From 032d4efa1eabaf4636499cce564045e014b5ab0d Mon Sep 17 00:00:00 2001
From: muddymudskipper <thomas.wilmering@gmail.com>
Date: Sat, 29 Jun 2024 14:45:08 +0100
Subject: [PATCH 1/7] valid range of "Maximum RAM Percentage" parameter in
 Validate plugin

---
 CHANGELOG.md                          | 5 +++++
 cmem_plugin_reason/plugin_validate.py | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e481e71..675718e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,11 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](http://keepachangelog.com/) and this project adheres to [Semantic Versioning](https://semver.org/)
 
+## [Unreleased] 2024-06-28
+
+### Fixed
+
+- valid range of "Maximum RAM Percentage" parameter in Validate plugin (1-100)
 
 ## [1.0.0alpha3] 2024-06-28
 
diff --git a/cmem_plugin_reason/plugin_validate.py b/cmem_plugin_reason/plugin_validate.py
index f2c8969..8a5a487 100644
--- a/cmem_plugin_reason/plugin_validate.py
+++ b/cmem_plugin_reason/plugin_validate.py
@@ -110,7 +110,7 @@ def __init__(  # noqa: PLR0913
                 validate_filename(md_filename)
             except:  # noqa: E722
                 errors += "Invalid filename for parameter Output filename. "
-        if max_ram_percentage not in range(1, 100):
+        if max_ram_percentage not in range(1, 101):
             errors += "Invalid value for parameter Maximum RAM Percentage. "
         if errors:
             raise ValueError(errors[:-1])

From 3da2194e8e64d63cd9b3c783f815e220786d15ce Mon Sep 17 00:00:00 2001
From: muddymudskipper <thomas.wilmering@gmail.com>
Date: Sat, 29 Jun 2024 14:47:04 +0100
Subject: [PATCH 2/7] edit CHANGELOG

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 675718e..6776ce0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,7 +4,7 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](http://keepachangelog.com/) and this project adheres to [Semantic Versioning](https://semver.org/)
 
-## [Unreleased] 2024-06-28
+## [Unreleased]
 
 ### Fixed
 

From e635ba988f5b37bd08cacb292c44b30c1c43d08d Mon Sep 17 00:00:00 2001
From: muddymudskipper <thomas.wilmering@gmail.com>
Date: Sat, 29 Jun 2024 15:39:58 +0100
Subject: [PATCH 3/7] edit parameter validation

---
 CHANGELOG.md                          |  4 ++
 cmem_plugin_reason/plugin_reason.py   | 20 +++----
 cmem_plugin_reason/plugin_validate.py | 25 ++++----
 poetry.lock                           | 82 +++++++++++++--------------
 4 files changed, 65 insertions(+), 66 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6776ce0..9858111 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,10 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/) and this p
 
 - valid range of "Maximum RAM Percentage" parameter in Validate plugin (1-100)
 
+### Change
+
+- completed validation for IRI parameters
+
 ## [1.0.0alpha3] 2024-06-28
 
 ### Added
diff --git a/cmem_plugin_reason/plugin_reason.py b/cmem_plugin_reason/plugin_reason.py
index 6934de7..838aa15 100644
--- a/cmem_plugin_reason/plugin_reason.py
+++ b/cmem_plugin_reason/plugin_reason.py
@@ -172,9 +172,9 @@
     ],
 )
 class ReasonPlugin(WorkflowPlugin):
-    """Robot reasoning plugin"""
+    """Reason plugin"""
 
-    def __init__(  # noqa: PLR0913
+    def __init__(  # noqa: PLR0913, C901
         self,
         data_graph_iri: str = "",
         ontology_graph_iri: str = "",
@@ -197,7 +197,6 @@ def __init__(  # noqa: PLR0913
         annotate_inferred_axioms: bool = False,
         max_ram_percentage: int = MAX_RAM_PERCENTAGE_DEFAULT,
     ) -> None:
-        """Init"""
         self.axioms = {
             "SubClass": sub_class,
             "EquivalentClass": equivalent_class,
@@ -216,14 +215,12 @@ def __init__(  # noqa: PLR0913
         }
 
