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Next pass at improving make_html_table, using metadata to generate column headers now.

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This commit is contained in:
Greg Von Kuster
2008-03-19 14:33:43 +00:00
parent a5544c752b
commit 11040a4616
4 changed files with 69 additions and 130 deletions
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lib/galaxy/datatypes/data.py
+33
View File
@@ -102,6 +102,39 @@ class Data( object ):
"""Set the peek and blurb text"""
dataset.peek = ''
dataset.blurb = 'data'
def make_html_peek_rows( self, dataset, skipchars=[] ):
out = [""]
comments = []
data = dataset.peek
lines = data.splitlines()
for line in lines:
line = line.strip()
if not line:
continue
comment = False
for skipchar in skipchars:
if line.startswith( skipchar ):
comments.append( line )
comment = True
break
if comment:
continue
elems = line.split( '\t' )
while len( comments ) > 0: # Keep comments
out.append( '<tr><td colspan="100%">' )
out.append( escape( comments.pop(0) ) )
out.append( '</td></tr>' )
out.append( '<tr>' )
for elem in elems: # valid data
elem = escape( elem )
out.append( '<td>%s</td>' % elem )
out.append( '</tr>' )
# Peek may consist only of comments
while len( comments ) > 0:
out.append( '<tr><td colspan="100%">' )
out.append( escape( comments.pop(0) ) )
out.append( '</td></tr>' )
return "".join( out )
def display_peek(self, dataset):
"""Returns formated html of peek"""
try:
lib/galaxy/datatypes/interval.py
+18 -48
View File
@@ -172,57 +172,27 @@ class Interval( Tabular ):
def make_html_table( self, dataset, skipchars=[] ):
"""Create HTML table, used for displaying peek"""
out = ['<table cellspacing="0" cellpadding="3">']
first = True
comments = []
try:
data = dataset.peek
lines = data.splitlines()
for line in lines:
line = line.strip()
if not line:
continue
comment = False
for skipchar in skipchars:
if line.startswith( skipchar ):
comments.append( line )
comment = True
break
if comment:
continue
elems = line.split( '\t' )
if first: # Generate column header
first = False
out.append('<tr>')
for index, elem in enumerate( elems ):
if index+1 == dataset.metadata.chromCol:
out.append( '<th>%s.Chrom</th>' % ( index+1 ) )
elif index+1 == dataset.metadata.startCol:
out.append( '<th>%s.Start</th>' % ( index+1 ) )
elif index+1 == dataset.metadata.endCol:
out.append( '<th>%s.End</th>' % ( index+1 ) )
elif dataset.metadata.strandCol and ( index+1 == dataset.metadata.strandCol ):
out.append( '<th>%s.Strand</th>' % ( index+1 ) )
elif dataset.metadata.nameCol and ( index+1 == dataset.metadata.nameCol ):
out.append( '<th>%s.Name</th>' % ( index+1 ) )
else:
out.append( '<th>%s</th>' % ( index+1 ) )
out.append('</tr>')
while len( comments ) > 0: # Keep comments
out.append( '<tr><td colspan="100%">' )
out.append( escape( comments.pop( 0 ) ) )
out.append( '</td></tr>' )
out.append( '<tr>' ) # body
for elem in elems:
elem = escape( elem )
out.append( '<td>%s</td>' % elem )
out.append( '</tr>' )
# Peek may consis only of comments
while len( comments ) > 0:
out.append( '<tr><td colspan="100%">' )
out.append( escape( comments.pop(0) ) )
out.append( '</td></tr>' )
# Generate column header
out.append('<tr>')
for i in range( 1, dataset.metadata.columns+1 ):
if i == dataset.metadata.chromCol:
out.append( '<th>%s.Chrom</th>' % i )
elif i == dataset.metadata.startCol:
out.append( '<th>%s.Start</th>' % i )
elif i == dataset.metadata.endCol:
out.append( '<th>%s.End</th>' % i )
elif dataset.metadata.strandCol and i == dataset.metadata.strandCol:
out.append( '<th>%s.Strand</th>' % i )
elif dataset.metadata.nameCol and i == dataset.metadata.nameCol:
out.append( '<th>%s.Name</th>' % i )
else:
out.append( '<th>%s</th>' % i )
out.append('</tr>')
out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) )
out.append( '</table>' )
out = ''.join( out )
