Merge branch 'develop' into Issue_38

Author: ajnelson-nist

.gitmodules

@@ -1,6 +1,3 @@
 [submodule "dependencies/CASE"]
 	path = dependencies/CASE
 	url = https://github.com/casework/CASE.git
-[submodule "dependencies/CASE-Examples-QC"]
-	path = dependencies/CASE-Examples-QC
-	url = https://github.com/ajnelson-nist/CASE-Examples-QC.git

CONTRIBUTE.md

@@ -6,9 +6,10 @@
 1. After cloning this repository, ensure the CASE submodule is checked out.  This can be done with either `git submodule init && git submodule update`, `make .git_submodule_init.done.log`, or `make check`.
 2. Update the CASE submodule pointer to the new tagged release.
 3. The version of CASE is also hard-coded in [`case_utils/ontology/version_info.py`](case_utils/ontology/version_info.py).  Edit the variable `CURRENT_CASE_VERSION`.
-4. From the top source directory, run `make clean`.  This guarantees a clean state of this repository as well as the ontology submodules.
-5. Still from the top source directory, run `make`.
-6. Any new `.ttl` files will be created under [`case_utils/ontology/`](case_utils/ontology/).  Use `git add` to add each of them.  (The patch-weight of these files could overshadow manual revisions, so it is fine to commit the built files after the manual changes are committed.)
+4. A list of built versions of CASE is also hard-coded in [`case_utils/ontology/version_info.py`](case_utils/ontology/version_info.py).  Edit the variable `built_version_choices_list`.
+5. From the top source directory, run `make clean`.  This guarantees a clean state of this repository as well as the ontology submodules.
+6. Still from the top source directory, run `make`.
+7. Any new `.ttl` files will be created under [`case_utils/ontology/`](case_utils/ontology/).  Use `git add` to add each of them.  (The patch-weight of these files could overshadow manual revisions, so it is fine to commit the built files separately from the manual changes being committed.  Preferably, commit the built files *before* manual changes - this prevents later issues with a `git bisect` that relies on CI passing.)
 
 Here is a sample sequence of shell commands to run the build:
 