         errors = ""
-        iris = {
-            "Data graph IRI": data_graph_iri,
-            "Ontology graph IRI": ontology_graph_iri,
-            "Result graph IRI": result_graph_iri,
-        }
-        not_iri = sorted([k for k, v in iris.items() if not validators.url(v)])
-        if not_iri:
-            errors += f"Invalid IRI for parameters: {', '.join(not_iri)}. "
+        if not validators.url(data_graph_iri):
+            errors += 'Invalid IRI for parameter "Data graph IRI". '
+        if not validators.url(ontology_graph_iri):
+            errors += 'Invalid IRI for parameter "Ontology graph IRI". '
+        if not validators.url(result_graph_iri):
+            errors += 'Invalid IRI for parameter "Result graph IRI". '
         if result_graph_iri and result_graph_iri == data_graph_iri:
             errors += "Result graph IRI cannot be the same as the data graph IRI. "
         if result_graph_iri and result_graph_iri == ontology_graph_iri:
@@ -241,7 +238,6 @@ def __init__(  # noqa: PLR0913
             errors += 'Invalid value for parameter "Maximum RAM Percentage". '
         if errors:
             raise ValueError(errors[:-1])
-
         self.data_graph_iri = data_graph_iri
         self.ontology_graph_iri = ontology_graph_iri
         self.result_graph_iri = result_graph_iri
diff --git a/cmem_plugin_reason/plugin_validate.py b/cmem_plugin_reason/plugin_validate.py
index 8a5a487..c82d91a 100644
--- a/cmem_plugin_reason/plugin_validate.py
+++ b/cmem_plugin_reason/plugin_validate.py
@@ -22,7 +22,7 @@
 from cmem_plugin_base.dataintegration.plugins import WorkflowPlugin
 from cmem_plugin_base.dataintegration.types import BoolParameterType, StringParameterType
 from cmem_plugin_base.dataintegration.utils import setup_cmempy_user_access
-from pathvalidate import validate_filename
+from pathvalidate import is_valid_filename
 
 from cmem_plugin_reason.utils import (
     MAX_RAM_PERCENTAGE_DEFAULT,
@@ -85,7 +85,7 @@
     ],
 )
 class ValidatePlugin(WorkflowPlugin):
-    """Example Workflow Plugin: Random Values"""
+    """Validate plugin"""
 
     def __init__(  # noqa: PLR0913
         self,
@@ -100,18 +100,17 @@ def __init__(  # noqa: PLR0913
     ) -> None:
         errors = ""
         if not validators.url(ontology_graph_iri):
-            errors += "Invalid IRI for parameter Ontology graph IRI. "
-        if reasoner not in REASONERS:
-            errors += "Invalid value for parameter Reasoner. "
+            errors += 'Invalid IRI for parameter "Ontology graph IRI." '
         if produce_graph and not validators.url(output_graph_iri):
-            errors += "Invalid IRI for parameter Output graph IRI. "
-        if write_md:
-            try:
-                validate_filename(md_filename)
-            except:  # noqa: E722
-                errors += "Invalid filename for parameter Output filename. "
+            errors += 'Invalid IRI for parameter "Output graph IRI". '
+        if produce_graph and output_graph_iri == ontology_graph_iri:
+            errors += "Output graph IRI cannot be the same as the Ontology graph IRI. "
+        if reasoner not in REASONERS:
+            errors += 'Invalid value for parameter "Reasoner". '
+        if write_md and not is_valid_filename(md_filename):
+            errors += 'Invalid filename for parameter "Output filename". '
         if max_ram_percentage not in range(1, 101):
-            errors += "Invalid value for parameter Maximum RAM Percentage. "
+            errors += 'Invalid value for parameter "Maximum RAM Percentage". '
         if errors:
             raise ValueError(errors[:-1])
 
@@ -121,7 +120,7 @@ def __init__(  # noqa: PLR0913
         self.output_graph_iri = output_graph_iri
         self.write_md = write_md
         self.stop_at_inconsistencies = stop_at_inconsistencies
-        self.md_filename = md_filename if md_filename and write_md else "mdfile.md"
+        self.md_filename = md_filename if write_md else "mdfile.md"
         self.max_ram_percentage = max_ram_percentage
         self.temp = f"reason_{uuid4().hex}"
 
diff --git a/poetry.lock b/poetry.lock
index ce33ffb..61c0e7c 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -485,48 +485,48 @@ files = [
 
