def get_sql_store(self):
"""Create a new SQL store object from the configured graph_cache file or return a cached value.
"""
if self.sql_store is None:
conn = sqlite3.connect(self.graph_cache, check_same_thread=False)
# don't do this for now, since we get the aliases as keys() which would require further mapping:
#conn.row_factory = sqlite3.Row
self.sql_store = sqlstore.SqliteStore(dbfile=self.graph_cache,
conn=conn,
loglevel=self.loglevel)
return self.sql_store
def run(input_files: KGTKFiles,
**options):
"""Run Kypher query according to the provided command-line arguments.
"""
try:
import_modules()
debug = options.get('_debug', False)
expert = options.get('_expert', False)
loglevel = debug and 1 or 0
if debug and expert:
loglevel = 2
print('OPTIONS:', options)
# normalize path objects to strings:
inputs = [str(f) for f in KGTKArgumentParser.get_input_file_list(input_files)]
if len(inputs) == 0:
raise KGTKException('At least one input needs to be supplied')
output = options.get('output')
if output == '-':
output = sys.stdout
if isinstance(output, str):
output = sqlstore.open_to_write(output, mode='wt')
parameters = parse_query_parameters(regular=options.get('regular_paras') or [],
string=options.get('string_paras') or [],
lqstring=options.get('lqstring_paras') or [])
try:
graph_cache = options.get('graph_cache_file')
store = sqlstore.SqliteStore(graph_cache, create=not os.path.exists(graph_cache), loglevel=loglevel)
query = kyquery.KgtkQuery(inputs, store, loglevel=loglevel,
options=options.get('input_file_options'),
query=options.get('query'),
match=options.get('match'),
where=options.get('where'),
ret=options.get('return_'),
order=options.get('order'),
skip=options.get('skip'),
limit=options.get('limit'),
parameters=parameters,
index=options.get('index'))
explain = options.get('explain')
if explain is not None:
result = query.explain(explain)
output.write(result)
else:
result = query.execute()
# we are forcing \n line endings here instead of \r\n, since those
# can be re/imported efficiently with the new SQLite import command;
# we force `escapechar' back to None to avoid generation of double
# backslashes as in 'Buffalo \'66', which in turn will now raise errors
# if separators in fields are encountered (which seems what we want):
csvwriter = csv.writer(output, dialect=None, delimiter='\t',
quoting=csv.QUOTE_NONE, quotechar=None,
lineterminator='\n',
escapechar=None)
if not options.get('no_header'):
csvwriter.writerow(query.result_header)
csvwriter.writerows(result)
output.flush()
finally:
store.close()
if output is not None and output is not sys.stdout:
output.close()
except sh.SignalException_SIGPIPE:
# hack to work around Python3 issue when stdout is gone when we try to report an exception;
# without this we get an ugly 'Exception ignored...' msg when we quit with head or a pager:
sys.stdout = os.fdopen(1)
except KGTKException as e:
raise e
except Exception as e:
raise KGTKException(str(e) + '\n')
def run(input_files: KGTKFiles, **options):
"""Run Kypher query according to the provided command-line arguments.
"""
try:
options = preprocess_query_options(input_files=input_files, **options)
show_cache = options.get('show_cache')
inputs = options.get('input_files')
if len(inputs) == 0 and not show_cache:
raise KGTKException('At least one input needs to be supplied')
output = options['output']
loglevel = options.get('loglevel')
store = None
try:
graph_cache = options.get('graph_cache_file')
store = sqlstore.SqliteStore(graph_cache, create=not os.path.exists(graph_cache),
loglevel=loglevel, readonly=options.get('readonly'))
if show_cache:
store.describe_meta_tables(out=sys.stdout)
return
imports = options.get('import')
imports and exec('import ' + imports, sqlstore.__dict__)
query = kyquery.KgtkQuery(inputs, store, loglevel=loglevel,
options=options.get('input_file_options'),
query=options.get('query'),
match=options.get('match'),
where=options.get('where'),
optionals=options.get('optionals'),
with_=options.get('with'),
ret=options.get('return'),
order=options.get('order'),
skip=options.get('skip'),
limit=options.get('limit'),
parameters=options.get('parameters'),
index=options.get('index_mode'),
force=options.get('force'))
explain = options.get('explain')
if explain is not None:
result = query.explain(explain)
output.write(result)
else:
result = query.execute()
# we are forcing \n line endings here instead of \r\n, since those
# can be re/imported efficiently with the new SQLite import command;
# we force `escapechar' back to None to avoid generation of double
# backslashes as in 'Buffalo \'66', which in turn will now raise errors
# if separators in fields are encountered (which seems what we want):
csvwriter = csv.writer(output, dialect=None, delimiter='\t',
quoting=csv.QUOTE_NONE, quotechar=None,
lineterminator='\n',
escapechar=None)
if not options.get('no_header'):
csvwriter.writerow(query.result_header)
csvwriter.writerows(result)
output.flush()
finally:
if store is not None:
store.close()
if output is not None and output is not sys.stdout:
output.close()
except sh.SignalException_SIGPIPE:
# hack to work around Python3 issue when stdout is gone when we try to report an exception;
# without this we get an ugly 'Exception ignored...' msg when we quit with head or a pager:
sys.stdout = os.fdopen(1)
except KGTKException as e:
raise e
except Exception as e:
raise KGTKException(str(e) + '\n')