CMOR functions

CMOR module.

Checking compliance

Module for checking iris cubes against their CMOR definitions.

Classes:

`CMORCheck`(cube, var_info[, frequency, ...])	Class used to check the CMOR-compliance of the data.
`CheckLevels`(value)	Level of strictness of the checks.

Exceptions:

CMORCheckError

Exception raised when a cube does not pass the CMORCheck.

Functions:

`cmor_check`(cube, cmor_table, mip, ...)	Check if cube conforms to variable's CMOR definition.
`cmor_check_data`(cube, cmor_table, mip, ...)	Check if data conforms to variable's CMOR definition.
`cmor_check_metadata`(cube, cmor_table, mip, ...)	Check if metadata conforms to variable's CMOR definition.

class esmvalcore.cmor.check.CMORCheck(cube, var_info, frequency=None, fail_on_error=False, check_level=CheckLevels.DEFAULT, automatic_fixes=False)[source]

Bases: object

Class used to check the CMOR-compliance of the data.

It can also fix some minor errors and does some minor data homogeneization:

Parameters:

cube (iris.cube.Cube:) – Iris cube to check.
var_info (variables_info.VariableInfo) – Variable info to check.
frequency (str) – Expected frequency for the data.
fail_on_error (bool) – If true, CMORCheck stops on the first error. If false, it collects all possible errors before stopping.
automatic_fixes (bool) – If True, CMORCheck will try to apply automatic fixes for any detected error, if possible.
check_level (CheckLevels) – Level of strictness of the checks.

frequency

Expected frequency for the data.

Type:: str

Attributes:

ALTERNATIVE_GENERIC_LEV_COORDS

Methods:

`check_data`([logger])	Check the cube data.
`check_metadata`([logger])	Check the cube metadata.
`has_debug_messages`()	Check if there are reported debug messages.
`has_errors`()	Check if there are reported errors.
`has_warnings`()	Check if there are reported warnings.
`report`(level, message, *args)	Report a message from the checker.
`report_critical`(message, *args)	Report an error.
`report_debug_message`(message, *args)	Report a debug message.
`report_debug_messages`()	Report detected debug messages to the given logger.
`report_error`(message, *args)	Report a normal error.
`report_errors`()	Report detected errors.
`report_warning`(message, *args)	Report a warning level error.
`report_warnings`()	Report detected warnings to the given logger.

ALTERNATIVE_GENERIC_LEV_COORDS = {'alevel': {'CMIP5': ['alt40', 'plevs'], 'CMIP6': ['alt16', 'plev3'], 'obs4MIPs': ['alt16', 'plev3']}, 'zlevel': {'CMIP3': ['pressure']}}

check_data(logger=None)[source]

Check the cube data.

Performs all the tests that require to have the data in memory. Assumes that metadata is correct, so you must call check_metadata prior to this.

It will also report some warnings in case of minor errors.

Parameters:: logger (logging.Logger) – Given logger.
Raises:: CMORCheckError – If errors are found. If fail_on_error attribute is set to True, raises as soon as an error is detected. If set to False, it perform all checks and then raises.

check_metadata(logger=None)[source]

Check the cube metadata.

Perform all the tests that do not require to have the data in memory.

It will also report some warnings in case of minor errors and homogenize some data:

Equivalent calendars will all default to the same name.

Time units will be set to days since 1850-01-01

Parameters:: logger (logging.Logger) – Given logger.
Raises:: CMORCheckError – If errors are found. If fail_on_error attribute is set to True, raises as soon as an error is detected. If set to False, it perform all checks and then raises.

has_debug_messages()[source]

Check if there are reported debug messages.

Returns:: True if there are pending debug messages, False otherwise.
Return type:: bool

has_errors()[source]

Check if there are reported errors.

Returns:: True if there are pending errors, False otherwise.
Return type:: bool

has_warnings()[source]

Check if there are reported warnings.

