pytest-wdl
stable
Contents:
}
}
}
}
}
}
}
}
)
)
)
pytest_wdl
pytest-wdl
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B
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C
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D
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E
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F
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G
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H
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I
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J
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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Y
A
alias() (pytest_wdl.url_schemes.UrlHandler method)
as_dict() (pytest_wdl.config.UserConfiguration method)
assert_bam_files_equal() (in module pytest_wdl.data_types.bam)
assert_binary_files_equal() (in module pytest_wdl.data_types)
assert_contents_equal() (pytest_wdl.data_types.DataFile method)
assert_text_files_equal() (in module pytest_wdl.data_types)
B
bam_to_sam() (in module pytest_wdl.data_types.bam)
BamDataFile (class in pytest_wdl.data_types.bam)
BaseResponse (class in pytest_wdl.url_schemes)
C
chdir() (in module pytest_wdl.utils)
cleanup() (in module pytest_wdl.config)
(pytest_wdl.config.UserConfiguration method)
collect() (pytest_wdl.loader.WdlTestsModule method)
compare_files_with_hash() (in module pytest_wdl.utils)
compare_gzip() (in module pytest_wdl.data_types)
context_dir() (in module pytest_wdl.utils)
COORDINATE (pytest_wdl.data_types.bam.Sorting attribute)
create_data_file() (in module pytest_wdl.core)
create_executor() (in module pytest_wdl.core)
CromwellLocalExecutor (class in pytest_wdl.executors.cromwell_local)
CromwellServerExecutor (class in pytest_wdl.executors.cromwell_server)
D
DATA_TYPES (in module pytest_wdl.core)
DataDirs (class in pytest_wdl.core)
DataFile (class in pytest_wdl.data_types)
DataManager (class in pytest_wdl.core)
DataResolver (class in pytest_wdl.core)
default_executors() (in module pytest_wdl.fixtures)
default_user_config_file() (in module pytest_wdl.config)
DefaultDataFile (class in pytest_wdl.data_types)
diff_bam_columns() (in module pytest_wdl.data_types.bam)
diff_default() (in module pytest_wdl.data_types)
diff_vcf_columns() (in module pytest_wdl.data_types.vcf)
DigestsNotEqualError
download_file() (in module pytest_wdl.localizers)
(pytest_wdl.providers.dx.DxResponse method)
(pytest_wdl.url_schemes.BaseResponse method)
(pytest_wdl.url_schemes.Response method)
DxInputsFormatter (class in pytest_wdl.providers.dx)
DxResponse (class in pytest_wdl.providers.dx)
DxUrlHandler (class in pytest_wdl.providers.dx)
DxWdlExecutor (class in pytest_wdl.providers.dx)
E
ensure_path() (in module pytest_wdl.utils)
env_map() (in module pytest_wdl.utils)
ExecutionFailedError
Executor (class in pytest_wdl.executors)
ExecutorError
EXECUTORS (in module pytest_wdl.core)
exit_status_str() (pytest_wdl.executors.ExecutionFailedError property)
F
find_executable_path() (in module pytest_wdl.utils)
find_in_classpath() (in module pytest_wdl.utils)
find_project_path() (in module pytest_wdl.utils)
format_inputs() (pytest_wdl.executors.InputsFormatter method)
(pytest_wdl.providers.dx.DxInputsFormatter method)
format_value() (pytest_wdl.executors.InputsFormatter method)
(pytest_wdl.providers.dx.DxInputsFormatter method)
G
get_content_length() (pytest_wdl.url_schemes.BaseResponse method)
(pytest_wdl.url_schemes.ResponseWrapper method)
get_dict() (pytest_wdl.core.DataManager method)
get_executor_defaults() (pytest_wdl.config.UserConfiguration method)
get_instance() (in module pytest_wdl.config)
(pytest_wdl.executors.InputsFormatter class method)
get_list() (pytest_wdl.core.DataManager method)
get_provider_defaults() (pytest_wdl.config.UserConfiguration method)
get_target_name() (in module pytest_wdl.executors)
H
handles() (pytest_wdl.providers.dx.DxUrlHandler property)
(pytest_wdl.url_schemes.UrlHandler property)
hash_file() (in module pytest_wdl.utils)
http_headers() (pytest_wdl.localizers.UrlLocalizer property)
I
import_dirs() (in module pytest_wdl.fixtures)
import_paths() (in module pytest_wdl.fixtures)
InputsFormatter (class in pytest_wdl.executors)
install_schemes() (in module pytest_wdl.url_schemes)
is_executable() (in module pytest_wdl.utils)
J
JavaExecutor (class in pytest_wdl.executors)
JsonDataFile (class in pytest_wdl.data_types.json)
JsonLocalizer (class in pytest_wdl.localizers)
JsonWdlTestsModule (class in pytest_wdl.loader)
L
LinkLocalizer (class in pytest_wdl.localizers)
localize() (pytest_wdl.localizers.JsonLocalizer method)
(pytest_wdl.localizers.LinkLocalizer method)
(pytest_wdl.localizers.Localizer method)
