Usage reference
Pipestat offers a CLI that can be access via the pipestat command in the shell. It offers complete control over reporting, inspecting, etc, via a series of subcommands.
Here you can see the command-line usage instructions for the main command and for each subcommand:
pipestat --help
version: 0.12.1
usage: pipestat [-h] [--version] [--silent] [--verbosity V] [--logdev] {report,inspect,remove,retrieve,status,init,summarize,link,serve,history} ...
pipestat - report pipeline results
positional arguments:
{report,inspect,remove,retrieve,status,init,summarize,link,serve,history}
report Report a result.
inspect Inspect a database.
remove Remove a result.
retrieve Retrieve a result.
status Manage pipeline status.
init Initialize generic config file
summarize Generates HTML Report
link Create symlinks of reported files
serve Initializes pipestatreader API
history Retrieve history of reported results for one record identifier
options:
-h, --help show this help message and exit
--version show program's version number and exit
--silent Silence logging. Overrides verbosity.
--verbosity V Set logging level (1-5 or logging module level name)
--logdev Expand content of logging message format.
Pipestat standardizes reporting of pipeline results and pipeline status management.
It formalizes a way for pipeline developers and downstream tools developers to communicate
-- results produced by a pipeline can easily andreliably become an input for downstream analyses.
A PipestatManager object exposes an API for interacting with the results and pipeline status and
can be backed by either a YAML-formatted file or a database.
pipestat report --help
usage: pipestat report [-h] [-n N] [-f F] [-c C] [-a] [-s S] [--status-schema ST]
[--flag-dir FD] [-p P] -i I [-r R] -v V [-o] [-t]
Report a result.
options:
-h, --help show this help message and exit
-n N, --project-name N Name of the pipeline to report result for. If not provided
'PIPESTAT_PROJECT_NAME' env var will be used. Currently not
set
-f F, --results-file F Path to the YAML file where the results will be stored.
This file will be used as pipestat backend and to restore
the reported results across sessions
-c C, --config C Path to the YAML configuration file. If not provided
'PIPESTAT_CONFIG' env var will be used. Currently not set
-a, --database-only Whether the reported data should not be stored in the
memory, only in the database.
-s S, --schema S Path to the schema that defines the results that can be
reported. If not provided 'PIPESTAT_RESULTS_SCHEMA' env var
will be used. Currently not set
--status-schema ST Path to the status schema. Default will be used if not
provided: /home/drc/GITHUB/pipestat/pipestat/venv/lib/pytho
n3.10/site-packages/pipestat/schemas/status_schema.yaml
--flag-dir FD Path to the flag directory in case YAML file is the
pipestat backend.
-p P, --pipeline-type P project or sample level pipeline type.
-i I, --result-identifier I ID of the result to report; needs to be defined in the
schema
-r R, --record-identifier R ID of the record to report the result for. If not provided
'PIPESTAT_RECORD_IDENTIFIER' env var will be used.
Currently not set
-v V, --value V Value of the result to report
-o, --overwrite Whether the result should override existing ones in case of
name clashes
-t, --skip-convert Whether skip result type conversion into the required class
in case it does not meet the schema requirements
pipestat inspect --help
usage: pipestat inspect [-h] [-n N] [-f F] [-c C] [-a] [-s S] [--status-schema ST]
[--flag-dir FD] [-p P] [-d]
Inspect a database.
options:
-h, --help show this help message and exit
-n N, --project-name N Name of the pipeline to report result for. If not provided
'PIPESTAT_PROJECT_NAME' env var will be used. Currently not set
-f F, --results-file F Path to the YAML file where the results will be stored. This
file will be used as pipestat backend and to restore the
reported results across sessions
-c C, --config C Path to the YAML configuration file. If not provided
'PIPESTAT_CONFIG' env var will be used. Currently not set
-a, --database-only Whether the reported data should not be stored in the memory,
only in the database.
-s S, --schema S Path to the schema that defines the results that can be
reported. If not provided 'PIPESTAT_RESULTS_SCHEMA' env var
will be used. Currently not set
--status-schema ST Path to the status schema. Default will be used if not
provided:
/home/drc/GITHUB/pipestat/pipestat/venv/lib/python3.10/site-
packages/pipestat/schemas/status_schema.yaml
--flag-dir FD Path to the flag directory in case YAML file is the pipestat
backend.
-p P, --pipeline-type P project or sample level pipeline type.
-d, --data Whether to display the data
pipestat remove --help
usage: pipestat remove [-h] [-n N] [-f F] [-c C] [-a] [-s S] [--status-schema ST]
[--flag-dir FD] [-p P] -i I [-r R]
Remove a result.
options:
-h, --help show this help message and exit
-n N, --project-name N Name of the pipeline to report result for. If not provided
'PIPESTAT_PROJECT_NAME' env var will be used. Currently not
set
-f F, --results-file F Path to the YAML file where the results will be stored.
This file will be used as pipestat backend and to restore
the reported results across sessions
-c C, --config C Path to the YAML configuration file. If not provided
'PIPESTAT_CONFIG' env var will be used. Currently not set
-a, --database-only Whether the reported data should not be stored in the
memory, only in the database.
