Merge pull request #131 from casework/release-1.2.0

Release 1.2.0

Author: plbt5

.gitignore

@@ -4,10 +4,10 @@
 # Unit testing files
 .*.done.log
 .*.ttl
+venv
 
 # Pycharm files
 .idea
 
 # Protege files
-catalog-v001.xml
 .project

CONTRIBUTE.md

@@ -4,3 +4,14 @@
 ## Testing prerelease states
 
 Practices for users interested in testing prerelease states are documented on the [Cyber Domain Ontology website](https://cyberdomainontology.org/ontology/development/#testing-prereleases).
+
+
+## Using Protégé catalog files
+
+Interested users of `catalog-v001.xml` files, e.g. users of [Protégé](https://protege.stanford.edu/), can use these XML files to interact with CASE as local files.  To do so, CASE must be `git-clone`'d with Git submodules also cloned.  This can be done with the following commands:
+
+* `git clone --recursive https://github.com/casework/CASE.git` (all users)
+* `git clone https://github.com/casework/CASE.git ; cd CASE ; make` (macOS or Linux users)
+   - The narrowest setup operation strictly for purposes of supporting the `catalog-v001.xml` files is to run `make .git_submodule_init.done.log` instead of the default `make all`.
+
+Protégé should not require network connectivity to load imported ontologies after the above commands are run.

ChangeLog

@@ -1,3 +1,6 @@
+2023-03-28
+	* (0cb7b85) UCO Issue 449: Enable generating Protégé catalog files
+
 2022-11-22
 	* ONT-491: Release CASE 1.1.0, with release notes at https://caseontology.org/releases/1.1.0/
 

Makefile

@@ -13,9 +13,12 @@
 
 SHELL := /bin/bash
 
-PYTHON3 ?= $(shell which python3.9 2>/dev/null || which python3.8 2>/dev/null || which python3.7 2>/dev/null || which python3.6 2>/dev/null || which python3)
+PYTHON3 ?= $(shell which python3)
 
-all:
+all: \
+  .venv.done.log
+	$(MAKE) \
+	  --directory ontology
 
 # This recipe guarantees that 'git submodule init' and 'git submodule update' have run at least once.
 # The recipe avoids running 'git submodule update' more than once, in case a user is testing with the submodule at a different commit than what CASE tracks.
@@ -38,8 +41,32 @@ all:
 	  .lib.done.log
 	touch $@
 
+# The two CASE-Utility... files are to trigger rebuilds based on command-line interface changes or version increments.
+.venv.done.log: \
+  .git_submodule_init.done.log \
+  dependencies/UCO/dependencies/CASE-Utility-SHACL-Inheritance-Reviewer/case_shacl_inheritance_reviewer/__init__.py \
+  dependencies/UCO/dependencies/CASE-Utility-SHACL-Inheritance-Reviewer/setup.cfg \
+  dependencies/UCO/requirements.txt
+	rm -rf venv
+	$(PYTHON3) -m venv \
+	  venv
+	source venv/bin/activate \
+	  && pip install \
+	    --upgrade \
+	    pip \
+	    setuptools \
+	    wheel
+	source venv/bin/activate \
+	  && pip install \
+	    dependencies/UCO/dependencies/CASE-Utility-SHACL-Inheritance-Reviewer
+	source venv/bin/activate \
+	  && pip install \
+	    --requirement dependencies/UCO/requirements.txt
+	touch $@
+
 check: \
-  .lib.done.log
+  .lib.done.log \
+  .venv.done.log
 	$(MAKE) \
 	  --directory ontology \
 	  check
@@ -70,3 +97,17 @@ clean:
 	  )
 	@rm -f \
 	  .*.done.log
+	@rm -rf \
+	  venv
+
+dependencies/UCO/dependencies/CASE-Utility-SHACL-Inheritance-Reviewer/case_shacl_inheritance_reviewer/__init__.py: \
+  .git_submodule_init.done.log
+	$(MAKE) \
+	  --directory dependencies/UCO \
+	  dependencies/CASE-Utility-SHACL-Inheritance-Reviewer/case_shacl_inheritance_reviewer/__init__.py
+
+dependencies/UCO/dependencies/CASE-Utility-SHACL-Inheritance-Reviewer/setup.cfg: \
+  .git_submodule_init.done.log
+	$(MAKE) \
+	  --directory dependencies/UCO \
+	  dependencies/CASE-Utility-SHACL-Inheritance-Reviewer/setup.cfg

dependencies/UCO

@@ -0,0 +1,2 @@
+https://ontology.caseontology.org/	${top_srcdir}/ontology/
+https://ontology.unifiedcyberontology.org/	${top_srcdir}/dependencies/UCO/ontology/

etc/dependency_files.tsv

@@ -11,18 +11,38 @@
 #
 # We would appreciate acknowledgement if the software is used.
 
-all:
+SHELL := /bin/bash
 
 top_srcdir := ..
 
