feat: e2e tests for filter by insertions

GenSpectrum · Sep 13, 2023 · fe8f0b9 · fe8f0b9
1 parent 3376cb7
commit fe8f0b9
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Showing 25 changed files with 513 additions and 218 deletions.
diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/OpenApiDocs.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/OpenApiDocs.kt
@@ -11,6 +11,8 @@ import org.genspectrum.lapis.config.SequenceFilterFields
 import org.genspectrum.lapis.controller.AGGREGATED_GROUP_BY_FIELDS_DESCRIPTION
 import org.genspectrum.lapis.controller.AGGREGATED_REQUEST_SCHEMA
 import org.genspectrum.lapis.controller.AGGREGATED_RESPONSE_SCHEMA
+import org.genspectrum.lapis.controller.AMINO_ACID_INSERTIONS_PROPERTY
+import org.genspectrum.lapis.controller.AMINO_ACID_INSERTIONS_SCHEMA
 import org.genspectrum.lapis.controller.AMINO_ACID_MUTATIONS_PROPERTY
 import org.genspectrum.lapis.controller.AMINO_ACID_MUTATIONS_RESPONSE_SCHEMA
 import org.genspectrum.lapis.controller.AMINO_ACID_MUTATIONS_SCHEMA
@@ -25,6 +27,8 @@ import org.genspectrum.lapis.controller.LIMIT_DESCRIPTION
 import org.genspectrum.lapis.controller.LIMIT_PROPERTY
 import org.genspectrum.lapis.controller.LIMIT_SCHEMA
 import org.genspectrum.lapis.controller.MIN_PROPORTION_PROPERTY
+import org.genspectrum.lapis.controller.NUCLEOTIDE_INSERTIONS_PROPERTY
+import org.genspectrum.lapis.controller.NUCLEOTIDE_INSERTIONS_SCHEMA
 import org.genspectrum.lapis.controller.NUCLEOTIDE_MUTATIONS_PROPERTY
 import org.genspectrum.lapis.controller.NUCLEOTIDE_MUTATIONS_RESPONSE_SCHEMA
 import org.genspectrum.lapis.controller.NUCLEOTIDE_MUTATIONS_SCHEMA
@@ -35,7 +39,9 @@ import org.genspectrum.lapis.controller.ORDER_BY_FIELDS_SCHEMA
 import org.genspectrum.lapis.controller.ORDER_BY_PROPERTY
 import org.genspectrum.lapis.controller.REQUEST_SCHEMA_WITH_MIN_PROPORTION
 import org.genspectrum.lapis.controller.SEQUENCE_FILTERS_SCHEMA
+import org.genspectrum.lapis.request.AminoAcidInsertion
 import org.genspectrum.lapis.request.AminoAcidMutation
+import org.genspectrum.lapis.request.NucleotideInsertion
 import org.genspectrum.lapis.request.NucleotideMutation
 import org.genspectrum.lapis.request.OrderByField
 import org.genspectrum.lapis.response.COUNT_PROPERTY
@@ -51,6 +57,8 @@ fun buildOpenApiSchema(sequenceFilterFields: SequenceFilterFields, databaseConfi
     val sequenceFilters = requestProperties +
         Pair(NUCLEOTIDE_MUTATIONS_PROPERTY, nucleotideMutations()) +
         Pair(AMINO_ACID_MUTATIONS_PROPERTY, aminoAcidMutations()) +
+        Pair(NUCLEOTIDE_INSERTIONS_PROPERTY, nucleotideInsertions()) +
+        Pair(AMINO_ACID_INSERTIONS_PROPERTY, aminoAcidInsertions()) +
         Pair(ORDER_BY_PROPERTY, orderByPostSchema()) +
         Pair(LIMIT_PROPERTY, limitSchema()) +
         Pair(OFFSET_PROPERTY, offsetSchema()) +
@@ -130,6 +138,8 @@ fun buildOpenApiSchema(sequenceFilterFields: SequenceFilterFields, databaseConfi
                     ),
                 )
                 .addSchemas(AMINO_ACID_MUTATIONS_SCHEMA, aminoAcidMutations())
+                .addSchemas(NUCLEOTIDE_INSERTIONS_SCHEMA, nucleotideInsertions())
+                .addSchemas(AMINO_ACID_INSERTIONS_SCHEMA, aminoAcidInsertions())
                 .addSchemas(ORDER_BY_FIELDS_SCHEMA, orderByGetSchema())
                 .addSchemas(LIMIT_SCHEMA, limitSchema())
                 .addSchemas(OFFSET_SCHEMA, offsetSchema())
@@ -160,6 +170,8 @@ private fun mapToOpenApiType(type: MetadataType): String = when (type) {
     MetadataType.DATE -> "string"
     MetadataType.INT -> "integer"
     MetadataType.FLOAT -> "number"
+    MetadataType.NUCLEOTIDE_INSERTION -> "string"
+    MetadataType.AMINO_ACID_INSERTION -> "string"
 }
 
