igvf-client

The Python client is autogenerated based on this IGVF OpenAPI specification, which exposes search, collection, and other read endpoints from the IGVF Data Portal.

Note while the API endpoints are relatively stable, the underlying data model is still evolving, and changing fields/types can cause breaking changes. The latest version of the client reflects the latest version of the schema used by the API.

API version: 54.0.1
Package version: 54.0.1
Generator version: 7.7.0
Build package: org.openapitools.codegen.languages.PythonClientCodegen

Requirements.

Python 3.9+

Installation & Usage

Pip install:

$ pip install igvf-client

Or clone the repo and and install:

$ git clone https://github.com/IGVF-DACC/igvf-python-client
$ cd igvf-python-client
$ pip install -e .

Then import the package:

$ python
>>> import igvf_client

Examples

from igvf_client import IgvfApi

api = IgvfApi()

# Search for Software that matches query `abc`.
r = api.search(query='abc', type=['Software'])

# Print total number of results and list of results in `@graph`.
print(r.total)
print(r.graph)

# Pull first item, unwrap to underlying Software item with `actual_instance`.
software_item = r.graph[0].actual_instance

# Print Software item and specific fields.
print(software_item)
print(software_item.id)
print(software_item.description)

# Get the Lab item based on the lab @id in the Software item.
lab = api.get_by_id(software_item.lab)

# Print lab and specific field.
print(lab)
print(lab.title)

Optional authorization

You can make authenticated requests (e.g. to view unreleased data) if you pass the access key/secret key associated with your user when instantiating the client.

from igvf_client import Configuration
from igvf_client import ApiClient
from igvf_client import IgvfApi

config = Configuration(
    access_key = os.environ["IGVF_ACCESS_KEY"],
    secret_access_key = os.environ["IGVF_SECRET_ACCESS_KEY"]
)

client = ApiClient(config)

api = IgvfApi(client)

api.sequence_files(status=['in progress']).total # 8878

More examples

See other examples in examples.ipynb and test_endpoints.py

Refer to the documentation for a full specification of endpoint inputs and outputs and model fields.

Documentation for API Endpoints

General Endpoints

All URIs are relative to https://api.data.igvf.org

Class	Method	HTTP request	Description
IgvfApi	get_by_id	GET /{resource_id}	Get item information
IgvfApi	search	GET /search	Search for items on the IGVF Data Portal.
IgvfApi	schemas	GET /profiles	Retrieve JSON schemas for all item types
IgvfApi	schema_for_item_type	GET /profiles/{item_type}	Retrieve JSON schema for item type
IgvfApi	report	GET /multireport.tsv	Generate a TSV file report based on search query. All results are returned.
IgvfApi	download	GET /{file_id}/@@download	Download file.
IgvfApi	batch_download	GET /batch-download	List files to download based on search query. All results are returned.

