def get_mapfile_drs(self):
try:
_cfg = SectionParser(section='config:{}'.format(self.project), directory=self.config_dir)
mapfile_drs = _cfg.get('mapfile_drs')
_cfg.reset()
except (NoConfigOption, NoConfigSection):
mapfile_drs = None
return mapfile_drs
def yield_xml_from_card(card_path):
"""
Yields XML path from run.card and config.card attributes.
:param str card_path: Directory including run.card and config.card
:returns: The XML paths to use
:rtype: *iter*
"""
# Check cards exist
if RUN_CARD not in os.listdir(card_path):
raise NoRunCardFound(card_path)
else:
run_card = os.path.join(card_path, RUN_CARD)
if CONF_CARD not in os.listdir(card_path):
raise NoConfigCardFound(card_path)
else:
conf_card = os.path.join(card_path, CONF_CARD)
# Extract config info from config.card
config = SectionParser('UserChoices')
config.read(conf_card)
xml_attrs = dict()
xml_attrs['root'] = FILEDEF_ROOT
xml_attrs['longname'] = config.get('longname').strip('"')
xml_attrs['experimentname'] = config.get('experimentname').strip('"')
if config.has_option('modelname'):
xml_attrs['modelname'] = config.get('modelname').strip('"')
else:
xml_attrs['modelname'] = 'IPSL-CM6A-LR'
xml_attrs['member'] = config.get('member').strip('"')
# Extract first and last simulated years from run.card
with open(run_card, 'r') as f:
lines = f.read().split('\n')
# Get run table without header
lines = [line for line in lines if line.count('|') == 8][1:]
year_start = int(lines[0].split()[3][:4])
year_end = int(lines[-1].split()[5][:4])
for year in range(year_start, year_end + 1):
xml_attrs['year'] = str(year)
yield FILEDEF_DIRECTORY_FORMAT.format(**xml_attrs)
def yield_xml_from_card(card_path):
"""
Yields XML path from run.card and config.card attributes.
:param str card_path: Directory including run.card and config.card
:returns: The XML paths to use
:rtype: *iter*
"""
# Check cards exist
if RUN_CARD not in os.listdir(card_path):
raise NoRunCardFound(card_path)
else:
run_card = os.path.join(card_path, RUN_CARD)
if CONF_CARD not in os.listdir(card_path):
raise NoConfigCardFound(card_path)
else:
conf_card = os.path.join(card_path, CONF_CARD)
# Extract config info from config.card
config = SectionParser('UserChoices')
config.read(conf_card)
xml_attrs = dict()
xml_attrs['root'] = FILEDEF_ROOT
xml_attrs['longname'] = config.get('longname').strip('"')
xml_attrs['experimentname'] = config.get('experimentname').strip('"')
if config.has_option('modelname'):
xml_attrs['modelname'] = config.get('modelname').strip('"')
else:
xml_attrs['modelname'] = 'IPSL-CM6A-LR'
xml_attrs['member'] = config.get('member').strip('"')
# Extract first and last simulated years from run.card
with open(run_card, 'r') as f:
lines = f.read().split('\n')
# Get run table without header
lines = [line for line in lines if line.count('|') == 8][1:]
year_start = int(lines[0].split()[3][:4])
year_end = int(lines[-1].split()[5][:4])
for year in range(year_start, year_end + 1):
xml_attrs['year'] = str(year)
yield FILEDEF_DIRECTORY_FORMAT.format(**xml_attrs)
def is_simulation_completed(card_path):
"""
Returns True if the simulation is completed.
:param str card_path: Directory including run.card
:returns: True if the simulation is completed
:rtype: *boolean*
"""
# Check cards exist
if RUN_CARD not in os.listdir(card_path):
raise NoRunCardFound(card_path)
else:
run_card = os.path.join(card_path, RUN_CARD)
# Extract info from cards
config = SectionParser('Configuration')
config.read(run_card)
return config.get('periodstate').strip('"') == 'Completed'
def is_simulation_completed(card_path):
"""
Returns True if the simulation is completed.
