details: http://www.bx.psu.edu/hg/galaxy/rev/e27e392806df changeset: 2437:e27e392806df user: Greg Von Kuster <greg@bx.psu.edu> date: Tue Jun 09 10:28:27 2009 -0400 description: Merge genetics.py 1 file(s) affected in this change: lib/galaxy/datatypes/genetics.py diffs (159 lines): diff -r 2c6720a9130c -r e27e392806df lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py Mon Jun 08 21:02:41 2009 -0400 +++ b/lib/galaxy/datatypes/genetics.py Tue Jun 09 10:28:27 2009 -0400 @@ -17,6 +17,7 @@ from galaxy import util from cgi import escape import urllib +from galaxy.web import url_for from galaxy.datatypes import metadata from galaxy.datatypes.metadata import MetadataElement #from galaxy.datatypes.data import Text @@ -80,7 +81,7 @@ for site_name, site_url in util.get_ucsc_by_build(dataset.dbkey): if site_name in app.config.ucsc_display_sites: site_url = site_url.replace('/hgTracks?','/hgGenome?') # for genome graphs - display_url = urllib.quote_plus( "%s/display_as?id=%i&display_app=%s" % (base_url, dataset.id, type) ) + display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s" % (base_url, url_for( controller='root' ), dataset.id, type)) sl = ["%sdb=%s" % (site_url,dataset.dbkey ),] sl.append("&hgGenome_dataSetName=%s&hgGenome_dataSetDescription=%s" % (dataset.name, 'GalaxyGG_data')) sl.append("&hgGenome_formatType=best%20guess&hgGenome_markerType=best%20guess") @@ -116,8 +117,8 @@ class Rgenetics(Html): """class to use for rgenetics""" """Add metadata elements""" - MetadataElement( name="base_name", desc="base name for all transformed versions of this genetic dataset", default="galaxy", readonly=True) + file_ext="html" composite_type = 'auto_primary_file' @@ -234,7 +235,128 @@ """fake class to distinguish different species of Rgenetics data collections """ file_ext="snptest" + +class RexpBase( Html ): + """base class for BioC data structures in Galaxy + must be constructed with the pheno data in place since that + goes into the metadata for each instance""" + """Add metadata elements""" + MetadataElement( name="columns", default=0, desc="Number of columns", readonly=True, visible=False ) + MetadataElement( name="column_names", default=[], desc="Column names", readonly=True,visible=True ) + MetadataElement( name="base_name", + desc="base name for all transformed versions of this genetic dataset", readonly=True) + MetadataElement( name="pheno_path", + desc="Path to phenotype data for this experiment", readonly=True) + MetadataElement( name="pheno", + desc="Phenotype data for this experiment", readonly=True) + + file_ext = None + + def set_peek( self, dataset ): + """expects a .pheno file in the extra_files_dir - ugh + note that R is wierd and does not include the row.name in + the header. why?""" + p = file(dataset.metadata.pheno_path,'r').readlines() + head = p[0].strip().split('\t') + head.insert(0,'ChipFileName') # fix R write.table b0rken-ness + p[0] = '\t'.join(head) + p = '\n'.join(p) + dataset.peek = p + dataset.metadata.pheno = p + dataset.blurb = 'R loadable BioC expression object for the Rexpression Galaxy toolkit' + + # stolen from Tabular + # class Tabular( data.Text ): + """Tab delimited data""" + + """Add metadata elements""" + def init_meta( self, dataset, copy_from=None ): + if copy_from: + dataset.metadata = copy_from.metadata + + + #def set_readonly_meta( self, dataset, skip=0, **kwd ): + # """Resets the values of readonly metadata elements.""" + # RexpBase.set_meta( self, dataset, skip=skip ) + + def set_readonly_meta( self, dataset, **kwd ): + """Resets the values of readonly metadata elements.""" + RexpBase.set_meta( self, dataset ) + + #def set_meta( self, dataset, skip=0, **kwd ): + def set_meta( self, dataset, **kwd ): + + """ + NOTE we apply the tabular machinary to the phenodata extracted + from a BioC eSet or affybatch. + + """ + if not dataset.peek: + dataset.set_peek() + pk = dataset.peek # use the peek which is the pheno data insead of dataset (!) + if pk: + p = pk.split('\n') + h = p[0].strip().split('\t') # hope is header + h = [escape(x) for x in h] + dataset.metadata.column_names = h + dataset.metadata.columns = len(h) + else: + dataset.metadata.column_names = [] + dataset.metadata.columns = 0 + + def make_html_table( self, dataset): + """Create HTML table, used for displaying peek""" + out = ['<table cellspacing="0" cellpadding="3">',] + try: + # Generate column header + pk = dataset.peek + p = pk.split('\n') + for i,row in enumerate(p): + lrow = row.strip().split('\t') + if i == 0: + orow = ['<th>%s</th>' % escape(x) for x in lrow] + orow.insert(0,'<tr>') + orow.append('</tr>') + else: + orow = ['<td>%s</td>' % escape(x) for x in lrow] + orow.insert(0,'<tr>') + orow.append('</tr>') + out.append(''.join(orow)) + out.append( '</table>' ) + out = "\n".join( out ) + except Exception, exc: + out = "Can't create peek %s" % str( exc ) + return out + + def display_peek( self, dataset ): + """Returns formatted html of peek""" + if not dataset.peek: + dataset.set_peek() + return self.make_html_table( dataset ) + + def get_mime(self): + """Returns the mime type of the datatype""" + return 'application/gzip' + + def sniff(self): + """ can we be bothered looking for the signature or loading via rpy? + """ + return true + +class AffyBatch( RexpBase ): + """derived class for BioC data structures in Galaxy """ + file_ext = "affybatch" + + +class ESet( RexpBase ): + """derived class for BioC data structures in Galaxy """ + file_ext = "eset" + + +class MAList( RexpBase ): + """derived class for BioC data structures in Galaxy """ + file_ext = "malist" if __name__ == '__main__':