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
Configure by setting PIPESTAT_CONFIG env var
version: 0.6.0
usage: pipestat [-h] [--version] [--silent] [--verbosity V] [--logdev]
{report,inspect,remove,retrieve,status,init,summarize,link,serve}
...
pipestat - report pipeline results
positional arguments:
{report,inspect,remove,retrieve,status,init,summarize,link,serve}
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
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 and
reliably 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
Configure by setting PIPESTAT_CONFIG env var
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
Configure by setting PIPESTAT_CONFIG env var
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
Configure by setting PIPESTAT_CONFIG env var
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
Configure by setting PIPESTAT_CONFIG env var
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
Configure by setting PIPESTAT_CONFIG env var
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
Configure by setting PIPESTAT_CONFIG env var
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
Configure by setting PIPESTAT_CONFIG env var
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.