def read_sdf_item(self, parsing_results):
"""
:param parsing_results: sth like
(Pdb) parsing_results
(['DSSTox_RID', '22308'], {})
"""
# for now just assuming the data header (e.g. DSSTox_RID) is URI-safe
header = parsing_results[0]
value = ' '.join(parsing_results[1:])
# if header == 'ActivityOutcome_NCTRER':
# print('%s\t%s' % (value, str(self._curr_res)))
# if header.startswith('Activity'):
# return
contains_dot = '.' in value
is_negative = value.strip().startswith('-')
if is_negative:
tmp = value.strip()[1:]
else:
tmp = value.strip()
is_num = tmp.replace('.', '').isnumeric()
if is_num and contains_dot:
dtype = self.xsd_double
elif is_num and not is_negative:
dtype = self.xsd_nnint
elif is_num and is_negative:
dtype = self.xsd_int
else:
dtype = XSD.term('string')
prop = self._register_and_build_property(header, dtype)
if self._props_data.get(prop) is None:
self._props_data[prop] = []
self._props_data[prop].append((self._curr_res, value))
# -*- coding: utf-8 -*-
"""
https://www.w3.org/TR/shacl/#core-components-value-type
"""
import rdflib
from datetime import date, time, datetime
from rdflib.term import Literal
from rdflib.namespace import RDF, XSD
from pyshacl.constraints.constraint_component import ConstraintComponent
from pyshacl.consts import SH, RDFS_subClassOf, RDF_type,\
SH_IRI, SH_BlankNode, SH_Literal, SH_IRIOrLiteral, SH_BlankNodeOrIRI,\
SH_BlankNodeORLiteral
from pyshacl.errors import ConstraintLoadError
RDF_langString = RDF.term('langString')
XSD_string = XSD.term('string')
XSD_integer = XSD.term('integer')
XSD_float = XSD.term('float')
XSD_boolean = XSD.term('boolean')
XSD_date = XSD.term('date')
XSD_time = XSD.term('time')
XSD_dateTime = XSD.term('dateTime')
SH_class = SH.term('class')
SH_datatype = SH.term('datatype')
SH_nodeKind = SH.term('nodeKind')
SH_ClassConstraintComponent = SH.term('ClassConstraintComponent')
SH_DatatypeConstraintComponent = SH.term('DatatypeConstraintComponent')
SH_NodeKindConstraintComponent = SH.term('NodeKindConstraintComponent')
"""
https://www.w3.org/TR/shacl/#core-components-count
"""
from typing import Dict, List
from rdflib.namespace import XSD
from rdflib.term import Literal
from pyshacl.constraints.constraint_component import ConstraintComponent
from pyshacl.consts import SH
from pyshacl.errors import ConstraintLoadError
from pyshacl.pytypes import GraphLike
from pyshacl.rdfutil import stringify_node
XSD_integer = XSD.term('integer')
SH_minCount = SH.term('minCount')
SH_maxCount = SH.term('maxCount')
SH_MinCountConstraintComponent = SH.term('MinCountConstraintComponent')
SH_MaxCountConstraintComponent = SH.term('MaxCountConstraintComponent')
class MinCountConstraintComponent(ConstraintComponent):
"""
sh:minCount specifies the minimum number of value nodes that satisfy the condition. If the minimum cardinality value is 0 then this constraint is always satisfied and so may be omitted.
Link:
https://www.w3.org/TR/shacl/#MinCountConstraintComponent
Textual Definition:
If the number of value nodes is less than $minCount, there is a validation result.
