Thanks Marco,

OK, that seems to still be part of the Galaxy core:

https://github.com/galaxyproject/galaxy/blob/dev/tools/genomespace/genomespace_importer.xml

I think you need to file a bug with the main GitHub repository (or Trello).

Looking at genomespace_importer.xml I don't see how the hidden URL
parameter is used, but I would still guess it just needs a <sanitizer> tag
to to allow the percent sign for any URL-encoded characters to be passed.

Peter

On Wed, Oct 21, 2015 at 3:01 PM, Marco Ocana <moc...@broadinstitute.org> wrote:
> Hi Peter,
>
> I am getting the metadata for the tool from:
>
> https://usegalaxy.org/api/tools/genomespace_importer
>
> Thanks
>
> Marco
>
> On Wed, Oct 21, 2015 at 8:01 AM, Peter Cock <p.j.a.c...@googlemail.com>
> wrote:
>>
>> Hi Marco,
>>
>> I'd lay money on the the tool parameter sanitization done in Cheetah
>> intended to avoid any command insertion into the shell command.
>> This can be configured within the tool definition using the <sanitizer>
>> tag set:
>>
>>
>> https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Csanitizer.3E_tag_set
>>
>> Which genomespace_importer are you working from (URL please)?
>>
>> Peter
>>
>> On Wed, Oct 21, 2015 at 3:20 AM, Marco Ocana <moc...@broadinstitute.org>
>> wrote:
>> > 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
>> >
>> > {
>> >
>> >   "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";,
>> >
>> >     "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_faX20fastaX20fastq/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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