This repository was part of HCA DCP/1 and is not maintained anymore. DCP/2 development of this component continues in the forked repository at https://github.com/ebi-ait/ingest-client.
This repository contains the hca-ingest Python package library which can be shared across ingest services.
pip install hca-ingest
To use the Ingest API interface in your python script
from 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
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 |
Requirements for this project are listed in 2 files: requirements.txt and requirements-dev.txt.
The requirements-dev.txt file contains dependencies specific for development, and needs to be
installed:
pip install -r requirements.txt
pip install -r requirements-dev.txt
Note: This package is currently only compatible with Python 3.
To run all the tests, use nose package:
nosetests
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.
-
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. This PyPI project is currently owned privately and may require access rights to change. Alternatively, the project name insetup.pycan be changed so that it can be built and uploaded to a different PyPI entry. -
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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