Merge branch 'main' into fix-sequenceNameQuoting

include/silo/preprocessing/preprocessor.h

@@ -3,11 +3,11 @@
 #include "silo/config/database_config.h"
 #include "silo/config/preprocessing_config.h"
 #include "silo/preprocessing/preprocessing_database.h"
+#include "silo/storage/pango_lineage_alias.h"
 #include "silo/storage/reference_genomes.h"
 
 namespace silo {
 class Database;
-class PangoLineageAliasLookup;
 
 namespace preprocessing {
 
@@ -18,12 +18,14 @@ class Preprocessor {
    config::DatabaseConfig database_config;
    PreprocessingDatabase preprocessing_db;
    ReferenceGenomes reference_genomes_;
+   PangoLineageAliasLookup alias_lookup_;
 
   public:
    Preprocessor(
-      const config::PreprocessingConfig preprocessing_config,
-      const config::DatabaseConfig database_config,
-      const ReferenceGenomes& reference_genomes
+      config::PreprocessingConfig preprocessing_config,
+      config::DatabaseConfig database_config,
+      const ReferenceGenomes& reference_genomes,
+      PangoLineageAliasLookup alias_lookup
    );
 
    Database preprocess();
@@ -65,7 +67,6 @@ class Preprocessor {
    Database buildDatabase(
       const preprocessing::Partitions& partition_descriptor,
       const std::string& order_by_clause,
-      const silo::PangoLineageAliasLookup& alias_key,
       const std::filesystem::path& intermediate_results_directory
    );
 

include/silo/storage/pango_lineage_alias.h

@@ -3,6 +3,7 @@
 #include <cstdint>
 #include <filesystem>
 #include <functional>
+#include <optional>
 #include <string>
 #include <unordered_map>
 #include <vector>
@@ -49,7 +50,7 @@ class PangoLineageAliasLookup {
    ) const;
 
    static silo::PangoLineageAliasLookup readFromFile(
-      const std::filesystem::path& pango_lineage_alias_file
+      const std::optional<std::filesystem::path>& pango_lineage_alias_file
    );
 };
 

include/silo/test/query_fixture.test.h

@@ -16,6 +16,7 @@
 #include "silo/preprocessing/preprocessor.h"
 #include "silo/preprocessing/sql_function.h"
 #include "silo/query_engine/query_engine.h"
+#include "silo/storage/pango_lineage_alias.h"
 #include "silo/storage/reference_genomes.h"
 
 namespace silo::test {
@@ -67,6 +68,7 @@ struct QueryTestData {
    const std::vector<nlohmann::json> ndjson_input_data;
    const silo::config::DatabaseConfig database_config;
    const silo::ReferenceGenomes reference_genomes;
+   const silo::PangoLineageAliasLookup alias_lookup;
 };
 
 struct QueryTestScenario {
@@ -117,7 +119,10 @@ class QueryTestFixture : public ::testing::TestWithParam<QueryTestScenario> {
       file.close();
 
       silo::preprocessing::Preprocessor preprocessor(
-         config_with_input_dir, test_data.database_config, test_data.reference_genomes
+         config_with_input_dir,
+         test_data.database_config,
+         test_data.reference_genomes,
+         test_data.alias_lookup
       );
       DataContainer::database = std::make_unique<Database>(preprocessor.preprocess());
 

src/silo/database.test.cpp

@@ -26,7 +26,12 @@ silo::Database buildTestDatabase() {
    const auto reference_genomes =
       silo::ReferenceGenomes::readFromFile(config.getReferenceGenomeFilename());
 
-   silo::preprocessing::Preprocessor preprocessor(config, database_config, reference_genomes);
+   const auto alias_lookup =
+      silo::PangoLineageAliasLookup::readFromFile(config.getPangoLineageDefinitionFilename());
+
+   silo::preprocessing::Preprocessor preprocessor(
+      config, database_config, reference_genomes, alias_lookup
+   );
    return preprocessor.preprocess();
 }
 
@@ -52,7 +57,12 @@ TEST(DatabaseTest, shouldSuccessfullyBuildDatabaseWithoutPartitionBy) {
    const auto reference_genomes =
       silo::ReferenceGenomes::readFromFile(config.getReferenceGenomeFilename());
 