 private fun primitiveSequenceFilterFieldSchemas(sequenceFilterFields: SequenceFilterFields) =
@@ -242,6 +254,35 @@ private fun aminoAcidMutations() =
                 ),
         )
 
+private fun nucleotideInsertions() =
+    Schema<List<NucleotideInsertion>>()
+        .type("array")
+        .items(
+            Schema<String>()
+                .type("string")
+                .example("ins_123:ATT")
+                .description(
+                    """
+                    |A nucleotide insertion in the format "ins_(\<sequenceName\>:)?\<position\>:\<insertion\>".  
+                    |If the sequenceName is not provided, LAPIS will use the default sequence name.  
+                    """.trimMargin(),
+                ),
+        )
+
+private fun aminoAcidInsertions() =
+    Schema<List<AminoAcidInsertion>>()
+        .type("array")
+        .items(
+            Schema<String>()
+                .type("string")
+                .example("ins_ORF1:123:ATT")
+                .description(
+                    """
+                    |A amino acid insertion in the format "ins_\<gene\>:\<position\>:\<insertion\>".  
+                    """.trimMargin(),
+                ),
+        )
+
 private fun orderByGetSchema() = Schema<List<String>>()
     .type("array")
     .items(orderByFieldStringSchema())

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/config/DatabaseConfig.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/config/DatabaseConfig.kt
@@ -32,6 +32,12 @@ enum class MetadataType {
 
     @JsonProperty("float")
     FLOAT,
+
+    @JsonProperty("insertion")
+    NUCLEOTIDE_INSERTION,
+
+    @JsonProperty("aaInsertion")
+    AMINO_ACID_INSERTION,
 }
 
 data class DatabaseFeature(val name: String)

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/config/SequenceFilterFields.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/config/SequenceFilterFields.kt
@@ -39,6 +39,8 @@ private fun mapToSequenceFilterFields(databaseMetadata: DatabaseMetadata) = when
         "${databaseMetadata.name}From" to SequenceFilterFieldType.FloatFrom(databaseMetadata.name),
         "${databaseMetadata.name}To" to SequenceFilterFieldType.FloatTo(databaseMetadata.name),
     )
+    MetadataType.NUCLEOTIDE_INSERTION -> emptyList()
+    MetadataType.AMINO_ACID_INSERTION -> emptyList()
 }
 
 private fun mapToSequenceFilterFieldsFromFeatures(databaseFeature: DatabaseFeature) = when (databaseFeature.name) {

