feat: have no default sequence by default, implement default amino ac…

…id sequence from config closes #454
GenSpectrum · Jul 16, 2024 · 16898ff · 16898ff
1 parent 069edd8
commit 16898ff
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Showing 6 changed files with 250 additions and 11 deletions.
diff --git a/include/silo/config/database_config.h b/include/silo/config/database_config.h
@@ -36,7 +36,8 @@ class DatabaseSchema {
 
 class DatabaseConfig {
   public:
-   std::string default_nucleotide_sequence;
+   std::optional<std::string> default_nucleotide_sequence;
+   std::optional<std::string> default_amino_acid_sequence;
    DatabaseSchema schema;
 
    [[nodiscard]] std::optional<DatabaseMetadata> getMetadata(const std::string& name) const;

diff --git a/src/silo/config/database_config.cpp b/src/silo/config/database_config.cpp
@@ -38,6 +38,9 @@ ValueType silo::config::toDatabaseValueType(std::string_view type) {
 
 namespace {
 
+const std::string DEFAULT_NUCLEOTIDE_SEQUENCE_KEY = "defaultNucleotideSequence";
+const std::string DEFAULT_AMINO_ACID_SEQUENCE_KEY = "defaultAminoAcidSequence";
+
 std::string toString(ValueType type) {
    switch (type) {
       case ValueType::STRING:
@@ -63,10 +66,15 @@ struct convert<silo::config::DatabaseConfig> {
    static bool decode(const Node& node, silo::config::DatabaseConfig& config) {
       config.schema = node["schema"].as<silo::config::DatabaseSchema>();
 
-      if (node["defaultNucleotideSequence"].IsDefined()) {
-         config.default_nucleotide_sequence = node["defaultNucleotideSequence"].as<std::string>();
-      } else {
-         config.default_nucleotide_sequence = "main";
+      if (node[DEFAULT_NUCLEOTIDE_SEQUENCE_KEY].IsDefined() &&
+          !node[DEFAULT_NUCLEOTIDE_SEQUENCE_KEY].IsNull()) {
+         config.default_nucleotide_sequence =
+            node[DEFAULT_NUCLEOTIDE_SEQUENCE_KEY].as<std::string>();
+      }
+      if (node[DEFAULT_AMINO_ACID_SEQUENCE_KEY].IsDefined() &&
+          !node[DEFAULT_AMINO_ACID_SEQUENCE_KEY].IsNull()) {
+         config.default_amino_acid_sequence =
+            node[DEFAULT_AMINO_ACID_SEQUENCE_KEY].as<std::string>();
       }
 
       SPDLOG_TRACE("Resulting database config: {}", config);
@@ -77,8 +85,11 @@ struct convert<silo::config::DatabaseConfig> {
       Node node;
       node["schema"] = config.schema;
 
-      if (config.default_nucleotide_sequence != "main") {
-         node["defaultNucleotideSequence"] = config.default_nucleotide_sequence;
+      if (config.default_nucleotide_sequence.has_value()) {
+         node[DEFAULT_NUCLEOTIDE_SEQUENCE_KEY] = *config.default_nucleotide_sequence;
+      }
+      if (config.default_amino_acid_sequence.has_value()) {
+         node[DEFAULT_AMINO_ACID_SEQUENCE_KEY] = *config.default_amino_acid_sequence;
       }
       return node;
    }
@@ -233,8 +244,13 @@ DatabaseConfig DatabaseConfigReader::parseYaml(const std::string& yaml) const {
 ) -> decltype(ctx.out()) {
    return fmt::format_to(
       ctx.out(),
-      "{{ default_nucleotide_sequence: '{}', schema: {} }}",
-      database_config.default_nucleotide_sequence,
+      "{{ default_nucleotide_sequence: '{}', default_amino_acid_sequence: '{}', schema: {} }}",
+      database_config.default_nucleotide_sequence.has_value()
+         ? *database_config.default_nucleotide_sequence
+         : "null",
+      database_config.default_amino_acid_sequence.has_value()
+         ? *database_config.default_nucleotide_sequence
+         : "null",
       database_config.schema
    );
 }

diff --git a/src/silo/config/database_config.test.cpp b/src/silo/config/database_config.test.cpp
@@ -138,6 +138,8 @@ TEST(DatabaseConfigReader, shouldReadConfigWithCorrectParameters) {
    ASSERT_EQ(config.schema.metadata[8].name, "qc_value");
    ASSERT_EQ(config.schema.metadata[8].type, ValueType::FLOAT);
    ASSERT_EQ(config.schema.metadata[8].generate_index, false);
+   ASSERT_EQ(config.default_nucleotide_sequence, std::nullopt);
+   ASSERT_EQ(config.default_amino_acid_sequence, std::nullopt);
 }
 
