feat: allow lower case letters for mutations and insertions in varian…

…t queries
GenSpectrum · Dec 19, 2023 · fe3f8da · fe3f8da
1 parent 7e48b26
commit fe3f8da
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Showing 3 changed files with 101 additions and 36 deletions.
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
@@ -60,11 +60,11 @@ aaInsertionQuery: insertionKeyword gene ':' position ':' aaInsertionSymbol+;
 aaInsertionSymbol: possiblyAmbiguousAaSymbol | '?';
 
 nextcladePangolineageQuery: nextcladePangoLineagePrefix pangolineageQuery;
-nextcladePangoLineagePrefix: 'nextcladePangoLineage:' | 'NEXTCLADEPANGOLINEAGE:';
+nextcladePangoLineagePrefix: 'nextcladePangoLineage:' | 'NEXTCLADEPANGOLINEAGE:' | 'nextcladepangolineage:';
 
 nextstrainCladeLineageQuery: nextstrainCladePrefix nextstrainCladeQuery;
-nextstrainCladePrefix: 'nextstrainClade:'| 'NEXTSTRAINCLADE:';
-nextstrainCladeQuery: NUMBER NUMBER nextstrainCladeCharacter | 'RECOMBINANT';
+nextstrainCladePrefix: 'nextstrainClade:'| 'NEXTSTRAINCLADE:' | 'nextstrainclade:';
+nextstrainCladeQuery: NUMBER NUMBER nextstrainCladeCharacter | 'RECOMBINANT' | 'recombinant';
 nextstrainCladeCharacter: A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z;
 
 gisaidCladeLineageQuery: gisaidCladePrefix gisaidCladeNomenclature;
@@ -75,37 +75,46 @@ gisaid_clade_character: A | B | C | D | E | F | G | H | I | J | K | L | M | N |
 
 // lexer rules
 
-A: 'A';
-B: 'B';
-C: 'C';
-D: 'D';
-E: 'E';
-F: 'F';
-G: 'G';
-H: 'H';
-I: 'I';
-J: 'J';
-K: 'K';
-L: 'L';
-M: 'M';
-N: 'N';
-O: 'O';
-P: 'P';
-Q: 'Q';
-R: 'R';
-S: 'S';
-T: 'T';
-U: 'U';
-V: 'V';
-W: 'W';
-X: 'X';
-Y: 'Y';
-Z: 'Z';
+A: 'A' | 'a';
+B: 'B' | 'b';
+C: 'C' | 'c';
+D: 'D' | 'd';
+E: 'E' | 'e';
+F: 'F' | 'f';
+G: 'G' | 'g';
+H: 'H' | 'h';
+I: 'I' | 'i';
+J: 'J' | 'j';
+K: 'K' | 'k';
+L: 'L' | 'l';
+M: 'M' | 'm';
+N: 'N' | 'n';
+O: 'O' | 'o';
+P: 'P' | 'p';
+Q: 'Q' | 'q';
+R: 'R' | 'r';
+S: 'S' | 's';
+T: 'T' | 't';
+U: 'U' | 'u';
+V: 'V' | 'v';
+W: 'W' | 'w';
+X: 'X' | 'x';
+Y: 'Y' | 'y';
+Z: 'Z' | 'z';
 MINUS: '-';
 DOT: '.';
 ASTERISK: '*';
 
 NUMBER: [0-9];
 WHITESPACE: [ \r\n\t] -> skip;
 
-ORF: 'ORF1A' | 'ORF1B' | 'ORF3A' | 'ORF6' | 'ORF7A' | 'ORF7B' | 'ORF8' | 'ORF9B';
+ORF1A: 'ORF1A' | 'orf1a';
+ORF1B: 'ORF1B' | 'orf1b';
+ORF3A: 'ORF3A' | 'orf3a';
+ORF6: 'ORF6' | 'orf6';
+ORF7A: 'ORF7A' | 'orf7a';
+ORF7B: 'ORF7B' | 'orf7b';
+ORF8: 'ORF8' | 'orf8';
+ORF9B: 'ORF9B' | 'orf9b';
+
+ORF: ORF1A | ORF1B | ORF3A | ORF6 | ORF7A | ORF7B | ORF8 | ORF9B;
diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/model/VariantQueryCustomListener.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/model/VariantQueryCustomListener.kt
@@ -48,7 +48,7 @@ class VariantQueryCustomListener : VariantQueryBaseListener(), ParseTreeListener
 
         val expression = when (val secondSymbol = ctx.nucleotideMutationQuerySecondSymbol()) {
             null -> HasNucleotideMutation(null, position)
-            else -> NucleotideSymbolEquals(null, position, secondSymbol.text)
+            else -> NucleotideSymbolEquals(null, position, secondSymbol.text.uppercase())
         }
 
         expressionStack.addLast(expression)
@@ -99,7 +99,7 @@ class VariantQueryCustomListener : VariantQueryBaseListener(), ParseTreeListener
         expressionStack.addLast(
             NucleotideInsertionContains(
                 ctx.position().text.toInt(),
-                value,
+                value.uppercase(),
             ),
         )
     }
@@ -112,7 +112,7 @@ class VariantQueryCustomListener : VariantQueryBaseListener(), ParseTreeListener
 
         val expression = when (val aaSymbol = ctx.possiblyAmbiguousAaSymbol()) {
             null -> HasAminoAcidMutation(ctx.gene().text, position)
-            else -> AminoAcidSymbolEquals(ctx.gene().text, position, aaSymbol.text)
+            else -> AminoAcidSymbolEquals(ctx.gene().text, position, aaSymbol.text.uppercase())
         }
 
