Setting prefix explicitly in excelparser

ontopy/excelparser.py

@@ -9,15 +9,18 @@
 
 Note that correct case is mandatory.
 """
-from typing import Tuple, Union, Sequence
+import os
+from typing import Tuple, Union
 import warnings
 
 import pandas as pd
+import numpy as np
 import pyparsing
 
 import ontopy
 from ontopy import get_ontology
 from ontopy.utils import EMMOntoPyException, NoSuchLabelError
+from ontopy.utils import ReadCatalogError, read_catalog
 from ontopy.manchester import evaluate
 import owlready2  # pylint: disable=C0411
 
@@ -97,20 +100,31 @@ def create_ontology_from_excel(  # pylint: disable=too-many-arguments
                     imported ontology.
 
     """
-    # Get imported ontologies from optional "Imports" sheet
-    if not imports:
-        imports = []
+    web_protocol = "http://", "https://", "ftp://"
+
+    def _relative_to_absolute_paths(path):
+        if isinstance(path, str):
+            if not path.startswith(web_protocol):
+                path = os.path.dirname(excelpath) + "/" + str(path)
+        return path
+
     try:
-        imports_frame = pd.read_excel(
+        imports = pd.read_excel(
             excelpath, sheet_name=imports_sheet_name, skiprows=[1]
         )
     except ValueError:
-        pass
+        imports = pd.DataFrame()
     else:
-        # Strip leading and trailing white spaces in path
-        imports.extend(
-            imports_frame["Imported ontologies"].str.strip().to_list()
+        # Strip leading and trailing white spaces in paths
+        imports.replace(r"^\s+", "", regex=True).replace(
+            r"\s+$", "", regex=True
         )
+        # Set empty strings to nan
+        imports = imports.replace(r"^\s*$", np.nan, regex=True)
+        if "Imported ontologies" in imports.columns:
+            imports["Imported ontologies"] = imports[
+                "Imported ontologies"
+            ].apply(_relative_to_absolute_paths)
 
     # Read datafile TODO: Some magic to identify the header row
     conceptdata = pd.read_excel(
@@ -131,7 +145,7 @@ def create_ontology_from_excel(  # pylint: disable=too-many-arguments
 def create_ontology_from_pandas(  # pylint:disable=too-many-locals,too-many-branches,too-many-statements,too-many-arguments
     data: pd.DataFrame,
     metadata: pd.DataFrame,
-    imports: list,
+    imports: pd.DataFrame,
     base_iri: str = "http://emmo.info/emmo/domain/onto#",
     base_iri_from_metadata: bool = True,
     catalog: dict = None,
@@ -332,7 +346,6 @@ def create_ontology_from_pandas(  # pylint:disable=too-many-locals,too-many-bran
             all_added_rows.extend(added_rows)
 
     # Add properties in a second loop
-
     for index in all_added_rows:
         row = data.loc[index]
         properties = row["Relations"]
@@ -379,14 +392,15 @@ def create_ontology_from_pandas(  # pylint:disable=too-many-locals,too-many-bran
     concepts_with_errors["in_imported_ontologies"] = concepts_with_errors[
         "already_defined"
     ].intersection(imported_concepts)
+
     return onto, catalog, concepts_with_errors
 
 
 def get_metadata_from_dataframe(  # pylint: disable=too-many-locals,too-many-branches,too-many-statements
     metadata: pd.DataFrame,
     base_iri: str,
     base_iri_from_metadata: bool = True,
-    imports: Sequence = (),
+    imports: pd.DataFrame = None,
     catalog: dict = None,
 ) -> Tuple[ontopy.ontology.Ontology, dict]:
     """Create ontology with metadata from pd.DataFrame"""
@@ -409,12 +423,29 @@ def get_metadata_from_dataframe(  # pylint: disable=too-many-locals,too-many-bra
     # Add imported ontologies
     catalog = {} if catalog is None else catalog
     locations = set()
-    for location in imports:
+    for _, row in imports.iterrows():
+        # for location in imports:
+        location = row["Imported ontologies"]
         if not pd.isna(location) and location not in locations:
             imported = onto.world.get_ontology(location).load()
             onto.imported_ontologies.append(imported)
             catalog[imported.base_iri.rstrip("#/")] = location
+            try:
+                cat = read_catalog(location.rsplit("/", 1)[0])
+                catalog.update(cat)
+            except ReadCatalogError:
+                warnings.warn(f"Catalog for {imported} not found.")
             locations.add(location)
+        # set defined prefix
+        if not pd.isna(row["prefix"]):
+            # set prefix for all ontologies with same 'base_iri_root'
+            if not pd.isna(row["base_iri_root"]):
+                onto.set_common_prefix(
+                    iri_base=row["base_iri_root"], prefix=row["prefix"]
+                )
+            # If base_root not given, set prefix only to top ontology
+            else:
+                imported.prefix = row["prefix"]
 