 TEST(DatabaseConfigReader, shouldThrowExceptionWhenConfigFileDoesNotExist) {
@@ -224,4 +226,40 @@ TEST(DatabaseConfigReader, shouldReadConfigWithoutPartitionBy) {
    ASSERT_EQ(config.schema.partition_by, std::nullopt);
 }
 
+TEST(DatabaseConfigReader, shouldReadConfigWithDefaultSequencesSet) {
+   const auto* yaml = R"-(
+schema:
+  instanceName: dummy without partitionBy
+  metadata:
+    - name: primaryKey
+      type: string
+  primaryKey: primaryKey
+defaultNucleotideSequence: defaultNuc
+defaultAminoAcidSequence: defaultAA
+)-";
+
+   const DatabaseConfig& config = DatabaseConfigReader().parseYaml(yaml);
+
+   ASSERT_EQ(config.default_nucleotide_sequence, "defaultNuc");
+   ASSERT_EQ(config.default_amino_acid_sequence, "defaultAA");
+}
+
+TEST(DatabaseConfigReader, shouldReadConfigWithDefaultSequencesSetButNull) {
+   const auto* yaml = R"-(
+schema:
+  instanceName: dummy without partitionBy
+  metadata:
+    - name: primaryKey
+      type: string
+  primaryKey: primaryKey
+defaultNucleotideSequence: null
+defaultAminoAcidSequence: null
+)-";
+
+   const DatabaseConfig& config = DatabaseConfigReader().parseYaml(yaml);
+
+   ASSERT_EQ(config.default_nucleotide_sequence, std::nullopt);
+   ASSERT_EQ(config.default_amino_acid_sequence, std::nullopt);
+}
+
 }  // namespace
diff --git a/src/silo/database.cpp b/src/silo/database.cpp
@@ -76,7 +76,7 @@ std::optional<std::string> Database::getDefaultSequenceName<Nucleotide>() const
 
 template <>
 std::optional<std::string> Database::getDefaultSequenceName<AminoAcid>() const {
-   return std::nullopt;
+   return database_config.default_amino_acid_sequence;
 }
 