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/LapisController.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/LapisController.kt
@@ -42,6 +42,9 @@ const val AMINO_ACID_MUTATIONS_RESPONSE_SCHEMA = "AminoAcidMutationsResponse"
 
 const val NUCLEOTIDE_MUTATIONS_SCHEMA = "NucleotideMutations"
 const val AMINO_ACID_MUTATIONS_SCHEMA = "AminoAcidMutations"
+const val NUCLEOTIDE_INSERTIONS_SCHEMA = "NucleotideInsertions"
+const val AMINO_ACID_INSERTIONS_SCHEMA = "AminoAcidInsertions"
+
 const val ORDER_BY_FIELDS_SCHEMA = "OrderByFields"
 const val LIMIT_SCHEMA = "Limit"
 const val OFFSET_SCHEMA = "Offset"
@@ -102,8 +105,10 @@ class LapisController(
         @RequestParam
         aminoAcidMutations: List<AminoAcidMutation>?,
         @RequestParam
+        @Parameter(schema = Schema(ref = "#/components/schemas/$NUCLEOTIDE_INSERTIONS_SCHEMA"))
         nucleotideInsertions: List<NucleotideInsertion>?,
         @RequestParam
+        @Parameter(schema = Schema(ref = "#/components/schemas/$AMINO_ACID_INSERTIONS_SCHEMA"))
         aminoAcidInsertions: List<AminoAcidInsertion>?,
         @Parameter(
             schema = Schema(ref = "#/components/schemas/$LIMIT_SCHEMA"),
@@ -188,8 +193,10 @@ class LapisController(
         @RequestParam
         dataFormat: String? = null,
         @RequestParam
+        @Parameter(schema = Schema(ref = "#/components/schemas/$NUCLEOTIDE_INSERTIONS_SCHEMA"))
         nucleotideInsertions: List<NucleotideInsertion>?,
         @RequestParam
+        @Parameter(schema = Schema(ref = "#/components/schemas/$AMINO_ACID_INSERTIONS_SCHEMA"))
         aminoAcidInsertions: List<AminoAcidInsertion>?,
     ): String {
         val request = SequenceFiltersRequestWithFields(
@@ -254,8 +261,10 @@ class LapisController(
         @RequestParam
         dataFormat: String? = null,
         @RequestParam
+        @Parameter(schema = Schema(ref = "#/components/schemas/$NUCLEOTIDE_INSERTIONS_SCHEMA"))
         nucleotideInsertions: List<NucleotideInsertion>?,
         @RequestParam
+        @Parameter(schema = Schema(ref = "#/components/schemas/$AMINO_ACID_INSERTIONS_SCHEMA"))
         aminoAcidInsertions: List<AminoAcidInsertion>?,
     ): String {
         val request = SequenceFiltersRequestWithFields(
@@ -296,7 +305,7 @@ class LapisController(
         responses = [ApiResponse(responseCode = "200")],
     )
     fun postAggregatedAsCsv(
-        @Parameter(schema = Schema(ref = "#/components/schemas/$DETAILS_REQUEST_SCHEMA"))
+        @Parameter(schema = Schema(ref = "#/components/schemas/$AGGREGATED_REQUEST_SCHEMA"))
         @RequestBody
         request: SequenceFiltersRequestWithFields,
     ): String {
@@ -310,7 +319,7 @@ class LapisController(
         responses = [ApiResponse(responseCode = "200")],
     )
     fun postAggregatedAsTsv(
-        @Parameter(schema = Schema(ref = "#/components/schemas/$DETAILS_REQUEST_SCHEMA"))
+        @Parameter(schema = Schema(ref = "#/components/schemas/$AGGREGATED_REQUEST_SCHEMA"))
         @RequestBody
         request: SequenceFiltersRequestWithFields,
     ): String {
@@ -365,8 +374,10 @@ class LapisController(
         @RequestParam
         dataFormat: String? = null,
         @RequestParam
+        @Parameter(schema = Schema(ref = "#/components/schemas/$NUCLEOTIDE_INSERTIONS_SCHEMA"))
         nucleotideInsertions: List<NucleotideInsertion>?,
         @RequestParam
+        @Parameter(schema = Schema(ref = "#/components/schemas/$AMINO_ACID_INSERTIONS_SCHEMA"))
         aminoAcidInsertions: List<AminoAcidInsertion>?,
     ): LapisResponse<List<NucleotideMutationResponse>> {
         val mutationProportionsRequest = MutationProportionsRequest(
@@ -427,8 +438,10 @@ class LapisController(
         @RequestParam
         offset: Int? = null,
         @RequestParam
+        @Parameter(schema = Schema(ref = "#/components/schemas/$NUCLEOTIDE_INSERTIONS_SCHEMA"))
         nucleotideInsertions: List<NucleotideInsertion>?,
         @RequestParam
