Patch Imported in 5618:b9fdb88da530.
Thanks!
Dan
On Mar 16, 2011, at 11:50 AM, Jim Johnson wrote:
> Request is issue#494
> https://bitbucket.org/galaxy/galaxy-central/issue/494/support-sub-dirs-in-extra_files_path-patch
>
> I'm finding that some qiime metagenomics applications build HTML results with
> an inherent directory structure. For some other applications, e.g. FastQC,
> I've been able to flatten the hierarchy and edit the html, but that appears
> problematic for qiime.
>
> Galaxy hasn't supported a dataset extra_files_path hierarchy, though the
> developers don't seem opposed to the idea:
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-October/003605.html
>
> I added a route in lib/galaxy/web/buildapp.pyand modified the dataset
> download code to traverse a hierarchy in lib/galaxy/web/controllers/dataset.py
> I don't think these add any security vulnerabilities, (I tried the obvious
> ../../ ).
>
> $ hg diff lib/galaxy/web/buildapp.py
> diff -r 6ae06d89fec7 lib/galaxy/web/buildapp.py
> --- a/lib/galaxy/web/buildapp.pyWed Mar 16 09:01:57 2011 -0400
> +++ b/lib/galaxy/web/buildapp.pyWed Mar 16 10:24:13 2011 -0500
> @@ -94,6 +94,8 @@
> webapp.add_route( '/async/:tool_id/:data_id/:data_secret',
> controller='async', action='index', tool_id=None, data_id=None,
> data_secret=None )
> webapp.add_route( '/:controller/:action', action='index' )
> webapp.add_route( '/:action', controller='root', action='index' )
> +# allow for subdirectories in extra_files_path
> +webapp.add_route( '/datasets/:dataset_id/display/{filename:.+?}',
> controller='dataset', action='display', dataset_id=None, filename=None)
> webapp.add_route( '/datasets/:dataset_id/:action/:filename',
> controller='dataset', action='index', dataset_id=None, filename=None)
> webapp.add_route(
> '/display_application/:dataset_id/:app_name/:link_name/:user_id/:app_action/:action_param',
> controller='dataset', action='display_application', dataset_id=None,
> user_id=None, app_name = None, link_name = None, app_action = None,
> action_param = None )
> webapp.add_route( '/u/:username/d/:slug', controller='dataset',
> action='display_by_username_and_slug' )
> $
> $ hg diff lib/galaxy/web/controllers/dataset.py
> diff -r 6ae06d89fec7 lib/galaxy/web/controllers/dataset.py
> --- a/lib/galaxy/web/controllers/dataset.py Wed Mar 16 09:01:57 2011 -0400
> +++ b/lib/galaxy/web/controllers/dataset.py Wed Mar 16 10:24:29 2011 -0500
> @@ -266,17 +266,18 @@
> log.exception( "Unable to add composite parent %s to
> temporary library download archive" % data.file_name)
> msg = "Unable to create archive for download, please
> report this error"
> messagetype = 'error'
> -flist = glob.glob(os.path.join(efp,'*.*')) # glob returns
> full paths
> -for fpath in flist:
> -efp,fname = os.path.split(fpath)
> -try:
> -archive.add( fpath,fname )
> -except IOError:
> -error = True
> -log.exception( "Unable to add %s to temporary
> library download archive" % fname)
> -msg = "Unable to create archive for download, please
> report this error"
> -messagetype = 'error'
> -continue
> +for root, dirs, files in os.walk(efp):
> +for fname in files:
> +fpath = os.path.join(root,fname)
> +rpath = os.path.relpath(fpath,efp)
> +try:
> +archive.add( fpath,rpath )
> +except IOError:
> +error = True
> +log.exception( "Unable to add %s to temporary
> library download archive" % rpath)
> +msg = "Unable to create archive for download,
> please report this error"
> +messagetype = 'error'
> +continue
> if not error:
> if params.do_action == 'zip':
> archive.close()
>
>
>
>
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