hubmap-commons

commons

This repository contains the code supporting several HuBMAP restful microservices.

Getting Started

The hubmap commons library is available through PyPi via the command:

pip install hubmap-commons

The hubmap-commons requirements can be found here

Contents

The code includes:

• activity.py (deprecated) creates Cyhper statements for creating and getting HuBMAP Activitiy node types

• autherror.py a class to handle authentiation errors

• entity.py(deprecated) a base class that executes many Cypher queries against Neo4j to return information about the HuBMAP Entity nodes

• file_helper.py contains methods to execute files and parse files

• globus_file_helper.py contains methods for creating Globus directories

• hm_auth.py contains several methods and classes relating to system security

• hubmap_const.py a file that maintains the names and strings used in the code and the Neo4j system

• neo4j_connection.py(deprecated) provides connections to Neo4j and some generic Cypher statements (e.g. CREATE and UPDATE)

• neo4j_driver.py creates a neo4j.Driver singleton instance

• provenance.py(deprecated) extracts provenance related information from a token

• schema_tools.py checks a JSON structure vs a schema definition using two main methods.

  • check_json_matches_schema(jsondata, schema_filename: str, base_path: str = "", base_uri: str = "") Checks the given json data against the jsonschema in the given schema file, raising an exception on error. The exception text includes one or more validation error messages.
  • assert_json_matches_schema(jsondata, schema_filename: str, base_path: str = "", base_uri: str = "") Raises AssertionError if the schema in schema_filename is invalid, or if the given jsondata does not match the schema.

• stirng_helper.py contains several string related functions (listToCommaSeparated, getYesNo, etc.)

• test_ws.py contains a test Web Service. This service can be run by copying hubmap_commons/common_app.conf.example to hubmap_commons/common_app.conf and providing a Globus client id and secret (available at https://developers.globus.org) then directly running test_ws.py from the hubmap_commons/ directory. The service has a useful /login method that can be used to generate Globus auth tokens for testing. Note: For much of HuBMAP a Globus "nexus" token used to access the globus Nexus APIs. To generate a nexus token the Client ID must be authorized for this. Client IDs are available from the developers of this repository to generate nexus tokens for use against HuBMAP APIs.

• uuid_generator.py(deprecated) this is a wrapper for calls to the /hmuuid Web Service

• type_cliet.py(deprecated and removed) provides a singleton client for retrieving information about different assay types