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"""Module to manage the different data conventions supported by EarthDiagnostics"""
import shutil
import re
import threading
from bscearth.utils.date import parse_date, chunk_start_date, chunk_end_date, previous_day, add_hours
from bscearth.utils.log import Log
from earthdiagnostics.frequency import Frequency, Frequencies
from earthdiagnostics.modelingrealm import ModelingRealms
from earthdiagnostics.variable import VariableType
def __init__(self, name, config):
self.config = config
self.name = name
self.lat_name = 'lat'
self.lon_name = 'lon'
self.time_separator = '-'
self.lock = threading.Lock()
self._checked_vars = list()
"""
Get the final scratch_masks path
Parameters
----------
scratch_masks: str
Returns
-------
str
"""
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def get_file_path(self, startdate, member, domain, var, cmor_var, chunk, frequency,
grid=None, year=None, date_str=None):
"""
Return the path to a concrete file
Parameters
----------
startdate: str
member: int
domain: ModelingRealm
var: str
cmor_var: Variable
chunk: int or None
frequency: Frequency or str
grid: str or None
year: int or None
date_str: str or None
Returns
-------
str
Raises
------
ValueError
If you provide two or more parameters from chunk, year or date_str or none at all
"""
if frequency is None:
frequency = self.config.frequency
frequency = Frequency.parse(frequency)
folder_path = self.get_cmor_folder_path(startdate, member, domain, var, frequency, grid, cmor_var)
file_name = self.get_file_name(startdate, member, domain, var, cmor_var, frequency,
chunk, year, date_str, grid)
filepath = os.path.join(folder_path, file_name)
return filepath
def get_file_name(self, startdate, member, domain, var, cmor_var, frequency, chunk, year, date_str, grid, ):
"""
Get filename for a given configuration
Parameters
----------
startdate: str
member: int
domain: ModelingRealm
var: str
cmor_var: Variable
frequency: Frequency
chunk: int or None
year: int or None
date_str: str or None
grid: str or None
Returns
-------
str
Raises
------
NotImplementedError:
If not implemented by derived classes
"""
raise NotImplementedError
def get_cmor_folder_path(self, startdate, member, domain, var, frequency, grid, cmor_var):
"""
Get the folder path following current CMOR convention
Parameters
----------
startdate: str
member: int
domain: ModelingRealm
var: str
frequency: Frequency
grid: str
cmor_var: Variable
Returns
-------
str
Raises
------
NotImplementedError:
If not implemented by derived classes
"""
raise NotImplementedError
def get_startdate_path(self, startdate):
"""
Return the path to the startdate's CMOR folder
Parameters
----------
startdate: str
Returns
-------
str
"""
return os.path.join(self.config.data_dir, self.config.experiment.expid, 'cmorfiles', self.config.cmor.activity,
self.config.experiment.institute, self.config.experiment.model,
self.experiment_name(startdate))
def experiment_name(self, startdate):
"""
Get experiment name, appending startdate if needed
Parameters
----------
startdate: str
Returns
-------
str
"""
if self.config.cmor.append_startdate:
return '{}S{}'.format(self.config.experiment.experiment_name, startdate)
else:
return self.config.experiment.experiment_name
def get_member_str(self, member):
"""
Transalate member number to member string
Parameters
----------
member: int
Returns
-------
str
Raises
------
NotImplementedError:
If not implemented by derived classes
"""
def create_links(self, startdate, member=None):
"""
Create links for a given startdate or member
Parameters
----------
startdate: str
member: int or None
"""
if member is not None:
member_str = self.get_member_str(member)
else:
member_str = None
Log.info('Creating links for CMOR files ({0})', startdate)
path = self.get_startdate_path(startdate)
self._link_startdate(path, member_str)
Log.debug('Links ready')
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raise NotImplementedError
def create_link(self, domain, filepath, frequency, var, grid, move_old, vartype):
"""
Create file link
Parameters
----------
