Merge pull request #577 from VariantEffect/feature/bencap/550/vrs-digest-in-post-mapped-csv

feat: output VRS digest with post mapped HGVS strings

Author: bencap

src/mavedb/lib/score_sets.py

@@ -1,17 +1,16 @@
-from collections import Counter
 import csv
 import io
 import logging
-from operator import attrgetter
 import re
-from typing import Any, BinaryIO, Iterable, List, Optional, TYPE_CHECKING, Sequence, Literal
+from collections import Counter
+from operator import attrgetter
+from typing import TYPE_CHECKING, Any, BinaryIO, Iterable, List, Literal, Optional, Sequence
 
-from mavedb.models.mapped_variant import MappedVariant
 import numpy as np
 import pandas as pd
 from pandas.testing import assert_index_equal
 from sqlalchemy import Integer, and_, cast, func, or_, select
-from sqlalchemy.orm import Session, aliased, contains_eager, joinedload, Query, selectinload
+from sqlalchemy.orm import Query, Session, aliased, contains_eager, joinedload, selectinload
 
 from mavedb.lib.exceptions import ValidationError
 from mavedb.lib.logging.context import logging_context, save_to_logging_context
@@ -26,7 +25,7 @@
 from mavedb.lib.mave.utils import is_csv_null
 from mavedb.lib.validation.constants.general import null_values_list
 from mavedb.lib.validation.utilities import is_null as validate_is_null
-from mavedb.lib.variants import get_hgvs_from_post_mapped, is_hgvs_g, is_hgvs_p
+from mavedb.lib.variants import get_digest_from_post_mapped, get_hgvs_from_post_mapped, is_hgvs_g, is_hgvs_p
 from mavedb.models.contributor import Contributor
 from mavedb.models.controlled_keyword import ControlledKeyword
 from mavedb.models.doi_identifier import DoiIdentifier
@@ -36,6 +35,7 @@
 from mavedb.models.experiment_controlled_keyword import ExperimentControlledKeywordAssociation
 from mavedb.models.experiment_publication_identifier import ExperimentPublicationIdentifierAssociation
 from mavedb.models.experiment_set import ExperimentSet
+from mavedb.models.mapped_variant import MappedVariant
 from mavedb.models.publication_identifier import PublicationIdentifier
 from mavedb.models.refseq_identifier import RefseqIdentifier
 from mavedb.models.refseq_offset import RefseqOffset
@@ -547,6 +547,7 @@ def get_score_set_variants_as_csv(
     if include_post_mapped_hgvs:
         namespaced_score_set_columns["mavedb"].append("post_mapped_hgvs_g")
         namespaced_score_set_columns["mavedb"].append("post_mapped_hgvs_p")
+        namespaced_score_set_columns["mavedb"].append("post_mapped_vrs_digest")
     for namespace in namespaces:
         namespaced_score_set_columns[namespace] = []
     if include_custom_columns:
@@ -596,7 +597,9 @@ def get_score_set_variants_as_csv(
         if limit:
             variants_query = variants_query.limit(limit)
         variants = db.scalars(variants_query).all()
-    rows_data = variants_to_csv_rows(variants, columns=namespaced_score_set_columns, namespaced=namespaced, mappings=mappings)  # type: ignore
+    rows_data = variants_to_csv_rows(
+        variants, columns=namespaced_score_set_columns, namespaced=namespaced, mappings=mappings
+    )  # type: ignore
     rows_columns = [
         (
             f"{namespace}.{col}"
@@ -701,6 +704,9 @@ def variant_to_csv_row(
                 value = hgvs_str
             else:
                 value = ""
+        elif column_key == "post_mapped_vrs_digest":
+            digest = get_digest_from_post_mapped(mapping.post_mapped) if mapping and mapping.post_mapped else None
+            value = digest if digest is not None else ""
         if is_null(value):
             value = na_rep
         key = f"mavedb.{column_key}" if namespaced else column_key

src/mavedb/lib/variants.py

@@ -1,7 +1,6 @@
 import re
 from typing import Any, Optional
 
-
 HGVS_G_REGEX = re.compile(r"(^|:)g\.")
 HGVS_P_REGEX = re.compile(r"(^|:)p\.")
 
