Welcome to jsonldschema’s documentation!¶

Utilities for semantic comparison of JSON-LD-schemas¶

class compareEntities.EntityCoverage(schema_a, context_a, schema_b, context_b)[source]¶

A class that compute the overlap between two JSON schemas semantic values taken from context files. This operation is not commutative. Thus, to find out if the schema/context pairs are equivalent, we need to run both semDiff(s_a, c_a, s_b, c_b) and semDiff(s_b, c_b, s_a, c_a)

Parameters:	schema_a – the content of the first schema context_a – the context content bound to the first schema schema_b – the content of the second schema context_b – the context content bound to the second schema

class compareNetwork.NetworkCoverage(networks_array)[source]¶: This class compute the coverage of entities (schemas) among two networks (set of schemas) by comparing the semantic base type of each schema. :param networks_array: an array containing the two networks to compare

class fullDiff.FullSemDiff(contexts, network_1, network_2)[source]¶: A class that computes the coverage at entity level and extracts ‘semantic synonyms’ (named twins in the code). It will then compute the coverage at attribute level between ‘semantic synonyms’.

class mergeEntities.EntityMerge(schema1, context1, schema2, context2)[source]¶: A class that merge two schemas based on their semantic annotations

Utilities FOR PREPARING FUNCTIONS INPUT¶

Utilities to validate JSON-schemas and instances¶

jsonschema_validator.validate_instance(schemapath, schemafile, instancepath, instancefile, error_printing, store)[source]¶: Validate a JSON instance againsts a JSON schema.

jsonschema_validator.validate_schema(path, schema_file_name)[source]¶: Validate a JSON schema given the folder/path and file name of the schema file.

jsonschema_validator.validate_schema_file(schema_file)[source]¶: Validate a JSON schema given the schema file.

class miflowcyt_validate.FlowRepoClient(mapping, base_schema, client_id)[source]¶

A class that provides functionality to download experiments from the FlowRepository (https://flowrepository.org/), transform the XML into JSON and validate the instances against their schema. The transformation from XML to JSON relies on the JSONBender library (https://github.com/Onyo/jsonbender).

static get_mapping(mapping_file_name)[source]¶: Build the mapping dictionary based on the given mapping file :param mapping_file_name: the name of the mapping file :return mapping: the mapping of the fields

get_user_content_id(client_identifier)[source]¶: Return all IDs found in the user content XML :param client_identifier: the user content ID :return: a list of all IDs there were identified in the variable returned by the API

static grab_experiment_from_api(client_identifier, item_identifier)[source]¶: Retrieve the experimental metadata and return it as a python object :param client_identifier: the client identifier (apiKey) :param item_identifier: the item identifier that should be retrieved :return: the python object obtained from the XML

static grab_user_content(client_identifier)[source]¶

Grab all content for a given user ID as an XML and outputs it as a JSON. This method will grab all public experiments plus those only accessible to the user ID.

Args:: client_identifier: the user ID
Returns: response the dictionary containing the XML

make_validation(number_of_items)[source]¶

Method to run the mapping for the given number of items

Args: number_of_items (int): the number of items to process
Returns: errors (dict): a dictionary containing the list of errors for all processed items

static validate_instance_from_file(instance, item_id, schema_name)[source]¶: Method to output the extracted JSON into a file and validate it against the given schema :param instance: the instance to output into a file :param item_id: the instance ID needed to create the file name :param schema_name: the schema to check against :return errors: a list of fields that have an error for this instance

class miflowcyt_validate.FlowRepoClient(mapping, base_schema, client_id)[source]

A class that provides functionality to download experiments from the FlowRepository (https://flowrepository.org/), transform the XML into JSON and validate the instances against their schema. The transformation from XML to JSON relies on the JSONBender library (https://github.com/Onyo/jsonbender).

static get_mapping(mapping_file_name)[source]: Build the mapping dictionary based on the given mapping file :param mapping_file_name: the name of the mapping file :return mapping: the mapping of the fields

get_user_content_id(client_identifier)[source]: Return all IDs found in the user content XML :param client_identifier: the user content ID :return: a list of all IDs there were identified in the variable returned by the API

static grab_experiment_from_api(client_identifier, item_identifier)[source]: Retrieve the experimental metadata and return it as a python object :param client_identifier: the client identifier (apiKey) :param item_identifier: the item identifier that should be retrieved :return: the python object obtained from the XML

static grab_user_content(client_identifier)[source]

Grab all content for a given user ID as an XML and outputs it as a JSON. This method will grab all public experiments plus those only accessible to the user ID.