Returns:: True if there are pending warnings, False otherwise.
Return type:: bool

report(level, message, *args)[source]

Report a message from the checker.

Parameters:

level (CheckLevels) – Message level
message (str) – Message to report
args – String format args for the message

Raises:

CMORCheckError – If fail on error is set, it is thrown when registering an error message

report_critical(message, *args)[source]

Report an error.

If fail_on_error is set to True, raises automatically. If fail_on_error is set to False, stores it for later reports.

Parameters:

message (str: unicode) – Message for the error.
*args – arguments to format the message string.

report_debug_message(message, *args)[source]

Report a debug message.

Parameters:

message (str: unicode) – Message for the debug logger.
*args – arguments to format the message string

report_debug_messages()[source]

Report detected debug messages to the given logger.

Parameters:: logger (logging.Logger) – Given logger.

report_error(message, *args)[source]

Report a normal error.

Parameters:

message (str: unicode) – Message for the error.
*args – arguments to format the message string.

report_errors()[source]

Report detected errors.

Raises:: CMORCheckError – If any errors were reported before calling this method.

report_warning(message, *args)[source]

Report a warning level error.

Parameters:

message (str: unicode) – Message for the warning.
*args – arguments to format the message string.

report_warnings()[source]

Report detected warnings to the given logger.

Parameters:: logger (logging.Logger) – Given logger

exception esmvalcore.cmor.check.CMORCheckError[source]

Bases: Exception

Exception raised when a cube does not pass the CMORCheck.

args

with_traceback(): Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class esmvalcore.cmor.check.CheckLevels(value)

Bases: IntEnum

Level of strictness of the checks.

- DEBUG

Type:: Report any debug message that the checker wants to communicate.

- STRICT

Type:: Fail if there are warnings regarding compliance of CMOR standards.

- DEFAULT

Type:: Fail if cubes present any discrepancy with CMOR standards.

- RELAXED

Type:: Fail if cubes present severe discrepancies with CMOR standards.

- IGNORE

Type:: Do not fail for any discrepancy with CMOR standards.

Attributes:

`DEBUG`
`DEFAULT`
`IGNORE`
`RELAXED`
`STRICT`

DEBUG = 1

DEFAULT = 3

IGNORE = 5

RELAXED = 4

STRICT = 2

esmvalcore.cmor.check.cmor_check(cube, cmor_table, mip, short_name, frequency, check_level)[source]

Check if cube conforms to variable’s CMOR definition.

Equivalent to calling cmor_check_metadata and cmor_check_data consecutively.

Parameters:

cube (iris.cube.Cube) – Data cube to check.
cmor_table (str) – CMOR definitions to use.
mip – Variable’s mip.
short_name (str) – Variable’s short name.
frequency (str) – Data frequency.
check_level (enum.IntEnum) – Level of strictness of the checks.

esmvalcore.cmor.check.cmor_check_data(cube, cmor_table, mip, short_name, frequency, check_level=CheckLevels.DEFAULT)[source]

Check if data conforms to variable’s CMOR definition.

The checks performed at this step require the data in memory.

Parameters:

cube (iris.cube.Cube) – Data cube to check.
cmor_table (str) – CMOR definitions to use.
mip – Variable’s mip.
short_name (str) – Variable’s short name
frequency (str) – Data frequency
check_level (CheckLevels) – Level of strictness of the checks.

esmvalcore.cmor.check.cmor_check_metadata(cube, cmor_table, mip, short_name, frequency, check_level=CheckLevels.DEFAULT)[source]

Check if metadata conforms to variable’s CMOR definition.

None of the checks at this step will force the cube to load the data.

Parameters:

cube (iris.cube.Cube) – Data cube to check.
cmor_table (str) – CMOR definitions to use.
mip – Variable’s mip.
short_name (str) – Variable’s short name.
frequency (str) – Data frequency.
check_level (CheckLevels) – Level of strictness of the checks.

Automatically fixing issues

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.

