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: {pdf, latexpdf}. 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: {pdf, latexpdf}. 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: {pdf, latexpdf}. Default value: pdf.
- --specifications-only
(bool) Only outputs the dataset specification document. Default value: False.
Default: False