Thanks Nate.
Maybe you could explain how to use/implement composite datatypes so
I can understand fully how it works?
The mvb file created is just a list of files i.e.
The contents of Test.mvb could be:
a.txt
b.img
c.log
So, to get composite datatypes to "work" do I have to upload "a.txt", "b.img"
and "c.log" and also "Test.mvb"? If so how does Test.mvb know about "a.txt,
b.img and c.log" as they will have been renamed as dataset_'id'.dat? The tool
takes only "Test.mvb" as input and obviously the contents are still "a.txt",
"b.img" and "c.log".
I don't see how it would work only uploading "Test.mvb" if the contents aren't
also uploaded at the same time?
Or am I getting confused? Please can you explain further?
If running the tool on the command line. The Test.mvb file is opened and each
file is read and operated on and a resultant file containing new files
returned...
Thanks
Neil
-----Original Message-----
From: Nate Coraor [mailto:n...@bx.psu.edu]
Sent: Thursday, 4 October 2012 2:09 AM
To: Burdett, Neil (ICT Centre, Herston - RBWH)
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Uploading composite datatypes.....
On Oct 2, 2012, at 11:44 PM, <neil.burd...@csiro.au> <neil.burd...@csiro.au>
wrote:
> Hi,
> I was under the impression that when a composite datatype (basic) file is
> uploaded then the files contained within the composite file are also uploaded
> is this not the case?
>
> I was hoping my script would be able to have a file as an input. The file
> contains multiple files. Each one would then be examined and outputted in
> turn...
>
> my xml file looks like this:
> <tool id="reorient_studies" name="Reorient images"> <description>for
> CTE surface</description>
> <!-- <command
> interpreter="bash">/usr/local/MILXView.12.08.2/BashScripts/CTESurface/
> tools/reorient_studies.sh $input $installDir $outputDir
> ${os.path.join( input.extra_files_path, '%s.nii.gz' %
> input.metadata.base_name )} --> <command
> interpreter="bash">/usr/local/MILXView.12.08.2/BashScripts/CTESurface/tools/reorient_studies.sh
> $input $installDir $outputDir </command> <inputs>
> <param format="mvb" name="input" type="data" label="Input File" />
> <param type="text" name="installDir" value="/usr/local/MILXView.12.08.2/"
> label="Atlas" />
> <param type="text" name="outputDir" value="CTE_SURFACE/"
> label="White Matter" /> </inputs> <outputs>
> <data format="input" name="output_mvb" from_work_dir="temp.mvb" />
> </outputs>
>
> (mvb is a new datatype i've added)
>
> datatypes_conf.xml :
>
> <datatype extension="mvb" type="galaxy.datatypes.data:Mvb"
> display_in_upload="true"/>
>
> data.py :
>
> class Mvb( Text ):
> MetadataElement( name="base_name", desc="base name for all transformed
> versions of this genetic dataset", readonly=True, set_in_upload=True)
> composite_type = 'basic'
> file_ext="mvb"
> allow_datatype_change = False
>
> def __init__( self, **kwd ):
> Text.__init__( self, **kwd )
> #self.add_composite_file( '215_T1_MRI_biasCorr.nii.gz', is_binary =
> True )
> #self.add_composite_file( 'VOTE_215_T1_MRI_hard_csf.nii.gz', is_binary
> = True )
> self.add_composite_file( '%s.nii.gz', description = 'Input
> File', substitute_name_with_metadata = 'base_name', is_binary = True )
>
> However, when I uploaded my backup.mvb file. It uploads the file and
> contents, but doesn't upload the files listed in the *.mvb file.
> Should it do this? Otherwise why have a composite datatype, as in this
> case it's simply acting like a text file
Hi Neil,
Is the mvb file some sort of container that actually contains multiple files in
one file? This isn't quite how composite datasets work. In Galaxy, a
composite dataset is multiple different files on disk that are referred to as a
single dataset.
--nate
>
> Thanks
> Neil
>
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