First version of added namespace search in get_by_label

examples/emmodoc/classes.md

@@ -54,11 +54,10 @@ branch of mereotopology.
 %BRANCHDOC MathematicalModel
 %BRANCHDOC MathematicalOperator
 %BRANCHDOC Metrological
-%BRANCHDOC PhysicalDimension     rankdir=RL
+%BRANCHDOC hasMetrologicalReference   rankdir=RL
 %BRANCHDOC PhysicalQuantity
 %BRANCHDOC Number
 %BRANCHDOC MeasurementUnit
-%BRANCHDOC UTF8
 %BRANCHDOC SIBaseUnit
 %BRANCHDOC SISpecialUnit        rankdir=RL
 %BRANCHDOC PrefixedUnit
@@ -71,7 +70,6 @@ branch of mereotopology.
 %BRANCHDOC Reductionistic
 %BRANCHDOC Expression
 
-%BRANCHDOC Physicalistic
 %BRANCHDOC ElementaryParticle
 #%BRANCHDOC Subatomic
 %BRANCHDOC Matter

examples/emmodoc/emmo.md

@@ -21,4 +21,4 @@
 %BRANCHFIG EMMORelation   caption='The complete taxonomy of EMMO relations.' terminated=0 relations=all edgelabels=0
 
 %HEADER "The taxonomy of EMMO classes"     level=2
-%BRANCHFIG EMMO           caption='The almost complete taxonomy of EMMO classes. Only physical quantities and constants are left out.' terminated=0 relations=isA edgelabels=0 leaves=PhysicalDimension,BaseQuantity,DerivedQuantity,ExactConstant,MeasuredConstant,SIBaseUnit,SISpecialUnit,MetricPrefix,UTF8
+%BRANCHFIG EMMO           caption='The almost complete taxonomy of EMMO classes. Only physical quantities and constants are left out.' terminated=0 relations=isA edgelabels=0 leaves=hasMetrologicalReference,BaseQuantity,DerivedQuantity,ExactConstant,MeasuredConstant,SIBaseUnit,SISpecialUnit,MetricPrefix

ontopy/excelparser.py

@@ -17,6 +17,7 @@
 import pandas as pd
 import numpy as np
 import pyparsing
+import defusedxml.ElementTree as ET
 
 import ontopy
 from ontopy import get_ontology
@@ -521,7 +522,7 @@ def get_metadata_from_dataframe(  # pylint: disable=too-many-locals,too-many-bra
             try:
                 cat = read_catalog(location.rsplit("/", 1)[0])
                 catalog.update(cat)
-            except ReadCatalogError:
+            except (ReadCatalogError, ET.ParseError):  # Issue 840
                 warnings.warn(f"Catalog for {imported} not found.")
             locations.add(location)
         # set defined prefix

ontopy/graph.py

@@ -109,6 +109,9 @@
         "hasOutput": {"color": "darkviolet", "style": "dotted"},
         "hasInput": {"color": "darkviolet"},
         "hasTemporaryParticipant": {"color": "darkviolet", "style": "dashed"},
+        "refersTo": {"color": "cyan", "style": "dotted"},
+        "hasReferent": {"color": "cyan"},
+        "providesInterpretation": {"color": "pink", "style": "dashed"},
     },
     "inverse": {"arrowhead": "inv"},
     "default_dataprop": {"color": "green", "constraint": "false"},

ontopy/ontology.py

@@ -110,18 +110,13 @@ def get_ontology(
         base_iri = base_iri.as_uri() if isinstance(base_iri, Path) else base_iri
 
         if base_iri == "emmo":
-            base_iri = (
-                "http://emmo-repo.github.io/versions/1.0.0-beta4/emmo.ttl"
-            )
+            base_iri = "https://w3id.org/emmo/"
         elif base_iri == "emmo-inferred":
-            base_iri = (
-                "https://emmo-repo.github.io/versions/1.0.0-beta4/"
-                "emmo-inferred.ttl"
-            )
+            base_iri = "https://w3id.org/emmo/inferred"
         elif base_iri == "emmo-development":
             base_iri = (
-                "https://emmo-repo.github.io/versions/1.0.0-beta5/"
-                "emmo-inferred.ttl"
+                "https://raw.githubusercontent.com/emmo-repo/EMMO/"
+                "refs/heads/dev/emmo.ttl"
             )
 
         if base_iri in self.ontologies:
@@ -317,33 +312,42 @@ def get_by_label(
         *,
         label_annotations: str = None,
         prefix: str = None,
+        namespace: str = None,
         imported: bool = True,
         colon_in_label: bool = None,
     ):
         """Returns entity with label annotation `label`.
 
