Merge branch 'master' into international-edition

constraints.txt

@@ -17,7 +17,7 @@ beautifulsoup4==4.12.3
 bidict==0.23.1
 bleach==6.1.0
 bmt==1.1.4
-cachetools==5.3.2
+cachetools==5.3.3
 cattrs==23.2.3
 certifi==2024.2.2
 cffi==1.16.0
@@ -85,7 +85,7 @@ importlib-metadata==7.0.1
 importlib_resources==6.1.2
 inflection==0.5.1
 iniconfig==2.0.0
-ipykernel==6.29.2
+ipykernel==6.29.3
 ipython==8.22.1
 ipywidgets==8.1.2
 isodate==0.6.1
@@ -114,7 +114,7 @@ jsonstreams==0.6.0
 jupyter==1.0.0
 jupyter-console==6.6.3
 jupyter-events==0.9.0
-jupyter-lsp==2.2.2
+jupyter-lsp==2.2.3
 jupyter_client==8.6.0
 jupyter_core==5.7.1
 jupyter_server==2.12.5
@@ -123,14 +123,14 @@ jupyterlab==4.1.2
 jupyterlab_pygments==0.3.0
 jupyterlab_server==2.25.3
 jupyterlab_widgets==3.0.10
-keyring==24.3.0
+keyring==24.3.1
 kgcl-rdflib==0.5.0
 kgcl_schema==0.6.4
 kgx==2.2.5
 kiwisolver==1.4.5
 lark==1.1.9
 lightrdf==0.4.0
-linkml==1.7.4
+linkml==1.7.5
 linkml-dataops==0.1.0
 linkml-renderer==0.3.0
 linkml-runtime==1.7.2
@@ -139,15 +139,15 @@ lxml==5.1.0
 Markdown==3.5.2
 markdown-it-py==3.0.0
 MarkupSafe==2.1.5
-marshmallow==3.20.2
+marshmallow==3.21.0
 matplotlib==3.8.3
 matplotlib-inline==0.1.6
 matplotlib-venn==0.11.10
 mdurl==0.1.2
 mergedeep==1.3.4
 mistune==3.0.2
 mkdocs==1.5.3
-mkdocs-material==9.5.11
+mkdocs-material==9.5.12
 mkdocs-material-extensions==1.3.1
 mkdocs-mermaid2-plugin==0.6.0
 mkdocs-table-reader-plugin==2.1.0
@@ -163,7 +163,7 @@ neo4j==4.4.11
 nest-asyncio==1.6.0
 networkx==3.2.1
 nh3==0.2.15
-notebook==7.1.0
+notebook==7.1.1
 notebook_shim==0.2.4
 numpy==1.26.4
 oaklib==0.5.25
@@ -173,7 +173,7 @@ ontobio==2.8.22
 ontodev-cogs==0.3.3
 ontodev-gizmos==0.3.2
 ontoportal-client==0.0.4
-openai==1.12.0
+openai==1.13.3
 openpyxl==3.1.2
 ordered-set==4.1.0
 overrides==7.7.0
@@ -206,7 +206,7 @@ py==1.11.0
 pyasn1==0.5.1
 pyasn1-modules==0.3.0
 pycparser==2.21
-pydantic==2.6.2
+pydantic==2.6.3
 pydantic_core==2.16.3
 pydotplus==2.0.2
 PyGithub==2.2.0
@@ -238,7 +238,7 @@ ratelimit==2.2.1
 rdflib==7.0.0
 rdflib-jsonld==0.6.1
 rdflib-shim==1.0.3
-readme-renderer==42.0
+readme_renderer==43.0
 recommonmark==0.7.1
 referencing==0.33.0
 regex==2023.12.25
@@ -250,7 +250,7 @@ rfc3339-validator==0.1.4
 rfc3986==2.0.0
 rfc3986-validator==0.1.1
 rfc3987==1.3.8
-rich==13.7.0
+rich==13.7.1
 rpds-py==0.18.0
 rsa==4.9
 ruamel.yaml==0.18.6

docker/odklite/Dockerfile

@@ -87,6 +87,11 @@ ENTRYPOINT ["/usr/local/sbin/odkuser-entrypoint.sh"]
 # secure_path is enabled by default in Debian/Ubuntu, disable it
 RUN sed -i '/secure_path/d' /etc/sudoers
 
