feat: allow string arrays as filter for string and pango lineage fields

#507
GenSpectrum · Dec 19, 2023 · 4d06713 · 4d06713
1 parent 83c1b3e
commit 4d06713
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Showing 47 changed files with 1,960 additions and 1,746 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
@@ -41,6 +41,7 @@ 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.GetRequestSequenceFilters
 import org.genspectrum.lapis.request.MutationProportionsRequest
 import org.genspectrum.lapis.request.NucleotideInsertion
 import org.genspectrum.lapis.request.NucleotideMutation
@@ -84,7 +85,7 @@ class LapisController(
     fun aggregated(
         @PrimitiveFieldFilters
         @RequestParam
-        sequenceFilters: Map<String, String>?,
+        sequenceFilters: GetRequestSequenceFilters?,
         @FieldsToAggregateBy
         @RequestParam
         fields: List<Field>?,
@@ -139,7 +140,7 @@ class LapisController(
     fun getAggregatedAsCsv(
         @PrimitiveFieldFilters
         @RequestParam
-        sequenceFilters: Map<String, String>?,
+        sequenceFilters: GetRequestSequenceFilters?,
         @FieldsToAggregateBy
         @RequestParam
         fields: List<Field>?,
@@ -192,7 +193,7 @@ class LapisController(
     fun getAggregatedAsTsv(
         @PrimitiveFieldFilters
         @RequestParam
-        sequenceFilters: Map<String, String>?,
+        sequenceFilters: GetRequestSequenceFilters?,
         @FieldsToAggregateBy
         @RequestParam
         fields: List<Field>?,
@@ -284,7 +285,7 @@ class LapisController(
     fun getNucleotideMutations(
         @PrimitiveFieldFilters
         @RequestParam
-        sequenceFilters: Map<String, String>?,
+        sequenceFilters: GetRequestSequenceFilters?,
         @RequestParam(required = false)
         @NucleotideMutations
         nucleotideMutations: List<NucleotideMutation>?,
@@ -339,7 +340,7 @@ class LapisController(
     fun getNucleotideMutationsAsCsv(
         @PrimitiveFieldFilters
         @RequestParam
-        sequenceFilters: Map<String, String>?,
+        sequenceFilters: GetRequestSequenceFilters?,
         @RequestParam(required = false)
         @NucleotideMutations
         nucleotideMutations: List<NucleotideMutation>?,
@@ -388,7 +389,7 @@ class LapisController(
     fun getNucleotideMutationsAsTsv(
         @PrimitiveFieldFilters
         @RequestParam
-        sequenceFilters: Map<String, String>?,
+        sequenceFilters: GetRequestSequenceFilters?,
         @RequestParam(required = false)
         @NucleotideMutations
         nucleotideMutations: List<NucleotideMutation>?,
@@ -477,7 +478,7 @@ class LapisController(
     fun getAminoAcidMutations(
         @PrimitiveFieldFilters
         @RequestParam
-        sequenceFilters: Map<String, String>?,
+        sequenceFilters: GetRequestSequenceFilters?,
         @RequestParam(required = false)
         @NucleotideMutations
         nucleotideMutations: List<NucleotideMutation>?,
@@ -528,7 +529,7 @@ class LapisController(
     fun getAminoAcidMutationsAsCsv(
         @PrimitiveFieldFilters
         @RequestParam
-        sequenceFilters: Map<String, String>?,
+        sequenceFilters: GetRequestSequenceFilters?,
         @RequestParam(required = false)
         @NucleotideMutations
         nucleotideMutations: List<NucleotideMutation>?,
@@ -577,7 +578,7 @@ class LapisController(
     fun getAminoAcidMutationsAsTsv(
         @PrimitiveFieldFilters
         @RequestParam
-        sequenceFilters: Map<String, String>?,
+        sequenceFilters: GetRequestSequenceFilters?,
         @RequestParam(required = false)
         @NucleotideMutations
         nucleotideMutations: List<NucleotideMutation>?,
@@ -682,7 +683,7 @@ class LapisController(
     fun getDetailsAsJson(
         @PrimitiveFieldFilters
         @RequestParam
-        sequenceFilters: Map<String, String>?,
+        sequenceFilters: GetRequestSequenceFilters?,
         @DetailsFields
         @RequestParam
         fields: List<Field>?,
@@ -735,7 +736,7 @@ class LapisController(
     fun getDetailsAsCsv(
         @PrimitiveFieldFilters
         @RequestParam
-        sequenceFilters: Map<String, String>?,
+        sequenceFilters: GetRequestSequenceFilters?,
         @DetailsFields
         @RequestParam
         fields: List<Field>?,
@@ -785,7 +786,7 @@ class LapisController(
     fun getDetailsAsTsv(
         @PrimitiveFieldFilters
         @RequestParam
-        sequenceFilters: Map<String, String>?,
+        sequenceFilters: GetRequestSequenceFilters?,
         @DetailsFields
         @RequestParam
         fields: List<Field>?,
@@ -874,7 +875,7 @@ class LapisController(
     fun getNucleotideInsertions(
         @PrimitiveFieldFilters
         @RequestParam
-        sequenceFilters: Map<String, String>?,
+        sequenceFilters: GetRequestSequenceFilters?,
         @InsertionsOrderByFields
         @RequestParam
         orderBy: List<OrderByField>?,
@@ -926,7 +927,7 @@ class LapisController(
     fun getNucleotideInsertionsAsCsv(
         @PrimitiveFieldFilters
         @RequestParam
-        sequenceFilters: Map<String, String>?,
+        sequenceFilters: GetRequestSequenceFilters?,
         @InsertionsOrderByFields
         @RequestParam
         orderBy: List<OrderByField>?,
@@ -977,7 +978,7 @@ class LapisController(
     fun getNucleotideInsertionsAsTsv(
         @PrimitiveFieldFilters
         @RequestParam
-        sequenceFilters: Map<String, String>?,
+        sequenceFilters: GetRequestSequenceFilters?,
         @InsertionsOrderByFields
         @RequestParam
         orderBy: List<OrderByField>?,
@@ -1072,7 +1073,7 @@ class LapisController(
     fun getAminoAcidInsertions(
         @PrimitiveFieldFilters
         @RequestParam
-        sequenceFilters: Map<String, String>?,
+        sequenceFilters: GetRequestSequenceFilters?,
         @InsertionsOrderByFields
         @RequestParam
         orderBy: List<OrderByField>?,
@@ -1124,7 +1125,7 @@ class LapisController(
     fun getAminoAcidInsertionsAsCsv(
         @PrimitiveFieldFilters
         @RequestParam
-        sequenceFilters: Map<String, String>?,
+        sequenceFilters: GetRequestSequenceFilters?,
         @InsertionsOrderByFields
         @RequestParam
         orderBy: List<OrderByField>?,
@@ -1175,7 +1176,7 @@ class LapisController(
     fun getAminoAcidInsertionsAsTsv(
         @PrimitiveFieldFilters
         @RequestParam
-        sequenceFilters: Map<String, String>?,
+        sequenceFilters: GetRequestSequenceFilters?,
         @InsertionsOrderByFields
         @RequestParam
         orderBy: List<OrderByField>?,
@@ -1271,7 +1272,7 @@ class LapisController(
         @PathVariable(name = "gene", required = true) gene: String,
         @PrimitiveFieldFilters
         @RequestParam
-        sequenceFilters: Map<String, String>?,
+        sequenceFilters: GetRequestSequenceFilters?,
         @AminoAcidSequencesOrderByFields
         @RequestParam
         orderBy: List<OrderByField>?,