domain: ModelingRealm
filepath: str
frequency: Frequency
var: str
grid: str
move_old: bool
vartype: VariableType
"""
freq_str = frequency.folder_name(vartype)
if not grid:
grid = 'original'
variable_folder = domain.get_varfolder(var, self.config.experiment.ocean_timestep,
self.config.experiment.atmos_timestep)
vargrid_folder = domain.get_varfolder(var, self.config.experiment.ocean_timestep,
self.config.experiment.atmos_timestep, grid=grid)
self.lock.acquire()
try:
expid = self.config.experiment.expid
if grid == 'original':
link_path = os.path.join(self.config.data_dir, expid, freq_str, variable_folder)
Utils.create_folder_tree(link_path)
else:
link_path = os.path.join(self.config.data_dir, expid, freq_str, vargrid_folder)
Utils.create_folder_tree(link_path)
default_path = os.path.join(self.config.data_dir, expid, freq_str, variable_folder)
original_path = os.path.join(self.config.data_dir, expid, freq_str,
vargrid_folder.replace('-{0}_f'.format(grid), '-original_f'))
if os.path.islink(default_path):
os.remove(default_path)
elif os.path.isdir(default_path):
shutil.move(default_path, original_path)
os.symlink(link_path, default_path)
if move_old and link_path not in self._checked_vars:
self._checked_vars.append(link_path)
old_path = os.path.join(self.config.data_dir, expid, freq_str,
'old_{0}'.format(os.path.basename(link_path)))
regex = re.compile(var + '_[0-9]{6,8}[.]nc')
for filename in os.listdir(link_path):
if regex.match(filename):
Utils.create_folder_tree(old_path)
Utils.move_file(os.path.join(link_path, filename),
os.path.join(old_path, filename))
link_path = os.path.join(link_path, os.path.basename(filepath))
if os.path.lexists(link_path):
os.remove(link_path)
if not os.path.exists(filepath):
raise ValueError('Original file {0} does not exists'.format(filepath))
relative_path = os.path.relpath(filepath, os.path.dirname(link_path))
os.symlink(relative_path, link_path)
except Exception:
raise
finally:
self.lock.release()
def _get_time_component(self, chunk, date_str, frequency, startdate, year):
if len([x for x in (chunk, date_str, year) if x is not None]) > 1:
raise ValueError('Only one of the parameters chunk, year or date_str may be provided')
time_bound = self._get_chunk_time_bounds(startdate, chunk, frequency)
elif year:
if frequency != Frequencies.yearly:
raise ValueError('Year may be provided instead of chunk only if frequency is "yr"')
time_bound = str(year)
else:
raise ValueError('Time info not provided')
def _get_chunk_time_bounds(self, startdate, chunk, frequency):
chunk_start = chunk_start_date(start, chunk, self.config.experiment.chunk_size, 'month',
self.config.experiment.calendar)
chunk_end = chunk_end_date(chunk_start, self.config.experiment.chunk_size, 'month',
self.config.experiment.calendar)
chunk_end = previous_day(chunk_end, self.config.experiment.calendar)
time_bound = "{0:04}{1:02}{4}{2:04}{3:02}".format(chunk_start.year, chunk_start.month, chunk_end.year,
chunk_end.month, self.time_separator)
return time_bound
def _check_var_presence(self, folder, current_count, startdate, member, domain, chunk, freq):
for var in os.listdir(folder):
cmor_var = self.config.var_manager.get_variable(var, True)
var_path = self.get_file_path(startdate, member, domain, var, cmor_var, chunk, frequency=freq)
if os.path.isfile(var_path):
current_count += 1
if current_count >= self.config.cmor.min_cmorized_vars:
break
return current_count
def is_cmorized(self, startdate, member, chunk, domain):
"""
Check if a given chunk is cmorized for a given domain
Parameters
----------
startdate: str
member: str
chunk: int
domain: ModelingRealm
Returns
-------
bool
Raises
------
NotImplementedError:
If not implemented by the derived classes
"""
class Cmor2Convention(DataConvention):
def get_file_name(self, startdate, member, domain, var, cmor_var, frequency, chunk, year, date_str, grid, ):
"""
Get filename for a given configuration
Parameters
----------
startdate: str
member: int
domain: ModelingRealm
var: str
cmor_var: Variable
frequency: Frequency
chunk: int or None
year: int or None
date_str: str or None
grid: str or None
Returns
-------