 template <>

diff --git a/src/silo/test/default_sequence.test.cpp b/src/silo/test/default_sequence.test.cpp
@@ -0,0 +1,183 @@
+#include <nlohmann/json.hpp>
+
+#include <optional>
+
+#include "silo/test/query_fixture.test.h"
+
+using silo::ReferenceGenomes;
+using silo::config::DatabaseConfig;
+using silo::config::ValueType;
+using silo::test::QueryTestData;
+using silo::test::QueryTestScenario;
+
+namespace {
+const std::string VALUE_SEGMENT_1 = "A";
+const std::string VALUE_SEGMENT_2 = "C";
+
+const nlohmann::json DATA_DIFFERENT_FROM_REFERENCE = {
+   {"metadata", {{"primaryKey", "id"}}},
+   {"alignedNucleotideSequences", {{"segment1", VALUE_SEGMENT_1}, {"segment2", VALUE_SEGMENT_2}}},
+   {"unalignedNucleotideSequences", {{"segment1", nullptr}, {"segment2", nullptr}}},
+   {"alignedAminoAcidSequences",
+    {{"gene1", VALUE_SEGMENT_1 + "*"}, {"gene2", VALUE_SEGMENT_2 + "*"}}},
+   {"nucleotideInsertions", {{"segment1", {"1:AAA"}}, {"segment2", {"1:GGG"}}}},
+   {"aminoAcidInsertions", {{"gene1", {"1:AAA"}}, {"gene2", {"1:GGG"}}}}
+};
+
+const nlohmann::json DATA_EQUALS_TO_REFERENCE = {
+   {"metadata", {{"primaryKey", "equal to reference"}}},
+   {"alignedNucleotideSequences", {{"segment1", "T"}, {"segment2", "T"}}},
+   {"unalignedNucleotideSequences", {{"segment1", nullptr}, {"segment2", nullptr}}},
+   {"alignedAminoAcidSequences", {{"gene1", "T*"}, {"gene2", "T*"}}},
+   {"nucleotideInsertions", {{"segment1", {}}, {"segment2", {}}}},
+   {"aminoAcidInsertions", {{"gene1", {}}, {"gene2", {}}}}
+};
+
+const auto DATABASE_CONFIG = DatabaseConfig{
+   .default_nucleotide_sequence = "segment1",
+   .default_amino_acid_sequence = "gene1",
+   .schema =
+      {.instance_name = "dummy name",
+       .metadata = {{.name = "primaryKey", .type = ValueType::STRING}},
+       .primary_key = "primaryKey"}
+};
+
+const auto REFERENCE_GENOMES = ReferenceGenomes{
+   {{"segment1", "T"}, {"segment2", "T"}},
+   {{"gene1", "T*"}, {"gene2", "T*"}},
+};
+
+const QueryTestData TEST_DATA{
+   .ndjson_input_data = {DATA_DIFFERENT_FROM_REFERENCE, DATA_EQUALS_TO_REFERENCE},
+   .database_config = DATABASE_CONFIG,
+   .reference_genomes = REFERENCE_GENOMES
+};
+
+nlohmann::json createQueryWithFilter(const nlohmann::json filter) {
+   return {{"action", {{"type", "Details"}}}, {"filterExpression", filter}};
+}
+
+const nlohmann::json EXPECTED_RESULT = {{{"primaryKey", "id"}}};
+
+const QueryTestScenario NUCLEOTIDE_EQUALS_NO_SEQUENCE_NAME = {
+   .name = "nucleotideEqualsWithoutSegmentTakesDefaultSequence",
+   .query = createQueryWithFilter(
+      {{"type", "NucleotideEquals"}, {"position", 1}, {"symbol", VALUE_SEGMENT_1}}
+   ),
+   .expected_query_result = EXPECTED_RESULT
+};
+
+const QueryTestScenario NUCLEOTIDE_EQUALS_NO_SEQUENCE_NAME_FILTER_BY_WRONG_VALUE = {
+   .name = "nucleotideEqualsWithoutSegmentFilterByWrongValue",
+   .query = createQueryWithFilter(
+      {{"type", "NucleotideEquals"}, {"position", 1}, {"symbol", VALUE_SEGMENT_2}}
+   ),
+   .expected_query_result = nlohmann::json::array()
+};
+
+const QueryTestScenario NUCLEOTIDE_EQUALS_SEGMENT_1 = {
+   .name = "nucleotideEqualsSegment1",
+   .query = createQueryWithFilter(
+      {{"type", "NucleotideEquals"},
+       {"sequenceName", "segment1"},
+       {"position", 1},
+       {"symbol", VALUE_SEGMENT_1}}
+   ),
+   .expected_query_result = EXPECTED_RESULT
+};
+
+const QueryTestScenario NUCLEOTIDE_EQUALS_SEGMENT_2 = {
+   .name = "nucleotideEqualsSegment2",
+   .query = createQueryWithFilter(
+      {{"type", "NucleotideEquals"},
+       {"sequenceName", "segment2"},
