feat: add lineage queries for nextstrain, nextclade and gisaid

lapis2/build.gradle

@@ -36,6 +36,7 @@ dependencies {
     }
     testImplementation 'com.ninja-squad:springmockk:4.0.2'
     testImplementation 'org.mock-server:mockserver-netty:5.15.0'
+    implementation "org.jetbrains.kotlin:kotlin-stdlib"
 }
 
 

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

@@ -16,6 +16,12 @@ single:
   nucleotide_mutation
   | pangolineage_query
   | n_of_query
+  | nucleotide_insertion
+  | aa_mutation
+  | aa_insertion
+  | nextclade_pangolineage_query
+  | nextstrain_clade_lineage_query
+  | gisaid_clade_lineage_query
   ;
 
 nucleotide_mutation : nucleotide_symbol? position ambigous_nucleotide_symbol?;
@@ -34,6 +40,30 @@ n_of_match_exactly: 'EXACTLY-';
 n_of_number_of_matchers: NUMBER+;
 n_of_exprs: expr (',' expr)*;
 
+nucleotide_insertion: 'ins_' position ':' (ambigous_nucleotide_symbol | '?')+;
+
+aa_mutation: gene ':' aa_symbol? position 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;
+gene: covid_gene;
+covid_gene : E | M | N | S | ORF;
+
+aa_insertion: 'ins_' gene ':' (ambigous_aa_symbol | '?')+;
+
+nextclade_pangolineage_query: nextclade_pango_lineage_prefix pangolineage_query;
+nextclade_pango_lineage_prefix: 'nextcladePangoLineage:';
+
+nextstrain_clade_lineage_query: nextstrain_clade_prefix nextstrain_clade_query;
+nextstrain_clade_prefix: '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_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;
+
+
 // lexer rules
 
 A: 'A';
@@ -68,3 +98,5 @@ ASTERISK: '*';
 
 NUMBER: [0-9];
 WHITESPACE: [ \r\n\t] -> skip;
+
+ORF: 'ORF1A' | 'ORF1B' | 'ORF3A' | 'ORF6' | 'ORF7A' | 'ORF7B' | 'ORF8' | 'ORF9B';

lapis2/src/main/kotlin/org/genspectrum/lapis/controller/ExceptionHandler.kt

@@ -65,6 +65,21 @@ class ExceptionHandler : ResponseEntityExceptionHandler() {
                 ),
             )
     }
+
+    @ExceptionHandler(NotImplementedError::class)
+    fun handleNotImplementedError(e: NotImplementedError): ResponseEntity<String> {
+        return ResponseEntity
+            .status(HttpStatus.NOT_IMPLEMENTED)
+            .contentType(MediaType.APPLICATION_JSON)
+            .body(
+                jacksonObjectMapper().writeValueAsString(
+                    LapisHttpErrorResponse(
+                        "Not implemented",
+                        "${e.message}",
+                    ),
+                ),
+            )
+    }
 }
 
 data class LapisHttpErrorResponse(val title: String, val message: String)

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

@@ -1,10 +1,16 @@
 package org.genspectrum.lapis.model
 
 import VariantQueryBaseListener
+import VariantQueryParser.Aa_insertionContext
+import VariantQueryParser.Aa_mutationContext
 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.OrContext
 import VariantQueryParser.Pangolineage_queryContext
@@ -82,4 +88,28 @@ class VariantQueryCustomListener : VariantQueryBaseListener(), ParseTreeListener
 
         expressionStack.addLast(NOf(n, matchExactly, children.reversed()))
     }
+
+    override fun enterNucleotide_insertion(ctx: Nucleotide_insertionContext?) {
+        throw NotImplementedError("Nucleotide insertions are not supported yet.")
+    }
+
+    override fun enterAa_mutation(ctx: Aa_mutationContext?) {
+        throw NotImplementedError("Amino acid mutations are not supported yet.")
+    }
+
+    override fun enterAa_insertion(ctx: Aa_insertionContext?) {
+        throw NotImplementedError("Amino acid insertions are not supported yet.")
+    }
+
+    override fun enterNextclade_pangolineage_query(ctx: Nextclade_pangolineage_queryContext?) {
+        throw NotImplementedError("Nextclade pango lineages are not supported yet.")
+    }
+
+    override fun enterNextstrain_clade_query(ctx: Nextstrain_clade_queryContext?) {
+        throw NotImplementedError("Nextstrain clade lineages are not supported yet.")
+    }
+
+    override fun enterGisaid_clade_lineage_query(ctx: Gisaid_clade_lineage_queryContext?) {
+        throw NotImplementedError("Gisaid clade lineages are not supported yet.")
+    }
 }

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

@@ -216,6 +216,78 @@ class VariantQueryFacadeTest {
         MatcherAssert.assertThat(result, Matchers.equalTo(expectedResult))
     }
 
+    @Test
+    fun `given a variant variantQuery with a 'Insertion' expression the map should throw an error`() {
+        val variantQuery = "ins_1234:GAG"
+
+        val exception = assertThrows<NotImplementedError> { underTest.map(variantQuery) }
+
+        MatcherAssert.assertThat(
+            exception.message,
+            Matchers.equalTo("Nucleotide insertions are not supported yet."),
+        )
+    }
+
+    @Test
+    fun `given a valid variant variantQuery with a 'AA mutation' expression the map should throw an error`() {
+        val variantQuery = "S:N501Y"
+
+        val exception = assertThrows<NotImplementedError> { underTest.map(variantQuery) }
+
+        MatcherAssert.assertThat(
+            exception.message,
+            Matchers.equalTo("Amino acid mutations are not supported yet."),
+        )
+    }
+
+    @Test
+    fun `given a valid variant variantQuery with a 'AA insertion' expression the map should throw an error`() {
+        val variantQuery = "ins_S:N501EPE"
+
+        val exception = assertThrows<NotImplementedError> { underTest.map(variantQuery) }
+
+        MatcherAssert.assertThat(
+            exception.message,
+            Matchers.equalTo("Amino acid insertions are not supported yet."),
+        )
+    }
+
+    @Test
+    fun `given a valid variant variantQuery with a 'nextclade pango lineage' expression the map should throw an error`() {
+        val variantQuery = "nextcladePangoLineage:BA.5*"
+
+        val exception = assertThrows<NotImplementedError> { underTest.map(variantQuery) }
+
+        MatcherAssert.assertThat(
+            exception.message,
+            Matchers.equalTo("Nextclade pango lineages are not supported yet."),
+        )
+    }
+
+    @Test
+    fun `given a valid variant variantQuery with a 'Nextstrain clade lineage' expression the map should throw an error`() {
+        val variantQuery = "nextstrainClade:22B"
+
+        val exception = assertThrows<NotImplementedError> { underTest.map(variantQuery) }
+
+        MatcherAssert.assertThat(
+            exception.message,
+            Matchers.equalTo("Nextstrain clade lineages are not supported yet."),
+        )
+    }
+
+    @Test
+    fun `given a valid variant variantQuery with a 'Gisaid clade lineage' expression the map should throw an error`() {
+        val variantQuery = "gisaid:AB"
+
+        val exception = assertThrows<NotImplementedError> { underTest.map(variantQuery) }
+
+        MatcherAssert.assertThat(
+            exception.message,
+            Matchers.equalTo("Gisaid clade lineages are not supported yet."),
+        )
+    }
+
     @Test
     fun `given a variantQuery with a exact 'Nof' expression then map should return the corresponding SiloQuery`() {
         val variantQuery = "[exactly-3-of: 123A, 234T, 345G]"