edit parameters

eccenca · Aug 14, 2024 · 3fa1408 · 3fa1408
1 parent 984c880
commit 3fa1408
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Showing 6 changed files with 49 additions and 44 deletions.
diff --git a/cmem_plugin_reason/plugin_reason.py b/cmem_plugin_reason/plugin_reason.py
@@ -5,7 +5,6 @@
 from pathlib import Path
 from tempfile import TemporaryDirectory
 from time import time
-from warnings import simplefilter
 
 import validators.url
 from cmem.cmempy.dp.proxy.graph import get
@@ -19,13 +18,11 @@
 from cmem_plugin_base.dataintegration.types import BoolParameterType, StringParameterType
 from cmem_plugin_base.dataintegration.utils import setup_cmempy_user_access
 from inflection import underscore
-from urllib3.exceptions import InsecureRequestWarning
 
 from cmem_plugin_reason.utils import (
     MAX_RAM_PERCENTAGE_DEFAULT,
     MAX_RAM_PERCENTAGE_PARAMETER,
     ONTOLOGY_GRAPH_IRI_PARAMETER,
-    OUTPUT_GRAPH_IRI_PARAMETER,
     REASON_DOC,
     REASONERS,
     VALIDATE_PROFILES_PARAMETER,
@@ -40,7 +37,6 @@
 )
 
 environ["SSL_VERIFY"] = "false"
-simplefilter("ignore", category=InsecureRequestWarning)
 
 
 @Plugin(
@@ -50,15 +46,27 @@
     documentation=REASON_DOC,
     parameters=[
         ONTOLOGY_GRAPH_IRI_PARAMETER,
-        OUTPUT_GRAPH_IRI_PARAMETER,
         VALIDATE_PROFILES_PARAMETER,
         MAX_RAM_PERCENTAGE_PARAMETER,
+        PluginParameter(
+            param_type=GraphParameterType(
+                allow_only_autocompleted_values=False,
+                classes=[
+                    "https://vocab.eccenca.com/di/Dataset",
+                    "http://rdfs.org/ns/void#Dataset",
+                    "http://www.w3.org/2002/07/owl#Ontology",
+                ],
+            ),
+            name="output_graph_iri",
+            label="Output graph IRI",
+            description="""The IRI of the output graph for the inconsistency validation. ⚠️ Existing
+            graphs will be overwritten.""",
+        ),
         PluginParameter(
             param_type=ChoiceParameterType(REASONERS),
             name="reasoner",
             label="Reasoner",
             description="Reasoner option. Additionally, select axiom generators below.",
-            default_value="",
         ),
         PluginParameter(
             param_type=GraphParameterType(
@@ -212,10 +220,10 @@ class ReasonPlugin(WorkflowPlugin):
 
     def __init__(  # noqa: PLR0913 C901
         self,
-        data_graph_iri: str = "",
-        ontology_graph_iri: str = "",
-        output_graph_iri: str = "",
-        reasoner: str = "",
+        data_graph_iri: str,
+        ontology_graph_iri: str,
+        output_graph_iri: str,
+        reasoner: str,
         class_assertion: bool = False,
         data_property_characteristic: bool = False,
         disjoint_classes: bool = False,
@@ -260,9 +268,9 @@ def __init__(  # noqa: PLR0913 C901
             errors += 'Invalid IRI for parameter "Ontology graph IRI". '
         if not validators.url(output_graph_iri):
             errors += 'Invalid IRI for parameter "Result graph IRI". '
-        if output_graph_iri and output_graph_iri == data_graph_iri:
+        if output_graph_iri == data_graph_iri:
             errors += "Result graph IRI cannot be the same as the data graph IRI. "
-        if output_graph_iri and output_graph_iri == ontology_graph_iri:
+        if output_graph_iri == ontology_graph_iri:
             errors += "Result graph IRI cannot be the same as the ontology graph IRI. "
         if reasoner not in REASONERS:
             errors += 'Invalid value for parameter "Reasoner". '

diff --git a/cmem_plugin_reason/plugin_validate.py b/cmem_plugin_reason/plugin_validate.py
@@ -5,7 +5,6 @@
 from pathlib import Path
 from tempfile import TemporaryDirectory
 from time import time
-from warnings import simplefilter
 
 import validators.url
 from cmem.cmempy.dp.proxy.graph import get
@@ -14,18 +13,17 @@
 from cmem_plugin_base.dataintegration.description import Icon, Plugin, PluginParameter
 from cmem_plugin_base.dataintegration.entity import Entities, Entity, EntityPath, EntitySchema
 from cmem_plugin_base.dataintegration.parameter.choice import ChoiceParameterType
+from cmem_plugin_base.dataintegration.parameter.graph import GraphParameterType
 from cmem_plugin_base.dataintegration.plugins import WorkflowPlugin
 from cmem_plugin_base.dataintegration.ports import FixedNumberOfInputs, FixedSchemaPort
 from cmem_plugin_base.dataintegration.types import BoolParameterType, StringParameterType
 from cmem_plugin_base.dataintegration.utils import setup_cmempy_user_access
 from pathvalidate import is_valid_filename
-from urllib3.exceptions import InsecureRequestWarning
 