str
"""
if cmor_var is None:
cmor_table = domain.get_table(frequency, self.config.data_convention)
else:
cmor_table = cmor_var.get_table(frequency, self.config.data_convention)
time_bound = self._get_time_component(chunk, date_str, frequency, startdate, year)
time_bound = '_{0}.nc'.format(time_bound)
file_name = '{0}_{1}_{2}_{3}_S{4}_{5}{6}'.format(var, cmor_table.name, self.config.experiment.model,
self.experiment_name(startdate), startdate,
return file_name
def get_cmor_folder_path(self, startdate, member, domain, var, frequency, grid, cmor_var):
folder_path = os.path.join(self.get_startdate_path(startdate), str(frequency), domain.name, var)
if grid and grid != 'original':
folder_path = os.path.join(folder_path, grid)
folder_path = os.path.join(folder_path, self.get_member_str(member))
if self.config.cmor.version:
folder_path = os.path.join(folder_path, self.config.cmor.version)
return folder_path
def get_member_str(self, member):
"""
Transalate member number to member string
Parameters
----------
member: int
Returns
-------
str
Raises
------
NotImplementedError:
If not implemented by derived classes
"""
return template.format(member + 1 - self.config.experiment.member_count_start,
self.config.cmor.initialization_number)
def _link_startdate(self, path, member_str):
for freq in os.listdir(path):
Log.debug('Creating links for frequency {0}', freq)
frequency = Frequency.parse(freq)
for domain in os.listdir(os.path.join(path, freq)):
Log.debug('Creating links for domain {0}', domain)
for var in os.listdir(os.path.join(path, freq, domain)):
for member in os.listdir(os.path.join(path, freq, domain, var)):
if member_str is not None and member_str != member:
continue
for name in os.listdir(os.path.join(path, freq, domain, var, member)):
filepath = os.path.join(path, freq, domain, var, member, name)
if os.path.isfile(filepath):
self.create_link(ModelingRealms.parse(domain), filepath, frequency, var, "", False,
else:
for filename in os.listdir(filepath):
self.create_link(ModelingRealms.parse(domain), os.path.join(filepath, filename),
frequency, var, "", False, vartype=VariableType.MEAN)
def is_cmorized(self, startdate, member, chunk, domain):
"""
Check if a given chunk is cmorized for a given domain
Parameters
----------
startdate: str
member: str
chunk: int
domain: ModelingRealm
Returns
-------
bool
"""
startdate_path = self.get_startdate_path(startdate)
if not os.path.isdir(startdate_path):
return False
count = 0
for freq in os.listdir(startdate_path):
domain_path = os.path.join(startdate_path, freq, domain.name)
if os.path.isdir(domain_path):
count = self._check_var_presence(domain_path, count, startdate, member, domain, chunk, freq)
if count >= self.config.cmor.min_cmorized_vars:
return True
return False
"""
Return the path to the startdate's CMOR folder
Parameters
----------
startdate: str
Returns
-------
str
"""
return os.path.join(self.config.data_dir, self.config.experiment.expid, 'cmorfiles',
self.config.experiment.institute,
self.config.experiment.model, self.experiment_name(startdate), 'S' + startdate)
class PrefaceConvention(Cmor2Convention):
Parameters
----------
name: str
config: Config
"""
def __init__(self, name, config):
super(PrefaceConvention, self).__init__(name, config)
self.time_separator = '_'
def get_startdate_path(self, startdate):
"""
Return the path to the startdate's CMOR folder
Parameters
----------
startdate: str
Returns
-------
str
"""
return os.path.join(self.config.data_dir, self.config.experiment.expid, 'cmorfiles',
self.config.experiment.institute,
self.experiment_name(startdate), 'S' + startdate)
class Cmor3Convention(DataConvention):
"""
Base class for CMOR3-based conventions
Parameters
----------
name: str
config: Config
"""
def __init__(self, name, config):
super(Cmor3Convention, self).__init__(name, config)
self.lat_name = 'latitude'
self.lon_name = 'longitude'
def get_scratch_masks(self, scratch_masks):
"""
Get the final scratch_masks path
Adds a folder matching the convention name to the configured path
Parameters
----------
scratch_masks: str
Returns
-------
str
"""
