refactor: rename lineage_index config to generate_lineage_index

GenSpectrum · Oct 16, 2024 · 0336600 · 0336600
1 parent 1d9f6f7
commit 0336600
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Showing 19 changed files with 47 additions and 44 deletions.
diff --git a/include/silo/config/database_config.h b/include/silo/config/database_config.h
@@ -21,7 +21,7 @@ class DatabaseMetadata {
    std::string name;
    ValueType type;
    bool generate_index;
-   bool lineage_index;
+   bool generate_lineage_index;
 
    [[nodiscard]] ColumnType getColumnType() const;
 };

diff --git a/src/silo/config/database_config.cpp b/src/silo/config/database_config.cpp
@@ -141,10 +141,10 @@ struct convert<silo::config::DatabaseMetadata> {
       } else {
          metadata.generate_index = false;
       }
-      if (node["lineageIndex"].IsDefined()) {
-         metadata.lineage_index = node["lineageIndex"].as<bool>();
+      if (node["generateLineageIndex"].IsDefined()) {
+         metadata.generate_lineage_index = node["generateLineageIndex"].as<bool>();
       } else {
-         metadata.lineage_index = false;
+         metadata.generate_lineage_index = false;
       }
       return true;
    }
@@ -153,8 +153,8 @@ struct convert<silo::config::DatabaseMetadata> {
       node["name"] = metadata.name;
       node["type"] = toString(metadata.type);
       node["generateIndex"] = metadata.generate_index;
-      if (metadata.lineage_index) {
-         node["lineageIndex"] = true;
+      if (metadata.generate_lineage_index) {
+         node["generateLineageIndex"] = true;
       }
       return node;
    }

diff --git a/src/silo/config/database_config.test.cpp b/src/silo/config/database_config.test.cpp
@@ -45,7 +45,7 @@ namespace {
 struct TestParameter {
    ValueType value_type;
    bool generate_index;
-   bool lineage_index;
+   bool generate_lineage_index;
    ColumnType expected_column_type;
 };
 
@@ -85,7 +85,7 @@ INSTANTIATE_TEST_SUITE_P(
       TestParameter{
          .value_type = ValueType::STRING,
          .generate_index = true,
-         .lineage_index = true,
+         .generate_lineage_index = true,
          .expected_column_type = ColumnType::INDEXED_STRING
       },
       TestParameter{
@@ -130,11 +130,11 @@ TEST(DatabaseConfigReader, shouldReadConfigWithCorrectParameters) {
    ASSERT_EQ(config.schema.metadata[5].name, "pango_lineage");
    ASSERT_EQ(config.schema.metadata[5].type, ValueType::STRING);
    ASSERT_EQ(config.schema.metadata[5].generate_index, true);
-   ASSERT_EQ(config.schema.metadata[5].lineage_index, true);
+   ASSERT_EQ(config.schema.metadata[5].generate_lineage_index, true);
    ASSERT_EQ(config.schema.metadata[6].name, "division");
    ASSERT_EQ(config.schema.metadata[6].type, ValueType::STRING);
    ASSERT_EQ(config.schema.metadata[6].generate_index, true);
-   ASSERT_EQ(config.schema.metadata[6].lineage_index, false);
+   ASSERT_EQ(config.schema.metadata[6].generate_lineage_index, false);
    ASSERT_EQ(config.schema.metadata[7].name, "age");
    ASSERT_EQ(config.schema.metadata[7].type, ValueType::INT);
    ASSERT_EQ(config.schema.metadata[7].generate_index, false);

diff --git a/src/silo/config/util/config_repository.cpp b/src/silo/config/util/config_repository.cpp
@@ -26,27 +26,27 @@ std::map<std::string, ValueType> validateMetadataDefinitions(const DatabaseConfi
          throw ConfigException("Metadata " + metadata.name + " is defined twice in the config");
       }
 
