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refactor: type safe checking for validation and caching of ndjson-fil…
…e-emptiness
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,33 @@ | ||
| #pragma once | ||
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| #include <filesystem> | ||
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| namespace silo { | ||
| class ReferenceGenomes; | ||
| } | ||
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| namespace silo::config { | ||
| class DatabaseConfig; | ||
| } | ||
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| namespace silo::preprocessing { | ||
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| class ValidatedNdjsonFile { | ||
| std::filesystem::path file_name; | ||
| bool empty; | ||
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| ValidatedNdjsonFile(std::filesystem::path file_name, bool empty); | ||
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| public: | ||
| std::filesystem::path getFileName() const; | ||
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| bool isEmpty() const; | ||
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| static ValidatedNdjsonFile validateFileAgainstConfig( | ||
| const std::filesystem::path& file_name, | ||
| const silo::config::DatabaseConfig& database_config, | ||
| const silo::ReferenceGenomes& reference_genomes | ||
| ); | ||
| }; | ||
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| } // namespace silo::preprocessing |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,58 @@ | ||
| #include "silo/preprocessing/validated_ndjson_file.h" | ||
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| #include <spdlog/spdlog.h> | ||
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| #include "silo/config/database_config.h" | ||
| #include "silo/preprocessing/metadata_info.h" | ||
| #include "silo/preprocessing/preprocessing_exception.h" | ||
| #include "silo/preprocessing/sequence_info.h" | ||
| #include "silo/storage/reference_genomes.h" | ||
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| namespace silo::preprocessing { | ||
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| ValidatedNdjsonFile::ValidatedNdjsonFile(std::filesystem::path file_name, bool empty) | ||
| : file_name(std::move(file_name)), | ||
| empty(empty) {} | ||
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| std::filesystem::path ValidatedNdjsonFile::getFileName() const { | ||
| return file_name; | ||
| } | ||
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| bool ValidatedNdjsonFile::isEmpty() const { | ||
| return empty; | ||
| } | ||
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| ValidatedNdjsonFile ValidatedNdjsonFile::validateFileAgainstConfig( | ||
| const std::filesystem::path& file_name, | ||
| const silo::config::DatabaseConfig& database_config, | ||
| const silo::ReferenceGenomes& reference_genomes | ||
| ) { | ||
| SPDLOG_DEBUG("build - checking whether the file '{}' exists: ", file_name.string()); | ||
| if (!std::filesystem::exists(file_name)) { | ||
| throw silo::preprocessing::PreprocessingException( | ||
| fmt::format("The specified input file {} does not exist.", file_name.string()) | ||
| ); | ||
| } | ||
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| SPDLOG_DEBUG("build - checking whether the file '{}' is not a directory: ", file_name.string()); | ||
| if (std::filesystem::is_directory(file_name)) { | ||
| throw silo::preprocessing::PreprocessingException( | ||
| fmt::format("The specified input file {} is a directory.", file_name.string()) | ||
| ); | ||
| } | ||
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| bool empty = MetadataInfo::isNdjsonFileEmpty(file_name); | ||
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| SPDLOG_DEBUG("build - checking whether the file '{}' is empty: ", file_name.string()); | ||
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| if (!empty) { | ||
| SPDLOG_DEBUG("build - validating metadata file '{}' with config", file_name.string()); | ||
| MetadataInfo::validateNdjsonFile(file_name, database_config); | ||
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| SPDLOG_DEBUG("build - validating metadata file '{}' with config", file_name.string()); | ||
| SequenceInfo::validateNdjsonFile(reference_genomes, file_name); | ||
| } | ||
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| return ValidatedNdjsonFile(file_name, empty); | ||
| } | ||
| } // namespace silo::preprocessing |