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import glob
from datetime import datetime
import os
from autosubmit.config.log import Log
from autosubmit.date.chunk_date_lib import parse_date, chunk_start_date, chunk_end_date, previous_day
from earthdiagnostics.cmorizer import Cmorizer
from earthdiagnostics.datamanager import DataManager, NetCDFFile
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from earthdiagnostics.utils import TempFile, Utils
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class CMORManager(DataManager):
"""
Data manager class for CMORized experiments
"""
def __init__(self, config):
super(CMORManager, self).__init__(config)
data_folders = self.config.data_dir.split(':')
self.config.data_dir = None
for data_folder in data_folders:
if os.path.isdir(os.path.join(data_folder, self.experiment.expid)):
self.config.data_dir = data_folder
break
if not self.config.data_dir:
raise Exception('Can not find model data')
def get_file(self, domain, var, startdate, member, chunk, grid=None, box=None, frequency=None):
"""
Copies a given file from the CMOR repository to the scratch folder and returns the path to the scratch's copy
:param domain: CMOR domain
:type domain: str
:param var: variable name
:type var: str
:param startdate: file's startdate
:type startdate: str
:param member: file's member
:type member: int
:param chunk: file's chunk
:type chunk: int
:param grid: file's grid (only needed if it is not the original)
:type grid: str|NoneType
:param box: file's box (only needed to retrieve sections or averages)
:type box: Box
:param frequency: file's frequency (only needed if it is different from the default)
:type frequency: str
:return: path to the copy created on the scratch folder
:rtype: str
"""
filepath = self.get_file_path(startdate, member, domain, var, chunk, frequency, box, grid, None, None)
temp_path = TempFile.get()
Utils.copy_file(filepath, temp_path)
return temp_path
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def get_file_path(self, startdate, member, domain, var, chunk, frequency,
box=None, grid=None, year=None, date_str=None):
"""
Returns the path to a concrete file
:param startdate: file's startdate
:type startdate: str
:param member: file's member
:type member: int
:param domain: file's domain
:type domain: str
:param var: file's var
:type var: str
:param chunk: file's chunk
:type chunk: int
:param frequency: file's frequency
:type frequency: str
:param box: file's box
:type box: Box
:param grid: file's grid
:type grid: str
:param year: file's year
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:param date_str: date string to add directly. Overrides year or chunk configurations
:type date_str: str
:return: path to the file
:rtype: str
"""
if not frequency:
frequency = self.config.frequency
var = self._get_final_var_name(box, var)
folder_path = self._get_full_cmor_folder_path(startdate, member, domain, var, frequency, grid)
file_name = self._get_cmor_file_name(startdate, member, domain, var, frequency, chunk, year, date_str)
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filepath = os.path.join(folder_path, file_name)
return filepath
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def _get_cmor_file_name(self, startdate, member, domain, var, frequency, chunk, year, date_str):
domain_abreviattion = Variable.get_table_name(domain, frequency)
if chunk is not None:
time_bound = self._get_chunk_time_bounds(startdate, chunk)
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elif year:
if frequency is not 'yr':
raise ValueError('Year may be provided instead of chunk only if frequency is "yr"')
time_bound = str(year)
elif date_str:
time_bound = date_str
else:
raise ValueError('Chunk, year and date_str can not be None at the same time')
file_name = '{0}_{1}_{2}_{3}_S{4}_r{5}i1p1_{6}.nc'.format(var, domain_abreviattion, self.experiment.model,
self.experiment.experiment_name, startdate,
member + 1,
time_bound)
return file_name
def _get_full_cmor_folder_path(self, startdate, member, domain, var, frequency, grid):
folder_path = os.path.join(self._get_startdate_path(startdate), frequency, domain, var)
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if grid:
folder_path = os.path.join(folder_path, grid)
folder_path = os.path.join(folder_path, 'r{0}i1p1'.format(member + 1))
return folder_path
def _get_chunk_time_bounds(self, startdate, chunk):
start = parse_date(startdate)
chunk_start = chunk_start_date(start, chunk, self.experiment.chunk_size, 'month', 'standard')
chunk_end = chunk_end_date(chunk_start, self.experiment.chunk_size, 'month', 'standard')
chunk_end = previous_day(chunk_end, 'standard')
time_bound = "{0:04}{1:02}-{2:04}{3:02}".format(chunk_start.year, chunk_start.month, chunk_end.year,
chunk_end.month)
return time_bound
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def link_file(self, domain, var, startdate, member, chunk=None, grid=None, box=None,
frequency=None, year=None, date_str=None, move_old=False):
"""
Creates the link of a given file from the CMOR repository.