+# Install a script that provides information about the ODK and its tools
+COPY scripts/odk-info.sh /tools/odk-info
+RUN chmod 755 /tools/odk-info
+RUN sed -i s/@@ODK_IMAGE_VERSION@@/$ODK_VERSION/ /tools/odk-info
+
 # Install the ODK itself.
 COPY odk/make-release-assets.py /tools
 COPY odk/odk.py /tools

odk/odk.py

@@ -565,6 +565,9 @@ class OntologyProject(JsonSchemaMixin):
 
     edit_format : str = "owl"
     """Format in which the edit file is managed, either obo or owl"""
+
+    run_as_root: bool = False
+    """if true, all commands will be executed into the container under the identity of the super-user. Use this if you have custom workflows that require admin rights (e.g. to install Debian packages not provided in the ODK)."""
 
     robot_version: Optional[str] = None
     """Only set this if you want to pin to a specific robot version"""

scripts/odk-info.sh

@@ -0,0 +1,57 @@
+#!/bin/bash
+
+show_odk_version=1
+show_tools_version=0
+show_all_python_packages=0
+
+while [ -n "$1" ]; do
+case $1 in
+--tools)
+    show_tools_version=1
+    shift
+    ;;
+
+--all-python)
+    show_all_python_packages=1
+    shift
+    ;;
+
+--all)
+    show_tools_version=1
+    show_all_python_packages=1
+    shift
+    ;;
+
+*)
+    echo "Usage: odkinfo [--tools|--all-python|--all]"
+    exit
+    ;;
+esac
+done
+
+if [ $show_odk_version -eq 1 ]; then
+    echo "ODK Image @@ODK_IMAGE_VERSION@@"
+fi
+
+if [ $show_tools_version -eq 1 ]; then
+    robot --version
+    amm --version
+    echo "DOSDP-Tools v$(dosdp-tools --version | sed -ne 's/^.*version: //;s/,.*$//p')"
+    if type -p Konclude > /dev/null ; then
+        echo "Konclude $(Konclude -h | sed -nre 's/^.*Version (.*) - .*$/\1/p')"
+    fi
+    if type -p jena.version > /dev/null ; then
+        echo "Jena v$(jena.version)"
+    fi
+    if type -p relation-graph > /dev/null ; then
+        echo "Relation-Graph v$(relation-graph --version | sed -ne 's/^.*version: //;s/,.*$//p')"
+    fi
+    if type -p runoak > /dev/null ; then
+        echo "Ontology Access Kit v$(python3 -m pip show oaklib | sed -ne 's/^Version: //p')"
+    fi
+fi
+
+if [ $show_all_python_packages -eq 1 ]; then
+    echo "Python packages:"
+    python3 -m pip list
+fi

template/src/ontology/Makefile.jinja2

@@ -134,9 +134,8 @@ reason_test: $(EDIT_PREPROCESSED)
 
 .PHONY: odkversion
 odkversion:
-	echo "ODK Makefile version: $(ODK_VERSION_MAKEFILE) (this is the version of the ODK with which this Makefile was generated, \
-        not the version of the ODK you are running)" &&\
-	echo "ROBOT version (ODK): " && $(ROBOT) --version
+	@echo "ODK Makefile $(ODK_VERSION_MAKEFILE)"
+	@odk-info --tools
 
 {%- if project.config_hash %}
 .PHONY: config_check

template/src/ontology/run.sh.jinja2

@@ -58,8 +58,8 @@ ODK_TAG=${ODK_TAG:-latest}
 ODK_JAVA_OPTS={% if project.robot_java_args is defined and project.robot_java_args|length %}${ODK_JAVA_OPTS:-{{ project.robot_java_args }}}{% else %}${ODK_JAVA_OPTS:--Xmx8G}{% endif %}
 ODK_DEBUG=${ODK_DEBUG:-no}
 
-ODK_USER_ID=${ODK_USER_ID:-$(id -u)}
-ODK_GROUP_ID=${ODK_GROUP_ID:-$(id -g)}
+ODK_USER_ID=${ODK_USER_ID:-{% if project.run_as_root %}0{% else %}$(id -u){% endif %}}
+ODK_GROUP_ID=${ODK_GROUP_ID:-{% if project.run_as_root %}0{% else %}$(id -g){% endif %}}
 
 # Convert OWLAPI_* environment variables to the OWLAPI as Java options
 # See http://owlcs.github.io/owlapi/apidocs_4/org/semanticweb/owlapi/model/parameters/ConfigurationOptions.html