-      const auto must_be_string = metadata.lineage_index;
+      const auto must_be_string = metadata.generate_lineage_index;
       if (metadata.type != ValueType::STRING && must_be_string) {
          throw ConfigException(
             "Metadata '" + metadata.name +
-            "' lineage_index is set, but the column is not of type STRING."
+            "' generateLineageIndex is set, but the column is not of type STRING."
          );
       }
 
       const auto must_not_generate_index_on_type = metadata.type != ValueType::STRING;
       if (metadata.generate_index && must_not_generate_index_on_type) {
          throw ConfigException(
             "Metadata '" + metadata.name +
-            "' generate_index is set, but generating an index is only allowed for types STRING"
+            "' generateIndex is set, but generating an index is only allowed for types STRING"
          );
       }
 
-      const auto must_generate_index = metadata.lineage_index;
+      const auto must_generate_index = metadata.generate_lineage_index;
       if (!metadata.generate_index && must_generate_index) {
          throw ConfigException(
             "Metadata '" + metadata.name +
-            "' lineage_index is set, generate_index must also be set."
+            "' generateLineageIndex is set, generateIndex must also be set."
          );
       }
 
@@ -65,11 +65,11 @@ void validateDateToSortBy(
 
    const std::string date_to_sort_by = config.schema.date_to_sort_by.value();
    if (metadata_map.find(date_to_sort_by) == metadata_map.end()) {
-      throw ConfigException("date_to_sort_by '" + date_to_sort_by + "' is not in metadata");
+      throw ConfigException("dateToSortBy '" + date_to_sort_by + "' is not in metadata");
    }
 
    if (metadata_map[date_to_sort_by] != ValueType::DATE) {
-      throw ConfigException("date_to_sort_by '" + date_to_sort_by + "' must be of type DATE");
+      throw ConfigException("dateToSortBy '" + date_to_sort_by + "' must be of type DATE");
    }
 }
 
@@ -86,12 +86,14 @@ void validatePartitionBy(const DatabaseConfig& config) {
       [&](const DatabaseMetadata& metadata) { return metadata.name == partition_by; }
    );
    if (partition_by_metadata == config.schema.metadata.end()) {
-      throw ConfigException("partition_by '" + partition_by + "' is not in metadata");
+      throw ConfigException("partitionBy '" + partition_by + "' is not in metadata");
    }
 
-   if (partition_by_metadata->type != ValueType::STRING || !partition_by_metadata->lineage_index) {
+   if (partition_by_metadata->type != ValueType::STRING ||
+       !partition_by_metadata->generate_lineage_index) {
       throw ConfigException(
-         "partition_by '" + partition_by + "' must be of type STRING and needs 'lineageIndex' set"
+         "partitionBy '" + partition_by +
+         "' must be of type STRING and needs 'generateLineageIndex' set"
       );
    }
 }

diff --git a/src/silo/config/util/config_repository.test.cpp b/src/silo/config/util/config_repository.test.cpp
@@ -15,7 +15,7 @@ using silo::config::ValueType;
 class ConfigReaderMock : public silo::config::DatabaseConfigReader {
   public:
    ConfigReaderMock() = default;
-   ConfigReaderMock(const ConfigReaderMock& /*other*/){};
+   ConfigReaderMock(const ConfigReaderMock& /*other*/) {};
 