:param str card_path: Directory including run.card
:returns: True if the simulation is completed
:rtype: *boolean*
"""
# Check cards exist
if RUN_CARD not in os.listdir(card_path):
raise NoRunCardFound(card_path)
else:
run_card = os.path.join(card_path, RUN_CARD)
# Extract info from cards
config = SectionParser('Configuration')
config.read(run_card)
return config.get('periodstate').strip('"') == 'Completed'
class ProcessingContext(object):
"""
Encapsulates the processing context/information for main process.
:param ArgumentParser args: The command-line arguments parser
:returns: The processing context
:rtype: *ProcessingContext*
"""
def __init__(self, args):
self.pbar = args.pbar
self.config_dir = args.i
self.project = args.project
self.directory = args.directory
self.mapfile_name = args.mapfile
self.outdir = args.outdir
self.notes_title = args.tech_notes_title
self.notes_url = args.tech_notes_url
self.no_version = args.no_version
self.threads = args.max_threads
self.use_pool = (self.threads > 1)
self.dataset = args.dataset
if not args.no_cleanup:
self.clean()
self.no_cleanup = args.no_cleanup
self.no_checksum = args.no_checksum
self.dir_filter = args.ignore_dir
self.file_filter = []
if args.include_file:
self.file_filter.extend([(f, False) for f in args.include_file])
else:
# Default includes netCDF only
self.file_filter.append(('^.*\.nc$', False))
if args.exclude_file:
# Default exclude hidden files
self.file_filter.extend([(f, True) for f in args.exclude_file])
else:
self.file_filter.append(('^\..*$', True))
self.all = args.all_versions
if self.all:
self.no_version = False
self.version = None
if args.version:
self.version = 'v{}'.format(args.version)
if args.latest_symlink:
self.version = 'latest'
self.scan_errors = None
self.scan_files = None
self.scan_err_log = logging.getLogger().handlers[0].baseFilename
self.nb_map = None
def __enter__(self):
# Get checksum client
self.checksum_type = self.get_checksum_type()
# Init configuration parser
self.cfg = SectionParser(section='project:{}'.format(self.project),
directory=self.config_dir)
self.facets = self.cfg.get_facets('dataset_id')
self.pattern = self.cfg.translate('directory_format',
filename_pattern=True)
# Get mapfile DRS is set in configuration file
try:
self.mapfile_drs = self.cfg.get('mapfile_drs')
except NoConfigOption:
self.mapfile_drs = None
# Init data collector
if self.pbar:
self.sources = VersionedPathCollector(
sources=self.directory,
data=self,
dir_format=self.cfg.translate('directory_format'))
else:
self.sources = VersionedPathCollector(
sources=self.directory,
data=self,
spinner=False,
dir_format=self.cfg.translate('directory_format'))
# Init file filter
for file_filter in self.file_filter:
self.sources.FileFilter[uuid()] = file_filter
# Init dir filter
self.sources.PathFilter['base_filter'] = (self.dir_filter, True)
if self.all:
# Pick up all encountered versions by adding "/latest" exclusion
self.sources.PathFilter['version_filter'] = ('/latest', True)
elif self.version:
# Pick up the specified version only (--version flag) by adding "/v{version}" inclusion
# If --latest-symlink, --version is set to "latest"
self.sources.PathFilter['version_filter'] = '/{}'.format(
self.version)
# Init progress bar
if self.pbar:
nfiles = len(self.sources)
self.pbar = tqdm(
desc='Mapfile(s) generation',
total=nfiles,
bar_format=
'{desc}: {percentage:3.0f}% | {n_fmt}/{total_fmt} files',
ncols=100,
file=sys.stdout)
# Init threads pool
if self.use_pool:
self.pool = ThreadPool(int(self.threads))
return self
def __exit__(self, *exc):
# Close threads pool
if self.use_pool:
self.pool.close()
self.pool.join()
