Decouple the parsers actions (#658)

* Decouple the following operations that the parser was responsible for: get the graph of the ontology, put the ontology in the namespace registry.

* Modify the unit tests to accommodate the new changes.

* Make the `Ontology` class directly accesible from the `ontology` module.

examples/ontology_example.py

@@ -1,6 +1,6 @@
 """An example explaining how to access an installed ontology."""
 
-from osp.core.ontology.oclass_composition import Composition  # Used later.
+from osp.core.ontology.oclass_composition import Composition
 
 # Please install the both the city ontology: $pico install city,
 # and the European Materials & Modelling Ontology (EMMO): $pico install emmo.

osp/core/namespaces.py

@@ -18,7 +18,7 @@
 
 
 try:
-    _namespace_registry.load(_path)
+    _namespace_registry.load_graph_file(_path)
 except RuntimeError:
     _logger.critical("Could not load installed ontologies.", exc_info=1)
 

osp/core/ontology/__init__.py

@@ -1,6 +1,9 @@
+from osp.core.ontology.installation import OntologyInstallationManager
+from osp.core.ontology.parser.parser import Parser
 from osp.core.ontology.oclass import OntologyClass
+from osp.core.ontology.ontology import Ontology
+from osp.core.ontology.attribute import OntologyAttribute
 from osp.core.ontology.entity import OntologyEntity
 from osp.core.ontology.relationship import OntologyRelationship
-from osp.core.ontology.attribute import OntologyAttribute
-from osp.core.ontology.parser import Parser
-from osp.core.ontology.installation import OntologyInstallationManager
+from osp.core.ontology.oclass_composition import Composition
+from osp.core.ontology.oclass_restriction import Restriction

osp/core/ontology/installation.py

@@ -4,12 +4,12 @@
 import logging
 import shutil
 import tempfile
-from osp.core.ontology.parser import Parser
+from osp.core.ontology.parser.parser import OntologyParser
 
 logger = logging.getLogger(__name__)
 
 
-class OntologyInstallationManager():
+class OntologyInstallationManager:
     """This class handles the installation of ontologies."""
 
     def __init__(self, namespace_registry=None, path=None):
@@ -81,7 +81,7 @@ def _get_remaining_packages(self, remove_packages):
         installed_pkgs = dict(self.get_installed_packages(return_path=True))
         for pkg in remove_packages:
             if pkg.endswith(".yml") and os.path.exists(pkg):
-                pkg = Parser.get_identifier(pkg)
+                pkg = OntologyParser.get_parser(pkg).identifier
             if pkg in installed_pkgs:
                 remove_pkgs.add(pkg)
             else:
@@ -105,7 +105,7 @@ def _get_replaced_packages(self, new_packages):
         """
         installed = dict(self.get_installed_packages(return_path=True))
         for pkg in new_packages:
-            installed[Parser.get_identifier(pkg)] = pkg
+            installed[OntologyParser.get_parser(pkg).identifier] = pkg
         return installed.values()
 
     def _get_new_packages(self, packages):
@@ -120,7 +120,7 @@ def _get_new_packages(self, packages):
         result = set(packages)
         installed = set(self.get_installed_packages())
         for pkg in packages:
-            identifier = Parser.get_identifier(pkg)
+            identifier = OntologyParser.get_parser(pkg).identifier
             if identifier in installed:
                 logger.info("Skipping package %s with identifier %s, "
                             "because it is already installed."
@@ -142,16 +142,15 @@ def _install(self, files, filter_func, clear):
         if clear:
             self.namespace_registry.clear()
             installed = set()
+            shutil.rmtree(self.path)
+            os.makedirs(self.path)
         files = self._sort_for_installation(filter_func(files), installed)
-        parser = Parser(parser_namespace_registry=self.namespace_registry)
         for file in files:
-            parser.parse(file)
+            parser = OntologyParser.get_parser(file)
+            self.namespace_registry.load_parser(parser)
+            # serialize the result
+            parser.install(self.path)
         self.namespace_registry.update_namespaces()
-        # serialize the result
-        if clear:
-            shutil.rmtree(self.path)
-            os.makedirs(self.path)
-        parser.store(self.path)
         self.namespace_registry.store(self.path)
 
     def _sort_for_installation(self, files, installed):
@@ -167,8 +166,8 @@ def _sort_for_installation(self, files, installed):
             List[str]: The sorted list of file paths.
         """
         result = list()
-        files = {Parser.get_identifier(f): f for f in files}
-        requirements = {n: Parser.get_requirements(f) for
+        files = {OntologyParser.get_parser(f).identifier: f for f in files}
+        requirements = {n: OntologyParser.get_parser(f).requirements for
                         n, f in files.items()}
 
