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refactor + docs
This commit is contained in:
Martin Cech
@@ -297,6 +297,14 @@ API Controllers
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:undoc-members:
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:show-inheritance:
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:mod:`lda_datasets` Module
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--------------------------
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.. automodule:: galaxy.webapps.galaxy.api.lda_datasets
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:members:
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:undoc-members:
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:show-inheritance:
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:mod:`libraries` Module
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-----------------------
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@@ -28,8 +28,17 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
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@web.expose_api
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def show( self, trans, id, **kwd ):
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"""
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GET /api/libraries/datasets/{encoded_dataset_id}
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Displays information about the dataset identified by the lda ID.
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show( self, trans, id, **kwd )
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* GET /api/libraries/datasets/{encoded_dataset_id}:
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Displays information about the dataset identified by the encoded id.
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:type id: an encoded id string
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:param id: the encoded id of the dataset to query
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:rtype: dictionary
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:returns: detailed dataset information from
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:func:`galaxy.web.base.controller.UsesVisualizationMixin.get_library_dataset.to_dict()`
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"""
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# Get dataset.
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try:
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@@ -55,9 +64,25 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
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@web.expose
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def download( self, trans, format, **kwd ):
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"""
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GET /api/libraries/datasets/download/{format}
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GET multiple params: ldda_ids = []
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Downloads dataset(s) in the requested format or plain.
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download( self, trans, format, **kwd )
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* GET /api/libraries/datasets/download/{format}
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.. code-block::
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example:
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GET localhost:8080/api/libraries/datasets/download/tbz?ldda_ids%255B%255D=a0d84b45643a2678&ldda_ids%255B%255D=fe38c84dcd46c828
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:type format: string
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:param format: string representing requested archive format
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.. note:: supported formats are: zip, tgz, tbz, uncompressed
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:type lddas[]: an array
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:param lddas[]: an array of encoded ids
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:rtype: file
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:returns: either archive with the requested datasets packed inside or a single uncompressed dataset
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:raises: MessageException, ItemDeletionException, ItemAccessibilityException, HTTPBadRequest, OSError, IOError, ObjectNotFound
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"""
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lddas = []
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datasets_to_download = kwd['ldda_ids%5B%5D']
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@@ -117,108 +142,101 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
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log.exception( "Unexpected error %s in create archive for download" % sys.exc_info()[0] )
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trans.response.status = 500
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return "Unable to create archive for download, please report - %s" % sys.exc_info()[0]
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if True:
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composite_extensions = trans.app.datatypes_registry.get_composite_extensions()
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seen = []
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for ldda in lddas:
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# if ldda.dataset.state in [ 'new', 'upload', 'queued', 'running', 'empty', 'discarded' ]:
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# continue
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ext = ldda.extension
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is_composite = ext in composite_extensions
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path = ""
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parent_folder = ldda.library_dataset.folder
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while parent_folder is not None:
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# Exclude the now-hidden "root folder"
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if parent_folder.parent is None:
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path = os.path.join( parent_folder.library_root[0].name, path )
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break
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path = os.path.join( parent_folder.name, path )
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parent_folder = parent_folder.parent
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path += ldda.name
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while path in seen:
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path += '_'
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seen.append( path )
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zpath = os.path.split(path)[-1] # comes as base_name/fname
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outfname,zpathext = os.path.splitext(zpath)
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if is_composite:
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# need to add all the components from the extra_files_path to the zip
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if zpathext == '':
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zpath = '%s.html' % zpath # fake the real nature of the html file
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composite_extensions = trans.app.datatypes_registry.get_composite_extensions()
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seen = []
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for ldda in lddas:
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ext = ldda.extension
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is_composite = ext in composite_extensions
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path = ""
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parent_folder = ldda.library_dataset.folder
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while parent_folder is not None:
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# Exclude the now-hidden "root folder"
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if parent_folder.parent is None:
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path = os.path.join( parent_folder.library_root[0].name, path )
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break
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path = os.path.join( parent_folder.name, path )
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parent_folder = parent_folder.parent
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path += ldda.name
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while path in seen:
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path += '_'
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seen.append( path )
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zpath = os.path.split(path)[-1] # comes as base_name/fname
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outfname,zpathext = os.path.splitext(zpath)
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if is_composite: # need to add all the components from the extra_files_path to the zip
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if zpathext == '':
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zpath = '%s.html' % zpath # fake the real nature of the html file
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try:
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if format=='zip':
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archive.add( ldda.dataset.file_name, zpath ) # add the primary of a composite set
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else:
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archive.add( ldda.dataset.file_name, zpath, check_file=True ) # add the primary of a composite set
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except IOError:
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log.exception( "Unable to add composite parent %s to temporary library download archive" % ldda.dataset.file_name)
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trans.response.status = 500
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return "Unable to create archive for download, please report this error"
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except ObjectNotFound:
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log.exception( "Requested dataset %s does not exist on the host." % ldda.dataset.file_name )
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trans.response.status = 500
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return "Requested dataset does not exist on the host."