 [[package]]
 name = "memray"
-version = "1.13.1"
+version = "1.13.2"
 description = "A memory profiler for Python applications"
 optional = false
 python-versions = ">=3.7.0"
 files = [
-    {file = "memray-1.13.1-cp310-cp310-macosx_10_14_x86_64.whl", hash = "sha256:5aa567b5f7a3f67b40194dcaa3ef06557ebf088e67f7ee41e7154b9747dbbd8d"},
-    {file = "memray-1.13.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:94eefd57a5e4f27ab97e976d732027957b15e3b9b561a643388dd1417380461d"},
-    {file = "memray-1.13.1-cp310-cp310-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:22263e294faffda1f8097b0d6e1d2283ca35a537d3e8f608244f48fd3f58d490"},
-    {file = "memray-1.13.1-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:8e3a5eb9bc01cdc2f916bae1615301347aaa252deb983d8277b0c9e4d4410e73"},
-    {file = "memray-1.13.1-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:f4917e333290802d91d1823f34365670628b2b0804dba93150c79bf8b855f8d5"},
-    {file = "memray-1.13.1-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:4270998b8fcd5f1a9c8faff2ad4f46fed57191160e78183357eba7dc32d93a1b"},
-    {file = "memray-1.13.1-cp311-cp311-macosx_10_14_x86_64.whl", hash = "sha256:71c5c8bb5d7ad19b3027efc48a792cb35bda7b9e1662b2c5f23af3f8f7374eae"},
-    {file = "memray-1.13.1-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:dadd7afa44df07074f4d887587e8241e085d9727fcf5b5097930c05ad054027a"},
-    {file = "memray-1.13.1-cp311-cp311-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:9d9e2604dd2b2025d5f0012e848cbc5357a15a4d27297cde5f76dd2fccb1873f"},
-    {file = "memray-1.13.1-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:74871ef2047f30d0f98994f56563fa8be85515679fbc398006246339ff4ace7d"},
-    {file = "memray-1.13.1-cp311-cp311-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:3d6bdaf8a4499f8dc3e1f6781cab13f95ed052f77b0a2ca0ef63ac851296cc9b"},
-    {file = "memray-1.13.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:748c7ba3180d84a5ce6dfc413e7f6127d887341ea75ddbffee150e0124cf810c"},
-    {file = "memray-1.13.1-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:659c8ddcae04bd8bc627836663a90eec077d831d904dc8ed7ce42a64a96fe8d2"},
-    {file = "memray-1.13.1-cp312-cp312-macosx_10_14_x86_64.whl", hash = "sha256:a86f80ced0bdf49e2cc637e112664dce6ded43a802c0fe99ea826f1a717fa252"},
-    {file = "memray-1.13.1-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:06d5f9ab8b4952631c030bfba74a385686f2da11471e13d838184b32d6582edb"},
-    {file = "memray-1.13.1-cp312-cp312-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:e33f8320e8578d16e371b90cd2c792e1414bfe28173c7f977d6b440686a66625"},
-    {file = "memray-1.13.1-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:c2c9896719d82240291f7ac81ba2509a8065f4a7829fc8219e0890e68877f497"},
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+    {file = "memray-1.13.2-cp37-cp37m-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:8c7ba0bd98323c71a5f2cafa81e74d232e9d1c7437682fdf1cb8833ec2c70f08"},
+    {file = "memray-1.13.2-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:d00ba714d6f8fe32fbfdf75f2d1b6755edcd7c6835efc4a65fa58943c0b53e62"},
+    {file = "memray-1.13.2-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:3bef98aaf398cb7f47669808d5febdad4323050f32f6e73ec3bfc6f7c04aacb0"},
+    {file = "memray-1.13.2-cp37-cp37m-musllinux_1_1_x86_64.whl", hash = "sha256:300c3710d6ddd291d6b53402e11c0de5818223e58e21ca1d42817f36dee29b24"},
+    {file = "memray-1.13.2-cp38-cp38-macosx_10_14_x86_64.whl", hash = "sha256:5e63552376567283a388e67382534017909891df8500d92e2dad1ebd3762d5b1"},
+    {file = "memray-1.13.2-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:4f09742556da269712cc89a7acaaa0825db15547ac1d03490f09ba3c2bf381f3"},
+    {file = "memray-1.13.2-cp38-cp38-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:6c5595539579f3f662acf794d8ac2fd3f23d3a24c4aea893a15b307c2727c3c8"},
+    {file = "memray-1.13.2-cp38-cp38-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:60176bf3015a155233d8cfaf7a6141eedc3ce5e89231892a96e162c073fb42cd"},
+    {file = "memray-1.13.2-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:bfa76dce73e6ee263d254345affc8bf7d4db8f899b7af396a0f5e37899f28aac"},
+    {file = "memray-1.13.2-cp38-cp38-musllinux_1_1_x86_64.whl", hash = "sha256:59bcb96af1a3462626575de4763c88217d9c1561d8c166c9a10f00a0c19ad8d1"},
+    {file = "memray-1.13.2-cp39-cp39-macosx_10_14_x86_64.whl", hash = "sha256:cdd35bf96776c27ffb326c2c4b6f9b50d9461b25f98574df98771593768eb803"},
+    {file = "memray-1.13.2-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:48449deeb65de71c0fda4ce9b539a9f35fe2634af3bcac367167903bab25cff0"},
+    {file = "memray-1.13.2-cp39-cp39-manylinux_2_12_i686.manylinux2010_i686.whl", hash = "sha256:71021329db86e03840fe210c5a6581500a069736e6f8835b2dae9c8e6be96302"},
+    {file = "memray-1.13.2-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl", hash = "sha256:db87adfbf05cec117b75cdafb7e2627d649b72f15a191e106375ee0acdd54b53"},
+    {file = "memray-1.13.2-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:6305ea70ddd15b9897abcc6f234b8aa94d4135146381b3d68fc97ec2d8d3f7ec"},
+    {file = "memray-1.13.2-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:1f38100fedec5c318c00654864ff2e6e8b8ffdb472206047e300337c2d55bb37"},
+    {file = "memray-1.13.2.tar.gz", hash = "sha256:355803182ea4a61dcb456c4c1e765f929123fc2b6998ba44efa4ae32b763e05b"},
 ]
 