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/MultiSegmentedSequenceController.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/MultiSegmentedSequenceController.kt
@@ -17,6 +17,7 @@ import org.genspectrum.lapis.openApi.Offset
 import org.genspectrum.lapis.openApi.PrimitiveFieldFilters
 import org.genspectrum.lapis.request.AminoAcidInsertion
 import org.genspectrum.lapis.request.AminoAcidMutation
+import org.genspectrum.lapis.request.GetRequestSequenceFilters
 import org.genspectrum.lapis.request.NucleotideInsertion
 import org.genspectrum.lapis.request.NucleotideMutation
 import org.genspectrum.lapis.request.OrderByField
@@ -47,7 +48,7 @@ class MultiSegmentedSequenceController(
         @PathVariable(name = "segment", required = true) segment: String,
         @PrimitiveFieldFilters
         @RequestParam
-        sequenceFilters: Map<String, String>?,
+        sequenceFilters: GetRequestSequenceFilters?,
         @NucleotideSequencesOrderByFields
         @RequestParam
         orderBy: List<OrderByField>?,

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/SingleSegmentedSequenceController.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/controller/SingleSegmentedSequenceController.kt
@@ -18,6 +18,7 @@ import org.genspectrum.lapis.openApi.Offset
 import org.genspectrum.lapis.openApi.PrimitiveFieldFilters
 import org.genspectrum.lapis.request.AminoAcidInsertion
 import org.genspectrum.lapis.request.AminoAcidMutation
+import org.genspectrum.lapis.request.GetRequestSequenceFilters
 import org.genspectrum.lapis.request.NucleotideInsertion
 import org.genspectrum.lapis.request.NucleotideMutation
 import org.genspectrum.lapis.request.OrderByField
@@ -47,7 +48,7 @@ class SingleSegmentedSequenceController(
     fun getAlignedNucleotideSequences(
         @PrimitiveFieldFilters
         @RequestParam
-        sequenceFilters: Map<String, String>?,
+        sequenceFilters: GetRequestSequenceFilters?,
         @NucleotideSequencesOrderByFields
         @RequestParam
         orderBy: List<OrderByField>?,

