# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Daniel Blankenberg dan@bx.psu.edu # Date 1289329026 18000 # Node ID 7c60d74ba2df4488df90d08ed0ae9c7cc3871222 # Parent 9ee40043b826b3bc1e29f84996f9fe14dd119a45 Aggressively sanitize metadata parameter values when provided on the upload form and which are subsequently used for filename substitution.
--- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -155,6 +155,26 @@ def sanitize_param(value): print value raise Exception, 'Unknown parameter type (%s)' % ( type( value ) )
+valid_filename_chars = set( string.ascii_letters + string.digits + '_.' ) +invalid_filenames = [ '', '.', '..' ] +def sanitize_for_filename( text, default=None ): + """ + Restricts the characters that are allowed in a filename portion; Returns default value or a unique id string if result is not a valid name. + Method is overly aggressive to minimize possible complications, but a maximum length is not considered. + """ + out = [] + for c in text: + if c in valid_filename_chars: + out.append( c ) + else: + out.append( '_' ) + out = ''.join( out ) + if out in invalid_filenames: + if default is None: + return sanitize_for_filename( str( unique_id() ) ) + return default + return out + class Params: """ Stores and 'sanitizes' parameters. Alphanumeric characters and the
--- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -12,7 +12,7 @@ import StringIO, os, urllib from galaxy.datatypes import sniff from galaxy.util.bunch import Bunch from galaxy.util.odict import odict -from galaxy.util import json, relpath +from galaxy.util import json, relpath, sanitize_for_filename
class Group( object ): def __init__( self ): @@ -335,10 +335,14 @@ class UploadDataset( Group ): dataset.composite_files = {} #load metadata files_metadata = context.get( self.metadata_ref, {} ) + metadata_name_substition_default_dict = dict( [ ( composite_file.substitute_name_with_metadata, d_type.metadata_spec[ composite_file.substitute_name_with_metadata ].default ) for composite_file in d_type.composite_files.values() if composite_file.substitute_name_with_metadata ] ) for meta_name, meta_spec in d_type.metadata_spec.iteritems(): if meta_spec.set_in_upload: if meta_name in files_metadata: - dataset.metadata[ meta_name ] = files_metadata[ meta_name ] + meta_value = files_metadata[ meta_name ] + if meta_name in metadata_name_substition_default_dict: + meta_value = sanitize_for_filename( meta_value, default = metadata_name_substition_default_dict[ meta_name ] ) + dataset.metadata[ meta_name ] = meta_value dataset.precreated_name = dataset.name = self.get_composite_dataset_name( context ) if dataset.datatype.composite_type == 'auto_primary_file': #replace sniff here with just creating an empty file