diff --git a/Taskfile.yml b/Taskfile.yml index 430cd8c..488399d 100644 --- a/Taskfile.yml +++ b/Taskfile.yml @@ -3,24 +3,19 @@ version: '3' tasks: install_dependencies: - cmds: - - pip install poetry + - pip install poetry install: - cmds: - - poetry install + - poetry install code_formating: - cmds: - - poetry run black shaclgen tests + - poetry run black shaclgen tests code_formating_check: - cmds: - - poetry run black --check shaclgen tests + - poetry run black --check shaclgen tests test: - cmds: - - poetry run pytest -rP --cov=shaclgen --cov-report=term-missing + - poetry run pytest -rP --cov=shaclgen --cov-report=term-missing ci: cmds: @@ -28,3 +23,11 @@ tasks: - task: install - task: test - task: code_formating_check + +# Aliases +# +# Should be new syntax onece v4 is out: +# https://github.com/go-task/task/issues/675 + + black: + - task: code_formating diff --git a/poetry.lock b/poetry.lock index 9cb50cf..ce8c583 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,39 +1,33 @@ -[[package]] -name = "atomicwrites" -version = "1.4.0" -description = "Atomic file writes." -category = "main" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" - -[[package]] -name = "attrs" -version = "21.4.0" -description = "Classes Without Boilerplate" -category = "main" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" - -[package.extras] -dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"] -docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"] -tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "cloudpickle"] -tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "cloudpickle"] +# This file is automatically @generated by Poetry and should not be changed by hand. 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schema import click -from sys import stdout +from sys import stdout, stderr from rdflib import Graph from rdflib.util import guess_format +from rdflib.namespace import NamespaceManager +from loguru import logger +import json +import pkg_resources @click.command() @@ -51,7 +55,33 @@ help="use implicit class targets with RDFS", default=False, ) -def main(graphs, ontology, output, serial, prefixes, namespace, implicit_class_target): +@click.option( + "--logfile", + help="Specify a logfile", + default=None, +) +@click.option( + "--loglevel", + help="Specify the standard output loglevel", + default="INFO", +) +@click.option( + "--logfilelevel", + help="Specify the loglevel for the logfile", + default="DEBUG", +) +def main( + graphs, + ontology, + output, + serial, + prefixes, + namespace, + implicit_class_target, + logfile, + loglevel, + logfilelevel, +): """ ---------------------------Shaclgen--------------------------- @@ -89,16 +119,35 @@ def main(graphs, ontology, output, serial, prefixes, namespace, implicit_class_t """ + logger.remove() + logger.add(stderr, level=loglevel) + if logfile: + logger.add(logfile, level=logfilelevel) + source_graph = Graph() for graph in graphs: source_graph.parse(graph, format=guess_format(graph)) + path = "prefixes/namespaces.json" + filepath = pkg_resources.resource_filename(__name__, path) + + namespaces = NamespaceManager(graph=Graph()) + + with open(filepath, "r", encoding="utf-8") as fin: + for prefix, namespace_iri in json.load(fin).items(): + namespaces.bind(prefix, namespace_iri) + + if prefixes: + with open(prefixes, "r", encoding="utf-8") as fin: + for prefix, namespace_iri in json.load(fin).items(): + namespaces.bind(prefix, namespace_iri) + g = None if ontology: - g = schema(source_graph, prefixes) + g = schema(source_graph, namespaces) else: - g = data_graph(source_graph, prefixes) + g = data_graph(source_graph, namespaces) shape_graph = g.gen_graph( namespace=namespace, implicit_class_target=implicit_class_target ) diff --git a/shaclgen/constraint.py b/shaclgen/constraint.py deleted file mode 100644 index d37e7fc..0000000 --- a/shaclgen/constraint.py +++ /dev/null @@ -1,6 +0,0 @@ -# -*- coding: utf-8 -*- -""" -Created on Wed Feb 26 15:47:44 2020 - -@author: alexi -""" diff --git a/shaclgen/generator.py b/shaclgen/generator.py index ed66305..c5ee0e2 100644 --- a/shaclgen/generator.py +++ b/shaclgen/generator.py @@ -3,7 +3,7 @@ class Generator: - def __init__(self, graph: Graph, prefixes=None): + def __init__(self, graph: Graph, namespaces=None): pass def sh_label_gen(self, uri): diff --git a/shaclgen/schema.py b/shaclgen/schema.py index 6025c05..0004851 100644 --- a/shaclgen/schema.py +++ b/shaclgen/schema.py @@ -1,11 +1,10 @@ +from loguru import logger from rdflib import Graph, Namespace from rdflib.namespace import XSD, RDF, RDFS, OWL, SH from rdflib.namespace import NamespaceManager from rdflib.term import URIRef, Literal, BNode import collections -import json from rdflib.collection import Collection -import pkg_resources from .generator import Generator """ @@ -17,7 +16,7 @@ class schema(Generator): - def __init__(self, graph: Graph, prefixes=None): + def __init__(self, graph: Graph, namespaces=None): self.G = graph self.CLASSES = collections.OrderedDict() @@ -39,21 +38,12 @@ def __init__(self, graph: Graph, prefixes=None): XSD.nonPositiveInteger, ] - path = "prefixes/namespaces.json" - filepath = pkg_resources.resource_filename(__name__, path) - - self.namespaces = NamespaceManager(graph=Graph()) + if namespaces: + self.namespaces = namespaces + else: + self.namespaces = NamespaceManager(graph=Graph()) self.namespaces.bind("sh", SH) - with open(filepath, "r", encoding="utf-8") as fin: - for prefix, namespace in json.load(fin).items(): - self.namespaces.bind(prefix, namespace) - - if prefixes: - with open(prefixes, "r", encoding="utf-8") as fin: - for prefix, namespace in json.load(fin).items(): - self.namespaces.bind(prefix, namespace) - def extract_props(self): properties = [] self.PROPS = {} @@ -207,9 +197,13 @@ def extract_restrictions(self): self.REST[rest]["value"] = rest_val[0] def gen_graph(self, namespace=None, implicit_class_target=False): + logger.info("Start Extraction of the Ontology") + logger.info("Properties …") self.extract_props() + logger.info("Classes …") self.extract_classes() self.extract_restrictions() + logger.info("Write resulting SHACL Graph …") ng = Graph(namespace_manager=self.namespaces) if namespace is not None: diff --git a/shaclgen/shaclgen.py b/shaclgen/shaclgen.py index 5b43e70..abb50de 100644 --- a/shaclgen/shaclgen.py +++ b/shaclgen/shaclgen.py @@ -1,97 +1,127 @@ -from rdflib import Namespace, URIRef, BNode, Literal, Graph +from loguru import logger +from rdflib import Namespace, Literal, Graph import rdflib -import json import collections -from rdflib.namespace import XSD, RDF, SH +from rdflib.namespace import RDF, RDFS, SH from rdflib.namespace import NamespaceManager -import pkg_resources from .generator import Generator +SHGEN = Namespace("http://shaclgen/") + class data_graph(Generator): - def __init__(self, graph: Graph, prefixes=None): + def __init__(self, graph: Graph, namespaces=None): self.G = graph self.CLASSES = collections.OrderedDict() self.PROPS = collections.OrderedDict() self.OUT = [] - path = "prefixes/namespaces.json" - filepath = pkg_resources.resource_filename(__name__, path) - - self.namespaces = NamespaceManager(graph=Graph()) + if namespaces: + self.namespaces = namespaces + else: + self.namespaces = NamespaceManager(graph=Graph()) self.namespaces.bind("sh", SH) - - with open(filepath, "r", encoding="utf-8") as fin: - for prefix, namespace in json.load(fin).items(): - self.namespaces.bind(prefix, namespace) - - if