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SynBioDex / SBOLExplorer

MIT License
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Serious bug with distributed search #24

Closed cjmyers closed 4 years ago

cjmyers commented 5 years ago

When a synbiohub cannot be reached (like SBH Utah that is down right now), it crashes SBOLExplorer. It appears you are missing a try/catch to error out properly in this instance.

michael13162 commented 5 years ago

This should be fixed. Needs testing.

cjmyers commented 5 years ago

Also, dumps file appears to be missing even with distributed search off.

cjmyers commented 5 years ago

Running uclust b'usearch v10.0.240_i86linux32, 4.0Gb RAM (16.4Gb total), 6 cores\n(C) Copyright 2013-17 Robert C. Edgar, all rights reserved.\nhttp://drive5.com/usearch\n\nLicense: michael13162@gmail.com\n\n' Running uclust complete parts: 0 hits: 0 Returning error float division by zero Successfully updated config Successfully updated config Query for sequences endpoint: http://virtuoso:8890/sparql? Successfully updated config 00:01 101Mb 100.0% Reading usearch/sequences.fsa 00:01 119Mb 100.0% DF
00:01 120Mb 48557 seqs, 45124 uniques, 42942 singletons (95.2%) 00:01 120Mb Min size 1, median 1, max 50, avg 1.08 00:01 121Mb 100.0% DB 00:01 122Mb Sort length... done. 10000 20000 30000 40000 48557 Query for sequences complete Running uclust Successfully updated config Returning error [Errno 2] No such file or directory: 'dumps/uri2rank_dump' Returning error [Errno 2] No such file or directory: 'dumps/uri2rank_dump' Successfully updated config Query for sequences endpoint: http://virtuoso:8890/sparql? Successfully updated config 03:53 237Mb 35.1% 15807 clusters, max size 10, avg 1.1

usearch/usearch10.0.240_i86linux32 -cluster_fast usearch/sequences.fsa -id 0.8 -sort length -uc usearch/uclust_results.uc

---Fatal error--- Empty file usearch/sequences.fsa

yu-eric commented 4 years ago

Should be fixed. See https://github.com/SynBioDex/SBOLExplorer/issues/27#issuecomment-579093008.

cjmyers commented 4 years ago

Ok, closing