"""
# -*- coding: utf-8 -*-
from rdflib import Literal
from rdflib.namespace import XSD
from pyshacl.rdfutil import clone_graph
from pyshacl.shape import Shape
from pyshacl.errors import RuleLoadError, ReportableRuntimeError
from pyshacl.consts import SH_construct
from pyshacl.sparql_query_helper import SPARQLQueryHelper
from pyshacl.rules.shacl_rule import SHACLRule
XSD_string = XSD.term('string')
class SPARQLRule(SHACLRule):
__slots__ = ("_constructs", "_qh")
def __init__(self, shape, rule_node):
"""
:param shape:
:type shape: Shape
:param rule_node:
:type rule_node: rdflib.Identifier
"""
super(SPARQLRule, self).__init__(shape, rule_node)
construct_nodes = set(self.shape.sg.objects(self.node, SH_construct))
if len(construct_nodes) < 1:
raise RuleLoadError("No sh:construct on SPARQLRule",
"https://www.w3.org/TR/shacl-af/#SPARQLRule")
self._constructs = []
def _init_ontology(self):
# ---------------------- basic vocabulary elements --------------------
self.xsd_nnint = XSD.term('nonNegativeInteger')
self.xsd_int = XSD.term('integer')
self.xsd_bool = XSD.term('boolean')
self.xsd_double = XSD.term('double')
a = RDF.term('type')
rdfs_dom = RDFS.term('domain')
rdfs_rnge = RDFS.term('range')
rdfs_subcls_of = RDFS.term('subClassOf')
owl_class = OWL.term('Class')
owl_dtype_prop = OWL.term('DatatypeProperty')
owl_obj_prop = OWL.term('ObjectProperty')
# --------------------------- basic classes ---------------------------
# dllont:Molecule
self.cls_molecule = URIRef(self._ont_uri_prefix + 'Molecule')
self._g.add((self.cls_molecule, a, owl_class))
# dllont:Atom
self.cls_atom = URIRef(self._ont_uri_prefix + 'Atom')
self._g.add((self.cls_atom, a, owl_class))
# dllont:AtomSymbol
self.cls_atom_symbol = URIRef(self._ont_uri_prefix + 'AtomSymbol')
self._g.add((self.cls_atom_symbol, a, owl_class))
# ----------------- atom stereo parity class hierarchy ----------------
# dllont:AtomParity
cls_atom_parity = URIRef(self._ont_uri_prefix + 'AtomParity')
self._g.add((cls_atom_parity, a, owl_class))
# dllont:AtomParityNotStereo, dllont:AtomParityOdd,
# dllont:AtomParityEven, dllont:AtomParityEitherOrUnmarkedStereoCenter
for val in atom_stereo_parity_mapping.values():
cls = self._get_cls_uri(
self._atom_stereo_parity_type_to_cls_local_part, val)
self._g.add((cls, a, owl_class))
self._g.add((cls, rdfs_subcls_of, cls_atom_parity))
# ----------------- hydrogen count resources and class ----------------
# dllont:HydrogenCount
self.cls_hydrogen_count = \
URIRef(self._ont_uri_prefix + 'HydrogenCount')
self._g.add((self.cls_hydrogen_count, a, owl_class))
for val in hydrogen_count_mapping.values():
if val is not None:
hc_res = URIRef(self._resource_uri_prefix + val.lower())
self._g.add((hc_res, a, self.cls_hydrogen_count))
# ------------------------ bond class hierarchy -----------------------
# dllont:Bond
self.cls_bond = URIRef(self._ont_uri_prefix + 'Bond')
self._g.add((self.cls_bond, a, owl_class))
# dllont:SingleBond, dllont:DoubleBond, dllont:TripleBond,
# dllont:AromaticBond, dllont:SingleOrDoubleBond,
# dllont:SingleOrAromaticBond, dllont:DoubleOrAromaticBond
for val in bond_type_mapping.values():