@@ -29,6 +30,6 @@ pushd case_utils/ontology
 popd
 make check
 # Assuming `make check` passes:
+git commit -m "Build CASE 0.6.0 monolithic .ttl files" case_utils/ontology/case-0.6.0-subclasses.ttl case_utils/ontology/case-0.6.0.ttl
 git commit -m "Update CASE ontology pointer to version 0.6.0" dependencies/CASE case_utils/ontology/version_info.py
-git commit -m "Build CASE 0.6.0.ttl" case_utils/ontology/case-0.6.0.ttl
 ```

Makefile

@@ -32,16 +32,6 @@ all: \
 	cd dependencies \
 	  && git diff . \
 	    | cat
-	git submodule init dependencies/CASE-Examples-QC
-	git submodule update dependencies/CASE-Examples-QC
-	# Build an ontology terms list, which has a side effect of initiating further submodules.
-	$(MAKE) \
-	  --directory dependencies/CASE-Examples-QC \
-	  .git_submodule_init.done.log \
-	  .venv.done.log
-	$(MAKE) \
-	  --directory dependencies/CASE-Examples-QC/tests \
-	  ontology_vocabulary.txt
 	test -r dependencies/CASE/ontology/master/case.ttl \
 	  || (git submodule init dependencies/CASE && git submodule update dependencies/CASE)
 	test -r dependencies/CASE/ontology/master/case.ttl
@@ -91,10 +81,6 @@ clean:
 	        tests/examples \
 	        || true \
 	  )
-	@#Remove flag files that are normally set after deeper submodules and rdf-toolkit are downloaded.
-	@rm -f \
-	  dependencies/CASE-Examples-QC/.git_submodule_init.done.log \
-	  dependencies/CASE-Examples-QC/.lib.done.log
 
 # This recipe guarantees timestamp update order, and is otherwise intended to be a no-op.
 dependencies/CASE/ontology/master/case.ttl: \

case_utils/__init__.py

@@ -11,22 +11,6 @@
 #
 # We would appreciate acknowledgement if the software is used.
 
-__version__ = "0.3.0"
-
-import typing
-import warnings
-
-import rdflib.util  # type: ignore
+__version__ = "0.4.0"
 
 from . import local_uuid
-
-
-def guess_format(
-    fpath: str, fmap: typing.Optional[typing.Dict[str, str]] = None
-) -> typing.Optional[str]:
-    warnings.warn(
-        "The functionality in case_utils.guess_format is now upstream.  Please revise your code to use rdflib.util.guess_format.  The function arguments remain the same.  case_utils.guess_format will be removed in case_utils 0.4.0.",
-        DeprecationWarning,
-    )
-
-    return rdflib.util.guess_format(fpath, fmap)  # type: ignore

case_utils/case_file/__init__.py

@@ -15,7 +15,7 @@
 This module creates a graph object that provides a basic UCO characterization of a single file.  The gathered metadata is among the more "durable" file characteristics, i.e. characteristics that would remain consistent when transferring a file between locations.
 """
 
-__version__ = "0.2.0"
+__version__ = "0.3.0"
 
 import datetime
 import hashlib
@@ -234,7 +234,7 @@ def main() -> None:
 
     output_format = None
     if args.output_format is None:
-        output_format = case_utils.guess_format(args.out_graph)
+        output_format = rdflib.util.guess_format(args.out_graph)
     else:
         output_format = args.output_format
 

case_utils/case_sparql_construct/__init__.py

@@ -15,7 +15,7 @@
 This script executes a SPARQL CONSTRUCT query, returning a graph of the generated triples.
 """
 
-__version__ = "0.2.0"
+__version__ = "0.2.1"
 
 import argparse
 import logging
@@ -42,8 +42,6 @@ def main() -> None:
         else logging.INFO
     )
 
-    built_version_choices_list = ["none", "case-" + CURRENT_CASE_VERSION]
-
     parser.add_argument("-d", "--debug", action="store_true")
     parser.add_argument(
         "--built-version",
@@ -105,7 +103,7 @@ def main() -> None:
 
     output_format = None
     if args.output_format is None:
-        output_format = case_utils.guess_format(args.out_graph)
+        output_format = rdflib.util.guess_format(args.out_graph)
     else:
         output_format = args.output_format
 

case_utils/case_sparql_select/__init__.py

@@ -26,7 +26,7 @@
 Should a more complex query be necessary, an outer, wrapping SELECT query would let this script continue to function.
 """
 
-__version__ = "0.4.0"
+__version__ = "0.4.1"
 
 import argparse
 import binascii
@@ -57,8 +57,6 @@ def main() -> None:
         else logging.INFO
     )
 
-    built_version_choices_list = ["none", "case-" + CURRENT_CASE_VERSION]
-
     parser.add_argument("-d", "--debug", action="store_true")
     parser.add_argument(
         "--built-version",

case_utils/case_validate/__init__.py

@@ -29,7 +29,7 @@
 details.)
 """
 
-__version__ = "0.1.0"
+__version__ = "0.1.1"
 
 import argparse
 import importlib.resources
@@ -63,8 +63,6 @@ def main() -> None:
         else logging.INFO
     )
 
-    built_version_choices_list = ["none", "case-" + CURRENT_CASE_VERSION]
-
     # Add arguments specific to case_validate.
     parser.add_argument(
         "-d", "--debug", action="store_true", help="Output additional runtime messages."

case_utils/namespace.py

@@ -26,13 +26,13 @@
 NS_CASE_INVESTIGATION = rdflib.Namespace(
     "https://ontology.caseontology.org/case/investigation/"
 )
-NS_UCO_ACTION = rdflib.Namespace("https://unifiedcyberontology.org/ontology/uco/action#")
-NS_UCO_CORE = rdflib.Namespace("https://unifiedcyberontology.org/ontology/uco/core#")
-NS_UCO_LOCATION = rdflib.Namespace("https://unifiedcyberontology.org/ontology/uco/location#")
+NS_UCO_ACTION = rdflib.Namespace("https://ontology.unifiedcyberontology.org/uco/action/")
+NS_UCO_CORE = rdflib.Namespace("https://ontology.unifiedcyberontology.org/uco/core/")
+NS_UCO_LOCATION = rdflib.Namespace("https://ontology.unifiedcyberontology.org/uco/location/")
 NS_UCO_OBSERVABLE = rdflib.Namespace(
-    "https://unifiedcyberontology.org/ontology/uco/observable#"
+    "https://ontology.unifiedcyberontology.org/uco/observable/"
 )
-NS_UCO_TYPES = rdflib.Namespace("https://unifiedcyberontology.org/ontology/uco/types#")
+NS_UCO_TYPES = rdflib.Namespace("https://ontology.unifiedcyberontology.org/uco/types/")
 NS_UCO_VOCABULARY = rdflib.Namespace(
-    "https://unifiedcyberontology.org/ontology/uco/vocabulary#"
+    "https://ontology.unifiedcyberontology.org/uco/vocabulary/"
 )