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A library to communicate with the Human Cell Atlas ingest API hosted by the EBI for creation and management of HCA project submissions.

Project description

PyPI

Ingest Client

This repository contains the hca-ingest Python package library which can be shared across ingest services.

Installation

pip install hca-ingest

Usage

API package

To use the Ingest API interface in your python script

from hca_ingest.api.ingestapi import IngestApi

Configure the ingest url to be used by setting the environment variable for INGEST_API

INGEST_API=http://localhost:8080

Schema template package

The schema template package provides convenient lookup of properties in the HCA JSON schema. Each property in the JSON schema is represented as a simple key that is prefixed with the schema name.

The first element is the short name for the schema followed by the property. e.g the key for the biomaterial_id property in the donor_organism schema is donor_organism.biomaterial_core.biomaterial_id.

The schema template provides access to attributes of each key that is useful for developing schema aware applications that need to query or generate JSON documents against the JSON schema.

Key Description Examples
{key}.schema.high_level_entity Tells you if the property is part of type, module or core schema donor_organism.biomaterial_core.schema.high_level_entity = core, donor_organism.schema.high_level_entity = type, donor_organism.medical_history.schema.high_level_entity = module
{key}.schema.domain_entity Tells you if the property is in a biomaterial, file, process, protocol, analysis or project schema donor_organism.schema.domain_entity = biomaterial, dissociation_protocol.schema.domain_entity = protocol, dissociation_protocol.schema.domain_entity = protocol, sequence_file.schema.domain_entity = File
{key}.schema.module Tells you the name of the schema where this property is defined donor_organism.schema.domain_entity = biomaterial, dissociation_protocol.schema.module = dissociation_protocol, dissociation_protocol.schema.module = dissociation_protocol, donor_organism.medical_history.schema.module = medical_history
{key}.schema.url Gives you the full URL to the schema where this property is defined donor_organism.medical_history.schema.url = https://schema.humancellatlas.org/module/biomaterial/5.1.0/medical_history
{key}.value_type Tells you the expected value stype for this property. Can be one of object, string, integer donor_organism.medical_history.medication.value_type = string, sequence_file.lane_index.value_type = integer, sequence_file.file_core.value_type = object
{key}.multivalue Tells you in the value is a single value or an array of values sequence_file.insdc_run.multivalue = True
{key}.user_friendly The user friendly name for the property sequence_file.insdc_run.multivalue = INSDC run
{key}.description A short description of the property sequence_file.insdc_run.multivalue = An INSDC (International Nucleotide Sequence Database Collaboration) run accession. Accession must start with DRR, ERR, or SRR.
{key}.format Tell you if the property has a specific format, like a date format project.contact.email.format = email
{key}.required Tells you if the property is required donor_organism.biomaterial_core.biomaterial_id.required = True
{key}.identifiable Tells you if the property is an identifiable field for the current entity donor_organism.biomaterial_core.biomaterial_id.identifiable = True, donor_organism.biomaterial_core.biomaterial_name.identifiable = False
{key}.external_reference Tells you if the property is globaly identifiable and therefore retrievable a retrievable object from ingest donor_organism.uuid.external_reference = True
{key}.example An example of the expected value for this property project.contact.contact_name.example = John,D,Doe

Developer Notes

This package is currently only compatible with Python 3.

Requirements

Requirements for this project are listed in 2 files: requirements.txt and dev-requirements.txt. The dev-requirements.txt file contains dependencies specific for development

The requirement files (requirements.txt, dev-requirements.txt) are generated using pip-compile from pip-tools

pip-compile requirements.in
pip-compile dev-requirements.in

The direct dependencies are listed in requirements.in, dev-requirements.in input files.

Install dependencies

  • by using pip-sync from pip-tools
pip-sync requirements.txt dev-requirements.txt
  • or by just using pip install
    pip install -r requirements.txt
    pip install -r dev-requirements.txt

Upgrade dependencies

To update all packages, periodically re-run pip-compile --upgrade

To update a specific package to the latest or a specific version use the --upgrade-package or -P flag:

pip-compile --upgrade-package requests

See more options in the pip-compile documentation .

Running the Tests

To run all the tests, use unittest package:

python -m unittest 

Developing Code in Editable Mode

Using pip's editable mode, client projects can refer to the latest code in this repository directly without installing it through PyPI. This can be done either by manually cloning the code base:

pip install -e path/to/ingest-client

or by having pip do it automatically by providing a reference to this repository:

pip install -e \
git+https://github.com/HumanCellAtlas/ingest-client.git\
#egg=hca_ingest

For more information on version control support with pip, refer to the VCS support documentation.

Publish to PyPI

  1. Create PyPI Account through the registration page.

    Take note that PyPI requires email addresses to be verified before publishing.

  2. Package the project for distribution.

     python setup.py sdist
    

    Take note that setup.py is configured to build a distribution with name hca-ingest.

  3. Install Twine

     pip install twine        
    
  4. Upload the distribution package to PyPI.

     twine upload dist/*
    

    Running python setup.py sdist will create a package in the dist directory of the project base directory. Specific packages can be chosen if preferred instead of the wildcard *:

     twine upload dist/hca_ingest-0.1a0.tar.gz
    

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