feat(lapis2): implement boolean columns

resolves #740
GenSpectrum · Apr 24, 2024 · 57e0691 · 57e0691
1 parent b424e0c
commit 57e0691
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Showing 16 changed files with 244 additions and 116 deletions.
diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/config/DatabaseConfig.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/config/DatabaseConfig.kt
@@ -33,6 +33,9 @@ enum class MetadataType {
     @JsonProperty("float")
     FLOAT,
 
+    @JsonProperty("boolean")
+    BOOLEAN,
+
     @JsonProperty("insertion")
     NUCLEOTIDE_INSERTION,
 

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/config/SequenceFilterFields.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/config/SequenceFilterFields.kt
@@ -88,6 +88,13 @@ private fun mapToSequenceFilterField(databaseMetadata: DatabaseMetadata) =
             ),
         )
 
+        MetadataType.BOOLEAN -> listOf(
+            SequenceFilterField(
+                name = databaseMetadata.name,
+                type = SequenceFilterFieldType.Boolean,
+            ),
+        )
+
         MetadataType.NUCLEOTIDE_INSERTION -> emptyList()
         MetadataType.AMINO_ACID_INSERTION -> emptyList()
     }
@@ -113,6 +120,8 @@ sealed class SequenceFilterFieldType(val openApiType: kotlin.String) {
 
     data object Date : SequenceFilterFieldType("string")
 
+    data object Boolean : SequenceFilterFieldType("boolean")
+
     data object VariantQuery : SequenceFilterFieldType("string")
 
     data class DateFrom(val associatedField: SequenceFilterFieldName) : SequenceFilterFieldType("string")

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/model/SiloFilterExpressionMapper.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/model/SiloFilterExpressionMapper.kt
@@ -13,6 +13,7 @@ import org.genspectrum.lapis.request.NucleotideMutation
 import org.genspectrum.lapis.silo.AminoAcidInsertionContains
 import org.genspectrum.lapis.silo.AminoAcidSymbolEquals
 import org.genspectrum.lapis.silo.And
+import org.genspectrum.lapis.silo.BooleanEquals
 import org.genspectrum.lapis.silo.DateBetween
 import org.genspectrum.lapis.silo.FloatBetween
 import org.genspectrum.lapis.silo.FloatEquals
@@ -73,6 +74,7 @@ class SiloFilterExpressionMapper(
                 Filter.IntBetween -> mapToIntBetweenFilter(siloColumnName, values)
                 Filter.FloatEquals -> mapToFloatEqualsFilter(siloColumnName, values)
                 Filter.FloatBetween -> mapToFloatBetweenFilter(siloColumnName, values)
+                Filter.BooleanEquals -> mapToBooleanEqualsFilters(siloColumnName, values)
             }
         }
 
@@ -109,6 +111,7 @@ class SiloFilterExpressionMapper(
             SequenceFilterFieldType.Float -> Pair(field.name, Filter.FloatEquals)
             is SequenceFilterFieldType.FloatFrom -> Pair(type.associatedField, Filter.FloatBetween)
             is SequenceFilterFieldType.FloatTo -> Pair(type.associatedField, Filter.FloatBetween)
+            SequenceFilterFieldType.Boolean -> Pair(field.name, Filter.BooleanEquals)
 
             null -> throw BadRequestException(
                 "'$key' is not a valid sequence filter key. Valid keys are: " +
@@ -169,6 +172,20 @@ class SiloFilterExpressionMapper(
         values: List<SequenceFilterValue>,
     ) = Or(values[0].values.map { StringEquals(siloColumnName, it) })
 
+    private fun mapToBooleanEqualsFilters(
+        siloColumnName: SequenceFilterFieldName,
+        values: List<SequenceFilterValue>,
+    ) = Or(
+        values[0].values.map {
+            val value = try {
+                it.lowercase().toBooleanStrict()
+            } catch (e: IllegalArgumentException) {
+                throw BadRequestException("'$it' is not a valid boolean.")
+            }
+            BooleanEquals(siloColumnName, value)
+        },
+    )
+
     private fun mapToVariantQueryFilter(variantQuery: String): SiloFilterExpression {
         if (variantQuery.isBlank()) {
             throw BadRequestException("variantQuery must not be empty")
@@ -382,6 +399,7 @@ class SiloFilterExpressionMapper(
         IntBetween,
         FloatEquals,
         FloatBetween,
+        BooleanEquals,
     }
 
     private val variantQueryTypes = listOf(Filter.PangoLineage)

