Feature/SQLite persistence

[JGsouzaa]

SQLite feature developed based on #11

*Development Summary:

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[sqlite.rs file (NEW FILE)]:

Implemented the following functions:

• check_db
• _createdb
• _check_schema
• _fill_projects_table
• _check_initial_row
• store_run
• store_mutants
• check_mutation_folder
• get_files_from_folder
• get_file_diff
• get_hash_from_diff
• update_status_mutant
• update_command_to_test_mutant
• update_mutants_table

Implemented the following tests:

• test_db_creation_and_seed
• test_store_run_creates_row
• test_store_mutants_inserts_rows
• test_update_status_mutant
• test_update_command_mutant

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[main.rs file (MODIFICATIONS)]:

Implemented the following logic:

• Added mod sqlite.rs
• Optional SQLite flag for mutation + handler
• Optional SQLite flag for analyze with --run_id + handler

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[lib.rs file (MODIFICATIONS)]:

• sqlite.rs module

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[git_changes.rs file (MODIFICATIONS)]:

• get_commit_hash function implementation

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[error.rs file (MODIFICATIONS)]:

• Added Sqlite and MissingDbPath errors

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[analyze.rs file (MODIFICATIONS)]:

• Adapted run_analysis signature to get db_path and run_id
• Added update_status_mutant and update_command_to_test_mutant on current logic
• Changed find_mutation_folders visibility to public so it can be called from the sqlite.rs module

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[Cargo.toml file (MODIFICATIONS)]:

• Added rusqlite and sha2 dependencies

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*Additional comments:

• strategy, config_json from the current execution config -> NOT IMPLEMENTED

• The database schema follows the issue documentation entirely, with only one exception on table mutant that was inserted an additional column called file_name to query on analyze section

• Apart from the code tests, the following functional tests were performed manually:

  • (mutate) -> --sqlite flag optional, normal behavior {OK}

  • (mutate --sqlite ) -> Creates/open "db/mutation.db" and uses it {OK}

  • (mutate --sqlite results.db) -> Creates/open "db/results.db" and uses it {OK}

  • (mutate --sqlite ...) -> Verify INSERT OR IGNORE INTO projects (name, repository_url) VALUES ('Bitcoin Core', 'https://github.com/bitcoin/bitcoin'); {OK}

  • (mutate --sqlite...) -> General behavior: Open DB (create if missing) Ensure projects seed (bitcoin core), create run, insert mutants {OK}

  • (analyze --sqlite) -> Asks for run_id {OK}

  • (analyze --sqlite <db_file> <run_id> ) -> Record standard commands {OK}

  • (analyze <without file (-f ...)> --sqlite <run_id> ...) -> Record only for run_id, behave like analyze normally {OK}

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*Further implementations suggestion:

• Modify logic when grabbing file extensions (current supports only for .cpp, .h and .py files)
• Implement help options for flag --sqlite
• Insert one more table column on table runs indicating the total number of mutants generated
• Explore options for compress the data on column "diff" on table "mutants" if diffs become hard to store and read
• Implement a folder called bcore-mutation on the project that it's running to hold "db" and "mutants" folders apart from original project

[brunoerg]

I think the correct flag here is --runid, not --run_id.

Suggested change

	bcore-mutation analyze --sqlite --run_id <run id number>
	bcore-mutation analyze --sqlite --runid <run id number>

[brunoerg]

Please, you should better organize your commits by squashing some of them.