Command Line Interface

Run the workflow

usage: morphology_workflows [-h] [-c CONFIG_PATH] [-l]
                            [-ll {DEBUG,INFO,WARNING,ERROR,CRITICAL}]
                            [-lf LOG_FILE] [-w WORKERS]
                            [-dg CREATE_DEPENDENCY_GRAPH]
                            {Curate,Annotate,Repair} ...

Positional Arguments

workflow

Possible choices: Curate, Annotate, Repair

Possible workflows

Named Arguments

-c, --config-path

Path to the Luigi config file

-l, --local-scheduler

Use Luigi’s local scheduler instead of master scheduler.

Default: False

-ll, --log-level

Possible choices: DEBUG, INFO, WARNING, ERROR, CRITICAL

Logger level.

Default: “INFO”

-lf, --log-file

Logger file.

-w, --workers

Number of workers that luigi can summon.

Default: 1

-dg, --create-dependency-graph

Create the dependency graph of a workflow instead of running it. Pass either ‘ascii’ to print the graph to screen or a path to render it as an image (depending on the extension of the given path).

Sub-commands:

Curate

Run Curation phase.

morphology_workflows Curate [-h] [--rerun] [--tag-output]
                            [--result-path CURATE_--RESULT-PATH]
                            [--dataset-df CURATE_--DATASET-DF]
                            [--data-dir CURATE_--DATA-DIR]
                            [--custom-task-name CURATE_--CUSTOM-TASK-NAME]
                            [--nb-processes CURATE_--NB-PROCESSES]
                            [--redirect-stdout [CURATE_--REDIRECT-STDOUT]]
                            [--report-path CURATE_--REPORT-PATH]
                            [--generate-report [CURATE_--GENERATE-REPORT]]
                            [--report-type CURATE_--REPORT-TYPE]
                            [--report-config CURATE_--REPORT-CONFIG]
                            [--specifications-only]

Named Arguments

--rerun

Trigger to force the task to rerun. Default value: False.

Default: False

--tag-output

(bool) Add a tag suffix to the output directory. Default value: False.

Default: False

--result-path

(str) Path to the global output directory.

--dataset-df

(str) Path to the input dataset.

--data-dir

(str) name of folder to store addittional files created by a task (the provided validation function must take this as argument). Default value: data.

--custom-task-name

(str) An optional custom name given to the task (the class name is used if not provided).

--nb-processes

(int) The number of parallel processes to use.

--redirect-stdout

(bool) Capture stdout from the validation function to make it work with progress bar. Disable it if you want to use PDB inside the validation function.

--report-path

(str) Path to the workflow report.

--generate-report

(bool) Trigger the report generation. Default value: True.

--report-type

(str) Type of report (‘pdf’: basic, ‘latexpdf’: beautiful). Choices: {latexpdf, pdf}. Default value: pdf.

--report-config

(dict) The configuration used by Sphinx to build the report.

--specifications-only

(bool) Only outputs the dataset specification document. Default value: False.

Default: False

Annotate

Run Annotation phase.

morphology_workflows Annotate [-h] [--rerun] [--tag-output]
                              [--result-path ANNOTATE_--RESULT-PATH]
                              [--dataset-df ANNOTATE_--DATASET-DF]
                              [--data-dir ANNOTATE_--DATA-DIR]
                              [--custom-task-name ANNOTATE_--CUSTOM-TASK-NAME]
                              [--nb-processes ANNOTATE_--NB-PROCESSES]
                              [--redirect-stdout [ANNOTATE_--REDIRECT-STDOUT]]
                              [--report-path ANNOTATE_--REPORT-PATH]
                              [--generate-report [ANNOTATE_--GENERATE-REPORT]]
                              [--report-type ANNOTATE_--REPORT-TYPE]
                              [--report-config ANNOTATE_--REPORT-CONFIG]
                              [--specifications-only]

Named Arguments

--rerun

Trigger to force the task to rerun. Default value: False.

Default: False

--tag-output

(bool) Add a tag suffix to the output directory. Default value: False.

Default: False

--result-path

(str) Path to the global output directory.

--dataset-df

(str) Path to the input dataset.

--data-dir

(str) name of folder to store addittional files created by a task (the provided validation function must take this as argument). Default value: data.

--custom-task-name

(str) An optional custom name given to the task (the class name is used if not provided).

--nb-processes

(int) The number of parallel processes to use.

--redirect-stdout

(bool) Capture stdout from the validation function to make it work with progress bar. Disable it if you want to use PDB inside the validation function.

--report-path

(str) Path to the workflow report.

--generate-report

(bool) Trigger the report generation. Default value: True.

--report-type

(str) Type of report (‘pdf’: basic, ‘latexpdf’: beautiful). Choices: {latexpdf, pdf}. Default value: pdf.

--report-config

(dict) The configuration used by Sphinx to build the report.

--specifications-only

(bool) Only outputs the dataset specification document. Default value: False.

Default: False

Repair

Run Repair phase.

morphology_workflows Repair [-h] [--rerun] [--tag-output]
                            [--result-path REPAIR_--RESULT-PATH]
                            [--dataset-df REPAIR_--DATASET-DF]
                            [--data-dir REPAIR_--DATA-DIR]
                            [--custom-task-name REPAIR_--CUSTOM-TASK-NAME]
                            [--nb-processes REPAIR_--NB-PROCESSES]
                            [--redirect-stdout [REPAIR_--REDIRECT-STDOUT]]
                            [--report-path REPAIR_--REPORT-PATH]
                            [--generate-report [REPAIR_--GENERATE-REPORT]]
                            [--report-type REPAIR_--REPORT-TYPE]
                            [--specifications-only]

Named Arguments

--rerun

Trigger to force the task to rerun. Default value: False.

Default: False

--tag-output

(bool) Add a tag suffix to the output directory. Default value: False.

Default: False

--result-path

(str) Path to the global output directory.

--dataset-df

(str) Path to the input dataset.

--data-dir

(str) name of folder to store addittional files created by a task (the provided validation function must take this as argument). Default value: data.

--custom-task-name

(str) An optional custom name given to the task (the class name is used if not provided).

--nb-processes

(int) The number of parallel processes to use.

--redirect-stdout

(bool) Capture stdout from the validation function to make it work with progress bar. Disable it if you want to use PDB inside the validation function.

--report-path

(str) Path to the workflow report.

--generate-report

(bool) Trigger the report generation. Default value: True.

--report-type

(str) Type of report (‘pdf’: basic, ‘latexpdf’: beautiful). Choices: {latexpdf, pdf}. Default value: pdf.

--specifications-only

(bool) Only outputs the dataset specification document. Default value: False.

Default: False