feat: add Maybe and bracket expression

Author: Jonas Kellerer

lapis2/src/main/antlr/org/genspectrum/lapis/model/variantqueryparser/VariantQuery.g4

@@ -8,6 +8,8 @@ expr:
   | '!' expr         # Not
   | expr '&' expr    # And
   | expr '|' expr    # Or
+  | '(' expr ')'     # Parentesis
+  | 'MAYBE(' expr ')' # Maybe
   ;
 
 single:

lapis2/src/main/kotlin/org/genspectrum/lapis/model/VariantQueryCustomListener.kt

@@ -2,11 +2,13 @@ package org.genspectrum.lapis.model
 
 import VariantQueryBaseListener
 import VariantQueryParser.AndContext
+import VariantQueryParser.MaybeContext
 import VariantQueryParser.NotContext
 import VariantQueryParser.Nucleotide_mutationContext
 import VariantQueryParser.OrContext
 import org.antlr.v4.runtime.tree.ParseTreeListener
 import org.genspectrum.lapis.silo.And
+import org.genspectrum.lapis.silo.Maybe
 import org.genspectrum.lapis.silo.Not
 import org.genspectrum.lapis.silo.NucleotideSymbolEquals
 import org.genspectrum.lapis.silo.Or
@@ -44,4 +46,9 @@ class VariantQueryCustomListener : VariantQueryBaseListener(), ParseTreeListener
         val children = listOf(expressionStack.removeLast(), expressionStack.removeLast()).reversed()
         expressionStack.addLast(Or(children))
     }
+
+    override fun exitMaybe(ctx: MaybeContext?) {
+        val child = expressionStack.removeLast()
+        expressionStack.addLast(Maybe(child))
+    }
 }

lapis2/src/main/kotlin/org/genspectrum/lapis/silo/SiloQuery.kt

@@ -44,3 +44,5 @@ data class And(val children: List<SiloFilterExpression>) : SiloFilterExpression(
 data class Or(val children: List<SiloFilterExpression>) : SiloFilterExpression("Or")
 
 data class Not(val child: SiloFilterExpression) : SiloFilterExpression("Not")
+
+data class Maybe(val child: SiloFilterExpression) : SiloFilterExpression("Maybe")

lapis2/src/test/kotlin/org/genspectrum/lapis/model/VariantQueryFacadeTest.kt

@@ -1,6 +1,7 @@
 package org.genspectrum.lapis.model
 
 import org.genspectrum.lapis.silo.And
+import org.genspectrum.lapis.silo.Maybe
 import org.genspectrum.lapis.silo.Not
 import org.genspectrum.lapis.silo.NucleotideSymbolEquals
 import org.genspectrum.lapis.silo.Or
@@ -28,7 +29,7 @@ class VariantQueryFacadeTest {
     }
 
     @Test
-    fun `given a variant variantQuery with an and expression the map should return the corresponding SiloQuery`() {
+    fun `given a variant variantQuery with an 'And' expression the map should return the corresponding SiloQuery`() {
         val variantQuery = "300G & 400"
 
         val result = underTest.map(variantQuery)
@@ -43,7 +44,7 @@ class VariantQueryFacadeTest {
     }
 
     @Test
-    fun `given a variant variantQuery with two and expression the map should return the corresponding SiloQuery`() {
+    fun `given a variant variantQuery with two 'And' expression the map should return the corresponding SiloQuery`() {
         val variantQuery = "300G & 400- & 500B"
 
         val result = underTest.map(variantQuery)
@@ -63,7 +64,7 @@ class VariantQueryFacadeTest {
     }
 
     @Test
-    fun `given a variant variantQuery with a not expression the map should return the corresponding SiloQuery`() {
+    fun `given a variant variantQuery with a 'Not' expression the map should return the corresponding SiloQuery`() {
         val variantQuery = "!300G"
 
         val result = underTest.map(variantQuery)
@@ -73,7 +74,7 @@ class VariantQueryFacadeTest {
     }
 
     @Test
-    fun `given a variant variantQuery with an Or expression the map should return the corresponding SiloQuery`() {
+    fun `given a variant variantQuery with an 'Or' expression the map should return the corresponding SiloQuery`() {
         val variantQuery = "300G | 400"
 
         val result = underTest.map(variantQuery)
@@ -86,4 +87,34 @@ class VariantQueryFacadeTest {
         )
         MatcherAssert.assertThat(result, Matchers.equalTo(expectedResult))
     }
+
+    @Test
+    fun `given a variant variantQuery with an bracket expression the map should return the corresponding SiloQuery`() {
+        val variantQuery = "300C & (400A | 500G)"
+
+        val result = underTest.map(variantQuery)
+
+        val expectedResult = And(
+            listOf(
+                NucleotideSymbolEquals(300, "C"),
+                Or(
+                    listOf(
+                        NucleotideSymbolEquals(400, "A"),
+                        NucleotideSymbolEquals(500, "G"),
+                    ),
+                ),
+            ),
+        )
+        MatcherAssert.assertThat(result, Matchers.equalTo(expectedResult))
+    }
+
+    @Test
+    fun `given a variant variantQuery with a 'Maybe' expression the map should return the corresponding SiloQuery`() {
+        val variantQuery = "MAYBE(300G)"
+
+        val result = underTest.map(variantQuery)
+
+        val expectedResult = Maybe(NucleotideSymbolEquals(300, "G"))
+        MatcherAssert.assertThat(result, Matchers.equalTo(expectedResult))
+    }
 }

lapis2/src/test/kotlin/org/genspectrum/lapis/silo/SiloQueryTest.kt

@@ -221,6 +221,19 @@ class SiloQueryTest {
                 }
                 """,
             ),
+            Arguments.of(
+                Maybe(StringEquals("theColumn", "theValue")),
+                """
+                {
+                    "type": "Maybe",
+                    "child": {
+                        "type": "StringEquals",
+                        "column": "theColumn",
+                        "value": "theValue"
+                    }
+                }
+                """,
+            ),
         )
     }
 }