igvf-async-client

Unless you have a specific need for an async Python client, you are probably looking for the synchronous IGVF Python 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: 101.2.0
• Package version: 101.2.0
• Generator version: 7.8.0
• Build package: org.openapitools.codegen.languages.PythonClientCodegen

Requirements.

Python 3.9+

Installation & Usage

Pip install:

$ pip install igvf-async-client

Or clone the repo and and install:

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

Then import the package:

$ python -m asyncio
>>> import igvf_async_client

Examples

(Must use an async runtime, e.g. $ python -m asyncio.)

from igvf_async_client import AsyncIgvfApi

api = AsyncIgvfApi()

# Search for Software that matches query `abc`.
r = await 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 = await api.get_by_id(software_item.lab)

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

See other examples in async_example.ipynb and test_endpoint.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
AsyncIgvfApi	search	GET /search	Search for items on the IGVF Data Portal.
AsyncIgvfApi	schemas	GET /profiles	Retrieve JSON schemas for all item types
AsyncIgvfApi	schema_for_item_type	GET /profiles/{item_type}	Retrieve JSON schema for item type
AsyncIgvfApi	report	GET /multireport.tsv	Generate a TSV file report based on search query. All results are returned.
AsyncIgvfApi	get_by_id	GET /{resource_id}	Get item information
AsyncIgvfApi	download	GET /{file_id}/@@download	Download file.
AsyncIgvfApi	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
AsyncIgvfApi	access_keys	GET /access-keys/@@listing	List items in the AccessKey collection.
AsyncIgvfApi	alignment_files	GET /alignment-files/@@listing	List items in the AlignmentFile collection.
AsyncIgvfApi	analysis_sets	GET /analysis-sets/@@listing	List items in the AnalysisSet collection.
AsyncIgvfApi	analysis_step_versions	GET /analysis-step-versions/@@listing	List items in the AnalysisStepVersion collection.
AsyncIgvfApi	analysis_steps	GET /analysis-steps/@@listing	List items in the AnalysisStep collection.
AsyncIgvfApi	assay_terms	GET /assay-terms/@@listing	List items in the AssayTerm collection.
AsyncIgvfApi	auxiliary_sets	GET /auxiliary-sets/@@listing	List items in the AuxiliarySet collection.
AsyncIgvfApi	awards	GET /awards/@@listing	List items in the Award collection.
AsyncIgvfApi	biomarkers	GET /biomarkers/@@listing	List items in the Biomarker collection.
AsyncIgvfApi	configuration_files	GET /configuration-files/@@listing	List items in the ConfigurationFile collection.
AsyncIgvfApi	construct_library_sets	GET /construct-library-sets/@@listing	List items in the ConstructLibrarySet collection.
AsyncIgvfApi	crispr_modifications	GET /crispr-modifications/@@listing	List items in the CrisprModification collection.
AsyncIgvfApi	curated_sets	GET /curated-sets/@@listing	List items in the CuratedSet collection.
AsyncIgvfApi	degron_modifications	GET /degron-modifications/@@listing	List items in the DegronModification collection.
AsyncIgvfApi	documents	GET /documents/@@listing	List items in the Document collection.
AsyncIgvfApi	genes	GET /genes/@@listing	List items in the Gene collection.
AsyncIgvfApi	human_donors	GET /human-donors/@@listing	List items in the HumanDonor collection.
AsyncIgvfApi	image_files	GET /image-files/@@listing	List items in the ImageFile collection.
AsyncIgvfApi	images	GET /images/@@listing	List items in the Image collection.
AsyncIgvfApi	in_vitro_systems	GET /in-vitro-systems/@@listing	List items in the InVitroSystem collection.
AsyncIgvfApi	index_files	GET /index-files/@@listing	List items in the IndexFile collection.
AsyncIgvfApi	institutional_certificates	GET /institutional-certificates/@@listing	List items in the InstitutionalCertificate collection.
AsyncIgvfApi	labs	GET /labs/@@listing	List items in the Lab collection.
AsyncIgvfApi	matrix_files	GET /matrix-files/@@listing	List items in the MatrixFile collection.
AsyncIgvfApi	measurement_sets	GET /measurement-sets/@@listing	List items in the MeasurementSet collection.
AsyncIgvfApi	model_files	GET /model-files/@@listing	List items in the ModelFile collection.
AsyncIgvfApi	model_sets	GET /model-sets/@@listing	List items in the ModelSet collection.
AsyncIgvfApi	mpra_quality_metrics	GET /mpra-quality-metrics/@@listing	List items in the MpraQualityMetric collection.
AsyncIgvfApi	multiplexed_samples	GET /multiplexed-samples/@@listing	List items in the MultiplexedSample collection.
AsyncIgvfApi	open_reading_frames	GET /open-reading-frames/@@listing	List items in the OpenReadingFrame collection.
AsyncIgvfApi	pages	GET /pages/@@listing	List items in the Page collection.
AsyncIgvfApi	perturb_seq_quality_metrics	GET /perturb-seq-quality-metrics/@@listing	List items in the PerturbSeqQualityMetric collection.
AsyncIgvfApi	phenotype_terms	GET /phenotype-terms/@@listing	List items in the PhenotypeTerm collection.
AsyncIgvfApi	phenotypic_features	GET /phenotypic-features/@@listing	List items in the PhenotypicFeature collection.
AsyncIgvfApi	platform_terms	GET /platform-terms/@@listing	List items in the PlatformTerm collection.
AsyncIgvfApi	prediction_sets	GET /prediction-sets/@@listing	List items in the PredictionSet collection.
AsyncIgvfApi	primary_cells	GET /primary-cells/@@listing	List items in the PrimaryCell collection.
AsyncIgvfApi	publications	GET /publications/@@listing	List items in the Publication collection.
AsyncIgvfApi	reference_files	GET /reference-files/@@listing	List items in the ReferenceFile collection.
AsyncIgvfApi	rodent_donors	GET /rodent-donors/@@listing	List items in the RodentDonor collection.
AsyncIgvfApi	sample_terms	GET /sample-terms/@@listing	List items in the SampleTerm collection.
AsyncIgvfApi	sequence_files	GET /sequence-files/@@listing	List items in the SequenceFile collection.
AsyncIgvfApi	signal_files	GET /signal-files/@@listing	List items in the SignalFile collection.
AsyncIgvfApi	single_cell_atac_seq_quality_metrics	GET /single-cell-atac-seq-quality-metrics/@@listing	List items in the SingleCellAtacSeqQualityMetric collection.
AsyncIgvfApi	single_cell_rna_seq_quality_metrics	GET /single-cell-rna-seq-quality-metrics/@@listing	List items in the SingleCellRnaSeqQualityMetric collection.
AsyncIgvfApi	software	GET /software/@@listing	List items in the Software collection.
AsyncIgvfApi	software_versions	GET /software-versions/@@listing	List items in the SoftwareVersion collection.
AsyncIgvfApi	sources	GET /sources/@@listing	List items in the Source collection.
AsyncIgvfApi	starr_seq_quality_metrics	GET /starr-seq-quality-metrics/@@listing	List items in the StarrSeqQualityMetric collection.
AsyncIgvfApi	tabular_files	GET /tabular-files/@@listing	List items in the TabularFile collection.
AsyncIgvfApi	technical_samples	GET /technical-samples/@@listing	List items in the TechnicalSample collection.
AsyncIgvfApi	tissues	GET /tissues/@@listing	List items in the Tissue collection.
AsyncIgvfApi	treatments	GET /treatments/@@listing	List items in the Treatment collection.
AsyncIgvfApi	users	GET /users/@@listing	List items in the User collection.
AsyncIgvfApi	whole_organisms	GET /whole-organisms/@@listing	List items in the WholeOrganism collection.
AsyncIgvfApi	workflows	GET /workflows/@@listing	List items in the Workflow collection.

