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
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 --output-file=- > requirements.txt
pip-compile dev-requirements.in --output-file=- > dev-requirements.txt
The direct dependencies are listed in requirements.in, dev-requirements.in input files.
Install dependencies
- by using
pip-syncfrompip-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
-
Create PyPI Account through the registration page.
Take note that PyPI requires email addresses to be verified before publishing.
-
Package the project for distribution.
python setup.py sdistTake note that
setup.pyis configured to build a distribution with namehca-ingest. -
Install Twine
pip install twine -
Upload the distribution package to PyPI.
twine upload dist/*Running
python setup.py sdistwill create a package in thedistdirectory 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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