Removing the SAM datatype for class Bam and resetting changes with sn…

…iff.py

lib/galaxy/datatypes/binary.py

@@ -18,7 +18,6 @@
 from galaxy import util
 from galaxy.datatypes import metadata
 from galaxy.datatypes.metadata import DictParameter, ListParameter, MetadataElement, MetadataParameter
-from galaxy.datatypes.tabular import Sam
 from galaxy.util import FILENAME_VALID_CHARS, nice_size, sqlite, which
 from . import data, dataproviders
 
@@ -223,7 +222,7 @@ class GenericAsn1Binary( Binary ):
 
 
 @dataproviders.decorators.has_dataproviders
-class Bam( Binary, Sam ):
+class Bam( Binary ):
     """Class describing a BAM binary file"""
     edam_format = "format_2572"
     edam_data = "data_0863"
@@ -238,9 +237,13 @@ class Bam( Binary, Sam ):
     MetadataElement( name="reference_names", default=[], desc="Chromosome Names", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value=[] )
     MetadataElement( name="reference_lengths", default=[], desc="Chromosome Lengths", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value=[] )
     MetadataElement( name="bam_header", default={}, desc="Dictionary of BAM Headers", param=MetadataParameter, readonly=True, visible=False, optional=True, no_value={} )
+    MetadataElement( name="columns", default=0, desc="Number of columns", readonly=True, visible=False, no_value=0 )
+    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__(self, **kwd):
         super( Bam, self ).__init__( **kwd )
+        self.column_names = ['QNAME', 'FLAG', 'RNAME', 'POS', 'MAPQ', 'CIGAR', 'MRNM', 'MPOS', 'ISIZE', 'SEQ', 'QUAL', 'OPT' ]
 
     def _get_samtools_version( self ):
         version = '0.0.0'
@@ -429,6 +432,8 @@ def set_meta( self, dataset, overwrite=True, **kwd ):
             dataset.metadata.read_groups = [ read_group['ID'] for read_group in dataset.metadata.bam_header.get( 'RG', [] ) if 'ID' in read_group ]
             dataset.metadata.sort_order = dataset.metadata.bam_header.get( 'HD', {} ).get( 'SO', None )
             dataset.metadata.bam_version = dataset.metadata.bam_header.get( 'HD', {} ).get( 'VN', None )
+            dataset.metadata.columns = 12
+            dataset.metadata.column_types = ['str', 'int', 'str', 'int', 'int', 'str', 'str', 'int', 'int', 'str', 'str', 'str']
         except:
             # Per Dan, don't log here because doing so will cause datasets that
             # fail metadata to end in the error state

lib/galaxy/datatypes/sniff.py

@@ -16,8 +16,8 @@
 
 from six import text_type
 
-from galaxy import datatypes
 from galaxy import util
+from galaxy.datatypes.binary import Binary
 from galaxy.util import (
     compression_utils,
     multi_byte,
@@ -487,7 +487,7 @@ def handle_uploaded_dataset_file( filename, datatypes_registry, ext='auto', is_m
         ext = guess_ext( filename, sniff_order=datatypes_registry.sniff_order, is_multi_byte=is_multi_byte )
 
     if check_binary( filename ):
-        if not datatypes.binary.Binary.is_ext_unsniffable(ext) and not datatypes_registry.get_datatype_by_extension( ext ).sniff( filename ):
+        if not Binary.is_ext_unsniffable(ext) and not datatypes_registry.get_datatype_by_extension( ext ).sniff( filename ):
             raise InappropriateDatasetContentError( 'The binary uploaded file contains inappropriate content.' )
     elif check_html( filename ):
         raise InappropriateDatasetContentError( 'The uploaded file contains inappropriate HTML content.' )