fix(lapis): nucleotideInsertionContains correctly handles segment

GenSpectrum · Jun 3, 2024 · d840a48 · d840a48
1 parent 46a0efa
commit d840a48
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Showing 5 changed files with 32 additions and 18 deletions.
diff --git a/lapis/src/main/kotlin/org/genspectrum/lapis/model/SiloFilterExpressionMapper.kt b/lapis/src/main/kotlin/org/genspectrum/lapis/model/SiloFilterExpressionMapper.kt
@@ -86,10 +86,10 @@ class SiloFilterExpressionMapper(
 
         return And(
             filterExpressions +
-                nucleotideMutationExpressions +
-                aminoAcidMutationExpressions +
-                nucleotideInsertionExpressions +
-                aminoAcidInsertionExpressions,
+                    nucleotideMutationExpressions +
+                    aminoAcidMutationExpressions +
+                    nucleotideInsertionExpressions +
+                    aminoAcidInsertionExpressions,
         )
     }
 
@@ -115,7 +115,7 @@ class SiloFilterExpressionMapper(
 
             null -> throw BadRequestException(
                 "'$key' is not a valid sequence filter key. Valid keys are: " +
-                    allowedSequenceFilterFields.fields.values.joinToString { it.name },
+                        allowedSequenceFilterFields.fields.values.joinToString { it.name },
             )
         }
         return Pair(filterExpressionId, type)
@@ -128,13 +128,13 @@ class SiloFilterExpressionMapper(
     ) {
         val containsAdvancedVariantQuery = allowedSequenceFiltersWithType.keys.any { it.second == Filter.VariantQuery }
         val containsSimpleVariantQuery = allowedSequenceFiltersWithType.keys.any { it.second in variantQueryTypes } ||
-            nucleotideMutations.isNotEmpty() ||
-            aaMutations.isNotEmpty()
+                nucleotideMutations.isNotEmpty() ||
+                aaMutations.isNotEmpty()
 
         if (containsAdvancedVariantQuery && containsSimpleVariantQuery) {
             throw BadRequestException(
                 "variantQuery filter cannot be used with other variant filters such as: " +
-                    variantQueryTypes.joinToString(", "),
+                        variantQueryTypes.joinToString(", "),
             )
         }
 
@@ -147,7 +147,7 @@ class SiloFilterExpressionMapper(
             if (intBetweenFilterForSameColumn != null) {
                 throw BadRequestException(
                     "Cannot filter by exact int field '$intEqualsColumnName' " +
-                        "and by int range field '${intBetweenFilterForSameColumn[0].originalKey}'.",
+                            "and by int range field '${intBetweenFilterForSameColumn[0].originalKey}'.",
                 )
             }
         }
@@ -161,7 +161,7 @@ class SiloFilterExpressionMapper(
             if (floatBetweenFilterForSameColumn != null) {
                 throw BadRequestException(
                     "Cannot filter by exact float field '$floatEqualsColumnName' " +
-                        "and by float range field '${floatBetweenFilterForSameColumn[0].originalKey}'.",
+                            "and by float range field '${floatBetweenFilterForSameColumn[0].originalKey}'.",
                 )
             }
         }
@@ -216,7 +216,7 @@ class SiloFilterExpressionMapper(
         if (exactDateFilters.isNotEmpty() && dateRangeFilters.isNotEmpty()) {
             throw BadRequestException(
                 "Cannot filter by exact date field '${exactDateFilters[0].originalKey}' " +
-                    "and by date range field '${dateRangeFilters[0].originalKey}'.",
+                        "and by date range field '${dateRangeFilters[0].originalKey}'.",
             )
         }
 
