diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py index bf547fd35f7..e96e32b4b68 100644 --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -95,8 +95,9 @@ class Tabular( data.Text ): if elems[0].lower().startswith(str): proceed = True break - elif format =='tabular' and i > 1: + elif ( format =='tabular' or format == "customtrack" or format == 'gbrowsetrack' ) and i > 1: proceed = True + if proceed: """Set the columns metadata attribute""" if elems_len != dataset.metadata.columns: diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py index deb6e550ed8..bee420f394c 100644 --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -218,22 +218,6 @@ class JobWrapper( object ): job = model.Job.get( self.job_id ) incoming = dict( [ ( p.name, p.value ) for p in job.parameters ] ) incoming = self.tool.params_from_strings( incoming, self.app ) - """ - Call set_meta on each tabular input dataset if metadata is missing. This - is a temporary work-around to ensure columns metadata attribute is set. - This code will be eliminated soon... - """ - """ - gvk: commented out on 9/6/2007 - This code seems to be causing concurrent update problems in the database. - At the current time, tabular datasets are missing the 'column_types' metadata attribute, which is currently - used only for the ColumnListParameter tool parameter. To be safe, I'm calling Tabular().set_meta() there - anyway, so we don't need this. Also, when we run Dan's script again, it will eliminate the need for this. - - for dataset_assoc in job.input_datasets: - dataset = dataset_assoc.dataset - if issubclass(type(dataset.datatype), type(self.app.datatypes_registry.get_datatype_by_extension('tabular'))) and dataset.missing_meta(): - Tabular().set_meta(dataset) - """ # Resore input / output data lists inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] ) out_data = dict( [ ( da.name, da.dataset ) for da in job.output_datasets ] ) diff --git a/lib/galaxy/tools/parameters.py b/lib/galaxy/tools/parameters.py index 96408835210..f708a085a1c 100644 --- a/lib/galaxy/tools/parameters.py +++ b/lib/galaxy/tools/parameters.py @@ -584,9 +584,8 @@ class ColumnListParameter( SelectToolParameter ): assert dataset is not None, "Error retrieving required dataset for ColumnListParameter" - if dataset.missing_meta(): - """Just to be safe...""" - Tabular().set_meta(dataset) + """Just to be safe...""" + Tabular().set_meta(dataset) if self.numerical: for i, col in enumerate( dataset.metadata.column_types ):