Squashed commit of the following:

commit 5a13047 Author: TheMadBug <[email protected]> Date: Sun Jul 14 00:50:04 2024 +1000 Put more progress debug in one_off_fix_symbolic_variants commit 7e3090d Author: TheMadBug <[email protected]> Date: Sat Jul 13 23:54:08 2024 +1000 Revert change that upgrade upgrade script to use sha before sha was in use commit 9c54168 Author: TheMadBug <[email protected]> Date: Sat Jul 13 23:51:14 2024 +1000 Update dependency of migrations (requires sha to be in place) commit f75e9a4 Author: TheMadBug <[email protected]> Date: Sat Jul 13 20:13:01 2024 +1000 Update deploy check to handle if Symbolic variants are disbaled commit 1499a26 Author: TheMadBug <[email protected]> Date: Sat Jul 13 20:07:51 2024 +1000 Fix error report on deploy check commit aaac12f Author: TheMadBug <[email protected]> Date: Sat Jul 13 20:05:08 2024 +1000 Include error message for hgvs test commit 0c460bd Author: Dave Lawrence <[email protected]> Date: Fri Jul 12 17:20:31 2024 +0930 issue #1114 - setting to reject symbolic variants
SACGF · Jul 15, 2024 · a8419be · a8419be
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Showing 3 changed files with 24 additions and 11 deletions.
diff --git a/snpdb/management/commands/one_off_fix_symbolic_variants.py b/snpdb/management/commands/one_off_fix_symbolic_variants.py
@@ -19,12 +19,14 @@ def add_arguments(self, parser):
     def handle(self, *args, **options):
         long_sequences = Sequence.objects.all().annotate(seq_length=Length("seq")).filter(seq_length__gte=1000)
         long_variants = Variant.objects.filter(Q(locus__ref__in=long_sequences) | Q(alt__in=long_sequences))
+        print(f"Long variant count = {long_variants.count()}")
 
         base_lookup = {s: Sequence.objects.get(seq=s) for s in ["G", "A", "T", "C", "<DEL>", "<DUP>"]}
         not_symbolic = []
         dry_run = options["dry_run"]
 
         for genome_build in GenomeBuild.builds_with_annotation():
+            print(f"Genome build {genome_build}")
             self._find_bad_symbolic_via_clinvar(dry_run, genome_build, "<DEL>")  # DELISN stored as DEL
             self._find_bad_symbolic_via_clinvar(dry_run, genome_build, "<DUP>")  # INS stored as DUP
             num_deleted = 0
@@ -107,19 +109,25 @@ def _find_bad_symbolic_via_clinvar(self, dry_run: bool, genome_build, alt_seq):
             ClinVar.objects.filter(version__genome_build=genome_build, variant__alt__seq=alt_seq).values_list(
                 "clinvar_variation_id", flat=True))
 
+        print(f"{genome_build} Found clinvar {alt_seq} count = {clinvar_variation_del.count()}")
+
         clinvar_variation_original = {}
 
         for cv in ClinVar.objects.filter(version__genome_build=genome_build,
                                          clinvar_variation_id__in=clinvar_variation_del).exclude(
                 variant__alt__seq=alt_seq):
             clinvar_variation_original[cv.clinvar_variation_id] = cv.variant
 
+        print(f"{genome_build} clinvar_variation_original_count = {len(clinvar_variation_original)}")
+
         clinvar_variation_bad = {}
         for cv in ClinVar.objects.filter(version__genome_build=genome_build,
                                          clinvar_variation_id__in=clinvar_variation_original,
                                          variant__alt__seq=alt_seq):
             clinvar_variation_bad[cv.clinvar_variation_id] = cv.variant
 
+        print(f"{genome_build} clinvar_variation_bad = {len(clinvar_variation_bad)}")
+
         for clinvar_variation_id, bad_variant in clinvar_variation_bad.items():
             original_variant = clinvar_variation_original[clinvar_variation_id]
             print(f"{bad_variant} should have been {original_variant}")

diff --git a/snpdb/migrations/0117_one_off_inv_symbolic.py b/snpdb/migrations/0117_one_off_inv_symbolic.py
@@ -8,7 +8,7 @@
 from django.db import migrations
 from django.db.models import Q
 
-from library.utils import sha256sum_str
+from library.utils import sha256sum_str, md5sum_str
 
 
 def _one_off_inv_symbolic(apps, _schema_editor):
@@ -41,7 +41,7 @@ def _one_off_inv_symbolic(apps, _schema_editor):
         base_lookup = {s: Sequence.objects.get(seq=s) for s in "GATC"}
         symbolic_alt = "<INV>"
         inv, _ = Sequence.objects.get_or_create(seq=symbolic_alt,
-                                                seq_sha256_hash=sha256sum_str(symbolic_alt),
+                                                seq_md5_hash=md5sum_str(symbolic_alt),
                                                 length=len(symbolic_alt))  # This is wrong, but will remove this eventually
 
         # There are so few of these, that we can just do them 1 by 1

diff --git a/variantgrid/deployment_validation/library_version_checks.py b/variantgrid/deployment_validation/library_version_checks.py
@@ -2,6 +2,7 @@
 
 from genes.hgvs.hgvs_converter import HGVSConverterType
 from snpdb.models import VariantCoordinate
+from variantgrid import settings
 
 
 def check_library_versions() -> dict:
@@ -15,8 +16,10 @@ def _test_biocommons_hgvs():
         matcher.get_variant_coordinate("NC_000006.12:g.49949407_49949408=")
 
         # Check it can handle contig names as chrom names
-        vc = VariantCoordinate(chrom="NC_000006.12", position=386486, ref="A", alt="<DUP>", svlen=5000)
-        matcher.variant_coordinate_to_g_hgvs(vc)
+        if settings.VARIANT_SYMBOLIC_ALT_ENABLED:
+            # only do this test if symbolic variants are supported
+            vc = VariantCoordinate(chrom="NC_000006.12", position=386486, ref="A", alt="<DUP>", svlen=5000)
+            matcher.variant_coordinate_to_g_hgvs(vc)
 
     minimum_versions = {
         "cdot": (0, 2, 21),
@@ -34,12 +37,14 @@ def _test_biocommons_hgvs():
                 version_str = metadata.version(name)
                 version = tuple(int(i) for i in version_str.split("."))
                 assert version >= version_required, "Library %s (%s) requires version >= %s" % (name, version, version_required)
-            valid = True
-        except:
-            valid = False
-        library_version_valid[name] = {
-            "valid": valid,
-            "fix": "Upgrade the library using the version in requirements.txt",
-        }
+            library_version_valid[name] = {
+                "valid": True,
+                "fix": f"All good",
+            }
+        except Exception as ex:
+            library_version_valid[name] = {
+                "valid": False,
+                "fix": f"Upgrade the library using the version in requirements.txt - error {ex}",
+            }
 
     return library_version_valid