bugfix allow fields with periods in name (#1033)

Author: bpblanken

v03_pipeline/lib/misc/nested_field.py

@@ -2,9 +2,11 @@
 
 
 def parse_nested_field(t: hl.MatrixTable | hl.Table, fields: str):
-    # Grab the field and continually select it from the hail table.
     expression = t
-    for field in fields.split('.'):
+    # Behavior here allows only a single nested field.
+    # Additional nesting is considered to be part of the
+    # name of the field. e.g. `gnomadv4.1_AF`.
+    for field in fields.split('.', maxsplit=1):
         # Select from multi-allelic list.
         if field.endswith('#'):
             expression = expression[field[:-1]][

v03_pipeline/lib/misc/nested_field_test.py

@@ -18,6 +18,7 @@ def test_parse_nested_field(self):
                     'alleles': ['A', 'C'],
                     'a': hl.Struct(d=1),
                     'b': hl.Struct(e=[2, 9]),
+                    'h': hl.Struct(**{'i.j': 1}),
                     'a_index': 1,
                 },
                 {
@@ -29,6 +30,7 @@ def test_parse_nested_field(self):
                     'alleles': ['A', 'C'],
                     'a': hl.Struct(d=3),
                     'b': hl.Struct(e=[4, 5]),
+                    'h': hl.Struct(**{'i.j': 2}),
                     'a_index': 1,
                 },
             ],
@@ -37,6 +39,7 @@ def test_parse_nested_field(self):
                 alleles=hl.tarray(hl.tstr),
                 a=hl.tstruct(d=hl.tint32),
                 b=hl.tstruct(e=hl.tarray(hl.tint32)),
+                h=hl.tstruct(**{'i.j': hl.tint32}),
                 a_index=hl.tint32,
             ),
             key=['locus', 'alleles'],
@@ -45,6 +48,7 @@ def test_parse_nested_field(self):
             d=parse_nested_field(ht, 'a.d'),
             e=parse_nested_field(ht, 'b.e#'),
             f=parse_nested_field(ht, 'a'),
+            g=parse_nested_field(ht, 'h.i.j'),
         )
         self.assertListEqual(
             ht.collect(),
@@ -59,6 +63,7 @@ def test_parse_nested_field(self):
                     d=1,
                     e=2,
                     f=hl.Struct(d=1),
+                    g=1,
                 ),
                 hl.Struct(
                     locus=hl.Locus(
@@ -70,6 +75,7 @@ def test_parse_nested_field(self):
                     d=3,
                     e=4,
                     f=hl.Struct(d=3),
+                    g=2,
                 ),
             ],
         )