 from cmem_plugin_reason.utils import (
     MAX_RAM_PERCENTAGE_DEFAULT,
     MAX_RAM_PERCENTAGE_PARAMETER,
     ONTOLOGY_GRAPH_IRI_PARAMETER,
-    OUTPUT_GRAPH_IRI_PARAMETER,
     REASONERS,
     VALIDATE_DOC,
     VALIDATE_PROFILES_PARAMETER,
@@ -40,7 +38,6 @@
 )
 
 environ["SSL_VERIFY"] = "false"
-simplefilter("ignore", category=InsecureRequestWarning)
 
 
 @Plugin(
@@ -52,20 +49,34 @@
         ONTOLOGY_GRAPH_IRI_PARAMETER,
         MAX_RAM_PERCENTAGE_PARAMETER,
         VALIDATE_PROFILES_PARAMETER,
-        OUTPUT_GRAPH_IRI_PARAMETER,
+        PluginParameter(
+            param_type=GraphParameterType(
+                allow_only_autocompleted_values=False,
+                classes=[
+                    "https://vocab.eccenca.com/di/Dataset",
+                    "http://rdfs.org/ns/void#Dataset",
+                    "http://www.w3.org/2002/07/owl#Ontology",
+                ],
+            ),
+            name="output_graph_iri",
+            label="Output graph IRI",
+            description="""The IRI of the output graph for the inconsistency validation. ⚠️ Existing
+            graphs will be overwritten.""",
+            default_value="",
+        ),
         PluginParameter(
             param_type=ChoiceParameterType(REASONERS),
             name="reasoner",
             label="Reasoner",
             description="Reasoner option.",
-            default_value="",
         ),
         PluginParameter(
             param_type=StringParameterType(),
             name="md_filename",
             label="Output filename",
             description="The filename of the Markdown file with the explanation of "
             "inconsistencies.⚠️ Existing files will be overwritten.",
+            default_value="",
         ),
         PluginParameter(
             param_type=BoolParameterType(),
@@ -91,8 +102,8 @@ class ValidatePlugin(WorkflowPlugin):
 
     def __init__(  # noqa: PLR0913 C901
         self,
-        ontology_graph_iri: str = "",
-        reasoner: str = "elk",
+        ontology_graph_iri: str,
+        reasoner: str,
         output_graph_iri: str = "",
         md_filename: str = "",
         validate_profile: bool = False,
@@ -268,5 +279,6 @@ def execute(self, inputs: None, context: ExecutionContext) -> Entities | None:
                 operation_desc="ontologies validated.",
             )
         )
+
         with TemporaryDirectory() as self.temp:
             return self._execute(context)
diff --git a/cmem_plugin_reason/utils.py b/cmem_plugin_reason/utils.py
@@ -65,21 +65,6 @@
     default_value=False,
 )
 
-OUTPUT_GRAPH_IRI_PARAMETER = PluginParameter(
-    param_type=GraphParameterType(
-        allow_only_autocompleted_values=False,
-        classes=[
-            "https://vocab.eccenca.com/di/Dataset",
-            "http://rdfs.org/ns/void#Dataset",
-            "http://www.w3.org/2002/07/owl#Ontology",
-        ],
-    ),
-    name="output_graph_iri",
-    label="Output graph IRI",
-    description="""The IRI of the output graph for the inconsistency validation. ⚠️ Existing graphs
-    graphs will be overwritten.""",
-)
-
 
 def create_xml_catalog_file(dir_: str, graphs: dict) -> None:
     """Create XML catalog file"""

diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -22,7 +22,6 @@ python = "^3.11"
 validators = "^0.33.0"
 pathvalidate = "^3.2.0"
 defusedxml = "^0.7.1"
-urllib3 = "^2.2.2"
 inflection = "^0.5.1"
 
 [tool.poetry.dependencies.cmem-plugin-base]

diff --git a/tests/test_reason.py b/tests/test_reason.py
@@ -90,6 +90,7 @@ def test_validate(errors: str) -> str:
         result = ValidatePlugin(
             ontology_graph_iri=VALIDATE_ONTOLOGY_GRAPH_IRI,
             output_graph_iri=OUTPUT_GRAPH_IRI,
+            reasoner="elk",
             validate_profile=True,
             md_filename=MD_FILENAME,
             output_entities=True,