prefixes: - with open(prefixes, "r", encoding="utf-8") as fin: - for prefix, namespace in json.load(fin).items(): - self.namespaces.bind(prefix, namespace) + self.namespaces.bind("shgen", SHGEN) def extract_classes(self): types_query = "select distinct ?class_ { ?s rdf:type ?class_ }" for row in self.G.query(types_query, initNs={"rdf": RDF}): + logger.debug(f"Class: {row.class_}") self.CLASSES[row.class_] = {"label": self.sh_label_gen(row.class_)} def extract_props(self): prop_query = "select distinct ?prop { ?s ?prop ?o . filter(?prop != rdf:type)}" - prop_subj_classes = "select distinct ?class_ {{ ?sub {prop} ?o ; a ?class_ . }}" - for property_row in self.G.query(prop_query, initNs={"rdf": RDF}): + for property_row in self.G.query(prop_query, initNs={"rdf": RDF, "rdfs": RDFS}): prop = property_row.prop + logger.debug(f"Property: {prop}") self.PROPS[prop] = { "nodekind": None, "cardinality": None, "classes": [], + "exceptions": [], "label": self.sh_label_gen(prop), } - for class_row in self.G.query(prop_subj_classes.format(prop=prop.n3())): - class_ = class_row.class_ - self.PROPS[prop]["classes"].append(self.CLASSES[class_]["label"]) + + self.extract_props_subj_types(prop) if len(self.PROPS[prop]["classes"]) == 1: self.PROPS[prop]["type"] = "unique" else: self.PROPS[prop]["type"] = "repeat" - def extract_constraints(self): + self.extract_props_obj_types(prop) - for prop in self.PROPS.keys(): - types = [] - classes = [] - datatypes = [] - for s, p, o in self.G.triples((None, prop, None)): - nodeType = type(o) - if not types: - types.append(nodeType) - elif nodeType not in types: - # currently only one type is handled per property - break - if nodeType == URIRef: - for _, _, objectClass in self.G.triples((o, RDF.type, None)): - classes.append(objectClass) - elif nodeType == Literal: - datatypes.append( - o.datatype or XSD.langString if o.language else XSD.string - ) + def extract_props_subj_types(self, prop): + logger.debug(f"Property subject types: {prop}") + prop_subject_type = "select distinct ?class_ {{ ?sub {prop} ?o ; a ?class_ . }}" - if len(set(types)) == 1: - if types[0] == URIRef: - self.PROPS[prop]["nodekind"] = "IRI" - self.PROPS[prop]["objectclasses"] = classes - elif types[0] == BNode: - self.PROPS[prop]["nodekind"] = "BNode" - elif types[0] == Literal: - self.PROPS[prop]["nodekind"] = "Literal" + try: + class_property_result = self.G.query( + prop_subject_type.format(prop=prop.n3()) + ) + for class_row in class_property_result: + class_ = class_row.class_ + self.PROPS[prop]["classes"].append(self.CLASSES[class_]["label"]) + except Exception as e: + logger.error(e) + self.PROPS[prop]["exceptions"].append( + {"exception": e, "query": prop_subject_type.format(prop=prop.n3())} + ) + + def extract_props_obj_types(self, prop): + logger.debug(f"Property object types: {prop}") + prop_object_type = """ + select distinct ?literal ?dt ?blank ?iri ?class_ {{ + ?s {prop} ?obj . + optional {{ ?obj a ?class_ }} + bind(isLiteral(?obj) as ?literal) + bind(datatype(?obj) as ?dt) + bind(isBlank(?obj) as ?blank) + bind(isIRI(?obj) as ?iri) + }}""" + + try: + nodekinds = [] + datatypes = [] + objectclasses = [] + + property_object_result = self.G.query( + prop_object_type.format(prop=prop.n3()) + ) + for object_type_row in property_object_result: + if object_type_row.literal: + nodekinds.append("Literal") + datatypes.append(object_type_row.dt) + elif object_type_row.blank: + nodekinds.append("BNode") + elif object_type_row.iri: + nodekinds.append("IRI") + + if object_type_row.blank or object_type_row.iri: + if object_type_row.class_: + objectclasses.append(object_type_row.class_) + + if len(set(nodekinds)) == 1: + self.PROPS[prop]["nodekind"] = nodekinds[0] + if nodekinds[0] == "Literal": if