"""
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
"""
import copy
import errno
import glob
import json
import logging
import os
from functools import total_ordering
from collections import Counter
from pathlib import Path
import yaml
logger = logging.getLogger(__name__)
CMOR_TABLES = {}
"""dict of str, obj: CMOR info objects."""
[docs]def get_var_info(project, mip, short_name):
"""Get variable information.
Parameters
----------
project : str
Dataset's project.
mip : str
Variable's cmor table.
short_name : str
Variable's short name.
"""
return CMOR_TABLES[project].get_variable(mip, short_name)
[docs]def read_cmor_tables(cfg_developer=None):
"""Read cmor tables required in the configuration.
Parameters
----------
cfg_developer : dict of str
Parsed config-developer file
"""
if cfg_developer is None:
cfg_file = Path(__file__).parent.parent / 'config-developer.yml'
with cfg_file.open() as file:
cfg_developer = yaml.safe_load(file)
cwd = os.path.dirname(os.path.realpath(__file__))
var_alt_names_file = os.path.join(cwd, 'variable_alt_names.yml')
with open(var_alt_names_file, 'r') as yfile:
alt_names = yaml.safe_load(yfile)
custom = CustomInfo()
CMOR_TABLES.clear()
CMOR_TABLES['custom'] = custom
install_dir = os.path.dirname(os.path.realpath(__file__))
for table in cfg_developer:
CMOR_TABLES[table] = _read_table(
cfg_developer, table, install_dir, custom, alt_names)
def _read_table(cfg_developer, table, install_dir, custom, alt_names):
project = cfg_developer[table]
cmor_type = project.get('cmor_type', 'CMIP5')
default_path = os.path.join(install_dir, 'tables', cmor_type.lower())
table_path = project.get('cmor_path', default_path)
table_path = os.path.expandvars(os.path.expanduser(table_path))
cmor_strict = project.get('cmor_strict', True)
default_table_prefix = project.get('cmor_default_table_prefix', '')
if cmor_type == 'CMIP3':
return CMIP3Info(
table_path,
default=custom,
strict=cmor_strict,
alt_names=alt_names,
)
if cmor_type == 'CMIP5':
return CMIP5Info(
table_path,
default=custom,
strict=cmor_strict,
alt_names=alt_names
)
if cmor_type == 'CMIP6':
return CMIP6Info(
table_path,
default=custom,
strict=cmor_strict,
default_table_prefix=default_table_prefix,
alt_names=alt_names,
)
raise ValueError(f'Unsupported CMOR type {cmor_type}')
[docs]class InfoBase():
"""
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
"""
def __init__(self, default, alt_names, strict):
if alt_names is None:
alt_names = ""
self.default = default
self.alt_names = alt_names
self.strict = strict
self.tables = {}
[docs] def get_table(self, table):
"""
Search and return the table info.
Parameters
----------
table: basestring
Table name
Returns
-------
TableInfo
Return the TableInfo object for the requested table if
found, returns None if not
"""
return self.tables.get(table)
[docs] def get_variable(self, table_name, short_name, derived=False):
"""
Search and return the variable info.
Parameters
----------
table_name: basestring
Table name
short_name: basestring
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
-------
VariableInfo
Return the VariableInfo object for the requested variable if
found, returns None if not
"""
alt_names_list = self._get_alt_names_list(short_name)
table = self.get_table(table_name)
if table:
for alt_names in alt_names_list:
try:
return table[alt_names]
except KeyError:
pass
var_info = self._look_in_all_tables(alt_names_list)
if not var_info:
var_info = self._look_in_default(
derived, alt_names_list, table_name)
if var_info:
var_info = var_info.copy()
var_info = self._update_frequency_from_mip(table_name, var_info)
return var_info
def _look_in_default(self, derived, alt_names_list, table_name):
var_info = None
if (not self.strict or derived):
for alt_names in alt_names_list:
var_info = self.default.get_variable(table_name, alt_names)
if var_info:
break
return var_info
def _look_in_all_tables(self, alt_names_list):
var_info = None
if not self.strict:
for alt_names in alt_names_list:
var_info = self._look_all_tables(alt_names)
if var_info:
break
return var_info
def _get_alt_names_list(self, short_name):
alt_names_list = [short_name]
for alt_names in self.alt_names:
if short_name in alt_names:
alt_names_list.extend(
[alt_name for alt_name in alt_names
if alt_name not in alt_names_list])
return alt_names_list
def _update_frequency_from_mip(self, table_name, var_info):
mip_info = self.get_table(table_name)
if mip_info:
var_info.frequency = mip_info.frequency
return var_info
def _look_all_tables(self, alt_names):
for table_vars in sorted(self.tables.values()):
if alt_names in table_vars:
return table_vars[alt_names]
return None
[docs]class CMIP6Info(InfoBase):
"""
Class to read CMIP6-like data request.
