# # Copyright The NOMAD Authors. # # This file is part of NOMAD. See https://nomad-lab.eu for further info. # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. # ''' This module describes all configurable parameters for the nomad python code. The configuration is used for all executed python code including API, worker, CLI, and other scripts. To use the configuration in your own scripts or new modules, simply import this module. All parameters are structured into objects for two reasons. First, to have categories. Second, to allow runtime manipulation that is not effected by python import logic. The categories are choosen along infrastructure components: ``mongo``, ``elastic``, etc. This module also provides utilities to read the configuration from environment variables and .yaml files. This is done automatically on import. The precedence is env over .yaml over defaults. .. autoclass:: nomad.config.NomadConfig .. autofunction:: nomad.config.apply .. autofunction:: nomad.config.load_config ''' import logging import os import os.path import yaml import warnings try: from nomad import gitinfo except ImportError: git_root = os.path.join(os.path.dirname(__file__), '..') cwd = os.getcwd() os.chdir(git_root) os.system('./gitinfo.sh') os.chdir(cwd) from nomad import gitinfo warnings.filterwarnings('ignore', message='numpy.dtype size changed') warnings.filterwarnings('ignore', message='numpy.ufunc size changed') class NomadConfig(dict): ''' A class for configuration categories. It is a dict subclass that uses attributes as key/value pairs. ''' def __init__(self, **kwargs): super().__init__(**kwargs) def __getattr__(self, name): if name in self: return self[name] else: raise AttributeError("No such attribute: " + name) def __setattr__(self, name, value): self[name] = value def __delattr__(self, name): if name in self: del self[name] else: raise AttributeError("No such attribute: " + name) CELERY_WORKER_ROUTING = 'worker' CELERY_QUEUE_ROUTING = 'queue' rabbitmq = NomadConfig( host='localhost', user='rabbitmq', password='rabbitmq' ) def rabbitmq_url(): return 'pyamqp://%s:%s@%s//' % (rabbitmq.user, rabbitmq.password, rabbitmq.host) celery = NomadConfig( max_memory=64e6, # 64 GB timeout=1800, # 1/2 h acks_late=True, routing=CELERY_QUEUE_ROUTING, priorities={ 'Upload.process_upload': 5, 'Upload.delete_upload': 9, 'Upload.publish_upload': 10 } ) fs = NomadConfig( tmp='.volumes/fs/tmp', staging='.volumes/fs/staging', public='.volumes/fs/public', local_tmp='/tmp', prefix_size=2, working_directory=os.getcwd() ) elastic = NomadConfig( host='localhost', port=9200, index_name='nomad_fairdi_calcs', materials_index_name='nomad_fairdi_materials' ) keycloak = NomadConfig( server_url='https://nomad-lab.eu/fairdi/keycloak/auth/', realm_name='fairdi_nomad_test', username='admin', password='password', client_id='nomad_public', client_secret=None, oasis=False) mongo = NomadConfig( host='localhost', port=27017, db_name='nomad_fairdi' ) logstash = NomadConfig( enabled=False, host='localhost', tcp_port='5000', level=logging.DEBUG ) services = NomadConfig( api_host='localhost', api_port=8000, api_base_path='/fairdi/nomad/latest', api_secret='defaultApiSecret', api_chaos=0, admin_user_id='00000000-0000-0000-0000-000000000000', not_processed_value='not processed', unavailable_value='unavailable', https=False, https_upload=False, upload_limit=10, force_raw_file_decoding=False, download_scan_size=500, download_scan_timeout=u'30m' ) oasis = NomadConfig( central_nomad_api_url='https://nomad-lab.eu/prod/rae/api', central_nomad_deployment_id='nomad-lab.eu/prod/rae' ) tests = NomadConfig( default_timeout=30 ) def api_url(ssl: bool = True, api: str = 'api'): base_url = '%s://%s/%s' % ( 'https' if services.https and ssl else 'http', services.api_host.strip('/'), services.api_base_path.strip('/')) return '%s/%s' % (base_url.strip('/'), api) def gui_url(page: str = None): base = api_url(True)[:-3] if base.endswith('/'): base = base[:-1] if page is not None: return '%s/gui/%s' % (base, page) return '%s/gui' % base def check_config(): """Used to check that the current configuration is valid. Should only be called once after the final config is loaded. Raises: AssertionError: if there is a contradiction or invalid values in the config file settings. """ # The AFLOW symmetry information is checked once on import proto_symmetry_tolerance = normalize.prototype_symmetry_tolerance symmetry_tolerance = normalize.symmetry_tolerance if proto_symmetry_tolerance != symmetry_tolerance: raise AssertionError( "The AFLOW prototype information is outdated due to changed tolerance " "for symmetry detection. Please update the AFLOW prototype information " "by running the CLI command 'nomad admin ops prototype-update " "--matches-only'." ) if normalize.springer_db_path and not os.path.exists(normalize.springer_db_path): normalize.springer_db_path = None mail = NomadConfig( enabled=False, with_login=False, host='', port=8995, user='', password='', from_address='support@nomad-lab.eu', cc_address='support@nomad-lab.eu' ) normalize = NomadConfig( # The system size limit for running the dimensionality analysis. For very # large systems the dimensionality analysis will get too expensive. system_classification_with_clusters_threshold=64, # Symmetry tolerance controls the precision used by spglib in order to find # symmetries. The atoms are allowed to move 1/2*symmetry_tolerance from # their symmetry positions in order for spglib to still detect symmetries. # The unit is angstroms. The value of 0.1 is used e.g. by Materials Project # according to # https://pymatgen.org/pymatgen.symmetry.analyzer.html#pymatgen.symmetry.analyzer.SpacegroupAnalyzer symmetry_tolerance=0.1, # The symmetry tolerance used in aflow prototype matching. Should only be # changed before re-running the prototype detection. prototype_symmetry_tolerance=0.1, # Maximum number of atoms in the single cell of a 2D material for it to be # considered valid. max_2d_single_cell_size=7, # The distance tolerance between atoms for grouping them into the same # cluster. Used in detecting system type. cluster_threshold=2.5, # Defines the "bin size" for rounding cell angles for the material hash angle_rounding=float(10.0), # unit: degree # The threshold for a system to be considered "flat". Used e.g. when # determining if a 2D structure is purely 2-dimensional to allow extra rigid # transformations that are improper in 3D but proper in 2D. flat_dim_threshold=0.1, # The threshold for point equality in k-space. Unit: 1/m. k_space_precision=150e6, # The energy threshold for how much a band can be on top or below the fermi # level in order to detect a gap. Unit: Joule. band_structure_energy_tolerance=1.6022e-20, # 0.1 eV springer_db_path=os.path.join( os.path.dirname(os.path.abspath(__file__)), 'normalizing/data/springer.msg' ) ) paths = NomadConfig( similarity="", ) client = NomadConfig( user='leonard.hofstadter@nomad-fairdi.tests.de', password='password', url='http://nomad-lab.eu/prod/rae/api' ) datacite = NomadConfig( mds_host='https://mds.datacite.org', enabled=False, prefix='10.17172', user='*', password='*' ) meta = NomadConfig( version='0.9.9', commit=gitinfo.commit, release='devel', default_domain='dft', service='unknown nomad service', name='novel materials discovery (NOMAD)', description='A FAIR data sharing platform for materials science data', homepage='https://nomad-lab.eu', source_url='https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR', maintainer_email='markus.scheidgen@physik.hu-berlin.de', deployment_id='nomad-lab.eu/prod/rae' ) gitlab = NomadConfig( private_token='not set' ) auxfile_cutoff = 100 parser_matching_size = 150 * 80 # 150 lines of 80 ASCII characters per line console_log_level = logging.WARNING max_upload_size = 32 * (1024 ** 3) raw_file_strip_cutoff = 1000 use_empty_parsers = False reprocess_unmatched = True metadata_file_name = 'nomad' metadata_file_extensions = ('json', 'yaml', 'yml') def normalize_loglevel(value, default_level=logging.INFO): plain_value = value if plain_value is None: return default_level else: try: return int(plain_value) except ValueError: return getattr(logging, plain_value) transformations = { 'console_log_level': normalize_loglevel, 'logstash_level': normalize_loglevel } # use std python logger, since logging is not configured while loading configuration logger = logging.getLogger(__name__) def apply(key, value) -> None: ''' Changes the config according to given key and value. The keys are interpreted as paths to config values with ``_`` as a separator. E.g. ``fs_staging`` leading to ``config.fs.staging`` ''' path = list(reversed(key.split('_'))) child_segment = None current_value = None child_config = globals() child_key = None try: while len(path) > 0: if child_segment is None: child_segment = path.pop() else: child_segment += '_' + path.pop() if child_segment in child_config: current_value = child_config[child_segment] if current_value is None: if len(path) == 0: raise KeyError continue if isinstance(current_value, NomadConfig): child_config = current_value current_value = None child_segment = None else: if len(path) > 0: raise KeyError() child_key = child_segment break if child_key is None or current_value is None: raise KeyError() except KeyError: return if not isinstance(value, type(current_value)): try: value = transformations.get(key, type(current_value))(value) except Exception as e: logger.error( 'config key %s value %s has wrong type: %s' % (key, str(value), str(e))) child_config[child_key] = value def load_config(config_file: str = os.environ.get('NOMAD_CONFIG', 'nomad.yaml')) -> None: ''' Loads the configuration from the ``config_file`` and environment. Arguments: config_file: Override the configfile, default is file stored in env variable NOMAD_CONFIG or ``nomad.yaml``. ''' # load yaml and override defaults (only when not in test) if os.path.exists(config_file): with open(config_file, 'r') as stream: try: config_data = yaml.load(stream, Loader=getattr(yaml, 'FullLoader')) except yaml.YAMLError as e: logger.error('cannot read nomad config', exc_info=e) def adapt(config, new_config, child_key=None): for key, value in new_config.items(): if key in config: if child_key is None: qualified_key = key else: qualified_key = '%s_%s' % (child_key, key) current_value = config[key] if isinstance(value, dict) and isinstance(current_value, NomadConfig): adapt(current_value, value, qualified_key) else: if not isinstance(value, type(current_value)): try: value = transformations.get(qualified_key, type(current_value))(value) except Exception as e: logger.error( 'config key %s value %s has wrong type: %s' % (key, str(value), str(e))) else: config[key] = value logger.debug('override config key %s with value %s' % (key, str(value))) else: logger.error('config key %s does not exist' % key) if config_data is not None: adapt(globals(), config_data) # load env and override yaml and defaults kwargs = { key[len('NOMAD_'):].lower(): value for key, value in os.environ.items() if key.startswith('NOMAD_') } for key, value in kwargs.items(): apply(key, value) check_config() load_config()