Functions:

`fix_data`(cube, short_name, project, dataset, mip)	Fix cube data if fixes add present and check it anyway.
`fix_file`(file, short_name, project, dataset, ...)	Fix files before ESMValTool can load them.
`fix_metadata`(cubes, short_name, project, ...)	Fix cube metadata if fixes are required and check it anyway.

esmvalcore.cmor.fix.fix_data(cube, short_name, project, dataset, mip, frequency=None, check_level=CheckLevels.DEFAULT, **extra_facets)[source]

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 Extra Facets.

Returns:

Fixed and checked cube.

Return type:

iris.cube.Cube

Raises:

CMORCheckError – If the checker detects errors in the data that it can not fix.

esmvalcore.cmor.fix.fix_file(file: Path, short_name: str, project: str, dataset: str, mip: str, output_dir: Path, add_unique_suffix: bool = False, **extra_facets) → Path[source]

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 (Path) – 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 (Path) – Output directory for fixed files.
add_unique_suffix (bool, optional (default: False)) – Adds a unique suffix to output_dir for thread safety.
**extra_facets (dict, optional) – Extra facets are mainly used for data outside of the big projects like CMIP, CORDEX, obs4MIPs. For details, see Extra Facets.

Returns:

Path to the fixed file.

Return type:

Path

esmvalcore.cmor.fix.fix_metadata(cubes, short_name, project, dataset, mip, frequency=None, check_level=CheckLevels.DEFAULT, **extra_facets)[source]

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 Extra Facets.

Returns:

Fixed and checked cube.

Return type:

iris.cube.Cube

Raises:

CMORCheckError – If the checker detects errors in the metadata that it can not fix.

Functions for fixing issues

Functions for fixing specific issues with datasets.

Functions:

`add_altitude_from_plev`(cube)	Add altitude coordinate from pressure level coordinate.
`add_plev_from_altitude`(cube)	Add pressure level coordinate from altitude coordinate.

esmvalcore.cmor.fixes.add_altitude_from_plev(cube)[source]

Add altitude coordinate from pressure level coordinate.

Parameters:: cube (iris.cube.Cube) – Input cube.
Raises:: ValueError – cube does not contain coordinate air_pressure.

esmvalcore.cmor.fixes.add_plev_from_altitude(cube)[source]

Add pressure level coordinate from altitude coordinate.

Parameters:: cube (iris.cube.Cube) – Input cube.
Raises:: ValueError – cube does not contain coordinate altitude.

Using CMOR tables

CMOR information reader for ESMValTool.

Read variable information from CMOR 2 and CMOR 3 tables and make it easily available for the other components of ESMValTool

Classes:

`CMIP3Info`(cmor_tables_path[, default, ...])	Class to read CMIP3-like data request.
`CMIP5Info`(cmor_tables_path[, default, ...])	Class to read CMIP5-like data request.
`CMIP6Info`(cmor_tables_path[, default, ...])	Class to read CMIP6-like data request.
`CoordinateInfo`(name)	Class to read and store coordinate information.
`CustomInfo`([cmor_tables_path])	Class to read custom var info for ESMVal.
`InfoBase`(default, alt_names, strict)	Base class for all table info classes.
`JsonInfo`()	Base class for the info classes.
`TableInfo`(args, *kwargs)	Container class for storing a CMOR table.
`VariableInfo`(table_type, short_name)	Class to read and store variable information.

Data:

CMOR_TABLES

CMOR info objects.

Functions:

`get_var_info`(project, mip, short_name)	Get variable information.
`read_cmor_tables`([cfg_developer])	Read cmor tables required in the configuration.

class esmvalcore.cmor.table.CMIP3Info(cmor_tables_path, default=None, alt_names=None, strict=True)[source]

Bases: CMIP5Info

Class to read CMIP3-like data request.

