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feat: return structured mutation and insertion responses #718
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@fengelniederhammer
fengelniederhammer committed Apr 3, 2024
1 parent c8872ba commit 0a5a7be
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Showing 16 changed files with 624 additions and 273 deletions.
1 change: 1 addition & 0 deletions .github/workflows/lapis2.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -137,6 +137,7 @@ jobs:

- name: Start SILO and LAPIS and Run Tests
run: |
docker compose -f lapis2/docker-compose.yml pull
docker compose -f lapis2/docker-compose.yml up -d --wait
cd siloLapisTests && npm run test
env:
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7 changes: 7 additions & 0 deletions lapis2-docs/src/components/QueryGenerator/QueryTypeSelectionState.ts
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Expand Up @@ -101,11 +101,18 @@ function getFieldsThatAreAlwaysPresent(selection: Selection): ResultField[] {
{ name: 'mutation', type: 'string', nullable: false },
{ name: 'proportion', type: 'string', nullable: false },
{ name: 'count', type: 'integer', nullable: false },
{ name: 'sequenceName', type: 'string', nullable: true },
{ name: 'mutationFrom', type: 'string', nullable: false },
{ name: 'mutationTo', type: 'string', nullable: false },
{ name: 'position', type: 'integer', nullable: false },
];
case 'insertions':
return [
{ name: 'insertion', type: 'string', nullable: false },
{ name: 'count', type: 'integer', nullable: false },
{ name: 'insertedSymbols', type: 'string', nullable: false },
{ name: 'sequenceName', type: 'string', nullable: false },
{ name: 'position', type: 'integer', nullable: false },
];
case 'details':
case 'nucleotideSequences':
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Binary file modified lapis2-docs/src/images/concepts/example_nucleotide_mutation_response_200.png
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Binary file modified lapis2-docs/src/images/concepts/example_nucleotide_mutation_schema.png
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49 changes: 35 additions & 14 deletions lapis2/src/main/kotlin/org/genspectrum/lapis/model/SiloQueryModel.kt
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Original file line number Diff line number Diff line change
Expand Up @@ -50,13 +50,23 @@ class SiloQueryModel(
),
)
return data.map {
val sequenceName =
if (referenceGenomeSchema.isSingleSegmented()) it.mutation else "${it.sequenceName}:${it.mutation}"
val mutation = if (referenceGenomeSchema.isSingleSegmented()) {
it.mutation
} else {
"${it.sequenceName}:${it.mutation}"
}

NucleotideMutationResponse(
sequenceName,
it.count,
it.proportion,
mutation = mutation,
count = it.count,
proportion = it.proportion,
sequenceName = when (referenceGenomeSchema.isSingleSegmented()) {
true -> null
false -> it.sequenceName
},
mutationFrom = it.mutationFrom,
mutationTo = it.mutationTo,
position = it.position,
)
}
}
Expand All @@ -77,9 +87,13 @@ class SiloQueryModel(
)
return data.map {
AminoAcidMutationResponse(
"${it.sequenceName}:${it.mutation}",
it.count,
it.proportion,
mutation = "${it.sequenceName}:${it.mutation}",
count = it.count,
proportion = it.proportion,
sequenceName = it.sequenceName,
mutationFrom = it.mutationFrom,
mutationTo = it.mutationTo,
position = it.position,
)
}
}
Expand Down Expand Up @@ -110,11 +124,15 @@ class SiloQueryModel(
)

return data.map {
val sequenceName = if (referenceGenomeSchema.isSingleSegmented()) "" else "${it.sequenceName}:"

NucleotideInsertionResponse(
"ins_${sequenceName}${it.position}:${it.insertions}",
it.count,
insertion = it.insertion,
count = it.count,
insertedSymbols = it.insertedSymbols,
position = it.position,
sequenceName = when (referenceGenomeSchema.isSingleSegmented()) {
true -> null
false -> it.sequenceName
},
)
}
}
Expand All @@ -133,8 +151,11 @@ class SiloQueryModel(

