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Better handling of creating peek for tabular files when metadata is missing.

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This commit is contained in:
Daniel Blankenberg
2013-10-11 15:03:13 -04:00
parent 18237898d1
commit e9d2043132
1 changed files with 10 additions and 6 deletions
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lib/galaxy/datatypes/tabular.py
+10 -6
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@@ -33,8 +33,6 @@ class Tabular( data.Text ):
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 @@ class Tabular( data.Text ):
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 @@ class Tabular( data.Text ):
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 @@ class Tabular( data.Text ):
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>' )