Stripping chr prefixes for queries via API (#402)

Related-Issue: #402 Projected-Results-Impact: none
varfish-org · Mar 24, 2022 · 2a671bc · 2a671bc
1 parent 66b6fa7
commit 2a671bc
Show file tree

Hide file tree

Showing 3 changed files with 21 additions and 9 deletions.
diff --git a/variants/query_presets.py b/variants/query_presets.py
@@ -773,25 +773,25 @@ class _ChromosomePresets:
     }
     #: Presets for the "autosomes" chromosome/region/gene settings
     autosomes: typing.Dict[str, typing.Any] = {
-        "genomic_region": tuple(f"chr{num}" for num in range(1, 23)),
+        "genomic_region": tuple(f"{num}" for num in range(1, 23)),
         "gene_allowlist": (),
         "gene_blocklist": (),
     }
     #: Presets for the "X-chromosome" chromosome/region/gene settings
     x_chromosome: typing.Dict[str, typing.Any] = {
-        "genomic_region": ("chrX",),
+        "genomic_region": ("X",),
         "gene_allowlist": (),
         "gene_blocklist": (),
     }
     #: Presets for the "Y-chromosomes" chromosome/region/gene settings
     y_chromosome: typing.Dict[str, typing.Any] = {
-        "genomic_region": ("chrY",),
+        "genomic_region": ("Y",),
         "gene_allowlist": (),
         "gene_blocklist": (),
     }
     #: Presets for the "mitochondrial" chromosome/region/gene settings
     mt_chromosome: typing.Dict[str, typing.Any] = {
-        "genomic_region": ("chrMT",),
+        "genomic_region": ("MT",),
         "gene_allowlist": (),
         "gene_blocklist": (),
     }

diff --git a/variants/query_schemas.py b/variants/query_schemas.py
@@ -8,6 +8,7 @@
 import typing
 
 import attr
+import attrs
 import cattr
 from jsonschema import Draft7Validator, validators
 
@@ -137,8 +138,14 @@ class GenomicRegionV1:
     chromosome: str
     range: typing.Optional[RangeV1] = None
 
+    def with_chr_stripped(self):
+        chromosome = self.chromosome
+        if chromosome.startswith("chr"):
+            chromosome = chromosome[len("chr") :]
+        return GenomicRegionV1(chromosome, self.range)
+
     def to_str(self):
-        if not range:
+        if not self.range:
             return self.chromosome
         else:
             return "%s:%d-%d" % (self.chromosome, self.range.start, self.range.end)
@@ -427,6 +434,11 @@ def convert_query_json_to_small_variant_filter_form_v1(
     tmp = copy.deepcopy(query_json)
     DefaultValidatingDraft7Validator(SCHEMA_QUERY_V1).validate(tmp)
     query = cattr.structure(tmp, CaseQueryV1)
+    if query.genomic_region:
+        query = attrs.evolve(
+            query,
+            genomic_region=list(map(GenomicRegionV1.with_chr_stripped, query.genomic_region)),
+        )
     return QueryJsonToFormConverter().convert(case, query)
 
 

diff --git a/variants/tests/test_query_presets.py b/variants/tests/test_query_presets.py
@@ -1311,7 +1311,7 @@ def testToSettingsAutosomes(self):
         self.assertEqual(
             query_presets.Chromosomes.AUTOSOMES.to_settings(),
             {
-                "genomic_region": tuple(f"chr{num}" for num in range(1, 23)),
+                "genomic_region": tuple(f"{num}" for num in range(1, 23)),
                 "gene_allowlist": (),
                 "gene_blocklist": (),
             },
@@ -1320,19 +1320,19 @@ def testToSettingsAutosomes(self):
     def testToSettingsXChromosome(self):
         self.assertEqual(
             query_presets.Chromosomes.X_CHROMOSOME.to_settings(),
-            {"genomic_region": ("chrX",), "gene_allowlist": (), "gene_blocklist": (),},
+            {"genomic_region": ("X",), "gene_allowlist": (), "gene_blocklist": (),},
         )
 
     def testToSettingsYChromosome(self):
         self.assertEqual(
             query_presets.Chromosomes.Y_CHROMOSOME.to_settings(),
-            {"genomic_region": ("chrY",), "gene_allowlist": (), "gene_blocklist": (),},
+            {"genomic_region": ("Y",), "gene_allowlist": (), "gene_blocklist": (),},
         )
 
     def testToSettingsMTChromosome(self):
         self.assertEqual(
             query_presets.Chromosomes.MT_CHROMOSOME.to_settings(),
-            {"genomic_region": ("chrMT",), "gene_allowlist": (), "gene_blocklist": (),},
+            {"genomic_region": ("MT",), "gene_allowlist": (), "gene_blocklist": (),},
         )