 [package.dependencies]
@@ -1048,13 +1048,13 @@ files = [
 
 [[package]]
 name = "textual"
-version = "0.70.0"
+version = "0.71.0"
 description = "Modern Text User Interface framework"
 optional = false
 python-versions = "<4.0,>=3.8"
 files = [
-    {file = "textual-0.70.0-py3-none-any.whl", hash = "sha256:774bf45782193760ca273b915fd685cada37d0836237d61dc57d5bcdbe2c7ddb"},
-    {file = "textual-0.70.0.tar.gz", hash = "sha256:9ca3f615b5cf442246325e40ef8255424c42b4241d3c62f9c0f96951bab82b1e"},
+    {file = "textual-0.71.0-py3-none-any.whl", hash = "sha256:60500cc63ffd98a4aff8679976a1530d5e99a881e13bb040d26558a2c45f49d8"},
+    {file = "textual-0.71.0.tar.gz", hash = "sha256:a38a3bd7e450ed173b59ab1c93a3aa8174d95bc5c79647f220a50243236ce70a"},
 ]
 
 [package.dependencies]

From ee90828fd8fd3299980f4c155327fadc3fd02344 Mon Sep 17 00:00:00 2001
From: muddymudskipper <thomas.wilmering@gmail.com>
Date: Sat, 29 Jun 2024 15:54:22 +0100
Subject: [PATCH 4/7] edits

---
 cmem_plugin_reason/plugin_reason.py   | 4 +---
 cmem_plugin_reason/plugin_validate.py | 7 +------
 2 files changed, 2 insertions(+), 9 deletions(-)

diff --git a/cmem_plugin_reason/plugin_reason.py b/cmem_plugin_reason/plugin_reason.py
index 838aa15..0267af2 100644
--- a/cmem_plugin_reason/plugin_reason.py
+++ b/cmem_plugin_reason/plugin_reason.py
@@ -1,7 +1,6 @@
 """Reasoning workflow plugin module"""
 
 import shlex
-from collections.abc import Sequence
 from datetime import UTC, datetime
 from pathlib import Path
 from subprocess import run
@@ -12,7 +11,6 @@
 from cmem.cmempy.dp.proxy.graph import get
 from cmem_plugin_base.dataintegration.context import ExecutionContext
 from cmem_plugin_base.dataintegration.description import Icon, Plugin, PluginParameter
-from cmem_plugin_base.dataintegration.entity import Entities
 from cmem_plugin_base.dataintegration.parameter.graph import GraphParameterType
 from cmem_plugin_base.dataintegration.plugins import WorkflowPlugin
 from cmem_plugin_base.dataintegration.types import BoolParameterType, StringParameterType
@@ -315,7 +313,7 @@ def clean_up(self, graphs: dict) -> None:
         except (OSError, FileNotFoundError) as err:
             self.log.warning(f"Cannot remove directory {self.temp} ({err})")
 
-    def execute(self, inputs: Sequence[Entities], context: ExecutionContext) -> None:  # noqa: ARG002
+    def execute(self, inputs: tuple, context: ExecutionContext) -> None:  # noqa: ARG002
         """Execute plugin"""
         setup_cmempy_user_access(context.user)
         graphs = get_graphs_tree((self.data_graph_iri, self.ontology_graph_iri))
diff --git a/cmem_plugin_reason/plugin_validate.py b/cmem_plugin_reason/plugin_validate.py
index c82d91a..3fca096 100644
--- a/cmem_plugin_reason/plugin_validate.py
+++ b/cmem_plugin_reason/plugin_validate.py
@@ -1,7 +1,6 @@
 """Ontology consistency validation workflow plugin module"""
 
 import shlex
-from collections.abc import Sequence
 from datetime import UTC, datetime
 from pathlib import Path
 from subprocess import run
@@ -189,11 +188,7 @@ def clean_up(self, graphs: dict) -> None:
         except (OSError, FileNotFoundError) as err:
             self.log.warning(f"Cannot remove directory {self.temp} ({err})")
 
-    def execute(
-        self,
-        inputs: Sequence[Entities],  # noqa: ARG002
-        context: ExecutionContext,
-    ) -> Entities | None:
+    def execute(self, inputs: tuple, context: ExecutionContext) -> Entities | None:  # noqa: ARG002
         """Run the workflow operator."""
         setup_cmempy_user_access(context.user)
         graphs = get_graphs_tree((self.ontology_graph_iri,))

