From 11040a4616cbffc667b9ae5dc88d814702e6a6ef Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Wed, 19 Mar 2008 14:33:43 +0000
Subject: [PATCH] Next pass at improving make_html_table, using metadata to
 generate column headers now.

---
 lib/galaxy/datatypes/data.py     | 33 +++++++++++
 lib/galaxy/datatypes/interval.py | 66 ++++++---------------
 lib/galaxy/datatypes/sequence.py |  2 +-
 lib/galaxy/datatypes/tabular.py  | 98 ++++++--------------------------
 4 files changed, 69 insertions(+), 130 deletions(-)

diff --git a/lib/galaxy/datatypes/data.py b/lib/galaxy/datatypes/data.py
index 4807b76c6e8..d982485c1c8 100644
--- a/lib/galaxy/datatypes/data.py
+++ b/lib/galaxy/datatypes/data.py
@@ -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:
diff --git a/lib/galaxy/datatypes/interval.py b/lib/galaxy/datatypes/interval.py
index 2b77b6e4cbe..1bd2b7f712d 100644
--- a/lib/galaxy/datatypes/interval.py
+++ b/lib/galaxy/datatypes/interval.py
@@ -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
diff --git a/lib/galaxy/datatypes/sequence.py b/lib/galaxy/datatypes/sequence.py
index 5d9cf7df819..8835539bcf5 100644
--- a/lib/galaxy/datatypes/sequence.py
+++ b/lib/galaxy/datatypes/sequence.py
@@ -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:
diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py
index 3e64fc206e3..7c8c8af362c 100644
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -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: