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https://github.com/chanzuckerberg/cellxgene.git
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59f989d26f
* initial support for corpora schema conventions * remove debugging print * add corpora util module * tests * lint * PR review edits * PR changes * more PR changes * more PR chnages * PR fixes * formatting * PR updates * lint * PR review
91 lines
3.2 KiB
Python
91 lines
3.2 KiB
Python
"""
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Corpora schema conventions support. Helper functions for reading.
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https://github.com/chanzuckerberg/corpora-data-portal/blob/main/backend/schema/corpora_schema.md
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https://github.com/chanzuckerberg/corpora-data-portal/blob/main/backend/schema/corpora_schema_h5ad_implementation.md
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"""
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import collections
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import json
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from server.cli.upgrade import validate_version_str
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def corpora_get_versions_from_anndata(adata):
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"""
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Given an AnnData object, return:
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* None - if not a Corpora object
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* [ corpora_schema_version, corpora_encoding_version ] - if a Corpora object
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Implements the identification protocol defined in the specification.
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"""
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# per Corpora AnnData spec, this is a corpora file if the following is true
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if "version" not in adata.uns_keys():
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return None
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version = adata.uns["version"]
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if not isinstance(version, collections.abc.Mapping) or "corpora_schema_version" not in version:
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return None
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corpora_schema_version = version.get("corpora_schema_version")
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corpora_encoding_version = version.get("corpora_encoding_version")
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# TODO: spec says these must be SEMVER values, so check.
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if validate_version_str(corpora_schema_version) and validate_version_str(corpora_encoding_version):
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return [corpora_schema_version, corpora_encoding_version]
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def corpora_is_version_supported(corpora_schema_version, corpora_encoding_version):
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return (
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corpora_schema_version
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and corpora_encoding_version
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and corpora_schema_version.startswith("1.")
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and corpora_encoding_version.startswith("0.1.")
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)
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def corpora_get_props_from_anndata(adata):
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"""
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Get Corpora dataset properties from an AnnData
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"""
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versions = corpora_get_versions_from_anndata(adata)
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if versions is None:
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return None
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[corpora_schema_version, corpora_encoding_version] = versions
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version_is_supported = corpora_is_version_supported(corpora_schema_version, corpora_encoding_version)
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if not version_is_supported:
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raise ValueError("Unsupported Corpora schema version")
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required_simple_fields = [
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"version",
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"title",
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"layer_descriptions",
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"organism",
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"organism_ontology_term_id",
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"project_name",
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"project_description",
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]
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# Spec says some values encoded as JSON due to the inability of AnnData to store complex types.
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required_json_fields = ["contributors", "project_links"]
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optional_simple_fields = ["preprint_doi", "publication_doi", "default_embedding", "default_field", "tags"]
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corpora_props = {}
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for key in required_simple_fields:
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if key not in adata.uns:
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raise KeyError(f"missing Corpora schema field {key}")
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corpora_props[key] = adata.uns[key]
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for key in required_json_fields:
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if key not in adata.uns:
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raise KeyError(f"missing Corpora schema field {key}")
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try:
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corpora_props[key] = json.loads(adata.uns[key])
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except json.JSONDecodeError:
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raise json.JSONDecodeError(f"Corpora schema field {key} is expected to be a valid JSON string")
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for key in optional_simple_fields:
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if key in adata.uns:
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corpora_props[key] = adata.uns[key]
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return corpora_props
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