Parameters:

cmor_tables_path (str) – Path to the folder containing the Tables folder with the json files
default (object) – Default table to look variables on if not found
strict (bool) – If False, will look for a variable in other tables if it can not be found in the requested one

Methods:

`get_table`(table)	Search and return the table info.
`get_variable`(table_name, short_name[, derived])	Search and return the variable info.

get_table(table)

Search and return the table info.

Parameters:: table (str) – Table name
Returns:: Return the TableInfo object for the requested table if found, returns None if not
Return type:: TableInfo

get_variable(table_name, short_name, derived=False)

Search and return the variable info.

Parameters:

table_name (str) – Table name
short_name (str) – Variable’s short name
derived (bool, optional) – Variable is derived. Info retrieval for derived variables always look on the default tables if variable is not find in the requested table

Returns:

Return the VariableInfo object for the requested variable if found, returns None if not

Return type:

VariableInfo

class esmvalcore.cmor.table.CMIP5Info(cmor_tables_path, default=None, alt_names=None, strict=True)[source]

Bases: InfoBase

Class to read CMIP5-like data request.

Parameters:

cmor_tables_path (str) – Path to the folder containing the Tables folder with the json files
default (object) – Default table to look variables on if not found
strict (bool) – If False, will look for a variable in other tables if it can not be found in the requested one

Methods:

`get_table`(table)	Search and return the table info.
`get_variable`(table_name, short_name[, derived])	Search and return the variable info.

get_table(table)[source]

Search and return the table info.

Parameters:: table (str) – Table name
Returns:: Return the TableInfo object for the requested table if found, returns None if not
Return type:: TableInfo

get_variable(table_name, short_name, derived=False)

Search and return the variable info.

Parameters:

table_name (str) – Table name
short_name (str) – Variable’s short name
derived (bool, optional) – Variable is derived. Info retrieval for derived variables always look on the default tables if variable is not find in the requested table

Returns:

Return the VariableInfo object for the requested variable if found, returns None if not

Return type:

VariableInfo

class esmvalcore.cmor.table.CMIP6Info(cmor_tables_path, default=None, alt_names=None, strict=True, default_table_prefix='')[source]

Bases: InfoBase

Class to read CMIP6-like data request.

This uses CMOR 3 json format

Parameters:

cmor_tables_path (str) – Path to the folder containing the Tables folder with the json files
default (object) – Default table to look variables on if not found
strict (bool) – If False, will look for a variable in other tables if it can not be found in the requested one

Methods:

`get_table`(table)	Search and return the table info.
`get_variable`(table_name, short_name[, derived])	Search and return the variable info.

get_table(table)[source]

Search and return the table info.

Parameters:: table (str) – Table name
Returns:: Return the TableInfo object for the requested table if found, returns None if not
Return type:: TableInfo

get_variable(table_name, short_name, derived=False)

Search and return the variable info.

Parameters:

table_name (str) – Table name
short_name (str) – Variable’s short name
derived (bool, optional) – Variable is derived. Info retrieval for derived variables always look on the default tables if variable is not find in the requested table

Returns:

Return the VariableInfo object for the requested variable if found, returns None if not

Return type:

VariableInfo

esmvalcore.cmor.table.CMOR_TABLES: dict[str, Union[esmvalcore.cmor.table.CMIP3Info, esmvalcore.cmor.table.CMIP5Info, esmvalcore.cmor.table.CMIP6Info, esmvalcore.cmor.table.CustomInfo]] = {'CESM': <esmvalcore.cmor.table.CMIP6Info object>, 'CMIP3': <esmvalcore.cmor.table.CMIP3Info object>, 'CMIP5': <esmvalcore.cmor.table.CMIP5Info object>, 'CMIP6': <esmvalcore.cmor.table.CMIP6Info object>, 'CORDEX': <esmvalcore.cmor.table.CMIP5Info object>, 'EMAC': <esmvalcore.cmor.table.CMIP6Info object>, 'ICON': <esmvalcore.cmor.table.CMIP6Info object>, 'IPSLCM': <esmvalcore.cmor.table.CMIP6Info object>, 'OBS': <esmvalcore.cmor.table.CMIP5Info object>, 'OBS6': <esmvalcore.cmor.table.CMIP6Info object>, 'ana4mips': <esmvalcore.cmor.table.CMIP5Info object>, 'custom': <esmvalcore.cmor.table.CustomInfo object>, 'native6': <esmvalcore.cmor.table.CMIP6Info object>, 'obs4MIPs': <esmvalcore.cmor.table.CMIP6Info object>}

CMOR info objects.

