fix(validate-data): enable usage of other ontologies besides the defa…

…ult ontology (DEV-4263) (#1235)

src/dsp_tools/commands/validate_data/models/data_deserialised.py

@@ -3,6 +3,15 @@
 from abc import ABC
 from dataclasses import dataclass
 
+from lxml import etree
+
+
+@dataclass
+class XMLProject:
+    shortcode: str
+    root: etree._Element
+    used_ontologies: set[str]
+
 
 @dataclass
 class ProjectDeserialised:

src/dsp_tools/commands/validate_data/validate_data.py

@@ -11,17 +11,20 @@
 from dsp_tools.commands.validate_data.deserialise_input import deserialise_xml
 from dsp_tools.commands.validate_data.make_data_rdf import make_data_rdf
 from dsp_tools.commands.validate_data.models.data_deserialised import ProjectDeserialised
+from dsp_tools.commands.validate_data.models.data_deserialised import XMLProject
 from dsp_tools.commands.validate_data.models.data_rdf import DataRDF
 from dsp_tools.commands.validate_data.models.validation import RDFGraphs
 from dsp_tools.commands.validate_data.models.validation import ValidationReport
 from dsp_tools.commands.validate_data.reformat_validaton_result import reformat_validation_graph
 from dsp_tools.commands.validate_data.sparql.construct_shacl import construct_shapes_graph
+from dsp_tools.models.exceptions import InputError
 from dsp_tools.utils.xml_utils import parse_xml_file
 from dsp_tools.utils.xml_utils import remove_comments_from_element_tree
 from dsp_tools.utils.xml_utils import transform_into_localnames
 from dsp_tools.utils.xml_validation import validate_xml
 
 LIST_SEPARATOR = "\n    - "
+KNORA_API = "http://api.knora.org/ontology/knora-api/v2#"
 
 
 def validate_data(filepath: Path, api_url: str, dev_route: bool, save_graphs: bool) -> bool:  # noqa: ARG001 (unused argument)
@@ -141,27 +144,54 @@ def _validate(validator: ShaclValidator, rdf_graphs: RDFGraphs) -> ValidationRep
 
 
 def _get_data_info_from_file(file: Path, api_url: str) -> tuple[DataRDF, str]:
-    cleaned_root = _parse_and_clean_file(file, api_url)
-    deserialised: ProjectDeserialised = deserialise_xml(cleaned_root)
+    xml_project = _parse_and_clean_file(file, api_url)
+    deserialised: ProjectDeserialised = deserialise_xml(xml_project.root)
     rdf_data: DataRDF = make_data_rdf(deserialised.data)
     return rdf_data, deserialised.info.shortcode
 
 
-def _parse_and_clean_file(file: Path, api_url: str) -> etree._Element:
+def _parse_and_clean_file(file: Path, api_url: str) -> XMLProject:
     root = parse_xml_file(file)
     root = remove_comments_from_element_tree(root)
     validate_xml(root)
     root = transform_into_localnames(root)
     return _replace_namespaces(root, api_url)
 
 
-def _replace_namespaces(root: etree._Element, api_url: str) -> etree._Element:
-    with open("src/dsp_tools/resources/validate_data/replace_namespace.xslt", "rb") as xslt_file:
-        xslt_data = xslt_file.read()
+def _replace_namespaces(root: etree._Element, api_url: str) -> XMLProject:
+    new_root = deepcopy(root)
     shortcode = root.attrib["shortcode"]
     default_ontology = root.attrib["default-ontology"]
-    namespace = f"{api_url}/ontology/{shortcode}/{default_ontology}/v2#"
-    xslt_root = etree.XML(xslt_data)
-    transform = etree.XSLT(xslt_root)
-    replacement_value = etree.XSLT.strparam(namespace)
-    return transform(root, replacementValue=replacement_value).getroot()
+    namespace_lookup = _make_namespace_lookup(api_url, shortcode, default_ontology)
+    for ele in new_root.iterdescendants():
+        if (found := ele.attrib.get("restype")) or (found := ele.attrib.get("name")):
+            split_found = found.split(":")
+            if len(split_found) == 1:
+                ele.set("restype" if "restype" in ele.attrib else "name", f"{KNORA_API}{found}")
+            elif len(split_found) == 2:
+                if len(split_found[0]) == 0:
+                    found_namespace = namespace_lookup[default_ontology]
+                elif not (namespace := namespace_lookup.get(split_found[0])):
+                    found_namespace = _construct_namespace(api_url, shortcode, split_found[0])
+                    namespace_lookup[split_found[0]] = found_namespace
+                else:
+                    found_namespace = namespace
+                ele.set("restype" if "restype" in ele.attrib else "name", f"{found_namespace}{split_found[1]}")
+            else:
+                raise InputError(
+                    f"It is not permissible to have a colon in a property or resource class name. "
+                    f"Please correct the following: {found}"
+                )
+    return XMLProject(
+        shortcode=shortcode,
+        root=new_root,
+        used_ontologies=set(namespace_lookup.values()),
+    )
+
+
+def _make_namespace_lookup(api_url: str, shortcode: str, default_onto: str) -> dict[str, str]:
+    return {default_onto: _construct_namespace(api_url, shortcode, default_onto), "knora-api": KNORA_API}
+
+
+def _construct_namespace(api_url: str, shortcode: str, onto_name: str) -> str:
+    return f"{api_url}/ontology/{shortcode}/{onto_name}/v2#"