This uses CMOR 3 json format
Parameters
----------
cmor_tables_path: basestring
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
"""
def __init__(self,
cmor_tables_path,
default=None,
alt_names=None,
strict=True,
default_table_prefix=''):
super().__init__(default, alt_names, strict)
cmor_tables_path = self._get_cmor_path(cmor_tables_path)
self._cmor_folder = os.path.join(cmor_tables_path, 'Tables')
if glob.glob(os.path.join(self._cmor_folder, '*_CV.json')):
self._load_controlled_vocabulary()
self.default_table_prefix = default_table_prefix
self.var_to_freq = {}
self._load_coordinates()
for json_file in glob.glob(os.path.join(self._cmor_folder, '*.json')):
if 'CV_test' in json_file or 'grids' in json_file:
continue
try:
self._load_table(json_file)
except Exception:
msg = f"Exception raised when loading {json_file}"
# Logger may not be ready at this stage
if logger.handlers:
logger.error(msg)
else:
print(msg)
raise
@staticmethod
def _get_cmor_path(cmor_tables_path):
if os.path.isdir(cmor_tables_path):
return cmor_tables_path
cwd = os.path.dirname(os.path.realpath(__file__))
cmor_tables_path = os.path.join(cwd, 'tables', cmor_tables_path)
if os.path.isdir(cmor_tables_path):
return cmor_tables_path
raise ValueError(
'CMOR tables not found in {}'.format(cmor_tables_path))
def _load_table(self, json_file):
with open(json_file) as inf:
raw_data = json.loads(inf.read())
if not self._is_table(raw_data):
return
table = TableInfo()
header = raw_data['Header']
table.name = header['table_id'].split(' ')[-1]
self.tables[table.name] = table
generic_levels = header['generic_levels'].split()
table.frequency = header.get('frequency', '')
self.var_to_freq[table.name] = {}
for var_name, var_data in raw_data['variable_entry'].items():
var = VariableInfo('CMIP6', var_name)
var.read_json(var_data, table.frequency)
self._assign_dimensions(var, generic_levels)
table[var_name] = var
self.var_to_freq[table.name][var_name] = var.frequency
if not table.frequency:
var_freqs = (var.frequency for var in table.values())
table_freq, _ = Counter(var_freqs).most_common(1)[0]
table.frequency = table_freq
self.tables[table.name] = table
def _assign_dimensions(self, var, generic_levels):
for dimension in var.dimensions:
if dimension in generic_levels:
coord = CoordinateInfo(dimension)
coord.generic_level = True
coord.axis = 'Z'
else:
try:
coord = self.coords[dimension]
except KeyError:
logger.exception(
'Can not find dimension %s for variable %s', dimension,
var)
raise
var.coordinates[dimension] = coord
def _load_coordinates(self):
self.coords = {}
for json_file in glob.glob(
os.path.join(self._cmor_folder, '*coordinate*.json')):
with open(json_file) as inf:
table_data = json.loads(inf.read())
for coord_name in table_data['axis_entry'].keys():
coord = CoordinateInfo(coord_name)
coord.read_json(table_data['axis_entry'][coord_name])
self.coords[coord_name] = coord
def _load_controlled_vocabulary(self):
self.activities = {}
self.institutes = {}
for json_file in glob.glob(os.path.join(self._cmor_folder,
'*_CV.json')):
with open(json_file) as inf:
table_data = json.loads(inf.read())
try:
exps = table_data['CV']['experiment_id']
for exp_id in exps:
activity = exps[exp_id]['activity_id'][0].split(' ')
self.activities[exp_id] = activity
except (KeyError, AttributeError):
pass
try:
sources = table_data['CV']['source_id']
for source_id in sources:
institution = sources[source_id]['institution_id']
self.institutes[source_id] = institution
except (KeyError, AttributeError):
pass
[docs] def get_table(self, table):
"""
Search and return the table info.
