From 7cb1bb2e47e6a815e8ff72b35db68ce907ced2dd Mon Sep 17 00:00:00 2001 From: Greg Von Kuster Date: Mon, 1 Oct 2007 14:07:34 +0000 Subject: [PATCH] Fix for cor2 tool functional test, also set columns and column-types meta data attributes to be invisible for all tabular data types. --- lib/galaxy/datatypes/interval.py | 10 +++++----- lib/galaxy/datatypes/tabular.py | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/lib/galaxy/datatypes/interval.py b/lib/galaxy/datatypes/interval.py index 1cd3a260ab6..02d86f216b2 100644 --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -220,7 +220,7 @@ class Bed( Interval ): MetadataElement( name="startCol", default=2, desc="Start column", param=metadata.ColumnParameter ) MetadataElement( name="endCol", default=3, desc="End column", param=metadata.ColumnParameter ) MetadataElement( name="strandCol", desc="Strand column (click box & select)", param=metadata.ColumnParameter, optional=True, no_value=0 ) - MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True ) + MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True, visible=False ) def missing_meta( self, dataset ): """Checks for empty meta values""" @@ -380,8 +380,8 @@ class Gff( Tabular ): file_ext = "gff" """Add metadata elements""" - MetadataElement( name="columns", default=9, desc="Number of columns", readonly=True ) - MetadataElement( name="column_types", default=['str','str','str','int','int','int','str','str','str'], desc="Column types", readonly=True ) + MetadataElement( name="columns", default=9, desc="Number of columns", readonly=True, visible=False ) + MetadataElement( name="column_types", default=['str','str','str','int','int','int','str','str','str'], desc="Column types", readonly=True, visible=False ) def __init__(self, **kwd): """Initialize datatype, by adding GBrowse display app""" @@ -504,7 +504,7 @@ class Gff3( Gff ): valid_gff3_phase = ['.', '0', '1', '2'] """Add metadata elements""" - MetadataElement( name="column_types", default=['str','str','str','int','int','float','str','int','list'], desc="Column types", readonly=True ) + MetadataElement( name="column_types", default=['str','str','str','int','int','float','str','int','list'], desc="Column types", readonly=True, visible=False ) def __init__(self, **kwd): """Initialize datatype, by adding GBrowse display app""" @@ -602,7 +602,7 @@ class Wiggle( Tabular ): """Tab delimited data in wiggle format""" file_ext = "wig" - MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True ) + MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True, visible=False ) def make_html_table(self, data): return Tabular.make_html_table(self, data, skipchar='#') diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py index 5e8f88aada5..8a9c6532c89 100644 --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -32,7 +32,7 @@ class Tabular( data.Text ): return True return False - def set_meta( self, dataset, skip=0 ): + def set_meta( self, dataset, skip=1 ): """ Tries to determine the number of columns as well as those columns that contain numerical values in the dataset. A skip parameter is