Command Line Interface¶
Run the workflow
usage: morphology-workflows [-h] [--version] [-c CONFIG_PATH] [-m]
[-ll {DEBUG,INFO,WARNING,ERROR,CRITICAL}]
[-lf LOG_FILE] [-w WORKERS]
[-dg CREATE_DEPENDENCY_GRAPH]
[-dgdpi DEPENDENCY_GRAPH_DPI]
{Initialize,Fetch,Placeholders,Curate,Annotate,Repair}
...
Positional Arguments¶
- workflow
Possible choices: Initialize, Fetch, Placeholders, Curate, Annotate, Repair
Possible workflows
Named Arguments¶
- --version
show program’s version number and exit
- -c, --config-path
Path to the Luigi config file.
- -m, --master-scheduler
Use Luigi’s master scheduler instead of local scheduler.
Default: False
- -ll, --log-level
Possible choices: DEBUG, INFO, WARNING, ERROR, CRITICAL
Logger level (this will ignore the luigi ‘logging_conf_file’ argument).
- -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 a path to render it as an image (depending on the extension of the given path).
- -dgdpi, --dependency-graph-dpi
The DPI used for the dependency graph export.
Sub-commands¶
Initialize¶
Create default inputs for a given workflow that users can then update according to their needs. Usually, the initialization consists in one of these two types:
the morphologies are fetched from an online database.
the morphologies are provided by the user.
In the first case, the ‘–input-dir’ argument should usually not be used. In the second case, the ‘–source-database’ argument should usually not be used.
morphology-workflows Initialize [-h]
[--source-database {NeuroMorpho,BBP-Nexus,Allen,MouseLight}]
[--input-dir INPUT_DIR]
[--output-dir OUTPUT_DIR]
[--dataset-filename DATASET_FILENAME]
Named Arguments¶
- --source-database
Possible choices: NeuroMorpho, BBP-Nexus, Allen, MouseLight
The database from which the morphologies will be fetched.
- --input-dir
The directory containing the input morphologies if they are not fetched from a database.
- --output-dir
The directory in which the project inputs will be exported.
- --dataset-filename
The name of the CSV file to which the dataset will be exported.
Default: “dataset.csv”
Fetch¶
Fetch morphologies from the given source.
The JSON configuration file should contain a list of objects where each object is a config set:
[ { "brain_region": "AHN", "nb_morphologies": 2, "seed": 0 }, { "brain_region": "VISp", "nb_morphologies": 2, "seed": 0 } ]
morphology-workflows Fetch [-h] [--rerun] [--tag-output]
[--source FETCH_SOURCE]
[--config-file FETCH_CONFIG_FILE]
[--result-path FETCH_RESULT_PATH]
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
- --source
(str) The source used to download the morphologies Choices: {NeuroMorpho, BBP-Nexus, Allen, MouseLight}.
- --config-file
(str) Path to the JSON config file
- --result-path
(str) Path to the output directory. Default value: morphologies.
Placeholders¶
Compute the placeholders for a given region and mtype set from a given config.
morphology-workflows Placeholders [-h] [--rerun] [--tag-output]
[--config PLACEHOLDERS_CONFIG]
[--input-dir PLACEHOLDERS_INPUT_DIR]
[--result-path PLACEHOLDERS_RESULT_PATH]
[--nb-jobs PLACEHOLDERS_NB_JOBS]
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
- --config
(str) (optional) The path to the JSON config file.
- --input-dir
(str) (optional) The directory containing the morphologies and their metadata file.
- --result-path
(str) Path to the output file (can be CSV or JSON file). Default value: placeholders.csv.
- --nb-jobs
(int) Number of jobs used by parallel tasks. Permitted values: int in [1, 10000000000). Default value: 1.
Curate¶
Run Curation phase.
(click on steps in the image for more details)
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) (optional) Path to the global output directory.
- --dataset-df
(str) (optional) 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.
(click on steps in the image for more details)
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) (optional) Path to the global output directory.
- --dataset-df
(str) (optional) 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.
(click on steps in the image for more details)
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) (optional) Path to the global output directory.
- --dataset-df
(str) (optional) 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