Hi,

I am encountering a problem executing the genomespace_importer tool using
the Galaxy API.

The tool works just fine to copy files in GenomeSpace into Galay a history
dataset EXCEPT when the GenomeSpace file URL includes a space (" ") of any
sort.

Below is an example problem request (the GenomeSpace URL is public, so you
should be able to try it if you like).

Note that the "URL" parameter includes a couple of %20 which are supposed
to url-encode the space character.


*POST https://usegalaxy.org/api/tools?key=XXXXXX
<https://usegalaxy.org/api/tools?key=XXXXXX>*

*{*

*  "history_id": "039421d939e31170",*

*  "tool_id": "genomespace_importer",*

*  "inputs": {*

*    "URL":
"https://dm.genomespace.org/datamanager/file/Home/Public/RecipeData/SequenceData_fa%20fasta%20fastq/RNA-Seq.fastq
<https://dm.genomespace.org/datamanager/file/Home/Public/RecipeData/SequenceData_fa%20fasta%20fastq/RNA-Seq.fastq>",*

*    "gs-token": null*

*  }*

*}*

The job is accepted by Galaxy but eventually it fails. An HTTP error occurs
during the execution of the job.

I looked through the logs in GenomeSpace. Turns out that the URL being used
by Galaxy to do a GET on the file is

*https://gsui.genomespace.org/datamanager/v1.0/file/Home/Public/RecipeData/SequenceData_fa
<https://gsui.genomespace.org/datamanager/v1.0/file/Home/Public/RecipeData/SequenceData_fa>X20fastaX20fastq/RNA-Seq.fastq*

The "percents" are converted to X (I made the Xs bigger for emphasis).

I attempted a couple of other experiments in the tool job submission, using
actual space characters instead of %20. I also tried using the + instead of
space.

In both of these attempts, the exact same file path in the URL param was
used for the GenomeSpace GET, leading to a BAD REQUEST error with the
actual space character and NOT FOUND error with the + .

So the question is: what kind of decoding is going on in the Galaxy
genomespace_importer tool and how do I get rid of the Xs?

Thanks

Marco
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