feat: allow lower case for insertions

GenSpectrum · Dec 18, 2023 · 79c9f2d · 79c9f2d
1 parent 74cfa74
commit 79c9f2d
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Showing 4 changed files with 10 additions and 2 deletions.
diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/request/AminoAcidInsertion.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/request/AminoAcidInsertion.kt
@@ -29,7 +29,7 @@ data class AminoAcidInsertion(val position: Int, val gene: String, val insertion
             val insertions = matchGroups["insertions"]?.value?.replace(
                 LAPIS_INSERTION_AMBIGUITY_SYMBOL,
                 SILO_INSERTION_AMBIGUITY_SYMBOL,
-            )
+            )?.uppercase()
                 ?: throw BadRequestException(
                     "Invalid amino acid insertion: $aminoAcidInsertion: Did not find insertions",
                 )

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/request/NucleotideInsertion.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/request/NucleotideInsertion.kt
@@ -27,7 +27,7 @@ data class NucleotideInsertion(val position: Int, val insertions: String, val se
             val insertions = matchGroups["insertions"]?.value?.replace(
                 LAPIS_INSERTION_AMBIGUITY_SYMBOL,
                 SILO_INSERTION_AMBIGUITY_SYMBOL,
-            )
+            )?.uppercase()
                 ?: throw BadRequestException(
                     "Invalid nucleotide insertion: $nucleotideInsertion: Did not find insertions",
                 )

diff --git a/lapis2/src/test/kotlin/org/genspectrum/lapis/request/AminoAcidInsertionTest.kt b/lapis2/src/test/kotlin/org/genspectrum/lapis/request/AminoAcidInsertionTest.kt
@@ -80,6 +80,10 @@ class AminoAcidInsertionTest {
                     "\"ins_gene:123:AB.*?CD\"",
                     AminoAcidInsertion(123, "gene", "AB.*.*CD"),
                 ),
+                Arguments.of(
+                    "\"ins_gene:123:abCd\"",
+                    AminoAcidInsertion(123, "gene", "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
@@ -88,6 +88,10 @@ class NucleotideInsertionTest {
                     "\"ins_segment:123:AB.*?CD\"",
                     NucleotideInsertion(123, "AB.*.*CD", "segment"),
                 ),
+                Arguments.of(
+                    "\"ins_segment:123:abCd\"",
+                    NucleotideInsertion(123, "ABCD", "segment"),
+                ),
             )
 
         @JvmStatic