mirror of
https://github.com/chanzuckerberg/cellxgene.git
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fb61bd6e9c
This splits the backend into two parts: the local backend for desktop cellxgene and the AWS backend for hosted cellxgene. The local backend is in local_server while the hosted remains in server. The general idea is to copy everything from server to local_server, pull unneeded stuff out of local_server, and keep server as-is for this PR. Not touching server means all the infra and deployment code will continue working just as it did before so we can make those changes incrementally.
79 lines
2.9 KiB
Python
79 lines
2.9 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 local_server.cli.upgrade import validate_version_str
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from local_server.common.utils.corpora_constants import CorporaConstants
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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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corpora_props = {}
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for key in CorporaConstants.REQUIRED_SIMPLE_METADATA_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 CorporaConstants.OPTIONAL_JSON_ENCODED_METADATA_FIELD:
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if key not in adata.uns:
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continue
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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 CorporaConstants.OPTIONAL_SIMPLE_METADATA_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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