From b66f3c57b440e7c92e83a31854a0a0e4da5147e6 Mon Sep 17 00:00:00 2001
From: muddymudskipper <thomas.wilmering@gmail.com>
Date: Sun, 30 Jun 2024 13:00:50 +0100
Subject: [PATCH 5/7] move cleanup to utils.py, annotate inferred axioms not
 advanced parameter

---
 CHANGELOG.md                          |  3 ++-
 cmem_plugin_reason/plugin_reason.py   | 25 +++++--------------------
 cmem_plugin_reason/plugin_validate.py | 23 ++++++-----------------
 cmem_plugin_reason/utils.py           | 16 +++++++++++++++-
 4 files changed, 28 insertions(+), 39 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9858111..fd55505 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,9 +10,10 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/) and this p
 
 - valid range of "Maximum RAM Percentage" parameter in Validate plugin (1-100)
 
-### Change
+### Changed
 
 - completed validation for IRI parameters
+- "Annnotate inferred subclass axioms" is now not an advanced parameter
 
 ## [1.0.0alpha3] 2024-06-28
 
diff --git a/cmem_plugin_reason/plugin_reason.py b/cmem_plugin_reason/plugin_reason.py
index 0267af2..31c8399 100644
--- a/cmem_plugin_reason/plugin_reason.py
+++ b/cmem_plugin_reason/plugin_reason.py
@@ -25,6 +25,7 @@
     ROBOT,
     create_xml_catalog_file,
     get_graphs_tree,
+    remove_temp,
     send_result,
 )
 
@@ -57,7 +58,7 @@
             param_type=StringParameterType(),
             name="result_graph_iri",
             label="Result graph IRI",
-            description="The IRI of the output graph for the reasoning result. ⚠️ Existing graph "
+            description="The IRI of the output graph for the reasoning result. ⚠️ Existing graphs "
             "will be overwritten.",
         ),
         PluginParameter(
@@ -162,10 +163,9 @@
             param_type=BoolParameterType(),
             name="annotate_inferred_axioms",
             label="Annnotate inferred subclass axioms",
-            description="Annotate inferred subclass axioms. ⚠️ This parameter can only be enabled "
-            "if the only enabled axiom generator is SubClass.",
+            description="⚠️ This parameter can only be enabled if the only enabled axiom generator "
+            "is SubClass.",
             default_value=False,
-            advanced=True,
         ),
     ],
 )
@@ -211,7 +211,6 @@ def __init__(  # noqa: PLR0913, C901
             "ObjectPropertyRange": object_property_range,
             "ObjectPropertyDomain": object_property_domain,
         }
-
         errors = ""
         if not validators.url(data_graph_iri):
             errors += 'Invalid IRI for parameter "Data graph IRI". '
@@ -299,20 +298,6 @@ def reason(self, graphs: dict) -> None:
                 raise OSError(response.stderr.decode())
             raise OSError("ROBOT error")
 
-    def clean_up(self, graphs: dict) -> None:
-        """Remove temporary files"""
-        files = ["catalog-v001.xml", "result.ttl"]
-        files += list(graphs.values())
-        for file in files:
-            try:
-                (Path(self.temp) / file).unlink()
-            except (OSError, FileNotFoundError) as err:
-                self.log.warning(f"Cannot remove file {file} ({err})")
-        try:
-            Path(self.temp).rmdir()
-        except (OSError, FileNotFoundError) as err:
-            self.log.warning(f"Cannot remove directory {self.temp} ({err})")
-
     def execute(self, inputs: tuple, context: ExecutionContext) -> None:  # noqa: ARG002
         """Execute plugin"""
         setup_cmempy_user_access(context.user)
@@ -322,4 +307,4 @@ def execute(self, inputs: tuple, context: ExecutionContext) -> None:  # noqa: AR
         self.reason(graphs)
         setup_cmempy_user_access(context.user)
         send_result(self.result_graph_iri, Path(self.temp) / "result.ttl")
-        self.clean_up(graphs)
+        remove_temp(self, ["catalog-v001.xml", "result.ttl", *graphs.values()])
diff --git a/cmem_plugin_reason/plugin_validate.py b/cmem_plugin_reason/plugin_validate.py
index 3fca096..fa55ad3 100644
--- a/cmem_plugin_reason/plugin_validate.py
+++ b/cmem_plugin_reason/plugin_validate.py
@@ -32,6 +32,7 @@
     ROBOT,
     create_xml_catalog_file,
     get_graphs_tree,
+    remove_temp,
     send_result,
 )
 
