def parse(in_data):
"""Parses a samtools flagstat result into a dictionary.
:param in_data: Input flagstat contents.
:type in_data: str or file handle
:returns: Parsed flagstat values.
:rtype: dict
"""
with get_handle(in_data) as fh:
contents = fh.read(_MAX_SIZE)
f = partial(search, contents, caster=int)
parsed = (
("total", f(_RE_TOTAL)),
("duplicates", f(_RE_DUPLICATES)),
("secondary", f(_RE_SECONDARY)),
("supplementary", f(_RE_SUPPLEMENTARY)),
("mapped", f(_RE_MAPPED)),
("paired_sequencing", f(_RE_PAIRED_SEQ)),
("paired", f(_RE_PAIRED_BAM)),
("paired_proper", f(_RE_PAIRED_PROPER)),
("read1", f(_RE_READ1)),
("read2", f(_RE_READ2)),
("singleton", f(_RE_SINGLETON)),
("diff_chrom", f(_RE_DIFF)),
("diff_chrom_mapq", f(_RE_DIFF_MIN)),
)
payload = {
"pass_qc": {k: v[0] for k, v in parsed if v[0] is not None},
"fail_qc": {k: v[1] for k, v in parsed if v[1] is not None},
}
if len(payload["pass_qc"]) == 0 and len(payload["fail_qc"]) == 0:
raise click.BadParameter("Cannot parse input flagstat file.")
return payload
def main():
handle = None
try:
#
# Create a handle
#
handle = get_handle(tenant_id)
#
# Create a table
#
statement = 'Create table if not exists ' + table_name + '(id integer, \
sid integer, name string, primary key(shard(sid), id))'
print('Creating table: ' + statement)
request = TableRequest().set_statement(statement).set_table_limits(
TableLimits(30, 10, 1))
handle.do_table_request(request, 50000, 3000)
print('After create table')
#
# Put a few rows
#
request = PutRequest().set_table_name(table_name)
for i in range(10):
value = {'id': i, 'sid': 0, 'name': 'myname' + str(i)}
request.set_value(value)
handle.put(request)
print('After put of 10 rows')
#
# Multiple write a few rows
#
request = WriteMultipleRequest()
for i in range(10):
value = {'id': i, 'sid': 0, 'name': 'newname' + str(i)}
request.add(
PutRequest().set_value(value).set_table_name(table_name), True)
result = handle.write_multiple(request)
print('After multiple write: ' + str(result))
#
# Prepare a statement
#
statement = 'select * from ' + table_name + ' where id > 2 and id < 8'
request = PrepareRequest().set_statement(statement)
prepared_result = handle.prepare(request)
print('After prepare the statement: ' + statement)
#
# Query, using the prepared statement
#
request = QueryRequest().set_prepared_statement(prepared_result)
print('Query results for the prepared statement: ')
while True:
result = handle.query(request)
for r in result.get_results():
print('\t' + str(r))
if request.is_done():
break
#
# Multiple delete the rows
#
request = MultiDeleteRequest().set_table_name(table_name).set_key(
{'sid': 0})
result = handle.multi_delete(request)
print('After multiple delete: ' + str(result))
#
# Query again to show deletions, using the prepared statement
#
request = QueryRequest().set_prepared_statement(prepared_result)
print('Query results for the prepared statement (should be no rows): ')
while True:
result = handle.query(request)
for r in result.get_results():
print('\t' + str(r))
if request.is_done():
break
#
# Drop the table
#
if drop_table:
request = TableRequest().set_statement('drop table if exists ' +
table_name)
handle.do_table_request(request, 40000, 2000)
print('After drop table')
else:
print('Not dropping table')
print('Example is complete')
except Exception as e:
print(e)
traceback.print_exc()
finally:
# If the handle isn't closed Python will not exit properly
if handle is not None:
handle.close()
def main():
handle = None
try:
#
# Create a handle
#
handle = get_handle(tenant_id)
#
# Create a table
#
statement = 'Create table if not exists ' + table_name + '(id integer, \
sid integer, name string, primary key(shard(sid), id))'
print('Creating table: ' + statement)
request = TableRequest().set_statement(statement).set_table_limits(
TableLimits(30, 10, 1))
result = handle.table_request(request)
#
# Table creation can take time, depending on the state of the system.
# If if fails after 40s, re-run the program
#
result.wait_for_state(handle, table_name, State.ACTIVE, 50000, 3000)
print('After create table')
#
# Put a few rows
#
request = PutRequest().set_table_name(table_name)
for i in range(10):
value = {'id': i, 'sid': 0, 'name': 'myname' + str(i)}
request.set_value(value)
handle.put(request)
print('After put of 10 rows')
#
# Get the row
#
request = GetRequest().set_key({
'id': 1,
'sid': 0
}).set_table_name(table_name)
result = handle.get(request)
print('After get: ' + str(result))
#
# Query, using a range
#
statement = 'select * from ' + table_name + ' where id > 2 and id < 8'
request = QueryRequest().set_statement(statement)
result = handle.query(request)
print('Query results for: ' + statement)
for r in result.get_results():
print('\t' + str(r))
#
# Delete the row
#
request = DeleteRequest().set_key({
'id': 1,
'sid': 0
}).set_table_name(table_name)
result = handle.delete(request)
print('After delete: ' + str(result))
#
# Get again to show deletion
#
request = GetRequest().set_key({
'id': 1,
'sid': 0
}).set_table_name(table_name)
result = handle.get(request)
print('After get (should be None): ' + str(result))
#
# Drop the table
#
if drop_table:
request = TableRequest().set_statement('drop table if exists ' +
table_name)
result = handle.table_request(request)