+all: \
+  all-investigation \
+  all-master \
+  all-vocabulary
+
 .PHONY: \
+  all-investigation \
+  all-master \
+  all-vocabulary \
   check-investigation \
   check-master \
   check-vocabulary \
   clean-investigation \
   clean-master \
   clean-vocabulary
 
+all-investigation:
+	$(MAKE) \
+	  --directory investigation
+
+all-master:
+	$(MAKE) \
+	  --directory master
+
+all-vocabulary:
+	$(MAKE) \
+	  --directory vocabulary
+
 check: \
   check-master \
   check-investigation \

etc/domain_directories.tsv

@@ -11,9 +11,16 @@
 #
 # We would appreciate acknowledgement if the software is used.
 
+SHELL := /bin/bash
+
 top_srcdir := ../..
 
-all:
+uco_srcdir := $(top_srcdir)/dependencies/UCO
+
+ttl_basenames := investigation.ttl
+
+all: \
+  catalog-v001.xml
 
 .check-investigation.ttl: \
   $(top_srcdir)/.lib.done.log \
@@ -26,11 +33,32 @@ all:
 	  --target-format turtle
 	mv _$@ $@
 
+catalog-v001.xml: \
+  $(top_srcdir)/.venv.done.log \
+  $(top_srcdir)/etc/domain_directories.tsv \
+  $(top_srcdir)/etc/dependency_files.tsv \
+  $(uco_srcdir)/ontology/uco/action/catalog-v001.xml \
+  $(uco_srcdir)/ontology/uco/role/catalog-v001.xml \
+  $(uco_srcdir)/src/create-catalog-v001.xml.py
+	rm -f _$@
+	source $(top_srcdir)/venv/bin/activate \
+	  && python3 $(uco_srcdir)/src/create-catalog-v001.xml.py \
+	    --catalog-xml $(uco_srcdir)/ontology/uco/action/catalog-v001.xml \
+	    --catalog-xml $(uco_srcdir)/ontology/uco/role/catalog-v001.xml \
+	    _$@ \
+	    $(top_srcdir)/etc/domain_directories.tsv \
+	    $(top_srcdir)/etc/dependency_files.tsv \
+	    "$(top_srcdir)" \
+	    $(ttl_basenames)
+	mv _$@ $@
+
 check: \
-  .check-investigation.ttl
+  .check-investigation.ttl \
+  catalog-v001.xml
 	diff investigation.ttl .check-investigation.ttl
 
 clean:
 	@rm -f \
 	  .check-*.ttl \
-	  _*
+	  _* \
+	  catalog-v001.xml

ontology/Makefile

@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<catalog xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog" prefer="public">
+    <uri id="User Entered Import Resolution" uri="../../dependencies/UCO/dependencies/collections-ontology/collections.owl" name="http://purl.org/co"/>
+    <uri id="User Entered Import Resolution" uri="../../dependencies/UCO/dependencies/error/docs/current/error.ttl" name="http://purl.org/spar/error"/>
+    <uri id="User Entered Import Resolution" uri="../../dependencies/UCO/ontology/co/co.ttl" name="https://ontology.unifiedcyberontology.org/co/1.2.0"/>
+    <uri id="User Entered Import Resolution" uri="../../dependencies/UCO/ontology/uco/action/action.ttl" name="https://ontology.unifiedcyberontology.org/uco/action/1.2.0"/>
+    <uri id="User Entered Import Resolution" uri="../../dependencies/UCO/ontology/uco/core/core.ttl" name="https://ontology.unifiedcyberontology.org/uco/core/1.2.0"/>
+    <uri id="User Entered Import Resolution" uri="../../dependencies/UCO/ontology/uco/location/location.ttl" name="https://ontology.unifiedcyberontology.org/uco/location/1.2.0"/>
+    <uri id="User Entered Import Resolution" uri="../../dependencies/UCO/ontology/uco/pattern/pattern.ttl" name="https://ontology.unifiedcyberontology.org/uco/pattern/1.2.0"/>
+    <uri id="User Entered Import Resolution" uri="../../dependencies/UCO/ontology/uco/role/role.ttl" name="https://ontology.unifiedcyberontology.org/uco/role/1.2.0"/>
+    <uri id="User Entered Import Resolution" uri="../../dependencies/UCO/ontology/uco/types/types.ttl" name="https://ontology.unifiedcyberontology.org/uco/types/1.2.0"/>
+    <uri id="User Entered Import Resolution" uri="../../dependencies/UCO/ontology/uco/vocabulary/vocabulary.ttl" name="https://ontology.unifiedcyberontology.org/uco/vocabulary/1.2.0"/>
+    <uri id="User Entered Import Resolution" uri="../vocabulary/vocabulary.ttl" name="https://ontology.caseontology.org/case/vocabulary/1.2.0"/>
+    <uri id="User Entered Import Resolution" uri="investigation.ttl" name="https://ontology.caseontology.org/case/investigation"/>
+</catalog>