def get_file_name(self, startdate, member, domain, var, cmor_var, frequency, chunk, year, date_str, grid, ):
"""
Get filename for a given configuration
Parameters
----------
startdate: str
member: int
domain: ModelingRealm
var: str
cmor_var: Variable
frequency: Frequency
chunk: int or None
year: int or None
date_str: str or None
grid: str or None
Returns
-------
str
"""
if cmor_var is None:
cmor_table = domain.get_table(frequency, self.config.data_convention)
else:
cmor_table = cmor_var.get_table(frequency, self.config.data_convention)
time_bound = self._get_time_component(chunk, date_str, frequency, startdate, year)
time_bound = '_{0}.nc'.format(time_bound)
if not grid:
if domain in [ModelingRealms.ocnBgchem, ModelingRealms.seaIce, ModelingRealms.ocean]:
grid = self.config.cmor.default_ocean_grid
else:
grid = self.config.cmor.default_atmos_grid
if self.config.cmor.append_startdate:
subexp_id = 's{}-'.format(startdate)
else:
subexp_id = ''
file_name = '{var_name}_{table}_{model}_{exp_id}_{subexp_id}{member}_{grid}{time}'.format(
var_name=var,
table=cmor_table.name,
model=self.config.experiment.model,
exp_id=self.experiment_name(startdate),
subexp_id=subexp_id,
member=self.get_member_str(member),
grid=grid,
time=time_bound)
def _get_chunk_time_bounds(self, startdate, chunk, frequency):
start = parse_date(startdate)
chunk_start = chunk_start_date(start, chunk, self.config.experiment.chunk_size, 'month',
self.config.experiment.calendar)
chunk_end = chunk_end_date(chunk_start, self.config.experiment.chunk_size, 'month',
self.config.experiment.calendar)
chunk_end = previous_day(chunk_end, self.config.experiment.calendar)
time_bound = "{0:04}{1:02}{4}{2:04}{3:02}".format(chunk_start.year, chunk_start.month, chunk_end.year,
chunk_end.month, self.time_separator)
elif frequency == Frequencies.daily:
chunk_end = previous_day(chunk_end, self.config.experiment.calendar)
time_bound = "{0.year:04}{0.month:02}{0.day:02}{2}" \
"{1.year:04}{1.month:02}{1.day:02}".format(chunk_start, chunk_end, self.time_separator)
elif frequency.frequency.endswith('hr'):
chunk_end = add_hours(chunk_end, -int(frequency.frequency[:-2]), self.config.experiment.calendar)
time_bound = "{0.year:04}{0.month:02}{0.day:02}{0.hour:02}{0.minute:02}{2}" \
"{1.year:04}{1.month:02}{1.day:02}{1.hour:02}{1.minute:02}".format(chunk_start,
def get_cmor_folder_path(self, startdate, member, domain, var, frequency, grid, cmor_var):
if not self.config.cmor.version:
raise ValueError('CMOR version is mandatory for PRIMAVERA and CMIP6')
if not grid:
if domain in [ModelingRealms.ocnBgchem, ModelingRealms.seaIce, ModelingRealms.ocean]:
grid = self.config.cmor.default_ocean_grid
else:
grid = self.config.cmor.default_atmos_grid
if cmor_var is None:
table_name = domain.get_table(frequency, self.config.data_convention).name
else:
table_name = cmor_var.get_table(frequency, self.config.data_convention).name
folder_path = os.path.join(self.get_startdate_path(startdate), self.get_member_str(member),
table_name, var,
grid, self.config.cmor.version)
return folder_path
def _link_startdate(self, path, member_str):
for member in os.listdir(path):
for table in os.listdir(os.path.join(path, member)):
frequency = self.config.var_manager.tables[table].frequency
Log.debug('Creating links for table {0}', table)
for var in os.listdir(os.path.join(path, member, table)):
cmor_var = self.config.var_manager.get_variable(var, silent=True)
domain = cmor_var.domain
domain = self.config.var_manager.tables[table].domain
for grid in os.listdir(os.path.join(path, member, table, var)):
if member_str is not None and member_str != member:
continue
for name in os.listdir(os.path.join(path, member, table, var, grid)):
filepath = os.path.join(path, member, table, var, grid, name)
if os.path.isfile(filepath):
self.create_link(domain, filepath, frequency, var, "", False,
vartype=VariableType.MEAN)
else:
for filename in os.listdir(filepath):
cmorfile = os.path.join(filepath, filename)
self.create_link(domain, cmorfile, frequency, var, "",
False, vartype=VariableType.MEAN)
def experiment_name(self, startdate):
"""
Get experiment name.