-s S, --schema S Path to the schema that defines the results that can be
reported. If not provided 'PIPESTAT_RESULTS_SCHEMA' env var
will be used. Currently not set
--status-schema ST Path to the status schema. Default will be used if not
provided: /home/drc/GITHUB/pipestat/pipestat/venv/lib/pytho
n3.10/site-packages/pipestat/schemas/status_schema.yaml
--flag-dir FD Path to the flag directory in case YAML file is the
pipestat backend.
-p P, --pipeline-type P project or sample level pipeline type.
-i I, --result-identifier I ID of the result to report; needs to be defined in the
schema
-r R, --record-identifier R ID of the record to report the result for. If not provided
'PIPESTAT_RECORD_IDENTIFIER' env var will be used.
Currently not set
pipestat retrieve --help
usage: pipestat retrieve [-h] [-n N] [-f F] [-c C] [-a] [-s S] [--status-schema ST]
[--flag-dir FD] [-p P] [-r R]
Retrieve a result.
options:
-h, --help show this help message and exit
-n N, --project-name N Name of the pipeline to report result for. If not provided
'PIPESTAT_PROJECT_NAME' env var will be used. Currently not
set
-f F, --results-file F Path to the YAML file where the results will be stored.
This file will be used as pipestat backend and to restore
the reported results across sessions
-c C, --config C Path to the YAML configuration file. If not provided
'PIPESTAT_CONFIG' env var will be used. Currently not set
-a, --database-only Whether the reported data should not be stored in the
memory, only in the database.
-s S, --schema S Path to the schema that defines the results that can be
reported. If not provided 'PIPESTAT_RESULTS_SCHEMA' env var
will be used. Currently not set
--status-schema ST Path to the status schema. Default will be used if not
provided: /home/drc/GITHUB/pipestat/pipestat/venv/lib/pytho
n3.10/site-packages/pipestat/schemas/status_schema.yaml
--flag-dir FD Path to the flag directory in case YAML file is the
pipestat backend.
-p P, --pipeline-type P project or sample level pipeline type.
-r R, --record-identifier R ID of the record to report the result for. If not provided
'PIPESTAT_RECORD_IDENTIFIER' env var will be used.
Currently not set
pipestat status --help
usage: pipestat status [-h] {set,get} ...
Manage pipeline status.
positional arguments:
{set,get}
set Set status.
get Get status.
options:
-h, --help show this help message and exit
pipestat status get --help
usage: pipestat status get [-h] [-n N] [-f F] [-c C] [-a] [-s S] [--status-schema ST]
[--flag-dir FD] [-r R] [-p P]
Get status.
options:
-h, --help show this help message and exit
-n N, --project-name N Name of the pipeline to report result for. If not provided
'PIPESTAT_PROJECT_NAME' env var will be used. Currently not
set
-f F, --results-file F Path to the YAML file where the results will be stored.
This file will be used as pipestat backend and to restore
the reported results across sessions
-c C, --config C Path to the YAML configuration file. If not provided
'PIPESTAT_CONFIG' env var will be used. Currently not set
-a, --database-only Whether the reported data should not be stored in the
memory, only in the database.
-s S, --schema S Path to the schema that defines the results that can be
reported. If not provided 'PIPESTAT_RESULTS_SCHEMA' env var
will be used. Currently not set
--status-schema ST Path to the status schema. Default will be used if not
provided: /home/drc/GITHUB/pipestat/pipestat/venv/lib/pytho
n3.10/site-packages/pipestat/schemas/status_schema.yaml
--flag-dir FD Path to the flag directory in case YAML file is the
pipestat backend.
-r R, --record-identifier R ID of the record to report the result for. If not provided
'PIPESTAT_RECORD_IDENTIFIER' env var will be used.
Currently not set
-p P, --pipeline-type P project or sample level pipeline type.
pipestat status set --help
usage: pipestat status set [-h] [-n N] [-f F] [-c C] [-a] [-s S] [--status-schema ST]
[--flag-dir FD] [-r R] [-p P]
status_identifier
Set status.
positional arguments:
status_identifier Status identifier to set.
options:
-h, --help show this help message and exit
-n N, --project-name N Name of the pipeline to report result for. If not provided
'PIPESTAT_PROJECT_NAME' env var will be used. Currently not
set
-f F, --results-file F Path to the YAML file where the results will be stored.
This file will be used as pipestat backend and to restore
the reported results across sessions
-c C, --config C Path to the YAML configuration file. If not provided
'PIPESTAT_CONFIG' env var will be used. Currently not set
-a, --database-only Whether the reported data should not be stored in the
memory, only in the database.
-s S, --schema S Path to the schema that defines the results that can be
reported. If not provided 'PIPESTAT_RESULTS_SCHEMA' env var
will be used. Currently not set
--status-schema ST Path to the status schema. Default will be used if not
provided: /home/drc/GITHUB/pipestat/pipestat/venv/lib/pytho
n3.10/site-packages/pipestat/schemas/status_schema.yaml
--flag-dir FD Path to the flag directory in case YAML file is the
pipestat backend.
-r R, --record-identifier R ID of the record to report the result for. If not provided
'PIPESTAT_RECORD_IDENTIFIER' env var will be used.
Currently not set
-p P, --pipeline-type P project or sample level pipeline type.