@@ -112,7 +113,6 @@ def __init__(  # noqa: PLR0913
             errors += 'Invalid value for parameter "Maximum RAM Percentage". '
         if errors:
             raise ValueError(errors[:-1])
-
         self.ontology_graph_iri = ontology_graph_iri
         self.reasoner = reasoner
         self.produce_graph = produce_graph
@@ -174,20 +174,6 @@ def make_resource(self, context: ExecutionContext) -> None:
             replace=True,
         )
 
-    def clean_up(self, graphs: dict) -> None:
-        """Remove temporary files"""
-        files = ["catalog-v001.xml", "output.ttl", self.md_filename]
-        files += list(graphs.values())
-        for file in files:
-            try:
-                (Path(self.temp) / file).unlink()
-            except (OSError, FileNotFoundError) as err:
-                self.log.warning(f"Cannot remove file {file} ({err})")
-        try:
-            Path(self.temp).rmdir()
-        except (OSError, FileNotFoundError) as err:
-            self.log.warning(f"Cannot remove directory {self.temp} ({err})")
-
     def execute(self, inputs: tuple, context: ExecutionContext) -> Entities | None:  # noqa: ARG002
         """Run the workflow operator."""
         setup_cmempy_user_access(context.user)
@@ -195,10 +181,13 @@ def execute(self, inputs: tuple, context: ExecutionContext) -> Entities | None:
         self.get_graphs(graphs, context)
         create_xml_catalog_file(self.temp, graphs)
         self.validate(graphs)
+        files = ["catalog-v001.xml", self.md_filename, *graphs.values()]
+        if self.produce_graph:
+            files.append("output.ttl")
 
         text = (Path(self.temp) / self.md_filename).read_text()
         if text == "No explanations found.":
-            self.clean_up(graphs)
+            remove_temp(self, files)
             return None
 
         if self.produce_graph:
@@ -209,7 +198,7 @@ def execute(self, inputs: tuple, context: ExecutionContext) -> Entities | None:
             setup_cmempy_user_access(context.user)
             self.make_resource(context)
 
-        self.clean_up(graphs)
+        remove_temp(self, files)
 
         if self.stop_at_inconsistencies:
             raise RuntimeError("Inconsistencies found in Ontology.")
diff --git a/cmem_plugin_reason/utils.py b/cmem_plugin_reason/utils.py
index 0b06e25..c0e37fa 100644
--- a/cmem_plugin_reason/utils.py
+++ b/cmem_plugin_reason/utils.py
@@ -1,4 +1,4 @@
-"""Common functions"""
+"""Common constants and functions"""
 
 import re
 import unicodedata
@@ -10,6 +10,7 @@
 from cmem_plugin_base.dataintegration.description import PluginParameter
 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.types import IntParameterType
 from defusedxml import minidom
 
@@ -105,3 +106,16 @@ def send_result(iri: str, filepath: Path) -> None:
         replace=True,
         content_type="text/turtle",
     )
+
+
+def remove_temp(plugin: WorkflowPlugin, files: list) -> None:
+    """Remove temproray files"""
+    for file in files:
+        try:
+            (Path(plugin.temp) / file).unlink()
+        except (OSError, FileNotFoundError) as err:
+            plugin.log.warning(f"Cannot remove file {file} ({err})")
+    try:
+        Path(plugin.temp).rmdir()
+    except (OSError, FileNotFoundError) as err:
+        plugin.log.warning(f"Cannot remove directory {plugin.temp} ({err})")

From 70932eb88f3d84d738bd20900f9e322170f72680 Mon Sep 17 00:00:00 2001
From: muddymudskipper <thomas.wilmering@gmail.com>
Date: Mon, 1 Jul 2024 09:53:14 +0100
Subject: [PATCH 6/7] remove "annotate inferred axioms" parameter, edit README

---
 CHANGELOG.md                          |  4 +-
 README-public.md                      |  2 +-
 README.md                             | 57 +++++++++++++++++++++++++--
 cmem_plugin_reason/plugin_reason.py   | 18 +--------
 cmem_plugin_reason/plugin_validate.py |  5 ++-
 cmem_plugin_reason/utils.py           |  4 +-
 6 files changed, 62 insertions(+), 28 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index fd55505..092309d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,8 +12,8 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/) and this p
 
 ### Changed
 
-- completed validation for IRI parameters
-- "Annnotate inferred subclass axioms" is now not an advanced parameter
+- complete validation for IRI parameters
+- Remove "Annnotate inferred subclass axioms" parameter
 
 ## [1.0.0alpha3] 2024-06-28
 
diff --git a/README-public.md b/README-public.md
index b6d5a71..4500bbf 100644
--- a/README-public.md
+++ b/README-public.md
@@ -1,6 +1,6 @@
 # cmem-plugin-reason
 
-This [eccenca](https://eccenca.com) [Corporate Memory](https://documentation.eccenca.com) workflow plugin performs reasoning using [ROBOT](http://robot.obolibrary.org/). It takes an OWL ontology and a data graph as inputs and writes the reasoning result to a specified graph.
+This [eccenca](https://eccenca.com) [Corporate Memory](https://documentation.eccenca.com) workflow plugin performs reasoning using [ROBOT](http://robot.obolibrary.org/).
 
