Source code for esmvalcore.cmor.fix

"""Apply automatic fixes for known errors in cmorized data.

All functions in this module will work even if no fixes are available
for the given dataset. Therefore is recommended to apply them to all
variables to be sure that all known errors are fixed.
"""
import logging
from collections import defaultdict

from iris.cube import CubeList

from ._fixes.fix import Fix
from .check import CheckLevels, _get_cmor_checker

logger = logging.getLogger(__name__)


[docs]def fix_file(file, short_name, project, dataset, mip, output_dir, **extra_facets): """Fix files before ESMValTool can load them. This fixes are only for issues that prevent iris from loading the cube or that cannot be fixed after the cube is loaded. Original files are not overwritten. Parameters ---------- file: str Path to the original file. short_name: str Variable's short name. project: str Project of the dataset. dataset: str Name of the dataset. mip: str Variable's MIP. output_dir: str Output directory for fixed files. **extra_facets: dict, optional Extra facets are mainly used for data outside of the big projects like CMIP, CORDEX, obs4MIPs. For details, see :ref:`extra_facets`. Returns ------- str: Path to the fixed file. """ # Update extra_facets with variable information given as regular arguments # to this function extra_facets.update({ 'short_name': short_name, 'project': project, 'dataset': dataset, 'mip': mip, }) for fix in Fix.get_fixes(project=project, dataset=dataset, mip=mip, short_name=short_name, extra_facets=extra_facets): file = fix.fix_file(file, output_dir) return file
[docs]def fix_metadata(cubes, short_name, project, dataset, mip, frequency=None, check_level=CheckLevels.DEFAULT, **extra_facets): """Fix cube metadata if fixes are required and check it anyway. This method collects all the relevant fixes for a given variable, applies them and checks the resulting cube (or the original if no fixes were needed) metadata to ensure that it complies with the standards of its project CMOR tables. Parameters ---------- cubes: iris.cube.CubeList Cubes to fix. short_name: str Variable's short name. project: str Project of the dataset. dataset: str Name of the dataset. mip: str Variable's MIP. frequency: str, optional Variable's data frequency, if available. check_level: CheckLevels Level of strictness of the checks. Set to default. **extra_facets: dict, optional Extra facets are mainly used for data outside of the big projects like CMIP, CORDEX, obs4MIPs. For details, see :ref:`extra_facets`. Returns ------- iris.cube.Cube: Fixed and checked cube. Raises ------ CMORCheckError If the checker detects errors in the metadata that it can not fix. """ # Update extra_facets with variable information given as regular arguments # to this function extra_facets.update({ 'short_name': short_name, 'project': project, 'dataset': dataset, 'mip': mip, 'frequency': frequency, }) fixes = Fix.get_fixes(project=project, dataset=dataset, mip=mip, short_name=short_name, extra_facets=extra_facets) fixed_cubes = [] by_file = defaultdict(list) for cube in cubes: by_file[cube.attributes.get('source_file', '')].append(cube) for cube_list in by_file.values(): cube_list = CubeList(cube_list) for fix in fixes: cube_list = fix.fix_metadata(cube_list) cube = _get_single_cube(cube_list, short_name, project, dataset) checker = _get_cmor_checker(frequency=frequency, table=project, mip=mip, short_name=short_name, check_level=check_level, fail_on_error=False, automatic_fixes=True) cube = checker(cube).check_metadata() cube.attributes.pop('source_file', None) fixed_cubes.append(cube) return fixed_cubes
def _get_single_cube(cube_list, short_name, project, dataset): if len(cube_list) == 1: return cube_list[0] cube = None for raw_cube in cube_list: if raw_cube.var_name == short_name: cube = raw_cube break if not cube: raise ValueError( f'More than one cube found for variable {short_name} in ' f'{project}:{dataset} but none of their var_names match the ' f'expected.\nFull list of cubes encountered: {cube_list}' ) logger.warning( 'Found variable %s in %s:%s, but there were other present in ' 'the file. Those extra variables are usually metadata ' '(cell area, latitude descriptions) that was not saved ' 'according to CF-conventions. It is possible that errors appear ' 'further on because of this. \nFull list of cubes encountered: %s', short_name, project, dataset, cube_list) return cube
[docs]def fix_data(cube, short_name, project, dataset, mip, frequency=None, check_level=CheckLevels.DEFAULT, **extra_facets): """Fix cube data if fixes add present and check it anyway. This method assumes that metadata is already fixed and checked. This method collects all the relevant fixes for a given variable, applies them and checks resulting cube (or the original if no fixes were needed) metadata to ensure that it complies with the standards of its project CMOR tables. Parameters ---------- cube: iris.cube.Cube Cube to fix. short_name: str Variable's short name. project: str Project of the dataset. dataset: str Name of the dataset. mip: str Variable's MIP. frequency: str, optional Variable's data frequency, if available. check_level: CheckLevels Level of strictness of the checks. Set to default. **extra_facets: dict, optional Extra facets are mainly used for data outside of the big projects like CMIP, CORDEX, obs4MIPs. For details, see :ref:`extra_facets`. Returns ------- iris.cube.Cube: Fixed and checked cube. Raises ------ CMORCheckError If the checker detects errors in the data that it can not fix. """ # Update extra_facets with variable information given as regular arguments # to this function extra_facets.update({ 'short_name': short_name, 'project': project, 'dataset': dataset, 'mip': mip, 'frequency': frequency, }) for fix in Fix.get_fixes(project=project, dataset=dataset, mip=mip, short_name=short_name, extra_facets=extra_facets): cube = fix.fix_data(cube) checker = _get_cmor_checker(frequency=frequency, table=project, mip=mip, short_name=short_name, fail_on_error=False, automatic_fixes=True, check_level=check_level) cube = checker(cube).check_data() return cube