Parameters
----------
table: basestring
Table name
Returns
-------
TableInfo
Return the TableInfo object for the requested table if
found, returns None if not
"""
try:
return self.tables[table]
except KeyError:
return self.tables.get(''.join((self.default_table_prefix, table)))
@staticmethod
def _is_table(table_data):
if 'variable_entry' not in table_data:
return False
if 'Header' not in table_data:
return False
return True
[docs]@total_ordering
class TableInfo(dict):
"""Container class for storing a CMOR table."""
def __init__(self, *args, **kwargs):
"""Create a new TableInfo object for storing VariableInfo objects."""
super(TableInfo, self).__init__(*args, **kwargs)
self.name = ''
self.frequency = ''
self.realm = ''
def __eq__(self, other):
return (self.name, self.frequency, self.realm) == \
(other.name, other.frequency, other.realm)
def __ne__(self, other):
return (self.name, self.frequency, self.realm) != \
(other.name, other.frequency, other.realm)
def __lt__(self, other):
return (self.name, self.frequency, self.realm) < \
(other.name, other.frequency, other.realm)
[docs]class JsonInfo(object):
"""
Base class for the info classes.
Provides common utility methods to read json variables
"""
def __init__(self):
self._json_data = {}
def _read_json_variable(self, parameter, default=''):
"""
Read a json parameter in json_data.
Parameters
----------
parameter: str
parameter to read
Returns
-------
str
Option's value or empty string if parameter is not present
"""
if parameter not in self._json_data:
return default
return str(self._json_data[parameter])
def _read_json_list_variable(self, parameter):
"""
Read a json list parameter in json_data.
Parameters
----------
parameter: str
parameter to read
Returns
-------
str
Option's value or empty list if parameter is not present
"""
if parameter not in self._json_data:
return []
return self._json_data[parameter]
[docs]class VariableInfo(JsonInfo):
"""Class to read and store variable information."""
def __init__(self, table_type, short_name):
"""
Class to read and store variable information.
Parameters
----------
short_name: str
variable's short name
"""
super(VariableInfo, self).__init__()
self.table_type = table_type
self.modeling_realm = []
"""Modeling realm"""
self.short_name = short_name
"""Short name"""
self.standard_name = ''
"""Standard name"""
self.long_name = ''
"""Long name"""
self.units = ''
"""Data units"""
self.valid_min = ''
"""Minimum admitted value"""
self.valid_max = ''
"""Maximum admitted value"""
self.frequency = ''
"""Data frequency"""
self.positive = ''
"""Increasing direction"""
self.dimensions = []
"""List of dimensions"""
self.coordinates = {}
"""Coordinates
This is a dict with the names of the dimensions as keys and
CoordinateInfo objects as values.
"""
self._json_data = None
[docs] def copy(self):
"""
Return a shallow copy of VariableInfo.
Returns
-------
VariableInfo
Shallow copy of this object
"""
return copy.copy(self)
[docs] def read_json(self, json_data, default_freq):
"""
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
"""
self._json_data = json_data
self.standard_name = self._read_json_variable('standard_name')
self.long_name = self._read_json_variable('long_name')
self.units = self._read_json_variable('units')
self.valid_min = self._read_json_variable('valid_min')
self.valid_max = self._read_json_variable('valid_max')
self.positive = self._read_json_variable('positive')
self.modeling_realm = self._read_json_variable(
'modeling_realm').split()
self.frequency = self._read_json_variable('frequency', default_freq)
self.dimensions = self._read_json_variable('dimensions').split()
[docs]class CoordinateInfo(JsonInfo):
"""Class to read and store coordinate information."""
def __init__(self, name):
"""
Class to read and store coordinate information.