bond_cls = self._get_bond_cls_uri(val)
self._g.add((bond_cls, a, owl_class))
for sdf_type in self._bond_type_to_cls_local_part[val][1]:
super_cls = self._get_bond_cls_uri(sdf_type)
self._g.add((bond_cls, rdfs_subcls_of, super_cls))
# ------------------- bond isomerism class hierarchy ------------------
# dllont:NonStereoBond
non_st_bond_cls = self._get_cls_uri(
self._bond_stereo_to_cls_local_part, 'Not stereo')
self._g.add((non_st_bond_cls, a, owl_class))
self._g.add((non_st_bond_cls, rdfs_subcls_of, self.cls_bond))
# dllont:SingleBondEitherUpOrDownStereochemistry
either_up_or_down_cls = self._get_cls_uri(
self._bond_stereo_to_cls_local_part, 'Either')
self._g.add((either_up_or_down_cls, a, owl_class))
self._g.add((
either_up_or_down_cls,
rdfs_subcls_of,
self._get_bond_cls_uri('Single')
))
# dllont:SingleBondUpStereochemistry
up_stereo_cls = self._get_cls_uri(
self._bond_stereo_to_cls_local_part, 'Up')
self._g.add((up_stereo_cls, a, owl_class))
self._g.add((up_stereo_cls, rdfs_subcls_of, either_up_or_down_cls))
# dllont:SingleBondDownStereochemistry
down_stereo_cls = self._get_cls_uri(
self._bond_stereo_to_cls_local_part, 'Down')
self._g.add((down_stereo_cls, a, owl_class))
self._g.add((down_stereo_cls, rdfs_subcls_of, either_up_or_down_cls))
cls_double_bond = self._get_bond_cls_uri('Double')
# dllont:DoubleBondDeriveCisOrTransIsomerismFromXYZCoords
derive_iso_cls = self._get_cls_uri(
self._bond_stereo_to_cls_local_part,
'Use x-, y-, z-coords from atom block to determine cis or trans')
self._g.add((derive_iso_cls, a, owl_class))
self._g.add((derive_iso_cls, rdfs_subcls_of, cls_double_bond))
# dllont:DoubleBondEitherCisOrTransIsomerism
cis_or_trans_cls = self._get_cls_uri(
self._bond_stereo_to_cls_local_part,
'Either cis or trans double bond')
self._g.add((cis_or_trans_cls, a, owl_class))
self._g.add((cis_or_trans_cls, rdfs_subcls_of, cls_double_bond))
# -------------------------- topology classes -------------------------
# dllont:BondTopology
topology_cls = URIRef(self._ont_uri_prefix + 'BondTopology')
self._g.add((topology_cls, a, owl_class))
# dllont:EitherRingOrChainTopology
either_topo_cls = self._get_cls_uri(
self._bond_topology_to_cls_local_part, 'Either')
self._g.add((either_topo_cls, a, owl_class))
self._g.add((either_topo_cls, rdfs_subcls_of, topology_cls))
# dllont:RingTopology
ring_topo_cls = self._get_cls_uri(
self._bond_topology_to_cls_local_part, 'Ring')
self._g.add((ring_topo_cls, a, owl_class))
self._g.add((ring_topo_cls, rdfs_subcls_of, either_topo_cls))
# dllont:ChainTopology
chain_topo_cls = self._get_cls_uri(
self._bond_topology_to_cls_local_part, 'Chain')
self._g.add((chain_topo_cls, a, owl_class))
self._g.add((chain_topo_cls, rdfs_subcls_of, either_topo_cls))
# --------------- reacting center status class hierarchy --------------
# dllont:ReactingCenterStatus
react_center_status_cls = URIRef(
self._ont_uri_prefix + 'ReactingCenterStatus')
self._g.add((react_center_status_cls, a, owl_class))
