DNA Sequence Search (Blast) getting errors and returning an empty result to the GUI

[Don-Isdale]

Investigation revealed several issues, which are fixed :

• some of the files / directories had a permission configuration which didn't allow the blastn process created by the blast server container to read them
  Changes made : changed the file permissions
• the files are on a volume which was not passed to the blastn process created by the blast server container
  Changes made : added those volumes to the configuration of the blast server container
  Note : this solution will have to be generalised to enable it to be committed in the Pretzel source repository, e.g. by reading the volume configuration from the environment file.
• the path of the blast database directory passed to the blastn command was configured for the AWS instance not the development server
  Changes made : changed the path configuration used on the development server

[Don-Isdale]

Testing

Tested with the same DNA Sequence and reference which was getting the error.

The Blast search results are now received OK.
The axes are not displayed - that is likely a database configuration issue and will be handled separately.

[Don-Isdale]

Similarly improve error reporting to GUI for VCF Genotype Search errors

The same function has been applied also in handling an error response from a VCF Genotype Search / Lookup.
124a823 genotype-search show HTML error text, ensure vcfGenotypeSamplesSelectedAll is defined, handle undefined lookupBlock.

Error shown in GUI

Error: VCF file is not configured