chore: renaming functions in preparation for TextValue verification

src/dsp_tools/commands/xmlupload/check_consistency_with_ontology.py

@@ -5,7 +5,10 @@
 from lxml import etree
 from regex import Pattern
 
-from dsp_tools.commands.xmlupload.models.ontology_diagnose_models import InvalidOntologyElements, OntoCheckInformation
+from dsp_tools.commands.xmlupload.models.ontology_lookup_models import ProjectOntosInformation
+from dsp_tools.commands.xmlupload.models.ontology_problem_models import (
+    InvalidOntologyElementsInData,
+)
 from dsp_tools.commands.xmlupload.ontology_client import OntologyClient
 from dsp_tools.models.exceptions import UserError
 
@@ -14,7 +17,7 @@
 genericPrefixedOntology: Pattern[str] = regex.compile(r"^[\w\-]+:\w+$")
 
 
-def do_xml_consistency_check(onto_client: OntologyClient, root: etree._Element) -> None:
+def do_xml_consistency_check_with_ontology(onto_client: OntologyClient, root: etree._Element) -> None:
     """
     This function takes an OntologyClient and the root of an XML.
     It retrieves the ontologies from the server.
@@ -28,21 +31,24 @@ def do_xml_consistency_check(onto_client: OntologyClient, root: etree._Element)
      Raises:
          UserError: if there are any invalid properties or classes
     """
-    onto_check_info = OntoCheckInformation(
-        default_ontology_prefix=onto_client.default_ontology, onto_lookup=onto_client.get_all_ontologies_from_server()
+    onto_check_info = ProjectOntosInformation(
+        default_ontology_prefix=onto_client.default_ontology,
+        onto_lookup=onto_client.get_all_ontologies_from_server(),
     )
-    classes, properties = _get_all_classes_and_properties(root)
-    _find_problems_in_classes_and_properties(classes, properties, onto_check_info)
+    classes_in_data, properties_in_data = _get_all_classes_and_properties_from_data(root)
+    _find_if_all_classes_and_properties_exist_in_onto(classes_in_data, properties_in_data, onto_check_info)
 
 
-def _find_problems_in_classes_and_properties(
-    classes: dict[str, list[str]], properties: dict[str, list[str]], onto_check_info: OntoCheckInformation
+def _find_if_all_classes_and_properties_exist_in_onto(
+    classes_in_data: dict[str, list[str]],
+    properties_in_data: dict[str, list[str]],
+    onto_check_info: ProjectOntosInformation,
 ) -> None:
-    class_problems = _diagnose_all_classes(classes, onto_check_info)
-    property_problems = _diagnose_all_properties(properties, onto_check_info)
+    class_problems = _check_if_all_class_types_exist(classes_in_data, onto_check_info)
+    property_problems = _check_if_all_properties_exist(properties_in_data, onto_check_info)
     if not class_problems and not property_problems:
         return None
-    problems = InvalidOntologyElements(
+    problems = InvalidOntologyElementsInData(
         classes=class_problems, properties=property_problems, ontos_on_server=list(onto_check_info.onto_lookup.keys())
     )
     msg, df = problems.execute_problem_protocol()
@@ -56,15 +62,17 @@ def _find_problems_in_classes_and_properties(
     raise UserError(msg)
 
 
-def _get_all_classes_and_properties(root: etree._Element) -> tuple[dict[str, list[str]], dict[str, list[str]]]:
-    cls_dict = _get_all_class_types_and_ids(root)
+def _get_all_classes_and_properties_from_data(
+    root: etree._Element,
+) -> tuple[dict[str, list[str]], dict[str, list[str]]]:
+    cls_dict = _get_all_class_types_and_ids_from_data(root)
     prop_dict: dict[str, list[str]] = {}
     for resource in root.iterchildren(tag="resource"):
         prop_dict = _get_all_property_names_and_resource_ids_one_resource(resource, prop_dict)
     return cls_dict, prop_dict
 
 
-def _get_all_class_types_and_ids(root: etree._Element) -> dict[str, list[str]]:
+def _get_all_class_types_and_ids_from_data(root: etree._Element) -> dict[str, list[str]]:
     cls_dict: dict[str, list[str]] = {}
     for resource in root.iterchildren(tag="resource"):
         restype = resource.attrib["restype"]
@@ -88,18 +96,18 @@ def _get_all_property_names_and_resource_ids_one_resource(
     return prop_dict
 
 
-def _diagnose_all_classes(
-    classes: dict[str, list[str]], onto_check_info: OntoCheckInformation
+def _check_if_all_class_types_exist(
+    classes: dict[str, list[str]], onto_check_info: ProjectOntosInformation
 ) -> list[tuple[str, list[str], str]]:
     problem_list = []
     for cls_type, ids in classes.items():
-        if problem := _diagnose_class(cls_type, onto_check_info):
+        if problem := _check_if_one_class_type_exists(cls_type, onto_check_info):
             problem_list.append((cls_type, ids, problem))
     return problem_list
 
