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Jonas Kellerer
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feat: add lineage queries for nextstrain, nextclade and gisaid
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‎lapis2/build.gradle

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@@ -36,6 +36,7 @@ dependencies {
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}
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testImplementation 'com.ninja-squad:springmockk:4.0.2'
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testImplementation 'org.mock-server:mockserver-netty:5.15.0'
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implementation "org.jetbrains.kotlin:kotlin-stdlib"
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}
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‎lapis2/src/main/antlr/org/genspectrum/lapis/model/variantqueryparser/VariantQuery.g4

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@@ -16,6 +16,12 @@ single:
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nucleotide_mutation
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| pangolineage_query
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| n_of_query
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| nucleotide_insertion
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| aa_mutation
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| aa_insertion
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| nextclade_pangolineage_query
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| nextstrain_clade_lineage_query
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| gisaid_clade_lineage_query
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;
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nucleotide_mutation : nucleotide_symbol? position ambigous_nucleotide_symbol?;
@@ -34,6 +40,30 @@ n_of_match_exactly: 'EXACTLY-';
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n_of_number_of_matchers: NUMBER+;
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n_of_exprs: expr (',' expr)*;
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nucleotide_insertion: 'ins_' position ':' (ambigous_nucleotide_symbol | '?')+;
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aa_mutation: gene ':' aa_symbol? position ambigous_aa_symbol?;
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aa_symbol: A | R | N | D | C | E | Q | G | H | I | L | K | M | F | P | S | T | W | Y | V | ASTERISK;
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ambigous_aa_symbol: aa_symbol | X | MINUS | DOT;
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gene: covid_gene;
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covid_gene : E | M | N | S | ORF;
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aa_insertion: 'ins_' gene ':' (ambigous_aa_symbol | '?')+;
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nextclade_pangolineage_query: nextclade_pango_lineage_prefix pangolineage_query;
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nextclade_pango_lineage_prefix: 'nextcladePangoLineage:';
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nextstrain_clade_lineage_query: nextstrain_clade_prefix nextstrain_clade_query;
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nextstrain_clade_prefix: 'nextstrainClade:';
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nextstrain_clade_query: NUMBER NUMBER nextstrain_clade_character | 'RECOMBINANT';
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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;
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gisaid_clade_lineage_query: gisaid_clade_prefix gisaid_clade_query;
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gisaid_clade_prefix: 'gisaid:';
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gisaid_clade_query: gisaid_clade_character gisaid_clade_character?;
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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;
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// lexer rules
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A: 'A';
@@ -68,3 +98,5 @@ ASTERISK: '*';
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NUMBER: [0-9];
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WHITESPACE: [ \r\n\t] -> skip;
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ORF: 'ORF1A' | 'ORF1B' | 'ORF3A' | 'ORF6' | 'ORF7A' | 'ORF7B' | 'ORF8' | 'ORF9B';

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

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

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

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

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

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

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