-   silo::preprocessing::Preprocessor preprocessor(config, database_config, reference_genomes);
+   const auto alias_lookup =
+      silo::PangoLineageAliasLookup::readFromFile(config.getPangoLineageDefinitionFilename());
+
+   silo::preprocessing::Preprocessor preprocessor(
+      config, database_config, reference_genomes, alias_lookup
+   );
    auto database = preprocessor.preprocess();
 
    const auto simple_database_info = database.getDatabaseInfo();

src/silo/preprocessing/preprocessor.cpp

@@ -28,12 +28,14 @@ constexpr std::string_view FASTA_EXTENSION = ".fasta";
 Preprocessor::Preprocessor(
    config::PreprocessingConfig preprocessing_config_,
    config::DatabaseConfig database_config_,
-   const ReferenceGenomes& reference_genomes
+   const ReferenceGenomes& reference_genomes,
+   PangoLineageAliasLookup alias_lookup
 )
     : preprocessing_config(std::move(preprocessing_config_)),
       database_config(std::move(database_config_)),
       preprocessing_db(preprocessing_config.getPreprocessingDatabaseLocation(), reference_genomes),
-      reference_genomes_(reference_genomes) {}
+      reference_genomes_(reference_genomes),
+      alias_lookup_(std::move(alias_lookup)) {}
 
 Database Preprocessor::preprocess() {
    SPDLOG_INFO(
@@ -50,14 +52,6 @@ Database Preprocessor::preprocess() {
       throw silo::preprocessing::PreprocessingException(error);
    }
 
-   SPDLOG_INFO("preprocessing - building alias key");
-   const auto pango_lineage_definition_filename =
-      preprocessing_config.getPangoLineageDefinitionFilename();
-   PangoLineageAliasLookup alias_key;
-   if (pango_lineage_definition_filename.has_value()) {
-      alias_key = PangoLineageAliasLookup::readFromFile(pango_lineage_definition_filename.value());
-   }
-
    const auto& ndjson_input_filename = preprocessing_config.getNdjsonInputFilename();
    if (ndjson_input_filename.has_value()) {
       SPDLOG_INFO("preprocessing - ndjson pipeline chosen");
@@ -92,10 +86,7 @@ Database Preprocessor::preprocess() {
    SPDLOG_INFO("preprocessing - building database");
    preprocessing_db.refreshConnection();
    return buildDatabase(
-      partition_descriptor,
-      order_by_clause,
-      alias_key,
-      preprocessing_config.getIntermediateResultsDirectory()
+      partition_descriptor, order_by_clause, preprocessing_config.getIntermediateResultsDirectory()
    );
 }
 
@@ -462,12 +453,11 @@ void Preprocessor::createPartitionedTableForSequence(
 Database Preprocessor::buildDatabase(
    const preprocessing::Partitions& partition_descriptor,
    const std::string& order_by_clause,
-   const silo::PangoLineageAliasLookup& alias_key,
    const std::filesystem::path& intermediate_results_directory
 ) {
    Database database;
    database.database_config = database_config;
-   database.alias_key = alias_key;
+   database.alias_key = alias_lookup_;
    database.intermediate_results_directory = intermediate_results_directory;
    const DataVersion& data_version = DataVersion::mineDataVersion();
    SPDLOG_INFO("preprocessing - mining data data_version: {}", data_version.toString());

src/silo/preprocessing/preprocessor.test.cpp

@@ -118,7 +118,11 @@ TEST_P(PreprocessorTestFixture, shouldProcessDataSetWithMissingSequences) {
    const auto reference_genomes =
       silo::ReferenceGenomes::readFromFile(config.getReferenceGenomeFilename());
 
-   silo::preprocessing::Preprocessor preprocessor(config, database_config, reference_genomes);
+   const auto alias_lookup =
+      silo::PangoLineageAliasLookup::readFromFile(config.getPangoLineageDefinitionFilename());
+   silo::preprocessing::Preprocessor preprocessor(
+      config, database_config, reference_genomes, alias_lookup
+   );
    auto database = preprocessor.preprocess();
 
    const auto database_info = database.getDatabaseInfo();

src/silo/query_engine/filter_expressions/pango_lineage_filter.cpp

@@ -73,8 +73,8 @@ void from_json(const nlohmann::json& json, std::unique_ptr<PangoLineageFilter>&
       json.contains("value"), "The field 'value' is required in a PangoLineage expression"
    )
    CHECK_SILO_QUERY(
-      json["value"].is_string(),
-      "The field 'value' in a PangoLineage expression needs to be a string"
+      json["value"].is_string() || json["value"].is_null(),
+      "The field 'value' in a PangoLineage expression needs to be a string or null"
    )
    CHECK_SILO_QUERY(
       json.contains("includeSublineages"),
@@ -85,7 +85,7 @@ void from_json(const nlohmann::json& json, std::unique_ptr<PangoLineageFilter>&
       "The field 'includeSublineages' in a PangoLineage expression needs to be a boolean"
    )
    const std::string& column = json["column"];
-   const std::string& lineage = json["value"];
+   const std::string& lineage = json["value"].is_null() ? "" : json["value"].get<std::string>();
    const bool include_sublineages = json["includeSublineages"];
    filter = std::make_unique<PangoLineageFilter>(column, lineage, include_sublineages);
 }