     with onto:
         # Add title

ontopy/ontology.py

@@ -15,7 +15,7 @@
 from pathlib import Path
 from collections import defaultdict
 from collections.abc import Iterable
-from urllib.request import HTTPError
+from urllib.request import HTTPError, URLError
 
 import rdflib
 from rdflib.util import guess_format
@@ -40,6 +40,7 @@
     _validate_installed_version,
     LabelDefinitionError,
     ThingClassDefinitionError,
+    EMMOntoPyException,
 )
 
 if TYPE_CHECKING:
@@ -617,7 +618,13 @@ def getmtime(path):
             if fmt and fmt not in OWLREADY2_FORMATS:
                 # Convert filename to rdfxml before passing it to owlready2
                 graph = rdflib.Graph()
-                graph.parse(resolved_url, format=fmt)
+                try:
+                    graph.parse(resolved_url, format=fmt)
+                except URLError as err:
+                    raise EMMOntoPyException(
+                        "URL error", err, resolved_url
+                    ) from err
+
                 with tempfile.NamedTemporaryFile() as handle:
                     graph.serialize(destination=handle, format="xml")
                     handle.seek(0)

tests/testonto/excelparser/catalog-v001.xml → tests/test_excelparser/catalog-v001.xml

@@ -2,5 +2,8 @@
 <catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
     <group id="Folder Repository, directory=, recursive=true, Auto-Update=false, version=2" prefer="public" xml:base="">
         <uri name="https://raw.githubusercontent.com/emmo-repo/emmo-repo.github.io/master/versions/1.0.0-beta/emmo-inferred-chemistry" uri="https://raw.githubusercontent.com/emmo-repo/emmo-repo.github.io/master/versions/1.0.0-beta/emmo-inferred-chemistry2.ttl"/>
+        <uri name="http://ontology.info/ontology" uri="imported_onto/ontology.ttl"/>
+        <uri name="http://ontology.info/ontology/0.1.0" uri="imported_onto/ontology.ttl"/>
+        <uri name="http://ontology.info/ontology/0.1.0/subontology" uri="imported_onto/subontology.ttl"/>
     </group>
 </catalog>

tests/testonto/excelparser/fromexcelonto.ttl → tests/test_excelparser/fromexcelonto.ttl

@@ -12,7 +12,8 @@
         "Jesper Friis"@en,
         "Sylvain Gouttebroze"@en ;
     term:title "A test domain ontology"@en ;
-    owl:imports <https://raw.githubusercontent.com/emmo-repo/emmo-repo.github.io/master/versions/1.0.0-beta/emmo-inferred-chemistry> ;
+    owl:imports <http://ontology.info/ontology>,
+        <https://raw.githubusercontent.com/emmo-repo/emmo-repo.github.io/master/versions/1.0.0-beta/emmo-inferred-chemistry> ;
     owl:versionInfo "0.01"@en .
 
 :EMMO_0264be35-e8ad-5b35-a1a3-84b37bde22d1 a owl:Class ;
@@ -25,6 +26,10 @@
         :EMMO_4b32833e-0833-56a7-903c-28a6a8191fe8 ;
     core:prefLabel "FiniteTemporalPattern"@en .
 
+:EMMO_080262b7-4f7e-582b-916e-8274c73dd629 a owl:Class ;
+    rdfs:subClassOf <http://ontology.info/ontology#testclass> ;
+    core:prefLabel "ANewTestClass"@en .
+
 :EMMO_1c81f1eb-8b94-5e74-96de-1aeacbdb5b93 a owl:Class ;
     emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 "The boundary of a grain"@en ;
     rdfs:subClassOf :EMMO_472ed27e-ce08-53cb-8453-56ab363275c4 ;
@@ -58,6 +63,10 @@
         :EMMO_9fa9ca88-2891-538a-a8dd-ccb8a08b9890 ;
     core:prefLabel "FiniteSpatioTemporalPattern"@en .
 