return data.map {
AminoAcidInsertionResponse(
"ins_${it.sequenceName}:${it.position}:${it.insertions}",
it.count,
insertion = it.insertion,
count = it.count,
insertedSymbols = it.insertedSymbols,
position = it.position,
sequenceName = it.sequenceName,
)
}
}
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140 changes: 113 additions & 27 deletions lapis2/src/main/kotlin/org/genspectrum/lapis/openApi/OpenApiDocs.kt
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@ import io.swagger.v3.oas.models.OpenAPI
import io.swagger.v3.oas.models.media.ArraySchema
import io.swagger.v3.oas.models.media.BooleanSchema
import io.swagger.v3.oas.models.media.IntegerSchema
import io.swagger.v3.oas.models.media.NumberSchema
import io.swagger.v3.oas.models.media.Schema
import io.swagger.v3.oas.models.media.StringSchema
import org.genspectrum.lapis.config.DatabaseConfig
Expand Down Expand Up @@ -163,7 +164,11 @@ fun buildOpenApiSchema(
.description(
"The response contains the metadata of every sequence matching the sequence filters.",
)
.properties(nucleotideMutationProportionSchema()),
.properties(nucleotideMutationProportionSchema())
.required(
nucleotideMutationProportionSchema().keys
.filterNot { referenceGenomeSchema.isSingleSegmented() && it == "sequenceName" },
),
),
)
.addSchemas(NUCLEOTIDE_MUTATIONS_SCHEMA, nucleotideMutations())
Expand All @@ -175,7 +180,8 @@ fun buildOpenApiSchema(
.description(
"The response contains the metadata of every sequence matching the sequence filters.",
)
.properties(aminoAcidMutationProportionSchema()),
.properties(aminoAcidMutationProportionSchema())
.required(aminoAcidMutationProportionSchema().keys.toList()),
),
)
.addSchemas(
Expand All @@ -184,7 +190,11 @@ fun buildOpenApiSchema(
Schema<String>()
.type("object")
.description("Nucleotide Insertion data.")
.properties(nucleotideInsertionSchema()),
.properties(nucleotideInsertionSchema())
.required(
nucleotideInsertionSchema().keys
.filterNot { referenceGenomeSchema.isSingleSegmented() && it == "sequenceName" },
),
),
)
.addSchemas(
Expand All @@ -193,7 +203,8 @@ fun buildOpenApiSchema(
Schema<String>()
.type("object")
.description("Amino Acid Insertion data.")
.properties(aminoAcidInsertionSchema()),
.properties(aminoAcidInsertionSchema())
.required(aminoAcidInsertionSchema().keys.toList()),
),
)
.addSchemas(FIELDS_TO_AGGREGATE_BY_SCHEMA, fieldsArray(databaseConfig.schema.metadata))
Expand Down Expand Up @@ -372,42 +383,112 @@ private fun getAggregatedResponseProperties(filterProperties: Map<SequenceFilter
COUNT_PROPERTY to IntegerSchema().description("The number of sequences matching the filters."),
)

fun accessKeySchema() = StringSchema().description(ACCESS_KEY_DESCRIPTION)
fun accessKeySchema(): Schema<Any> = StringSchema().description(ACCESS_KEY_DESCRIPTION)

private fun nucleotideMutationProportionSchema() =
mapOf(
"mutation" to Schema<String>().type("string").example("T123C").description("The mutation that was found."),
"proportion" to Schema<String>().type("number").description("The proportion of sequences having the mutation."),
"count" to Schema<String>().type("integer")
.description("The number of sequences matching having the mutation."),
"mutation" to StringSchema()
.example("sequence1:G29741T")
.description(
"If the genome only contains one segment then this is: " +
"(mutationFrom)(position)(mutationTo)." +
"If it has more than one segment (e.g., influenza), then the sequence is contained here: " +
"(sequenceName):(mutationFrom)(position)" +
"(mutationTo)",
),
"proportion" to NumberSchema()
.example(0.54321)
.description(
"Number of sequences with this mutation divided by the total number sequences matching the " +
"given filter criteria with non-ambiguous reads at that position",
),
"count" to IntegerSchema()
.example(1234)
.description("Total number of sequences with this mutation matching the given sequence filter criteria"),
"sequenceName" to StringSchema()
.example("sequence1")
.description(
"The name of the segment in which the mutation occurs. Null if the genome is single-segmented.",
),
"mutationFrom" to StringSchema()
.example("G")
.description("The nucleotide symbol in the reference genome at the position of the mutation"),
"mutationTo" to StringSchema()
.example("T")
.description("The nucleotide symbol that the mutation changes to or '-' in case of a deletion"),
"position" to IntegerSchema()
.example(29741)
.description("The position in the reference genome where the mutation occurs"),
)