src/silo/storage/pango_lineage_alias.cpp

@@ -100,25 +100,32 @@ std::unordered_map<std::string, std::vector<std::string>> readFromJson(
 }  // namespace
 
 silo::PangoLineageAliasLookup silo::PangoLineageAliasLookup::readFromFile(
-   const std::filesystem::path& pango_lineage_alias_file
+   const std::optional<std::filesystem::path>& pango_lineage_alias_file
 ) {
-   if (!std::filesystem::exists(pango_lineage_alias_file)) {
+   if (!pango_lineage_alias_file.has_value()) {
+      SPDLOG_INFO("No pango lineage alias file provided. Using empty alias lookup.");
+      return {};
+   }
+
+   const auto& pango_lineage_alias_path = pango_lineage_alias_file.value();
+
+   if (!std::filesystem::exists(pango_lineage_alias_path)) {
       throw std::filesystem::filesystem_error(
-         "Alias key file " + pango_lineage_alias_file.string() + " does not exist",
+         "Alias key file " + pango_lineage_alias_path.string() + " does not exist",
          std::error_code()
       );
    }
 
-   if (pango_lineage_alias_file.extension() != ".json") {
+   if (pango_lineage_alias_path.extension() != ".json") {
       throw std::filesystem::filesystem_error(
-         "Alias key file " + pango_lineage_alias_file.string() + " is not a json file",
+         "Alias key file " + pango_lineage_alias_path.string() + " is not a json file",
          std::error_code()
       );
    }
 
-   SPDLOG_INFO("Read pango lineage alias from file: {}", pango_lineage_alias_file.string());
+   SPDLOG_INFO("Read pango lineage alias from file: {}", pango_lineage_alias_path.string());
 
-   return PangoLineageAliasLookup(readFromJson(pango_lineage_alias_file));
+   return PangoLineageAliasLookup(readFromJson(pango_lineage_alias_path));
 }
 