CMOR3 ignores append startdates as thery are added to the member str
Parameters
----------
startdate: str
Returns
-------
str
"""
return self.config.experiment.experiment_name
"""
Transalate member number to member string
Parameters
----------
member: int
Returns
-------
str
"""
template = 'r{0}i{1}p1f1'
return template.format(member + 1 - self.config.experiment.member_count_start,
self.config.cmor.initialization_number)
def is_cmorized(self, startdate, member, chunk, domain):
"""
Check if a given chunk is cmorized for a given domain
Parameters
----------
startdate: str
member: str
chunk: int
domain: ModelingRealm
Returns
-------
bool
"""
startdate_path = self.get_startdate_path(startdate)
if not os.path.isdir(startdate_path):
return False
count = 0
member_path = os.path.join(startdate_path, self.get_member_str(member))
if not os.path.isdir(member_path):
return False
freq = Frequencies.monthly
table = domain.get_table(freq, self.config.data_convention)
table_dir = os.path.join(member_path, table.name)
if not os.path.isdir(table_dir):
return False
count = self._check_var_presence(table_dir, count, startdate, member, domain, chunk, freq)
if count >= self.config.cmor.min_cmorized_vars:
return True
return False
class CMIP6Convention(Cmor3Convention):
class PrimaveraConvention(Cmor3Convention):
class MeteoFranceConvention(DataConvention):
def get_file_name(self, startdate, member, domain, var, cmor_var, frequency, chunk, year, date_str, grid,):
"""
Get filename for a given configuration
Parameters
----------
startdate: str
member: int
domain: ModelingRealm
var: str
cmor_var: Variable
frequency: Frequency
chunk: int or None
year: int or None
date_str: str or None
grid: str or None
Returns
-------
str
"""
if year is not None:
raise ValueError('Year not supported with MeteoFrance convention')
if date_str is not None:
raise ValueError('Date_str not supported with MeteoFrance convention')
if chunk is None:
raise ValueError('Chunk must be provided in MeteoFrance convention')
time_bound = self._get_chunk_time_bounds(startdate, chunk, frequency)
file_name = '{0}_{1}_{2}_{3}.nc'.format(var, frequency, time_bound, self.get_member_str(member))
return file_name
def get_cmor_folder_path(self, startdate, member, domain, var, frequency, grid, cmor_var):
folder_path = os.path.join(self.config.data_dir, self.experiment_name(startdate),
'H{0}'.format(chr(64 + int(startdate[4:6]))),
startdate[0:4])
return folder_path
def get_member_str(self, member):
"""
Transalate member number to member string
Parameters
----------
member: int
Returns
-------
str
"""
def _get_chunk_time_bounds(self, startdate, chunk, frequency):
chunk_start = chunk_start_date(start, chunk, self.config.experiment.chunk_size, 'month',
self.config.experiment.calendar)
time_bound = "{0:04}{1:02}".format(chunk_start.year, chunk_start.month)
return time_bound
def create_link(self, domain, filepath, frequency, var, grid, move_old, vartype):
"""
Create file link
In this convention, it does nothing
Parameters
----------
domain: ModelingRealm
filepath: str
frequency: Frequency
var: str
grid: str
move_old: bool
vartype: VariableType
"""
pass
def create_links(self, startdate, member=None):
"""
Create links for a given startdate or member
In this convention, it does nothing
Parameters
----------
startdate: str
member: int or None
"""
pass
def is_cmorized(self, startdate, member, chunk, domain):
"""
Check if a given chunk is cmorized for a given domain
Parameters
----------
startdate: str
member: str
chunk: int
domain: ModelingRealm
Returns
-------
bool
Raises
------
NotImplementedError:
If not implemented by the derived classes
"""