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SynBioDex / SBOLExplorer

MIT License
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Indexing is not working for distributed search #91

Open cjmyers opened 3 years ago

cjmyers commented 3 years ago

Indexing is failing when fetching information from synbiohub.org/?sparql instance.

yu-eric commented 3 years ago

Error Virtuoso S1T00 Error SR171: Transaction timed out is being thrown on the query:

https://synbiohub.org/sparql?query=%0A++++PREFIX+rdf%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F1999%2F02%2F22-rdf-syntax-ns%23%3E%0A++++PREFIX+dcterms%3A+%3Chttp%3A%2F%2Fpurl.org%2Fdc%2Fterms%2F%3E%0A++++PREFIX+dc%3A+%3Chttp%3A%2F%2Fpurl.org%2Fdc%2Felements%2F1.1%2F%3E%0A++++PREFIX+sbh%3A+%3Chttp%3A%2F%2Fwiki.synbiohub.org%2Fwiki%2FTerms%2Fsynbiohub%23%3E%0A++++PREFIX+synbiohub%3A+%3Chttp%3A%2F%2Fsynbiohub.org%23%3E%0A++++PREFIX+igem%3A+%3Chttp%3A%2F%2Fwiki.synbiohub.org%2Fwiki%2FTerms%2Figem%23%3E%0A++++PREFIX+prov%3A+%3Chttp%3A%2F%2Fwww.w3.org%2Fns%2Fprov%23%3E%0A++++PREFIX+sbol2%3A+%3Chttp%3A%2F%2Fsbols.org%2Fv2%23%3E%0A++++PREFIX+xsd%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F2001%2FXMLSchema%23%3E%0A++++PREFIX+rdfs%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F2000%2F01%2Frdf-schema%23%3E%0A++++PREFIX+purl%3A+%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2F%3E%0A++++PREFIX+ncbi%3A+%3Chttp%3A%2F%2Fwww.ncbi.nlm.nih.gov%23%3E%0A++++%0ASELECT+DISTINCT+%3Fparent+%3Fchild%0AWHERE%0A%7B%0A++++%3Fparent+sbh%3AtopLevel+%3Fparent+.%0A++++%3Fchild+sbh%3AtopLevel+%3Fchild+.%0A++++%7B+%3Fparent+%3FoneLink+%3Fchild+%7D+UNION+%7B+%3Fparent+%3FtwoLinkOne+%3Ftmp+.+%3Ftmp+%3FtwoLinkTwo+%3Fchild+%7D%0A%7D%0AOFFSET+560000+LIMIT+10000

yu-eric commented 3 years ago

SPARQL query (querying for links):

SELECT DISTINCT ?parent ?child
WHERE
{
    ?parent sbh:topLevel ?parent .
    ?child sbh:topLevel ?child .
    { ?parent ?oneLink ?child } UNION { ?parent ?twoLinkOne ?tmp . ?tmp ?twoLinkTwo ?child }
}
yu-eric commented 3 years ago

Reaches an OFFSET of 560,000 and 590,000 on two machines that I tried running indexing on (with distributed search turned on).

yu-eric commented 3 years ago

Looks to be fixed for now; will reopen if issue arises again.

yu-eric commented 3 years ago

EDIT: Looks like it is now hanging when queryling by parts. Additionally, synbiohub.org seems to be indexing by graph, may not be on the latest commit.