo/metadata/ont-config.yaml --solr-log /tmp/golr_timestamp.log --solr-purge --solr-load-ontology --solr-load-ontology-general

Will continue trying to get a lucky run. If the ontologies can be loaded separately (I assume they can), I'll split up the load.

cmungall commented 5 years ago

nothing changed I know of

On Fri, Dec 28, 2018 at 10:46 PM kltm notifications@github.com wrote:

I've been unable to get the job to run in Jenkins or manually. @cmungall https://github.com/cmungall Has anything significant changed in the load/NEO that you know of? Also, is there anything in the command that could be peeled out? It always seems to run for a while, then chokes on a

Exception in thread "main" org.apache.solr.client.solrj.SolrServerException: java.net.SocketException: Broken pipe (Write failed) at org.apache.solr.client.solrj.impl.CommonsHttpSolrServer.request(CommonsHttpSolrServer.java:475)

after a half to two and a half hours.

java -Xms1024M -DentityExpansionLimit=4086000 -Djava.awt.headless=true -Xmx192G -jar ./java/lib/owltools-runner-all.jar http://purl.obolibrary.org/obo/go/extensions/go-lego.owl http://purl.obolibrary.org/obo/eco.owl http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl http://purl.obolibrary.org/obo/cl/cl-basic.owl http://purl.obolibrary.org/obo/go/extensions/gorel.owl http://purl.obolibrary.org/obo/pato.owl http://purl.obolibrary.org/obo/po.owl http://purl.obolibrary.org/obo/chebi.owl http://purl.obolibrary.org/obo/uberon/basic.owl http://purl.obolibrary.org/obo/wbbt.owl http://purl.obolibrary.org/obo/go/extensions/go-modules-annotations.owl http://purl.obolibrary.org/obo/go/extensions/go-taxon-subsets.owl --log-info --merge-support-ontologies --merge-imports-closure --remove-subset-entities upperlevel --remove-disjoints --silence-elk --reasoner elk --solr-taxon-subset-name amigo_grouping_subset --solr-eco-subset-name go_groupings --ontology-pre-check --solr-url http://localhost:8080/solr/ --solr-config /home/bbop/local/src/git/amigo/metadata/ont-config.yaml --solr-log /tmp/golr_timestamp.log --solr-purge --solr-load-ontology --solr-load-ontology-general

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kltm commented 5 years ago

After a worrying number of retries, I believe that I've gotten at least a full load in piecemeal. For now, I've suspended the load-golr-noctua-neo job, as it can no longer apparently complete on its own. Something has changed with regards to the load recently; I've elevated this issue, but will likely start something new to either track the issue or rebuild this part within the new (and safer) environment of pipeline.

vanaukenk commented 5 years ago

Hi - I'm having a similar issue with a C. elegans gene, cyk-7, that I'm trying to annotate in Noctua.

It is not available in the autocomplete in the form or graph editor.

Here is its entry in our gpi file:

WB WBGene00015591 cyk-7 CYtoKinesis defect CELE_C08C3.4 gene taxon:6239 UniProtKB:P34325

That can be found here: ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/PRJNA13758/annotation/gene_product_info/c_elegans.PRJNA13758.current.gene_product_info.gpi.gz

Is the C. elegans gpi file being loaded into NEO?

We have discussed a similar issue with another gene in a separate ticket, but I don't think this ever got resolved:

https://github.com/geneontology/noctua/issues/580

kltm commented 5 years ago

@vanaukenk Your issue is a separate one--the above issue is about the loader, your issue seems to be about being in NEO, which is seems to not be:

sjcarbon@moiraine:/tmp$:) wget http://purl.obolibrary.org/obo/go/noctua/neo.owl
sjcarbon@moiraine:/tmp$:) grep "cyk-7" neo.owl | wc
      0       0       0

The source we have for you is

   source: ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/PRJNA13758/annotation/gene_product_info/c_elegans.PRJNA13758.current.gene_product_info.gpi.gz

with the last load a few days ago. If your GP is less recent than that, we should open up a new ticket.

vanaukenk commented 5 years ago

Thanks @kltm Then we should probably open a new ticket, since I can see the "cyk-7" entry in our source gpi file which was generated 2018-11-10. I'll create a new ticket.

kltm commented 5 years ago

You may want to try https://github.com/geneontology/neo for Chris--the entity does not appear in the NEO file as currently downloaded apparently (see my example above).

vanaukenk commented 5 years ago

Okay, I'll create a ticket in neo (there is also now one in https://github.com/geneontology/noctua)

Never mind - I see you've already done it. Thx.

vanaukenk commented 4 years ago

Closing this ticket, as I think the issues have been resolved. Please re-open if I'm mistaken.