# Decline outputs depending on the scan results
# Raise errors when one or several files have been skipped or failed
# Default is sys.exit(0)
if self.scan_files and not self.scan_errors:
# All files have been successfully scanned
# Print number of generated mapfiles
if self.pbar:
print('{}: {} (see {})'.format('Mapfile(s) generated',
self.nb_map, self.outdir))
logging.info('{} mapfile(s) generated'.format(self.nb_map))
logging.info('==> Scan completed ({} file(s) scanned)'.format(
self.scan_files))
if not self.scan_files and not self.scan_errors:
# Results list is empty = no files scanned/found
if self.pbar:
print('No files found')
logging.warning('==> No files found')
sys.exit(1)
if self.scan_files and self.scan_errors:
# Print number of scan errors in any case
if self.pbar:
print('{}: {} (see {})'.format('Scan errors', self.scan_errors,
self.scan_err_log))
logging.warning('{} file(s) have been skipped'
' (see {})'.format(self.scan_errors,
self.scan_err_log))
if self.scan_errors == self.scan_files:
# All files have been skipped or failed during the scan
logging.warning(
'==> All files have been ignored or have failed leading to no mapfile.'
)
sys.exit(3)
else:
# Some files have been skipped or failed during the scan
logging.info('==> Scan completed ({} file(s) scanned)'.format(
self.scan_files))
sys.exit(2)
def get_checksum_type(self):
"""
Gets the checksum type to use.
Be careful to Exception constants by reading two different sections.
:returns: The checksum type
:rtype: *str*
"""
if self.no_checksum:
return None
_cfg = SectionParser(section='DEFAULT', directory=self.config_dir)
if _cfg.has_option('checksum', section='DEFAULT'):
checksum_type = _cfg.get_options_from_table(
'checksum')[0][1].lower()
else: # Use SHA256 as default because esg.ini not mandatory in configuration directory
checksum_type = 'sha256'
if checksum_type not in checksum_types:
raise InvalidChecksumType(checksum_type)
return checksum_type
def clean(self):
"""
Clean directory from incomplete mapfiles.
Incomplete mapfiles from a previous run are silently removed.
"""
for root, _, filenames in os.walk(self.outdir):
for filename in fnmatch.filter(filenames,
'*{}'.format(WORKING_EXTENSION)):
os.remove(os.path.join(root, filename))
logging.info('{} cleaned'.format(self.outdir))
class ProcessingContext(object):
"""
Encapsulates the processing context/information for main process.
:param ArgumentParser args: Parsed command-line arguments
:returns: The processing context
:rtype: *ProcessingContext*
"""
def __init__(self, args):
self.pbar = args.pbar
self.config_dir = args.i
self.directory = args.directory
self.root = os.path.normpath(args.root)
self.rescan = args.rescan
self.commands_file = args.commands_file
self.overwrite_commands_file = args.overwrite_commands_file
self.upgrade_from_latest = args.upgrade_from_latest
self.set_values = {}
if args.set_value:
self.set_values = dict(args.set_value)
self.set_keys = {}
if args.set_key:
self.set_keys = dict(args.set_key)
self.threads = args.max_threads
self.use_pool = (self.threads > 1)
self.project = args.project
self.action = args.action
if args.copy:
self.mode = 'copy'
elif args.link:
self.mode = 'link'
elif args.symlink:
self.mode = 'symlink'
else:
self.mode = 'move'
self.version = args.version
DRSPath.TREE_VERSION = 'v{}'.format(args.version)
self.scan = True
self.scan_errors = None
self.scan_files = None
self.scan_err_log = logging.getLogger().handlers[0].baseFilename
if self.commands_file and self.action != 'todo':
print '"{}" action ignores "--commands-file" argument.'.format(
self.action)
self.commands_file = None
if self.overwrite_commands_file and not self.commands_file:
print '--overwrite-commands-file ignored'
def __enter__(self):
# Get checksum client
self.checksum_type = self.get_checksum_type()
