Index

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)