API Documentation

All modules above listed are under the “sct_dbtool” namespace.

Contents:

sct_dbtool.api – Server API

class sct_dbtool.api.APIClient(user: str, password: str, hostname='tristano.neuro.polymtl.ca', port=80)

The API client for the web management tool. This API client contains code only for retrieving the entire JSON dataset.

Parameters:

• user – username for the web management.
• password – password for the web management.
• hostname – the hostname for the web management.
• port – the port of the web management.

classmethod from_config(config: Dict)

Use this class method to create a new API client from a configuration dictionary.

Parameters:config – the configuration. Returns:a new configured APIClient instance.

get_dataset() → List[Dict]

Retrieves the entire dataset from the server.

Returns:list of items from the dataset.

sct_dbtool.sanity – Sanity Checks

class sct_dbtool.sanity.CheckEmptyDemographics(db_path: str)

This check will verify if the demographics field is present.

check(item: Dict)

Implement this function in the sub-classes to add the specific checks.

Parameters:item – each item of the database

class sct_dbtool.sanity.CheckFilesystemDB(db_path: str)

This check will verify if all files in file system are present in the database.

check(item: Dict)

Implement this function in the sub-classes to add the specific checks.

Parameters:item – each item of the database

teardown()

This function is called after finishing the checking on all database items. Before collecting diagnostic messages.

class sct_dbtool.sanity.CheckLabelVolumeConsistency(db_path: str)

This check will verify if the label is consistent with the volume (shapes).

check(item: Dict)

Implement this function in the sub-classes to add the specific checks.

Parameters:item – each item of the database

class sct_dbtool.sanity.CheckLabelVolumePath(db_path: str)

This check will verify if the label volume exists in the file system.

check(item: Dict)

Implement this function in the sub-classes to add the specific checks.

Parameters:item – each item of the database

class sct_dbtool.sanity.CheckMainVolumeNibabel(db_path: str)

This check will verify if nibabel is able to open the main volume.

check(item: Dict)

Implement this function in the sub-classes to add the specific checks.

Parameters:item – each item of the database

class sct_dbtool.sanity.CheckMainVolumePath(db_path: str)

This check will verify if the main volume exists in the file system.

check(item: Dict)

Implement this function in the sub-classes to add the specific checks.

Parameters:item – each item of the database

class sct_dbtool.sanity.Diagnostic(category: str, check_name: str, message: str, item: Dict)

This is a data class to represent the diagnostics.

Parameters:

• category – the diagnostic category (warning, error, info)
• check_name – the name of the check that generated the diagnostic.
• message – message generated by the check.
• item – the item related to the diagnostic.

class sct_dbtool.sanity.SanityCheck(category: str, db_path: str)

Extend this class to implement new sanity checks.

Parameters:

• category – category of the check (warning, error or info).
• db_path – the path to the database.

add_diagnostic(msg: str, item: Dict)

Add a new diagnostic message for the item.

Parameters:

• msg – message with details about the diagnostic.
• item – item who generated the diagnostic.

check(item: Dict)

Implement this function in the sub-classes to add the specific checks.

Parameters:item – each item of the database

collect_diagnostics() → List[sct_dbtool.sanity.Diagnostic]

This method will collect all diagnostics generated by each checking.

Returns:a list of diagnostics.

teardown()

This function is called after finishing the checking on all database items. Before collecting diagnostic messages.

sct_dbtool.sanity.class_inheritors(klass: Type) → Set[Type]

This method will search for all classes inheriting from the SanityCheck class.

Parameters:klass – the class to search for childs. Returns:list of the classes.

sct_dbtool.sanity.sanity_check(api_client: sct_dbtool.api.APIClient, arguments: Dict)

Main entry-point for the sanity checking.

Parameters:

• api_client – a configured instance of APIClient.
• arguments – the CLI arguments.

sct_dbtool.setup – CLI setup entry-point

sct_dbtool.setup.read_setup()

Read the system configuration file.

Returns:a dict with the configuration parameters.

sct_dbtool.setup.setup(arguments: Dict)

This method will ask user input to configure the system with the hostname, username, etc, for the web management access.

Parameters:arguments – the CLI arguments.

sct_dbtool.main – Main CLI entry-point

Naval Fate.

Usage:

sct_dbtool sanity <db_path> sct_dbtool setup sct_dbtool (-h | –help) sct_dbtool –version

Options:

-h –help Show this screen –version Show version