+        @Parameter(schema = Schema(ref = "#/components/schemas/$AMINO_ACID_INSERTIONS_SCHEMA"))
         aminoAcidInsertions: List<AminoAcidInsertion>?,
     ): String {
         val request = MutationProportionsRequest(
@@ -487,8 +500,10 @@ class LapisController(
         @RequestParam
         offset: Int? = null,
         @RequestParam
+        @Parameter(schema = Schema(ref = "#/components/schemas/$NUCLEOTIDE_INSERTIONS_SCHEMA"))
         nucleotideInsertions: List<NucleotideInsertion>?,
         @RequestParam
+        @Parameter(schema = Schema(ref = "#/components/schemas/$AMINO_ACID_INSERTIONS_SCHEMA"))
         aminoAcidInsertions: List<AminoAcidInsertion>?,
     ): String {
         val request = MutationProportionsRequest(
@@ -594,8 +609,10 @@ class LapisController(
         @RequestParam
         offset: Int? = null,
         @RequestParam
+        @Parameter(schema = Schema(ref = "#/components/schemas/$NUCLEOTIDE_INSERTIONS_SCHEMA"))
         nucleotideInsertions: List<NucleotideInsertion>?,
         @RequestParam
+        @Parameter(schema = Schema(ref = "#/components/schemas/$AMINO_ACID_INSERTIONS_SCHEMA"))
         aminoAcidInsertions: List<AminoAcidInsertion>?,
     ): LapisResponse<List<AminoAcidMutationResponse>> {
         val mutationProportionsRequest = MutationProportionsRequest(
@@ -656,8 +673,10 @@ class LapisController(
         @RequestParam
         offset: Int? = null,
         @RequestParam
+        @Parameter(schema = Schema(ref = "#/components/schemas/$NUCLEOTIDE_INSERTIONS_SCHEMA"))
         nucleotideInsertions: List<NucleotideInsertion>?,
         @RequestParam
+        @Parameter(schema = Schema(ref = "#/components/schemas/$AMINO_ACID_INSERTIONS_SCHEMA"))
         aminoAcidInsertions: List<AminoAcidInsertion>?,
     ): String {
         val mutationProportionsRequest = MutationProportionsRequest(
@@ -716,8 +735,10 @@ class LapisController(
         @RequestParam
         offset: Int? = null,
         @RequestParam
+        @Parameter(schema = Schema(ref = "#/components/schemas/$NUCLEOTIDE_INSERTIONS_SCHEMA"))
         nucleotideInsertions: List<NucleotideInsertion>?,
         @RequestParam
+        @Parameter(schema = Schema(ref = "#/components/schemas/$AMINO_ACID_INSERTIONS_SCHEMA"))
         aminoAcidInsertions: List<AminoAcidInsertion>?,
     ): String {
         val mutationProportionsRequest = MutationProportionsRequest(
@@ -842,8 +863,10 @@ class LapisController(
         @RequestParam
         dataFormat: String? = null,
         @RequestParam
+        @Parameter(schema = Schema(ref = "#/components/schemas/$NUCLEOTIDE_INSERTIONS_SCHEMA"))
         nucleotideInsertions: List<NucleotideInsertion>?,
         @RequestParam
+        @Parameter(schema = Schema(ref = "#/components/schemas/$AMINO_ACID_INSERTIONS_SCHEMA"))
         aminoAcidInsertions: List<AminoAcidInsertion>?,
     ): LapisResponse<List<DetailsData>> {
         val request = SequenceFiltersRequestWithFields(
@@ -901,8 +924,10 @@ class LapisController(
         @RequestParam
         offset: Int? = null,
         @RequestParam
+        @Parameter(schema = Schema(ref = "#/components/schemas/$NUCLEOTIDE_INSERTIONS_SCHEMA"))
         nucleotideInsertions: List<NucleotideInsertion>?,
         @RequestParam
+        @Parameter(schema = Schema(ref = "#/components/schemas/$AMINO_ACID_INSERTIONS_SCHEMA"))
         aminoAcidInsertions: List<AminoAcidInsertion>?,
     ): String {
         val request = SequenceFiltersRequestWithFields(
@@ -958,8 +983,10 @@ class LapisController(
         @RequestParam
         offset: Int? = null,
         @RequestParam
+        @Parameter(schema = Schema(ref = "#/components/schemas/$NUCLEOTIDE_INSERTIONS_SCHEMA"))
         nucleotideInsertions: List<NucleotideInsertion>?,
         @RequestParam
+        @Parameter(schema = Schema(ref = "#/components/schemas/$AMINO_ACID_INSERTIONS_SCHEMA"))
         aminoAcidInsertions: List<AminoAcidInsertion>?,
     ): String {
         val request = SequenceFiltersRequestWithFields(

