Added new operators for statistics preprocesor (e.g., percentile) and allowed arbitrary kwargs

esmvalcore/_recipe/check.py

@@ -3,19 +3,21 @@
 
 import logging
 import os
-import re
 import subprocess
+from inspect import getfullargspec
 from pprint import pformat
 from shutil import which
 from typing import Any, Iterable
 
 import isodate
 import yamale
 
+import esmvalcore.preprocessor
 from esmvalcore.exceptions import InputFilesNotFound, RecipeError
 from esmvalcore.local import _get_start_end_year, _parse_period
 from esmvalcore.preprocessor import TIME_PREPROCESSORS, PreprocessingTask
-from esmvalcore.preprocessor._multimodel import STATISTIC_MAPPING
+from esmvalcore.preprocessor._multimodel import _get_operator_and_kwargs
+from esmvalcore.preprocessor._shared import get_iris_aggregator
 from esmvalcore.preprocessor._supplementary_vars import (
     PREPROCESSOR_SUPPLEMENTARIES,
 )
@@ -256,20 +258,6 @@ def extract_shape(settings):
                 "{}".format(', '.join(f"'{k}'".lower() for k in valid[key])))
 
 
-def _verify_statistics(statistics, step):
-    """Raise error if multi-model statistics cannot be verified."""
-    valid_names = ['std'] + list(STATISTIC_MAPPING.keys())
-    valid_patterns = [r"^(p\d{1,2})(\.\d*)?$"]
-
-    for statistic in statistics:
-        if not (statistic in valid_names
-                or re.match(r'|'.join(valid_patterns), statistic)):
-            raise RecipeError(
-                "Invalid value encountered for `statistic` in preprocessor "
-                f"{step}. Valid values are {valid_names} "
-                f"or patterns matching {valid_patterns}. Got '{statistic}'.")
-
-
 def _verify_span_value(span):
     """Raise error if span argument cannot be verified."""
     valid_names = ('overlap', 'full')
@@ -305,26 +293,8 @@ def _verify_ignore_scalar_coords(ignore_scalar_coords):
             f"{ignore_scalar_coords}.")
 
 
-def _verify_arguments(given, expected):
-    """Raise error if arguments cannot be verified."""
-    for key in given:
-        if key not in expected:
-            raise RecipeError(
-                f"Unexpected keyword argument encountered: {key}. Valid "
-                f"keywords are: {expected}.")
-
-
 def multimodel_statistics_preproc(settings):
     """Check that the multi-model settings are valid."""
-    valid_keys = [
-        'groupby',
-        'ignore_scalar_coords',
-        'keep_input_datasets',
-        'span',
-        'statistics',
-    ]
-    _verify_arguments(settings.keys(), valid_keys)
-
     span = settings.get('span', None)  # optional, default: overlap
     if span:
         _verify_span_value(span)
@@ -333,10 +303,6 @@ def multimodel_statistics_preproc(settings):
     if groupby:
         _verify_groupby(groupby)
 
-    statistics = settings.get('statistics', None)  # required
-    if statistics:
-        _verify_statistics(statistics, 'multi_model_statistics')
-
     keep_input_datasets = settings.get('keep_input_datasets', True)
     _verify_keep_input_datasets(keep_input_datasets)
 
@@ -346,21 +312,10 @@ def multimodel_statistics_preproc(settings):
 
 def ensemble_statistics_preproc(settings):
     """Check that the ensemble settings are valid."""
-    valid_keys = [
-        'ignore_scalar_coords',
-        'span',
-        'statistics',
-    ]
-    _verify_arguments(settings.keys(), valid_keys)
-
     span = settings.get('span', 'overlap')  # optional, default: overlap
     if span:
         _verify_span_value(span)
 
-    statistics = settings.get('statistics', None)
-    if statistics:
-        _verify_statistics(statistics, 'ensemble_statistics')
-
     ignore_scalar_coords = settings.get('ignore_scalar_coords', False)
     _verify_ignore_scalar_coords(ignore_scalar_coords)
 