test/integration/commands/validate_data/test_reformat_input.py

@@ -10,7 +10,7 @@ def test_to_data_rdf(data_xml: etree._Element) -> None:
     assert isinstance(res, ProjectDeserialised)
     assert res.info.shortcode == "9999"
     assert res.info.default_onto == "onto"
-    assert len(res.data.resources) == 14
+    assert len(res.data.resources) == 15
 
 
 if __name__ == "__main__":

test/integration/commands/validate_data/test_validate_data.py

@@ -4,7 +4,10 @@
 def test_to_data_rdf(data_xml: etree._Element) -> None:
     res_list = list(data_xml.iterdescendants(tag="resource"))
     all_types = {x.attrib["restype"] for x in res_list}
-    assert all_types == {"http://0.0.0.0:3333/ontology/9999/onto/v2#ClassWithEverything"}
+    assert all_types == {
+        "http://0.0.0.0:3333/ontology/9999/onto/v2#ClassWithEverything",
+        "http://0.0.0.0:3333/ontology/9999/second-onto/v2#SecondOntoClass",
+    }
     expected_names = {
         "http://0.0.0.0:3333/ontology/9999/onto/v2#testBoolean",
         "http://0.0.0.0:3333/ontology/9999/onto/v2#testColor",
@@ -15,9 +18,11 @@ def test_to_data_rdf(data_xml: etree._Element) -> None:
         "http://0.0.0.0:3333/ontology/9999/onto/v2#testListProp",
         "http://0.0.0.0:3333/ontology/9999/onto/v2#testHasLinkTo",
         "http://0.0.0.0:3333/ontology/9999/onto/v2#testRichtext",
+        "http://0.0.0.0:3333/ontology/9999/onto/v2#testSimpleText",
         "http://0.0.0.0:3333/ontology/9999/onto/v2#testTextarea",
         "http://0.0.0.0:3333/ontology/9999/onto/v2#testTimeValue",
         "http://0.0.0.0:3333/ontology/9999/onto/v2#testUriValue",
+        "http://0.0.0.0:3333/ontology/9999/second-onto/v2#testBoolean",
         "http://api.knora.org/ontology/knora-api/v2#hasColor",
         "http://api.knora.org/ontology/knora-api/v2#isRegionOf",
         "http://api.knora.org/ontology/knora-api/v2#hasGeometry",

test/integration/commands/validate_data/xml_fixtures.py

@@ -8,4 +8,4 @@
 
 @pytest.fixture
 def data_xml() -> etree._Element:
-    return _parse_and_clean_file(Path("testdata/validate-data/data/minimal_correct.xml"), "http://0.0.0.0:3333")
+    return _parse_and_clean_file(Path("testdata/validate-data/data/minimal_correct.xml"), "http://0.0.0.0:3333").root

testdata/validate-data/data/minimal_correct.xml

@@ -80,6 +80,15 @@
         </uri-prop>
     </resource>
 
+    <resource label="Class of second ontology" restype="second-onto:SecondOntoClass" id="second_onto_class">
+        <boolean-prop name="second-onto:testBoolean">
+            <boolean>true</boolean>
+        </boolean-prop>
+        <text-prop name=":testSimpleText">
+            <text encoding="utf8">Text</text>
+        </text-prop>
+    </resource>
+
     <region label="Region" id="region_1">
         <color-prop name="hasColor">
             <color permissions="prop-restricted">#5d1f1e</color>

testdata/validate-data/project.json

@@ -505,6 +505,44 @@
             ]
           }
         ]
+      },
+      {
+        "name": "second-onto",
+        "label": "Second Ontology",
+        "properties": [
+          {
+            "name": "testBoolean",
+            "super": [
+              "hasValue"
+            ],
+            "object": "BooleanValue",
+            "labels": {
+              "en": "Test Boolean of the second onto"
+            },
+            "gui_element": "Checkbox"
+          }
+        ],
+        "resources": [
+          {
+            "name": "SecondOntoClass",
+            "super": "Resource",
+            "labels": {
+              "en": "Resource with all cardinality options"
+            },
+            "cardinalities": [
+              {
+                "propname": ":testBoolean",
+                "cardinality": "0-1",
+                "gui_order": 0
+              },
+              {
+                "propname": "onto:testSimpleText",
+                "cardinality": "0-n",
+                "gui_order": 1
+              }
+            ]
+          }
+        ]
       }
     ]
   }