 }  // namespace silo

src/silo/test/pango_lineage_filter.test.cpp

@@ -0,0 +1,116 @@
+#include <nlohmann/json.hpp>
+
+#include <optional>
+
+#include "silo/test/query_fixture.test.h"
+
+using silo::PangoLineageAliasLookup;
+using silo::ReferenceGenomes;
+using silo::config::DatabaseConfig;
+using silo::config::ValueType;
+using silo::test::QueryTestData;
+using silo::test::QueryTestScenario;
+
+static const std::string SOME_BASE_PANGO_LINEAGE = "BASE.1";
+static const std::string SOME_SUBLINEAGE = "CHILD.1";
+
+nlohmann::json createDataWithPangoLineageValue(const std::string& primaryKey, std::string value) {
+   return {
+      {"metadata", {{"primaryKey", primaryKey}, {"pango_lineage", value}}},
+      {"alignedNucleotideSequences", {{"segment1", nullptr}}},
+      {"unalignedNucleotideSequences", {{"segment1", nullptr}}},
+      {"alignedAminoAcidSequences", {{"gene1", nullptr}}}
+   };
+}
+
+nlohmann::json createDataWithPangoLineageNullValue(const std::string& primaryKey) {
+   return {
+      {"metadata", {{"primaryKey", primaryKey}, {"pango_lineage", nullptr}}},
+      {"alignedNucleotideSequences", {{"segment1", nullptr}}},
+      {"unalignedNucleotideSequences", {{"segment1", nullptr}}},
+      {"alignedAminoAcidSequences", {{"gene1", nullptr}}}
+   };
+}
+const std::vector<nlohmann::json> DATA = {
+   createDataWithPangoLineageValue("id_0", SOME_BASE_PANGO_LINEAGE),
+   createDataWithPangoLineageValue("id_1", SOME_BASE_PANGO_LINEAGE),
+   createDataWithPangoLineageValue("id_2", SOME_SUBLINEAGE),
+   createDataWithPangoLineageNullValue("id_3")
+};
+
+const auto DATABASE_CONFIG = DatabaseConfig{
+   .default_nucleotide_sequence = "segment1",
+   .schema =
+      {.instance_name = "dummy name",
+       .metadata =
+          {{.name = "primaryKey", .type = ValueType::STRING},
+           {.name = "pango_lineage", .type = ValueType::PANGOLINEAGE, .generate_index = true}},
+       .primary_key = "primaryKey"}
+};
+
+const auto REFERENCE_GENOMES = ReferenceGenomes{
+   {{"segment1", "A"}},
+   {{"gene1", "*"}},
+};
+
+const auto ALIAS_LOOKUP = PangoLineageAliasLookup{{{"CHILD", {"BASE.1.1.1"}}}};
+
+const QueryTestData TEST_DATA{
+   .ndjson_input_data = {DATA},
+   .database_config = DATABASE_CONFIG,
+   .reference_genomes = REFERENCE_GENOMES,
+   .alias_lookup = ALIAS_LOOKUP
+};
+
+nlohmann::json createPangoLineageQuery(const nlohmann::json value, bool include_sublineages) {
+   return {
+      {"action", {{"type", "Details"}}},
+      {"filterExpression",
+       {{"type", "PangoLineage"},
+        {"column", "pango_lineage"},
+        {"value", value},
+        {"includeSublineages", include_sublineages}}}
+   };
+}
+
+const QueryTestScenario PANGO_LINEAGE_FILTER_SCENARIO = {
+   .name = "pangoLineageFilter",
+   .query = createPangoLineageQuery(SOME_BASE_PANGO_LINEAGE, false),
+   .expected_query_result = nlohmann::json(
+      {{{"primaryKey", "id_0"}, {"pango_lineage", SOME_BASE_PANGO_LINEAGE}},
+       {{"primaryKey", "id_1"}, {"pango_lineage", SOME_BASE_PANGO_LINEAGE}}}
+   )
+};
+
+const QueryTestScenario PANGO_LINEAGE_FILTER_INCLUDING_SUBLINEAGES_SCENARIO = {
+   .name = "pangoLineageFilterIncludingSublineages",
+   .query = createPangoLineageQuery(SOME_BASE_PANGO_LINEAGE, true),
+   .expected_query_result = nlohmann::json(
+      {{{"primaryKey", "id_0"}, {"pango_lineage", SOME_BASE_PANGO_LINEAGE}},
+       {{"primaryKey", "id_1"}, {"pango_lineage", SOME_BASE_PANGO_LINEAGE}},
+       {{"primaryKey", "id_2"}, {"pango_lineage", SOME_SUBLINEAGE}}}
+   )
+};
+
+const QueryTestScenario PANGO_LINEAGE_FILTER_NULL_SCENARIO = {
+   .name = "pangoLineageFilterNull",
+   .query = createPangoLineageQuery(nullptr, false),
+   .expected_query_result = nlohmann::json({{{"primaryKey", "id_3"}, {"pango_lineage", nullptr}}})
+};
+
+const QueryTestScenario PANGO_LINEAGE_FILTER_NULL_INCLUDING_SUBLINEAGES_SCENARIO = {
+   .name = "pangoLineageFilterNullIncludingSublineages",
+   .query = createPangoLineageQuery(nullptr, true),
+   .expected_query_result = nlohmann::json({{{"primaryKey", "id_3"}, {"pango_lineage", nullptr}}})
+};
+
+QUERY_TEST(
+   PangoLineageFilterTest,
+   TEST_DATA,
+   ::testing::Values(
+      PANGO_LINEAGE_FILTER_SCENARIO,
+      PANGO_LINEAGE_FILTER_INCLUDING_SUBLINEAGES_SCENARIO,
+      PANGO_LINEAGE_FILTER_NULL_SCENARIO,
+      PANGO_LINEAGE_FILTER_NULL_INCLUDING_SUBLINEAGES_SCENARIO
+   )
+);

src/silo_api/api.cpp

@@ -254,8 +254,13 @@ class SiloServer : public Poco::Util::ServerApplication {
       const auto reference_genomes =
          silo::ReferenceGenomes::readFromFile(preprocessing_config.getReferenceGenomeFilename());
 
+      SPDLOG_INFO("preprocessing - reading pango lineage alias");
+      const auto alias_lookup = silo::PangoLineageAliasLookup::readFromFile(
+         preprocessing_config.getPangoLineageDefinitionFilename()
+      );
+
       auto preprocessor = silo::preprocessing::Preprocessor(
-         preprocessing_config, database_config, reference_genomes
+         preprocessing_config, database_config, reference_genomes, alias_lookup
       );
 
       return preprocessor.preprocess();