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#!/usr/bin/env python
import argparse
import shutil
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import pkg_resources
import netCDF4
from bscearth.utils.date import *
from earthdiagnostics.constants import Basins
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from earthdiagnostics.cmormanager import CMORManager
from earthdiagnostics.threddsmanager import THREDDSManager
from earthdiagnostics.obsreconmanager import ObsReconManager
from earthdiagnostics.variable import VariableManager
from distutils.spawn import find_executable
:param config_file: path to the configuration file
:type config_file: str
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# Get the version number from the relevant file. If not, from autosubmit package
scriptdir = os.path.abspath(os.path.dirname(__file__))
if not os.path.exists(os.path.join(scriptdir, 'VERSION')):
scriptdir = os.path.join(scriptdir, os.path.pardir)
version_path = os.path.join(scriptdir, 'VERSION')
readme_path = os.path.join(scriptdir, 'README')
changes_path = os.path.join(scriptdir, 'CHANGELOG')
documentation_path = os.path.join(scriptdir, 'EarthDiagnostics.pdf')
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if os.path.isfile(version_path):
with open(version_path) as f:
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version = f.read().strip()
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version = pkg_resources.require("earthdiagnostics")[0].version
def __init__(self, config_file):
Log.info('Initialising Earth Diagnostics Version {0}', EarthDiags.version)
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self.config = Config(config_file)
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TempFile.scratch_folder = self.config.scratch_dir
cdftools.path = self.config.cdftools_path
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self.time = dict()
self.data_manager = None
self.threads = None
self.had_errors = False
Log.info('Running diags for experiment {0}, startdates {1}, members {2}', self.config.experiment.expid,
self.config.experiment.startdates, self.config.experiment.members)
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@staticmethod
def parse_args():
"""
Entry point for the Earth Diagnostics. For more detailed documentation, use -h option
"""
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# try:
parser = argparse.ArgumentParser(description='Main executable for Earth Diagnostics.')
parser.add_argument('-v', '--version', action='version', version=EarthDiags.version,
help="returns Earth Diagnostics's version number and exit")
parser.add_argument('--doc', action='store_true',
help="opens documentation and exits")
parser.add_argument('--clean', action='store_true',
help="clean the scratch folder and exits")
parser.add_argument('--report', action='store_true',
help="generates a report about the available files")
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parser.add_argument('-lf', '--logfile', choices=('EVERYTHING', 'DEBUG', 'INFO', 'RESULT', 'USER_WARNING',
'WARNING', 'ERROR', 'CRITICAL', 'NO_LOG'),
default='DEBUG', type=str,
help="sets file's log level.")
parser.add_argument('-lc', '--logconsole', choices=('EVERYTHING', 'DEBUG', 'INFO', 'RESULT', 'USER_WARNING',
'WARNING', 'ERROR', 'CRITICAL', 'NO_LOG'),
default='INFO', type=str,
help="sets console's log level")
parser.add_argument('-log', '--logfilepath', default=None, type=str)
parser.add_argument('-f', '--configfile', default='diags.conf', type=str)
args = parser.parse_args()
if args.doc:
Log.info('Opening documentation...')
doc_path = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'EarthDiagnostics.pdf')
Utils.execute_shell_command(('xdg-open', doc_path))
Log.result('Documentation opened!')
