diff --git a/corrlib/cli.py b/corrlib/cli.py index bdee36e..0e6d96a 100644 --- a/corrlib/cli.py +++ b/corrlib/cli.py @@ -108,7 +108,7 @@ def find( ), ) -> None: """ - Find a record in the given backlog. + Find a record in the backlog at hand. Through specifying it's ensemble and the measured correlator. """ results = find_record(path, ensemble, corr, code) if results.empty: @@ -147,9 +147,6 @@ def check(path: Path = typer.Option( "-d", ), ) -> None: - """ - Check the integrity of the repository. - """ full_integrity_check(path) diff --git a/corrlib/integrity.py b/corrlib/integrity.py index f660dfe..5f80aa3 100644 --- a/corrlib/integrity.py +++ b/corrlib/integrity.py @@ -1,34 +1,15 @@ import datetime as dt from pathlib import Path -from .tools import get_db_file, CONFIG_FILENAME +from .tools import get_db_file import pandas as pd import sqlite3 from .tracker import get import pyerrors.input.json as pj -import os -from configparser import ConfigParser from typing import Any -path_opts = ['db', 'projects_path', 'archive_path', 'toml_imports_path', 'import_scripts_path'] - - def has_valid_times(result: pd.Series) -> bool: - """ - Check, whether the result at hand has time-stamps that are sensible: - A recored is created first, then updated, with both times laying in the past. - - Parameters - ---------- - result: pd.Series - The result to check - - Returns - ------- - b: bool - True, if the timestamps make sense. - """ # we expect created_at <= updated_at <= now created_at = dt.datetime.fromisoformat(result['created_at']) updated_at = dt.datetime.fromisoformat(result['updated_at']) @@ -39,41 +20,15 @@ def has_valid_times(result: pd.Series) -> bool: return True def are_keys_unique(db: Path, table: str, col: str) -> bool: - """ - Check whether the strings listed in a column of a given table are unique. - - Parameters - ---------- - db: Path - The database to check. - table: str - The table to check. - col: str - The column to be checked for uniqueness. - - Returns - ------- - b: bool - True, if the strings are unique. - """ conn = sqlite3.connect(db) c = conn.cursor() - c.execute(f"SELECT COUNT( DISTINCT CAST({col} AS nvarchar(4000))), COUNT({col}) FROM {table};") + c.execute(f"SELECT COUNT( DISTINCT CAST(path AS nvarchar(4000))), COUNT({col}) FROM {table};") results = c.fetchall()[0] conn.close() return bool(results[0] == results[1]) def check_db_integrity(path: Path) -> None: - """ - Check intergrity of the database by checking the uniqueness of the record keys used to load the records - and ensuring that the timestamps of each record is sensible. Throws an error, if issues are detected. - - Parameters - ---------- - path: Path - Path to the backlog-library to check. - """ db = get_db_file(path) if not are_keys_unique(path / db, 'backlogs', 'path'): @@ -86,21 +41,11 @@ def check_db_integrity(path: Path) -> None: for _, result in results.iterrows(): if not has_valid_times(result): raise ValueError(f"Result with id {result[id]} has wrong time signatures.") + print("DB:\t✅") return def _check_db2paths(path: Path, meas_paths: list[str]) -> None: - """ - Check whether for each record in the given by meas_paths, we can find the data in the file as we expect. - Also check, whether there are unreachable records in the files. If either of the issues arise, throws an error. - - Parameters - ---------- - path: Path - Path to the backlog-library to check. - meas_paths: list[str] - List of measurement paths to check. - """ needed_data: dict[str, list[str]] = {} for mpath in meas_paths: file = mpath.split("::")[0] @@ -122,19 +67,11 @@ def _check_db2paths(path: Path, meas_paths: list[str]) -> None: for key in needed_data[file]: if key not in filedict.keys(): raise ValueError(f"Did not find data for key {key} that should be in file {file}.") + print("Links:\t✅") return def check_db_file_links(path: Path) -> None: - """ - Check whether for each record in the given correlator library, we can find the data in the file as we expect. - Also check, whether there are unreachable records in the files. If either of the issues arise, throws an error. - - Parameters - ---------- - path: Path - Path to the backlog-library to check. - """ db = get_db_file(path) search_expr = "SELECT path FROM 'backlogs'" conn = sqlite3.connect(path / db) @@ -142,90 +79,9 @@ def check_db_file_links(path: Path) -> None: _check_db2paths(path, list(results)) -def check_path_and_config(path: Path) -> None: - """ - Check whether the given path exists and the cinfigureation file can be found. - - Parameters - ---------- - path: Path - Path to the backlog-library to check. - """ - if not os.path.exists(path): - raise FileNotFoundError(f"Corrlib path {path} does not exist.") - config_path = path / CONFIG_FILENAME - if not os.path.exists(config_path): - raise FileNotFoundError(f"Configuration file {config_path} not found.") - - -def check_config_validity(path: Path) -> None: - """ - Check whether the configuration file of the given corrlib-dataset path is valid. - - Parameters - ---------- - path: Path - Path to the backlog-library to check. - """ - config = ConfigParser() - config_path = path / CONFIG_FILENAME - if os.path.exists(config_path): - config.read(config_path) - else: - raise FileNotFoundError("Configuration file not found.") - - if config.has_section('core'): - core_opts = ['version', 'tracker', 'cached'] - has_core_opts = [config.has_option('core', opt) for opt in core_opts] - if not all(has_core_opts): - raise ValueError("One of the options in the 'core' section ('version', 'tracker', 'cached') is missing.") - - if config.has_section('paths'): - has_path_opts = [config.has_option('paths', opt) for opt in path_opts] - if not all(has_path_opts): - raise ValueError("One of the options in the 'path' section ('db', 'projects_path', 'archive_path', 'toml_imports_path', 'import_scripts_path') is missing.") - - -def check_paths(path: Path) -> None: - """ - Check whether all paths demanded by the 'paths' section of the configuration-file exist. - - Parameters - ---------- - path: Path - Path to the backlog-library to check. - """ - config = ConfigParser() - config_path = path / CONFIG_FILENAME - if os.path.exists(config_path): - config.read(config_path) - else: - raise FileNotFoundError("Configuration file not found.") - has_paths = [os.path.exists(path / config.get('paths', opt)) for opt in path_opts] - if not all(has_paths): - raise FileNotFoundError("One of the paths specified in the configuration file is not present.") - - def full_integrity_check(path: Path) -> None: - """ - Aggregate all checks for easy validation of the backlog-library. - - Parameters - ---------- - path: Path - Path to the backlog-library to check. - """ - print("Run full integrity check...") - check_path_and_config(path) - print("(1/5) Path and config-file exist: ✅") - check_config_validity(path) - print("(2/5) Configuration is valid: ✅") - check_paths(path) - print("(3/5) Needed paths exist: ✅") check_db_integrity(path) - print("(4/5) Database is sane: ✅") check_db_file_links(path) - print("(5/5) DB2File and File2DB-links are sound: ✅") - print("Full integrity check: ✅") + print("Full:\t✅")