From 5a0ef385fb64198fff655a465c3de9bebfb6b3f4 Mon Sep 17 00:00:00 2001
From: Jonas Kellerer <jonas.kellerer@tngtech.com>
Date: Wed, 5 Apr 2023 12:45:07 +0200
Subject: [PATCH] feat: add Or expression to variantQuery

---
 .../model/variantqueryparser/VariantQuery.g4  |  1 +
 .../lapis/model/VariantQueryCustomListener.kt |  7 +++++++
 .../org/genspectrum/lapis/silo/SiloQuery.kt   |  2 ++
 .../lapis/model/VariantQueryFacadeTest.kt     | 16 +++++++++++++++
 .../genspectrum/lapis/silo/SiloQueryTest.kt   | 20 +++++++++++++++++++
 5 files changed, 46 insertions(+)

diff --git a/lapis2/src/main/antlr/org/genspectrum/lapis/model/variantqueryparser/VariantQuery.g4 b/lapis2/src/main/antlr/org/genspectrum/lapis/model/variantqueryparser/VariantQuery.g4
index a550c9a9..7363978e 100644
--- a/lapis2/src/main/antlr/org/genspectrum/lapis/model/variantqueryparser/VariantQuery.g4
+++ b/lapis2/src/main/antlr/org/genspectrum/lapis/model/variantqueryparser/VariantQuery.g4
@@ -7,6 +7,7 @@ expr:
   single             # Uni
   | '!' expr         # Not
   | expr '&' expr    # And
+  | expr '|' expr    # Or
   ;
 
 single:
diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/model/VariantQueryCustomListener.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/model/VariantQueryCustomListener.kt
index 2c7d205b..07c67033 100644
--- a/lapis2/src/main/kotlin/org/genspectrum/lapis/model/VariantQueryCustomListener.kt
+++ b/lapis2/src/main/kotlin/org/genspectrum/lapis/model/VariantQueryCustomListener.kt
@@ -4,10 +4,12 @@ import VariantQueryBaseListener
 import VariantQueryParser.AndContext
 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.Not
 import org.genspectrum.lapis.silo.NucleotideSymbolEquals
+import org.genspectrum.lapis.silo.Or
 import org.genspectrum.lapis.silo.SiloFilterExpression
 
 class VariantQueryCustomListener : VariantQueryBaseListener(), ParseTreeListener {
@@ -37,4 +39,9 @@ class VariantQueryCustomListener : VariantQueryBaseListener(), ParseTreeListener
         val child = expressionStack.removeLast()
         expressionStack.addLast(Not(child))
     }
+
+    override fun exitOr(ctx: OrContext?) {
+        val children = listOf(expressionStack.removeLast(), expressionStack.removeLast()).reversed()
+        expressionStack.addLast(Or(children))
+    }
 }
diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/silo/SiloQuery.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/silo/SiloQuery.kt
index 18423bf6..6a56430c 100644
--- a/lapis2/src/main/kotlin/org/genspectrum/lapis/silo/SiloQuery.kt
+++ b/lapis2/src/main/kotlin/org/genspectrum/lapis/silo/SiloQuery.kt
@@ -41,4 +41,6 @@ object True : SiloFilterExpression("True")
 
 data class And(val children: List<SiloFilterExpression>) : SiloFilterExpression("And")
 
+data class Or(val children: List<SiloFilterExpression>) : SiloFilterExpression("Or")
+
 data class Not(val child: SiloFilterExpression) : SiloFilterExpression("Not")
diff --git a/lapis2/src/test/kotlin/org/genspectrum/lapis/model/VariantQueryFacadeTest.kt b/lapis2/src/test/kotlin/org/genspectrum/lapis/model/VariantQueryFacadeTest.kt
index 21939199..d8283e2e 100644
--- a/lapis2/src/test/kotlin/org/genspectrum/lapis/model/VariantQueryFacadeTest.kt
+++ b/lapis2/src/test/kotlin/org/genspectrum/lapis/model/VariantQueryFacadeTest.kt
@@ -3,6 +3,7 @@ package org.genspectrum.lapis.model
 import org.genspectrum.lapis.silo.And
 import org.genspectrum.lapis.silo.Not
 import org.genspectrum.lapis.silo.NucleotideSymbolEquals
+import org.genspectrum.lapis.silo.Or
 import org.hamcrest.MatcherAssert
 import org.hamcrest.Matchers
 import org.junit.jupiter.api.BeforeEach
@@ -70,4 +71,19 @@ class VariantQueryFacadeTest {
         val expectedResult = Not(NucleotideSymbolEquals(300, "G"))
         MatcherAssert.assertThat(result, Matchers.equalTo(expectedResult))
     }
+
+    @Test
+    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)
+
+        val expectedResult = Or(
+            listOf(
+                NucleotideSymbolEquals(300, "G"),
+                NucleotideSymbolEquals(400, "-"),
+            ),
+        )
+        MatcherAssert.assertThat(result, Matchers.equalTo(expectedResult))
+    }
 }
diff --git a/lapis2/src/test/kotlin/org/genspectrum/lapis/silo/SiloQueryTest.kt b/lapis2/src/test/kotlin/org/genspectrum/lapis/silo/SiloQueryTest.kt
index f122c77d..e0453def 100644
--- a/lapis2/src/test/kotlin/org/genspectrum/lapis/silo/SiloQueryTest.kt
+++ b/lapis2/src/test/kotlin/org/genspectrum/lapis/silo/SiloQueryTest.kt
@@ -201,6 +201,26 @@ class SiloQueryTest {
                 }
                 """,
             ),
+            Arguments.of(
+                Or(listOf(StringEquals("theColumn", "theValue"), StringEquals("theOtherColumn", "theOtherValue"))),
+                """
+                {
+                    "type": "Or",
+                    "children": [
+                        {
+                        "type": "StringEquals",
+                        "column": "theColumn",
+                        "value": "theValue"
+                        },
+                        {
+                        "type": "StringEquals",
+                        "column": "theOtherColumn",
+                        "value": "theOtherValue"
+                        }
+                    ]
+                }
+                """,
+            ),
         )
     }
 }