Parameters
----------
name: str
coordinate's name
"""
super(CoordinateInfo, self).__init__()
self.name = name
self.generic_level = False
self.axis = ""
"""Axis"""
self.value = ""
"""Coordinate value"""
self.standard_name = ""
"""Standard name"""
self.long_name = ""
"""Long name"""
self.out_name = ""
"""
Out name
This is the name of the variable in the file
"""
self.var_name = ""
"""Short name"""
self.units = ""
"""Units"""
self.stored_direction = ""
"""Direction in which the coordinate increases"""
self.requested = []
"""Values requested"""
self.valid_min = ""
"""Minimum allowed value"""
self.valid_max = ""
"""Maximum allowed value"""
self.must_have_bounds = ""
"""Whether bounds are required on this dimension"""
[docs] def read_json(self, json_data):
"""
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
"""
self._json_data = json_data
self.axis = self._read_json_variable('axis')
self.value = self._read_json_variable('value')
self.out_name = self._read_json_variable('out_name')
self.var_name = self._read_json_variable('var_name')
self.standard_name = self._read_json_variable('standard_name')
self.long_name = self._read_json_variable('long_name')
self.units = self._read_json_variable('units')
self.stored_direction = self._read_json_variable('stored_direction')
self.valid_min = self._read_json_variable('valid_min')
self.valid_max = self._read_json_variable('valid_max')
self.requested = self._read_json_list_variable('requested')
self.must_have_bounds = self._read_json_variable('must_have_bounds')
[docs]class CMIP5Info(InfoBase):
"""
Class to read CMIP5-like data request.
Parameters
----------
cmor_tables_path: basestring
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
"""
def __init__(self, cmor_tables_path, default=None, alt_names=None,
strict=True):
super().__init__(default, alt_names, strict)
cmor_tables_path = self._get_cmor_path(cmor_tables_path)
self._cmor_folder = os.path.join(cmor_tables_path, 'Tables')
if not os.path.isdir(self._cmor_folder):
raise OSError(errno.ENOTDIR, "CMOR tables path is not a directory",
self._cmor_folder)
self.strict = strict
self.tables = {}
self.coords = {}
self._current_table = None
self._last_line_read = None
for table_file in glob.glob(os.path.join(self._cmor_folder, '*')):
if '_grids' in table_file:
continue
try:
self._load_table(table_file)
except Exception:
msg = f"Exception raised when loading {table_file}"
# Logger may not be ready at this stage
if logger.handlers:
logger.error(msg)
else:
print(msg)
raise
@staticmethod
def _get_cmor_path(cmor_tables_path):
if os.path.isdir(cmor_tables_path):
return cmor_tables_path
cwd = os.path.dirname(os.path.realpath(__file__))
cmor_tables_path = os.path.join(cwd, 'tables', cmor_tables_path)
return cmor_tables_path
def _load_table(self, table_file, table_name=''):
if table_name and table_name in self.tables:
# special case used for updating a table with custom variable file
table = self.tables[table_name]
else:
# default case: table name is first line of table file
table = None
self._read_table_file(table_file, table)
def _read_table_file(self, table_file, table=None):
with open(table_file) as self._current_table:
self._read_line()
while True:
key, value = self._last_line_read
if key == 'table_id':
table = TableInfo()
table.name = value[len('Table '):]
self.tables[table.name] = table
elif key == 'frequency':
table.frequency = value
elif key == 'modeling_realm':
table.realm = value
elif key == 'generic_levels':
for dim in value.split(' '):
coord = CoordinateInfo(dim)
coord.generic_level = True
coord.axis = 'Z'
self.coords[dim] = coord
elif key == 'axis_entry':
self.coords[value] = self._read_coordinate(value)
continue
elif key == 'variable_entry':
table[value] = self._read_variable(value, table.frequency)
continue
if not self._read_line():
return
def _read_line(self):
line = self._current_table.readline()
if line == '':
return False
if line.startswith('!'):
return self._read_line()
line = line.replace('\n', '')
if '!' in line:
line = line[:line.index('!')]
