refactor _get_observation_joinid into util function for reuse

cellxgene_schema_cli/cellxgene_schema/utils.py

@@ -1,11 +1,13 @@
 import logging
 import os
 import sys
+from base64 import b85encode
 from typing import List, Union
 
 import anndata as ad
 import numpy as np
 from scipy import sparse
+from xxhash import xxh3_64_intdigest
 
 logger = logging.getLogger(__name__)
 
@@ -144,3 +146,16 @@ def _enforce_canonical_format(df):
     if adata.raw:
         logger.info("enforce canonical format in raw.X")
         _enforce_canonical_format(adata.raw)
+
+
+def get_hash_digest_column(dataframe):
+    """
+    Get column with hash digest for each row in dataframe.
+    """
+
+    return (
+        dataframe.index.to_series()
+        .map(xxh3_64_intdigest)
+        .astype(np.uint64)
+        .apply(lambda v: b85encode(v.to_bytes(8, "big")).decode("ascii"))
+    )

cellxgene_schema_cli/cellxgene_schema/write_labels.py

@@ -1,17 +1,15 @@
 import logging
 import traceback
-from base64 import b85encode
 from typing import Dict, List, Optional
 
 import numpy as np
 import pandas as pd
-from xxhash import xxh3_64_intdigest
 
 from cellxgene_schema import ontology
 from cellxgene_schema.env import SCHEMA_REFERENCE_BASE_URL, SCHEMA_REFERENCE_FILE_NAME
 from cellxgene_schema.validate import ONTOLOGY_CHECKER, Validator
 
-from .utils import enforce_canonical_format, getattr_anndata
+from .utils import enforce_canonical_format, getattr_anndata, get_hash_digest_column
 
 logger = logging.getLogger(__name__)
 
@@ -361,7 +359,7 @@ def write_labels(self, add_labels_file: str):
 
         self.adata.uns["schema_version"] = self.validator.schema_version
         self.adata.uns["schema_reference"] = self._build_schema_reference_url(self.validator.schema_version)
-        self.adata.obs["observation_joinid"] = self._get_observation_joinid_column()
+        self.adata.obs["observation_joinid"] = get_hash_digest_column(self.adata.obs)
 
         enforce_canonical_format(self.adata)
 

cellxgene_schema_cli/tests/fixtures/examples_validate.py

@@ -3,9 +3,8 @@
 import numpy
 import anndata
 import os
-from base64 import b85encode
 from scipy import sparse
-from xxhash import xxh3_64_intdigest
+from cellxgene_schema.utils import get_hash_digest_column
 
 # -----------------------------------------------------------------#
 # General example information
@@ -120,12 +119,7 @@
     ],
 )
 
-obs_expected["observation_joinid"] = (
-    obs_expected.index.to_series()
-    .map(xxh3_64_intdigest)
-    .astype(numpy.uint64)
-    .apply(lambda v: b85encode(v.to_bytes(8, "big")).decode("ascii"))
-)
+obs_expected["observation_joinid"] = get_hash_digest_column(obs_expected)
 
 # ---
 # 2. Creating individual var components: valid object and valid object and with labels