Re: [galaxy-dev] Support for subdirs in dataset extra_files_path

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-ex...

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.py and 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.py Wed Mar 16 09:01:57 2011 -0400 +++ b/lib/galaxy/web/buildapp.py Wed 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()
  
  
  
  
  

---

Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/