More fixes related to metadata. Now only the GOPS tool tests are broken...

lib/galaxy/datatypes/interval.py

@@ -44,6 +44,7 @@ class Interval( Tabular ):
     MetadataElement( name="strandCol", desc="Strand column", param=metadata.ColumnParameter, optional=True )
     MetadataElement( name="dbkey", desc="Database/Build", default="?",
                      param=metadata.SelectParameter, multiple=False, values=util.dbnames )
+    MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True )
 
 
     def __init__(self, **kwd):
@@ -187,6 +188,7 @@ class Bed( Interval ):
     MetadataElement( name="strandCol", desc="Strand column", param=metadata.ColumnParameter, optional=True )
     MetadataElement( name="dbkey", desc="Database/Build", default=None,
                      param=metadata.SelectParameter, multiple=False, values=util.dbnames )
+    MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True )
     
     def missing_meta( self, dataset ):
         """Checks for empty meta values"""
@@ -204,18 +206,20 @@ class Bed( Interval ):
         valid_bed_data = False
         if dataset.has_data():
             for i, line in enumerate( file(dataset.file_name) ):
-                line = line.strip()
-                if len(line) > 0 and ( line.startswith('chr') or line.startswith('scaff') ):
+                line = line.rstrip('\r\n')
+                if line and len(line) > 0 and ( line.startswith('chr') or line.startswith('scaff') ):
                     valid_bed_data = True
                     elems = line.split("\t")
                     if len(elems) < 6:
-                        dataset.metadata.strandCol = 0
+                        dataset.metadata.is_strandCol = "false"
+                        dataset.metadata.strandCol = None
                         dataset.mark_metadata_changed()
                     break
                 if i == 30:
                     break
         if not valid_bed_data:
-            dataset.metadata.strandCol = 0
+            dataset.metadata.is_strandCol = "false"
+            dataset.metadata.strandCol = None
             dataset.mark_metadata_changed()
         
     def as_ucsc_display_file( self, dataset, **kwd ):
@@ -259,6 +263,7 @@ class Gff( Tabular ):
     """Add metadata elements"""
     MetadataElement( name="dbkey", desc="Database/Build", default="?",
                      param=metadata.SelectParameter, multiple=False, values=util.dbnames )
+    MetadataElement( name="columns", default=9, desc="Number of columns", readonly=True )
     
     def __init__(self, **kwd):
         """Initialize datatype, by adding GBrowse display app"""
@@ -331,6 +336,7 @@ class Wiggle( Tabular ):
     """Tab delimited data in wiggle format"""
     MetadataElement( name="dbkey", desc="Database/Build", default="?",
                      param=metadata.SelectParameter, multiple=False, values=util.dbnames )
+    MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True )
     
     def make_html_table(self, data):
         return Tabular.make_html_table(self, data, skipchar='#')

lib/galaxy/datatypes/tabular.py

@@ -19,10 +19,7 @@ class Tabular( data.Text ):
     """Tab delimited data"""
 
     """Add metadata elements"""
-    MetadataElement( name="columns",
-                     default=0,
-                     desc="Number of columns",
-                     readonly=True )
+    MetadataElement( name="columns", default=0, desc="Number of columns", readonly=True )
     MetadataElement( name="dbkey", desc="Database/Build", default="?",
                      param=metadata.SelectParameter, multiple=False, values=util.dbnames )
 
@@ -85,10 +82,14 @@ class Tabular( data.Text ):
             maxcols = 0
             count = 0
             for line in open( dataset.file_name ):
-                count += 1
-                if count > 1000: break
-                cols = len( line.split("\t") )
-                if cols > maxcols: maxcols = cols
+                line = line.rstrip('\r\n')
+                if line and not line.startswith( '#' ):
+                    count += 1
+                    if count > 1000: 
+                        break
+                    cols = len( line.split("\t") )
+                    if cols > maxcols: 
+                        maxcols = cols
             setattr( dataset.metadata, "columns", maxcols )
         except:
             pass        

test/functional/test_basic.py

@@ -41,7 +41,10 @@ class BasicFunctions(TwillTestCase):
         #
         #self.edit_data(hid=1, dbkey='hg15', chromCol='1', info='foo')
         #self.check_history('hg15 Testdata interval foo')
-        self.edit_data(hid=1, dbkey='hg16', is_strandCol='')
+        """
+        TODO: Ian make sure this test is functioning as you expect...
+        """
+        self.edit_data(hid=1, dbkey='hg16', is_strandCol="true")
         self.check_history('hg16 Testdata bed')
         
     def test_delete(self):