@@ -456,3 +411,65 @@ def reference_for_bias_preproc(products):
             f"{len(reference_products):d}{ref_products_str}Please also "
             f"ensure that the reference dataset is not excluded with the "
             f"'exclude' option")
+
+
+def statistics_preprocessors(settings: dict) -> None:
+    """Check options of statistics preprocessors."""
+    mm_stats = (
+        'multi_model_statistics',
+        'ensemble_statistics',
+    )
+    for (step, step_settings) in settings.items():
+
+        # For multi-model statistics, we need to check each entry of statistics
+        if step in mm_stats:
+            _check_mm_stat(step, step_settings)
+
+        # For other statistics, check optional kwargs for operator
+        elif '_statistics' in step:
+            _check_regular_stat(step, step_settings)
+
+
+def _check_regular_stat(step, step_settings):
+    """Check regular statistics (non-multi-model statistics) step."""
+    step_settings = dict(step_settings)
+
+    # Some preprocessors like climate_statistics use default 'mean' for
+    # operator. If 'operator' is missing for those preprocessors with no
+    # default, this will be detected in PreprocessorFile.check() later.
+    operator = step_settings.pop('operator', 'mean')
+
+    # If preprocessor does not exist, do nothing here; this will be detected in
+    # PreprocessorFile.check() later.
+    try:
+        preproc_func = getattr(esmvalcore.preprocessor, step)
+    except AttributeError:
+        return
+
+    # Ignore other preprocessor arguments, e.g., 'hours' for hourly_statistics
+    other_args = getfullargspec(preproc_func).args[1:]
+    operator_kwargs = {
+        k: v for (k, v) in step_settings.items() if k not in other_args
+    }
+    try:
+        get_iris_aggregator(operator, **operator_kwargs)
+    except ValueError as exc:
+        raise RecipeError(
+            f"Invalid options for {step}: {exc}"
+        )
+
+
+def _check_mm_stat(step, step_settings):
+    """Check multi-model statistic step."""
+    statistics = step_settings.get('statistics', [])
+    for stat in statistics:
+        try:
+            (operator, kwargs) = _get_operator_and_kwargs(stat)
+        except ValueError as exc:
+            raise RecipeError(str(exc))
+        try:
+            get_iris_aggregator(operator, **kwargs)
+        except ValueError as exc:
+            raise RecipeError(
+                f"Invalid options for {step}: {exc}"
+            )

esmvalcore/_recipe/recipe.py

@@ -19,10 +19,7 @@
 from esmvalcore.config._config import TASKSEP
 from esmvalcore.config._diagnostics import TAGS
 from esmvalcore.dataset import Dataset
-from esmvalcore.exceptions import (
-    InputFilesNotFound,
-    RecipeError,
-)
+from esmvalcore.exceptions import InputFilesNotFound, RecipeError
 from esmvalcore.local import (
     _dates_to_timerange,
     _get_multiproduct_filename,
@@ -39,6 +36,7 @@
     PreprocessorFile,
 )
 from esmvalcore.preprocessor._area import _update_shapefile_path
+from esmvalcore.preprocessor._multimodel import _get_stat_identifier
 from esmvalcore.preprocessor._other import _group_products
 from esmvalcore.preprocessor._regrid import (
     _spec_to_latlonvals,
@@ -416,9 +414,11 @@ def _update_multiproduct(input_products, order, preproc_dir, step):
     for identifier, products in _group_products(products, by_key=grouping):
         common_attributes = _get_common_attributes(products, settings)
 
-        for statistic in settings.get('statistics', []):
+        statistics = settings.get('statistics', [])
+        for statistic in statistics:
             statistic_attributes = dict(common_attributes)
-            statistic_attributes[step] = _get_tag(step, identifier, statistic)
+            stat_id = _get_stat_identifier(statistic)
+            statistic_attributes[step] = _get_tag(step, identifier, stat_id)
             statistic_attributes.setdefault('alias',
                                             statistic_attributes[step])
             statistic_attributes.setdefault('dataset',
@@ -432,7 +432,7 @@ def _update_multiproduct(input_products, order, preproc_dir, step):
             )  # Note that ancestors is set when running the preprocessor func.
             output_products.add(statistic_product)
             relevant_settings['output_products'][identifier][
-                statistic] = statistic_product
+                stat_id] = statistic_product
 
     return output_products, relevant_settings
 
@@ -637,6 +637,7 @@ def _update_preproc_functions(settings, dataset, datasets, missing_vars):
     _update_regrid_time(dataset, settings)
     if dataset.facets.get('frequency') == 'fx':
         check.check_for_temporal_preprocs(settings)
+    check.statistics_preprocessors(settings)
 
 
 def _get_preprocessor_task(datasets, profiles, task_name):

esmvalcore/cmor/_fixes/shared.py

@@ -107,7 +107,9 @@ def add_plev_from_altitude(cube):
             )
         pressure_coord = iris.coords.AuxCoord(pressure_points,
                                               bounds=pressure_bounds,
+                                              var_name='plev',
                                               standard_name='air_pressure',
+                                              long_name='pressure',
                                               units='Pa')
         cube.add_aux_coord(pressure_coord, cube.coord_dims(height_coord))
         return
@@ -145,7 +147,9 @@ def add_altitude_from_plev(cube):
             )
         altitude_coord = iris.coords.AuxCoord(altitude_points,
                                               bounds=altitude_bounds,
+                                              var_name='alt',
                                               standard_name='altitude',
+                                              long_name='altitude',
                                               units='m')
         cube.add_aux_coord(altitude_coord, cube.coord_dims(plev_coord))
         return