From ec87d99b36fcce4871790765ea0afecfae74fcd0 Mon Sep 17 00:00:00 2001
From: Alex Nelson <alexander.nelson@nist.gov>
Date: Tue, 6 Dec 2022 08:53:51 -0500
Subject: [PATCH 01/19] Add and test --use-prefixes flag for case_sparql_select

A follow-on patch will regenerate Make-managed files.

Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
---
 case_utils/case_sparql_select/__init__.py     | 10 ++++++
 .../.check-prefixed_results.html              | 18 +++++++++++
 .../.check-prefixed_results.md                |  4 +++
 tests/case_utils/case_sparql_select/Makefile  | 32 +++++++++++++++++++
 4 files changed, 64 insertions(+)
 create mode 100644 tests/case_utils/case_sparql_select/.check-prefixed_results.html
 create mode 100644 tests/case_utils/case_sparql_select/.check-prefixed_results.md

diff --git a/case_utils/case_sparql_select/__init__.py b/case_utils/case_sparql_select/__init__.py
index b753664..dcc704e 100644
--- a/case_utils/case_sparql_select/__init__.py
+++ b/case_utils/case_sparql_select/__init__.py
@@ -70,6 +70,11 @@ def main() -> None:
         action="store_true",
         help="Raise error if no results are returned for query.",
     )
+    parser.add_argument(
+        "--use-prefixes",
+        action="store_true",
+        help="Abbreviate node IDs according to graph's encoded prefixes.  (This will use prefixes in the graph, not the query.)",
+    )
     parser.add_argument(
         "out_table",
         help="Expected extensions are .html for HTML tables or .md for Markdown tables.",
@@ -124,6 +129,11 @@ def main() -> None:
                 # The render to ASCII is in support of this script rendering results for website viewing.
                 # .decode() is because hexlify returns bytes.
                 column_value = binascii.hexlify(column.toPython()).decode()
+            elif isinstance(column, rdflib.URIRef):
+                if args.use_prefixes:
+                    column_value = graph.namespace_manager.qname(column.toPython())
+                else:
+                    column_value = column.toPython()
             else:
                 column_value = column.toPython()
             if row_no == 0:
diff --git a/tests/case_utils/case_sparql_select/.check-prefixed_results.html b/tests/case_utils/case_sparql_select/.check-prefixed_results.html
new file mode 100644
index 0000000..10e210b
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-prefixed_results.html
@@ -0,0 +1,18 @@
+<table border="1" class="dataframe table table-bordered table-condensed">
+  <thead>
+    <tr style="text-align: right;">
+      <th></th>
+      <th>?nFile</th>
+    </tr>
+  </thead>
+  <tbody>
+    <tr>
+      <th>0</th>
+      <td>kb:file-1</td>
+    </tr>
+    <tr>
+      <th>1</th>
+      <td>kb:file-2</td>
+    </tr>
+  </tbody>
+</table>
\ No newline at end of file
diff --git a/tests/case_utils/case_sparql_select/.check-prefixed_results.md b/tests/case_utils/case_sparql_select/.check-prefixed_results.md
new file mode 100644
index 0000000..f49a624
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-prefixed_results.md
@@ -0,0 +1,4 @@
+|    | ?nFile    |
+|----|-----------|
+|  0 | kb:file-1 |
+|  1 | kb:file-2 |
\ No newline at end of file
diff --git a/tests/case_utils/case_sparql_select/Makefile b/tests/case_utils/case_sparql_select/Makefile
index 22a849b..4f36399 100644
--- a/tests/case_utils/case_sparql_select/Makefile
+++ b/tests/case_utils/case_sparql_select/Makefile
@@ -18,6 +18,8 @@ top_srcdir := $(shell cd ../../.. ; pwd)
 tests_srcdir := $(top_srcdir)/tests
 
 all: \
+  prefixed_results.html \
+  prefixed_results.md \
   subclass-explicit-none.md \
   subclass-implicit-any.md \
   w3-output.html \
@@ -37,8 +39,23 @@ all: \
 check: \
   check-w3-html \
   check-w3-markdown \
+  check-prefixed_results \
   check-subclass
 
