Mercurial > repos > bgruening > upload_testing
diff homer.py @ 56:07a5042bbe90
Uploaded
| author | bgruening |
|---|---|
| date | Mon, 12 Aug 2013 14:25:53 -0400 |
| parents | e9cd105a8856 |
| children |
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--- a/homer.py Mon Aug 12 09:06:47 2013 -0400 +++ b/homer.py Mon Aug 12 14:25:53 2013 -0400 @@ -1,14 +1,14 @@ """ HOMER special datatypes """ - +import os from galaxy.datatypes.data import get_file_peek from galaxy.datatypes.data import Text, Data from galaxy.datatypes.metadata import MetadataElement from galaxy.datatypes.images import Html -class TagDirectory( Text ): +class TagDirectory( Html ): """Base class for HOMER's Tag Directory datatype.""" file_ext = 'homer_tagdir' @@ -16,7 +16,7 @@ allow_datatype_change = False def __init__(self, **kwd): - Text.__init__( self, **kwd ) + Html.__init__( self, **kwd ) #self.add_composite_file('tagInfo.txt', description = 'basic configuration information', mimetype = 'text/html') # Contains basic configuration information self.add_composite_file('tagLengthDistribution.txt', description = 'histogram of read lengths used for alignment', mimetype = 'text/html') # File contains a histogram of read lengths used for alignment. self.add_composite_file('tagCountDistribution.txt', description = 'histogram of clonal read depth, showing the number of reads per unique position', mimetype = 'text/html') # File contains a histogram of clonal read depth, showing the number of reads per unique position. @@ -29,25 +29,23 @@ def regenerate_primary_file(self,dataset): """ - cannot do this until we are setting metadata + regenerate the index file after metadata generation """ - flist = os.listdir(dataset.extra_files_path) - rval = ['<html><head><title>CuffDiff Output</title></head>'] + rval = ['<html><head><title>HOMER database files</title></head>'] rval.append('<body>') rval.append('<p/>CuffDiff Outputs:<p/><ul>') - for i,fname in enumerate(flist): + for fname in os.listdir(dataset.extra_files_path): 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 = file( dataset.file_name, 'w' ) + f.write( '%s\n' % '\n'.join( rval ) ) f.close() - - def set_meta( self, dataset, **kwd ): - Text.set_meta( self, dataset, **kwd ) - self.regenerate_primary_file(dataset) - + if not dataset.info: + dataset.info = 'HOMER datatype object' + if not dataset.blurb: + dataset.blurb = 'Composite file - HOMER' + return True def generate_primary_file( self, dataset = None ): rval = ['<html><head><title>HOMER database files</title></head><ul>'] @@ -59,6 +57,11 @@ rval.append( '</ul></html>' ) return "\n".join( rval ) + def set_meta( self, dataset, **kwd ): + Html.set_meta( self, dataset, **kwd ) + self.regenerate_primary_file(dataset) + + def display_data(self, trans, data, preview=False, filename=None, to_ext=None, size=None, offset=None, **kwd): """Apparently an old display method, but still gets called.