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/model/SiloFilterExpressionMapper.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/model/SiloFilterExpressionMapper.kt
@@ -21,6 +21,7 @@ import org.genspectrum.lapis.silo.IntBetween
 import org.genspectrum.lapis.silo.IntEquals
 import org.genspectrum.lapis.silo.NucleotideInsertionContains
 import org.genspectrum.lapis.silo.NucleotideSymbolEquals
+import org.genspectrum.lapis.silo.Or
 import org.genspectrum.lapis.silo.PangoLineageEquals
 import org.genspectrum.lapis.silo.SiloFilterExpression
 import org.genspectrum.lapis.silo.StringEquals
@@ -30,7 +31,7 @@ import java.time.LocalDate
 import java.time.format.DateTimeParseException
 import java.util.Locale
 
-data class SequenceFilterValue(val type: SequenceFilterFieldType, val value: String, val originalKey: String)
+data class SequenceFilterValue(val type: SequenceFilterFieldType, val values: List<String>, val originalKey: String)
 
 typealias SequenceFilterFieldName = String
 
@@ -46,10 +47,10 @@ class SiloFilterExpressionMapper(
 
         val allowedSequenceFiltersWithType = sequenceFilters
             .sequenceFilters
-            .map { (key, value) ->
+            .map { (key, values) ->
                 val nullableField = allowedSequenceFilterFields.fields[key.lowercase(Locale.US)]
                 val (filterExpressionId, type) = mapToFilterExpressionIdentifier(nullableField, key)
-                filterExpressionId to SequenceFilterValue(type, value, key)
+                filterExpressionId to SequenceFilterValue(type, values, key)
             }
             .groupBy({ it.first }, { it.second })
 
@@ -62,10 +63,10 @@ class SiloFilterExpressionMapper(
         val filterExpressions = allowedSequenceFiltersWithType.map { (key, values) ->
             val (siloColumnName, filter) = key
             when (filter) {
-                Filter.StringEquals -> StringEquals(siloColumnName, values[0].value)
-                Filter.PangoLineage -> mapToPangoLineageFilter(siloColumnName, values[0].value)
+                Filter.StringEquals -> mapToStringEqualsFilters(siloColumnName, values)
+                Filter.PangoLineage -> mapToPangoLineageFilter(siloColumnName, values)
                 Filter.DateBetween -> mapToDateBetweenFilter(siloColumnName, values)
-                Filter.VariantQuery -> mapToVariantQueryFilter(values[0].value)
+                Filter.VariantQuery -> mapToVariantQueryFilter(values[0].values[0])
                 Filter.IntEquals -> mapToIntEqualsFilter(siloColumnName, values)
                 Filter.IntBetween -> mapToIntBetweenFilter(siloColumnName, values)
                 Filter.FloatEquals -> mapToFloatEqualsFilter(siloColumnName, values)
@@ -161,6 +162,11 @@ class SiloFilterExpressionMapper(
         }
     }
 
+    private fun mapToStringEqualsFilters(
+        siloColumnName: SequenceFilterFieldName,
+        values: List<SequenceFilterValue>,
+    ) = Or(values[0].values.map { StringEquals(siloColumnName, it) })
+
     private fun mapToVariantQueryFilter(variantQuery: String): SiloFilterExpression {
         if (variantQuery.isBlank()) {
             throw BadRequestException("variantQuery must not be empty")
@@ -208,7 +214,8 @@ class SiloFilterExpressionMapper(
     }
 
     private fun getAsDate(sequenceFilterValue: SequenceFilterValue?): LocalDate? {
-        val (_, value, originalKey) = sequenceFilterValue ?: return null
+        val (_, values, originalKey) = sequenceFilterValue ?: return null
+        val value = extractSingleFilterValue(values, originalKey)
 
         try {
             return LocalDate.parse(value)
@@ -219,22 +226,26 @@ class SiloFilterExpressionMapper(
 
     private fun mapToPangoLineageFilter(
         column: String,
-        value: String,
-    ) = when {
-        value.endsWith(".*") -> PangoLineageEquals(column, value.substringBeforeLast(".*"), includeSublineages = true)
-        value.endsWith('*') -> PangoLineageEquals(column, value.substringBeforeLast('*'), includeSublineages = true)
-        value.endsWith('.') -> throw BadRequestException(
-            "Invalid pango lineage: $value must not end with a dot. Did you mean '$value*'?",
-        )
+        values: List<SequenceFilterValue>,
+    ) = Or(
+        values[0].values.map {
+            when {
+                it.endsWith(".*") -> PangoLineageEquals(column, it.substringBeforeLast(".*"), includeSublineages = true)
+                it.endsWith('*') -> PangoLineageEquals(column, it.substringBeforeLast('*'), includeSublineages = true)
+                it.endsWith('.') -> throw BadRequestException(
+                    "Invalid pango lineage: $it must not end with a dot. Did you mean '$it*'?",
+                )
 
