Source code for jwst.associations.association

from import MutableMapping
from copy import deepcopy
from datetime import datetime
import json
import jsonschema
import logging
import re
import os
import warnings

from . import __version__
from .exceptions import (
from .lib.constraint import (
from stpipe.format_template import FormatTemplate
from .lib.ioregistry import IORegistry

__all__ = ['Association']

# Configure logging
logger = logging.getLogger(__name__)

# Timestamp template

[docs]class Association(MutableMapping): """Association Base Class Parameters ---------- version_id : str or None Version ID to use in the name of this association. If None, nothing is added. Raises ------ AssociationError If an item doesn't match. Attributes ---------- instance : dict-like The instance is the association data structure. See `data` below meta : dict Information about the association. data : dict The association. The format of this data structure is determined by the individual associations and, if defined, validated against their specified schema. schema_file : str The name of the output schema that an association must adhere to. """ registry = None """Registry this rule has been placed in.""" DEFAULT_FORCE_UNIQUE = False """Default whether to force constraints to use unique values.""" DEFAULT_REQUIRE_CONSTRAINT = True """Default require that the constraint exists or otherwise can be explicitly checked. """ DEFAULT_EVALUATE = False """Default do not evaluate input values""" GLOBAL_CONSTRAINT = None """Global constraints""" INVALID_VALUES = None """Attribute values that indicate the attribute is not specified. """ ioregistry = IORegistry() """The association IO registry""" def __init__( self, version_id=None, ): = dict() self.run_init_hook = True self.meta = {} self.version_id = version_id{ 'asn_type': 'None', 'asn_rule': self.asn_rule, 'version_id': self.version_id, 'code_version': __version__, }) # Setup constraints # These may be predefined by a rule. try: constraints = self.constraints except AttributeError: constraints = Constraint() if self.GLOBAL_CONSTRAINT is not None: constraints.append(self.GLOBAL_CONSTRAINT.copy()) self.constraints = constraints
[docs] @classmethod def create(cls, item, version_id=None): """Create association if item belongs Parameters ---------- item : dict The item to initialize the association with. version_id : str or None Version ID to use in the name of this association. If None, nothing is added. Returns ------- (association, reprocess_list) 2-tuple consisting of: - association or None: The association or, if the item does not match this rule, None - [ProcessList[, ...]]: List of items to process again. """ asn = cls(version_id=version_id) matches, reprocess = asn.add(item) if not matches: return None, reprocess return asn, reprocess
@property def asn_name(self): """Suggest filename for the association""" return 'unnamed_association' @classmethod def _asn_rule(cls): return cls.__name__ @property def asn_rule(self): """Name of the rule""" return self._asn_rule()
[docs] @classmethod def validate(cls, asn): """Validate an association against this rule Parameters ---------- asn : Association or association-like The association structure to examine Returns ------- valid : bool True if valid. Otherwise the `AssociationNotValidError` is raised Raises ------ AssociationNotValidError If there is some reason validation failed. Notes ----- The base method checks against the rule class' schema If the rule class does not define a schema, a warning is issued but the routine will return True. """ if not hasattr(cls, 'schema_file'): logger.warning( 'Cannot validate: {} has no schema. Presuming OK.'.format(cls) ) return True if isinstance(asn, cls): asn_data = else: asn_data = asn with open(cls.schema_file, 'r') as schema_file: asn_schema = json.load(schema_file) try: jsonschema.validate(asn_data, asn_schema) except (AttributeError, jsonschema.ValidationError) as err: logger.debug('Validation failed:\n%s', err) raise AssociationNotValidError('Validation failed') from err # Validate no path data for expnames for product in asn_data["products"]: members = product['members'] for member in members: fpath, fname = os.path.split(member["expname"]) if len(fpath) > 0: err_str = "'expname' contains path, but should only be a filename." err_str += " All input files should be in a single directory" err_str += ", so no path is needed." logger.debug(err_str) warnings.warn(err_str, UserWarning) return True
[docs] def dump(self, format='json', **kwargs): """Serialize the association Parameters ---------- format : str The format to use to dump the association into. kwargs : dict List of arguments to pass to the registered routines for the current association type. Returns ------- (name, serialized): Tuple where the first item is the suggested base name for the file. Second item is the serialization. Raises ------ AssociationError If the operation cannot be done AssociationNotValidError If the given association does not validate. """ if self.is_valid: return self.ioregistry[format].dump(self, **kwargs) else: raise AssociationNotValidError( 'Association {} is not valid'.format(self) )
[docs] @classmethod def load( cls, serialized, format=None, validate=True, **kwargs ): """Marshall a previously serialized association Parameters ---------- serialized : object The serialized form of the association. format : str or None The format to force. If None, try all available. validate : bool Validate against the class' defined schema, if any. kwargs : dict Other arguments to pass to the `load` method Returns ------- association : Association The association. Raises ------ AssociationNotValidError Cannot create or validate the association. Notes ----- The `serialized` object can be in any format supported by the registered I/O routines. For example, for `json` and `yaml` formats, the input can be either a string or a file object containing the string. """ if format is None: formats = [ format_func for format_name, format_func in cls.ioregistry.items() ] else: formats = [cls.ioregistry[format]] for format_func in formats: try: asn = format_func.load( cls, serialized, **kwargs ) except AssociationNotValidError: continue else: break else: raise AssociationNotValidError( 'Cannot translate "{}" to an association'.format(serialized) ) # Validate if validate: cls.validate(asn) return asn