:param move_old:
:param date_str:
:param year: if frequency is yearly, this parameter is used to give the corresponding year
:type year: int
:param domain: CMOR domain
:type domain: str
:param var: variable name
:type var: str
:param startdate: file's startdate
:type startdate: str
:param member: file's member
:type member: int
:param chunk: file's chunk
:type chunk: int
:param grid: file's grid (only needed if it is not the original)
:type grid: str
:param box: file's box (only needed to retrieve sections or averages)
:type box: Box
:param frequency: file's frequency (only needed if it is different from the default)
:type frequency: str
:return: path to the copy created on the scratch folder
:rtype: str
"""
var = self._get_final_var_name(box, var)
if not frequency:
frequency = self.config.frequency
domain = DataManager.correct_domain(domain)
filepath = self.get_file_path(startdate, member, domain, var, chunk, frequency, grid, year, date_str)
self._create_link(domain, filepath, frequency, var, grid, move_old)
def send_file(self, filetosend, domain, var, startdate, member, chunk=None, grid=None, region=None,
box=None, rename_var=None, frequency=None, year=None, date_str=None, move_old=False,
diagnostic=None, cmorized=False):
"""
Copies a given file to the CMOR repository. It also automatically converts to netCDF 4 if needed and can merge
with already existing ones as needed
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:param move_old: if true, moves files following older conventions that may be found on the links folder
:type move_old: bool
:param date_str: exact date_str to use in the cmorized file
:type: str
:param year: if frequency is yearly, this parameter is used to give the corresponding year
:type year: int
:param rename_var: if exists, the given variable will be renamed to the one given by var
:type rename_var: str
:param filetosend: path to the file to send to the CMOR repository
:type filetosend: str
:param region: specifies the region represented by the file. If it is defined, the data will be appended to the
CMOR repository as a new region in the file or will overwrite if region was already present
:type region: str
:param domain: CMOR domain
:type domain: str
:param var: variable name
:type var: str
:param startdate: file's startdate
:type startdate: str
:param member: file's member
:type member: int
:param chunk: file's chunk
:type chunk: int
:param grid: file's grid (only needed if it is not the original)
:type grid: str
:param box: file's box (only needed to retrieve sections or averages)
:type box: Box
:param frequency: file's frequency (only needed if it is different from the default)
:type frequency: str
:return: path to the copy created on the scratch folder
:rtype: str
"""
original_var = var
cmor_var = Variable.get_variable(var)
var = self._get_final_var_name(box, var)
if rename_var and rename_var != var:
Utils.rename_variable(filetosend, rename_var, var)
elif original_var != var:
Utils.rename_variable(filetosend, original_var, var)
if not frequency:
frequency = self.config.frequency
domain = DataManager.correct_domain(domain)
filepath = self.get_file_path(startdate, member, domain, var, chunk, frequency, box,
grid, year, date_str)
netcdf_file = NetCDFFile(filepath, filetosend, domain, var, cmor_var)
if diagnostic:
netcdf_file.add_diagnostic_history(diagnostic)
elif cmorized:
netcdf_file.add_cmorization_history()
else:
raise ValueError('You must provide a diagnostic or set cmorized to true to store data '
'using the CMORManager')
netcdf_file.send()
self._create_link(domain, filepath, frequency, var, grid, move_old)
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def get_year(self, domain, var, startdate, member, year, grid=None, box=None):
"""
Ge a file containing all the data for one year for one variable
:param domain: variable's domain
:type domain: str
:param var: variable's name
:type var: str
:param startdate: startdate to retrieve
:type startdate: str
:param member: member to retrieve
:type member: int
:param year: year to retrieve
:type year: int
:param grid: variable's grid
:type grid: str
:param box: variable's box
:type box: Box
:return:
"""
chunk_files = list()
for chunk in self.experiment.get_year_chunks(startdate, year):
chunk_files.append(self.get_file(domain, var, startdate, member, chunk, grid=grid, box=box))
if len(chunk_files) > 1:
temp = self._merge_chunk_files(chunk_files)
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else:
temp = chunk_files[0]
temp2 = self._select_data_of_given_year(temp, year)
os.remove(temp)
return temp2
@staticmethod
def _select_data_of_given_year(data_file, year):
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temp2 = TempFile.get()
Utils.cdo.selyear(str(year), input=data_file, output=temp2)
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return temp2
@staticmethod
def _merge_chunk_files(chunk_files):
temp = TempFile.get()
Utils.nco.ncrcat(input=' '.join(chunk_files), output=temp)
for chunk_file in chunk_files:
os.remove(chunk_file)
return temp
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# noinspection PyPep8Naming
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"""
Prepares the data to be used by the diagnostic.
If CMOR data is not created, it show a warning and closes. In the future, an automatic cmorization procedure
will be launched
If CMOR data is available but packed, the procedure will unpack it.
