1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/96242495c567/ Changeset: 96242495c567 User: martenson Date: 2014-05-09 00:55:57 Summary: pep 8, fixed decoding of folders again Affected #: 2 files
diff -r f2f32d8b8a06ff370145360b5c75c90e2e2447a9 -r 96242495c567a287bdb4bc26e05b70403c732f24 lib/galaxy/webapps/galaxy/api/folders.py --- a/lib/galaxy/webapps/galaxy/api/folders.py +++ b/lib/galaxy/webapps/galaxy/api/folders.py @@ -136,7 +136,7 @@
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 ) )
diff -r f2f32d8b8a06ff370145360b5c75c90e2e2447a9 -r 96242495c567a287bdb4bc26e05b70403c732f24 lib/galaxy/webapps/galaxy/api/library_contents.py --- a/lib/galaxy/webapps/galaxy/api/library_contents.py +++ b/lib/galaxy/webapps/galaxy/api/library_contents.py @@ -17,6 +17,7 @@ import logging log = logging.getLogger( __name__ )
+ class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems, UsesHistoryDatasetAssociationMixin ):
@expose_api @@ -26,7 +27,7 @@ * 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 @@ 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_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 @@ 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 @@ ``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 @@ # 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 @@ #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 @@ 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 @@ 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 @@ 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 @@ trans.response.status = 500 rval.update({ 'error': str( exc ) }) return rval - -
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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