Type:: dict of str, obj

class esmvalcore.cmor.table.CoordinateInfo(name)[source]

Bases: JsonInfo

Class to read and store coordinate information.

Attributes:

`axis`	Axis
`generic_lev_name`	Generic level name
`long_name`	Long name
`must_have_bounds`	Whether bounds are required on this dimension
`out_name`	Out name
`requested`	Values requested
`standard_name`	Standard name
`stored_direction`	Direction in which the coordinate increases
`units`	Units
`valid_max`	Maximum allowed value
`valid_min`	Minimum allowed value
`value`	Coordinate value
`var_name`	Short name

Methods:

read_json(json_data)

Read coordinate information from json.

axis: Axis

generic_lev_name: Generic level name

long_name: Long name

must_have_bounds: Whether bounds are required on this dimension

out_name

Out name

This is the name of the variable in the file

read_json(json_data)[source]

Read coordinate information from json.

Non-present options will be set to empty

Parameters:: json_data (dict) – dictionary created by the json reader containing coordinate information

requested: Values requested

standard_name: Standard name

stored_direction: Direction in which the coordinate increases

units: Units

valid_max: Maximum allowed value

valid_min: Minimum allowed value

value: Coordinate value

var_name: Short name

class esmvalcore.cmor.table.CustomInfo(cmor_tables_path=None)[source]

Bases: CMIP5Info

Class to read custom var info for ESMVal.

Parameters:: cmor_tables_path (str or None) – Full path to the table or name for the table if it is present in ESMValTool repository

Methods:

`get_table`(table)	Search and return the table info.
`get_variable`(table, short_name[, derived])	Search and return the variable info.

get_table(table)

Search and return the table info.

Parameters:: table (str) – Table name
Returns:: Return the TableInfo object for the requested table if found, returns None if not
Return type:: TableInfo

get_variable(table, short_name, derived=False)[source]

Search and return the variable info.

Parameters:

table (str) – Table name
short_name (str) – Variable’s short name
derived (bool, optional) – Variable is derived. Info retrieval for derived variables always look on the default tables if variable is not find in the requested table

Returns:

Return the VariableInfo object for the requested variable if found, returns None if not

Return type:

VariableInfo

class esmvalcore.cmor.table.InfoBase(default, alt_names, strict)[source]

Bases: object

Base class for all table info classes.

This uses CMOR 3 json format

Parameters:

default (object) – Default table to look variables on if not found
alt_names (list[list[str]]) – List of known alternative names for variables
strict (bool) – If False, will look for a variable in other tables if it can not be found in the requested one

Methods:

`get_table`(table)	Search and return the table info.
`get_variable`(table_name, short_name[, derived])	Search and return the variable info.

get_table(table)[source]

Search and return the table info.

Parameters:: table (str) – Table name
Returns:: Return the TableInfo object for the requested table if found, returns None if not
Return type:: TableInfo

get_variable(table_name, short_name, derived=False)[source]

Search and return the variable info.

Parameters:

table_name (str) – Table name
short_name (str) – Variable’s short name
derived (bool, optional) – Variable is derived. Info retrieval for derived variables always look on the default tables if variable is not find in the requested table

Returns:

Return the VariableInfo object for the requested variable if found, returns None if not

Return type:

VariableInfo

class esmvalcore.cmor.table.JsonInfo[source]

Bases: object

Base class for the info classes.