:return:
"""
# Check if cmorized and convert if not
for startdate, member in self.experiment.get_member_list():
if not self.config.cmor.force and not self.config.cmor.force_untar and self._is_cmorized(startdate, member):
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continue
if not self._unpack_cmor_files(member):
self._cmorize_member(startdate, member)
def _is_cmorized(self, startdate, member):
startdate_path = self._get_startdate_path(startdate)
if not os.path.exists(startdate_path):
return False
for freq in os.listdir(startdate_path):
freq_path = os.path.join(startdate_path, freq)
for domain in os.listdir(freq_path):
domain_path = os.path.join(freq_path, domain)
for var in os.listdir(domain_path):
member_path = os.path.join(domain_path, var, 'r{0}i1p1'.format(member + 1))
if os.path.exists(member_path):
return True
return False
def _cmorize_member(self, startdate, member):
start_time = datetime.now()
member_str = self.experiment.get_member_str(member)
Log.info('CMORizing startdate {0} member {1}. Starting at {0}', startdate, member_str, start_time)
cmorizer = Cmorizer(self, startdate, member)
cmorizer.cmorize_ocean()
cmorizer.cmorize_atmos()
Log.result('CMORized startdate {0} member {1}!\n\n', startdate, member_str, datetime.now() - start_time)
def _unpack_cmor_files(self, startdate, member):
if self.config.cmor.force:
return False
filepaths = self._get_transferred_cmor_data_filepaths(startdate, 'tar.gz')
if len(filepaths) > 0:
Log.info('Unzipping cmorized data...')
Utils.unzip(filepaths, True)
if not os.path.exists(self.cmor_path):
os.mkdir(self.cmor_path)
filepaths = self._get_transferred_cmor_data_filepaths(startdate, 'tar')
if len(filepaths) > 0:
Log.info('Unpacking cmorized data...')
Utils.untar(filepaths, self.cmor_path)
self._correct_paths(startdate)
self._create_links(startdate)
return True
return False
def _get_transferred_cmor_data_filepaths(self, startdate, extension):
tar_path = os.path.join(self.config.data_dir, self.experiment.expid, 'original_files', 'cmorfiles')
tar_original_files = os.path.join(self.config.data_dir, 'original_files', self.experiment.expid,
'cmorfiles')
file_name = 'CMOR?_{0}_{1}_{2}_*.{3}'.format(self.experiment.expid, startdate,
self.experiment.get_member_str(member), extension)
filepaths = glob.glob(os.path.join(tar_path, file_name))
filepaths += glob.glob(os.path.join(tar_path, 'outputs', file_name))
filepaths += glob.glob(os.path.join(tar_original_files, file_name))
filepaths += glob.glob(os.path.join(tar_original_files, 'outputs', file_name))
return filepaths
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def _correct_paths(self, startdate):
self._remove_extra_output_folder()
self._fix_model_as_experiment_error(startdate)
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def _fix_model_as_experiment_error(self, startdate):
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if self.experiment.experiment_name != self.experiment.model:
bad_path = os.path.join(self.cmor_path, self.experiment.institute, self.experiment.model,
self.experiment.model)
Log.debug('Correcting double model appearance')
for (dirpath, dirnames, filenames) in os.walk(bad_path, False):
for filename in filenames:
filepath = os.path.join(dirpath, filename)
good = filepath.replace('_{0}_output_'.format(self.experiment.model),
'_{0}_{1}_S{2}_'.format(self.experiment.model,
self.experiment.experiment_name,
startdate))
good = good.replace('/{0}/{0}'.format(self.experiment.model),
'/{0}/{1}'.format(self.experiment.model,
self.experiment.experiment_name))
Utils.move_file(filepath, good)
os.rmdir(dirpath)
Log.debug('Done')
def _remove_extra_output_folder(self):
bad_path = os.path.join(self.cmor_path, 'output', self.experiment.institute)
if os.path.exists(bad_path):
Log.debug('Moving CMOR files out of the output folder')
Utils.execute_shell_command(['mv', bad_path, os.path.join(bad_path, '..', '..')])
os.rmdir(os.path.join(self.cmor_path, 'output'))
Log.debug('Done')
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def _create_links(self, startdate):
Log.info('Creating links for CMOR files ()')
path = self._get_startdate_path(startdate)
for freq in os.listdir(path):
for domain in os.listdir(os.path.join(path, freq)):
for var in os.listdir(os.path.join(path, freq, domain)):
for member in os.listdir(os.path.join(path, freq, domain, var)):
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(domain, filepath, freq, var, "", False)
else:
for filename in os.listdir(filepath):
self._create_link(domain, os.path.join(filepath, filename), freq, var, "", False)
Log.info('Creating lings for CMOR files')
def _get_startdate_path(self, startdate):
"""
Returns the path to the startdate's CMOR folder
:param startdate: target startdate
:type startdate: str
:return: path to the startdate's CMOR folder
:rtype: str
"""
return os.path.join(self.config.data_dir, self.experiment.expid, 'cmorfiles', self.experiment.institute,
self.experiment.model, self.experiment.experiment_name, 'S' + startdate)