         expressionStack.addLast(expression)
@@ -123,7 +123,7 @@ class VariantQueryCustomListener : VariantQueryBaseListener(), ParseTreeListener
         expressionStack.addLast(
             AminoAcidInsertionContains(
                 ctx.position().text.toInt(),
-                value,
+                value.uppercase(),
                 ctx.gene().text,
             ),
         )
@@ -136,13 +136,13 @@ class VariantQueryCustomListener : VariantQueryBaseListener(), ParseTreeListener
     override fun enterNextstrainCladeQuery(ctx: NextstrainCladeQueryContext) {
         val value = when (ctx.text) {
             NEXTSTRAIN_CLADE_RECOMBINANT -> ctx.text.lowercase()
-            else -> ctx.text
+            else -> ctx.text.uppercase()
         }
         expressionStack.addLast(StringEquals(NEXTSTRAIN_CLADE_COLUMN, value))
     }
 
     override fun enterGisaidCladeNomenclature(ctx: VariantQueryParser.GisaidCladeNomenclatureContext) {
-        expressionStack.addLast(StringEquals(GISAID_CLADE_COLUMN, ctx.text))
+        expressionStack.addLast(StringEquals(GISAID_CLADE_COLUMN, ctx.text.uppercase()))
     }
 
     private fun addPangoLineage(

diff --git a/lapis2/src/test/kotlin/org/genspectrum/lapis/model/VariantQueryFacadeTest.kt b/lapis2/src/test/kotlin/org/genspectrum/lapis/model/VariantQueryFacadeTest.kt
@@ -269,6 +269,15 @@ class VariantQueryFacadeTest {
         assertThat(result, equalTo(NucleotideInsertionContains(1234, "GAG")))
     }
 
+    @Test
+    fun `given a variantQuery with a 'Insertion' expression with lower case letters then returns SILO query`() {
+        val variantQuery = "ins_1234:gAG"
+
+        val result = underTest.map(variantQuery)
+
+        assertThat(result, equalTo(NucleotideInsertionContains(1234, "GAG")))
+    }
+
     @Test
     fun `given a variantQuery with a 'Insertion' with wildcard expression then returns SILO query`() {
         val variantQuery = "ins_1234:G?A?G"
@@ -287,6 +296,24 @@ class VariantQueryFacadeTest {
         assertThat(result, equalTo(AminoAcidSymbolEquals("S", 501, "Y")))
     }
 
+    @Test
+    fun `given amino acid mutation expression with lower case letters then should map to AminoAcidSymbolEquals`() {
+        val variantQuery = "S:n501y"
+
+        val result = underTest.map(variantQuery)
+
+        assertThat(result, equalTo(AminoAcidSymbolEquals("S", 501, "Y")))
+    }
+
+    @Test
+    fun `given amino acid mutation expression with gene lower case letters then should map to AminoAcidSymbolEquals`() {
+        val variantQuery = "orf1a:N501Y"
+
+        val result = underTest.map(variantQuery)
+
+        assertThat(result, equalTo(AminoAcidSymbolEquals("ORF1A", 501, "Y")))
+    }
+
     @Test
     fun `given amino acid mutation expression without first symbol then should map to AminoAcidSymbolEquals`() {
         val variantQuery = "S:501Y"
@@ -323,6 +350,15 @@ class VariantQueryFacadeTest {
         assertThat(result, equalTo(AminoAcidInsertionContains(501, "EPE", "S")))
     }
 
+    @Test
+    fun `given a valid variantQuery with a 'AA insertion' expression with lower case then returns SILO query`() {
+        val variantQuery = "ins_S:501:ePe"
+
+        val result = underTest.map(variantQuery)
+
+        assertThat(result, equalTo(AminoAcidInsertionContains(501, "EPE", "S")))
+    }
+
     @Test
     fun `given a valid variantQuery with a 'AA insertion' with wildcard then returns SILO query`() {
         val variantQuery = "ins_S:501:E?E?"
@@ -341,6 +377,16 @@ class VariantQueryFacadeTest {
         assertThat(result, equalTo(StringEquals(NEXTSTRAIN_CLADE_COLUMN, "22B")))
     }
 
+    @Test
+    @Suppress("ktlint:standard:max-line-length")
+    fun `given a valid variantQuery with a 'NextstrainCladeLineage' expression in lower case then returns SILO query`() {
+        val variantQuery = "nextstrainClade:22b"
+
+        val result = underTest.map(variantQuery)
+
+        assertThat(result, equalTo(StringEquals(NEXTSTRAIN_CLADE_COLUMN, "22B")))
+    }
+
     @Test
     fun `given a valid variantQuery with a 'NextstrainCladeLineage' recombinant expression then returns SILO query`() {
         val variantQuery = "nextstrainClade:RECOMBINANT"
@@ -359,6 +405,16 @@ class VariantQueryFacadeTest {
         assertThat(result, equalTo(StringEquals(GISAID_CLADE_COLUMN, "X")))
     }
 
+    @Test
+    @Suppress("ktlint:standard:max-line-length")
+    fun `given a valid variantQuery with a single letter 'GisaidCladeLineage' expression with lower case then returns SILO query`() {
+        val variantQuery = "gisaid:x"
+
+        val result = underTest.map(variantQuery)
+
+        assertThat(result, equalTo(StringEquals(GISAID_CLADE_COLUMN, "X")))
+    }
+
     @Test
     fun `given a valid variantQuery with a 'GisaidCladeLineage' expression then returns SILO query`() {
         val variantQuery = "gisaid:AB"