         Arguments:
-           label: label so search for.
-               May be written as 'label' or 'prefix:label'.
-               get_by_label('prefix:label') ==
-               get_by_label('label', prefix='prefix').
-           label_annotations: a sequence of label annotation names to look up.
-               Defaults to the `label_annotations` property.
-           prefix: if provided, it should be the last component of
-               the base iri of an ontology (with trailing slash (/) or hash
-               (#) stripped off).  The search for a matching label will be
-               limited to this namespace.
-           imported: Whether to also look for `label` in imported ontologies.
-           colon_in_label: Whether to accept colon (:) in a label or name-part
-               of IRI.  Defaults to the `colon_in_label` property of `self`.
-               Setting this true cannot be combined with `prefix`.
+            label: label so search for.
+                May be written as 'label' or 'prefix:label'
+                get_by_label('prefix:label') is equivalent to
+                searching for both
+                get_by_label('label', prefix='prefix') and
+                get_by_label('label', namespace='prefix')
+            label_annotations: a sequence of label annotation names to look up.
+                Defaults to the `label_annotations` property.
+            prefix: if provided, it should be the last component of
+                the base iri of an ontology (with trailing slash (/) or hash
+                (#) stripped off).  The search for a matching label will be
+                limited to this ontology. `prefix` is ignored if `namespace`
+                is provided.
+            namespace: if provided, it should be the namespace of the entity.
+                It can be provided either as the whole namespace or only as the
+                last 'word' in the namespace, i.e. what is defined as the
+                namespace.name. `namespace` takes precedence over `prefix`.
+            imported: Whether to also look for `label` in imported ontologies.
+            colon_in_label: Whether to accept colon (:) in a label or name-part
+                of IRI.  Defaults to the `colon_in_label` property of `self`.
+                Setting this true cannot be combined with `prefix`.
 
         If several entities have the same label, only the one which is
         found first is returned.Use get_by_label_all() to get all matches.
 
-        Note, if different prefixes are provided in the label and via
-        the `prefix` argument a warning will be issued and the
-        `prefix` argument will take precedence.
+        Note, if namespace is provided directly in the first argument as
+        'namespace:label' it will be used as namespace and
+        any value given to the `namespace` argument will be
+        ignored.
 
         A NoSuchLabelError is raised if `label` cannot be found.
         """
@@ -358,23 +362,34 @@ def get_by_label(
 
         if colon_in_label is None:
             colon_in_label = self._colon_in_label
-        if colon_in_label:
-            if prefix:
-                raise ValueError(
-                    "`prefix` cannot be combined with `colon_in_label`"
+        if colon_in_label and prefix:
+            raise ValueError(
+                "`prefix` cannot be combined with `colon_in_label`"
+            )
+
+        splitlabel = label.split(":", 1)
+        if len(splitlabel) == 2 and not splitlabel[1].startswith("//"):
+            label = splitlabel[1]
+            if namespace and namespace != splitlabel[0]:
+                warnings.warn(
+                    f"Namespace given both as argument ({namespace}) "
+                    f"and in label as ({splitlabel[0]}). "
+                    "Namespace given in argument is ignored. "
                 )
-        else:
-            splitlabel = label.split(":", 1)
-            if len(splitlabel) == 2 and not splitlabel[1].startswith("//"):
-                label = splitlabel[1]
-                if prefix and prefix != splitlabel[0]:
-                    warnings.warn(
-                        f"Prefix given both as argument ({prefix}) "
-                        f"and in label ({splitlabel[0]}). "
-                        "Prefix given in argument takes precedence. "
-                    )
-                if not prefix:
-                    prefix = splitlabel[0]
+            namespace = splitlabel[0]
+
+        if namespace:
+            entityset = self.get_by_label_all(
+                label,
+                label_annotations=label_annotations,
+                namespace=namespace,
+            )
+            if len(entityset) == 1:
+                return entityset.pop()
+            raise NoSuchLabelError(
+                f"No label annotations matches for '{label}' "
+                f"with prefix '{prefix}'."
+            )
 
         if prefix:
             entityset = self.get_by_label_all(
@@ -384,11 +399,6 @@ def get_by_label(
             )
             if len(entityset) == 1:
                 return entityset.pop()
-            if len(entityset) > 1:
-                raise AmbiguousLabelError(
-                    f"Several entities have the same label '{label}' "
-                    f"with prefix '{prefix}'."
-                )
             raise NoSuchLabelError(
                 f"No label annotations matches for '{label}' "
                 f"with prefix '{prefix}'."
@@ -430,24 +440,30 @@ def get_by_label_all(
         label,
         label_annotations=None,
         prefix=None,
+        namespace=None,
         exact_match=False,
     ) -> "Set[Optional[owlready2.entity.EntityClass]]":
         """Returns set of entities with label annotation `label`.
 