len(set(datatypes)) == 1: self.PROPS[prop]["datatype"] = datatypes[0] + elif nodekinds[0] in ("IRI", "BNode"): + self.PROPS[prop]["objectclasses"] = objectclasses + except Exception as e: + logger.error(e) + self.PROPS[prop]["exceptions"].append( + {"exception": e, "query": prop_object_type.format(prop=prop.n3())} + ) def gen_graph(self, namespace=None, implicit_class_target=False): + logger.info("Start Extraction of the Data Graph") + logger.info("Classes …") self.extract_classes() + logger.info("Properties …") self.extract_props() - self.extract_constraints() + logger.info("Write resulting SHACL Graph …") ng = rdflib.Graph(namespace_manager=self.namespaces) if namespace is not None: @@ -120,6 +150,22 @@ def gen_graph(self, namespace=None, implicit_class_target=False): ng.add((EX[self.PROPS[p]["label"]], RDF.type, SH.PropertyShape)) ng.add((EX[self.PROPS[p]["label"]], SH.path, p)) + for exception in self.PROPS[p]["exceptions"]: + ng.add( + ( + EX[self.PROPS[p]["label"]], + SHGEN.exception, + Literal(str(exception["exception"])), + ) + ) + ng.add( + ( + EX[self.PROPS[p]["label"]], + SHGEN.query, + Literal(str(exception["query"])), + ) + ) + for class_prop in self.PROPS[p]["classes"]: ng.add((EX[class_prop], SH.property, EX[self.PROPS[p]["label"]])) if self.PROPS[p]["nodekind"] == "IRI": diff --git a/tests/test_minimal_integration.py b/tests/test_minimal_integration.py index ffec98a..c3e3a9a 100644 --- a/tests/test_minimal_integration.py +++ b/tests/test_minimal_integration.py @@ -307,3 +307,38 @@ def test_object_blank_node(): } """, ) + + +def test_property_loop(): + source_graph = Graph() + + data = """ + a ; + . + a ; + . + """ + + source_graph.parse(data=data, format="turtle") + + extraction_graph = data_graph(source_graph) + shacl_graph = extraction_graph.gen_graph() + + assertAskQuery( + shacl_graph, + """ + prefix sh: + prefix xsd: + ask { + ?nodeShapeA a sh:NodeShape ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:property ?property ; + sh:targetClass . + + ?property a sh:PropertyShape ; + sh:class ; + sh:nodeKind sh:IRI ; + sh:path . + } + """, + ) diff --git a/tests/test_node_types.py b/tests/test_node_types.py new file mode 100644 index 0000000..28ebf6d --- /dev/null +++ b/tests/test_node_types.py @@ -0,0 +1,282 @@ +from rdflib import Graph +from shaclgen.shaclgen import data_graph +from helpers import assertAskQuery + + +def test_object_class(): + source_graph = Graph() + + data = """ + a ; + ; + [a ] ; + 4 ; + true ; + "Literal" ; + "Literal"@en . + a . + """ + + source_graph.parse(data=data, format="turtle") + + extraction_graph = data_graph(source_graph) + shacl_graph = extraction_graph.gen_graph() + + assertAskQuery( + shacl_graph, + """ + prefix sh: + prefix xsd: + ask { + ?nodeShapeA a sh:NodeShape ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:property ?obj_property_iri, ?obj_property_bnode, ?data_property_int, ?data_property_bool, ?data_property_langstr, ?data_property_str ; + sh:targetClass . + + ?obj_property_iri a sh:PropertyShape ; + sh:class ; + sh:nodeKind sh:IRI ; + sh:path . + + ?obj_property_bnode a sh:PropertyShape ; + #sh:class ; + sh:nodeKind sh:BlankNode ; + sh:path . + + ?data_property_int a sh:PropertyShape ; + sh:datatype xsd:integer ; + sh:nodeKind sh:Literal ; + sh:path . + + ?data_property_bool a sh:PropertyShape ; + sh:datatype xsd:boolean ; + sh:nodeKind sh:Literal ; + sh:path . + + ?data_property_langstr a sh:PropertyShape ; + sh:datatype rdf:langString ; + sh:nodeKind sh:Literal ; + sh:path . + + ?data_property_str a sh:PropertyShape ; + sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:path . + + ?nodeShapeB a sh:NodeShape ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:targetClass . + + ?nodeShapeC