Collection Endpoints

All URIs are relative to https://api.data.igvf.org

Class	Method	HTTP request	Description
IgvfApi	access_keys	GET /access-keys/@@listing	List items in the AccessKey collection.
IgvfApi	alignment_files	GET /alignment-files/@@listing	List items in the AlignmentFile collection.
IgvfApi	analysis_sets	GET /analysis-sets/@@listing	List items in the AnalysisSet collection.
IgvfApi	analysis_step_versions	GET /analysis-step-versions/@@listing	List items in the AnalysisStepVersion collection.
IgvfApi	analysis_steps	GET /analysis-steps/@@listing	List items in the AnalysisStep collection.
IgvfApi	assay_terms	GET /assay-terms/@@listing	List items in the AssayTerm collection.
IgvfApi	auxiliary_sets	GET /auxiliary-sets/@@listing	List items in the AuxiliarySet collection.
IgvfApi	awards	GET /awards/@@listing	List items in the Award collection.
IgvfApi	biomarkers	GET /biomarkers/@@listing	List items in the Biomarker collection.
IgvfApi	configuration_files	GET /configuration-files/@@listing	List items in the ConfigurationFile collection.
IgvfApi	construct_library_sets	GET /construct-library-sets/@@listing	List items in the ConstructLibrarySet collection.
IgvfApi	crispr_modifications	GET /crispr-modifications/@@listing	List items in the CrisprModification collection.
IgvfApi	curated_sets	GET /curated-sets/@@listing	List items in the CuratedSet collection.
IgvfApi	degron_modifications	GET /degron-modifications/@@listing	List items in the DegronModification collection.
IgvfApi	documents	GET /documents/@@listing	List items in the Document collection.
IgvfApi	genes	GET /genes/@@listing	List items in the Gene collection.
IgvfApi	genome_browser_annotation_files	GET /genome-browser-annotation-files/@@listing	List items in the GenomeBrowserAnnotationFile collection.
IgvfApi	human_donors	GET /human-donors/@@listing	List items in the HumanDonor collection.
IgvfApi	image_files	GET /image-files/@@listing	List items in the ImageFile collection.
IgvfApi	images	GET /images/@@listing	List items in the Image collection.
IgvfApi	in_vitro_systems	GET /in-vitro-systems/@@listing	List items in the InVitroSystem collection.
IgvfApi	institutional_certificates	GET /institutional-certificates/@@listing	List items in the InstitutionalCertificate collection.
IgvfApi	labs	GET /labs/@@listing	List items in the Lab collection.
IgvfApi	matrix_files	GET /matrix-files/@@listing	List items in the MatrixFile collection.
IgvfApi	measurement_sets	GET /measurement-sets/@@listing	List items in the MeasurementSet collection.
IgvfApi	model_files	GET /model-files/@@listing	List items in the ModelFile collection.
IgvfApi	model_sets	GET /model-sets/@@listing	List items in the ModelSet collection.
IgvfApi	multiplexed_samples	GET /multiplexed-samples/@@listing	List items in the MultiplexedSample collection.
IgvfApi	open_reading_frames	GET /open-reading-frames/@@listing	List items in the OpenReadingFrame collection.
IgvfApi	pages	GET /pages/@@listing	List items in the Page collection.
IgvfApi	phenotype_terms	GET /phenotype-terms/@@listing	List items in the PhenotypeTerm collection.
IgvfApi	phenotypic_features	GET /phenotypic-features/@@listing	List items in the PhenotypicFeature collection.
IgvfApi	platform_terms	GET /platform-terms/@@listing	List items in the PlatformTerm collection.
IgvfApi	prediction_sets	GET /prediction-sets/@@listing	List items in the PredictionSet collection.
IgvfApi	primary_cells	GET /primary-cells/@@listing	List items in the PrimaryCell collection.
IgvfApi	publications	GET /publications/@@listing	List items in the Publication collection.
IgvfApi	reference_files	GET /reference-files/@@listing	List items in the ReferenceFile collection.
IgvfApi	rodent_donors	GET /rodent-donors/@@listing	List items in the RodentDonor collection.
IgvfApi	sample_terms	GET /sample-terms/@@listing	List items in the SampleTerm collection.
IgvfApi	sequence_files	GET /sequence-files/@@listing	List items in the SequenceFile collection.
IgvfApi	signal_files	GET /signal-files/@@listing	List items in the SignalFile collection.
IgvfApi	software	GET /software/@@listing	List items in the Software collection.
IgvfApi	software_versions	GET /software-versions/@@listing	List items in the SoftwareVersion collection.
IgvfApi	sources	GET /sources/@@listing	List items in the Source collection.
IgvfApi	tabular_files	GET /tabular-files/@@listing	List items in the TabularFile collection.
IgvfApi	technical_samples	GET /technical-samples/@@listing	List items in the TechnicalSample collection.
IgvfApi	tissues	GET /tissues/@@listing	List items in the Tissue collection.
IgvfApi	treatments	GET /treatments/@@listing	List items in the Treatment collection.
IgvfApi	users	GET /users/@@listing	List items in the User collection.
IgvfApi	whole_organisms	GET /whole-organisms/@@listing	List items in the WholeOrganism collection.
IgvfApi	workflows	GET /workflows/@@listing	List items in the Workflow collection.

Documentation for Models

About

Autogenerated Python client for the IGVF API

MIT License

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