GitHub - ISI-MIP/isimip-qc: A command line tool for the quality control of climate impact data of the ISIMIP project. (original) (raw)

A command line tool for the quality control of climate impact data of the ISIMIP project. It mainly covers tests of:

the file name against the protocol schemas and patterns
variables, dimensions and global attributes
data model and types
some consistency checks on the NetCDF time axis and
if the data is within a valid value range (when defined in the ISIMIP protocol)

Setup

The application is written in Python (> 3.11) uses only dependencies, which can be installed without administrator privileges. The installation of Python (and its developing packages), however differs from operating system to operating system. Optional Git is needed if the application is installed directly from GitHub. The installation of Python 3 and Git for different platforms is documented here.

The tool itself can be installed via pip. Usually you want to create a virtual environment first, but this is optional. The tool works also with pipx.

setup venv on Linux/macOS/Windows WSL

python3 -m venv env source env/bin/activate

setup venv on Windows cmd

python -m venv env call env\Scripts\activate.bat

install from the Python Package Index (PyPI), recommended

pip install isimip-qc

update from PyPI

pip install --upgrade isimip-qc

install directly from GitHub

pip install git+https://github.com/ISI-MIP/isimip-qc

update directly from GitHub

pip install --upgrade git+https://github.com/ISI-MIP/isimip-qc

Usage

The tool has several options which can be inspected using the help option -h, --help:

usage: isimip-qc [-h] [-c] [-m] [-O] [--unchecked-path UNCHECKED_PATH]
                 [--checked-path CHECKED_PATH] [--protocol-location PROTOCOL_LOCATIONS]
                 [--log-level LOG_LEVEL] [--show-time] [--show-path] [--log-path LOG_PATH]
                 [--log-path-level LOG_PATH_LEVEL] [--include INCLUDE] [--exclude EXCLUDE] [-f]
                 [-w] [-e] [--ignore-critical] [--skip-exp] [--match-only] [-r [MINMAX]] [-nt]
                 [--summary] [--fix] [--fix-datamodel [FIX_DATAMODEL]] [--check CHECK]
                 [--force-copy-move] [-V]
                 schema_path

Check ISIMIP files for matching protocol definitions

positional arguments:
  schema_path           ISIMIP schema_path, e.g. ISIMIP3a/OutputData/water_global

options:
  -h, --help            show this help message and exit
  -c, --copy            copy checked files to CHECKED_PATH if no warnings or errors were found
  -m, --move            move checked files to CHECKED_PATH if no warnings or errors were found
  -O, --overwrite       overwrite files in CHECKED_PATH if present. Default is False.
  --unchecked-path UNCHECKED_PATH
                        base path of the unchecked files
  --checked-path CHECKED_PATH
                        base path for the checked files
  --protocol-location PROTOCOL_LOCATIONS
                        URL or file path to the protocol when different from official repository
  --log-level LOG_LEVEL
                        log level (CRITICAL, ERROR, WARN, CHECKING, INFO, or DEBUG) [default:
                        CHECKING]
  --show-time           show time in console logs
  --show-path           show path in console logs
  --log-path LOG_PATH   base path for the individual log files
  --log-path-level LOG_PATH_LEVEL
                        log level for the individual log files [default: WARN]
  --include INCLUDE     patterns of files to include. Exclude those that don't match any.
  --exclude EXCLUDE     patterns of files to exclude. Include only those that don't match any.
  -f, --first-file      only process first file found in UNCHECKED_PATH
  -w, --stop-on-warnings
                        stop execution on warnings
  -e, --stop-on-errors  stop execution on errors
  --ignore-critical     allow fixing and copy/move files with critical issues found
  --skip-exp            skip test for valid experiment combination
  --match-only          only match the file name and skip all other checks
  -r [MINMAX], --minmax [MINMAX]
                        test values for valid range (slow). MINMAX denotes the length of the
                        ordered top list of outliers
  -nt, --skip-time-span-check
                        skip check for simulated time period
  --summary             append a summary with statistics about experiments and specifiers to the
                        output
  --fix                 try to fix warnings detected on the original files
  --fix-datamodel [FIX_DATAMODEL]
                        also fix warnings on data model found using NCCOPY or CDO (slow). Choose
                        preferred tool per lower case argument.
  --check CHECK         perform only one particular check
  --force-copy-move     copy or move files despite errors
  -V, --version         show program's version number and exit

The only mandatory argument is the schema_path, which specifies the pattern and schema to use. The schema_path consitst of the simulation_round, the product, and the sector separated by slashes, e.g. ISIMIP3a/OutputData/water_global. If the only argument used is schema_path, the current user path when calling the tool should be same as the directory of the files to be checked.

