From 667f487abdf9124af83cfce7c49486f4fb4a6412 Mon Sep 17 00:00:00 2001
From: Jonas Kellerer <jonas.kellerer@tngtech.com>
Date: Tue, 23 Jan 2024 15:00:05 +0100
Subject: [PATCH] feat: amino acid and nucleotide insertion filters are
 case-insensitive

---
 .../org/genspectrum/lapis/request/AminoAcidInsertion.kt       | 3 +++
 .../org/genspectrum/lapis/request/NucleotideInsertion.kt      | 3 +++
 .../org/genspectrum/lapis/request/AminoAcidInsertionTest.kt   | 4 ++++
 .../org/genspectrum/lapis/request/NucleotideInsertionTest.kt  | 4 ++++
 4 files changed, 14 insertions(+)

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/request/AminoAcidInsertion.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/request/AminoAcidInsertion.kt
index b991cbf85..68eac54f0 100644
--- a/lapis2/src/main/kotlin/org/genspectrum/lapis/request/AminoAcidInsertion.kt
+++ b/lapis2/src/main/kotlin/org/genspectrum/lapis/request/AminoAcidInsertion.kt
@@ -51,6 +51,9 @@ data class AminoAcidInsertion(val position: Int, val gene: String, val insertion
 private val AMINO_ACID_INSERTION_REGEX =
     Regex(
         """^ins_(?<gene>[a-zA-Z0-9_-]+):(?<position>\d+):(?<insertions>(([a-zA-Z?]|(\.\*))+))$""",
+        setOf(
+            RegexOption.IGNORE_CASE,
+        ),
     )
 
 @JsonComponent
diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/request/NucleotideInsertion.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/request/NucleotideInsertion.kt
index 0fdde101c..7af796895 100644
--- a/lapis2/src/main/kotlin/org/genspectrum/lapis/request/NucleotideInsertion.kt
+++ b/lapis2/src/main/kotlin/org/genspectrum/lapis/request/NucleotideInsertion.kt
@@ -51,6 +51,9 @@ data class NucleotideInsertion(val position: Int, val insertions: String, val se
 private val NUCLEOTIDE_INSERTION_REGEX =
     Regex(
         """^ins_((?<segment>[a-zA-Z0-9_-]+)(?=:):)?(?<position>\d+):(?<insertions>(([a-zA-Z?]|(\.\*))+))$""",
+        setOf(
+            RegexOption.IGNORE_CASE,
+        ),
     )
 
 @JsonComponent
diff --git a/lapis2/src/test/kotlin/org/genspectrum/lapis/request/AminoAcidInsertionTest.kt b/lapis2/src/test/kotlin/org/genspectrum/lapis/request/AminoAcidInsertionTest.kt
index 82b4661b6..2772f6740 100644
--- a/lapis2/src/test/kotlin/org/genspectrum/lapis/request/AminoAcidInsertionTest.kt
+++ b/lapis2/src/test/kotlin/org/genspectrum/lapis/request/AminoAcidInsertionTest.kt
@@ -88,6 +88,10 @@ class AminoAcidInsertionTest {
                     "\"ins_gEne1:123:ABCD\"",
                     AminoAcidInsertion(123, "gene1", "ABCD"),
                 ),
+                Arguments.of(
+                    "\"INs_gEne1:123:ABCD\"",
+                    AminoAcidInsertion(123, "gene1", "ABCD"),
+                ),
             )
 
         @JvmStatic
diff --git a/lapis2/src/test/kotlin/org/genspectrum/lapis/request/NucleotideInsertionTest.kt b/lapis2/src/test/kotlin/org/genspectrum/lapis/request/NucleotideInsertionTest.kt
index bff329746..4ce54c9a3 100644
--- a/lapis2/src/test/kotlin/org/genspectrum/lapis/request/NucleotideInsertionTest.kt
+++ b/lapis2/src/test/kotlin/org/genspectrum/lapis/request/NucleotideInsertionTest.kt
@@ -96,6 +96,10 @@ class NucleotideInsertionTest {
                     "\"ins_oTher_segmenT:123:ABCD\"",
                     NucleotideInsertion(123, "ABCD", "other_segment"),
                 ),
+                Arguments.of(
+                    "\"INs_123:AcCD\"",
+                    NucleotideInsertion(123, "ACCD", null),
+                ),
             )
 
         @JvmStatic