opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-16 07:19:13 +08:00
Code Issues Packages Projects Releases Wiki Activity

pep 8, fixed decoding of folders again

Browse Source
This commit is contained in:
Martin Cech
2014-05-08 18:55:57 -04:00
parent 6d0de9ba11
commit 3fb515224b
2 changed files with 19 additions and 21 deletions
Download Patch File Download Diff File Expand all files Collapse all files
lib/galaxy/webapps/galaxy/api/folders.py
+1 -1
View File
@@ -136,7 +136,7 @@ class FoldersController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinIt
def __cut_the_prefix(self, encoded_id):
if ( ( len( encoded_id ) % 2 == 1 ) and encoded_id.startswith( 'F' ) ):
if ( ( len( encoded_id ) % 16 == 1 ) and encoded_id.startswith( 'F' ) ):
return encoded_id[ 1: ]
else:
raise exceptions.MalformedId( 'Malformed folder id ( %s ) specified, unable to decode.' % str( encoded_id ) )
lib/galaxy/webapps/galaxy/api/library_contents.py
+18 -20
View File
@@ -17,6 +17,7 @@ from sqlalchemy.orm.exc import NoResultFound
import logging
log = logging.getLogger( __name__ )
class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems, UsesHistoryDatasetAssociationMixin ):
@expose_api
@@ -26,7 +27,7 @@ class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
* GET /api/libraries/{library_id}/contents:
Returns a list of library files and folders.
.. note:: May be slow! Returns all content traversing recursively through all folders.
.. note:: May be slow! Returns all content traversing recursively through all folders.
.. seealso:: :class:`galaxy.webapps.galaxy.api.FolderContentsController.index` for a non-recursive solution
:param library_id: encoded id string of the library
@@ -78,7 +79,7 @@ class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
except NoResultFound:
raise exceptions.RequestParameterInvalidException( 'No library found with the id provided.' )
except Exception, e:
raise exceptions.InternalServerError( 'Error loading from the database.' + str(e))
raise exceptions.InternalServerError( 'Error loading from the database.' + str(e))
if not ( trans.user_is_admin() or trans.app.security_agent.can_access_library( current_user_roles, library ) ):
raise exceptions.RequestParameterInvalidException( 'No library found with the id provided.' )
encoded_id = 'F' + trans.security.encode_id( library.root_folder.id )
@@ -122,7 +123,7 @@ class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
class_name, content_id = self.__decode_library_content_id( trans, id )
if class_name == 'LibraryFolder':
content = self.get_library_folder( trans, content_id, check_ownership=False, check_accessible=True )
rval = content.to_dict( view='element', value_mapper={ 'id' : trans.security.encode_id } )
rval = content.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id } )
rval[ 'id' ] = 'F' + str( rval[ 'id' ] )
rval[ 'parent_id' ] = 'F' + str( trans.security.encode_id( rval[ 'parent_id' ] ) )
rval[ 'parent_library_id' ] = trans.security.encode_id( rval[ 'parent_library_id' ] )
@@ -236,9 +237,9 @@ class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
encoded_id = trans.security.encode_id( v.id )
if create_type == 'folder':
encoded_id = 'F' + encoded_id
rval.append( dict( id = encoded_id,
name = v.name,
url = url_for( 'library_content', library_id=library_id, id=encoded_id ) ) )
rval.append( dict( id=encoded_id,
name=v.name,
url=url_for( 'library_content', library_id=library_id, id=encoded_id ) ) )
return rval
def _scan_json_block(self, meta, prefix=""):
@@ -276,7 +277,7 @@ class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
``library_contents.create`` will branch to this if called with 'from_hda_id'
in its payload.
"""
log.debug( '_copy_hda_to_library_folder: %s' %( str(( from_hda_id, library_id, folder_id, ldda_message )) ) )
log.debug( '_copy_hda_to_library_folder: %s' % ( str(( from_hda_id, library_id, folder_id, ldda_message )) ) )
#PRECONDITION: folder_id has already been altered to remove the folder prefix ('F')
#TODO: allow name and other, editable ldda attrs?
if ldda_message:
@@ -287,14 +288,14 @@ class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
# check permissions on (all three?) resources: hda, library, folder
#TODO: do we really need the library??
hda = self.get_dataset( trans, from_hda_id, check_ownership=True, check_accessible=True, check_state=True )
library = self.get_library( trans, library_id, check_accessible=True )
# library = self.get_library( trans, library_id, check_accessible=True )
folder = self.get_library_folder( trans, folder_id, check_accessible=True )
# TOOD: refactor to use check_user_can_add_to_library_item, eliminate boolean
# can_current_user_add_to_library_item.
if not self.can_current_user_add_to_library_item( trans, folder ):
trans.response.status = 403
return { 'error' : 'user has no permission to add to library folder (%s)' %( folder_id ) }
return { 'error': 'user has no permission to add to library folder (%s)' % ( folder_id ) }
ldda = self.copy_hda_to_library_folder( trans, hda, folder, ldda_message=ldda_message )
ldda_dict = ldda.to_dict()
@@ -304,11 +305,11 @@ class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
#TODO: grrr...
if 'not accessible to the current user' in str( exc ):
trans.response.status = 403
return { 'error' : str( exc ) }
return { 'error': str( exc ) }
else:
log.exception( exc )
trans.response.status = 500
return { 'error' : str( exc ) }
return { 'error': str( exc ) }
return rval
@@ -335,10 +336,10 @@ class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
converted_id = payload.pop( 'converted_dataset_id' )
content = self.get_library_dataset( trans, id, check_ownership=False, check_accessible=False )
content_conv = self.get_library_dataset( trans, converted_id, check_ownership=False, check_accessible=False )
assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation( parent = content.library_dataset_dataset_association,
dataset = content_conv.library_dataset_dataset_association,
file_type = content_conv.library_dataset_dataset_association.extension,
metadata_safe = True )
assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation( parent=content.library_dataset_dataset_association,
dataset=content_conv.library_dataset_dataset_association,
file_type=content_conv.library_dataset_dataset_association.extension,
metadata_safe=True )
trans.sa_session.add( assoc )
trans.sa_session.flush()
@@ -346,11 +347,10 @@ class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
if ( len( content_id ) % 16 == 0 ):
return 'LibraryDataset', content_id
elif ( content_id.startswith( 'F' ) ):
return 'LibraryFolder', content_id[1:]
return 'LibraryFolder', content_id[ 1: ]
else:
raise HTTPBadRequest( 'Malformed library content id ( %s ) specified, unable to decode.' % str( content_id ) )
@web.expose_api
def delete( self, trans, library_id, id, **kwd ):
"""
@@ -377,7 +377,7 @@ class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
if kwd.get( 'payload', None ):
purge = util.string_as_bool( kwd['payload'].get( 'purge', False ) )
rval = { 'id' : id }
rval = { 'id': id }
try:
ld = self.get_library_dataset( trans, id, check_ownership=False, check_accessible=True )
user_is_admin = trans.user_is_admin()
@@ -424,5 +424,3 @@ class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrar
trans.response.status = 500
rval.update({ 'error': str( exc ) })
return rval