Args:: client_identifier: the user ID
Returns: response the dictionary containing the XML

make_validation(number_of_items)[source]

Method to run the mapping for the given number of items

Args: number_of_items (int): the number of items to process
Returns: errors (dict): a dictionary containing the list of errors for all processed items

static validate_instance_from_file(instance, item_id, schema_name)[source]: Method to output the extracted JSON into a file and validate it against the given schema :param instance: the instance to output into a file :param item_id: the instance ID needed to create the file name :param schema_name: the schema to check against :return errors: a list of fields that have an error for this instance

CEDAR utilities¶

The CEDAR client will provide all the links the the CEDAR API functionnalities such as get, post and updates on templates, template elements, folders, instances ect …

class client.CEDARClient[source]¶

A client for the CEDAR API

create_folder(endpoint_type, api_key, target_folder_id, new_folder_name, new_folder_description)[source]¶

Create a folder with new_folder_name in the target_folder_id location

Parameters:	endpoint_type – (str) the type of server to prompt api_key – (str) your CEDAR user API key target_folder_id – (str) he CEDAR target folder’s ID where the new folder will be created new_folder_name – (str) the new folder name to create new_folder_description – (str) the new folder description to create
Returns:	(dict) a request response

create_template(endpoint_type, api_key, folder_id, template_file)[source]¶

Post a new schema to the selected folder id

Parameters:	endpoint_type – (str) the type of server to prompt api_key – (str) your CEDAR user API key folder_id – (str) the CEDAR target folder’s ID template_file – (str) the CEDAR target template’s ID
Returns:	(dict) a request response

create_template_element(endpoint_type, api_key, folder_id, template_resource)[source]¶

Create a new template element on the given server

Parameters:	endpoint_type – (str) the type of server to prompt api_key – (str) your CEDAR user API key folder_id – (str) the CEDAR target folder’s ID template_resource – (dict) the resource to post
Returns:	(dict) a request response

delete_folder(endpoint_type, api_key, folder_id)[source]¶

Delete a given folder from the server

Parameters:	endpoint_type – (str) the type of server to prompt api_key – (str) your CEDAR user API key folder_id – (str) the CEDAR target folder’s ID
Returns:	(dict) a request response

get_folder_content(endpoint_type, api_key, folder_id)[source]¶

Get the content of a folder from CEDAR

Parameters:	endpoint_type – (str) the type of server to prompt api_key – (str) your CEDAR user API key folder_id – (str) the CEDAR target folder’s ID
Returns:	(dict) a request response

static get_headers(api_key)[source]¶

Method to build the HTTP request header

Parameters:	api_key – (str) the API Key to your CEDAR account
Returns:	(dict) the HTTP headers

get_template_content(endpoint_type, api_key, template_id)[source]¶

Get the content of a CEDAR template

Parameters:	endpoint_type – (str) the type of server to prompt api_key – (str) your CEDAR user API key template_id – (str) the CEDAR target template’s ID
Returns:	(dict) a request response

get_users(endpoint_type, api_key)[source]¶

Method to get all users from the server

Parameters:	endpoint_type – (str) url to the CEDAR selected server api_key – (str) your CEDAR user API key
Returns:	(dict) a request response

static post(url, parameter, headers, directory)[source]¶

Method to post data to the CEDAR selected server and log the process

Parameters:	url – (str) the URL to the selected server parameter – (dict) parameters of the HTTP request headers – (dict) the header required by the HTTP request directory – (str) the directory where to saved the log file

static select_endpoint(server_type)[source]¶

Method to select the server (prod or dev)

Parameters:	server_type – (str) the type of server to select
Returns:	(str) the URL corresponding to the selected server

update_template(endpoint_type, api_key, template_file)[source]¶

Update the content of template_file into the selected template

Parameters:	endpoint_type – (str) “staging” or “production” api_key – (str) your CEDAR user API key template_file – (str) the full path to a local template JSON file
Returns:	(dict) a request response

upload_element(server_alias, api_key, schema_file, remote_folder_id)[source]¶

Upload a template element to the server

Parameters:	server_alias – (str) the type of server to prompt api_key – (str) your CEDAR user API key schema_file – (str) the full path to a local template element JSON file remote_folder_id – (str) the CEDAR target folder’s ID
Returns:	(dict) a request response

