Cerise
stable
Contents:
Introduction
Cerise Configuration
Specialising Cerise
Developer documentation
Indices and tables
Cerise
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Index
A
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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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P
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W
A
add_log() (cerise.back_end.test.mock_job.MockJob method)
(cerise.job_store.sqlite_job.SQLiteJob method)
B
BrokenJob (class in cerise.test.fixture_jobs)
C
cancel_job() (cerise.back_end.job_runner.JobRunner method)
cancellation_active (cerise.job_store.job_state.JobState attribute)
CANCELLED (cerise.job_store.job_state.JobState attribute)
cerise (module)
cerise.back_end (module)
cerise.back_end.cwl (module)
cerise.back_end.execution_manager (module)
cerise.back_end.file (module)
cerise.back_end.job_planner (module)
cerise.back_end.job_runner (module)
cerise.back_end.local_files (module)
cerise.back_end.remote_api (module)
cerise.back_end.remote_job_files (module)
cerise.back_end.test (module)
cerise.back_end.test.mock_job (module)
cerise.back_end.test.test_job_planner (module)
cerise.config (module)
cerise.front_end (module)
cerise.front_end.controllers (module)
cerise.job_store (module)
cerise.job_store.job_state (module)
cerise.job_store.sqlite_job (module)
cerise.job_store.sqlite_job_store (module)
cerise.run_back_end (module)
cerise.test (module)
cerise.test.fixture_jobs (module)
cerise.util (module)
close_file_systems() (cerise.config.Config method)
Config (class in cerise.config)
create_job() (cerise.job_store.sqlite_job_store.SQLiteJobStore method)
create_output_dir() (cerise.back_end.local_files.LocalFiles method)
critical() (cerise.back_end.test.mock_job.MockJob method)
(cerise.job_store.sqlite_job.SQLiteJob method)
D
debug() (cerise.back_end.test.mock_job.MockJob method)
(cerise.job_store.sqlite_job.SQLiteJob method)
delete_job() (cerise.back_end.remote_job_files.RemoteJobFiles method)
(cerise.job_store.sqlite_job_store.SQLiteJobStore method)
delete_output_dir() (cerise.back_end.local_files.LocalFiles method)
destage_job_output() (cerise.back_end.remote_job_files.RemoteJobFiles method)
E
error() (cerise.back_end.test.mock_job.MockJob method)
(cerise.job_store.sqlite_job.SQLiteJob method)
execute_jobs() (cerise.back_end.execution_manager.ExecutionManager method)
ExecutionManager (class in cerise.back_end.execution_manager)
F
File (class in cerise.back_end.file)
FileArrayJob (class in cerise.test.fixture_jobs)
FINISHED (cerise.job_store.job_state.JobState attribute)
G
get_base_url() (cerise.config.Config method)
get_basedir() (cerise.config.Config method)
get_cores_per_node() (cerise.config.Config method)
get_cwltool_result() (in module cerise.back_end.cwl)
get_database_location() (cerise.config.Config method)
get_file_system() (cerise.config.Config method)
get_files_from_binding() (in module cerise.back_end.cwl)
get_job() (cerise.job_store.sqlite_job_store.SQLiteJobStore method)
get_log_file() (cerise.config.Config method)
get_log_level() (cerise.config.Config method)
get_pid_file() (cerise.config.Config method)
get_projects() (cerise.back_end.remote_api.RemoteApi method)
get_queue_name() (cerise.config.Config method)
get_remote_cwl_runner() (cerise.config.Config method)
get_remote_refresh() (cerise.config.Config method)
get_required_num_cores() (in module cerise.back_end.cwl)
get_scheduler() (cerise.config.Config method)
get_scheduler_options() (cerise.config.Config method)