         # order the files
@@ -210,7 +209,6 @@ def pico_migrate(namespace_registry, path):
             files.append(os.path.join(d, file))
         shutil.rmtree(path)
         os.mkdir(path)
-
         installer = OntologyInstallationManager(namespace_registry, path)
         namespace_registry._load_cuba()
         installer.install(*files)

osp/core/ontology/namespace.py

@@ -8,7 +8,7 @@
 from osp.core.ontology.entity import OntologyEntity
 from osp.core.ontology.relationship import OntologyRelationship
 from osp.core.ontology.cuba import rdflib_cuba
-from osp.core.ontology.yml.case_insensitivity import \
+from osp.core.ontology.parser.yml.case_insensitivity import \
     get_case_insensitive_alternative as alt
 
 logger = logging.getLogger(__name__)

osp/core/ontology/namespace_registry.py

@@ -8,12 +8,14 @@
 from osp.core.ontology.oclass import OntologyClass
 from osp.core.ontology.relationship import OntologyRelationship
 from osp.core.ontology.attribute import OntologyAttribute
+from osp.core.ontology.ontology import Ontology
+from osp.core.ontology.parser.parser import OntologyParser
 from functools import lru_cache
 
 logger = logging.getLogger(__name__)
 
 
-class NamespaceRegistry():
+class NamespaceRegistry:
     """Stores all the loaded namespaces."""
 
     def __init__(self):
@@ -27,7 +29,7 @@ def __init__(self):
         self._namespaces = dict()
 
     def __iter__(self):
-        """Iterate over the installed namespace.
+        """Iterate over the installed namespaces.
 
         :return: An iterator over the namespaces.
         :rtype: Iterator[OntologyNamespace]
@@ -178,8 +180,10 @@ def from_bnode(self, bnode, btype=None):
             bnode (BNode): A blank node in the triple store.
             btype (URIRef): The rdf.type of the blank node.
         """
-        from osp.core.ontology.oclass_composition import get_composition
-        from osp.core.ontology.oclass_restriction import get_restriction
+        from osp.core.ontology.oclass_composition import \
+            get_composition
+        from osp.core.ontology.oclass_restriction import \
+            get_restriction
         t = btype or self._graph.value(bnode, rdflib.RDF.type)
 
         if t == rdflib.OWL.Restriction:
@@ -309,15 +313,15 @@ def store(self, path):
             for name, iri in self._namespaces.items():
                 print("%s\t%s" % (name, iri), file=f)
 
-    def load(self, path):
+    def load_graph_file(self, path):
         """Load the installed graph from at the given path.
 
         Args:
             path (Path): path to directory where the ontology has been
                 installed.
         """
         # Migrate old ontology formats if needed.
-        if os.path.exists(os.path.join(path, "yml")):
+        if os.path.exists(os.path.join(path, "parser/yml")):
             from osp.core.ontology.installation import pico_migrate
             pico_migrate(self, path)
         # Migrate to 3.5.3.1 format if needed.
@@ -356,5 +360,57 @@ def _load_cuba(self):
         self.bind("cuba",
                   rdflib.URIRef("http://www.osp-core.com/cuba#"))
 
+    def load_parser(self, parser: OntologyParser):
+        """Load new namespace(s) from a parser object.
+
+        Args:
+            parser (OntologyParser): the ontology parser from where to load
+                the new namespaces
+        """
+        namespaces = parser.namespaces.items() \
+            if isinstance(parser.namespaces, dict) else dict()
+        logger.info("Loading namespaces %s." %
+                    '; '.join([f'{name}, {uri}'
+                               for name, uri in namespaces]))
+        ontology = Ontology(from_parser=parser)
+        # Force default relationships to be installed before installing a new
+        # ontology.
+        self._check_default_relationship_installed(ontology)
+        # Merge ontology graph.
+        self._graph += ontology.graph
+        # Bind namespaces.
+        for name, iri in namespaces:
+            if not (
+                iri.endswith("#") or iri.endswith("/")
+            ):
+                iri += "#"
+            self.bind(name, iri)
+
+    def _check_default_relationship_installed(self, ontology: Ontology,
+                                              allow_types=frozenset(
+                                                  {rdflib.OWL.ObjectProperty,
+                                                   })
+                                              ):
+        found = False
+        # Check if it is in the namespace to be installed.
+        for s, p, o in ontology.graph.triples((ontology.default_relationship,
+                                               rdflib.RDF.type,
+                                               None)):
+            if o in allow_types:
+                found = True
+                break
+        # If not, found, find it in the namespace registry.
+        if not found:
+            try:
+                self.from_iri(ontology.default_relationship)
+                found = True
+            except KeyError:
+                pass
+        if not found:
+            raise ValueError(f'The default relationship '
+                             f'{ontology.default_relationship} defined for '
+                             f'the ontology package {ontology.identifier} '
+                             f'is not installed.')
+
 
 namespace_registry = NamespaceRegistry()