 
-def _diagnose_class(cls_type: str, onto_check_info: OntoCheckInformation) -> str | None:
-    prefix, cls_ = _get_prefix_and_prop_or_cls_identifier(cls_type, onto_check_info.default_ontology_prefix)
+def _check_if_one_class_type_exists(cls_type: str, onto_check_info: ProjectOntosInformation) -> str | None:
+    prefix, cls_ = _get_separate_prefix_and_iri_from_onto_prop_or_cls(cls_type, onto_check_info.default_ontology_prefix)
     if not prefix:
         return "Property name does not follow a known ontology pattern"
     if onto := onto_check_info.onto_lookup.get(prefix):
@@ -108,18 +116,20 @@ def _diagnose_class(cls_type: str, onto_check_info: OntoCheckInformation) -> str
         return "Unknown ontology prefix"
 
 
-def _diagnose_all_properties(
-    properties: dict[str, list[str]], onto_check_info: OntoCheckInformation
+def _check_if_all_properties_exist(
+    properties: dict[str, list[str]], onto_check_info: ProjectOntosInformation
 ) -> list[tuple[str, list[str], str]]:
     problem_list = []
     for prop_name, ids in properties.items():
-        if problem := _diagnose_property(prop_name, onto_check_info):
+        if problem := _check_if_one_property_exists(prop_name, onto_check_info):
             problem_list.append((prop_name, ids, problem))
     return problem_list
 
 
-def _diagnose_property(prop_name: str, onto_check_info: OntoCheckInformation) -> str | None:
-    prefix, prop = _get_prefix_and_prop_or_cls_identifier(prop_name, onto_check_info.default_ontology_prefix)
+def _check_if_one_property_exists(prop_name: str, onto_check_info: ProjectOntosInformation) -> str | None:
+    prefix, prop = _get_separate_prefix_and_iri_from_onto_prop_or_cls(
+        prop_name, onto_check_info.default_ontology_prefix
+    )
     if not prefix:
         return "Property name does not follow a known ontology pattern"
     if onto := onto_check_info.onto_lookup.get(prefix):
@@ -128,7 +138,7 @@ def _diagnose_property(prop_name: str, onto_check_info: OntoCheckInformation) ->
         return "Unknown ontology prefix"
 
 
-def _get_prefix_and_prop_or_cls_identifier(
+def _get_separate_prefix_and_iri_from_onto_prop_or_cls(
     prop_or_cls: str, default_ontology_prefix: str
 ) -> tuple[str, ...] | tuple[None, None]:
     if defaultOntologyColon.match(prop_or_cls):

src/dsp_tools/commands/xmlupload/models/ontology_lookup_models.py

@@ -0,0 +1,57 @@
+from dataclasses import dataclass, field
+from typing import Any
+
+
+@dataclass(frozen=True)
+class OntoInfo:
+    """This class saves the properties and the classes from an ontology."""
+
+    classes: list[str] = field(default_factory=list)
+    properties: list[str] = field(default_factory=list)
+
+
+@dataclass
+class ProjectOntosInformation:
+    """This class saves information needed to check the consistency with the ontology."""
+
+    default_ontology_prefix: str
+    onto_lookup: dict[str, OntoInfo]
+
+
+def extract_classes_properties_from_onto(onto_graph: list[dict[str, Any]]) -> OntoInfo:
+    """
+    This function takes an ontology graph from the DSP-API.
+    It extracts the classes and properties.
+    And saves them in an instance of the class Ontology.
+
+    Args:
+        onto_graph: graph from DSP-API
+
+    Returns:
+        Ontology instance with the classes and properties
+    """
+    classes = _get_all_cleaned_classes_from_graph(onto_graph)
+    properties = _get_all_cleaned_properties_from_graph(onto_graph)
+    return OntoInfo(classes, properties)
+
+
+def _get_all_cleaned_classes_from_graph(onto_graph: list[dict[str, Any]]) -> list[str]:
+    classes = _get_all_classes_from_graph(onto_graph)
+    return _remove_prefixes(classes)
+
+
+def _get_all_classes_from_graph(onto_graph: list[dict[str, Any]]) -> list[str]:
+    return [elem["@id"] for elem in onto_graph if elem.get("knora-api:isResourceClass")]
+
+
+def _get_all_cleaned_properties_from_graph(onto_graph: list[dict[str, Any]]) -> list[str]:
+    props = _get_all_properties_from_graph(onto_graph)
+    return _remove_prefixes(props)
+
+
+def _get_all_properties_from_graph(onto_graph: list[dict[str, Any]]) -> list[str]:
+    return [elem["@id"] for elem in onto_graph if not elem.get("knora-api:isResourceClass")]
+
+
+def _remove_prefixes(ontology_elements: list[str]) -> list[str]:
+    return [x.split(":")[1] for x in ontology_elements]

src/dsp_tools/commands/xmlupload/models/ontology_diagnose_models.py → src/dsp_tools/commands/xmlupload/models/ontology_problem_models.py