 ROBOT is published under the [BSD 3-Clause "New" or "Revised" License](https://choosealicense.com/licenses/bsd-3-clause/).
 Copyright © 2015, the Authors
diff --git a/README.md b/README.md
index dc019ad..370a27b 100644
--- a/README.md
+++ b/README.md
@@ -2,9 +2,7 @@
 
 # cmem-plugin-reason
 
-Reasoning with ROBOT
-
-This eccenca Corporate Memory workflow plugin performs reasoning using [ROBOT](http://robot.obolibrary.org/). It takes an OWL ontology and a data graph as inputs and writes the reasoning result to a specified graph.
+This [eccenca](https://eccenca.com) [Corporate Memory](https://documentation.eccenca.com) workflow plugin bundle contains plugins performing reasoning (Reason) and ontology consistency checking (Validate) using [ROBOT](http://robot.obolibrary.org/).
 
 [![eccenca Corporate Memory](https://img.shields.io/badge/eccenca-Corporate%20Memory-orange)](https://documentation.eccenca.com) [![workflow](https://github.com/eccenca/cmem-plugin-pyshacl/actions/workflows/check.yml/badge.svg)](https://github.com/eccenca/cmem-plugin-pyshacl/actions) [![pypi version](https://img.shields.io/pypi/v/cmem-plugin-reason)](https://pypi.org/project/cmem-plugin-reason/) [![license](https://img.shields.io/pypi/l/cmem-plugin-reason)](https://pypi.org/project/cmem-plugin-reasom)
 