# Init configuration parser
self.cfg = SectionParser(section='project:{}'.format(self.project),
directory=self.config_dir)
# check if --commands-file argument specifies existing file
self.check_existing_commands_file()
# Warn user about unconsidered hard-coded elements
for pattern_element in self.cfg.get('directory_format').strip().split(
"/"):
if not re.match(re.compile(r'%\([\w]+\)s'), pattern_element):
msg = 'Hard-coded DRS elements (as "{}") in "directory_format"' \
'are not supported.'.format(pattern_element)
if self.pbar:
print(msg)
logging.warning(msg)
break
self.facets = self.cfg.get_facets('directory_format')
self.pattern = self.cfg.translate('filename_format')
# Init DRS tree
self.tree = DRSTree(self.root, self.version, self.mode,
self.commands_file)
# Disable file scan if a previous DRS tree have generated using same context and no "list" action
if not self.rescan and self.action != 'list' and os.path.isfile(
TREE_FILE):
reader = load(TREE_FILE)
old_args = reader.next()
# Ensure that processing context is similar to previous step
if self.check_args(old_args):
self.scan = False
# Init data collector
if self.pbar:
self.sources = Collector(sources=self.directory, data=self)
else:
self.sources = Collector(sources=self.directory,
spinner=False,
data=self)
# Init file filter
# Only supports netCDF files
self.sources.FileFilter[uuid()] = ('^.*\.nc$', False)
# And exclude hidden files
self.sources.FileFilter[uuid()] = ('^\..*$', True)
# Init progress bar
if self.pbar:
nfiles = len(self.sources)
self.pbar = tqdm(
desc='Scanning incoming files',
total=nfiles,
bar_format=
'{desc}: {percentage:3.0f}% | {n_fmt}/{total_fmt} files',
ncols=100,
file=sys.stdout)
# Init threads pool
if self.use_pool:
self.pool = ThreadPool(int(self.threads))
return self
def check_existing_commands_file(self):
"""
Check for existing commands file,
and depending on ``--overwrite-commands-file`` setting,
either delete it or throw a fatal error.
"""
if self.commands_file and os.path.exists(self.commands_file):
if self.overwrite_commands_file:
os.remove(self.commands_file)
else:
print "File '{}' already exists and '--overwrite-commands-file'" \
"option not used.".format(self.commands_file)
sys.exit(1)
def __exit__(self, *exc):
# Close threads pool
if self.use_pool:
self.pool.close()
self.pool.join()
# Decline outputs depending on the scan results
# Raise errors when one or several files have been skipped or failed
# Default is sys.exit(0)
if self.scan_files and not self.scan_errors:
# All files have been successfully scanned
logging.info('==> Scan completed ({} file(s) scanned)'.format(
self.scan_files))
if not self.scan_files and not self.scan_errors:
# Results list is empty = no files scanned/found
if self.pbar:
print('No files found')
logging.warning('==> No files found')
sys.exit(1)
if self.scan_files and self.scan_errors:
if self.scan:
msg = 'Scan errors: {} (see {})'
else:
msg = 'Orginal scan errors: {} (previously written to {})'
# Print number of scan errors in any case
if self.pbar:
print(msg.format(self.scan_errors, self.scan_err_log))
logging.warning('{} file(s) have been skipped'
' (see {})'.format(self.scan_errors,
self.scan_err_log))
if self.scan_errors == self.scan_files:
# All files have been skipped or failed during the scan
logging.warning(
'==> All files have been ignored or have failed leading to no DRS tree.'
)
sys.exit(3)
else:
# Some files have been skipped or failed during the scan
logging.info('==> Scan completed ({} file(s) scanned)'.format(
self.scan_files))
sys.exit(2)
def get_checksum_type(self):
"""
Gets the checksum type to use.
Be careful to Exception constants by reading two different sections.
