# column 0; but the column really ought to be chosen by a command line
# argument, either by position or by column name (in header).
name_column = 0
# Extract just the taxon names from the table, as a vector, one entry per row.
ids = []
for row in rows:
ids.append(row[name_column])
# Invoke the Open Tree TNRS service.
# TBD: consider doing fuzzy matches as well (with a high threshold). Not
# clear what the user should do for names that don't uniquely resolve.
tnrs_return = opentreelib.tnrs_match_names(ids, do_approximate_matching=False)
# import pprint
# pprint.PrettyPrinter().pprint(tnrs_return)
# Process the wad of stuff that the TNRS returned. First, index the
# results by taxon name.
name_to_matches = {}
for lump in tnrs_return['results']:
name_to_matches[lump['id']] = lump['matches']
# Now add the OTT id as a new column at the right side of the table.
for row in rows:
name = row[name_column]
if name in name_to_matches:
def unique_ott_id(name):
tnrs_result = opentreelib.tnrs_match_names([name])
ottid = tnrs_result['results'][0]['matches'][0]['ot:ottId']
return ottid
# column 0; but the column really ought to be chosen by a command line
# argument, either by position or by column name (in header).
name_column = 0
# Extract just the taxon names from the table, as a vector, one entry per row.
ids = []
for row in rows:
ids.append(row[name_column])
# Invoke the Open Tree TNRS service.
# TBD: consider doing fuzzy matches as well (with a high threshold). Not
# clear what the user should do for names that don't uniquely resolve.
tnrs_return = opentreelib.tnrs_match_names(ids, do_approximate_matching=False)
# import pprint
# pprint.PrettyPrinter().pprint(tnrs_return)
# Process the wad of stuff that the TNRS returned. First, index the
# results by taxon name.
name_to_matches = {}
for lump in tnrs_return['results']:
name_to_matches[lump['id']] = lump['matches']
# Now add the OTT id as a new column at the right side of the table.
for row in rows:
name = row[name_column]
if name in name_to_matches:
def unique_ott_id(name):
tnrs_result = opentreelib.tnrs_match_names([name])
ottid = tnrs_result['results'][0]['matches'][0]['ot:ottId']
return ottid
