database scanning error

sequenceserver
#1

Regarding the following error reported by some of us (all CCed) -

Oops! Something went wonky.
Error:
undefined method downcase!' for nil:NilClass /Library/Ruby/Gems/2.0.0/gems/sequenceserver-1.0.2/lib/sequenceserver/database.rb:25:in initialize’
/Library/Ruby/Gems/2.0.0/gems/sequenceserver-1.0.2/lib/sequenceserver/database.rb:109:in new' /Library/Ruby/Gems/2.0.0/gems/sequenceserver-1.0.2/lib/sequenceserver/database.rb:109:in block (2 levels) in scan_databases_dir’
/Library/Ruby/Gems/2.0.0/gems/sequenceserver-1.0.2/lib/sequenceserver/database.rb:106:in each_line' /Library/Ruby/Gems/2.0.0/gems/sequenceserver-1.0.2/lib/sequenceserver/database.rb:106:in block in scan_databases_dir’

[…]

I have tried everything and I can’t reproduce this issue on neither Linux nor Mac. Neither on 32 bit system, nor on 64 bit system. Not when FASTA deflines are too long, not when FASTA defline contains funky characters.

So I have put some debug code in 1.0.3 update that tries to print more informative message that can help understand and debug the issue.

To all for whom deleting and re-creating BLAST database didn’t work, I request you update to 1.0.3 (gem install sequenceserver) and post back error output.

Thanks.

– Priyam

#2

Thanks to the debugging output introduced in 1.0.3 release for this bug and to our newest contributor (Alekhya) I have been able to debug and fix this issue.

The reason was, when entering a custom title during database creation the input wasn’t properly cleaned, thus leaving a trailing “\n”. When scanning for BLAST databases this “\n” would split the output on a new line, due to which parsing BLAST output would fail.

It was a regression - must have been introduced in improving the assisted setup. I sincerely apologise for the troubles this bug has caused.

This bug is fixed in the 1.0.4 release.

– Priyam