:returns: The checksum type
:rtype: *str*
"""
_cfg = SectionParser(section='DEFAULT', directory=self.config_dir)
if _cfg.has_option('checksum', section='DEFAULT'):
checksum_type = _cfg.get_options_from_table(
'checksum')[0][1].lower()
else: # Use SHA256 as default because esg.ini not mandatory in configuration directory
checksum_type = 'sha256'
if checksum_type not in checksum_types:
raise InvalidChecksumType(checksum_type)
return checksum_type
def check_args(self, old_args):
"""
Checks command-line argument to avoid discrepancies between ``esgprep drs`` steps.
:param *dict* old_args: The recorded arguments
:raises Error: If one argument differs
"""
for k in CONTROLLED_ARGS:
if self.__getattribute__(k) != old_args[k]:
logging.warning(
'"{}" argument has changed: "{}" instead of "{}". '
'File rescan needed.'.format(k, self.__getattribute__(k),
old_args[k]))
return False
return True
def __enter__(self):
# Get checksum client
self.checksum_type = self.get_checksum_type()
# Init configuration parser
self.cfg = SectionParser(section='project:{}'.format(self.project), directory=self.config_dir)
self.facets = self.cfg.get_facets('dataset_id')
# Get mapfile DRS is set in configuration file
try:
_cfg = SectionParser(section='config:{}'.format(self.project), directory=self.config_dir)
self.mapfile_drs = _cfg.get('mapfile_drs')
except (NoConfigOption, NoConfigSection):
self.mapfile_drs = None
# Init data collector
if self.directory:
# The source is a list of directories
# Instantiate file collector to walk through the tree
self.source_type = 'file'
if self.pbar:
self.sources = VersionedPathCollector(sources=self.directory,
data=self,
dir_format=self.cfg.translate('directory_format'))
else:
self.sources = VersionedPathCollector(sources=self.directory,
data=self,
spinner=False,
dir_format=self.cfg.translate('directory_format'))
# Translate directory format pattern
self.pattern = self.cfg.translate('directory_format', add_ending_filename=True)
# Init file filter
for regex, inclusive in self.file_filter:
self.sources.FileFilter.add(regex=regex, inclusive=inclusive)
# Init dir filter
self.sources.PathFilter.add(regex=self.dir_filter, inclusive=False)
if self.all:
# Pick up all encountered versions by adding "/latest" exclusion
self.sources.PathFilter.add(name='version_filter', regex='/latest', inclusive=False)
elif self.version:
# Pick up the specified version only (--version flag) by adding "/v{version}" inclusion
# If --latest-symlink, --version is set to "latest"
self.sources.PathFilter.add(name='version_filter', regex='/{}'.format(self.version))
else:
# Default behavior: pick up the latest version among encountered versions
self.sources.default = True
elif self.dataset_list:
# The source is a list of dataset from a TXT file
self.source_type = 'dataset'
self.sources = DatasetCollector(sources=[x.strip() for x in self.dataset_list.readlines() if x.strip()],
data=self,
spinner=False)
# Translate dataset_id format
self.pattern = self.cfg.translate('dataset_id', add_ending_version=True, sep='.')
else:
# The source is a dataset ID (potentially from stdin)
self.source_type = 'dataset'
self.sources = DatasetCollector(sources=[self.dataset_id],
data=self,
spinner=False)
# Translate dataset_id format
self.pattern = self.cfg.translate('dataset_id', add_ending_version=True, sep='.')
# Init progress bar
nfiles = len(self.sources)
if self.pbar and nfiles:
self.pbar = tqdm(desc='Mapfile(s) generation',
total=nfiles,
bar_format='{desc}: {percentage:3.0f}% | {n_fmt}/{total_fmt} '
+ SOURCE_TYPE[self.source_type],
ncols=100,
file=sys.stdout)
# Init threads pool
if self.use_pool:
self.pool = ThreadPool(int(self.threads))
return self