#
# Table drop can take time, depending on the state of the system.
# If this wait fails the table will still probably been dropped
#
result.wait_for_state(handle, table_name, State.DROPPED, 40000,
2000)
print('After drop table')
else:
print('Not dropping table')
print('Example is complete')
except Exception as e:
print(e)
traceback.print_exc()
finally:
# If the handle isn't closed Python will not exit properly
if handle is not None:
handle.close()
def main():
handle = None
try:
#
# Create a handle
#
handle = get_handle(tenant_id)
#
# List any existing tables for this tenant
#
print('Listing tables')
ltr = ListTablesRequest()
lr_result = handle.list_tables(ltr)
print('Existing tables: ' + str(lr_result))
#
# Create a table
#
statement = 'Create table if not exists ' + table_name + '(id integer, \
sid integer, name string, primary key(shard(sid), id))'
print('Creating table: ' + statement)
request = TableRequest().set_statement(statement).set_table_limits(
TableLimits(30, 10, 1))
result = handle.table_request(request)
#
# Table creation can take time, depending on the state of the system.
# If if fails after 40s, re-run the program
#
result.wait_for_state(handle, table_name, State.ACTIVE, 40000, 3000)
print('After create table')
#
# Create an index
#
statement = ('Create index if not exists ' + index_name + ' on ' +
table_name + '(name)')
print('Creating index: ' + statement)
request = TableRequest().set_statement(statement)
result = handle.table_request(request)
#
# Index creation can take time, depending on the state of the system.
# If if fails after 40s, re-run the program
#
result.wait_for_state(handle, table_name, State.ACTIVE, 40000, 3000)
print('After create index')
#
# Get the table
#
request = GetTableRequest().set_table_name(table_name)
result = handle.get_table(request)
print('After get table: ' + str(result))
#
# Get the indexes
#
request = GetIndexesRequest().set_table_name(table_name)
result = handle.get_indexes(request)
print('The indexes for: ' + table_name)
for idx in result.get_indexes():
print('\t' + str(idx))
#
# Get the table usage information
#
request = TableUsageRequest().set_table_name(table_name)
result = handle.get_table_usage(request)
print('The table usage information for: ' + table_name)
for record in result.get_usage_records():
print('\t' + str(record))
#
# Drop the table
#
if drop_table:
request = TableRequest().set_statement('drop table if exists ' +
table_name)
result = handle.table_request(request)
#
# Table drop can take time, depending on the state of the system.
# If this wait fails the table will still probably been dropped
#
result.wait_for_state(handle, table_name, State.DROPPED, 30000,
2000)
print('After drop table')
else:
print('Not dropping table')
print('Example is complete')
except Exception as e:
print(e)
traceback.print_exc()
finally:
# If the handle isn't closed Python will not exit properly
if handle is not None:
handle.close()
def main():
handle = None
try:
#
# Create a handle
#
handle = get_handle(tenant_id)
#
# List any existing tables for this tenant
#
print('Listing tables')
ltr = ListTablesRequest()
lr_result = handle.list_tables(ltr)
print('Existing tables: ' + str(lr_result))
#
# Create a table
#
statement = 'Create table if not exists ' + table_name + '(id integer, \
sid integer, name string, primary key(shard(sid), id))'
print('Creating table: ' + statement)
request = TableRequest().set_statement(statement).set_table_limits(
TableLimits(30, 10, 1))
handle.do_table_request(request, 40000, 3000)
print('After create table')
#
# Create an index
#
statement = ('Create index if not exists ' + index_name + ' on ' +
table_name + '(name)')
print('Creating index: ' + statement)
request = TableRequest().set_statement(statement)
handle.do_table_request(request, 40000, 3000)
print('After create index')
#
# Get the table
#
request = GetTableRequest().set_table_name(table_name)
result = handle.get_table(request)
print('After get table: ' + str(result))
#
# Get the indexes
#
request = GetIndexesRequest().set_table_name(table_name)
result = handle.get_indexes(request)
print('The indexes for: ' + table_name)
for idx in result.get_indexes():
print('\t' + str(idx))
#
# Get the table usage information, on-prem mode not supported
#
if not using_on_prem:
request = TableUsageRequest().set_table_name(table_name)
result = handle.get_table_usage(request)
print('The table usage information for: ' + table_name)
for record in result.get_usage_records():
print('\t' + str(record))
#
# Drop the index
#
request = TableRequest().set_statement(
'drop index ' + index_name + ' on ' + table_name)
handle.do_table_request(request, 30000, 2000)
print('After drop index')
#
# Drop the table
#
if drop_table:
request = TableRequest().set_statement(
'drop table if exists ' + table_name)
handle.do_table_request(request, 30000, 2000)
print('After drop table')
else:
print('Not dropping table')
print('Example is complete')
except Exception as e:
print(e)
traceback.print_exc()
finally:
# If the handle isn't closed Python will not exit properly
if handle is not None:
handle.close()
