fix: set default min proportion

See GenSpectrum/LAPIS-SILO#234
GenSpectrum · Dec 19, 2023 · d033b34 · d033b34
1 parent 79c9f2d
commit d033b34
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Showing 4 changed files with 38 additions and 14 deletions.
diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/LapisController.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/LapisController.kt
@@ -39,6 +39,7 @@ import org.genspectrum.lapis.openApi.REQUEST_SCHEMA_WITH_MIN_PROPORTION
 import org.genspectrum.lapis.request.AminoAcidInsertion
 import org.genspectrum.lapis.request.AminoAcidMutation
 import org.genspectrum.lapis.request.CommonSequenceFilters
+import org.genspectrum.lapis.request.DEFAULT_MIN_PROPORTION
 import org.genspectrum.lapis.request.Field
 import org.genspectrum.lapis.request.MutationProportionsRequest
 import org.genspectrum.lapis.request.NucleotideInsertion
@@ -290,7 +291,7 @@ class LapisController(
         @RequestParam(required = false)
         @AminoAcidMutations
         aminoAcidMutations: List<AminoAcidMutation>?,
-        @RequestParam minProportion: Double?,
+        @RequestParam(defaultValue = "$DEFAULT_MIN_PROPORTION") minProportion: Double?,
         @MutationsOrderByFields
         @RequestParam
         orderBy: List<OrderByField>?,
@@ -345,7 +346,7 @@ class LapisController(
         @RequestParam(required = false)
         @AminoAcidMutations
         aminoAcidMutations: List<AminoAcidMutation>?,
-        @RequestParam minProportion: Double?,
+        @RequestParam(defaultValue = "$DEFAULT_MIN_PROPORTION") minProportion: Double?,
         @MutationsOrderByFields
         @RequestParam
         orderBy: List<OrderByField>?,
@@ -394,7 +395,7 @@ class LapisController(
         @RequestParam(required = false)
         @AminoAcidMutations
         aminoAcidMutations: List<AminoAcidMutation>?,
-        @RequestParam minProportion: Double?,
+        @RequestParam(defaultValue = "$DEFAULT_MIN_PROPORTION") minProportion: Double?,
         @MutationsOrderByFields
         @RequestParam
         orderBy: List<OrderByField>?,
@@ -483,7 +484,7 @@ class LapisController(
         @RequestParam(required = false)
         @AminoAcidMutations
         aminoAcidMutations: List<AminoAcidMutation>?,
-        @RequestParam minProportion: Double?,
+        @RequestParam(defaultValue = "$DEFAULT_MIN_PROPORTION") minProportion: Double?,
         @MutationsOrderByFields
         @RequestParam
         orderBy: List<OrderByField>?,
@@ -534,7 +535,7 @@ class LapisController(
         @RequestParam(required = false)
         @AminoAcidMutations
         aminoAcidMutations: List<AminoAcidMutation>?,
-        @RequestParam minProportion: Double?,
+        @RequestParam(defaultValue = "$DEFAULT_MIN_PROPORTION") minProportion: Double?,
         @MutationsOrderByFields
         @RequestParam
         orderBy: List<OrderByField>?,
@@ -583,7 +584,7 @@ class LapisController(
         @RequestParam(required = false)
         @AminoAcidMutations
         aminoAcidMutations: List<AminoAcidMutation>?,
-        @RequestParam minProportion: Double?,
+        @RequestParam(defaultValue = "$DEFAULT_MIN_PROPORTION") minProportion: Double?,
         @MutationsOrderByFields
         @RequestParam
         orderBy: List<OrderByField>?,

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/request/MutationProportionsRequest.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/request/MutationProportionsRequest.kt
@@ -10,6 +10,8 @@ import org.genspectrum.lapis.controller.BadRequestException
 import org.genspectrum.lapis.controller.MIN_PROPORTION_PROPERTY
 import org.springframework.boot.jackson.JsonComponent
 
+const val DEFAULT_MIN_PROPORTION = 0.05
+
 data class MutationProportionsRequest(
     override val sequenceFilters: Map<String, String>,
     override val nucleotideMutations: List<NucleotideMutation>,
@@ -32,7 +34,7 @@ class MutationProportionsRequestDeserializer : JsonDeserializer<MutationProporti
         val codec = jsonParser.codec
 
         val minProportion = when (val minProportionNode = node.get(MIN_PROPORTION_PROPERTY)) {
-            null, is NullNode -> null
+            null, is NullNode -> DEFAULT_MIN_PROPORTION
             is NumericNode -> minProportionNode.doubleValue()
 
             else -> throw BadRequestException("minProportion must be a number")