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/openApi/OpenApiDocs.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/openApi/OpenApiDocs.kt
@@ -330,6 +330,7 @@ private fun mapToOpenApiType(type: MetadataType): String =
         MetadataType.FLOAT -> "number"
         MetadataType.NUCLEOTIDE_INSERTION -> "string"
         MetadataType.AMINO_ACID_INSERTION -> "string"
+        MetadataType.BOOLEAN -> "boolean"
     }
 
 private fun primitiveSequenceFilterFieldSchemas(sequenceFilterFields: SequenceFilterFields) =

diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/silo/SiloQuery.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/silo/SiloQuery.kt
@@ -216,6 +216,8 @@ sealed class SiloFilterExpression(val type: String)
 
 data class StringEquals(val column: String, val value: String) : SiloFilterExpression("StringEquals")
 
+data class BooleanEquals(val column: String, val value: Boolean?) : SiloFilterExpression("BooleanEquals")
+
 data class PangoLineageEquals(val column: String, val value: String, val includeSublineages: Boolean) :
     SiloFilterExpression("PangoLineage")
 

diff --git a/lapis2/src/test/kotlin/org/genspectrum/lapis/DummySequenceFilterFields.kt b/lapis2/src/test/kotlin/org/genspectrum/lapis/DummySequenceFilterFields.kt
@@ -31,6 +31,7 @@ val dummySequenceFilterFields = SequenceFilterFields(
         "floatField" to SequenceFilterFieldType.Float,
         "floatFieldTo" to SequenceFilterFieldType.FloatTo("floatField"),
         "floatFieldFrom" to SequenceFilterFieldType.FloatFrom("floatField"),
+        "test_boolean_column" to SequenceFilterFieldType.Boolean,
     )
         .map { (name, type) -> name.lowercase() to SequenceFilterField(name, type) }
         .toMap(),

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 +26,7 @@ class DatabaseConfigTest {
                 DatabaseMetadata(name = "region", type = MetadataType.STRING),
                 DatabaseMetadata(name = "country", type = MetadataType.STRING),
                 DatabaseMetadata(name = "pangoLineage", type = MetadataType.PANGO_LINEAGE),
+                DatabaseMetadata(name = "test_boolean_column", type = MetadataType.BOOLEAN),
                 DatabaseMetadata(name = "nucInsertion", type = MetadataType.NUCLEOTIDE_INSERTION),
                 DatabaseMetadata(name = "aaInsertion", type = MetadataType.AMINO_ACID_INSERTION),
             ),

diff --git a/lapis2/src/test/kotlin/org/genspectrum/lapis/model/SiloFilterExpressionMapperTest.kt b/lapis2/src/test/kotlin/org/genspectrum/lapis/model/SiloFilterExpressionMapperTest.kt
@@ -15,6 +15,7 @@ import org.genspectrum.lapis.request.SequenceFilters
 import org.genspectrum.lapis.silo.AminoAcidInsertionContains
 import org.genspectrum.lapis.silo.AminoAcidSymbolEquals
 import org.genspectrum.lapis.silo.And
+import org.genspectrum.lapis.silo.BooleanEquals
 import org.genspectrum.lapis.silo.DateBetween
 import org.genspectrum.lapis.silo.FloatBetween
 import org.genspectrum.lapis.silo.FloatEquals
@@ -448,6 +449,21 @@ class SiloFilterExpressionMapperTest {
         )
     }
 
+    @Test
+    fun `GIVEN a boolean equals with non-boolean value THEN should throw an error`() {
+        val filterParameter = getSequenceFilters(
+            mapOf(
+                "test_boolean_column" to "not a boolean",
+            ),
+        )
+
+        val exception = assertThrows<BadRequestException> { underTest.map(filterParameter) }
+        assertThat(
+            exception.message,
+            containsString("'not a boolean' is not a valid boolean."),
+        )
+    }
+
     @ParameterizedTest
     @MethodSource("getFilterParametersWithMultipleValues")
     fun `GIVEN multiple value for date field THEN throws an error`(
@@ -656,6 +672,17 @@ class SiloFilterExpressionMapperTest {
                         ),
                     ),
                 ),
+                Arguments.of(
+                    mapOf(
+                        "test_boolean_column" to listOf("true", "false"),
+                    ),
+                    And(
+                        Or(
+                            BooleanEquals("test_boolean_column", true),
+                            BooleanEquals("test_boolean_column", false),
+                        ),
+                    ),
+                ),
             )
     }
 

