Question: Modifying library dataset names with bioblend/the API
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Devon Ryan • 1.9k wrote:
I'm interested in linking a number of files into our local Galaxy instance using bioblend (or the Galaxy API directly if need be). The code for almost everything I need is simple enough, but there are some file names where Galaxy will strip off the file extensions. Namely, if one links in a file called "foo.fastq.gz", Galaxy will strip off the ".gz" suffix. That needs to stay there, since Galaxy is just linking in the files and not uncompressing them. I've not found an "update a library dataset name" method anywhere in bioblend or the API, but I assume I've just overlooked it (at least in the API). Can anyone point me in the right direction?
I am facing the same issue. And it is one of the reasons why I haven't gone into production with automatic library generation for our fastq files.
So far I just refer to the dataset peek where it says: 'gzipped file'
I have to add, I use file_type='fastq' in the "upload_from_galaxy_filesystem". Though, that should not make a difference....it just brings us back to the way Galaxy handles gzipped files.
Regards, Hans-Rudolf
I am afraid there is no API to update library dataset's name in Galaxy. However the proper solution for this seems to prevent galaxy from stripping suffix of linked data. Does this sound reasonable?
That might work. I'm a little concerned that that'll screw things up if someone tries to upload a gzipped file (I've had the most common wrappers modified to handle gzipped files...but that requires a proper file extension). Having said that, I suspect people almost never do that, so probably I'm worrying for nothing. Where is the extension stripping handled?
The other solution I can think of would be to have a cron job on the server with Galaxy that runs and periodically checks for and fixes names in the database. That'd be an easy enough thing to write I expect.