feat: allow upper and lowercase for queries

Author: Jonas Kellerer

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

@@ -13,53 +13,60 @@ expr:
   ;
 
 single:
-  nucleotide_mutation
+  nucleotide_mutation_query
   | pangolineage_query
   | n_of_query
-  | nucleotide_insertion
-  | aa_mutation
-  | aa_insertion
+  | nucleotide_insertion_query
+  | aa_mutation_query
+  | aa_insertion_query
   | nextclade_pangolineage_query
   | nextstrain_clade_lineage_query
   | gisaid_clade_lineage_query
   ;
 
-nucleotide_mutation : nucleotide_symbol? position ambigous_nucleotide_symbol?;
+nucleotide_mutation_query : nucleotide_mutation_query_first_symbol? position nucleotide_mutation_query_second_symbol?;
+nucleotide_mutation_query_first_symbol: nucleotide_symbol;
+nucleotide_mutation_query_second_symbol: possible_ambigous_nucleotide_symbol;
 position: NUMBER+;
 nucleotide_symbol: A | C | G | T;
-ambigous_nucleotide_symbol: nucleotide_symbol | M | R | W | S | Y | K | V | H | D | B | N | MINUS | DOT;
+ambigous_nucleotide_symbol: M | R | W | S | Y | K | V | H | D | B | N | MINUS | DOT;
+possible_ambigous_nucleotide_symbol: nucleotide_symbol | ambigous_nucleotide_symbol;
+
 
 pangolineage_query: pangolineage pangolineage_include_sublineages?;
 pangolineage: pangolineage_character pangolineage_character? pangolineage_character? pangolineage_number_component*;
 pangolineage_character: 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;
 pangolineage_number_component: '.' NUMBER NUMBER? NUMBER?;
 pangolineage_include_sublineages: DOT? ASTERISK;
 
-n_of_query: '[' n_of_match_exactly? n_of_number_of_matchers '-of:' n_of_exprs ']';
-n_of_match_exactly: 'EXACTLY-';
+n_of_query: '[' n_of_match_exactly? n_of_number_of_matchers no_of_of_keyword n_of_exprs ']';
+no_of_of_keyword: '-of:' | '-OF:';
+n_of_match_exactly: 'EXACTLY-' | 'exactly-';
 n_of_number_of_matchers: NUMBER+;
 n_of_exprs: expr (',' expr)*;
 
-nucleotide_insertion: 'ins_' position ':' (ambigous_nucleotide_symbol | '?')+;
+nucleotide_insertion_query: insertion_keyword position ':' (possible_ambigous_nucleotide_symbol | '?')+;
+insertion_keyword: 'ins_' | 'INS_';
 
-aa_mutation: gene ':' aa_symbol? position ambigous_aa_symbol?;
+aa_mutation_query: gene ':' aa_symbol? position possible_ambigous_aa_symbol?;
 aa_symbol: A | R | N | D | C | E | Q | G | H | I | L | K | M | F | P | S | T | W | Y | V | ASTERISK;
-ambigous_aa_symbol: aa_symbol | X | MINUS | DOT;
+ambigous_aa_symbol: X | MINUS | DOT;
+possible_ambigous_aa_symbol: aa_symbol | ambigous_aa_symbol;
 gene: covid_gene;
 covid_gene : E | M | N | S | ORF;
 
-aa_insertion: 'ins_' gene ':' (ambigous_aa_symbol | '?')+;
+aa_insertion_query: insertion_keyword gene ':' position ':' (possible_ambigous_aa_symbol | '?')+;
 
 nextclade_pangolineage_query: nextclade_pango_lineage_prefix pangolineage_query;
-nextclade_pango_lineage_prefix: 'nextcladePangoLineage:';
+nextclade_pango_lineage_prefix: 'nextcladePangoLineage:' | 'NEXTCLADEPANGOLINEAGE:';
 