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Log.set_console_level(args.logconsole)
Log.set_file_level(args.logfile)
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if Log.console_handler.level <= Log.DEBUG:
Utils.cdo.debug = True
Utils.nco.debug = False # This is due to a bug in nco. Must change when it's solved
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Utils.cdo.CDO = find_executable('cdo')
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if args.logfilepath:
Log.set_file(bscearth.utils.path.expand_path(args.logfilepath))
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config_file_path = bscearth.utils.path.expand_path(args.configfile)
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if not os.path.isfile(config_file_path):
Log.critical('Configuration file {0} can not be found', config_file_path)
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return False
try:
diags = EarthDiags(config_file_path)
if args.clean:
result = diags.clean()
elif args.report:
result = diags.report()
else:
result = diags.run()
finally:
TempFile.clean()
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def _create_dic_variables(self):
self.dic_variables = dict()
self.dic_variables['x'] = 'i'
self.dic_variables['y'] = 'j'
self.dic_variables['z'] = 'lev'
self.dic_variables['nav_lon'] = 'lon'
self.dic_variables['nav_lat'] = 'lat'
self.dic_variables['nav_lev'] = 'lev'
self.dic_variables['time_counter'] = 'time'
self.dic_variables['t'] = 'time'
self.had_errors = False
Log.debug('Using netCDF version {0}', netCDF4.getlibversion())
# Run diagnostics
Log.info('Running diagnostics')
work_manager = WorkManager(self.config, self.data_manager)
work_manager.prepare_job_list()
result = work_manager.run()
if self.config.auto_clean:
self._remove_scratch_dir()
self._read_basins_from_file('mask_regions.nc')
self._read_basins_from_file('mask_regions.3d.nc')
@staticmethod
def _read_basins_from_file(filename):
if not os.path.isfile(filename):
return
handler = Utils.openCdf(filename)
Basins().get_available_basins(handler)
handler.close()
def _prepare_scratch_dir(self):
if self.config.use_ramdisk:
self._remove_scratch_dir()
tempfile.mkdtemp(dir='/dev/shm')
os.symlink(tempfile.mkdtemp(dir='/dev/shm'), self.config.scratch_dir)
else:
if not os.path.exists(self.config.scratch_dir):
os.makedirs(self.config.scratch_dir)
os.chdir(self.config.scratch_dir)
def _prepare_data_manager(self):
if self.config.data_adaptor == 'CMOR':
self.data_manager = CMORManager(self.config)
elif self.config.data_adaptor == 'THREDDS':
self.data_manager = THREDDSManager(self.config)
elif self.config.data_adaptor == 'OBSRECON':
self.data_manager = ObsReconManager(self.config)
def clean(self):
Log.info('Removing scratch folder...')
Log.result('Scratch folder removed')
def _remove_scratch_dir(self):
if os.path.islink(self.config.scratch_dir):
shutil.rmtree(os.path.realpath(self.config.scratch_dir))
os.remove(self.config.scratch_dir)
elif os.path.isdir(self.config.scratch_dir):
shutil.rmtree(self.config.scratch_dir)
def report(self):
Log.info('Looking for existing vars...')
self._prepare_data_manager()
base_folder = self.config.report.path
if not base_folder:
base_folder = self.config.scratch_dir
Utils.create_folder_tree(base_folder)
for startdate in self.config.experiment.startdates:
for member in self.config.experiment.members:
results = self._get_variable_report(startdate, member)
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'{0}_{1}.report'.format(startdate,
self.config.experiment.get_member_str(member)))
self.create_report(report_path, results)
Log.result('Report finished')
return True
def _get_variable_report(self, startdate, member):
var_manager = VariableManager()
results = list()
for var in var_manager.get_all_variables():
for table, priority in var.tables:
if priority is None or priority > self.config.report.maximum_priority:
continue
if not self.data_manager.file_exists(var.domain, var.short_name, startdate, member, 1,
frequency=table.frequency):
Log.debug('Variable {0.short_name} not found in {1.name}', var, table)
else:
Log.result('Variable {0.short_name} found in {1.name}', var, table)
@staticmethod
def create_report(report_path, results):
tables = set([result[1].name for result in results])
for table in tables:
file_handler = open('{0}.{1}'.format(report_path, table), 'w')
table_results = [result for result in results if result[1].name == table]
file_handler.write('\nTable {0}\n'.format(table))
file_handler.write('===================================\n')
priorities = set([result[2] for result in table_results])
priorities = sorted(priorities)
for priority in priorities:
priority_results = [result[0] for result in table_results if result[2] == priority]
priority_results = sorted(priority_results, key=lambda v: v.short_name)
file_handler.write('\nMissing variables with priority {0}:\n'.format(priority))
file_handler.write('--------------------------------------\n')
file_handler.write('{0:12}: {1}\n'.format(var.short_name, var.standard_name))
def _prepare_mesh_files(self):
model_version = self.config.experiment.model_version
if not model_version:
Log.info('No model version defined. Skipping mesh files copy!')
