Will Trimble

Promote error correction scripts from sandbox

8

This is an attempt to bring two (of only three) CLI scripts that use ReadAligner up to date with the khmer codebase, `error_correct_pass2` and `correct-reads`. Tests were added, and the...

.filename must not contain path separator; this causes downstream applications to be unable to find the files and may be a security flaw.

This PR provides error containing shock id for failed processing-history requests error containing shock id for failed sequence-stats requests header containing shock id for failed downloads and the excel maintenance...

The /search resource will update the elasticsearch database (and indexes) and is used when metadata is updated or when jobs are created or destroyed. /search requires consistent job data, however,...

py.test -k test_apix_metagenome {"ERROR":"resource request failed\nUnsupported object class 'Project' in database 'WebAppBackend'. at /MG-RAST/site/lib/PPO/DBMaster.pm line 444.\n\n"} This error originates from lines 840-843 of metadata.pm, updating elasticsearch when no elasticsearch server...

py.test -k get_proj_metadata {"ERROR":"resource request failed\nBad arg length for Socket::pack_sockaddr_in, length is 0, should be 4 at /usr/lib/x86_64-linux-gnu/perl/5.24/Socket.pm line 157.\n\n"} This error is caused by memcached not running, and originates...

Adds option to turn hierarchy into string for csv output

When the first FASTQ read is longer than 16kbases, the FASTQ-format-checker fails, and FASTQ upload fails.