feat: allow loweer case for mutations

GenSpectrum · Dec 18, 2023 · caa8713 · caa8713
1 parent 45e931e
commit caa8713
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Showing 4 changed files with 21 additions and 4 deletions.
diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/request/AminoAcidMutation.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/request/AminoAcidMutation.kt
@@ -26,15 +26,15 @@ data class AminoAcidMutation(val gene: String, val position: Int, val symbol: St
             return AminoAcidMutation(
                 gene,
                 position,
-                matchGroups["symbolTo"]?.value,
+                matchGroups["symbolTo"]?.value?.uppercase(),
             )
         }
     }
 }
 
 private val AMINO_ACID_MUTATION_REGEX =
     Regex(
-        """^((?<gene>[a-zA-Z0-9_-]+):)(?<symbolFrom>[A-Z]?)(?<position>\d+)(?<symbolTo>[A-Z.-])?$""",
+        """^((?<gene>[a-zA-Z0-9_-]+):)(?<symbolFrom>[a-zA-Z]?)(?<position>\d+)(?<symbolTo>[a-zA-Z.-])?$""",
     )
 
 @JsonComponent

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/request/NucleotideMutation.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/request/NucleotideMutation.kt
@@ -24,15 +24,16 @@ data class NucleotideMutation(val sequenceName: String?, val position: Int, val
             return NucleotideMutation(
                 matchGroups["sequenceName"]?.value,
                 position,
-                matchGroups["symbolTo"]?.value,
+                matchGroups["symbolTo"]?.value?.uppercase(),
             )
         }
     }
 }
 
 private val NUCLEOTIDE_MUTATION_REGEX =
     Regex(
-        """^((?<sequenceName>[a-zA-Z0-9_-]+)(?=:):)?(?<symbolFrom>[A-Z]?)(?<position>\d+)(?<symbolTo>[A-Z.-])?$""",
+        @Suppress("ktlint:standard:max-line-length")
+        """^((?<sequenceName>[a-zA-Z0-9_-]+)(?=:):)?(?<symbolFrom>[a-zA-Z]?)(?<position>\d+)(?<symbolTo>[a-zA-Z.-])?$""",
     )
 
 @JsonComponent

diff --git a/lapis2/src/test/kotlin/org/genspectrum/lapis/request/AminoAcidMutationTest.kt b/lapis2/src/test/kotlin/org/genspectrum/lapis/request/AminoAcidMutationTest.kt
@@ -68,6 +68,10 @@ class AminoAcidMutationTest {
                     "\"ORF1b:123X\"",
                     AminoAcidMutation("ORF1b", 123, "X"),
                 ),
+                Arguments.of(
+                    "\"gene:123a\"",
+                    AminoAcidMutation("gene", 123, "A"),
+                ),
             )
 
         @JvmStatic

diff --git a/lapis2/src/test/kotlin/org/genspectrum/lapis/request/NucleotideMutationTest.kt b/lapis2/src/test/kotlin/org/genspectrum/lapis/request/NucleotideMutationTest.kt
@@ -68,6 +68,18 @@ class NucleotideMutationTest {
                     "\"sequence-Name_1:123X\"",
                     NucleotideMutation("sequence-Name_1", 123, "X"),
                 ),
+                Arguments.of(
+                    "\"g123A\"",
+                    NucleotideMutation(null, 123, "A"),
+                ),
+                Arguments.of(
+                    "\"G123a\"",
+                    NucleotideMutation(null, 123, "A"),
+                ),
+                Arguments.of(
+                    "\"g123a\"",
+                    NucleotideMutation(null, 123, "A"),
+                ),
             )
 
         @JvmStatic