         Arguments:
-           label: label so search for.
-               May be written as 'label' or 'prefix:label'.  Wildcard matching
-               using glob pattern is also supported if `exact_match` is set to
-               false.
-           label_annotations: a sequence of label annotation names to look up.
-               Defaults to the `label_annotations` property.
-           prefix: if provided, it should be the last component of
-               the base iri of an ontology (with trailing slash (/) or hash
-               (#) stripped off).  The search for a matching label will be
-               limited to this namespace.
-           exact_match: Do not treat "*" and brackets as special characters
-               when matching.  May be useful if your ontology has labels
-               containing such labels.
+            label: label so search for.
+                May be written as 'label' or 'prefix:label'.  Wildcard matching
+                using glob pattern is also supported if `exact_match` is set to
+                false.
+            label_annotations: a sequence of label annotation names to look up.
+                Defaults to the `label_annotations` property.
+            prefix: if provided, it should be the last component of
+                the base iri of an ontology (with trailing slash (/) or hash
+                (#) stripped off).  The search for a matching label will be
+                limited to this ontology. `prefix` is ignored if `namespace`
+                is provided.
+            namespace: if provided, it should be the namespace of the entity.
+                It can be provided either as the whole namespace or only as the
+                last 'word' in the namespace, i.e. what is defined as the
+                namespace.name. `namespace` takes precedence over `prefix`.
+            exact_match: Do not treat "*" and brackets as special characters
+                when matching.  May be useful if your ontology has labels
+                containing such labels.
 
         Returns:
             Set of all matching entities or an empty set if no matches
@@ -501,13 +517,27 @@ def get_by_label_all(
             entities.update(
                 ent for ent in self.get_entities() if ent.name in matches
             )
+        if namespace:
+            print("in namespace", namespace)
+            print("entities", entities)
+            for ent in entities:
+                print("ent.namespace", ent.namespace)
+                print("ent.namespace.name", ent.namespace.name)
+                print("namespace", namespace)
+                print(namespace in [ent.namespace.name, ent.namespace.base_iri])
+            return set(
+                ent
+                for ent in entities
+                if namespace in [ent.namespace.name, ent.namespace._base_iri]
+            )
 
         if prefix:
             return set(
                 ent
                 for ent in entities
                 if ent.namespace.ontology.prefix == prefix
             )
+
         return entities
 
     def _to_storids(self, sequence, create_if_missing=False):
@@ -564,23 +594,40 @@ def remove_label_annotation(self, iri):
 
     def set_common_prefix(
         self,
-        iri_base: str = "http://emmo.info/emmo",
+        iri_base: str = "https://w3id.org/emmo/inferred",
         prefix: str = "emmo",
         visited: "Optional[Set]" = None,
     ) -> None:
         """Set a common prefix for all imported ontologies
         with the same first part of the base_iri.
 
+        Note that this function might give unintended results.
+        I.e. if `https://w3id.org/emmo` is given as iri_base
+        all imported domain ontologies adhering to the
+        emmo standard for base_iri will be given the same
+        prefix as well as emmo itself.
+
+        The default is to set the prefix to emmo only for emmo-inferred.
+
         Args:
             iri_base: The start of the base_iri to look for. Defaults to
-                the emmo base_iri http://emmo.info/emmo
+                the emmo base_iri https://w3id.org/emmo/inferred
             prefix: the desired prefix. Defaults to emmo.
             visited: Ontologies to skip. Only intended for internal use.
         """
         if visited is None:
             visited = set()
         if self.base_iri.startswith(iri_base):
             self.prefix = prefix
+
+        # If importing emmo-inferred set prefix to emmo
+        if (
+            iri_base == "https://w3id.org/emmo/inferred"
+            and self.prefix == "inferred"
+            and prefix == "emmo"
+            and self.base_iri == "https://w3id.org/emmo#"
+        ):
+            self.prefix = prefix
         for onto in self.imported_ontologies:
             if not onto in visited:
                 visited.add(onto)
@@ -1331,7 +1378,6 @@ def properties(self, imported=False):
         )
         for s in self._get_obj_triples_po_s(rdf_type, rdf_property):
             if not s < 0:
-                # print(s, self._unabbreviate(s))
                 generator.append(self._unabbreviate(s))
                 # generator.append(self[self._unabbreviate(s)])
                 # generator.append(self.world._get_by_storid(s))

tests/ontopy_tests/test_graph.py

@@ -223,8 +223,7 @@ def test_emmo_graphs(emmo: "Ontology", tmpdir: "Path") -> None:
             emmo.Index,
             emmo.Subjective,
             emmo.NominalProperty,
-            emmo.ConventionalQuantitativeProperty,
-            emmo.ModelledQuantitativeProperty,
+            emmo.ConventionalProperty,
             emmo.Theorization,
             emmo.Experiment,
             emmo.Theory,