+check-prefixed_results: \
+  check-prefixed_results-html \
+  check-prefixed_results-md
+
+check-prefixed_results-html: \
+  .check-prefixed_results.html \
+  prefixed_results.html
+	diff $^
+
+check-prefixed_results-md: \
+  .check-prefixed_results.md \
+  prefixed_results.md
+	diff $^
+
 check-subclass: \
   check-subclass-explicit-none \
   check-subclass-implicit-any
@@ -71,6 +88,21 @@ clean:
 	  *.md \
 	  _*
 
+prefixed_results.%: \
+  $(tests_srcdir)/.venv.done.log \
+  $(top_srcdir)/case_utils/case_sparql_select/__init__.py \
+  $(top_srcdir)/case_utils/ontology/__init__.py \
+  $(top_srcdir)/case_utils/ontology/version_info.py \
+  subclass.json \
+  subclass.sparql
+	source $(tests_srcdir)/venv/bin/activate \
+	  && case_sparql_select \
+	    --use-prefixes \
+	    _$@ \
+	    subclass.sparql \
+	    subclass.json
+	mv _$@ $@
+
 subclass-explicit-none.md: \
   $(tests_srcdir)/.venv.done.log \
   $(top_srcdir)/case_utils/case_sparql_select/__init__.py \

From 46a9b8033df0ca752641d9664731c607b1f1d7b3 Mon Sep 17 00:00:00 2001
From: Alex Nelson <alexander.nelson@nist.gov>
Date: Tue, 6 Dec 2022 08:54:12 -0500
Subject: [PATCH 02/19] Regenerate Make-managed files

Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
---
 .../case_sparql_select/prefixed_results.html   | 18 ++++++++++++++++++
 .../case_sparql_select/prefixed_results.md     |  4 ++++
 2 files changed, 22 insertions(+)
 create mode 100644 tests/case_utils/case_sparql_select/prefixed_results.html
 create mode 100644 tests/case_utils/case_sparql_select/prefixed_results.md

diff --git a/tests/case_utils/case_sparql_select/prefixed_results.html b/tests/case_utils/case_sparql_select/prefixed_results.html
new file mode 100644
index 0000000..10e210b
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/prefixed_results.html
@@ -0,0 +1,18 @@
+<table border="1" class="dataframe table table-bordered table-condensed">
+  <thead>
+    <tr style="text-align: right;">
+      <th></th>
+      <th>?nFile</th>
+    </tr>
+  </thead>
+  <tbody>
+    <tr>
+      <th>0</th>
+      <td>kb:file-1</td>
+    </tr>
+    <tr>
+      <th>1</th>
+      <td>kb:file-2</td>
+    </tr>
+  </tbody>
+</table>
\ No newline at end of file
diff --git a/tests/case_utils/case_sparql_select/prefixed_results.md b/tests/case_utils/case_sparql_select/prefixed_results.md
new file mode 100644
index 0000000..f49a624
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/prefixed_results.md
@@ -0,0 +1,4 @@
+|    | ?nFile    |
+|----|-----------|
+|  0 | kb:file-1 |
+|  1 | kb:file-2 |
\ No newline at end of file

From 66becce691871c25123ba28b78c27f32934504f8 Mon Sep 17 00:00:00 2001
From: Alex Nelson <alexander.nelson@nist.gov>
Date: Tue, 6 Dec 2022 10:19:50 -0500
Subject: [PATCH 03/19] Have case_sparql_select output end with newline

No effects were observed on Make-managed files.

Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
---
 case_utils/case_sparql_select/__init__.py                      | 3 +++
 .../case_sparql_select/.check-subclass-explicit-none.md        | 2 +-
 .../case_sparql_select/.check-subclass-implicit-any.md         | 2 +-
 tests/case_utils/case_sparql_select/.check-w3-output.html      | 2 +-
 tests/case_utils/case_sparql_select/.check-w3-output.md        | 2 +-
 5 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/case_utils/case_sparql_select/__init__.py b/case_utils/case_sparql_select/__init__.py
index b753664..92c0e6b 100644
--- a/case_utils/case_sparql_select/__init__.py
+++ b/case_utils/case_sparql_select/__init__.py
@@ -153,6 +153,9 @@ def main() -> None:
 
     with open(args.out_table, "w") as out_fh:
         out_fh.write(table_text)
+        if table_text[-1] != "\n":
+            # End file with newline.
+            out_fh.write("\n")
 
 
 if __name__ == "__main__":
diff --git a/tests/case_utils/case_sparql_select/.check-subclass-explicit-none.md b/tests/case_utils/case_sparql_select/.check-subclass-explicit-none.md
index 5d9d1ef..587732b 100644
--- a/tests/case_utils/case_sparql_select/.check-subclass-explicit-none.md
+++ b/tests/case_utils/case_sparql_select/.check-subclass-explicit-none.md
@@ -1,3 +1,3 @@
 |    | ?nFile                       |
 |----|------------------------------|
-|  0 | http://example.org/kb/file-1 |
\ No newline at end of file
+|  0 | http://example.org/kb/file-1 |
diff --git a/tests/case_utils/case_sparql_select/.check-subclass-implicit-any.md b/tests/case_utils/case_sparql_select/.check-subclass-implicit-any.md
index 251fcf6..c94f185 100644
--- a/tests/case_utils/case_sparql_select/.check-subclass-implicit-any.md
+++ b/tests/case_utils/case_sparql_select/.check-subclass-implicit-any.md
@@ -1,4 +1,4 @@
 |    | ?nFile                       |
 |----|------------------------------|
 |  0 | http://example.org/kb/file-1 |
-|  1 | http://example.org/kb/file-2 |
\ No newline at end of file
+|  1 | http://example.org/kb/file-2 |
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output.html b/tests/case_utils/case_sparql_select/.check-w3-output.html
index aff9beb..bee5944 100644
--- a/tests/case_utils/case_sparql_select/.check-w3-output.html
+++ b/tests/case_utils/case_sparql_select/.check-w3-output.html
@@ -18,4 +18,4 @@
       <td>mailto:peter@example.org</td>
     </tr>
   </tbody>
-</table>
\ No newline at end of file
+</table>
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output.md b/tests/case_utils/case_sparql_select/.check-w3-output.md
index 77b05f4..af68b84 100644
--- a/tests/case_utils/case_sparql_select/.check-w3-output.md
+++ b/tests/case_utils/case_sparql_select/.check-w3-output.md
@@ -1,4 +1,4 @@
 |    | ?name             | ?mbox                    |
 |----|-------------------|--------------------------|
 |  0 | Johnny Lee Outlaw | mailto:jlow@example.com  |
-|  1 | Peter Goodguy     | mailto:peter@example.org |
\ No newline at end of file
+|  1 | Peter Goodguy     | mailto:peter@example.org |

From 9a2eb226939eb21222e851a6fb1149f3c61f8794 Mon Sep 17 00:00:00 2001
From: Alex Nelson <alexander.nelson@nist.gov>
Date: Tue, 6 Dec 2022 10:40:42 -0500
Subject: [PATCH 04/19] Designate new test files PRECIOUS

Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
---
 tests/case_utils/case_sparql_select/Makefile | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/case_utils/case_sparql_select/Makefile b/tests/case_utils/case_sparql_select/Makefile
index 4f36399..6431be7 100644
--- a/tests/case_utils/case_sparql_select/Makefile
+++ b/tests/case_utils/case_sparql_select/Makefile
@@ -33,6 +33,7 @@ all: \
   check-w3-markdown
 
 .PRECIOUS: \
+  prefixed_results.% \
   subclass-% \
   w3-output.%
 

From b13d78a97f6c6001bd95f0ad2da0c4520418c68e Mon Sep 17 00:00:00 2001
From: Alex Nelson <alexander.nelson@nist.gov>
Date: Tue, 6 Dec 2022 10:59:37 -0500
Subject: [PATCH 05/19] Add case_sparql_select CSV and TSV output

No effects were observed on Make-managed files.

Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
---
 case_utils/case_sparql_select/__init__.py     | 18 ++++++++++++---
 .../case_sparql_select/.check-w3-output.csv   |  3 +++
 .../case_sparql_select/.check-w3-output.tsv   |  3 +++
 tests/case_utils/case_sparql_select/Makefile  | 22 +++++++++++++++++--
 4 files changed, 41 insertions(+), 5 deletions(-)
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output.csv
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output.tsv

diff --git a/case_utils/case_sparql_select/__init__.py b/case_utils/case_sparql_select/__init__.py
index b753664..5b9e601 100644
--- a/case_utils/case_sparql_select/__init__.py
+++ b/case_utils/case_sparql_select/__init__.py
@@ -33,6 +33,7 @@
 import logging
 import os
 import sys
+import typing
 
 import pandas as pd  # type: ignore
 import rdflib.plugins.sparql
@@ -72,7 +73,7 @@ def main() -> None:
     )
     parser.add_argument(
         "out_table",
-        help="Expected extensions are .html for HTML tables or .md for Markdown tables.",
+        help="Expected extensions are .html for HTML tables, .md for Markdown tables, .csv for comma-separated values, and .tsv for tab-separated values.",
     )
     parser.add_argument(
         "in_sparql",
@@ -136,8 +137,19 @@ def main() -> None:
 
     df = pd.DataFrame(records, columns=variables)
 
-    table_text = None
-    if args.out_table.endswith(".html"):
+    table_text: typing.Optional[str] = None
+    if args.out_table.endswith(".csv") or args.out_table.endswith(".tsv"):
+        sep: str
+        if args.out_table.endswith(".csv"):
+            sep = ","
+        elif args.out_table.endswith(".tsv"):
+            sep = "\t"
+        else:
+            raise NotImplementedError(
+                "Output extension not implemented in CSV-style output."
+            )
+        table_text = df.to_csv(sep=sep)
+    elif args.out_table.endswith(".html"):
         # https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.to_html.html
         # Add CSS classes for CASE website Bootstrap support.
         table_text = df.to_html(classes=("table", "table-bordered", "table-condensed"))
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output.csv b/tests/case_utils/case_sparql_select/.check-w3-output.csv
new file mode 100644
index 0000000..063e950
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output.csv
@@ -0,0 +1,3 @@
+,?name,?mbox
+0,Johnny Lee Outlaw,mailto:jlow@example.com
+1,Peter Goodguy,mailto:peter@example.org
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output.tsv b/tests/case_utils/case_sparql_select/.check-w3-output.tsv
new file mode 100644
index 0000000..a4fdfca
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output.tsv
@@ -0,0 +1,3 @@
+	?name	?mbox
+0	Johnny Lee Outlaw	mailto:jlow@example.com
+1	Peter Goodguy	mailto:peter@example.org
diff --git a/tests/case_utils/case_sparql_select/Makefile b/tests/case_utils/case_sparql_select/Makefile
index 22a849b..fe74e32 100644
--- a/tests/case_utils/case_sparql_select/Makefile
+++ b/tests/case_utils/case_sparql_select/Makefile
@@ -20,23 +20,29 @@ tests_srcdir := $(top_srcdir)/tests
 all: \
   subclass-explicit-none.md \
   subclass-implicit-any.md \
+  w3-output.csv \
   w3-output.html \
-  w3-output.md
+  w3-output.md \
+  w3-output.tsv
 
 .PHONY: \
   check-subclass \
   check-subclass-explicit-none \
   check-subclass-implicit-any \
+  check-w3-csv \
   check-w3-html \
-  check-w3-markdown
+  check-w3-markdown \
+  check-w3-tsv
 