line = line.strip()
if not line:
self._last_line_read = ('', '')
else:
index = line.index(':')
self._last_line_read = (line[:index].strip(),
line[index + 1:].strip())
return True
def _read_coordinate(self, value):
coord = CoordinateInfo(value)
while self._read_line():
key, value = self._last_line_read
if key in ('variable_entry', 'axis_entry'):
return coord
if key == 'requested':
coord.requested.extend(
(val for val in value.split(' ') if val))
continue
if hasattr(coord, key):
setattr(coord, key, value)
return coord
def _read_variable(self, short_name, frequency):
var = VariableInfo('CMIP5', short_name)
var.frequency = frequency
while self._read_line():
key, value = self._last_line_read
if key in ('variable_entry', 'axis_entry'):
break
if key in ('dimensions', 'modeling_realm'):
setattr(var, key, value.split())
elif hasattr(var, key):
setattr(var, key, value)
for dim in var.dimensions:
var.coordinates[dim] = self.coords[dim]
return var
[docs] def get_table(self, table):
"""
Search and return the table info.
Parameters
----------
table: basestring
Table name
Returns
-------
TableInfo
Return the TableInfo object for the requested table if
found, returns None if not
"""
return self.tables.get(table)
[docs]class CMIP3Info(CMIP5Info):
"""
Class to read CMIP3-like data request.
Parameters
----------
cmor_tables_path: basestring
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
"""
def _read_table_file(self, table_file, table=None):
for dim in ('zlevel', ):
coord = CoordinateInfo(dim)
coord.generic_level = True
coord.axis = 'Z'
self.coords[dim] = coord
super()._read_table_file(table_file, table)
def _read_coordinate(self, value):
coord = super()._read_coordinate(value)
if not coord.out_name:
coord.out_name = coord.name
coord.var_name = coord.name
return coord
def _read_variable(self, short_name, frequency):
var = super()._read_variable(short_name, frequency)
var.frequency = None
var.modeling_realm = None
return var
[docs]class CustomInfo(CMIP5Info):
"""
Class to read custom var info for ESMVal.
Parameters
----------
cmor_tables_path: basestring or None
Full path to the table or name for the table if it is present in
ESMValTool repository
"""
def __init__(self, cmor_tables_path=None):
cwd = os.path.dirname(os.path.realpath(__file__))
self._cmor_folder = os.path.join(cwd, 'tables', 'custom')
self.tables = {}
self.var_to_freq = {}
table = TableInfo()
table.name = 'custom'
self.tables[table.name] = table
self._coordinates_file = os.path.join(
self._cmor_folder,
'CMOR_coordinates.dat',
)
self.coords = {}
self._read_table_file(self._coordinates_file, self.tables['custom'])
for dat_file in glob.glob(os.path.join(self._cmor_folder, '*.dat')):
if dat_file == self._coordinates_file:
continue
try:
self._read_table_file(dat_file, self.tables['custom'])
except Exception:
msg = f"Exception raised when loading {dat_file}"
# Logger may not be ready at this stage
if logger.handlers:
logger.error(msg)
else:
print(msg)
raise
[docs] def get_variable(self, table, short_name, derived=False):
"""
Search and return the variable info.
Parameters
----------
table: basestring
Table name
short_name: basestring
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
-------
VariableInfo
Return the VariableInfo object for the requested variable if
found, returns None if not
"""
return self.tables['custom'].get(short_name, None)
def _read_table_file(self, table_file, table=None):
with open(table_file) as self._current_table:
self._read_line()
while True:
key, value = self._last_line_read
if key == 'generic_levels':
for dim in value.split(' '):
coord = CoordinateInfo(dim)
coord.generic_level = True
coord.axis = 'Z'
self.coords[dim] = coord
elif key == 'axis_entry':
self.coords[value] = self._read_coordinate(value)
continue
elif key == 'variable_entry':
table[value] = self._read_variable(value, '')
continue
if not self._read_line():
return
read_cmor_tables()