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sniffing of xlsx file as blastxml #6849
On top of #6867 which should fix the issue it also looks like the blastxml sniffer on usegalaxy.org is a bit overeager, on my dev instance this is being sniffed as a regular xml datatype. Which is weird, since we ship the blastxml datatype. Any chance that somehow a tool shed installed datatype somehow interfered here ? They shouldn't, but might be worth checking.
Or maybe main is using a non-default sniff order ?
As per https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/blast.py#L64 the BLAST XML sniffer should be looking for files starting as follows (allowing for white space):
<?xml version="1.0"?>': <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd"> <BlastOutput>
<?xml version="1.0"?>': <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd"> <BlastOutput>
This has not diverged meaningfully from the standalone datatype definition which is still available on the tool shed:
From a visual inspection of the contents of the Excel file once unzipped into individual XML files, I struggle to understand how this could go wrong.
Could there be something off in the
Further more, even going back to the BLAST XML datatype when it was originally taken out of Galaxy, the essential BLAST XML sniffer logic has not changed:
i.e. Even some older version of the ToolShed definition from http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes is installed, the logic ought never to recognise the Excel file.