(pytest_wdl.localizers.StringLocalizer method)
(pytest_wdl.localizers.UrlLocalizer method)
Localizer (class in pytest_wdl.localizers)
log_source() (pytest_wdl.executors.miniwdl.MiniwdlExecutor static method)
login() (in module pytest_wdl.providers.dx)
M
MaxCallException
Method (class in pytest_wdl.url_schemes)
MiniwdlExecutor (class in pytest_wdl.executors.miniwdl)
module
pytest_wdl
pytest_wdl.config
pytest_wdl.core
pytest_wdl.data_types
pytest_wdl.data_types.bam
pytest_wdl.data_types.json
pytest_wdl.data_types.vcf
pytest_wdl.executors
pytest_wdl.executors.cromwell_local
pytest_wdl.executors.cromwell_server
pytest_wdl.executors.miniwdl
pytest_wdl.fixtures
pytest_wdl.loader
pytest_wdl.localizers
pytest_wdl.plugins
pytest_wdl.providers
pytest_wdl.providers.dx
pytest_wdl.url_schemes
pytest_wdl.utils
N
NAME (pytest_wdl.data_types.bam.Sorting attribute)
NONE (pytest_wdl.data_types.bam.Sorting attribute)
O
OPEN (pytest_wdl.url_schemes.Method attribute)
P
parse_wdl() (in module pytest_wdl.executors)
path() (pytest_wdl.data_types.DataFile property)
paths() (pytest_wdl.core.DataDirs property)
plugin_factory_map() (in module pytest_wdl.plugins)
PluginError
PluginFactory (class in pytest_wdl.plugins)
poll() (in module pytest_wdl.utils)
PollingException
project_root() (in module pytest_wdl.fixtures)
project_root_files() (in module pytest_wdl.fixtures)
proxies() (pytest_wdl.localizers.UrlLocalizer property)
pytest_collect_file() (in module pytest_wdl.loader)
pytest_collection() (in module pytest_wdl.loader)
pytest_wdl
module
pytest_wdl.config
module
pytest_wdl.core
module
pytest_wdl.data_types
module
pytest_wdl.data_types.bam
module
pytest_wdl.data_types.json
module
pytest_wdl.data_types.vcf
module
pytest_wdl.executors
module
pytest_wdl.executors.cromwell_local
module
pytest_wdl.executors.cromwell_server
module
pytest_wdl.executors.miniwdl
module
pytest_wdl.fixtures
module
pytest_wdl.loader
module
pytest_wdl.localizers
module
pytest_wdl.plugins
module
pytest_wdl.providers
module
pytest_wdl.providers.dx
module
pytest_wdl.url_schemes
module
pytest_wdl.utils
module
R
read() (pytest_wdl.url_schemes.BaseResponse method)
(pytest_wdl.url_schemes.ResponseWrapper method)
read_miniwdl_command_std() (pytest_wdl.executors.miniwdl.MiniwdlExecutor static method)
read_write_inputs() (in module pytest_wdl.executors)
REQUEST (pytest_wdl.url_schemes.Method attribute)
request() (pytest_wdl.url_schemes.UrlHandler method)
resolve() (pytest_wdl.core.DataResolver method)
resolve_file() (in module pytest_wdl.utils)
resolve_jar_file() (pytest_wdl.executors.JavaExecutor static method)
resolve_value_descriptor() (in module pytest_wdl.utils)
Response (class in pytest_wdl.url_schemes)
RESPONSE (pytest_wdl.url_schemes.Method attribute)
response() (pytest_wdl.url_schemes.UrlHandler method)
ResponseWrapper (class in pytest_wdl.url_schemes)
run_workflow() (pytest_wdl.executors.cromwell_local.CromwellLocalExecutor method)
(pytest_wdl.executors.cromwell_server.CromwellServerExecutor method)
(pytest_wdl.executors.Executor method)
(pytest_wdl.executors.miniwdl.MiniwdlExecutor method)
(pytest_wdl.providers.dx.DxWdlExecutor method)
runtest() (pytest_wdl.loader.TestItem method)
S
safe_string() (in module pytest_wdl.utils)
save() (pytest_wdl.config.UserConfiguration method)
scheme() (pytest_wdl.providers.dx.DxUrlHandler property)
(pytest_wdl.url_schemes.UrlHandler property)
set_compare_opts() (pytest_wdl.data_types.DataFile method)
set_instance() (in module pytest_wdl.config)
setup() (pytest_wdl.loader.TestItem method)
Sorting (class in pytest_wdl.data_types.bam)
StringLocalizer (class in pytest_wdl.localizers)
T
tempdir() (in module pytest_wdl.utils)
TestItem (class in pytest_wdl.loader)
TimeoutException
U
UrlHandler (class in pytest_wdl.url_schemes)
UrlLocalizer (class in pytest_wdl.localizers)
urlopen() (pytest_wdl.providers.dx.DxUrlHandler method)
(pytest_wdl.url_schemes.UrlHandler method)
user_config() (in module pytest_wdl.fixtures)
user_config_file() (in module pytest_wdl.fixtures)
UserConfiguration (class in pytest_wdl.config)
V
VcfDataFile (class in pytest_wdl.data_types.vcf)
verify() (pytest_wdl.localizers.Localizer method)
(pytest_wdl.localizers.UrlLocalizer method)
verify_digests() (in module pytest_wdl.utils)
W
WdlTestsModule (class in pytest_wdl.loader)
workflow_data() (in module pytest_wdl.fixtures)
workflow_data_descriptor_file() (in module pytest_wdl.fixtures)
workflow_data_descriptors() (in module pytest_wdl.fixtures)
workflow_data_resolver() (in module pytest_wdl.fixtures)
workflow_runner() (in module pytest_wdl.fixtures)
WorkflowRunner (class in pytest_wdl.fixtures)
Y
YamlWdlTestsModule (class in pytest_wdl.loader)
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