+       {"position", 1},
+       {"symbol", VALUE_SEGMENT_2}}
+   ),
+   .expected_query_result = EXPECTED_RESULT
+};
+
+const QueryTestScenario AMINO_ACID_EQUALS_NO_SEQUENCE_NAME = {
+   .name = "aminoAcidEqualsWithoutSequenceNameTakesDefaultSequence",
+   .query = createQueryWithFilter(
+      {{"type", "AminoAcidEquals"}, {"position", 1}, {"symbol", VALUE_SEGMENT_1}}
+   ),
+   .expected_query_result = EXPECTED_RESULT
+};
+
+const QueryTestScenario AMINO_ACID_EQUALS_NO_SEQUENCE_NAME_FILTER_BY_WRONG_VALUE = {
+   .name = "aminoAcidEqualsWithoutSequenceNameFilterByWrongValue",
+   .query = createQueryWithFilter(
+      {{"type", "AminoAcidEquals"}, {"position", 1}, {"symbol", VALUE_SEGMENT_2}}
+   ),
+   .expected_query_result = nlohmann::json::array()
+};
+
+const QueryTestScenario AMINO_ACID_EQUALS_GENE_1 = {
+   .name = "aminoAcidEqualsGene1",
+   .query = createQueryWithFilter(
+      {{"type", "AminoAcidEquals"},
+       {"sequenceName", "gene1"},
+       {"position", 1},
+       {"symbol", VALUE_SEGMENT_1}}
+   ),
+   .expected_query_result = EXPECTED_RESULT
+};
+
+const QueryTestScenario AMINO_ACID_EQUALS_GENE_2 = {
+   .name = "aminoAcidEqualsGene2",
+   .query = createQueryWithFilter(
+      {{"type", "AminoAcidEquals"},
+       {"sequenceName", "gene2"},
+       {"position", 1},
+       {"symbol", VALUE_SEGMENT_2}}
+   ),
+   .expected_query_result = EXPECTED_RESULT
+};
+
+const QueryTestScenario HAS_NUCLEOTIDE_MUTATION_WITHOUT_SEQUENCE_NAME = {
+   .name = "hasNucleotideMutationWithoutSequenceName",
+   .query = createQueryWithFilter({{"type", "HasNucleotideMutation"}, {"position", 1}}),
+   .expected_query_result = EXPECTED_RESULT
+};
+
+const QueryTestScenario HAS_AMINO_ACID_MUTATION_WITHOUT_SEQUENCE_NAME = {
+   .name = "hasAminoAcidMutationWithoutSequenceName",
+   .query = createQueryWithFilter({{"type", "HasAminoAcidMutation"}, {"position", 1}}),
+   .expected_query_result = EXPECTED_RESULT
+};
+
+const QueryTestScenario NUCLEOTIDE_INSERTION_CONTAINS_WITHOUT_SEQUENCE_NAME = {
+   .name = "nucleotideInsertionContainsWithoutSequenceName",
+   .query = createQueryWithFilter({{"type", "InsertionContains"}, {"value", "A"}, {"position", 1}}),
+   .expected_query_result = EXPECTED_RESULT
+};
+
+const QueryTestScenario AMINO_ACID_INSERTION_CONTAINS_WITHOUT_SEQUENCE_NAME = {
+   .name = "aminoAcidInsertionContainsWithoutSequenceName",
+   .query = createQueryWithFilter(
+      {{"type", "AminoAcidInsertionContains"}, {"value", "A"}, {"position", 1}}
+   ),
+   .expected_query_result = EXPECTED_RESULT
+};
+
+}  // namespace
+
+QUERY_TEST(
+   DefaultSequenceTest,
+   TEST_DATA,
+   ::testing::Values(
+      NUCLEOTIDE_EQUALS_NO_SEQUENCE_NAME,
+      NUCLEOTIDE_EQUALS_NO_SEQUENCE_NAME_FILTER_BY_WRONG_VALUE,
+      NUCLEOTIDE_EQUALS_SEGMENT_1,
+      NUCLEOTIDE_EQUALS_SEGMENT_2,
+      AMINO_ACID_EQUALS_NO_SEQUENCE_NAME,
+      AMINO_ACID_EQUALS_NO_SEQUENCE_NAME_FILTER_BY_WRONG_VALUE,
+      AMINO_ACID_EQUALS_GENE_1,
+      AMINO_ACID_EQUALS_GENE_2,
+      HAS_NUCLEOTIDE_MUTATION_WITHOUT_SEQUENCE_NAME,
+      HAS_AMINO_ACID_MUTATION_WITHOUT_SEQUENCE_NAME,
+      NUCLEOTIDE_INSERTION_CONTAINS_WITHOUT_SEQUENCE_NAME,
+      AMINO_ACID_INSERTION_CONTAINS_WITHOUT_SEQUENCE_NAME
+   )
+);
diff --git a/testBaseData/exampleDataset/database_config.yaml b/testBaseData/exampleDataset/database_config.yaml
@@ -26,4 +26,5 @@ schema:
       type: boolean
   primaryKey: gisaid_epi_isl
   dateToSortBy: date
-  partitionBy: pango_lineage
+  partitionBy: pango_lineage
+defaultNucleotideSequence: "main"