upload_resource(api_key, request_url, resource)[source]¶

Upload the given resource to the CEDAR server

Parameters:	api_key – (str) your CEDAR user API key request_url – (str) the CEDAR server URL to post to resource – (dict) the resource to upload
Returns:	(dict) a response text loaded as a dictionary

validate_element(server_alias, api_key, element)[source]¶

Method to validate a CEDAR template element

Parameters:	server_alias – (str) the URL to run the validation from api_key – (str) your CEDAR user API key element – (dict) the resource to validate as a template
Returns:	(dict) a request response

validate_instance(server_address, api_key, instance)[source]¶

Method to validate a JSON instance against the corresponding resource on CEDAR

Parameters:	server_address – (str) the CEDAR server URL api_key – (str) your CEDAR user API key instance – (dict) the resource to validate as an instance
Returns:	(dict) a request response

validate_resource(api_key, request_url, resource)[source]¶

Method to validate a resource against the server

Parameters:	api_key – (str) your CEDAR user API key request_url – (str) the URL to run the validation from resource – (dict) the resource to validate
Returns:	(dict) a request response

validate_template(server_alias, api_key, template)[source]¶

Method to validate a CEDAR template

Parameters:	server_alias – (str) the URL to run the validation from api_key – (str) your CEDAR user API key template – (dict) the resource to validate as a template
Returns:	(dict) a request response

The schema2cedar classes will help you transform your JSON schemas draft 04 into compatible CEDAR schemas

class schema2cedar.Schema2CedarBase[source]¶

The base converter class

Warning

This class should not be used! Use its children for converting to cedar template and template elements

static json_pretty_dump(json_object, output_file)[source]¶

Dump a given json in the given file

Parameters:	json_object (dict) – the input JSON to dump output_file (str) – the file to dump the JSON to
Returns:	the dumping result
Return type:	string

static set_context()[source]¶

Set the base context for a given template

Returns:	the base context

static set_prop_context(schema)[source]¶

Set the required context for the properties attribute of the given schema

Parameters:	schema – an input JSON schema
Returns:	the properties context required by CEDAR

static set_properties_base_item()[source]¶

Set the base properties required by CEDAR

Returns:	the base property dictionary

static set_required_item(schema)[source]¶

Set the required items that a CEDAR schema needs for a given schema

Parameters:	schema – the input schema
Returns:	the dictionary of required items

static set_stripped_properties(schema)[source]¶

Set the properties of a given schema

Parameters:	schema – the input schema
Returns:	a dictionary of properties

static set_sub_context(schema)[source]¶

Set the context required by CEDAR for each individual attribute/field for a given schema

Parameters:	schema – the input schema
Returns:	the dictionary of required context for each field

static set_template_element_property_minimals(sub_context, schema)[source]¶

Set the minimal elements of the properties attributes of a given schema and its sub-context

Parameters:	sub_context – the schema sub-context schema – the input schema
Returns:	(dict) a dictionary of the required properties for CEDAR conversion

class schema2cedar.Schema2CedarTemplate[source]¶

Schema 2 Template Converter, this is the one you want to use if you want to convert a schema into a template

convert_template(input_json_schema)[source]¶

Method to convert a given schema into a CEDAR template

Parameters:	input_json_schema – the input JSON schema
Returns:	the schema converted into a template

class schema2cedar.Schema2CedarTemplateElement[source]¶

Schema to TemplateElement converter.

Warning

Should only be used to convert schemas to template element. If you want to convert a schema to a template, use Schema2CedarTemplate (it will automatically create nested template elements for you)

convert_template_element(input_json_schema, **kwargs)[source]¶

Method to convert a given schema into a CEDAR template element

Parameters:	input_json_schema – the input schema kwargs – optional parameter to provide the field name referencing that schema
Returns:	the schema converted to a CEDAR template element

find_sub_specs(schema, sub_spec_container)[source]¶

Inspect a given schema to find and load its schemas dependencies

Return sub_spec_container:
Parameters:	schema – the input schema sub_spec_container – a container that will hold the dependencies
	the filled container with the schema dependencies

static load_sub_spec(path_to_load, parent_schema, field_key)[source]¶

Load the given sub schema into memory

Parameters:	path_to_load – path to the sub schema parent_schema – the parent schema that this sub-schema is referenced from field_key – the parent schema field name that this sub-schema is referenced from
Returns:	the string containing the loaded JSON schema