def refine(self):
self.init()
clusterings = self.cluster_splits_of_interest()
default_clustering_class = constants.merged_default if self.is_merged else constants.single_default
default_clustering_id = dbops.get_default_clustering_id(
default_clustering_class, clusterings)
d = interactive.InputHandler(self.args,
external_clustering={
'clusterings':
clusterings,
'default_clustering':
default_clustering_id
})
# set a more appropriate title
bins = sorted(list(self.bins))
if not self.title:
self.title = 'Refining %s%s from "%s"' % (
', '.join(bins[0:3]), ' (and %d more)' %
(len(bins) - 3) if len(bins) > 3 else '', self.collection_name)
d.title = textwrap.fill(self.title)
return d
def get_the_interactive_object(self,
base_path,
title="Unknown Title",
read_only=True):
"""Helper function to get an interactive object that is ready to be launched"""
args = copy.deepcopy(self.args)
args.title = title
args.read_only = read_only
J = lambda f: os.path.join(base_path, f)
F = lambda f: J(f) if os.path.exists(J(f)) else None
args.tree = F('treeFile')
args.fasta_file = F('fastaFile')
args.view_data = F('dataFile')
args.samples_db = F('samples.db')
args.profile_db = J('profile.db')
args.samples_information_db = F('samples.db')
args.additional_layers = F('additionalFile')
try:
d = interactive.InputHandler(args)
return {
"status": "ok",
"message": None,
"data": {
"d": d,
"args": args
}
}
except Exception, e:
return {"status": "error", "message": e.e, "data": None}
def refine(self):
self.init()
clusterings = self.cluster_splits_of_interest()
d = interactive.InputHandler(self.args,
external_clustering={
'clusterings': clusterings,
'default_clustering': 'tnf-cov'
})
# set a more appropriate title
bins = sorted(list(self.bins))
title = 'Refining %s%s from "%s"' % (
', '.join(bins[0:3]), ' (and %d more)' %
(len(bins) - 3) if len(bins) > 3 else '', self.collection_id)
d.title = textwrap.fill(title)
return d