diff --git a/lapis2/src/test/kotlin/org/genspectrum/lapis/silo/SiloQueryTest.kt b/lapis2/src/test/kotlin/org/genspectrum/lapis/silo/SiloQueryTest.kt
@@ -553,24 +553,50 @@ class SiloQueryTest {
                         ),
                     ),
                     """
-                {
-                    "type": "N-Of",
-                    "numberOfMatchers": 2,
-                    "matchExactly": true,
-                    "children": [
                         {
-                        "type": "StringEquals",
-                        "column": "theColumn",
-                        "value": "theValue"
-                        },
+                            "type": "N-Of",
+                            "numberOfMatchers": 2,
+                            "matchExactly": true,
+                            "children": [
+                                {
+                                "type": "StringEquals",
+                                "column": "theColumn",
+                                "value": "theValue"
+                                },
+                                {
+                                "type": "StringEquals",
+                                "column": "theOtherColumn",
+                                "value": "theOtherValue"
+                                }
+                            ]
+                        }
+                    """,
+                ),
+                Arguments.of(
+                    BooleanEquals(
+                        column = "theColumn",
+                        value = true,
+                    ),
+                    """
                         {
-                        "type": "StringEquals",
-                        "column": "theOtherColumn",
-                        "value": "theOtherValue"
+                            "type": "BooleanEquals",
+                            "column": "theColumn",
+                            "value": true
                         }
-                    ]
-                }
-                """,
+                    """,
+                ),
+                Arguments.of(
+                    BooleanEquals(
+                        column = "theColumn",
+                        value = null,
+                    ),
+                    """
+                        {
+                            "type": "BooleanEquals",
+                            "column": "theColumn",
+                            "value": null
+                        }
+                    """,
                 ),
             )
     }

diff --git a/lapis2/src/test/resources/config/testDatabaseConfig.yaml b/lapis2/src/test/resources/config/testDatabaseConfig.yaml
@@ -12,6 +12,8 @@ schema:
       type: string
     - name: pangoLineage
       type: pango_lineage
+    - name: test_boolean_column
+      type: boolean
     - name: nucInsertion
       type: insertion
     - name: aaInsertion

diff --git a/siloLapisTests/test/aggregatedQueries/filterByBoolean.json b/siloLapisTests/test/aggregatedQueries/filterByBoolean.json
@@ -0,0 +1,11 @@
+{
+  "testCaseName": "boolean equals",
+  "lapisRequest": {
+    "testBooleanColumn": true
+  },
+  "expected": [
+    {
+      "count": 34
+    }
+  ]
+}
diff --git a/siloLapisTests/test/aggregatedQueries/groupByBoolean.json b/siloLapisTests/test/aggregatedQueries/groupByBoolean.json
@@ -0,0 +1,19 @@
+{
+  "testCaseName": "boolean equals",
+  "lapisRequest": {
+    "fields": ["test_boolean_column"]
+  },
+  "expected": [
+    {
+      "count": 34,
+      "testBooleanColumn": true
+    },
+    {
+      "count": 33
+    },
+    {
+      "count": 33,
+      "testBooleanColumn": false
+    }
+  ]
+}
diff --git a/siloLapisTests/test/details.spec.ts b/siloLapisTests/test/details.spec.ts
@@ -20,6 +20,7 @@ describe('The /details endpoint', () => {
       pangoLineage: 'B.1.617.2',
       qcValue: undefined,
       region: undefined,
+      testBooleanColumn: undefined,
     });
   });
 
@@ -40,6 +41,7 @@ describe('The /details endpoint', () => {
       pangoLineage: 'B.1.617.2',
       qcValue: 0.96,
       region: 'Europe',
+      testBooleanColumn: false,
     });
   });
 
@@ -140,6 +142,7 @@ Solothurn	B.1	key_1002052
       pangoLineage: 'P.1',
       qcValue: 0.93,
       region: 'Europe',
+      testBooleanColumn: undefined,
     };
 
     const result = await lapisClient.postDetails1({
@@ -162,6 +165,7 @@ Solothurn	B.1	key_1002052
       pangoLineage: 'AY.43',
       qcValue: 0.98,
       region: 'Europe',
+      testBooleanColumn: true,
     };
 
     const result = await lapisClient.postDetails1({

diff --git a/siloLapisTests/testData/protectedTestDatabaseConfig.yaml b/siloLapisTests/testData/protectedTestDatabaseConfig.yaml
@@ -21,6 +21,8 @@ schema:
       type: int
     - name: qc_value
       type: float
+    - name: test_boolean_column
+      type: boolean
     - name: insertions
       type: insertion
     - name: aaInsertions