get_secondary_files() (in module cerise.back_end.cwl)
get_service_host() (cerise.config.Config method)
get_service_port() (cerise.config.Config method)
get_slots_per_node() (cerise.config.Config method)
get_store_location_client() (cerise.config.Config method)
get_store_location_service() (cerise.config.Config method)
get_time_limit() (in module cerise.back_end.cwl)
get_username() (cerise.config.Config method)
get_workflow_step_names() (in module cerise.back_end.cwl)
H
has_logging() (cerise.config.Config method)
HostnameJob (class in cerise.test.fixture_jobs)
I
id (cerise.back_end.test.mock_job.MockJob attribute)
(cerise.job_store.sqlite_job.SQLiteJob attribute)
index (cerise.back_end.file.File attribute)
info() (cerise.back_end.test.mock_job.MockJob method)
(cerise.job_store.sqlite_job.SQLiteJob method)
input_content (cerise.test.fixture_jobs.BrokenJob attribute)
(cerise.test.fixture_jobs.FileArrayJob attribute)
(cerise.test.fixture_jobs.HostnameJob attribute)
(cerise.test.fixture_jobs.InstallScriptTestJob attribute)
(cerise.test.fixture_jobs.MissingInputJob attribute)
(cerise.test.fixture_jobs.NoSuchStepJob attribute)
(cerise.test.fixture_jobs.NoWorkflowJob attribute)
(cerise.test.fixture_jobs.PartiallyFailingJob attribute)
(cerise.test.fixture_jobs.PassJob attribute)
(cerise.test.fixture_jobs.SecondaryFilesJob attribute)
(cerise.test.fixture_jobs.SlowJob attribute)
(cerise.test.fixture_jobs.WcJob attribute)
install() (cerise.back_end.remote_api.RemoteApi method)
InstallScriptTestJob (class in cerise.test.fixture_jobs)
InvalidJobError
is_final (cerise.job_store.job_state.JobState attribute)
is_remote (cerise.job_store.job_state.JobState attribute)
is_workflow() (in module cerise.back_end.cwl)
J
JobNotFound
JobPlanner (class in cerise.back_end.job_planner)
JobRunner (class in cerise.back_end.job_runner)
JobState (class in cerise.job_store.job_state)
L
list_jobs() (cerise.job_store.sqlite_job_store.SQLiteJobStore method)
local_input (cerise.back_end.test.mock_job.MockJob attribute)
(cerise.job_store.sqlite_job.SQLiteJob attribute)
local_input() (cerise.test.fixture_jobs.BrokenJob method)
(cerise.test.fixture_jobs.FileArrayJob method)
(cerise.test.fixture_jobs.HostnameJob method)
(cerise.test.fixture_jobs.InstallScriptTestJob method)
(cerise.test.fixture_jobs.LongRunningJob method)
(cerise.test.fixture_jobs.MissingInputJob method)
(cerise.test.fixture_jobs.NoSuchStepJob method)
(cerise.test.fixture_jobs.NoWorkflowJob method)
(cerise.test.fixture_jobs.PartiallyFailingJob method)
(cerise.test.fixture_jobs.PassJob method)
(cerise.test.fixture_jobs.SecondaryFilesJob method)
(cerise.test.fixture_jobs.SlowJob method)
(cerise.test.fixture_jobs.WcJob method)
local_input_files (cerise.test.fixture_jobs.BrokenJob attribute)
(cerise.test.fixture_jobs.FileArrayJob attribute)
(cerise.test.fixture_jobs.HostnameJob attribute)
(cerise.test.fixture_jobs.InstallScriptTestJob attribute)
(cerise.test.fixture_jobs.LongRunningJob attribute)
(cerise.test.fixture_jobs.MissingInputJob attribute)
(cerise.test.fixture_jobs.NoSuchStepJob attribute)
(cerise.test.fixture_jobs.NoWorkflowJob attribute)
(cerise.test.fixture_jobs.PartiallyFailingJob attribute)
(cerise.test.fixture_jobs.PassJob attribute)
(cerise.test.fixture_jobs.SecondaryFilesJob attribute)
(cerise.test.fixture_jobs.SlowJob attribute)
(cerise.test.fixture_jobs.WcJob attribute)
local_output (cerise.back_end.test.mock_job.MockJob attribute)
(cerise.job_store.sqlite_job.SQLiteJob attribute)