 nextstrain_clade_lineage_query: nextstrain_clade_prefix nextstrain_clade_query;
-nextstrain_clade_prefix: 'nextstrainClade:';
+nextstrain_clade_prefix: 'nextstrainClade:'| 'NEXTSTRAINCLADE:';
 nextstrain_clade_query: NUMBER NUMBER nextstrain_clade_character | 'RECOMBINANT';
 nextstrain_clade_character: 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;
 
 gisaid_clade_lineage_query: gisaid_clade_prefix gisaid_clade_query;
-gisaid_clade_prefix: 'gisaid:';
+gisaid_clade_prefix: ('gisaid:'| 'GISAID:');
 gisaid_clade_query: gisaid_clade_character gisaid_clade_character?;
 gisaid_clade_character: 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;
 

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

@@ -1,17 +1,17 @@
 package org.genspectrum.lapis.model
 
 import VariantQueryBaseListener
-import VariantQueryParser.Aa_insertionContext
-import VariantQueryParser.Aa_mutationContext
+import VariantQueryParser.Aa_insertion_queryContext
+import VariantQueryParser.Aa_mutation_queryContext
 import VariantQueryParser.AndContext
 import VariantQueryParser.Gisaid_clade_lineage_queryContext
 import VariantQueryParser.MaybeContext
 import VariantQueryParser.N_of_queryContext
 import VariantQueryParser.Nextclade_pangolineage_queryContext
 import VariantQueryParser.Nextstrain_clade_queryContext
 import VariantQueryParser.NotContext
-import VariantQueryParser.Nucleotide_insertionContext
-import VariantQueryParser.Nucleotide_mutationContext
+import VariantQueryParser.Nucleotide_insertion_queryContext
+import VariantQueryParser.Nucleotide_mutation_queryContext
 import VariantQueryParser.OrContext
 import VariantQueryParser.Pangolineage_queryContext
 import org.antlr.v4.runtime.tree.ParseTreeListener
@@ -31,12 +31,12 @@ class VariantQueryCustomListener : VariantQueryBaseListener(), ParseTreeListener
         return expressionStack.first()
     }
 
-    override fun enterNucleotide_mutation(ctx: Nucleotide_mutationContext?) {
+    override fun enterNucleotide_mutation_query(ctx: Nucleotide_mutation_queryContext?) {
         if (ctx == null) {
             return
         }
         val position = ctx.position().text.toInt()
-        val secondSymbol = ctx.ambigous_nucleotide_symbol()?.text ?: "-"
+        val secondSymbol = ctx.nucleotide_mutation_query_second_symbol()?.text ?: "-"
 
         val expr = NucleotideSymbolEquals(position, secondSymbol)
         expressionStack.addLast(expr)
@@ -89,15 +89,15 @@ class VariantQueryCustomListener : VariantQueryBaseListener(), ParseTreeListener
         expressionStack.addLast(NOf(n, matchExactly, children.reversed()))
     }
 
-    override fun enterNucleotide_insertion(ctx: Nucleotide_insertionContext?) {
+    override fun enterNucleotide_insertion_query(ctx: Nucleotide_insertion_queryContext?) {
         throw NotImplementedError("Nucleotide insertions are not supported yet.")
     }
 
-    override fun enterAa_mutation(ctx: Aa_mutationContext?) {
+    override fun enterAa_mutation_query(ctx: Aa_mutation_queryContext?) {
         throw NotImplementedError("Amino acid mutations are not supported yet.")
     }
 
-    override fun enterAa_insertion(ctx: Aa_insertionContext?) {
+    override fun enterAa_insertion_query(ctx: Aa_insertion_queryContext?) {
         throw NotImplementedError("Amino acid insertions are not supported yet.")
     }
 

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

@@ -242,7 +242,7 @@ class VariantQueryFacadeTest {
 
     @Test
     fun `given a valid variantQuery with a 'AA insertion' expression the map should throw an error`() {
-        val variantQuery = "ins_S:N501EPE"
+        val variantQuery = "ins_S:501:EPE"
 
         val exception = assertThrows<NotImplementedError> { underTest.map(variantQuery) }