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:
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activity.py(deprecated) creates Cyhper statements for creating and getting HuBMAP Activitiy node types -
autherror.py a class to handle authentiation errors
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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
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globus_file_helper.py contains methods for creating Globus directories
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hm_auth.py contains several methods and classes relating to system security
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hubmap_const.py a file that maintains the names and strings used in the code and the Neo4j system
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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
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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.
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stirng_helper.py contains several string related functions (listToCommaSeparated, getYesNo, etc.)
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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.
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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
1 maintainer
Metadata
1 maintainer
Release files for hubmap-commons 2.1.26
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| hubmap_commons-2.1.26-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 133.1 kB
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