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except:
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trans.response.status = 500
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return "Unknown error, please report this error"
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flist = glob.glob(os.path.join(ldda.dataset.extra_files_path,'*.*')) # glob returns full paths
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for fpath in flist:
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efp,fname = os.path.split(fpath)
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if fname > '':
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fname = fname.translate(trantab)
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try:
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if format=='zip':
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archive.add( ldda.dataset.file_name, zpath ) # add the primary of a composite set
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else:
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archive.add( ldda.dataset.file_name, zpath, check_file=True ) # add the primary of a composite set
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except IOError:
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log.exception( "Unable to add composite parent %s to temporary library download archive" % ldda.dataset.file_name)
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trans.response.status = 500
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return "Unable to create archive for download, please report this error"
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except ObjectNotFound:
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log.exception( "Requested dataset %s does not exist on the host." % ldda.dataset.file_name )
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trans.response.status = 500
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return "Requested dataset does not exist on the host."
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except:
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trans.response.status = 500
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return "Unknown error, please report this error"
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flist = glob.glob(os.path.join(ldda.dataset.extra_files_path,'*.*')) # glob returns full paths
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for fpath in flist:
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efp,fname = os.path.split(fpath)
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if fname > '':
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fname = fname.translate(trantab)
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try:
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if format=='zip':
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archive.add( fpath,fname )
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else:
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archive.add( fpath,fname, check_file=True )
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except IOError:
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log.exception( "Unable to add %s to temporary library download archive %s" % (fname,outfname))
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trans.response.status = 500
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return "Unable to create archive for download, please report this error"
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except ObjectNotFound:
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log.exception( "Requested dataset %s does not exist on the host." % fpath )
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trans.response.status = 500
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return "Requested dataset does not exist on the host."
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except:
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trans.response.status = 500
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return "Unknown error, please report this error"
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else: # simple case
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try:
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if format=='zip':
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archive.add( ldda.dataset.file_name, path )
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archive.add( fpath,fname )
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else:
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archive.add( ldda.dataset.file_name, path, check_file=True )
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archive.add( fpath,fname, check_file=True )
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except IOError:
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log.exception( "Unable to write %s to temporary library download archive" % ldda.dataset.file_name)
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log.exception( "Unable to add %s to temporary library download archive %s" % (fname,outfname))
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trans.response.status = 500
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return "Unable to create archive for download, please report this error"
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except ObjectNotFound:
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log.exception( "Requested dataset %s does not exist on the host." % ldda.dataset.file_name )
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log.exception( "Requested dataset %s does not exist on the host." % fpath )
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trans.response.status = 500
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return "Requested dataset does not exist on the host."
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return "Requested dataset does not exist on the host."
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except:
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trans.response.status = 500
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return "Unknown error, please report this error"
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if True:
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lname = 'selected_dataset'
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fname = lname.replace( ' ', '_' ) + '_files'
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if format == 'zip':
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archive.close()
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trans.response.set_content_type( "application/octet-stream" )
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trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % (fname,outext)
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archive = util.streamball.ZipBall(tmpf, tmpd)
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archive.wsgi_status = trans.response.wsgi_status()
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archive.wsgi_headeritems = trans.response.wsgi_headeritems()
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trans.response.status = 200
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return archive.stream
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else:
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trans.response.set_content_type( "application/x-tar" )
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trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % (fname,outext)
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archive.wsgi_status = trans.response.wsgi_status()
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archive.wsgi_headeritems = trans.response.wsgi_headeritems()
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trans.response.status = 200
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return archive.stream
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else: # simple case
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try:
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if format=='zip':
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archive.add( ldda.dataset.file_name, path )
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else:
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archive.add( ldda.dataset.file_name, path, check_file=True )
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except IOError:
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log.exception( "Unable to write %s to temporary library download archive" % ldda.dataset.file_name)
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trans.response.status = 500
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return "Unable to create archive for download, please report this error"
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except ObjectNotFound:
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log.exception( "Requested dataset %s does not exist on the host." % ldda.dataset.file_name )
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trans.response.status = 500
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return "Requested dataset does not exist on the host."
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except:
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trans.response.status = 500
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return "Unknown error, please report this error"
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lname = 'selected_dataset'
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fname = lname.replace( ' ', '_' ) + '_files'
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if format == 'zip':
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archive.close()
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trans.response.set_content_type( "application/octet-stream" )
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trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % (fname,outext)
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archive = util.streamball.ZipBall(tmpf, tmpd)
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archive.wsgi_status = trans.response.wsgi_status()
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archive.wsgi_headeritems = trans.response.wsgi_headeritems()
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trans.response.status = 200
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return archive.stream
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else:
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trans.response.set_content_type( "application/x-tar" )
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trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % (fname,outext)
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archive.wsgi_status = trans.response.wsgi_status()
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archive.wsgi_headeritems = trans.response.wsgi_headeritems()
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trans.response.status = 200
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return archive.stream
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elif format == 'uncompressed':
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if len(lddas) != 1:
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trans.response.status = 400
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