diff --git a/lapis2/src/test/kotlin/org/genspectrum/lapis/controller/LapisControllerTest.kt b/lapis2/src/test/kotlin/org/genspectrum/lapis/controller/LapisControllerTest.kt
@@ -3,9 +3,11 @@ package org.genspectrum.lapis.controller
 import com.fasterxml.jackson.databind.ObjectMapper
 import com.fasterxml.jackson.databind.node.IntNode
 import com.fasterxml.jackson.databind.node.TextNode
+import com.fasterxml.jackson.module.kotlin.readValue
 import com.ninjasquad.springmockk.MockkBean
 import io.mockk.every
 import org.genspectrum.lapis.model.SiloQueryModel
+import org.genspectrum.lapis.request.DEFAULT_MIN_PROPORTION
 import org.genspectrum.lapis.request.Field
 import org.genspectrum.lapis.request.MutationProportionsRequest
 import org.genspectrum.lapis.request.NucleotideMutation
@@ -170,7 +172,7 @@ class LapisControllerTest(
     @ParameterizedTest(name = "GET {0} without explicit minProportion")
     @MethodSource("getMutationEndpoints")
     fun `GET mutations without explicit minProportion`(endpoint: String) {
-        setupMutationMock(endpoint, null)
+        setupMutationMock(endpoint, DEFAULT_MIN_PROPORTION)
 
         mockMvc.perform(getSample("$endpoint?country=Switzerland"))
             .andExpect(status().isOk)
@@ -196,7 +198,7 @@ class LapisControllerTest(
     @ParameterizedTest(name = "POST {0} without explicit minProportion")
     @MethodSource("getMutationEndpoints")
     fun `POST mutations without explicit minProportion`(endpoint: String) {
-        setupMutationMock(endpoint, null)
+        setupMutationMock(endpoint, DEFAULT_MIN_PROPORTION)
 
         val request = postSample(endpoint)
             .content("""{"country": "Switzerland"}""")
@@ -245,13 +247,13 @@ class LapisControllerTest(
     @ParameterizedTest(name = "GET {0} only returns mutation, proportion and count")
     @MethodSource("getMutationEndpoints")
     fun `GET mutations only returns mutation, proportion and count`(endpoint: String) {
-        setupMutationMock(endpoint, null)
+        setupMutationMock(endpoint, DEFAULT_MIN_PROPORTION)
 
         val mvcResult = mockMvc.perform(getSample("$endpoint?country=Switzerland"))
             .andExpect(status().isOk)
             .andReturn()
 
-        val response = ObjectMapper().readValue(mvcResult.response.contentAsString, Map::class.java)
+        val response = ObjectMapper().readValue<Map<*, *>>(mvcResult.response.contentAsString)
         val data = response["data"] as List<*>
         val firstDataObject = data[0] as Map<*, *>
 
@@ -261,7 +263,7 @@ class LapisControllerTest(
 
     private fun setupMutationMock(
         endpoint: String,
-        minProportion: Double?,
+        minProportion: Double = DEFAULT_MIN_PROPORTION,
     ) {
         if (endpoint == "/nucleotideMutations") {
             every {

diff --git a/lapis2/src/test/kotlin/org/genspectrum/lapis/request/MutationProportionsRequestTest.kt b/lapis2/src/test/kotlin/org/genspectrum/lapis/request/MutationProportionsRequestTest.kt
@@ -57,6 +57,7 @@ class MutationProportionsRequestTest {
                         emptyList(),
                         emptyList(),
                         emptyList(),
+                        minProportion = DEFAULT_MIN_PROPORTION,
                     ),
                 ),
                 Arguments.of(
@@ -71,6 +72,7 @@ class MutationProportionsRequestTest {
                         emptyList(),
                         emptyList(),
                         emptyList(),
+                        minProportion = DEFAULT_MIN_PROPORTION,
                     ),
                 ),
                 Arguments.of(
@@ -85,6 +87,7 @@ class MutationProportionsRequestTest {
                         listOf(AminoAcidMutation("S", 501, "Y"), AminoAcidMutation("ORF1b", 12, null)),
                         emptyList(),
                         emptyList(),
+                        minProportion = DEFAULT_MIN_PROPORTION,
                     ),
                 ),
                 Arguments.of(
@@ -102,6 +105,7 @@ class MutationProportionsRequestTest {
                             NucleotideInsertion(12, "ABCD", null),
                         ),
                         emptyList(),
+                        minProportion = DEFAULT_MIN_PROPORTION,
                     ),
                 ),
                 Arguments.of(
@@ -119,6 +123,7 @@ class MutationProportionsRequestTest {
                             AminoAcidInsertion(501, "S", "Y"),
                             AminoAcidInsertion(12, "ORF1", "ABCD"),
                         ),
+                        minProportion = DEFAULT_MIN_PROPORTION,
                     ),
                 ),
                 Arguments.of(
@@ -135,14 +140,28 @@ class MutationProportionsRequestTest {
                     "accessKey": "some access key"                
                 }
                 """,
-                    MutationProportionsRequest(emptyMap(), emptyList(), emptyList(), emptyList(), emptyList()),
+                    MutationProportionsRequest(
+                        emptyMap(),
+                        emptyList(),
+                        emptyList(),
+                        emptyList(),
+                        emptyList(),
+                        minProportion = DEFAULT_MIN_PROPORTION,
+                    ),
                 ),
                 Arguments.of(
                     """
                 {
                 }
                 """,
-                    MutationProportionsRequest(emptyMap(), emptyList(), emptyList(), emptyList(), emptyList()),
+                    MutationProportionsRequest(
+                        emptyMap(),
+                        emptyList(),
+                        emptyList(),
+                        emptyList(),
+                        emptyList(),
+                        minProportion = DEFAULT_MIN_PROPORTION,
+                    ),
                 ),
             )