Command line interface

flexiznam

flexiznam [OPTIONS] COMMAND [ARGS]...

add-mouse

Add a single mouse to a project.

flexiznam add-mouse [OPTIONS]

Options

-p, --project_id <project_id>

Project ID.

-m, --mouse_name <mouse_name>

Name of the mouse for flexilims.

--mcms_animal_name <mcms_animal_name>

Name of the mouse on MCMS (if different from mouse_name).

--flexilims_username <flexilims_username>

Your username on flexilims.

--mcms_username <mcms_username>

Your username on mcms.

add-password

Edit or create password file

flexiznam add-password [OPTIONS]

Options

-a, --app <app>

Name of the service requiring the password (flexilims or mcms for instance).

-u, --username <username>

Username as required by the app.

-p, --password <password>

Password to add.

--password_file <password_file>

File to edit or create to add if not using the config folder

config

Create a configuration file if none exists.

flexiznam config [OPTIONS]

Options

-t, --template <template>

Template config file.

--config_folder <config_folder>

Folder containing the config file.

--update, --no-update

Update the config file to include all fields present in the default config. Will not change already defined fields.

process-yaml

Parse source_yaml and autogenerate a full yaml containing all datasets

flexiznam process-yaml [OPTIONS]

Options

-s, --source_yaml <source_yaml>

Required Manually generated yaml to seed automatic method.

-t, --target_yaml <target_yaml>

Path to outpout YAML file.

-r, --raw_data_folder <raw_data_folder>

Path to the root folder containing raw data

--overwrite, --no-overwrite

Overwrite the output if it exists.

yaml-to-flexilims

Create entries on flexilims corresponding to yaml

flexiznam yaml-to-flexilims [OPTIONS]

Options

-s, --source_yaml <source_yaml>

Required Clean yaml without any error.

-r, --raw_data_folder <raw_data_folder>

Path to the root folder containing raw data

-c, --conflicts <conflicts>

Default is abort to crash if there is a conflict, use skip to ignore and proceed