The options in detail

--config-file: Default values for the optional arguments are set in the code, but can also be provided via:
- a config file given by --config-file, or located at isimip.toml, ~/.isimip.toml, or /etc/isimip.toml. The config file needs to have a section isimip-qc and uses lower case variables and underscores, e.g.:

[isimip-qc]  
unchecked_path = "data/unchecked"  
checked_path = "data/checked"  
log_level = "INFO"  
log_path = "data/log"  
log_path_level = "INFO"  
minmax = true  # for the default value  
minmax = 5     # for a custom value

environment variables (in caps, with underscores, and with ISIMIP_ as prefix, e.g. ISIMIP_UNCHECKED_PATH).
-c, --copy and -m, --move: Copy or move files that have successfully passed the checks to a final destination. Effective only when no warnings have been found on the file.
'-O, --overwrite`: Allow overwriting of existing files in CHECKED_PATH. Default is to skip copy or move in case the target file is already present.
--unchecked-path UNCHECKED_PATH: Any files in this folder and its subfolders will be included into the list of files to test.
--checked-path CHECKED_PATH: Target folder for the --copy or --move operation. The subfolder structure below CHECKED_PATH will be created and filled according to the sub-structure found in UNCHECKED_PATH
--protocol-location PROTOCOL_LOCATIONS: For working with local copies of the ISIMIP protocol (append /output to the cloned repositories folder). Omit option for using the online GitHub protocol versions for ISIMIP2 or ISIMIP3. An internet connection is required for reading the online protocols.
--log-level LOG_LEVEL: Set the detail level of log output. Default is CHECKING. Log levels from CRITICAL to VRDETAIL will not show the file currently checked in the terminal but write all of them to the data file specific log file.
CRITICAL: only very severe errors
ERROR: all errors
WARN: warnings and all errors
VRDETAIL: same as CHECKING but with details on time and location of valid ranges violations when invoked with --minmax option. Very slow when violations are detected.
CHECKING: includes warnings and errors
SUMMARY: includes warnings, errors and the summary shown at the end
INFO: includes SUMMARY and details for successful checks
DEBUG: all the above plus details for some debugging cases.
--show-time: show the timestamp in console logs
--show-path: Show the path from where a log entry is written in console logs
--log-path LOG_PATH: Also write the logs to a file where the folder structure below LOG_PATH is taken from UNCHECKED_PATH.
--log-path-level LOG_PATH_LEVEL: The log level used for the file specific logs below LOG_PATH. The default is WARN and should suffice for most cases.
--include INCLUDE_LIST: Provide a comma-separated list of strings to include for the checks if any of them matches the file path or name, e.g. 'daily,dis' will only check *daily* or *discharge* files while skipping others.
--exclude EXCLUDE_LIST: Provide a comma-separated list of strings to exclude from the checks if any of them matches the file path or name, e.g. 'monthly,histsoc' will skip any *monthly* or *histsoc* files.
-f, --first-file: Only test the first file found in UNCHECKED_PATH. Useful for revealing issues that may occur on all your files.
-w, --stop-on-warnings: The tool will stop after the first file where WARNINGs have been identified.
-e, --stop-on-errors: The tool will stop after the first file where ERRORs have been identified.
--ignore-critical: allow fixing and copy/move files although critical issues were found. Caution, this might lead to unexpected behaviour.
--skip-exp: Skip test for valid experiment combination validation, e.g for secondary outputs.
-r [MINMAX], --minmax [MINMAX]: Test the data for valid ranges when defined in the protocol and outputs a toplist with exact time step and geographic location. MINMAX is optional, defaults to 10 and defines the length of the toplist. This test drastically slows down the run time of the tool as every data point is looked at.
-nt, --skip-time-span-check: Skip checking non-dialy data for proper coverage of simulation periods.
--fix: Activates a number of fixes for WARNINGs by taking the default values from the protocol, e.g. variable attributes and units. In additions an unique identifier (UUID), the version of this tool and the protocol version (by a git hash) are being written to the global attributes section of the NetCDF file. Attention: Fixes and are going to be applied on your original files in UNCHECKED_PATH.
--fix-datamodel [FIX_DATAMODEL]: Fixes to the data model and compression level of the NetCDF file can't be made on-the-fly with the libraries used by the tool. We here rely on the external tools cdo or nccopy (from the NetCDF library) to rewrite the entire file. Default is nccopy. Please try to create the files with the proper data model (compressed NETCDF4_CLASSIC) in your postprocessing chain before submitting them to the data server.
--check CHECK: Perform only one particular check. The list of CHECKs can be taken from the functions defined in the isimip_qc/checks/*.py files.
--force-copy-move: Copy or move files despite errors found during checks.