Mercurial > repos > jjohnson > cummerbund

changeset 10:45275147ac1e

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Add composite_file defs to datatype
author Jim Johnson <jj@umn.edu>
date Wed, 17 Oct 2012 12:00:55 -0500
parents b6427cdbf6d4
children 56bdf6d4ac9c
files cuffdata.py
diffstat 1 files changed, 38 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/cuffdata.py	Fri Oct 12 09:56:02 2012 -0500
+++ b/cuffdata.py	Wed Oct 17 12:00:55 2012 -0500
@@ -40,13 +40,50 @@
     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
         """
-        return '<html><head></head><body>AutoGenerated Primary File for Composite Dataset</body></html>'
+        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):
         """