This PR addresses issue #46. There has been a change to the java code to avoid deadlocks when blast finds only invalid characters, effectively clogging stdout. The web server now checks for non-DNA sequences and filters out fasta files that contain non-DNA characters. A similar check is performed for submitted RAYT protein files. If no valid DNA fasta remains, the user is returned to the sequence upload page.
Fixes included in this PR
execution of blast could lead to an infinite wait for long error messages. in this particular example the error was due to building a nucleotide db with a protein sequence. this error message filled the error buffer, which was not continuously read and hence led to a dead lock. both error input stream and stdout input stream are now contnuously read and hence a dead lock does not occur anymore.
Summary
This PR addresses issue #46. There has been a change to the java code to avoid deadlocks when blast finds only invalid characters, effectively clogging stdout. The web server now checks for non-DNA sequences and filters out fasta files that contain non-DNA characters. A similar check is performed for submitted RAYT protein files. If no valid DNA fasta remains, the user is returned to the sequence upload page.
Fixes included in this PR