Models documentation

Enum Models

Messages.py

Module regrouping enumerations containing messages.

It includes different kind of messages :

Messages returned during the parsing of lipid names by Pygoslin tool.
Messages that may be returned by the application in case of errors.
Messages returned by the application serving as information for users.
Messages related to the local “database” built at the start of the application.

class src.models.enums.Messages.ErrorMessages(value, names=<not given>, *values, module=None, qualname=None, type=None, start=1, boundary=None)

Regroups the error messages that the application may return.

BAD_REQUEST = 'Bad request - There is an error in the request.\rThere must be at least one query parameter named "lipid_names". It takes a lipid name as value and can be repeated.\rExample : /goslin/validate?lipid_name=value1&lipid_name=value2'

class src.models.enums.Messages.GoslinMessages(value, names=<not given>, *values, module=None, qualname=None, type=None, start=1, boundary=None)

Regroups messages that can be returned in the response obtained after parsing with Pygoslin tool.

LIPIDMAPS_REF_NOT_FOUND = 'Standardized name not link with any entry in the LipidMaps Structure Database'

LIPID_NOT_FOUND = 'Lipid not found'

NO_CLASS_NAME = 'UNDEFINED'

NO_FORMULA = 'The formula for this lipid could not be calculated.'

NO_MASS = 'The mass of this lipid could not be calculated.'

class src.models.enums.Messages.InformativeMessages(value, names=<not given>, *values, module=None, qualname=None, type=None, start=1, boundary=None)

Regroups the informative messages that the application may return.

ROOT = 'You are at the root of the Goslin API. Please refer to the Swagger documentation to know the existing endpoint.\rIt is available here : https://metabocloud.mesocentre.uca.fr/goslin/api/doc'

class src.models.enums.Messages.LocalDatabase(value, names=<not given>, *values, module=None, qualname=None, type=None, start=1, boundary=None)

Regroups messages related to the local database built from the LipidMaps Structure Database.

FILE_NOT_FOUND = 'The SDF file containing the LipidMaps Structure Database was not found. \n The local database could not be created.'

NO_LOCAL_DATABASE = 'Information coming from this database could not be retrieved (LipidMaps ID, InCHI key and SwissLipids ID). Error during the creation of the local database.'

class src.models.enums.Messages.State(value, names=<not given>, *values, module=None, qualname=None, type=None, start=1, boundary=None)

Regroups the different states that a parsing result can take.

FAILURE = 'Failure'

SUCCESS = 'Success'

UNCOMPLETED = 'Uncompleted'

Paths.py

Module regrouping enumerations containing paths.

It includes all paths used in the application.

class src.models.enums.Paths.Paths(value, names=<not given>, *values, module=None, qualname=None, type=None, start=1, boundary=None)

Paths used in the API.

LIPIDMAPS_DATABASE = 'http://mirror.dsi.uca.fr/metabocloud/structures.sdf': URL to the SDF file containing the LipidMaps Structure Database.

LIPID_CLASSES_SUPPORTED = './resources/lipid-list.csv': Relative path to the CSV file containing the lipid class that are supported by the Goslin tool. This file comes from the package pygoslin.

METADATA_JSON = './resources/goslin_about.json': Relative path to the template JSON file with the metadata of a microservice.

OPENAPI_DOC = 'https://metabocloud.mesocentre.uca.fr/goslin/api/doc': URL to the OpenAPI documentation.

OPENAPI_YAML = './resources/metabocloud-goslin.yaml': Relative path to the YAML OpenAPI specification.

Object Models

LipidMapsEntry.py

class src.models.objects.LipidMapsEntry.LipidMapsEntry(lipidmaps_id: str = None, inchi_key: str = None, standardized_name: str = None, swiss_lipids: str = None)

An Object model to store LipidMaps Structure Database entry

property inchi_key: str

Gets the InChI Key of the lipid.

Returns:: The InChI Key of the lipid.
Return type:: str

property lipidmaps_id: str

Gets the LipidMaps ID of the lipid.

Returns:: The LipidMaps ID of the lipid.
Return type:: str

property standardized_name: str

Gets the standardized name of the lipid.

Returns:: The standardized name of the lipid.
Return type:: str

property swiss_lipids: str

Gets the SwissLipids ID of the lipid.

Returns:: The SwissLipids ID of the lipid.
Return type:: str

to_dict()

Returns the model properties as a dictionary

Returns:: The model properties as a dictionary
Return type:: dict

Vars.py

class src.models.objects.Vars.Vars

Variables used in the API.

LIPIDMAPS_DATABASE = []: Variable which will store the local database built from the SDF file of the LipidMaps Structure Database during the launch of the application. It will be a list a dictionary where each dictionary will contain 4 keys : LIPIDMAPS_ID, INCHI_KEY, STANDARDIZED_NAME and SWISSLIPIDS_ID.

METADATA = {'SHA_1': None, 'SHORT_SHA_1': None, 'TIMESTAMP': None}: Variable which will store the metadata about the version of the microservice that will be retrieve during the launch of the application.