Split out the local backend (#2052)

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.
2026-10-03 08:38:12 +08:00 · 2021-02-18 12:58:22 -08:00
parent 036b5f8c0f
commit fb61bd6e9c
153 changed files with 14027 additions and 46 deletions
@@ -0,0 +1,78 @@
+"""
+Corpora schema conventions support.  Helper functions for reading.
+
+https://github.com/chanzuckerberg/corpora-data-portal/blob/main/backend/schema/corpora_schema.md
+
+https://github.com/chanzuckerberg/corpora-data-portal/blob/main/backend/schema/corpora_schema_h5ad_implementation.md
+"""
+import collections
+import json
+
+from local_server.cli.upgrade import validate_version_str
+from local_server.common.utils.corpora_constants import CorporaConstants
+
+
+def corpora_get_versions_from_anndata(adata):
+    """
+    Given an AnnData object, return:
+        * None - if not a Corpora object
+        * [ corpora_schema_version, corpora_encoding_version ] - if a Corpora object
+
+    Implements the identification protocol defined in the specification.
+    """
+
+    # per Corpora AnnData spec, this is a corpora file if the following is true
+    if "version" not in adata.uns_keys():
+        return None
+    version = adata.uns["version"]
+    if not isinstance(version, collections.abc.Mapping) or "corpora_schema_version" not in version:
+        return None
+
+    corpora_schema_version = version.get("corpora_schema_version")
+    corpora_encoding_version = version.get("corpora_encoding_version")
+
+    # TODO: spec says these must be SEMVER values, so check.
+    if validate_version_str(corpora_schema_version) and validate_version_str(corpora_encoding_version):
+        return [corpora_schema_version, corpora_encoding_version]
+
+
+def corpora_is_version_supported(corpora_schema_version, corpora_encoding_version):
+    return (
+        corpora_schema_version
+        and corpora_encoding_version
+        and corpora_schema_version.startswith("1.")
+        and corpora_encoding_version.startswith("0.1.")
+    )
+
+
+def corpora_get_props_from_anndata(adata):
+    """
+    Get Corpora dataset properties from an AnnData
+    """
+    versions = corpora_get_versions_from_anndata(adata)
+    if versions is None:
+        return None
+    [corpora_schema_version, corpora_encoding_version] = versions
+    version_is_supported = corpora_is_version_supported(corpora_schema_version, corpora_encoding_version)
+    if not version_is_supported:
+        raise ValueError("Unsupported Corpora schema version")
+
+    corpora_props = {}
+    for key in CorporaConstants.REQUIRED_SIMPLE_METADATA_FIELDS:
+        if key not in adata.uns:
+            raise KeyError(f"missing Corpora schema field {key}")
+        corpora_props[key] = adata.uns[key]
+
+    for key in CorporaConstants.OPTIONAL_JSON_ENCODED_METADATA_FIELD:
+        if key not in adata.uns:
+            continue
+        try:
+            corpora_props[key] = json.loads(adata.uns[key])
+        except json.JSONDecodeError:
+            raise json.JSONDecodeError(f"Corpora schema field {key} is expected to be a valid JSON string")
+
+    for key in CorporaConstants.OPTIONAL_SIMPLE_METADATA_FIELDS:
+        if key in adata.uns:
+            corpora_props[key] = adata.uns[key]
+
+    return corpora_props