code stringlengths 3 6.57k |
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logger.info("Checking if results are valid...") |
result_dict.copy() |
handle_result_kwargs.get("test_suite", None) |
handle_result_kwargs.get("test_name", None) |
handle_result_kwargs.get("category", None) |
SUITE_TO_FN.get(test_suite, None) |
logger.warning(f"No handle for suite {test_suite}") |
default_handle_result(**handle_result_kwargs) |
handle_fn(**handle_result_kwargs) |
RuntimeError(alert) |
read_groups_from_bam(bam_filename, use_libraries=False) |
pysam.AlignmentFile(bam_filename, "rb") |
print(read_groups) |
print(read_group) |
for (key, ignored) |
results.items() |
sorted(results_without_duplicates) |
read_groups_and_libraries_from_bam(bam_filename) |
pysam.AlignmentFile(bam_filename, "rb") |
print(read_groups) |
argparse.ArgumentParser(description="Show the read groups in a bam.") |
parser.add_argument('-p', "--pulldown", help="report read groups colon-delimited for pulldown", action='store_true') |
parser.add_argument('-l', "--libraries", help="report libraries instead of read groups", action='store_true') |
parser.add_argument('-b', "--both", help="report read groups and libraries", action='store_true') |
parser.add_argument("bam", help="bam for read groups") |
parser.parse_args() |
read_groups_and_libraries_from_bam(bam_filename) |
read_groups_to_libraries.items() |
print("{}\t{}".format(read_group, library) |
read_groups_from_bam(bam_filename, args.libraries) |
print(':'.join(read_groups) |
print(read_group) |
upgrade() |
sa.Column("user", sa.BigInteger() |
sa.Column("count", sa.BigInteger() |
sa.PrimaryKeyConstraint("user") |
downgrade() |
op.drop_table("stats") |
lcc.prop("main", "type") |
lcc.tags("scenarios", "many_contracts_in_one_trx") |
lcc.suite("Check scenario 'Create many contracts in a single transaction'") |
CreateManyContractsInOneTrx(BaseTest) |
__init__(self) |
super() |
__init__() |
self.get_byte_code("piggy", "code") |
setup_suite(self) |
super() |
setup_suite() |
self._connect_to_echopy_lib() |
lcc.set_step("Setup for {}".format(self.__class__.__name__) |
self.get_identifier("database") |
self.get_identifier("registration") |
lcc.log_info("Echo account is '{}'".format(self.echo_acc0) |
teardown_suite(self) |
self._disconnect_to_echopy_lib() |
super() |
teardown_suite() |
create_many_contracts_in_one_trx_scenario(self, get_random_integer_up_to_fifty) |
lcc.set_step("Create '{}' 'Piggy' contracts in the Echo network".format(number_of_contracts) |
self.collect_operations(operation, self.__database_api_identifier) |
range(number_of_contracts) |
list_operations.append(collected_operation) |
self.echo_ops.broadcast(echo=self.echo, list_operations=list_operations, log_broadcast=False) |
lcc.set_step("Check that all contracts created in the Echo network") |
broadcast_result.get("trx") |
get("operation_results") |
has_length(number_of_contracts) |
stage00_query(base_analysis) |
get_structureFile_standards(self,met_id_I) |
standards.met_id.like(met_id_I) |
all() |
print('no structure file found for ' + met_id_I) |
exit(-1) |
print(e) |
get_exactMassAndFormula_standards(self,met_id_I) |
standards.met_id.like(met_id_I) |
all() |
print('no mass and formula found for ' + met_id_I) |
exit(-1) |
print(e) |
get_Q1AndQ3MassAndMode_MSComponents(self,met_id_I) |
MS_components.met_id.like(met_id_I) |
MS_components.ms_mode.asc() |
MS_components.q1_mass.asc() |
MS_components.q3_mass.asc() |
all() |
mscomponents_O.append(mscomponents_1) |
print(e) |
get_row_MSComponents(self,met_id_I,ms_mode_I,ms_methodtype_I) |
MS_components.met_id.like(met_id_I) |
MS_components.ms_mode.like(ms_mode_I) |
MS_components.ms_methodtype.like(ms_methodtype_I) |
all() |
print('bad query for row in ms_components: ') |
print('met_id: ' + met_id_I + ', ms_mode_I: ' + ms_mode_I + ', ms_methodtype_I: ' + ms_methodtype_I) |
exit(-1) |
mscomponents_O.append(mscomponents_1) |
print(e) |
MS_components.met_id.like(met_id_I) |
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