--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cuffdata.py	Mon Feb 04 19:50:25 2013 -0500
@@ -0,0 +1,115 @@
+"""
+CuffData 
+"""
+import logging
+import os,os.path,re
+import galaxy.datatypes.data
+from galaxy.datatypes.images import Html
+from galaxy.datatypes.binary import Binary
+from galaxy import util
+from galaxy.datatypes.metadata import MetadataElement
+
+log = logging.getLogger(__name__)
+
+class CuffDiffData( Html ):
+    """
+    CuffDiff output files:
+    run.info
+    read_groups.info
+    cds.count_tracking
+    cds.diff
+    cds.fpkm_tracking
+    cds.read_group_tracking
+    cds_exp.diff
+    gene_exp.diff
+    genes.count_tracking
+    genes.fpkm_tracking
+    genes.read_group_tracking
+    isoform_exp.diff
+    isoforms.count_tracking
+    isoforms.fpkm_tracking
+    isoforms.read_group_tracking
+    promoters.diff
+    splicing.diff
+    tss_group_exp.diff
+    tss_groups.count_tracking
+    tss_groups.fpkm_tracking
+    tss_groups.read_group_tracking
+    """
+    file_ext = 'cuffdata'
+    is_binary = False
+    composite_type = 'auto_primary_file'
+    allow_datatype_change = False
+    def __init__( self, **kwd ):
+        Html.__init__( self, **kwd )
+        self.add_composite_file('run.info', description = 'run.info', mimetype = 'text/html', optional = True, is_binary = False )
+        self.add_composite_file('read_groups.info', description = 'read_groups.info', mimetype = 'text/html', optional = True, is_binary = False )
+        self.add_composite_file('cds.count_tracking', description = 'cds.count_tracking', mimetype = 'text/html', optional = True, is_binary = False )
+        self.add_composite_file('cds.diff', description = 'cds.diff', mimetype = 'text/html', optional = True, is_binary = False )
+        self.add_composite_file('cds.fpkm_tracking', description = 'cds.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False )
+        self.add_composite_file('cds.read_group_tracking', description = 'cds.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False )
+        self.add_composite_file('cds_exp.diff', description = 'cds_exp.diff', mimetype = 'text/html', optional = True, is_binary = False )
+        self.add_composite_file('gene_exp.diff', description = 'gene_exp.diff', mimetype = 'text/html', optional = True, is_binary = False )
+        self.add_composite_file('genes.count_tracking', description = 'genes.count_tracking', mimetype = 'text/html', optional = True, is_binary = False )
+        self.add_composite_file('genes.fpkm_tracking', description = 'genes.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False )
+        self.add_composite_file('genes.read_group_tracking', description = 'genes.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False )
+        self.add_composite_file('isoform_exp.diff', description = 'isoform_exp.diff', mimetype = 'text/html', optional = True, is_binary = False )
+        self.add_composite_file('isoforms.count_tracking', description = 'isoforms.count_tracking', mimetype = 'text/html', optional = True, is_binary = False )
+        self.add_composite_file('isoforms.fpkm_tracking', description = 'isoforms.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False )
+        self.add_composite_file('isoforms.read_group_tracking', description = 'isoforms.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False )
+        self.add_composite_file('promoters.diff', description = 'promoters.diff', mimetype = 'text/html', optional = True, is_binary = False )
+        self.add_composite_file('splicing.diff', description = 'splicing.diff', mimetype = 'text/html', optional = True, is_binary = False )
+        self.add_composite_file('tss_group_exp.diff', description = 'tss_group_exp.diff', mimetype = 'text/html', optional = True, is_binary = False )
+        self.add_composite_file('tss_groups.count_tracking', description = 'tss_groups.count_tracking', mimetype = 'text/html', optional = True, is_binary = False )
+        self.add_composite_file('tss_groups.fpkm_tracking', description = 'tss_groups.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False )
+        self.add_composite_file('tss_groups.read_group_tracking', description = 'tss_groups.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False )
+
+    def generate_primary_file( self, dataset = None ):
+        """ 
+        This is called only at upload to write the html file
+        cannot rename the datasets here - they come with the default unfortunately
+        """
+        rval = ['<html><head><title>CuffDiff Output</title></head>']
+        rval.append('<body>')
+        rval.append('<p/>CuffDiff Outputs:<p/><ul>')
+        for composite_name, composite_file in self.get_composite_files( dataset = dataset ).iteritems():
+            fn = composite_name
+            log.debug( "Velvet log info  %s %s %s" % ('JJ generate_primary_file',fn,composite_file))
+            opt_text = ''
+            if composite_file.optional:
+                opt_text = ' (optional)'
+            if composite_file.get('description'):
+                rval.append( '<li><a href="%s" type="text/plain">%s (%s)</a>%s</li>' % ( fn, fn, composite_file.get('description'), opt_text ) )
+            else:
+                rval.append( '<li><a href="%s" type="text/plain">%s</a>%s</li>' % ( fn, fn, opt_text ) )
+        rval.append( '</ul></body></html>' )
+        return "\n".join( rval )
+
+    def regenerate_primary_file(self,dataset):
+        """
+        cannot do this until we are setting metadata 
+        """
+        flist = os.listdir(dataset.extra_files_path)
+        rval = ['<html><head><title>CuffDiff Output</title></head>']
+        rval.append('<body>')
+        rval.append('<p/>CuffDiff Outputs:<p/><ul>')
+        for i,fname in enumerate(flist):
+            sfname = os.path.split(fname)[-1]
+            rval.append( '<li><a href="%s" type="text/html">%s</a>' % ( sfname, sfname ) )
+        rval.append( '</ul></body></html>' )
+        f = file(dataset.file_name,'w')
+        f.write("\n".join( rval ))
+        f.write('\n')
+        f.close()
+
+    def set_meta( self, dataset, **kwd ):
+        Html.set_meta( self, dataset, **kwd )
+        self.regenerate_primary_file(dataset)
+
+    def sniff( self, filename ):
+        return False
+
+class CuffDataDB( Binary ):
+    file_ext = 'cuffdata'
+    is_binary = True
+    allow_datatype_change = False