(cerise.test.fixture_jobs.FileArrayJob attribute)
(cerise.test.fixture_jobs.HostnameJob attribute)
(cerise.test.fixture_jobs.InstallScriptTestJob attribute)
(cerise.test.fixture_jobs.LongRunningJob attribute)
(cerise.test.fixture_jobs.NoSuchStepJob attribute)
(cerise.test.fixture_jobs.PartiallyFailingJob attribute)
(cerise.test.fixture_jobs.PassJob attribute)
(cerise.test.fixture_jobs.SecondaryFilesJob attribute)
(cerise.test.fixture_jobs.SlowJob attribute)
(cerise.test.fixture_jobs.WcJob attribute)
LocalFiles (class in cerise.back_end.local_files)
location (cerise.back_end.file.File attribute)
log (cerise.back_end.test.mock_job.MockJob attribute)
(cerise.job_store.sqlite_job.SQLiteJob attribute)
LongRunningJob (class in cerise.test.fixture_jobs)
M
make_config() (in module cerise.config)
MissingInputJob (class in cerise.test.fixture_jobs)
MockJob (class in cerise.back_end.test.mock_job)
N
name (cerise.back_end.file.File attribute)
(cerise.back_end.test.mock_job.MockJob attribute)
(cerise.job_store.sqlite_job.SQLiteJob attribute)
NoSuchStepJob (class in cerise.test.fixture_jobs)
NoWorkflowJob (class in cerise.test.fixture_jobs)
O
output_content (cerise.test.fixture_jobs.BrokenJob attribute)
(cerise.test.fixture_jobs.FileArrayJob attribute)
(cerise.test.fixture_jobs.HostnameJob attribute)
(cerise.test.fixture_jobs.InstallScriptTestJob attribute)
(cerise.test.fixture_jobs.LongRunningJob attribute)
(cerise.test.fixture_jobs.NoSuchStepJob attribute)
(cerise.test.fixture_jobs.NoWorkflowJob attribute)
(cerise.test.fixture_jobs.PartiallyFailingJob attribute)
(cerise.test.fixture_jobs.PassJob attribute)
(cerise.test.fixture_jobs.SecondaryFilesJob attribute)
(cerise.test.fixture_jobs.SlowJob attribute)
(cerise.test.fixture_jobs.WcJob attribute)
output_files (cerise.test.fixture_jobs.BrokenJob attribute)
(cerise.test.fixture_jobs.FileArrayJob attribute)
(cerise.test.fixture_jobs.HostnameJob attribute)
(cerise.test.fixture_jobs.InstallScriptTestJob attribute)
(cerise.test.fixture_jobs.LongRunningJob attribute)
(cerise.test.fixture_jobs.NoSuchStepJob attribute)
(cerise.test.fixture_jobs.NoWorkflowJob attribute)
(cerise.test.fixture_jobs.PartiallyFailingJob attribute)
(cerise.test.fixture_jobs.PassJob attribute)
(cerise.test.fixture_jobs.SecondaryFilesJob attribute)
(cerise.test.fixture_jobs.SlowJob attribute)
(cerise.test.fixture_jobs.WcJob attribute)
P
PartiallyFailingJob (class in cerise.test.fixture_jobs)
PassJob (class in cerise.test.fixture_jobs)
PERMANENT_FAILURE (cerise.job_store.job_state.JobState attribute)
plan_job() (cerise.back_end.job_planner.JobPlanner method)
please_delete (cerise.back_end.test.mock_job.MockJob attribute)
(cerise.job_store.sqlite_job.SQLiteJob attribute)
publish_job_output() (cerise.back_end.local_files.LocalFiles method)
R
remote_error (cerise.back_end.test.mock_job.MockJob attribute)
(cerise.job_store.sqlite_job.SQLiteJob attribute)
remote_input() (cerise.test.fixture_jobs.BrokenJob method)
(cerise.test.fixture_jobs.FileArrayJob method)
(cerise.test.fixture_jobs.HostnameJob method)
(cerise.test.fixture_jobs.MissingInputJob method)
(cerise.test.fixture_jobs.NoSuchStepJob method)
(cerise.test.fixture_jobs.NoWorkflowJob method)
(cerise.test.fixture_jobs.PartiallyFailingJob method)
(cerise.test.fixture_jobs.PassJob method)
(cerise.test.fixture_jobs.SecondaryFilesJob method)
(cerise.test.fixture_jobs.SlowJob method)
(cerise.test.fixture_jobs.WcJob method)
remote_input_files (cerise.test.fixture_jobs.BrokenJob attribute)
(cerise.test.fixture_jobs.FileArrayJob attribute)
