def get_taxon(self, ctx, ref):
"""
Retrieve the Taxon associated with this GenomeAnnotation.
@return Reference to TaxonAPI object
:param ref: instance of type "ObjectReference"
:returns: instance of type "ObjectReference"
"""
# ctx is the context object
# return variables are: returnVal
#BEGIN get_taxon
ga = GenomeAnnotationAPI_local(self.services, ctx['token'], ref)
returnVal = ga.get_taxon(ref_only=True)
#END get_taxon
# At some point might do deeper type checking...
if not isinstance(returnVal, basestring):
raise ValueError('Method get_taxon return value ' +
'returnVal is not type basestring as required.')
# return the results
return [returnVal]
'num_contigs' : 0,
'contig_lengths' : [],
'contig_ids' : [],
'source' : "KBase",
'source_id' : sys.argv[6],
# 'md5' : "",
'taxonomy' : "Unknown",
'gc_content' : 0.5,
'complete' : 1,
'features' : []
};
taxon = {};
success = 0;
try:
taxon = ga.get_taxon();
success = 1;
except Exception, e:
success = 0
if success == 1:
try:
gto['scientific_name'] = taxon.get_scientific_name()
except Exception, e:
success = 0
try:
gto['domain'] = taxon.get_domain()
except Exception, e:
success = 0
try:
gto['genetic_code'] = taxon.get_genetic_code()