out = "".join( out )
except Exception, exc:
out = "Can't create peek %s" % str( exc )
return out
lib/galaxy/datatypes/sequence.py
+1 -1
View File
@@ -148,7 +148,7 @@ class Maf( Alignment ):
line = line.strip()
if not line:
continue
out.append( '<tr><td>%s</td></tr>' % line )
out.append( '<tr><td>%s</td></tr>' % escape( line ) )
out.append( '</table>' )
out = "".join( out )
except Exception, exc:
lib/galaxy/datatypes/tabular.py
+17 -81
View File
@@ -88,48 +88,16 @@ class Tabular( data.Text ):
def make_html_table( self, dataset, skipchars=[] ):
"""Create HTML table, used for displaying peek"""
out = ['<table cellspacing="0" cellpadding="3">']
first = True
comments = []
try:
data = dataset.peek
lines = data.splitlines()
for line in lines:
line = line.strip()
if not line:
continue
comment = False
for skipchar in skipchars:
if line.startswith( skipchar ):
comments.append( line )
comment = True
break
if comment:
continue
elems = line.split("\t")
if first: # Generate column header
first = False
out.append('<tr>')
for index, elem in enumerate(elems):
out.append("<th>%s</th>" % (index+1))
out.append('</tr>')
while len(comments)>0: # Keep comments
out.append('<tr><td colspan="100%">')
out.append(escape(comments.pop(0)))
out.append('</td></tr>')
out.append('<tr>')
for elem in elems: # body
elem = escape(elem)
out.append("<td>%s</td>" % elem)
out.append('</tr>')
# Peek may consis only of comments
while len( comments ) > 0:
out.append( '<tr><td colspan="100%">' )
out.append( escape( comments.pop(0) ) )
out.append( '</td></tr>' )
out.append('</table>')
out = "".join(out)
# Generate column header
for i in range( 1, dataset.metadata.columns+1 ):
out.append( '<th>%s</th>' % str( i ) )
out.append( '</tr>' )
out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) )
out.append( '</table>' )
out = "".join( out )
except Exception, exc:
out = "Can't create peek %s" % exc
out = "Can't create peek %s" % str( exc )
return out
def display_peek( self, dataset ):
@@ -149,50 +117,18 @@ class Taxonomy( Tabular ):
def make_html_table( self, dataset, skipchars=[] ):
"""Create HTML table, used for displaying peek"""
out = ['<table cellspacing="0" cellpadding="3">']
first = True
comments = []
try:
data = dataset.peek
lines = data.splitlines()
for line in lines:
line = line.strip()
if not line:
continue
comment = False
for skipchar in skipchars:
if line.startswith( skipchar ):
comments.append( line )
comment = True
break
if comment:
continue
elems = line.split( '\t' )
if first: # Generate column header
first = False
out.append( '<tr>' )
for index, name in enumerate( self.column_names ):
out.append( "<th>%s.%s</th>" % ( str( index+1 ), name ) )
# This data type requires at least 24 columns in the data
num_col_headers = len( elems ) - len( self.column_names )
if num_col_headers > 0:
for index in range( len( self.column_names ), len( elems ) ):
out.append( "<th>%s</th>" % ( index+1 ) )
out.append( '</tr>' )
# Keep comments
while len( comments ) > 0:
out.append( '<tr><td colspan="100%">' )
out.append( escape( comments.pop( 0 ) ) )
out.append( '</td></tr>' )
out.append( '<tr>' ) # body
for elem in elems:
elem = escape( elem )
out.append( "<td>%s</td>" % elem )
# Generate column header
out.append( '<tr>' )
for i, name in enumerate( self.column_names ):
out.append( '<th>%s.%s</th>' % ( str( i+1 ), name ) )
# This data type requires at least 24 columns in the data
if dataset.metadata.columns - len( self.column_names ) > 0:
for i in range( len( self.column_names ), dataset.metadata.columns ):
out.append( '<th>%s</th>' % str( i+1 ) )
out.append( '</tr>' )
# Peek may consis only of comments
while len( comments ) > 0:
out.append( '<tr><td colspan="100%">' )
out.append( escape( comments.pop(0) ) )
out.append( '</td></tr>' )
out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) )
out.append( '</table>' )
out = "".join( out )
except Exception, exc: