From ce39e478f04ddb878b217cfdae66b19d3c3cd708 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Tue, 4 Mar 2008 21:55:16 +0000
Subject: [PATCH] Added new 'taxonomy' datatype to config file and registry,
 user can now manually set this datatype for upoaded files, but no sniffer yet
 exists.  First pass at bulding the history HTML for the dataset, but needs
 review.

---
 lib/galaxy/datatypes/registry.py |  2 ++
 lib/galaxy/datatypes/tabular.py  | 54 +++++++++++++++++++++++++++++++-
 universe_wsgi.ini.sample         |  1 +
 3 files changed, 56 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index a0ff29cf9b7..1c26da81b47 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -52,6 +52,7 @@ class Registry( object ):
                 'qualityscore': qualityscore.QualityScore(),
                 'scf'         : images.Scf(),
                 'tabular'     : tabular.Tabular(),
+                'taxonomy'    : tabular.Taxonomy(),
                 'txt'         : data.Text(),
                 'txtseq.zip'  : images.Txtseq(),
                 'wig'         : interval.Wiggle()
@@ -72,6 +73,7 @@ class Registry( object ):
                 'qualityscore': 'text/plain',
                 'scf'         : 'application/octet-stream',
                 'tabular'     : 'text/plain',
+                'taxonomy'    : 'text/plani',
                 'txt'         : 'text/plain',
                 'txtseq.zip'  : 'application/zip',
                 'wig'         : 'text/plain'
diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py
index 7722557d91b..1afaf8bf1c8 100644
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -130,4 +130,56 @@ class Tabular( data.Text ):
         return m_peek
 
 class Taxonomy( Tabular ):
-    pass
+    def __init__(self, **kwd):
+        """Initialize taxonomy datatype"""
+        Tabular.__init__( self, **kwd )
+        self.column_names = ['Name', 'GI', 'Root', 'Superkingdom', 'Kingdom', 'Subkingdom',
+                             'Superphylum', 'Phylum', 'Subphylum', 'Superclass', 'Class', 'Subclass',
+                             'Superorder', 'Order', 'Suborder', 'Superfamily', 'Family', 'Subfamily',
+                             'Tribe', 'Subtribe', 'Genus', 'Subgenus', 'Species', 'Subspecies'
+                             ]
+
+    def make_html_table( self, data, skipchar=None ):
+        """Create HTML table, used for displaying peek"""
+        out = ['<table cellspacing="0" cellpadding="3">']
+        first = True
+        comments = []
+        try:
+            lines =  data.splitlines()
+            for line in lines:
+                line = line.rstrip( '\r\n' )
+                if not line:
+                    continue
+                if skipchar and line.startswith( skipchar ):
+                    comments.append( line )
+                    continue
+
+                elems = line.split( '\t' )
+                # This data type requires at least 24 columns in the data
+                int_col_headers = len( elems ) - len( self.column_names )
+
+                if first: #generate header
+                    first = False
+                    out.append( '<tr>' )
+                    for index, elem in enumerate( elems[0:int_col_headers] ):
+                        out.append( "<th>%s</th>" % ( index+1 ) )
+                    for index, name in enumerate( self.column_names ):
+                        out.append( "<th>%s</th>" % name )
+                    out.append( '</tr>' )
+                
+                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 )
+                out.append( '</tr>' )
+            out.append( '</table>' )
+            out = "".join( out )
+        except Exception, exc:
+            out = "Can't create peek %s" % exc
+        return out
+
diff --git a/universe_wsgi.ini.sample b/universe_wsgi.ini.sample
index e8bcb30f775..87ac55f15af 100644
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -181,6 +181,7 @@ pdf = galaxy.datatypes.images:Image,application/pdf
 png = galaxy.datatypes.images:Image,image/png
 qualityscore = galaxy.datatypes.qualityscore:QualityScore
 scf = galaxy.datatypes.images:Scf,application/octet-stream
+taxonomy = galaxy.datatypes.tabular:Taxonomy
 tabular = galaxy.datatypes.tabular:Tabular
 txt = galaxy.datatypes.data:Text
 txtseq.zip = galaxy.datatypes.images:Txtseq,application/zip