private fun aminoAcidMutationProportionSchema() =
mapOf(
"mutation" to Schema<String>().type("string").example("ORF1a:123").description(
"A amino acid mutation that was found in the format \"\\<gene\\>:\\<position\\>",
),
"proportion" to Schema<String>().type("number").description("The proportion of sequences having the mutation."),
"count" to Schema<String>().type("integer")
.description("The number of sequences matching having the mutation."),
"mutation" to StringSchema()
.example("ORF1a:G29741T")
.description("Of the format (sequenceName):(mutationFrom)(position)(mutationTo)"),
"proportion" to NumberSchema()
.example(0.54321)
.description(
"Number of sequences with this mutation divided by the total number sequences matching the " +
"given filter criteria with non-ambiguous reads at that position",
),
"count" to IntegerSchema()
.example(42)
.description("Total number of sequences with this mutation matching the given sequence filter criteria"),
"sequenceName" to StringSchema()
.example("ORF1a")
.description("The name of the gene in which the mutation occurs."),
"mutationFrom" to StringSchema()
.example("G")
.description("The amino acid symbol in the reference genome at the position of the mutation"),
"mutationTo" to StringSchema()
.example("T")
.description("The amino acid symbol that the mutation changes to or '-' in case of a deletion"),
"position" to IntegerSchema()
.example(29741)
.description("The position in the reference genome where the mutation occurs"),
)

private fun nucleotideInsertionSchema() =
mapOf(
"insertion" to Schema<String>().type("string")
.example("ins_segment:123:AAT")
.description("The insertion that was found."),
"count" to Schema<String>().type("integer")
.description("The number of sequences matching having the insertion."),
"insertion" to StringSchema()
.example("ins_segment1:22204:CAGAAG")
.description(
"A nucleotide insertion in the format \"ins_(segment):(position):(insertedSymbols)\". " +
"If the pathogen has only one segment LAPIS will omit the segment name (\"ins_22204:CAGAAG\").",
),
"count" to IntegerSchema()
.example(42)
.description("Total number of sequences with this insertion matching the given sequence filter criteria"),
"insertedSymbols" to StringSchema()
.example("CAGAAG")
.description("The nucleotide symbols that were inserted at the given position"),
"position" to IntegerSchema()
.example(22204)
.description("The position in the reference genome where the insertion occurs"),
"sequenceName" to StringSchema()
.example("segment1")
.description(
"The name of the segment in which the insertion occurs. Null if the genome is single-segmented.",
),
)

private fun aminoAcidInsertionSchema() =
mapOf(
"insertion" to Schema<String>().type("string")
.example("ins_gene:123:AAT")
.description("The insertion that was found."),
"count" to Schema<String>().type("integer")
.description("The number of sequences matching having the insertion."),
"insertion" to StringSchema()
.example("ins_ORF1a:22204:CAGAAG")
.description("An amino acid insertion in the format \"ins_(gene):(position):(insertedSymbols)\"."),
"count" to IntegerSchema()
.description("Total number of sequences with this insertion matching the given sequence filter criteria."),
"insertedSymbols" to StringSchema()
.example("CAGAAG")
.description("The amino acid symbols that were inserted at the given position."),
"position" to IntegerSchema()
.example(22204)
.description("The position in the reference genome where the insertion occurs."),
"sequenceName" to StringSchema()
.example("ORF1a")
.description("The name of the gene in which the insertion occurs."),
)

private fun nucleotideMutations() =
Expand Down Expand Up @@ -512,9 +593,14 @@ private fun fieldsArray(
private fun aggregatedOrderByFieldsEnum(databaseConfig: DatabaseConfig) =
orderByFieldsEnum(databaseConfig.schema.metadata, listOf("count"))

private fun mutationsOrderByFieldsEnum() = orderByFieldsEnum(emptyList(), listOf("mutation", "count", "proportion"))
private fun mutationsOrderByFieldsEnum() =
orderByFieldsEnum(
emptyList(),
listOf("mutation", "count", "proportion", "sequenceName", "mutationFrom", "mutationTo", "position"),
)

private fun insertionsOrderByFieldsEnum() = orderByFieldsEnum(emptyList(), listOf("insertion", "count"))
private fun insertionsOrderByFieldsEnum() =
orderByFieldsEnum(emptyList(), listOf("insertion", "count", "position", "sequenceName", "insertedSymbols"))

private fun aminoAcidSequenceOrderByFieldsEnum(
referenceGenomeSchema: ReferenceGenomeSchema,
Expand Down
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