a sh:NodeShape ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:targetClass . + } + """, + ) + + +def test_object_class_iri(): + source_graph = Graph() + + data = """ + a ; + . + a . + """ + + source_graph.parse(data=data, format="turtle") + + extraction_graph = data_graph(source_graph) + shacl_graph = extraction_graph.gen_graph() + + assertAskQuery( + shacl_graph, + """ + prefix sh: + prefix xsd: + ask { + ?nodeShapeA a sh:NodeShape ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:property ?obj_property_iri ; + sh:targetClass . + + ?obj_property_iri a sh:PropertyShape ; + sh:class ; + sh:nodeKind sh:IRI ; + sh:path . + + ?nodeShapeB a sh:NodeShape ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:targetClass . + } + """, + ) + + +def test_object_class_bnode(): + source_graph = Graph() + + data = """ + a ; + [a ] . + """ + + source_graph.parse(data=data, format="turtle") + + extraction_graph = data_graph(source_graph) + shacl_graph = extraction_graph.gen_graph() + + assertAskQuery( + shacl_graph, + """ + prefix sh: + prefix xsd: + ask { + ?nodeShapeA a sh:NodeShape ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:property ?obj_property_bnode ; + sh:targetClass . + + ?obj_property_bnode a sh:PropertyShape ; + #sh:class ; + sh:nodeKind sh:BlankNode ; + sh:path . + + ?nodeShapeC a sh:NodeShape ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:targetClass . + } + """, + ) + + +def test_object_datatype_int(): + source_graph = Graph() + + data = """ + a ; + 4 . + """ + + source_graph.parse(data=data, format="turtle") + + extraction_graph = data_graph(source_graph) + shacl_graph = extraction_graph.gen_graph() + + assertAskQuery( + shacl_graph, + """ + prefix sh: + prefix xsd: + ask { + ?nodeShapeA a sh:NodeShape ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:property ?obj_property_int ; + sh:targetClass . + + ?data_property_int a sh:PropertyShape ; + sh:datatype xsd:integer ; + sh:nodeKind sh:Literal ; + sh:path . + } + """, + ) + + +def test_object_datatype_bool(): + source_graph = Graph() + + data = """ + a ; + true . + """ + + source_graph.parse(data=data, format="turtle") + + extraction_graph = data_graph(source_graph) + shacl_graph = extraction_graph.gen_graph() + + assertAskQuery( + shacl_graph, + """ + prefix sh: + prefix xsd: + ask { + ?nodeShapeA a sh:NodeShape ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:property ?data_property_bool ; + sh:targetClass . + + ?data_property_bool a sh:PropertyShape ; + sh:datatype xsd:boolean ; + sh:nodeKind sh:Literal ; + sh:path . + } + """, + ) + + +def test_object_datatype_str(): + source_graph = Graph() + + data = """ + a ; + "Literal" . + """ + + source_graph.parse(data=data, format="turtle") + + extraction_graph = data_graph(source_graph) + shacl_graph = extraction_graph.gen_graph() + + assertAskQuery( + shacl_graph, + """ + prefix sh: + prefix xsd: + ask { + ?nodeShapeA a sh:NodeShape ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:property ?data_property_str ; + sh:targetClass . + + ?data_property_str a sh:PropertyShape ; + sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:path . + } + """, + ) + + +def test_object_datatype_langstr(): + source_graph = Graph() + + data = """ + a ; + "Literal"@en . + """ + + source_graph.parse(data=data, format="turtle") + + extraction_graph = data_graph(source_graph) + shacl_graph = extraction_graph.gen_graph() + + assertAskQuery( + shacl_graph, + """ + prefix sh: + prefix xsd: + ask { + ?nodeShapeA a sh:NodeShape ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:property ?data_property_langstr; + sh:targetClass . + + ?data_property_langstr a sh:PropertyShape ; + sh:datatype rdf:langString ; + sh:nodeKind sh:Literal ; + sh:path . + } + """, + )