# dllont:Unmarked
react_unmarked_cls = self._get_cls_uri(
self._reacting_center_status_to_cls_local_part, 'unmarked')
self._g.add((react_unmarked_cls, a, owl_class))
self._g.add(
(react_unmarked_cls, rdfs_subcls_of, react_center_status_cls))
# dllont:ACenter
react_a_center_cls = self._get_cls_uri(
self._reacting_center_status_to_cls_local_part, 'a center')
self._g.add((react_a_center_cls, a, owl_class))
self._g.add(
(react_a_center_cls, rdfs_subcls_of, react_center_status_cls))
# dllont:NotACenter
react_not_a_center_cls = self._get_cls_uri(
self._reacting_center_status_to_cls_local_part, 'not a center')
self._g.add((react_not_a_center_cls, a, owl_class))
self._g.add(
(react_not_a_center_cls, rdfs_subcls_of, react_center_status_cls))
self._g.add((
react_a_center_cls,
OWL.term('disjointWith'),
react_not_a_center_cls
))
# dllont:NoChange
react_no_change_cls = self._get_cls_uri(
self._reacting_center_status_to_cls_local_part, 'no change')
self._g.add((react_no_change_cls, a, owl_class))
self._g.add(
(react_no_change_cls, rdfs_subcls_of, react_center_status_cls))
# FIXME: add class intersections
# dllont:BondMadeOrBroken
react_bond_made_or_broken_cls = self._get_cls_uri(
self._reacting_center_status_to_cls_local_part, 'bond made/broken')
self._g.add((react_bond_made_or_broken_cls, a, owl_class))
self._g.add((
react_bond_made_or_broken_cls,
rdfs_subcls_of,
react_center_status_cls
))
# dllont:BondOrderChanges
react_bond_order_change_cls = self._get_cls_uri(
self._reacting_center_status_to_cls_local_part,
'bond order changes')
self._g.add((react_bond_order_change_cls, a, owl_class))
self._g.add((
react_bond_order_change_cls,
rdfs_subcls_of,
react_center_status_cls
))
# dllont:BondMadeOrBrokenAndBondOrderChanges
react_bmob_and_boc_cls = self._get_cls_uri(
self._reacting_center_status_to_cls_local_part,
'bond made/broken + bond order changes')
self._g.add((react_bmob_and_boc_cls, a, owl_class))
self._g.add((
react_bmob_and_boc_cls,
rdfs_subcls_of,
react_bond_made_or_broken_cls
))
self._g.add((
react_bmob_and_boc_cls,
rdfs_subcls_of,
react_bond_order_change_cls
))
# dllont:BondMadeOrBrokenAndACenter
react_bmob_and_a_center_cls = self._get_cls_uri(
self._reacting_center_status_to_cls_local_part,
'bond made/broken + a center')
self._g.add((react_bmob_and_a_center_cls, a, owl_class))
self._g.add((
react_bmob_and_a_center_cls,
rdfs_subcls_of,
react_bond_made_or_broken_cls
))
self._g.add((
react_bmob_and_a_center_cls,
rdfs_subcls_of,
react_a_center_cls
))
# dllont:BondMadeOrBrokenAndBondOrderChangesAndACenter
react_bmob_and_boc_and_a_center_cls = self._get_cls_uri(
self._reacting_center_status_to_cls_local_part,
'bond made/broken + bond order changes + a center')
self._g.add((react_bmob_and_boc_and_a_center_cls, a, owl_class))
self._g.add((
react_bmob_and_boc_and_a_center_cls,
rdfs_subcls_of,
react_bmob_and_boc_cls
))
self._g.add((
react_bmob_and_boc_and_a_center_cls,
rdfs_subcls_of,
react_bmob_and_a_center_cls
))
self._g.add((
react_bmob_and_boc_and_a_center_cls,
rdfs_subcls_of,
react_a_center_cls