+:EMMO_e4e653eb-72cd-5dd6-a428-f506d9679774 a owl:Class ;
+    rdfs:subClassOf <http://ontology.info/subontology#testclass2> ;
+    core:prefLabel "AnotherNewTestClass"@en .
+
 :EMMO_e633d033-2af6-5f04-a706-dab826854fb1 a owl:Class ;
     emmo:EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 "The boundary of a subgrain"@en ;
     rdfs:subClassOf owl:Thing ;

tests/test_excelparser/imported_onto/catalog-v001.xml

@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
+    <group id="Folder Repository, directory=, recursive=true, Auto-Update=false, version=2" prefer="public" xml:base="">
+	    <uri name="http://ontology.info/ontology/0.1.0" uri="./ontology.ttl"/>
+	    <uri name="http://ontology.info/ontology/0.1.0/subontology" uri="./subontology.ttl"/>
+    </group>
+</catalog>

tests/test_excelparser/imported_onto/ontology.ttl

@@ -0,0 +1,18 @@
+@prefix : <http://ontology.info/ontology#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix xml: <http://www.w3.org/XML/1998/namespace> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
+@base <http://ontology.info/ontology> .
+
+<http://ontology.info/ontology> rdf:type owl:Ontology ;
+                             owl:versionIRI <http://ontology.info/ontology/0.1.0> ;
+                             owl:imports <http://ontology.info/ontology/0.1.0/subontology> ;
+			     owl:versionInfo "0.1.0" .
+
+
+:testclass rdf:type owl:Class ;
+    rdfs:subClassOf owl:Thing ;
+    skos:prefLabel "TestClass"@en .

tests/test_excelparser/imported_onto/subontology.ttl

@@ -0,0 +1,21 @@
+@prefix : <http://ontology.info/subontology#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix xml: <http://www.w3.org/XML/1998/namespace> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
+@base <http://ontology.info/subontology> .
+
+<http://ontology.info/subontology> rdf:type owl:Ontology ;
+    owl:versionIRI <http://ontology.info/ontology/0.1.0/subontology> .
+
+
+# Annotations
+skos:prefLabel rdf:type owl:AnnotationProperty .
+skos:altLabel rdf:type owl:AnnotationProperty .
+
+
+:testclass2 rdf:type owl:Class ;
+    rdfs:subClassOf owl:Thing ;
+    skos:prefLabel "TestClass2"@en .

tests/test_excelparser.py → tests/test_excelparser/test_excelparser.py

@@ -10,12 +10,10 @@
 
 def test_excelparser(repo_dir: "Path") -> None:
     """Basic test for creating an ontology from an Excel file."""
-    ontopath = (
-        repo_dir / "tests" / "testonto" / "excelparser" / "fromexcelonto.ttl"
-    )
+    ontopath = repo_dir / "tests" / "test_excelparser" / "fromexcelonto.ttl"
 
     onto = get_ontology(str(ontopath)).load()
-    xlspath = repo_dir / "tests" / "testonto" / "excelparser" / "onto.xlsx"
+    xlspath = repo_dir / "tests" / "test_excelparser" / "onto.xlsx"
     ontology, catalog, errors = create_ontology_from_excel(xlspath, force=True)
     assert onto == ontology
 

tests/test_load.py

@@ -8,7 +8,7 @@ def test_load(repo_dir: "Path", testonto: "Ontology") -> None:
     import pytest
 
     from ontopy import get_ontology
-    from ontopy.ontology import HTTPError
+    from ontopy.ontology import EMMOntoPyException
 
     # Check that the defaults works
     emmo = get_ontology("emmo").load()  # ttl format
@@ -36,8 +36,9 @@ def test_load(repo_dir: "Path", testonto: "Ontology") -> None:
     assert onto.Electrolyte.prefLabel.first() == "Electrolyte"
 
     with pytest.raises(
-        HTTPError,
-        match="HTTP Error 404: https://emmo.info/non-existing/ontology: Not Found",
+        EMMOntoPyException,
+        match="'URL error', <HTTPError 404: 'Not Found'>, 'http://emmo.info/non-existing/ontology'"
+        # match="HTTP Error 404: https://emmo.info/non-existing/ontology: Not Found",
     ):
         get_ontology("http://emmo.info/non-existing/ontology#").load()
 

tests/testonto/catalog-v001.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
     <group id="Folder Repository, directory=, recursive=true, Auto-Update=false, version=2" prefer="public" xml:base="">
-        <uri name="http://emmo.info/testonto/0.1.0" uri="testonto.ttl"/>
-        <uri name="http://emmo.info/testonto/0.1.0/models" uri="models.ttl"/>
+	    <uri name="http://emmo.info/testonto/0.1.0" uri="ontology.ttl"/>
+	    <uri name="http://emmo.info/testonto/0.1.0/models" uri="models.ttl"/>
     </group>
 </catalog>