@@ -48,6 +47,23 @@ def get_hgvs_from_post_mapped(post_mapped_vrs: Optional[Any]) -> Optional[str]:
     return variations_hgvs[0]
 
 
+def get_digest_from_post_mapped(post_mapped_vrs: Optional[Any]) -> Optional[str]:
+    """
+    Extract the digest value from a post-mapped VRS object.
+
+    Args:
+        post_mapped_vrs: A post-mapped VRS (Variation Representation Specification) object
+                        that may contain a digest field. Can be None.
+
+    Returns:
+        The digest string if present in the post_mapped_vrs object, otherwise None.
+    """
+    if not post_mapped_vrs:
+        return None
+
+    return post_mapped_vrs.get("digest")  # type: ignore
+
+
 # TODO (https://github.com/VariantEffect/mavedb-api/issues/440) Temporarily, we are using these functions to distinguish
 # genomic and protein HGVS strings produced by the mapper. Using hgvs.parser.Parser is too slow, and we won't need to do
 # this once the mapper extracts separate g., c., and p. post-mapped HGVS strings.

tests/lib/test_variants.py

@@ -1,15 +1,22 @@
 import pytest
 
-from mavedb.lib.variants import hgvs_from_vrs_allele, get_hgvs_from_post_mapped, is_hgvs_g, is_hgvs_p
-
+from mavedb.lib.variants import (
+    get_digest_from_post_mapped,
+    get_hgvs_from_post_mapped,
+    hgvs_from_vrs_allele,
+    is_hgvs_g,
+    is_hgvs_p,
+)
 from tests.helpers.constants import (
     TEST_HGVS_IDENTIFIER,
     TEST_VALID_POST_MAPPED_VRS_ALLELE_VRS1_X,
     TEST_VALID_POST_MAPPED_VRS_ALLELE_VRS2_X,
-    TEST_VALID_POST_MAPPED_VRS_HAPLOTYPE,
     TEST_VALID_POST_MAPPED_VRS_CIS_PHASED_BLOCK,
+    TEST_VALID_POST_MAPPED_VRS_HAPLOTYPE,
 )
 
+### Tests for hgvs_from_vrs_allele function ###
+
 
 def test_hgvs_from_vrs_allele_vrs_1():
     with pytest.raises(ValueError):
@@ -26,6 +33,9 @@ def test_hgvs_from_vrs_allele_invalid():
         hgvs_from_vrs_allele({"invalid_key": "invalid_value"})
 
 
+### Tests for get_hgvs_from_post_mapped function ###
+
+
 def test_get_hgvs_from_post_mapped_haplotype():
     with pytest.raises(ValueError):
         get_hgvs_from_post_mapped(TEST_VALID_POST_MAPPED_VRS_HAPLOTYPE)
@@ -61,6 +71,36 @@ def test_get_hgvs_from_post_mapped_invalid_structure():
         get_hgvs_from_post_mapped({"invalid_key": "InvalidType"})
 
 
+### Tests for get_digest_from_post_mapped function ###
+
+
+def test_get_digest_from_post_mapped_with_digest():
+    post_mapped_vrs = {"digest": "test_digest_value", "type": "Allele"}
+    result = get_digest_from_post_mapped(post_mapped_vrs)
+    assert result == "test_digest_value"
+
+
+def test_get_digest_from_post_mapped_without_digest():
+    post_mapped_vrs = {"type": "Allele", "other_field": "value"}
+
+    result = get_digest_from_post_mapped(post_mapped_vrs)
+
+    assert result is None
+
+
+def test_get_digest_from_post_mapped_none_input():
+    result = get_digest_from_post_mapped(None)
+    assert result is None
+
+
+def test_get_digest_from_post_mapped_empty_dict():
+    result = get_digest_from_post_mapped({})
+    assert result is None
+
+
+### Tests for is_hgvs_g and is_hgvs_p functions ###
+
+
 @pytest.mark.parametrize(
     "hgvs,expected",
     [

tests/routers/test_score_set.py

@@ -2706,6 +2706,7 @@ def test_download_variants_data_file(
             "hgvs_pro",
             "mavedb.post_mapped_hgvs_g",
             "mavedb.post_mapped_hgvs_p",
+            "mavedb.post_mapped_vrs_digest",
             "scores.score",
         ]
     )
@@ -2871,6 +2872,7 @@ def test_download_scores_counts_and_post_mapped_variants_file(
             "hgvs_pro",
             "mavedb.post_mapped_hgvs_g",
             "mavedb.post_mapped_hgvs_p",
+            "mavedb.post_mapped_vrs_digest",
             "scores.score",
             "scores.s_0",
             "scores.s_1",