))
# ------------------------ property definitions -----------------------
# dllont:number_of_atoms
self.prop_num_atoms = \
URIRef(self._ont_uri_prefix + 'number_of_atoms')
self._g.add((self.prop_num_atoms, a, owl_dtype_prop))
self._g.add((self.prop_num_atoms, rdfs_dom, self.cls_molecule))
self._g.add((self.prop_num_atoms, rdfs_rnge, self.xsd_nnint))
# dllont:number_of_bounds
self.prop_num_bounds = \
URIRef(self._ont_uri_prefix + 'number_of_bounds')
self._g.add((self.prop_num_bounds, a, owl_dtype_prop))
self._g.add((self.prop_num_bounds, rdfs_dom, self.cls_molecule))
self._g.add((self.prop_num_bounds, rdfs_rnge, self.xsd_nnint))
# dllont:number_of_atom_lists
self.prop_num_atom_lists = URIRef(
self._ont_uri_prefix + 'number_of_atom_lists')
self._g.add((self.prop_num_atom_lists, a, owl_dtype_prop))
self._g.add((self.prop_num_atom_lists, rdfs_dom, self.cls_molecule))
self._g.add((self.prop_num_atom_lists, rdfs_rnge, self.xsd_nnint))
# dllont:molecule_is_chiral
self.prop_molec_is_chiral = URIRef(
self._ont_uri_prefix + 'molecule_is_chiral')
self._g.add((self.prop_molec_is_chiral, a, owl_dtype_prop))
self._g.add((self.prop_molec_is_chiral, rdfs_dom, self.cls_molecule))
self._g.add((self.prop_molec_is_chiral, rdfs_rnge, self.xsd_bool))
# dllont:atom
self.prop_atom = URIRef(self._ont_uri_prefix + 'atom')
self._g.add((self.prop_atom, a, owl_obj_prop))
self._g.add((self.prop_atom, rdfs_dom, self.cls_molecule))
self._g.add((self.prop_atom, rdfs_rnge, self.cls_atom))
# dllont:atom_number
self.prop_atom_number = URIRef(self._ont_uri_prefix + 'atom_number')
self._g.add((self.prop_atom_number, a, owl_dtype_prop))
self._g.add((self.prop_atom_number, rdfs_dom, self.cls_atom))
self._g.add((self.prop_atom_number, rdfs_rnge, self.xsd_nnint))
# dllont:atom_coordinate_x
self.prop_coord_x = URIRef(self._ont_uri_prefix + 'atom_coordinate_x')
self._g.add((self.prop_coord_x, a, owl_dtype_prop))
self._g.add((self.prop_coord_x, rdfs_dom, self.cls_atom))
self._g.add((self.prop_coord_x, rdfs_rnge, self.xsd_double))
# dllont:atom_coordinate_y
self.prop_coord_y = URIRef(self._ont_uri_prefix + 'atom_coordinate_y')
self._g.add((self.prop_coord_y, a, owl_dtype_prop))
self._g.add((self.prop_coord_y, rdfs_dom, self.cls_atom))
self._g.add((self.prop_coord_y, rdfs_rnge, self.xsd_double))
# dllont:atom_coordinate_z
self.prop_coord_z = URIRef(self._ont_uri_prefix + 'atom_coordinate_z')
self._g.add((self.prop_coord_z, a, owl_dtype_prop))
self._g.add((self.prop_coord_z, rdfs_dom, self.cls_atom))
self._g.add((self.prop_coord_z, rdfs_rnge, self.xsd_double))
# dllont:atom_symbol
self.prop_atom_symbol = URIRef(self._ont_uri_prefix + 'atom_symbol')
self._g.add((self.prop_atom_symbol, a, owl_obj_prop))
self._g.add((self.prop_atom_symbol, rdfs_dom, self.cls_atom))
self._g.add((self.prop_atom_symbol, rdfs_rnge, self.cls_atom_symbol))
# dllont:mass_difference
self.prop_mass_difference = URIRef(
self._ont_uri_prefix + 'mass_difference')
self._g.add((self.prop_mass_difference, a, owl_dtype_prop))
self._g.add((self.prop_mass_difference, rdfs_dom, self.cls_atom))