@@ -1,32 +1,17 @@
 import itertools
-from dataclasses import dataclass, field
+from dataclasses import dataclass
 
 import pandas as pd
 
 separator = "\n    "
 list_separator = "\n    - "
-grand_separator = "\n----------------------------\n"
+medium_separator = "\n----------------------------\n"
+grand_separator = "\n\n---------------------------------------\n\n"
 maximum_prints = 50
 
 
 @dataclass(frozen=True)
-class OntoInfo:
-    """This class saves the properties and the classes from an ontology."""
-
-    classes: list[str] = field(default_factory=list)
-    properties: list[str] = field(default_factory=list)
-
-
-@dataclass
-class OntoCheckInformation:
-    """This class saves information needed to check the consistency with the ontology."""
-
-    default_ontology_prefix: str
-    onto_lookup: dict[str, OntoInfo]
-
-
-@dataclass(frozen=True)
-class InvalidOntologyElements:
+class InvalidOntologyElementsInData:
     """This class saves and prints out the information regarding ontology classes and properties
     that are in the XML but not the ontology."""
 
@@ -42,15 +27,14 @@ def execute_problem_protocol(self) -> tuple[str, pd.DataFrame | None]:
         Returns:
             the error message and a dataframe with the errors if they exceed 50 or None
         """
-        extra_separator = "\n\n---------------------------------------\n\n"
         msg = (
             f"\nSome property and/or class type(s) used in the XML are unknown.\n"
             f"The ontologies for your project on the server are:{list_separator}"
-            f"{list_separator.join(self.ontos_on_server)}{extra_separator}"
+            f"{list_separator.join(self.ontos_on_server)}{grand_separator}"
         )
         cls_msg = self._compose_problem_string_for_cls()
         if cls_msg:
-            msg += cls_msg + extra_separator
+            msg += cls_msg + grand_separator
         prop_msg = self._compose_problem_string_for_props()
         if prop_msg:
             msg += prop_msg
@@ -108,7 +92,7 @@ def _format_cls(cls_tup: tuple[str, list[str], str]) -> str:
 
             problems = [_format_cls(x) for x in self.classes]
 
-            return "The following resource(s) have an invalid resource type:\n\n" + grand_separator.join(problems)
+            return "The following resource(s) have an invalid resource type:\n\n" + medium_separator.join(problems)
         else:
             return None
 
@@ -126,6 +110,6 @@ def _format_prop(prop_tup: tuple[str, list[str], str]) -> str:
                 )
 
             problems = [_format_prop(x) for x in self.properties]
-            return "The following resource(s) have invalid property type(s):\n\n" + grand_separator.join(problems)
+            return "The following resource(s) have invalid property type(s):\n\n" + medium_separator.join(problems)
         else:
             return None

src/dsp_tools/commands/xmlupload/ontology_client.py

@@ -2,7 +2,7 @@
 from pathlib import Path
 from typing import Any, Protocol
 
-from dsp_tools.commands.xmlupload.models.ontology_diagnose_models import OntoInfo
+from dsp_tools.commands.xmlupload.models.ontology_lookup_models import OntoInfo, extract_classes_properties_from_onto
 from dsp_tools.models.exceptions import BaseError, UserError
 from dsp_tools.utils.connection import Connection
 from dsp_tools.utils.create_logger import get_logger
@@ -21,7 +21,10 @@ class OntologyClient(Protocol):
     ontology_names: list[str] = field(default_factory=list)
 
     def get_all_ontologies_from_server(self) -> dict[str, OntoInfo]:
-        """Get all the ontologies for a project and the knora-api ontology from the server."""
+        """Get all the ontologies for a project from the server."""
+
+    def get_knora_api_ontology_from_server(self) -> list[dict[str, Any]]:
+        """Get the knora-api ontology from the server."""
 
