def action(args):
engine = sqlalchemy.create_engine(args.url, echo=args.verbosity > 2)
tax = Taxonomy(engine, schema=args.schema)
records = list(yaml.load_all(args.new_nodes))
log.info('adding new nodes')
retval = None
for rec in records:
try:
record_type = rec.pop('type')
if record_type not in {'node', 'name'}:
raise ValueError
except (KeyError, ValueError):
log.error(
('Error in record for tax_id {tax_id}: "type" is '
'required and must be one of "node" or "name"').format(**rec))
retval = 1
continue
tax_id = rec['tax_id']
rec['source_name'] = rec.get('source_name') or args.source_name
try:
if record_type == 'node':
if not rec['source_name']:
log.error('Error: record has no source_name:\n{}'.format(
pprint.pformat(rec)))
raise ValueError
if tax.has_node(tax_id):
log.info('updating *node* "{tax_id}"'.format(**rec))
tax.update_node(**rec)
else:
log.info('new *node* "{tax_id}"'.format(**rec))
tax.add_node(**rec)
elif record_type == 'name':
for name in rec['names']:
name['tax_id'] = tax_id
# source_name may be provided at the record or name level
name['source_name'] = name.get(
'source_name') or rec['source_name']
if not name['source_name']:
log.error(
'Error: record has no source_name:\n {}'.format(
pprint.pformat(rec)))
raise ValueError
log.info('new *name* for "{tax_id}": "{tax_name}"'.format(
**name))
tax.add_name(**name)
except (ValueError, TypeError):
log.error('Error in record with tax_id {}'.format(rec['tax_id']))
log.error(''.join(traceback.format_exception(*sys.exc_info())))
retval = 1
engine.dispose()
if retval:
log.error('Error: some records were malformed')
return retval
def action(args):
engine = sqlalchemy.create_engine(args.url, echo=args.verbosity > 2)
tax = Taxonomy(engine, schema=args.schema)
nodes = list(get_new_nodes(args.new_nodes))
# check if there are any new ranks and exit if needed
node_ranks = set(n['rank'] for n in nodes)
for r in node_ranks:
if r not in tax.ranks:
msg = 'adding new ranks to taxonomy is not yet supported'
raise TaxonIntegrityError(msg)
ranksdict = tax.ranksdict()
ranksdict.update(dict([(n['tax_id'], n['rank']) for n in nodes]))
nodes = [verify_rank_integrity(n, ranksdict, tax.ranks) for n in nodes]
nodes = [verify_lineage_integrity(n, ranksdict, tax.ranks, tax) for n in nodes]
log.info('adding new nodes')
for d in nodes:
if args.source_name:
d['source_name'] = args.source_name
try:
tax.add_node(**d)
except sqlalchemy.exc.IntegrityError:
if args.update:
tax.update_node(**d)
else:
log.warn('node with tax_id %(tax_id)s already exists' % d)
else:
log.info('added new node with tax_id %(tax_id)s' % d)
engine.dispose()
def action(args):
engine = sqlalchemy.create_engine(args.url, echo=args.verbosity > 2)
tax = Taxonomy(engine, schema=args.schema)
records = list(yaml.load_all(args.new_nodes))
log.info('adding new nodes')
retval = None
for rec in records:
try:
record_type = rec.pop('type')
if record_type not in {'node', 'name'}:
raise ValueError
except (KeyError, ValueError):
log.error(('Error in record for tax_id {tax_id}: "type" is '
'required and must be one of "node" or "name"').format(**rec))
retval = 1
continue
tax_id = rec['tax_id']
rec['source_name'] = rec.get('source_name') or args.source_name
try:
if record_type == 'node':
if not rec['source_name']:
log.error('Error: record has no source_name:\n{}'.format(
pprint.pformat(rec)))
raise ValueError
if tax.has_node(tax_id):
log.info('updating *node* "{tax_id}"'.format(**rec))
tax.update_node(**rec)
else:
log.info('new *node* "{tax_id}"'.format(**rec))
tax.add_node(**rec)
elif record_type == 'name':
for name in rec['names']:
name['tax_id'] = tax_id
# source_name may be provided at the record or name level
name['source_name'] = name.get('source_name') or rec['source_name']
if not name['source_name']:
log.error(
'Error: record has no source_name:\n {}'.format(
pprint.pformat(rec)))
raise ValueError
log.info('new *name* for "{tax_id}": "{tax_name}"'.format(**name))
tax.add_name(**name)
except (ValueError, TypeError):
log.error('Error in record with tax_id {}'.format(rec['tax_id']))
log.error(''.join(traceback.format_exception(*sys.exc_info())))
retval = 1
engine.dispose()
if retval:
log.error('Error: some records were malformed')
return retval
def action(args):
dbname = args.database_file
new_nodes = args.new_nodes
source_name = args.source_name
engine = create_engine('sqlite:///%s' % dbname, echo=args.verbosity > 2)
tax = Taxonomy(engine, ncbi.RANKS)
log.warning('adding new nodes')
nodes = get_new_nodes(new_nodes)
for d in nodes:
if source_name:
d['source_name'] = source_name
try:
tax.add_node(**d)
except IntegrityError:
log.info('node with tax_id %(tax_id)s already exists' % d)
else:
log.info('added new node with tax_id %(tax_id)s' % d)
engine.dispose()
def action(args):
dbname = args.database_file
new_nodes = args.new_nodes
source_name = args.source_name
engine = create_engine('sqlite:///%s' % dbname, echo=args.verbosity > 2)
tax = Taxonomy(engine, ncbi.RANKS)
log.warning('adding new nodes')
nodes = get_new_nodes(new_nodes)
for d in nodes:
if source_name:
d['source_name'] = source_name
try:
tax.add_node(**d)
except IntegrityError:
log.info('node with tax_id %(tax_id)s already exists' % d)
else:
log.info('added new node with tax_id %(tax_id)s' % d)
engine.dispose()