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/request/AminoAcidInsertion.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/request/AminoAcidInsertion.kt
@@ -25,7 +25,7 @@ data class AminoAcidInsertion(val position: Int, val gene: String, val insertion
                     "Invalid amino acid insertion: $aminoAcidInsertion: Did not find gene",
                 )
 
-            val insertions = matchGroups["insertion"]?.value?.replace("?", ".*")
+            val insertions = matchGroups["insertions"]?.value?.replace("?", ".*")
                 ?: throw IllegalArgumentException(
                     "Invalid amino acid insertion: $aminoAcidInsertion: Did not find insertions",
                 )
@@ -41,7 +41,7 @@ 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+):(?<insertion>[a-zA-Z0-9?_-]+)?$""",
+        """^ins_(?<gene>[a-zA-Z0-9_-]+):(?<position>\d+):(?<insertions>(([a-zA-Z?]|(\.\*))+))$""",
     )
 
 @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
@@ -36,7 +36,7 @@ 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-Z0-9?_-]+)?$""",
+        """^ins_((?<segment>[a-zA-Z0-9_-]+)(?=:):)?(?<position>\d+):(?<insertions>(([a-zA-Z?]|(\.\*))+))$""",
     )
 
 @JsonComponent

diff --git a/lapis2/src/test/kotlin/org/genspectrum/lapis/config/DatabaseConfigTest.kt b/lapis2/src/test/kotlin/org/genspectrum/lapis/config/DatabaseConfigTest.kt
@@ -26,6 +26,8 @@ class DatabaseConfigTest {
                 DatabaseMetadata(name = "region", type = MetadataType.STRING),
                 DatabaseMetadata(name = "country", type = MetadataType.STRING),
                 DatabaseMetadata(name = "pangoLineage", type = MetadataType.PANGO_LINEAGE),
+                DatabaseMetadata(name = "nucInsertion", type = MetadataType.NUCLEOTIDE_INSERTION),
+                DatabaseMetadata(name = "aaInsertion", type = MetadataType.AMINO_ACID_INSERTION),
             ),
         )
         assertThat(
@@ -56,6 +58,8 @@ class DatabaseConfigWithoutFeaturesTest {
                 DatabaseMetadata(name = "region", type = MetadataType.STRING),
                 DatabaseMetadata(name = "country", type = MetadataType.STRING),
                 DatabaseMetadata(name = "pangoLineage", type = MetadataType.PANGO_LINEAGE),
+                DatabaseMetadata(name = "nucInsertion", type = MetadataType.NUCLEOTIDE_INSERTION),
+                DatabaseMetadata(name = "aaInsertion", type = MetadataType.AMINO_ACID_INSERTION),
             ),
         )
         assertThat(underTest.schema.features, `is`(emptyList()))