-        else -> PangoLineageEquals(column, value, includeSublineages = false)
-    }
+                else -> PangoLineageEquals(column, it, includeSublineages = false)
+            }
+        },
+    )
 
     private fun mapToIntEqualsFilter(
         siloColumnName: SequenceFilterFieldName,
         values: List<SequenceFilterValue>,
     ): SiloFilterExpression {
-        val value = values[0].value
+        val value = extractSingleFilterValue(values[0])
         try {
             return IntEquals(siloColumnName, value.toInt())
         } catch (exception: NumberFormatException) {
@@ -249,7 +260,7 @@ class SiloFilterExpressionMapper(
         siloColumnName: SequenceFilterFieldName,
         values: List<SequenceFilterValue>,
     ): SiloFilterExpression {
-        val value = values[0].value
+        val value = extractSingleFilterValue(values[0])
         try {
             return FloatEquals(siloColumnName, value.toDouble())
         } catch (exception: NumberFormatException) {
@@ -274,7 +285,8 @@ class SiloFilterExpressionMapper(
     private inline fun <reified T : SequenceFilterFieldType> findIntOfFilterType(
         dateRangeFilters: List<SequenceFilterValue>,
     ): Int? {
-        val (_, value, originalKey) = dateRangeFilters.find { (type, _, _) -> type is T } ?: return null
+        val (_, values, originalKey) = dateRangeFilters.find { (type, _, _) -> type is T } ?: return null
+        val value = extractSingleFilterValue(values, originalKey)
 
         try {
             return value.toInt()
@@ -300,7 +312,8 @@ class SiloFilterExpressionMapper(
     private inline fun <reified T : SequenceFilterFieldType> findFloatOfFilterType(
         dateRangeFilters: List<SequenceFilterValue>,
     ): Double? {
-        val (_, value, originalKey) = dateRangeFilters.find { (type, _, _) -> type is T } ?: return null
+        val (_, values, originalKey) = dateRangeFilters.find { (type, _, _) -> type is T } ?: return null
+        val value = extractSingleFilterValue(values, originalKey)
 
         try {
             return value.toDouble()
@@ -356,4 +369,14 @@ class SiloFilterExpressionMapper(
     }
 
     private val variantQueryTypes = listOf(Filter.PangoLineage)
+
+    private fun extractSingleFilterValue(value: SequenceFilterValue) =
+        extractSingleFilterValue(value.values, value.originalKey)
+
+    private fun extractSingleFilterValue(
+        values: List<String>,
+        originalKey: String,
+    ) = values.singleOrNull() ?: throw BadRequestException(
+        "Expected exactly one value for '$originalKey' but got ${values.size} values.",
+    )
 }
diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/openApi/OpenApiDocs.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/openApi/OpenApiDocs.kt
@@ -9,6 +9,7 @@ import org.genspectrum.lapis.config.MetadataType
 import org.genspectrum.lapis.config.OpennessLevel
 import org.genspectrum.lapis.config.ReferenceGenome
 import org.genspectrum.lapis.config.SequenceFilterFieldName
+import org.genspectrum.lapis.config.SequenceFilterFieldType
 import org.genspectrum.lapis.config.SequenceFilterFields
 import org.genspectrum.lapis.controller.AGGREGATED_GROUP_BY_FIELDS_DESCRIPTION
 import org.genspectrum.lapis.controller.AMINO_ACID_INSERTIONS_PROPERTY
@@ -282,7 +283,20 @@ private fun mapToOpenApiType(type: MetadataType): String =
 private fun primitiveSequenceFilterFieldSchemas(sequenceFilterFields: SequenceFilterFields) =
     sequenceFilterFields.fields
         .values
-        .associate { (fieldName, field) -> fieldName to Schema<String>().type(field.openApiType) }
+        .associate { (fieldName, field) -> fieldName to filterFieldSchema(field) }
+
+private fun filterFieldSchema(fieldType: SequenceFilterFieldType) =
+    when (fieldType) {
+        SequenceFilterFieldType.String, SequenceFilterFieldType.PangoLineage ->
+            Schema<String>().anyOf(
+                listOf(
+                    Schema<String>().type(fieldType.openApiType),
+                    arraySchema(Schema<String>().type(fieldType.openApiType)),
+                ),
+            )
+
+        else -> Schema<String>().type(fieldType.openApiType)
+    }
 
 private fun requestSchemaForCommonSequenceFilters(
     requestProperties: Map<SequenceFilterFieldName, Schema<out Any>>,