@@ -29,6 +27,7 @@ Alternatively, the _build_ and _installation_ process can be initiated with the
 ➜ task deploy
 ```
 
+# Reason
 ## Options
 
 ### Data graph IRI
@@ -46,7 +45,6 @@ The IRI of the output graph for the reasoning result.
 
 :warning: Existing graphs will be overwritten.
 
-
 ### Reasoner
 
 The following reasoner options are supported: 
@@ -84,3 +82,54 @@ parameters to include inferred axiom generators:
 - ObjectPropertyRange
 - ObjectPropertyDomain
 
+### Maximum RAM Percentage
+
+Maximum heap size for the Java virtual machine in the DI container running the reasoning process.
+
+:warning: Setting the percentage too high may result in an out of memory error.
+
+# Validate
+
+In case ontology inconsistencies are found, the plugin outputs the explanation as text in Markdown format using the path "text".
+
+## Options
+
+### Ontology graph IRI
+
+The IRI of the input ontology graph. The graph IRI is selected from a list of graphs of type`owl:Ontology`.
+
+### Reasoner
+
+The following reasoner options are supported: 
+- [ELK](https://code.google.com/p/elk-reasoner/) (elk)
+- [Expression Materializing Reasoner](http://static.javadoc.io/org.geneontology/expression-materializing-reasoner/0.1.3/org/geneontology/reasoner/ExpressionMaterializingReasoner.html) (emr)
+- [HermiT](http://www.hermit-reasoner.com/) (hermit)
+- [JFact](http://jfact.sourceforge.net/) (jfact)
+- [Structural Reasoner](http://owlcs.github.io/owlapi/apidocs_4/org/semanticweb/owlapi/reasoner/structural/StructuralReasoner.html) (structural)
+- [Whelk](https://github.com/balhoff/whelk) (whelk)
+
+### Produce output graph
+
+If enabled, an explanation graph is created.
+
+### Output graph IRI
+
+The IRI of the output graph for the reasoning result.
+
+:warning: Existing graphs will be overwritten.
+
+### Write markdown explanation file
+
+If enabled, an explanation markdown file is written to the project.
+
+:warning: Existing files will be overwritten.
+
+### Stop at inconsistencies
+
+Raise an error if inconsistencies are found. If enabled, the plugin does not output entities.
+
+### Maximum RAM Percentage
+
+Maximum heap size for the Java virtual machine in the DI container running the reasoning process.
+
+:warning: Setting the percentage too high may result in an out of memory error.
\ No newline at end of file
diff --git a/cmem_plugin_reason/plugin_reason.py b/cmem_plugin_reason/plugin_reason.py
index 31c8399..ab5908c 100644
--- a/cmem_plugin_reason/plugin_reason.py
+++ b/cmem_plugin_reason/plugin_reason.py
@@ -159,20 +159,12 @@
             description="",
             default_value=False,
         ),
-        PluginParameter(
-            param_type=BoolParameterType(),
-            name="annotate_inferred_axioms",
-            label="Annnotate inferred subclass axioms",
-            description="⚠️ This parameter can only be enabled if the only enabled axiom generator "
-            "is SubClass.",
-            default_value=False,
-        ),
     ],
 )
 class ReasonPlugin(WorkflowPlugin):
     """Reason plugin"""
 
-    def __init__(  # noqa: PLR0913, C901
+    def __init__(  # noqa: PLR0913
         self,
         data_graph_iri: str = "",
         ontology_graph_iri: str = "",
@@ -192,7 +184,6 @@ def __init__(  # noqa: PLR0913, C901
         sub_class: bool = True,
         sub_data_property: bool = False,
         sub_object_property: bool = False,
-        annotate_inferred_axioms: bool = False,
         max_ram_percentage: int = MAX_RAM_PERCENTAGE_DEFAULT,
     ) -> None:
         self.axioms = {
@@ -226,11 +217,6 @@ def __init__(  # noqa: PLR0913, C901
             errors += 'Invalid value for parameter "Reasoner". '
         if True not in self.axioms.values():
             errors += "No axiom generator selected. "
-        if annotate_inferred_axioms and [k for k, v in self.axioms.items() if v] != ["SubClass"]:
-            errors += (
-                'Parameter "Annnotate inferred subclass axioms" can only be enabled if the only '
-                "enabled axiom generator is SubClass. "
-            )
         if max_ram_percentage not in range(1, 101):
             errors += 'Invalid value for parameter "Maximum RAM Percentage". '
         if errors:
@@ -239,7 +225,6 @@ def __init__(  # noqa: PLR0913, C901
         self.ontology_graph_iri = ontology_graph_iri
         self.result_graph_iri = result_graph_iri
         self.reasoner = reasoner
-        self.annotate_inferred_axioms = str(annotate_inferred_axioms).lower()
         self.max_ram_percentage = max_ram_percentage
         self.temp = f"reason_{uuid4().hex}"
 
@@ -268,7 +253,6 @@ def reason(self, graphs: dict) -> None:
             "--collapse-import-closure false "
             f"reason --reasoner {self.reasoner} "
             f'--axiom-generators "{axioms}" '
-            f"--annotate-inferred-axioms {self.annotate_inferred_axioms} "
             f"--include-indirect true "
             f"--exclude-duplicate-axioms true "
             f"--exclude-owl-thing true "
diff --git a/cmem_plugin_reason/plugin_validate.py b/cmem_plugin_reason/plugin_validate.py
index fa55ad3..eea52ca 100644
--- a/cmem_plugin_reason/plugin_validate.py
+++ b/cmem_plugin_reason/plugin_validate.py
@@ -50,7 +50,8 @@
             param_type=BoolParameterType(),
             name="write_md",
             label="Write Markdown explanation file",
-            description="Write Markdownn file with explanation to project.",
+            description="Write Markdown file with explanation to project. ⚠️ Existing files will "
+            "be overwritten.",
             default_value=False,
         ),
         PluginParameter(
@@ -65,7 +66,7 @@
             name="output_graph_iri",
             label="Output graph IRI",
             description="The IRI of the output graph for the inconsistency validation. ⚠️ Existing "
-            "graph will be overwritten.",
+            "graphs will be overwritten.",
         ),
         PluginParameter(
             param_type=StringParameterType(),
diff --git a/cmem_plugin_reason/utils.py b/cmem_plugin_reason/utils.py
index c0e37fa..eea73a7 100644
--- a/cmem_plugin_reason/utils.py
+++ b/cmem_plugin_reason/utils.py
@@ -67,9 +67,9 @@ def convert_iri_to_filename(value: str) -> str:
     return value + ".nt"
 
 
-def create_xml_catalog_file(temp: str, graphs: dict) -> None:
+def create_xml_catalog_file(dir_: str, graphs: dict) -> None:
     """Create XML catalog file"""
-    file_name = Path(temp) / "catalog-v001.xml"
+    file_name = Path(dir_) / "catalog-v001.xml"
     catalog = Element("catalog")
     catalog.set("prefer", "public")
     catalog.set("xmlns", "urn:oasis:names:tc:entity:xmlns:xml:catalog")

From 72f974194e92cdd8c3732641f59dfb091856ac89 Mon Sep 17 00:00:00 2001
From: muddymudskipper <thomas.wilmering@gmail.com>
Date: Mon, 1 Jul 2024 10:03:00 +0100
Subject: [PATCH 7/7] edit changelog

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 092309d..98747bb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,7 +4,7 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](http://keepachangelog.com/) and this project adheres to [Semantic Versioning](https://semver.org/)
 
-## [Unreleased]
+## [1.0.0beta1] 2024-07-01
 
 ### Fixed