    MOCK_METHOD((DatabaseConfig), readConfig, (const std::filesystem::path&), (const override));
 };
@@ -44,7 +44,7 @@ TEST(ConfigRepository, shouldReadConfigWithoutErrors) {
                    {.name = "metadata1",
                     .type = ValueType::STRING,
                     .generate_index = true,
-                    .lineage_index = true},
+                    .generate_lineage_index = true},
                    {.name = "metadata2", .type = ValueType::DATE},
                 },
              .primary_key = "testPrimaryKey",
@@ -114,7 +114,7 @@ TEST(ConfigRepository, givenConfigWithDateToSortByThatIsNotConfiguredThenThrows)
          ConfigRepository(config_reader_mock).getValidatedConfig("test.yaml");
       },
       ThrowsMessage<ConfigException>(
-         ::testing::HasSubstr("date_to_sort_by 'notConfiguredDateToSortBy' is not in metadata")
+         ::testing::HasSubstr("dateToSortBy 'notConfiguredDateToSortBy' is not in metadata")
       )
    );
 }
@@ -138,7 +138,7 @@ TEST(ConfigRepository, givenDateToSortByThatIsNotADateThenThrows) {
          ConfigRepository(config_reader_mock).getValidatedConfig("test.yaml");
       },
       ThrowsMessage<ConfigException>(
-         ::testing::HasSubstr("date_to_sort_by 'not a date' must be of type DATE")
+         ::testing::HasSubstr("dateToSortBy 'not a date' must be of type DATE")
       )
    );
 }
@@ -163,7 +163,7 @@ TEST(ConfigRepository, givenConfigPartitionByThatIsNotConfiguredThenThrows) {
          ConfigRepository(config_reader_mock).getValidatedConfig("test.yaml");
       },
       ThrowsMessage<ConfigException>(
-         ::testing::HasSubstr("partition_by 'notConfiguredPartitionBy' is not in metadata")
+         ::testing::HasSubstr("partitionBy 'notConfiguredPartitionBy' is not in metadata")
       )
    );
 }
@@ -188,7 +188,7 @@ TEST(ConfigRepository, givenConfigPartitionByThatIsNotALineageThrows) {
          ConfigRepository(config_reader_mock).getValidatedConfig("test.yaml");
       },
       ThrowsMessage<silo::config::ConfigException>(::testing::HasSubstr(
-         "partition_by 'not a lineage' must be of type STRING and needs 'lineageIndex' set"
+         "partitionBy 'not a lineage' must be of type STRING and needs 'generateLineageIndex' set"
       ))
    );
 }
@@ -213,7 +213,7 @@ TEST(ConfigRepository, givenMetadataToGenerateIndexForThatIsNotStringThenThrows)
          ConfigRepository(config_reader_mock).getValidatedConfig("test.yaml");
       },
       ThrowsMessage<ConfigException>(
-         ::testing::HasSubstr("Metadata 'indexed date' generate_index is set, but generating an "
+         ::testing::HasSubstr("Metadata 'indexed date' generateIndex is set, but generating an "
                               "index is only allowed for types STRING")
       )
    );
@@ -227,7 +227,8 @@ TEST(ConfigRepository, givenLineageIndexAndNotGenerateThenThrows) {
            .metadata =
               {
                  {.name = "testPrimaryKey", .type = ValueType::STRING},
-                 {.name = "some lineage", .type = ValueType::STRING, .lineage_index = true},
+                 {.name = "some lineage", .type = ValueType::STRING, .generate_lineage_index = true
+                 },
               },
            .primary_key = "testPrimaryKey",
            .date_to_sort_by = std::nullopt,
@@ -239,8 +240,8 @@ TEST(ConfigRepository, givenLineageIndexAndNotGenerateThenThrows) {
          ConfigRepository(config_reader_mock).getValidatedConfig("test.yaml");
       },
       ThrowsMessage<ConfigException>(
-         ::testing::HasSubstr("Metadata 'some lineage' lineage_index is set, "
-                              "generate_index must also be set")
+         ::testing::HasSubstr("Metadata 'some lineage' generateLineageIndex is set, "
+                              "generateIndex must also be set")
       )
    );
 }
diff --git a/src/silo/database.cpp b/src/silo/database.cpp
@@ -603,7 +603,7 @@ void Database::initializeColumn(const config::DatabaseMetadata& metadata) {
          }
          return;
       case config::ColumnType::INDEXED_STRING: {
-         if (metadata.lineage_index) {
+         if (metadata.generate_lineage_index) {
             auto column = storage::column::IndexedStringColumn(lineage_tree);
             columns.indexed_string_columns.emplace(name, std::move(column));
          } else {

diff --git a/src/silo/test/lineage_filter.test.cpp b/src/silo/test/lineage_filter.test.cpp
@@ -54,7 +54,7 @@ const auto DATABASE_CONFIG = DatabaseConfig{
            {.name = "pango_lineage",
             .type = ValueType::STRING,
             .generate_index = true,
-            .lineage_index = true}},
+            .generate_lineage_index = true}},
        .primary_key = "primaryKey"}
 };
 

diff --git a/testBaseData/diverseSequenceNames/database_config.yaml b/testBaseData/diverseSequenceNames/database_config.yaml
@@ -16,7 +16,7 @@ schema:
     - name: pango_lineage
       type: string
       generateIndex: true
-      lineageIndex: true
+      generateLineageIndex: true
     - name: division
       type: string
       generateIndex: true

