1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a221a2734261/ Changeset: a221a2734261 User: dan Date: 2013-10-11 21:03:13 Summary: Better handling of creating peek for tabular files when metadata is missing. Affected #: 1 file diff -r 4eb6fc99fda92e240a1efaaf169c26effa70d429 -r a221a2734261849a49a0f42af6473d4fed06075d lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -33,8 +33,6 @@ MetadataElement( name="column_types", default=[], desc="Column types", param=metadata.ColumnTypesParameter, readonly=True, visible=False, no_value=[] ) MetadataElement( name="column_names", default=[], desc="Column names", readonly=True, visible=False, optional=True, no_value=[] ) - def init_meta( self, dataset, copy_from=None ): - data.Text.init_meta( self, dataset, copy_from=copy_from ) def set_meta( self, dataset, overwrite = True, skip = None, max_data_lines = 100000, max_guess_type_data_lines = None, **kwd ): """ Tries to determine the number of columns as well as those columns that @@ -199,10 +197,13 @@ if not column_names and dataset.metadata.column_names: column_names = dataset.metadata.column_names - column_headers = [None] * dataset.metadata.columns + columns = dataset.metadata.columns + if columns is None: + columns = dataset.metadata.spec.columns.no_value + column_headers = [None] * columns # fill in empty headers with data from column_names - for i in range( min( dataset.metadata.columns, len( column_names ) ) ): + for i in range( min( columns, len( column_names ) ) ): if column_headers[i] is None and column_names[i] is not None: column_headers[i] = column_names[i] @@ -213,7 +214,7 @@ i = int( getattr( dataset.metadata, name ) ) - 1 except: i = -1 - if 0 <= i < dataset.metadata.columns and column_headers[i] is None: + if 0 <= i < columns and column_headers[i] is None: column_headers[i] = column_parameter_alias.get(name, name) out.append( '<tr>' ) @@ -236,13 +237,16 @@ try: if not dataset.peek: dataset.set_peek() + columns = dataset.metadata.columns + if columns is None: + columns = dataset.metadata.spec.columns.no_value for line in dataset.peek.splitlines(): if line.startswith( tuple( skipchars ) ): out.append( '<tr><td colspan="100%%">%s</td></tr>' % escape( line ) ) elif line: elems = line.split( '\t' ) # we may have an invalid comment line or invalid data - if len( elems ) != dataset.metadata.columns: + if len( elems ) != columns: out.append( '<tr><td colspan="100%%">%s</td></tr>' % escape( line ) ) else: out.append( '<tr>' ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.