Re: [galaxy-dev] Spaces in GenomeSpaces file URLs from genomespace_importer tool

[Peter Cock]

See: https://trello.com/c/YBK8ZPFb/

Hopefully one of the Galaxy team can take a look.

Peter

On Wed, Oct 21, 2015 at 3:48 PM, Marco Ocana  wrote:
> Thanks for you help Peter.
> I have reported the problem using the built in Galaxy reporting tool from
> one of my failed jobs.
> I also created a Trello bug submission.
>
> Regards,
>
> Marco
>
> On Wed, Oct 21, 2015 at 10:15 AM, Peter Cock 
> wrote:
>>
>> 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  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 
>> wrote:
>> > Hi Peter,
>> >
>> > I am getting the metadata for the tool from:
>> >
>> > https://usegalaxy.org/api/tools/genomespace_importer
>> >
>> > Thanks
>> >
>> > Marco
>> >
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Re: [galaxy-dev] Spaces in GenomeSpaces file URLs from genomespace_importer tool

[Peter Cock]

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 
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  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=XX
>
> {
>
>   "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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