(cerise.test.fixture_jobs.HostnameJob attribute)
(cerise.test.fixture_jobs.MissingInputJob attribute)
(cerise.test.fixture_jobs.NoSuchStepJob attribute)
(cerise.test.fixture_jobs.NoWorkflowJob attribute)
(cerise.test.fixture_jobs.PartiallyFailingJob attribute)
(cerise.test.fixture_jobs.PassJob attribute)
(cerise.test.fixture_jobs.SecondaryFilesJob attribute)
(cerise.test.fixture_jobs.SlowJob attribute)
(cerise.test.fixture_jobs.WcJob attribute)
remote_input_path (cerise.back_end.test.mock_job.MockJob attribute)
(cerise.job_store.sqlite_job.SQLiteJob attribute)
remote_job_id (cerise.back_end.test.mock_job.MockJob attribute)
(cerise.job_store.sqlite_job.SQLiteJob attribute)
remote_output (cerise.back_end.test.mock_job.MockJob attribute)
(cerise.job_store.sqlite_job.SQLiteJob attribute)
remote_output() (cerise.test.fixture_jobs.BrokenJob method)
(cerise.test.fixture_jobs.FileArrayJob method)
(cerise.test.fixture_jobs.HostnameJob method)
(cerise.test.fixture_jobs.InstallScriptTestJob method)
(cerise.test.fixture_jobs.NoSuchStepJob method)
(cerise.test.fixture_jobs.NoWorkflowJob method)
(cerise.test.fixture_jobs.PartiallyFailingJob method)
(cerise.test.fixture_jobs.PassJob method)
(cerise.test.fixture_jobs.SecondaryFilesJob method)
(cerise.test.fixture_jobs.SlowJob method)
(cerise.test.fixture_jobs.WcJob method)
remote_stderr_path (cerise.back_end.test.mock_job.MockJob attribute)
(cerise.job_store.sqlite_job.SQLiteJob attribute)
remote_stdout_path (cerise.back_end.test.mock_job.MockJob attribute)
(cerise.job_store.sqlite_job.SQLiteJob attribute)
remote_system_err_path (cerise.back_end.test.mock_job.MockJob attribute)
(cerise.job_store.sqlite_job.SQLiteJob attribute)
remote_system_out_path (cerise.back_end.test.mock_job.MockJob attribute)
(cerise.job_store.sqlite_job.SQLiteJob attribute)
remote_workdir_path (cerise.back_end.test.mock_job.MockJob attribute)
(cerise.job_store.sqlite_job.SQLiteJob attribute)
remote_workflow_path (cerise.back_end.test.mock_job.MockJob attribute)
(cerise.job_store.sqlite_job.SQLiteJob attribute)
RemoteApi (class in cerise.back_end.remote_api)
RemoteJobFiles (class in cerise.back_end.remote_job_files)
required_num_cores (cerise.back_end.test.mock_job.MockJob attribute)
(cerise.job_store.sqlite_job.SQLiteJob attribute)
(cerise.test.fixture_jobs.BrokenJob attribute)
(cerise.test.fixture_jobs.FileArrayJob attribute)
(cerise.test.fixture_jobs.HostnameJob attribute)
(cerise.test.fixture_jobs.InstallScriptTestJob attribute)
(cerise.test.fixture_jobs.LongRunningJob attribute)
(cerise.test.fixture_jobs.MissingInputJob attribute)
(cerise.test.fixture_jobs.NoSuchStepJob attribute)
(cerise.test.fixture_jobs.NoWorkflowJob attribute)
(cerise.test.fixture_jobs.PartiallyFailingJob attribute)
(cerise.test.fixture_jobs.PassJob attribute)
(cerise.test.fixture_jobs.SecondaryFilesJob attribute)
(cerise.test.fixture_jobs.SlowJob attribute)
(cerise.test.fixture_jobs.WcJob attribute)
resolve_input() (cerise.back_end.local_files.LocalFiles method)
resolve_retry_count (cerise.back_end.test.mock_job.MockJob attribute)
(cerise.job_store.sqlite_job.SQLiteJob attribute)
resolve_secondary_files() (cerise.back_end.local_files.LocalFiles method)
RUNNING (cerise.job_store.job_state.JobState attribute)
RUNNING_CR (cerise.job_store.job_state.JobState attribute)
S
secondary_files (cerise.back_end.file.File attribute)
SecondaryFilesJob (class in cerise.test.fixture_jobs)
shutdown() (cerise.back_end.execution_manager.ExecutionManager method)