@@ -409,7 +409,11 @@ class SiloFilterExpressionMapper(
     }
 
     private fun toNucleotideInsertionFilter(nucleotideInsertion: NucleotideInsertion): NucleotideInsertionContains {
-        return NucleotideInsertionContains(nucleotideInsertion.position, nucleotideInsertion.insertions)
+        return NucleotideInsertionContains(
+            nucleotideInsertion.position,
+            nucleotideInsertion.insertions,
+            nucleotideInsertion.segment,
+        )
     }
 
     private fun toAminoAcidInsertionFilter(aminoAcidInsertion: AminoAcidInsertion): AminoAcidInsertionContains {

diff --git a/lapis/src/main/kotlin/org/genspectrum/lapis/model/VariantQueryCustomListener.kt b/lapis/src/main/kotlin/org/genspectrum/lapis/model/VariantQueryCustomListener.kt
@@ -131,6 +131,7 @@ class VariantQueryCustomListener(val referenceGenomeSchema: ReferenceGenomeSchem
             NucleotideInsertionContains(
                 ctx.position().text.toInt(),
                 value.uppercase(),
+                null,
             ),
         )
     }

diff --git a/lapis/src/main/kotlin/org/genspectrum/lapis/silo/SiloQuery.kt b/lapis/src/main/kotlin/org/genspectrum/lapis/silo/SiloQuery.kt
@@ -238,7 +238,8 @@ data class HasAminoAcidMutation(val sequenceName: String, val position: Int) :
 data class DateBetween(val column: String, val from: LocalDate?, val to: LocalDate?) :
     SiloFilterExpression("DateBetween")
 
-data class NucleotideInsertionContains(val position: Int, val value: String) : SiloFilterExpression("InsertionContains")
+data class NucleotideInsertionContains(val position: Int, val value: String, val sequenceName: String?) :
+    SiloFilterExpression("InsertionContains")
 
 data class AminoAcidInsertionContains(val position: Int, val value: String, val sequenceName: String) :
     SiloFilterExpression(

diff --git a/lapis/src/test/kotlin/org/genspectrum/lapis/model/SiloFilterExpressionMapperTest.kt b/lapis/src/test/kotlin/org/genspectrum/lapis/model/SiloFilterExpressionMapperTest.kt
@@ -370,7 +370,7 @@ class SiloFilterExpressionMapperTest {
         val result = underTest.map(filterParameter)
 
         val expected =
-            And(NucleotideInsertionContains(123, "ABCD"), NucleotideInsertionContains(999, "DEF"))
+            And(NucleotideInsertionContains(123, "ABCD", "segment"), NucleotideInsertionContains(999, "DEF", null))
         assertThat(result, equalTo(expected))
     }
 

diff --git a/lapis/src/test/kotlin/org/genspectrum/lapis/model/VariantQueryFacadeTest.kt b/lapis/src/test/kotlin/org/genspectrum/lapis/model/VariantQueryFacadeTest.kt
@@ -303,7 +303,15 @@ class VariantQueryFacadeTest {
 
         val result = underTest.map(variantQuery)
 
-        assertThat(result, equalTo(NucleotideInsertionContains(1234, "GAG")))
+        assertThat(result, equalTo(NucleotideInsertionContains(1234, "GAG", null)))
+    }
+
+    @Test
+    fun `given a variantQuery with a 'Insertion' expression with sequenceName throws`() {
+        //  COVID variant queries do not support segment name in insertion queries
+        val variantQuery = "ins_sequence:1234:GAG"
+
+        assertThrows<BadRequestException> { underTest.map(variantQuery) }
     }
 
     @Test
@@ -312,7 +320,7 @@ class VariantQueryFacadeTest {
 
         val result = underTest.map(variantQuery)
 
-        assertThat(result, equalTo(NucleotideInsertionContains(1234, "GAG")))
+        assertThat(result, equalTo(NucleotideInsertionContains(1234, "GAG", null)))
     }
 
     @Test
@@ -321,7 +329,7 @@ class VariantQueryFacadeTest {
 
         val result = underTest.map(variantQuery)
 
-        assertThat(result, equalTo(NucleotideInsertionContains(1234, "GAG")))
+        assertThat(result, equalTo(NucleotideInsertionContains(1234, "GAG", null)))
     }
 
     @Test
@@ -330,7 +338,7 @@ class VariantQueryFacadeTest {
 
         val result = underTest.map(variantQuery)
 
-        assertThat(result, equalTo(NucleotideInsertionContains(1234, "G.*A.*G")))
+        assertThat(result, equalTo(NucleotideInsertionContains(1234, "G.*A.*G", null)))
     }
 
     @Test
-Original file line number
+Diff line change
@@ Expand Up @@
                 NucleotideInsertionContains(
                     ctx.position().text.toInt(),
                     value.uppercase(),
+                    null,
                 ),
             )
         }
@@ Expand Down @@