diff --git a/testBaseData/diverseSequenceNamesAsNdjson/database_config.yaml b/testBaseData/diverseSequenceNamesAsNdjson/database_config.yaml
@@ -16,7 +16,7 @@ schema:
     - name: pango_lineage
       type: string
       generateIndex: true
-      lineageIndex: true
+      generateLineageIndex: true
     - name: division
       type: string
       generateIndex: true

diff --git a/testBaseData/emptyInputNdjson/database_config.yaml b/testBaseData/emptyInputNdjson/database_config.yaml
@@ -11,7 +11,7 @@ schema:
     - name: pango_lineage
       type: string
       generateIndex: true
-      lineageIndex: true
+      generateLineageIndex: true
     - name: division
       type: string
       generateIndex: true

diff --git a/testBaseData/emptyInputNdjsonUnpartitioned/database_config.yaml b/testBaseData/emptyInputNdjsonUnpartitioned/database_config.yaml
@@ -11,7 +11,7 @@ schema:
     - name: pango_lineage
       type: string
       generateIndex: true
-      lineageIndex: true
+      generateLineageIndex: true
     - name: division
       type: string
       generateIndex: true

diff --git a/testBaseData/emptyInputTsv/database_config.yaml b/testBaseData/emptyInputTsv/database_config.yaml
@@ -16,7 +16,7 @@ schema:
     - name: pango_lineage
       type: string
       generateIndex: true
-      lineageIndex: true
+      generateLineageIndex: true
     - name: division
       type: string
       generateIndex: true

diff --git a/testBaseData/exampleDataset/database_config.yaml b/testBaseData/exampleDataset/database_config.yaml
@@ -16,7 +16,7 @@ schema:
     - name: pango_lineage
       type: string
       generateIndex: true
-      lineageIndex: true
+      generateLineageIndex: true
     - name: division
       type: string
       generateIndex: true

diff --git a/testBaseData/exampleDataset1000Sequences/database_config.yaml b/testBaseData/exampleDataset1000Sequences/database_config.yaml
@@ -14,7 +14,7 @@ schema:
     - name: pangoLineage
       type: string
       generateIndex: true
-      lineageIndex: true
+      generateLineageIndex: true
     - name: division
       type: string
       generateIndex: true

diff --git a/testBaseData/exampleDatasetAsTsv/database_config.yaml b/testBaseData/exampleDatasetAsTsv/database_config.yaml
@@ -16,7 +16,7 @@ schema:
     - name: pango_lineage
       type: string
       generateIndex: true
-      lineageIndex: true
+      generateLineageIndex: true
     - name: division
       type: string
       generateIndex: true

diff --git a/testBaseData/test_database_config.yaml b/testBaseData/test_database_config.yaml
@@ -16,7 +16,7 @@ schema:
     - name: pango_lineage
       type: string
       generateIndex: true
-      lineageIndex: true
+      generateLineageIndex: true
     - name: division
       type: string
       generateIndex: true

diff --git a/testBaseData/test_database_config_without_partition_by.yaml b/testBaseData/test_database_config_without_partition_by.yaml
@@ -16,7 +16,7 @@ schema:
     - name: pango_lineage
       type: string
       generateIndex: true
-      lineageIndex: true
+      generateLineageIndex: true
     - name: division
       type: string
       generateIndex: true

diff --git a/testBaseData/tsvWithQuoteInPartitionBy/database_config.yaml b/testBaseData/tsvWithQuoteInPartitionBy/database_config.yaml
@@ -16,7 +16,7 @@ schema:
     - name: 'pango_"lineage'
       type: string
       generateIndex: true
-      lineageIndex: true
+      generateLineageIndex: true
     - name: division
       type: string
       generateIndex: true

diff --git a/testBaseData/unitTestDummyDataset/database_config.yaml b/testBaseData/unitTestDummyDataset/database_config.yaml
@@ -16,7 +16,7 @@ schema:
     - name: pango_lineage
       type: string
       generateIndex: true
-      lineageIndex: true
+      generateLineageIndex: true
     - name: division
       type: string
       generateIndex: true