Improve metadata validation

sc2ts/cli.py

@@ -636,9 +636,26 @@ def extend(
     help="Validate metadata",
     show_default=True,
 )
+@click.option(
+    "-s",
+    "--skip",
+    default=[],
+    help="Skip this metadata field during comparison",
+    show_default=True,
+    multiple=True,
+)
 @chunk_cache_size
 @verbose
-def validate(dataset, ts_file, deletions_as_missing, genotypes, metadata, chunk_cache_size, verbose):
+def validate(
+    dataset,
+    ts_file,
+    deletions_as_missing,
+    genotypes,
+    metadata,
+    skip,
+    chunk_cache_size,
+    verbose,
+):
     """
     Check that the specified trees correctly encode data
     """
@@ -649,7 +666,7 @@ def validate(dataset, ts_file, deletions_as_missing, genotypes, metadata, chunk_
     if genotypes:
         sc2ts.validate_genotypes(ts, ds, deletions_as_missing, show_progress=True)
     if metadata:
-        sc2ts.validate_metadata(ts, ds, show_progress=True)
+        sc2ts.validate_metadata(ts, ds, skip_fields=set(skip), show_progress=True)
 
 
 # @click.command()

sc2ts/validation.py

@@ -1,4 +1,5 @@
 import logging
+import unittest
 
 import numpy as np
 import numpy.testing as nt
@@ -30,15 +31,17 @@ def validate_genotypes(ts, dataset, deletions_as_missing=False, show_progress=Fa
     bar.close()
 
 
-def validate_metadata(ts, dataset, show_progress=False):
+def validate_metadata(ts, dataset, show_progress=False, skip_fields=set()):
 
     samples = ts.samples()[1:]
     bar = tqdm.tqdm(samples, desc="Metadata", disable=not show_progress)
     for u in bar:
         md1 = ts.node(u).metadata
-        del md1["sc2ts"]
+        keys = set(md1.keys()) - ({"sc2ts"} | skip_fields)
         md2 = dataset.metadata[md1["strain"]]
-        assert md1 == md2
+        md1 = {k: md1[k] for k in keys}
+        md2 = {k: md2[k] for k in keys}
+        unittest.TestCase().assertDictEqual(md1, md2)
 
 
 def validate(ts, dataset, deletions_as_missing=False, show_progress=False):