return
Log.info('Copying mesh files')
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con_files = self.config.con_files
model_version = self.config.experiment.model_version
restore_meshes = self.config.restore_meshes
mesh_mask = 'mesh_mask_nemo.{0}.nc'.format(model_version)
new_mask_glo = 'new_maskglo.{0}.nc'.format(model_version)
mask_regions = 'mask.regions.{0}.nc'.format(model_version)
mask_regions_3d = 'mask.regions.3d.{0}.nc'.format(model_version)
if self.config.mesh_mask:
mesh_mask_path = self.config.mesh_mask
else:
mesh_mask_path = os.path.join(con_files, mesh_mask)
if self.config.new_mask_glo:
new_mask_glo_path = self.config.new_mask_glo
else:
new_mask_glo_path = os.path.join(con_files, new_mask_glo)
if self.config.mask_regions:
mask_regions_path = self.config.mask_regions
else:
mask_regions_path = os.path.join(con_files, mask_regions)
if self.config.mask_regions_3d:
mask_regions_3d_path = self.config.mask_regions_3d
else:
mask_regions_3d_path = os.path.join(con_files, mask_regions_3d)
if self.config.scratch_masks:
Utils.create_folder_tree(self.config.scratch_masks)
Utils.give_group_write_permissions(self.config.scratch_masks)
mesh_mask_scratch_path = os.path.join(self.config.scratch_masks, mesh_mask)
if self._copy_file(mesh_mask_path, mesh_mask_scratch_path,
restore_meshes):
Utils.give_group_write_permissions(mesh_mask_scratch_path)
self._link_file(mesh_mask_scratch_path, 'mesh_hgr.nc')
self._link_file(mesh_mask_scratch_path, 'mesh_zgr.nc')
self._link_file(mesh_mask_scratch_path, 'mask.nc')
new_maskglo_scratch_path = os.path.join(self.config.scratch_masks, new_mask_glo)
if self._copy_file(new_mask_glo_path,
new_maskglo_scratch_path, restore_meshes):
Utils.give_group_write_permissions(new_maskglo_scratch_path)
self._link_file(new_maskglo_scratch_path, 'new_maskglo.nc')
mask_regions_scratch_path = os.path.join(self.config.scratch_masks, mask_regions)
if self._copy_file(mask_regions_path,
mask_regions_scratch_path, restore_meshes):
Utils.give_group_write_permissions(mask_regions_scratch_path)
self._link_file(mask_regions_scratch_path, 'mask_regions.nc')
mask_regions3d_scratch_path = os.path.join(self.config.scratch_masks, mask_regions_3d)
if self._copy_file(mask_regions_3d_path,
mask_regions3d_scratch_path, restore_meshes):
Utils.give_group_write_permissions(mask_regions3d_scratch_path)
self._link_file(mask_regions3d_scratch_path, 'mask_regions.3d.nc')
self._copy_file(mesh_mask_path, 'mesh_hgr.nc', restore_meshes)
self._link_file('mesh_hgr.nc', 'mesh_zgr.nc')
self._link_file('mesh_hgr.nc', 'mask.nc')
self._copy_file(new_mask_glo_path, 'new_maskglo.nc',
restore_meshes)
self._copy_file(mask_regions_path,
'mask_regions.nc', restore_meshes)
self._copy_file(mask_regions_3d_path,
'mask_regions.3d.nc', restore_meshes)
def _copy_file(self, source, destiny, force):
if not os.path.exists(source):
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Log.user_warning('File {0} is not available for {1}', destiny, self.config.experiment.model_version)
return False
if not force and os.path.exists(destiny):
if os.stat(source).st_size == os.stat(destiny).st_size:
Log.info('File {0} already exists', destiny)
return True
shutil.copy(source, destiny)
Log.info('File {0} ready', destiny)
Utils.rename_variables(destiny, self.dic_variables, False, True)
return True
def _link_file(self, source, destiny):
if not os.path.exists(source):
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Log.user_warning('File {0} is not available for {1}', destiny, self.config.experiment.model_version)
try:
os.remove(destiny)
except OSError:
pass
os.symlink(source, destiny)
Log.info('File {0} ready', destiny)
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if not EarthDiags.parse_args():
exit(1)
if __name__ == "__main__":