 
 @dataclass
@@ -42,12 +45,14 @@ def get_all_ontologies_from_server(self) -> dict[str, OntoInfo]:
             a dictionary with the ontology name as key and the ontology as value.
         """
         ontologies = self._get_all_ontology_jsons_from_server()
-        return {onto_name: deserialize_ontology(onto_graph) for onto_name, onto_graph in ontologies.items()}
+        return {
+            onto_name: extract_classes_properties_from_onto(onto_graph) for onto_name, onto_graph in ontologies.items()
+        }
 
     def _get_all_ontology_jsons_from_server(self) -> dict[str, list[dict[str, Any]]]:
         self._get_ontology_names_from_server()
         project_ontos = {onto: self._get_ontology_from_server(onto) for onto in self.ontology_names}
-        project_ontos["knora-api"] = self._get_knora_api_ontology_from_server()
+        project_ontos["knora-api"] = self.get_knora_api_ontology_from_server()
         return project_ontos
 
     def _get_ontology_names_from_server(self) -> None:
@@ -77,7 +82,16 @@ def _get_ontology_from_server(self, ontology_name: str) -> list[dict[str, Any]]:
             raise BaseError(f"Unexpected response from server: {res}") from e
         return onto_graph
 
-    def _get_knora_api_ontology_from_server(self) -> list[dict[str, Any]]:
+    def get_knora_api_ontology_from_server(self) -> list[dict[str, Any]]:
+        """
+        This function returns the knora-api ontology from the server.
+
+        Returns:
+            knora-api ontology in json format
+
+        Raises:
+            BaseError: if an unexpected response from the server occurred
+        """
         url = "/ontology/knora-api/v2#"
         try:
             res = self.con.get(url)
@@ -88,42 +102,3 @@ def _get_knora_api_ontology_from_server(self) -> list[dict[str, Any]]:
         except KeyError as e:
             raise BaseError(f"Unexpected response from server when retrieving knora-api ontology: {res}") from e
         return onto_graph
-
-
-def deserialize_ontology(onto_graph: list[dict[str, Any]]) -> OntoInfo:
-    """
-    This function takes an ontology graph from the DSP-API.
-    It extracts the classes and properties.
-    And saves them in an instance of the class Ontology.
-
-    Args:
-        onto_graph: graph from DSP-API
-
-    Returns:
-        Ontology instance with the classes and properties
-    """
-    classes = _get_all_cleaned_classes_from_graph(onto_graph)
-    properties = _get_all_cleaned_properties_from_graph(onto_graph)
-    return OntoInfo(classes, properties)
-
-
-def _get_all_cleaned_classes_from_graph(onto_graph: list[dict[str, Any]]) -> list[str]:
-    classes = _get_all_classes_from_graph(onto_graph)
-    return _remove_prefixes(classes)
-
-
-def _get_all_classes_from_graph(onto_graph: list[dict[str, Any]]) -> list[str]:
-    return [elem["@id"] for elem in onto_graph if elem.get("knora-api:isResourceClass")]
-
-
-def _get_all_cleaned_properties_from_graph(onto_graph: list[dict[str, Any]]) -> list[str]:
-    props = _get_all_properties_from_graph(onto_graph)
-    return _remove_prefixes(props)
-
-
-def _get_all_properties_from_graph(onto_graph: list[dict[str, Any]]) -> list[str]:
-    return [elem["@id"] for elem in onto_graph if not elem.get("knora-api:isResourceClass")]
-
-
-def _remove_prefixes(ontology_elements: list[str]) -> list[str]:
-    return [x.split(":")[1] for x in ontology_elements]

src/dsp_tools/commands/xmlupload/xmlupload.py

@@ -10,7 +10,7 @@
 
 from lxml import etree
 
-from dsp_tools.commands.xmlupload.check_consistency_with_ontology import do_xml_consistency_check
+from dsp_tools.commands.xmlupload.check_consistency_with_ontology import do_xml_consistency_check_with_ontology
 from dsp_tools.commands.xmlupload.iri_resolver import IriResolver
 from dsp_tools.commands.xmlupload.list_client import ListClient, ListClientLive
 from dsp_tools.commands.xmlupload.models.permission import Permissions
@@ -94,7 +94,7 @@ def xmlupload(
         default_ontology=default_ontology,
         save_location=config.diagnostics.save_location,
     )
-    do_xml_consistency_check(onto_client=ontology_client, root=root)
+    do_xml_consistency_check_with_ontology(onto_client=ontology_client, root=root)
 
     resources, permissions_lookup, stash = _prepare_upload(
         root=root,
@@ -104,11 +104,7 @@ def xmlupload(
     )
 
     project_client: ProjectClient = ProjectClientLive(con, config.shortcode)
-    if default_ontology not in project_client.get_ontology_name_dict():
-        raise UserError(
-            f"The default ontology '{default_ontology}' "
-            "specified in the XML file is not part of the project on the DSP server."
-        )
+
     list_client: ListClient = ListClientLive(con, project_client.get_project_iri())
 
     iri_resolver, failed_uploads = _upload(