Python Modules¶

The beacon_api package contains code to start an EGA Beacon API.

Note

In this file the information about the Beacon is registered. The information is parsed from beacon_api.conf.config.ini

`beacon_api.schemas`	Load JSON Schemas.
`beacon_api.api`	Beacon API endpoints.
`beacon_api.permissions`	Permissions Module.
`beacon_api.utils`	Utilities Module.
`beacon_api.conf`	Beacon Python Application Configuration.
`beacon_api.extensions`	Extensions Module.

API Schemas¶

Load JSON Schemas.

The JSON schemas represent a good method of checking that an endpoint’s requests/responses adhere to the API specification. Schemas available:

info.json - for the /info endpoint response;
query.json - for the /query endpoint request;
response.json - beacon API JSON response.

Example snippets from query.json:

    },
    "integer": {
      "$id": "$/definitions/integer",
      "type": "integer",
      "minimum": 0

  "required": [
    "referenceName",
    "referenceBases",
    "assemblyId"
  ],
  "properties": {
    "referenceName": {
      "$ref": "#/definitions/chromosome"
    },
    "mateName": {
      "$ref": "#/definitions/chromosome"
    },
    "start": {
      "$ref": "#/definitions/integer"
    },
    "end": {
      "$ref": "#/definitions/integer"
    },
    "startMin": {
      "$ref": "#/definitions/integer"
    },
    "startMax": {
      "$ref": "#/definitions/integer"
    },

      "type": "string",
      "default": "NONE",
      "enum": ["ALL", "HIT", "MISS", "NONE"]
    }
  },
  "dependencies": {
    "end": [
      "start"
    ],
    "startMin": [
      "startMax"
    ],
    "endMin": [
      "endMax"
    ],
    "startMax": ["startMin"],
    "endMax": ["endMin"],
    "mateName": {
      "oneOf": [{
        "required": [
          "start"
        ]
      },
      {
        "required": [
          "startMin"
        ],
        "not": {
          "required": [
            "endMin"
          ]

Beacon API¶

Beacon API endpoints.

The endpoints reflect the specification provided by: https://github.com/ga4gh-beacon/specification/blob/develop/beacon.md Endpoints:

/ - Information about the datasets in the Beacon;
/service-info - Information about the Beacon in GA4GH format (extra endpoint);
/query - querying/filtering datasets in the Beacon;

`beacon_api.api.info`	Info Endpoint.
`beacon_api.api.query`	Query Endpoint.
`beacon_api.api.exceptions`	Custom API exception reponses.

Utility Functions¶

Utilities Module.

Contains utilities such as database create/load, JSON schema validation, token authentication.

Also contains necessary functions for querying the DB and retrieving and transforming data to desired format.

Other functions include logging formatter.

`beacon_api.utils.logging`	Logging formatting.
`beacon_api.utils.db_load`	Beacon Database Loader.
`beacon_api.utils.validate_json`	JSON Request/Response Validation.
`beacon_api.utils.validate_jwt`	JSON Token authentication.
`beacon_api.utils.data_query`	Query DB and prepare data for response.

Permissions Addons¶

Permissions Module.

Module for getting permissions to datasets, more precisely CONTROLLED datasets. This module was designed to be addon based, where users of the beacon-python app can write their implementation for parsing a specific JWT token claim that contains CONTROLLED permissions to datasets.

Each file added in this module will consist of a function for parsing a permissions claim from a JWT token. Then this function MUST be added to utils.validate_jwt module in order to pass permissions when retrieving datasets from the database.

To avoid collisions check that your claim for permissions does not conflict with existing ones: https://www.iana.org/assignments/jwt/jwt.xhtml

beacon_api.permissions.ga4gh Parse permissions and statuses from ELIXIR token for GA4GH claim.

Configuration¶

Beacon Python Application Configuration.

beacon_api.conf.config DB Configuration.

Extensions¶

Extensions Module.

This module contains optional extensions to the Beacon Python Server. Currently we have two extensions:

handover - used to convey extra information regarding the Beacon service, or the dataset response;
mate fusion - used for finding breakend records.

`beacon_api.extensions.handover`	Prepare Handover.
`beacon_api.extensions.mate_name`	Prepare mate.

Index | Module Index