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 Thanks Neil
On Oct 2, 2012, at 11:44 PM, <Neil.Burdett@csiro.au> <Neil.Burdett@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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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:nate@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.Burdett@csiro.au> <Neil.Burdett@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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