self._g.add((self.prop_mass_difference, rdfs_rnge, self.xsd_double))
# dllont:charge
self.prop_charge = URIRef(self._ont_uri_prefix + 'charge')
self._g.add((self.prop_charge, a, owl_dtype_prop))
self._g.add((self.prop_charge, rdfs_dom, self.cls_atom))
self._g.add((self.prop_charge, rdfs_rnge, self.xsd_int))
# dllont:hydrogen_count
self.prop_hydrogen_count = URIRef(
self._ont_uri_prefix + 'hydrogen_count')
self._g.add((self.prop_hydrogen_count, a, owl_obj_prop))
self._g.add((self.prop_hydrogen_count, rdfs_dom, self.cls_atom))
self._g.add(
(self.prop_hydrogen_count, rdfs_rnge, self.cls_hydrogen_count))
# dllont:valence
self.prop_valence = URIRef(self._ont_uri_prefix + 'valence')
self._g.add((self.prop_valence, a, owl_dtype_prop))
self._g.add((self.prop_valence, rdfs_dom, self.cls_atom))
self._g.add((self.prop_valence, rdfs_rnge, self.xsd_nnint))
# dllont:h_atoms_allowed
self.prop_h_atoms_allowed = URIRef(
self._ont_uri_prefix + 'h_atoms_allowed')
self._g.add((self.prop_h_atoms_allowed, a, owl_dtype_prop))
self._g.add((self.prop_h_atoms_allowed, rdfs_dom, self.cls_atom))
self._g.add((self.prop_h_atoms_allowed, rdfs_rnge, self.xsd_bool))
# dllont:atom-atom_mapping_number
self.prop_atom_atom_mapping_nr = URIRef(
self._ont_uri_prefix + 'atom-atom_mapping_number')
self._g.add((self.prop_atom_atom_mapping_nr, a, owl_dtype_prop))
self._g.add((self.prop_atom_atom_mapping_nr, rdfs_dom, self.cls_atom))
self._g.add(
(self.prop_atom_atom_mapping_nr, rdfs_rnge, self.xsd_nnint))
# dllont:has_binding_with
self.prop_has_binding_with = URIRef(
self._ont_uri_prefix + 'has_binding_with')
self._g.add((
self.prop_has_binding_with,
a,
URIRef(OWL.term('SymmetricProperty'))
))
self._g.add((self.prop_has_binding_with, rdfs_dom, self.cls_atom))
self._g.add((self.prop_has_binding_with, rdfs_rnge, self.cls_atom))
# dllont:first_bound_atom
self.prop_first_bound_atom = URIRef(
self._ont_uri_prefix + 'first_bound_atom')
self._g.add((self.prop_first_bound_atom, a, owl_obj_prop))
self._g.add((self.prop_first_bound_atom, rdfs_dom, self.cls_bond))
self._g.add((self.prop_first_bound_atom, rdfs_rnge, self.cls_atom))
# dllont:second_bound_atom
self.prop_second_bound_atom = URIRef(
self._ont_uri_prefix + 'second_bound_atom')
self._g.add((self.prop_second_bound_atom, a, owl_obj_prop))
self._g.add((self.prop_second_bound_atom, rdfs_dom, self.cls_bond))
self._g.add((self.prop_second_bound_atom, rdfs_rnge, self.cls_atom))
# dllont:has_topology
self.prop_has_topology = URIRef(self._ont_uri_prefix + 'has_topology')
self._g.add((self.prop_has_topology, a, owl_obj_prop))
self._g.add((self.prop_has_topology, rdfs_dom, self.cls_bond))
self._g.add((self.prop_has_topology, rdfs_rnge, topology_cls))
# dllont:has_reacting_center_status
self.prop_has_rc_status = URIRef(
self._ont_uri_prefix + 'has_reacting_center_status')
self._g.add((self.prop_has_rc_status, a, owl_obj_prop))
self._g.add((self.prop_has_rc_status, rdfs_dom, self.cls_bond))
self._g.add(
(self.prop_has_rc_status, rdfs_rnge, react_center_status_cls))
