feat: allow features to be empty

GenSpectrum · Apr 27, 2023 · a5bf1ea · a5bf1ea
1 parent 88acb65
commit a5bf1ea
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Showing 4 changed files with 18 additions and 9 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
@@ -6,7 +6,7 @@ data class DatabaseSchema(
     val instanceName: String,
     val metadata: List<DatabaseMetadata>,
     val primaryKey: String,
-    val features: List<DatabaseFeature>,
+    val features: List<DatabaseFeature>?,
 )
 
 data class DatabaseMetadata(val name: String, val type: 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
@@ -6,17 +6,24 @@ data class SequenceFilterFields(val fields: Map<FieldName, SequenceFilterFieldTy
     companion object {
         private val nucleotideMutationsField = Pair("nucleotideMutations", SequenceFilterFieldType.MutationsList)
 
-        fun fromDatabaseConfig(databaseConfig: DatabaseConfig) = SequenceFilterFields(
-            fields = databaseConfig.schema.metadata
+        fun fromDatabaseConfig(databaseConfig: DatabaseConfig): SequenceFilterFields {
+            val metadataFields = databaseConfig.schema.metadata
                 .map(::mapToSequenceFilterFields)
                 .flatten()
-                .toMap() +
+                .toMap()
+            val staticFields = listOf(nucleotideMutationsField)
+
+            val featuresFields = if (databaseConfig.schema.features.isNullOrEmpty()) {
+                emptyMap<FieldName, SequenceFilterFieldType>()
+            } else {
                 databaseConfig.schema.features
                     .map(::mapToSequenceFilterFieldsFromFeatures)
                     .flatten()
-                    .toMap() +
-                nucleotideMutationsField,
-        )
+                    .toMap()
+            }
+
+            return SequenceFilterFields(fields = metadataFields + staticFields + featuresFields)
+        }
     }
 }
 
@@ -35,7 +42,7 @@ private fun mapToSequenceFilterFields(databaseMetadata: DatabaseMetadata) = when
 }
 
 private fun mapToSequenceFilterFieldsFromFeatures(databaseFeature: DatabaseFeature) = when (databaseFeature.name) {
-    "sarsCoV2VariantQuery" -> listOf(databaseFeature.name to SequenceFilterFieldType.VariantQuery)
+    "sarsCoV2VariantQuery" -> listOf("variantQuery" to SequenceFilterFieldType.VariantQuery)
     else -> throw IllegalArgumentException(
         "Unknown feature '${databaseFeature.name}'",
     )

diff --git a/lapis2/src/test/resources/config/testDatabaseConfig.yaml b/lapis2/src/test/resources/config/testDatabaseConfig.yaml
@@ -12,5 +12,5 @@ schema:
     - name: pangoLineage
       type: pango_lineage
   features:
-    - feature: sarsCoV2VariantQuery
+    - name: sarsCoV2VariantQuery
   primaryKey: gisaid_epi_isl
diff --git a/siloLapisTests/testDatabaseConfig.yaml b/siloLapisTests/testDatabaseConfig.yaml
@@ -11,4 +11,6 @@ schema:
       type: string
     - name: pangoLineage
       type: pango_lineage
+  features:
+    - name: sarsCoV2VariantQuery
   primaryKey: gisaid_epi_isl