Provides common utility methods to read json variables

class esmvalcore.cmor.table.TableInfo(*args, **kwargs)[source]

Bases: dict

Container class for storing a CMOR table.

Methods:

`clear`()
`copy`()
`fromkeys`([value])	Create a new dictionary with keys from iterable and values set to value.
`get`(key[, default])	Return the value for key if key is in the dictionary, else default.
`items`()
`keys`()
`pop`(k[,d])	If the key is not found, return the default if given; otherwise, raise a KeyError.
`popitem`()	Remove and return a (key, value) pair as a 2-tuple.
`setdefault`(key[, default])	Insert key with a value of default if key is not in the dictionary.
`update`([E, ]**F)	If E is present and has a .keys() method, then does: for k in E: D[k] = E[k] If E is present and lacks a .keys() method, then does: for k, v in E: D[k] = v In either case, this is followed by: for k in F: D[k] = F[k]
`values`()

clear() → None. Remove all items from D.

copy() → a shallow copy of D

fromkeys(value=None, /): Create a new dictionary with keys from iterable and values set to value.

get(key, default=None, /): Return the value for key if key is in the dictionary, else default.

items() → a set-like object providing a view on D's items

keys() → a set-like object providing a view on D's keys

pop(k[, d]) → v, remove specified key and return the corresponding value.: If the key is not found, return the default if given; otherwise, raise a KeyError.

popitem()

Remove and return a (key, value) pair as a 2-tuple.

Pairs are returned in LIFO (last-in, first-out) order. Raises KeyError if the dict is empty.

setdefault(key, default=None, /)

Insert key with a value of default if key is not in the dictionary.

Return the value for key if key is in the dictionary, else default.

update([E, ]**F) → None. Update D from dict/iterable E and F.: If E is present and has a .keys() method, then does: for k in E: D[k] = E[k] If E is present and lacks a .keys() method, then does: for k, v in E: D[k] = v In either case, this is followed by: for k in F: D[k] = F[k]

values() → an object providing a view on D's values

class esmvalcore.cmor.table.VariableInfo(table_type, short_name)[source]

Bases: JsonInfo

Class to read and store variable information.

Attributes:

`coordinates`	Coordinates
`dimensions`	List of dimensions
`frequency`	Data frequency
`long_name`	Long name
`modeling_realm`	Modeling realm
`positive`	Increasing direction
`short_name`	Short name
`standard_name`	Standard name
`units`	Data units
`valid_max`	Maximum admitted value
`valid_min`	Minimum admitted value

Methods:

`copy`()	Return a shallow copy of VariableInfo.
`read_json`(json_data, default_freq)	Read variable information from json.

coordinates

Coordinates

This is a dict with the names of the dimensions as keys and CoordinateInfo objects as values.

copy()[source]

Return a shallow copy of VariableInfo.

Returns:: Shallow copy of this object
Return type:: VariableInfo

dimensions: List of dimensions

frequency: Data frequency

long_name: Long name

modeling_realm: Modeling realm

positive: Increasing direction

read_json(json_data, default_freq)[source]

Read variable information from json.

Non-present options will be set to empty

Parameters:

json_data (dict) – dictionary created by the json reader containing variable information
default_freq (str) – Default frequency to use if it is not defined at variable level

short_name: Short name

standard_name: Standard name

units: Data units

valid_max: Maximum admitted value

valid_min: Minimum admitted value

esmvalcore.cmor.table.get_var_info(project, mip, short_name)[source]

Get variable information.

Parameters:

project (str) – Dataset’s project.
mip (str) – Variable’s cmor table.
short_name (str) – Variable’s short name.

esmvalcore.cmor.table.read_cmor_tables(cfg_developer: Path | None = None) → None[source]

Read cmor tables required in the configuration.

Parameters:

cfg_developer –

Path to config-developer.yml file.

Prior to v2.8.0 cfg_developer was an dict with the contents of config-developer.yml. This is deprecated and support will be removed in v2.10.0.