SlowJob (class in cerise.test.fixture_jobs)
source (cerise.back_end.file.File attribute)
SQLiteJob (class in cerise.job_store.sqlite_job)
SQLiteJobStore (class in cerise.job_store.sqlite_job_store)
stage_job() (cerise.back_end.remote_job_files.RemoteJobFiles method)
STAGING_IN (cerise.job_store.job_state.JobState attribute)
STAGING_IN_CR (cerise.job_store.job_state.JobState attribute)
STAGING_OUT (cerise.job_store.job_state.JobState attribute)
STAGING_OUT_CR (cerise.job_store.job_state.JobState attribute)
start_job() (cerise.back_end.job_runner.JobRunner method)
state (cerise.back_end.test.mock_job.MockJob attribute)
(cerise.job_store.sqlite_job.SQLiteJob attribute)
SUBMITTED (cerise.job_store.job_state.JobState attribute)
SUCCESS (cerise.job_store.job_state.JobState attribute)
SYSTEM_ERROR (cerise.job_store.job_state.JobState attribute)
T
TEMPORARY_FAILURE (cerise.job_store.job_state.JobState attribute)
test_job_planner_init() (in module cerise.back_end.test.test_job_planner)
test_plan_job() (in module cerise.back_end.test.test_job_planner)
time_limit (cerise.back_end.test.mock_job.MockJob attribute)
(cerise.job_store.sqlite_job.SQLiteJob attribute)
(cerise.test.fixture_jobs.BrokenJob attribute)
(cerise.test.fixture_jobs.FileArrayJob attribute)
(cerise.test.fixture_jobs.HostnameJob attribute)
(cerise.test.fixture_jobs.InstallScriptTestJob attribute)
(cerise.test.fixture_jobs.LongRunningJob attribute)
(cerise.test.fixture_jobs.MissingInputJob attribute)
(cerise.test.fixture_jobs.NoSuchStepJob attribute)
(cerise.test.fixture_jobs.NoWorkflowJob attribute)
(cerise.test.fixture_jobs.PartiallyFailingJob attribute)
(cerise.test.fixture_jobs.PassJob attribute)
(cerise.test.fixture_jobs.SecondaryFilesJob attribute)
(cerise.test.fixture_jobs.SlowJob attribute)
(cerise.test.fixture_jobs.WcJob attribute)
to_cwl_state_string (cerise.job_store.job_state.JobState attribute)
translate_runner_location() (cerise.back_end.remote_api.RemoteApi method)
translate_workflow() (cerise.back_end.remote_api.RemoteApi method)
try_transition() (cerise.back_end.test.mock_job.MockJob method)
(cerise.job_store.sqlite_job.SQLiteJob method)
U
update_available() (cerise.back_end.remote_api.RemoteApi method)
update_job() (cerise.back_end.job_runner.JobRunner method)
(cerise.back_end.remote_job_files.RemoteJobFiles method)
W
WAITING (cerise.job_store.job_state.JobState attribute)
WAITING_CR (cerise.job_store.job_state.JobState attribute)
warning() (cerise.back_end.test.mock_job.MockJob method)
(cerise.job_store.sqlite_job.SQLiteJob method)
WcJob (class in cerise.test.fixture_jobs)
workflow (cerise.back_end.test.mock_job.MockJob attribute)
(cerise.job_store.sqlite_job.SQLiteJob attribute)
(cerise.test.fixture_jobs.BrokenJob attribute)
(cerise.test.fixture_jobs.FileArrayJob attribute)
(cerise.test.fixture_jobs.HostnameJob attribute)
(cerise.test.fixture_jobs.InstallScriptTestJob attribute)
(cerise.test.fixture_jobs.LongRunningJob attribute)
(cerise.test.fixture_jobs.MissingInputJob attribute)
(cerise.test.fixture_jobs.NoSuchStepJob attribute)
(cerise.test.fixture_jobs.NoWorkflowJob attribute)
(cerise.test.fixture_jobs.PartiallyFailingJob attribute)
(cerise.test.fixture_jobs.PassJob attribute)
(cerise.test.fixture_jobs.SecondaryFilesJob attribute)
(cerise.test.fixture_jobs.SlowJob attribute)
(cerise.test.fixture_jobs.WcJob attribute)
workflow_content (cerise.back_end.test.mock_job.MockJob attribute)
(cerise.job_store.sqlite_job.SQLiteJob attribute)
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