From caa8713df7887f01187957167a388af7705a36b5 Mon Sep 17 00:00:00 2001
From: Jonas Kellerer <jonas.kellerer@tngtech.com>
Date: Thu, 14 Dec 2023 17:09:28 +0100
Subject: [PATCH] feat: allow loweer case for mutations

---
 .../genspectrum/lapis/request/AminoAcidMutation.kt   |  4 ++--
 .../genspectrum/lapis/request/NucleotideMutation.kt  |  5 +++--
 .../lapis/request/AminoAcidMutationTest.kt           |  4 ++++
 .../lapis/request/NucleotideMutationTest.kt          | 12 ++++++++++++
 4 files changed, 21 insertions(+), 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
index 420f9b60..3bc8fb8a 100644
--- a/lapis2/src/main/kotlin/org/genspectrum/lapis/request/AminoAcidMutation.kt
+++ b/lapis2/src/main/kotlin/org/genspectrum/lapis/request/AminoAcidMutation.kt
@@ -26,7 +26,7 @@ data class AminoAcidMutation(val gene: String, val position: Int, val symbol: St
             return AminoAcidMutation(
                 gene,
                 position,
-                matchGroups["symbolTo"]?.value,
+                matchGroups["symbolTo"]?.value?.uppercase(),
             )
         }
     }
@@ -34,7 +34,7 @@ data class AminoAcidMutation(val gene: String, val position: Int, val symbol: St
 
 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
index aec265a6..98ecc08d 100644
--- a/lapis2/src/main/kotlin/org/genspectrum/lapis/request/NucleotideMutation.kt
+++ b/lapis2/src/main/kotlin/org/genspectrum/lapis/request/NucleotideMutation.kt
@@ -24,7 +24,7 @@ data class NucleotideMutation(val sequenceName: String?, val position: Int, val
             return NucleotideMutation(
                 matchGroups["sequenceName"]?.value,
                 position,
-                matchGroups["symbolTo"]?.value,
+                matchGroups["symbolTo"]?.value?.uppercase(),
             )
         }
     }
@@ -32,7 +32,8 @@ data class NucleotideMutation(val sequenceName: String?, val position: Int, val
 
 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
index 8405a0e4..b9208bfd 100644
--- 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
index 15e2173b..bbdd3f44 100644
--- 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