Add schema subcommand (#1939)

Add the `cellxgene schema apply` and `cellxgene schema validate` subcommands. The first takes an h5ad file and a yaml with config information and produces a new h5ad that follows the cellxgene data integration schema. The second takes an h5ad and checks if it follows the schema version written into its metadata. Both are currently marked as "experimental" as the primary intended users are still at CZI.
2026-10-09 19:00:56 +08:00 · 2020-11-02 08:26:37 -08:00
parent b9e132a00c
commit 78176f9711
20 changed files with 2224 additions and 0 deletions
@@ -0,0 +1,56 @@
+import os
+import unittest
+
+import pandas as pd
+
+from server.test import FIXTURES_ROOT
+from server.converters.schema import gene_symbol
+
+
+class TestHGNCSymbolChecker(unittest.TestCase):
+
+    def setUp(self):
+        self.test_hgnc_path = os.path.join(FIXTURES_ROOT, "hgnc_example.txt.gz")
+        self.hgnc_checker = gene_symbol.HGNCSymbolChecker.from_hgnc_records(self.test_hgnc_path)
+
+    def test_symbol_upgrade(self):
+        self.assertEqual(self.hgnc_checker.upgrade_symbol("SEPT1"), "SEPTIN1")
+        self.assertEqual(self.hgnc_checker.upgrade_symbol("ADRB2R"), "ADRB2")
+        self.assertEqual(self.hgnc_checker.upgrade_symbol("BAR"), "ADRB2")
+        self.assertEqual(self.hgnc_checker.upgrade_symbol("sept1"), "SEPTIN1")
+        self.assertEqual(self.hgnc_checker.upgrade_symbol("AdRb2R"), "ADRB2")
+        self.assertEqual(self.hgnc_checker.upgrade_symbol("bar"), "ADRB2")
+
+        # Strip off seurat endings when appropriate
+        self.assertEqual(self.hgnc_checker.upgrade_symbol("SEPT1.1"), "SEPTIN1")
+        self.assertEqual(self.hgnc_checker.upgrade_symbol("ADRB2-1"), "ADRB2")
+
+        # DIFF6 is ambiguous so don't upgrade it
+        self.assertEqual(self.hgnc_checker.upgrade_symbol("DIFF6"), "DIFF6")
+        self.assertEqual(self.hgnc_checker.upgrade_symbol("diff6"), "diff6")
+
+        # ARG1 is approved
+        self.assertEqual(self.hgnc_checker.upgrade_symbol("ARG1"), "ARG1")
+        self.assertEqual(self.hgnc_checker.upgrade_symbol("arg1"), "ARG1")
+
+        # HAP1 is both approved and withdrawn
+        self.assertEqual(self.hgnc_checker.upgrade_symbol("HAP1"), "HAP1")
+        self.assertEqual(self.hgnc_checker.upgrade_symbol("hap1"), "HAP1")
+
+        # Leave unknown symbols alone
+        self.assertEqual(self.hgnc_checker.upgrade_symbol("NOTASYMBOL"), "NOTASYMBOL")
+        self.assertEqual(self.hgnc_checker.upgrade_symbol("notasymbol"), "notasymbol")
+
+    def test_check_symbol(self):
+        self.assertEqual(self.hgnc_checker.check_symbol("SEPT1"), gene_symbol.SymbolStatus.UPGRADABLE)
+        self.assertEqual(self.hgnc_checker.check_symbol("DIFF6"), gene_symbol.SymbolStatus.AMBIGUOUS)
+        self.assertEqual(self.hgnc_checker.check_symbol("NOTASYMBOL"), gene_symbol.SymbolStatus.UNKNOWN)
+
+        # HAP1 is one of the approved and withdrawn symbols
+        self.assertEqual(self.hgnc_checker.check_symbol("HAP1"), gene_symbol.SymbolStatus.APPROVED)
+
+    def test_upgrade_index(self):
+        index = pd.Index(["SEPT1", "DIFF6", "NOTASYMBOL", "bar", "SEPTIN1"])
+        var_df = pd.DataFrame([[0] * len(index)], index=index)
+        upgraded_index = gene_symbol.get_upgraded_var_index(var_df, hgnc_path=self.test_hgnc_path)
+        self.assertEqual(upgraded_index.tolist(), ["SEPTIN1", "DIFF6", "NOTASYMBOL", "ADRB2", "SEPTIN1"])