@property def is_valid(self): """Check if association is valid""" try: self.__class__.validate(self) except AssociationNotValidError: return False return True
[docs] def add(self, item, check_constraints=True): """Add the item to the association Parameters ---------- item : dict The item to add. check_constraints : bool If True, see if the item should belong to this association. If False, just add it. Returns ------- (match, reprocess_list) 2-tuple consisting of: - bool : True if match - [ProcessList[, ...]]: List of items to process again. """ if self.is_item_member(item): return True, [] match = not check_constraints if check_constraints: match, reprocess = self.check_and_set_constraints(item) if match: if self.run_init_hook: self._init_hook(item) self.run_init_hook = False self._add(item) # If a constraint `force_match` exists, set the `match` # result to the value of the constraint. try: force_match = self.constraints['force_match'].value except (KeyError, TypeError): pass else: if force_match is not None: match = force_match return match, reprocess
[docs] def check_and_set_constraints(self, item): """Check whether the given dictionaries match parameters for for this association Parameters ---------- item : dict The parameters to check/set for this association. This can be a list of dictionaries. Returns ------- (match, reprocess) 2-tuple consisting of: - bool : Did constraint match? - [ProcessItem[, ...]]: List of items to process again. """ cached_constraints = deepcopy(self.constraints) match, reprocess = cached_constraints.check_and_set(item) if match: self.constraints = cached_constraints # Set the association type for all reprocessed items. for process_list in reprocess: if process_list.rules is None: process_list.rules = [type(self)] return match, reprocess
[docs] def match_constraint(self, item, constraint, conditions): """Generic constraint checking Parameters ---------- item : dict The item to retrieve the values from constraint : str The name of the constraint conditions : dict The conditions structure Returns ------- (matches, reprocess_list) 2-tuple consisting of: - bool : True if the all constraints are satisfied - [ProcessList[, ...]]: List of items to process again. """ reprocess = [] evaled_str = conditions['inputs'](item) if conditions['value'] is not None: if not meets_conditions( evaled_str, conditions['value'] ): return False, reprocess # At this point, the constraint has passed. # Fix the conditions. escaped_value = re.escape(evaled_str) conditions['found_values'].add(escaped_value) if conditions['value'] is None or \ conditions.get('force_unique', self.DEFAULT_FORCE_UNIQUE): conditions['value'] = escaped_value conditions['force_unique'] = False # That's all folks return True, reprocess
[docs] def finalize(self): """Finalize association Finalize or close-off this association. Perform validations, modifications, etc. to ensure that the association is complete. Returns ------- associations : [association[, ...]] or None List of fully-qualified associations that this association represents. `None` if a complete association cannot be produced. """ if self.is_valid: return [self] else: return None
[docs] def is_item_member(self, item): """Check if item is already a member of this association Parameters ---------- item : dict The item to add. Returns ------- is_item_member : bool True if item is a member. """ raise NotImplementedError( 'Association.is_item_member must be implemented by a specific association rule.' )
def _init_hook(self, item): """Post-check and pre-item-adding initialization.""" pass def _add(self, item): """Add a item, association-specific""" raise NotImplementedError( 'Association._add must be implemented by a specific association rule.' ) def _add_items(self, items, **kwargs): """ Force adding items to the association Parameters ---------- items : [object[, ...]] A list of items to make members of the association. Notes ----- This is a low-level shortcut into adding members, such as file names, to an association. All defined shortcuts and other initializations are by-passed, resulting in a potentially unusable association. """ try: self['members'].update(items) except KeyError: self['members'] = items # ################################################# # Methods required for implementing MutableMapping # ################################################# def __getitem__(self, key): return[self.__keytransform__(key)] def __setitem__(self, key, value):[self.__keytransform__(key)] = value def __delitem__(self, key): del[self.__keytransform__(key)] def __iter__(self): return iter( def __len__(self): return len( def __keytransform__(self, key): return key
[docs] def keys(self): return
[docs] def items(self): return
[docs] def values(self): return
# ######### # Utilities # ######### def finalize(asns): """Finalize associations by calling their `finalize_hook` method Notes ----- This is a functioning example of a finalize callback, and can be used as the generic callback. Suggested usage is as follows: .. code-block:: python from jwst.associations.association import finalize as generic_finalize RegistryMarker.callback('finalize')(generic_finalize) """ finalized_asns = list(filter( lambda asn: asn is not None, map(lambda asn: asn.finalize(), asns) )) return finalized_asns def make_timestamp(): timestamp = datetime.utcnow().strftime( _TIMESTAMP_TEMPLATE ) return timestamp # Define default product name filling format_product = FormatTemplate()