Documentation for Models

• ATACBamSummaryStats
• ATACFragmentSummaryStats
• ATACFragmentsAlignmentStats
• AccessKey
• AccessKeyResults
• AlignmentFile
• AlignmentFileResults
• AnalysisSet
• AnalysisSetResults
• AnalysisStep
• AnalysisStepResults
• AnalysisStepVersion
• AnalysisStepVersionResults
• AssayTerm
• AssayTermResults
• Attachment
• Attachment1
• AuxiliarySet
• AuxiliarySetResults
• Award
• AwardResults
• Biomarker
• BiomarkerResults
• ConfigurationFile
• ConfigurationFileResults
• ConstructLibrarySet
• ConstructLibrarySetResults
• CrisprModification
• CrisprModificationResults
• CuratedSet
• CuratedSetResults
• DegronModification
• DegronModificationResults
• Document
• DocumentResults
• Gene
• GeneLocation
• GeneLocation1
• GeneResults
• HumanDonor
• HumanDonorResults
• Image
• ImageFile
• ImageFileResults
• ImageResults
• InVitroSystem
• InVitroSystemResults
• IndexFile
• IndexFileResults
• InstitutionalCertificate
• InstitutionalCertificateResults
• Item
• ItemType
• Lab
• LabResults
• Limit
• Locus
• Locus1
• MatrixFile
• MatrixFileResults
• MeasurementSet
• MeasurementSetResults
• ModelFile
• ModelFileResults
• ModelSet
• ModelSetResults
• MpraQualityMetric
• MpraQualityMetricResults
• MultiplexedSample
• MultiplexedSampleResults
• NoResultsResponse
• NoResultsResponseColumnsValue
• NoResultsResponseFacetGroupsInner
• NoResultsResponseFacetsInner
• NoResultsResponseFiltersInner
• NoResultsResponseSortValue
• OpenReadingFrame
• OpenReadingFrameResults
• Page
• PageLayout
• PageLayoutComponents
• PageResults
• PerturbSeqQualityMetric
• PerturbSeqQualityMetricResults
• PhenotypeTerm
• PhenotypeTermResults
• PhenotypicFeature
• PhenotypicFeatureResults
• PlatformTerm
• PlatformTermResults
• PredictionSet
• PredictionSetResults
• PrimaryCell
• PrimaryCellResults
• Publication
• PublicationResults
• RNASeqKBInfo
• ReferenceFile
• ReferenceFileResults
• RelatedDonor
• RodentDonor
• RodentDonorResults
• SampleTerm
• SampleTermResults
• SearchFacet
• SearchResultItem
• SearchResults
• SequenceFile
• SequenceFileResults
• SignalFile
• SignalFileResults
• SingleCellAtacSeqQualityMetric
• SingleCellAtacSeqQualityMetricResults
• SingleCellRnaSeqQualityMetric
• SingleCellRnaSeqQualityMetricResults
• Software
• SoftwareResults
• SoftwareVersion
• SoftwareVersionResults
• Source
• SourceResults
• StarrSeqQualityMetric
• StarrSeqQualityMetricResults
• TabularFile
• TabularFileResults
• TechnicalSample
• TechnicalSampleResults
• Tile
• Tissue
• TissueResults
• Treatment
• TreatmentResults
• User
• UserResults
• WholeOrganism
• WholeOrganismResults
• Workflow
• WorkflowResults

Documentation For Authorization

Authentication schemes defined for the API:

basicAuth

• Type: HTTP basic authentication

Author

Optional authorization

import os

from igvf_async_client import Configuration
from igvf_async_client import ApiClient
from igvf_async_client import AsyncIgvfApi

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

client = ApiClient(config)

api = AsyncIgvfApi(client)