 .PRECIOUS: \
   subclass-% \
   w3-output.%
 
 check: \
+  check-w3-csv \
   check-w3-html \
   check-w3-markdown \
+  check-w3-tsv \
   check-subclass
 
 check-subclass: \
@@ -53,6 +59,11 @@ check-subclass-implicit-any: \
   subclass-implicit-any.md
 	diff $^
 
+check-w3-csv: \
+  .check-w3-output.csv \
+  w3-output.csv
+	diff $^
+
 check-w3-html: \
   .check-w3-output.html \
   w3-output.html
@@ -63,12 +74,19 @@ check-w3-markdown: \
   w3-output.md
 	diff $^
 
+check-w3-tsv: \
+  .check-w3-output.tsv \
+  w3-output.tsv
+	diff $^
+
 clean:
 	@rm -rf \
 	  __pycache__
 	@rm -f \
+	  *.csv \
 	  *.html \
 	  *.md \
+	  *.tsv \
 	  _*
 
 subclass-explicit-none.md: \

From 894d7b171cdcadf3e52659d686ca1ecc46ee61b8 Mon Sep 17 00:00:00 2001
From: Alex Nelson <alexander.nelson@nist.gov>
Date: Tue, 6 Dec 2022 11:26:02 -0500
Subject: [PATCH 06/19] Update documentation comment

Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
---
 case_utils/case_sparql_select/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/case_utils/case_sparql_select/__init__.py b/case_utils/case_sparql_select/__init__.py
index 5c50e78..424848c 100644
--- a/case_utils/case_sparql_select/__init__.py
+++ b/case_utils/case_sparql_select/__init__.py
@@ -164,7 +164,7 @@ def main() -> None:
     with open(args.out_table, "w") as out_fh:
         out_fh.write(table_text)
         if table_text[-1] != "\n":
-            # End file with newline.
+            # End file with newline.  CSV and TSV modes end with a built-in newline.
             out_fh.write("\n")
 
 

From 22306b9bd8437d0e714cb131fd8812ea687a8e73 Mon Sep 17 00:00:00 2001
From: Alex Nelson <alexander.nelson@nist.gov>
Date: Tue, 6 Dec 2022 13:29:03 -0500
Subject: [PATCH 07/19] Align test files with new behavior

A follow-on patch will address Make-managed files.

Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
---
 .../case_utils/case_sparql_select/.check-prefixed_results.html  | 2 +-
 tests/case_utils/case_sparql_select/.check-prefixed_results.md  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/case_utils/case_sparql_select/.check-prefixed_results.html b/tests/case_utils/case_sparql_select/.check-prefixed_results.html
index 10e210b..4b41f69 100644
--- a/tests/case_utils/case_sparql_select/.check-prefixed_results.html
+++ b/tests/case_utils/case_sparql_select/.check-prefixed_results.html
@@ -15,4 +15,4 @@
       <td>kb:file-2</td>
     </tr>
   </tbody>
-</table>
\ No newline at end of file
+</table>
diff --git a/tests/case_utils/case_sparql_select/.check-prefixed_results.md b/tests/case_utils/case_sparql_select/.check-prefixed_results.md
index f49a624..f07d435 100644
--- a/tests/case_utils/case_sparql_select/.check-prefixed_results.md
+++ b/tests/case_utils/case_sparql_select/.check-prefixed_results.md
@@ -1,4 +1,4 @@
 |    | ?nFile    |
 |----|-----------|
 |  0 | kb:file-1 |
-|  1 | kb:file-2 |
\ No newline at end of file
+|  1 | kb:file-2 |

From c4a9f584b2f6cc4c41b92e4c8e5df73124ad72ca Mon Sep 17 00:00:00 2001
From: Alex Nelson <alexander.nelson@nist.gov>
Date: Tue, 6 Dec 2022 13:31:04 -0500
Subject: [PATCH 08/19] Remove Make-managed files

This directory had not been tracking the non-dot files.

Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
---
 tests/case_utils/case_sparql_select/.gitignore |  1 +
 .../case_sparql_select/prefixed_results.html   | 18 ------------------
 .../case_sparql_select/prefixed_results.md     |  4 ----
 3 files changed, 1 insertion(+), 22 deletions(-)
 delete mode 100644 tests/case_utils/case_sparql_select/prefixed_results.html
 delete mode 100644 tests/case_utils/case_sparql_select/prefixed_results.md

diff --git a/tests/case_utils/case_sparql_select/.gitignore b/tests/case_utils/case_sparql_select/.gitignore
index 0ae4849..9d94989 100644
--- a/tests/case_utils/case_sparql_select/.gitignore
+++ b/tests/case_utils/case_sparql_select/.gitignore
@@ -1,2 +1,3 @@
+prefixed*
 subclass-*.md
 w3-output.*
diff --git a/tests/case_utils/case_sparql_select/prefixed_results.html b/tests/case_utils/case_sparql_select/prefixed_results.html
deleted file mode 100644
index 10e210b..0000000
--- a/tests/case_utils/case_sparql_select/prefixed_results.html
+++ /dev/null
@@ -1,18 +0,0 @@
-<table border="1" class="dataframe table table-bordered table-condensed">
-  <thead>
-    <tr style="text-align: right;">
-      <th></th>
-      <th>?nFile</th>
-    </tr>
-  </thead>
-  <tbody>
-    <tr>
-      <th>0</th>
-      <td>kb:file-1</td>
-    </tr>
-    <tr>
-      <th>1</th>
-      <td>kb:file-2</td>
-    </tr>
-  </tbody>
-</table>
\ No newline at end of file
diff --git a/tests/case_utils/case_sparql_select/prefixed_results.md b/tests/case_utils/case_sparql_select/prefixed_results.md
deleted file mode 100644
index f49a624..0000000
--- a/tests/case_utils/case_sparql_select/prefixed_results.md
+++ /dev/null
@@ -1,4 +0,0 @@
-|    | ?nFile    |
-|----|-----------|
-|  0 | kb:file-1 |
-|  1 | kb:file-2 |
\ No newline at end of file

From 70ed1e54185e0d76875a0532aa5407421af0ea44 Mon Sep 17 00:00:00 2001
From: Alex Nelson <alexander.nelson@nist.gov>
Date: Tue, 6 Dec 2022 13:42:57 -0500
Subject: [PATCH 09/19] Run pre-commit autoupdate, pinning flake8 at 5.0.4

`flake8` 6.0.0 requires Python >= 3.8.  Python 3.7 goes EOL on
2023-06-27, so we will stay with flake8 < 6.0.0 until then.

The `flake8` issue was previously seen in case-prov PR 55.

References:
* https://github.com/casework/CASE-Implementation-PROV-O/pull/55
* https://www.python.org/downloads/
* https://peps.python.org/pep-0537/

Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
---
 .pre-commit-config.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index c952e8e..d6274fe 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,10 +1,10 @@
 repos:
   - repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 22.10.0
     hooks:
       - id: black
   - repo: https://github.com/pycqa/flake8
-    rev: 4.0.1
+    rev: 5.0.4
     hooks:
       - id: flake8
   - repo: https://github.com/pycqa/isort

From d1fc533ccfb13fb787ec7dc1860bf863fcbda591 Mon Sep 17 00:00:00 2001
From: Alex Nelson <alexander.nelson@nist.gov>
Date: Tue, 6 Dec 2022 13:53:56 -0500
Subject: [PATCH 10/19] Link documentation as with other if-elif branches

Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
---
 case_utils/case_sparql_select/__init__.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/case_utils/case_sparql_select/__init__.py b/case_utils/case_sparql_select/__init__.py
index fc45de2..56fea8b 100644
--- a/case_utils/case_sparql_select/__init__.py
+++ b/case_utils/case_sparql_select/__init__.py
@@ -149,6 +149,7 @@ def main() -> None:
 
     table_text: typing.Optional[str] = None
     if args.out_table.endswith(".csv") or args.out_table.endswith(".tsv"):
+        # https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.to_csv.html
         sep: str
         if args.out_table.endswith(".csv"):
             sep = ","

From e9ab5607695257510bd087f83244b94b2d8ce09b Mon Sep 17 00:00:00 2001
From: Alex Nelson <alexander.nelson@nist.gov>
Date: Tue, 6 Dec 2022 15:39:51 -0500
Subject: [PATCH 11/19] Cross CSV and TSV output testing with prefix testing

No effects were observed on Make-managed files.

Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
---
 .../.check-prefixed_results.csv                  |  3 +++
 .../.check-prefixed_results.tsv                  |  3 +++
 tests/case_utils/case_sparql_select/Makefile     | 16 +++++++++++++++-
 3 files changed, 21 insertions(+), 1 deletion(-)
 create mode 100644 tests/case_utils/case_sparql_select/.check-prefixed_results.csv
 create mode 100644 tests/case_utils/case_sparql_select/.check-prefixed_results.tsv

diff --git a/tests/case_utils/case_sparql_select/.check-prefixed_results.csv b/tests/case_utils/case_sparql_select/.check-prefixed_results.csv
new file mode 100644
index 0000000..60d4b78
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-prefixed_results.csv
@@ -0,0 +1,3 @@
+,?nFile
+0,kb:file-1
+1,kb:file-2
diff --git a/tests/case_utils/case_sparql_select/.check-prefixed_results.tsv b/tests/case_utils/case_sparql_select/.check-prefixed_results.tsv
new file mode 100644
index 0000000..9dac11d
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-prefixed_results.tsv
@@ -0,0 +1,3 @@
+	?nFile
+0	kb:file-1
+1	kb:file-2
diff --git a/tests/case_utils/case_sparql_select/Makefile b/tests/case_utils/case_sparql_select/Makefile
index 23d082d..68f11ec 100644
--- a/tests/case_utils/case_sparql_select/Makefile
+++ b/tests/case_utils/case_sparql_select/Makefile
@@ -18,8 +18,10 @@ top_srcdir := $(shell cd ../../.. ; pwd)
 tests_srcdir := $(top_srcdir)/tests
 
 all: \
+  prefixed_results.csv \
   prefixed_results.html \
   prefixed_results.md \
+  prefixed_results.tsv \
   subclass-explicit-none.md \
   subclass-implicit-any.md \
   w3-output.csv \
@@ -50,8 +52,15 @@ check: \
   check-subclass
 
 check-prefixed_results: \
+  check-prefixed_results-csv \
   check-prefixed_results-html \
-  check-prefixed_results-md
+  check-prefixed_results-md \
+  check-prefixed_results-tsv
+
+check-prefixed_results-csv: \
+  .check-prefixed_results.csv \
+  prefixed_results.csv
+	diff $^
 
 check-prefixed_results-html: \
   .check-prefixed_results.html \
@@ -63,6 +72,11 @@ check-prefixed_results-md: \
   prefixed_results.md
 	diff $^
 
+check-prefixed_results-tsv: \
+  .check-prefixed_results.tsv \
+  prefixed_results.tsv
+	diff $^
+
 check-subclass: \
   check-subclass-explicit-none \
   check-subclass-implicit-any

From 98d4c6b7bf0081b18ad8e135167efcec5e35235a Mon Sep 17 00:00:00 2001
From: Alex Nelson <alexander.nelson@nist.gov>
Date: Wed, 7 Dec 2022 15:42:43 -0500
Subject: [PATCH 12/19] Refactor case_sparql_select code

This patch is code-motion to give function names to chunks of
`case_sparql_select:main`.

Some upcoming patch series are going to add features that, when taken
together, introduce non-trivial parameter-value cross-dependencies.

Moving functionality to functions enables combinatoric testing in a
`pytest` space, rather than resorting to copying, pasting, and tweaking
many Makefile lines.  A future patch series will add the `pytest`
script.

Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
---
 case_utils/case_sparql_select/__init__.py | 195 ++++++++++++++--------
 1 file changed, 127 insertions(+), 68 deletions(-)

diff --git a/case_utils/case_sparql_select/__init__.py b/case_utils/case_sparql_select/__init__.py
index eaa98cb..8b25f30 100644
--- a/case_utils/case_sparql_select/__init__.py
+++ b/case_utils/case_sparql_select/__init__.py
@@ -49,74 +49,44 @@
 _logger = logging.getLogger(os.path.basename(__file__))
 
 
-def main() -> None:
-    parser = argparse.ArgumentParser()
-
-    # Configure debug logging before running parse_args, because there could be an error raised before the construction of the argument parser.
-    logging.basicConfig(
-        level=logging.DEBUG
-        if ("--debug" in sys.argv or "-d" in sys.argv)
-        else logging.INFO
-    )
-
-    parser.add_argument("-d", "--debug", action="store_true")
-    parser.add_argument(
-        "--built-version",
-        choices=tuple(built_version_choices_list),
-        default="case-" + CURRENT_CASE_VERSION,
-        help="Ontology version to use to supplement query, such as for subclass querying.  Does not require networking to use.  Default is most recent CASE release.  Passing 'none' will mean no pre-built CASE ontology versions accompanying this tool will be included in the analysis.",
-    )
-    parser.add_argument(
-        "--disallow-empty-results",
-        action="store_true",
-        help="Raise error if no results are returned for query.",
-    )
-    parser.add_argument(
-        "--use-prefixes",
-        action="store_true",
-        help="Abbreviate node IDs according to graph's encoded prefixes.  (This will use prefixes in the graph, not the query.)",
-    )
-    parser.add_argument(
-        "out_table",
-        help="Expected extensions are .html for HTML tables, .md for Markdown tables, .csv for comma-separated values, and .tsv for tab-separated values.",
-    )
-    parser.add_argument(
-        "in_sparql",
-        help="File containing a SPARQL SELECT query.  Note that prefixes not mapped with a PREFIX statement will be mapped according to their first occurrence among input graphs.",
-    )
-    parser.add_argument("in_graph", nargs="+")
-    args = parser.parse_args()
-
-    graph = rdflib.Graph()
-    for in_graph_filename in args.in_graph:
-        graph.parse(in_graph_filename)
-
-    # Inherit prefixes defined in input context dictionary.
-    nsdict = {k: v for (k, v) in graph.namespace_manager.namespaces()}
-
-    select_query_text = None
-    with open(args.in_sparql, "r") as in_fh:
-        select_query_text = in_fh.read().strip()
-    _logger.debug("select_query_text = %r." % select_query_text)
-
-    if "subClassOf" in select_query_text:
-        case_utils.ontology.load_subclass_hierarchy(
-            graph, built_version=args.built_version
-        )
-
+def query_text_to_variables(select_query_text: str) -> typing.List[str]:
     # Build columns list from SELECT line.
     select_query_text_lines = select_query_text.split("\n")
     select_line = [
         line for line in select_query_text_lines if line.startswith("SELECT ")
     ][0]
     variables = select_line.replace(" DISTINCT", "").replace("SELECT ", "").split(" ")
+    return variables
+
+
+def graph_and_query_to_data_frame(
+    graph: rdflib.Graph,
+    select_query_text: str,
+    *args: typing.Any,
+    built_version: str = "case-" + CURRENT_CASE_VERSION,
+    disallow_empty_results: bool = False,
+    use_prefixes: bool = False,
+    **kwargs: typing.Any,
+) -> pd.DataFrame:
+    # Inherit prefixes defined in input context dictionary.
+    nsdict = {k: v for (k, v) in graph.namespace_manager.namespaces()}
+
+    # Avoid side-effects on input parameter.
+    if "subClassOf" in select_query_text:
+        _graph = rdflib.Graph()
+        _graph += graph
+        case_utils.ontology.load_subclass_hierarchy(_graph, built_version=built_version)
+    else:
+        _graph = graph
+
+    variables = query_text_to_variables(select_query_text)
 
     tally = 0
     records = []
     select_query_object = rdflib.plugins.sparql.processor.prepareQuery(
         select_query_text, initNs=nsdict
     )
-    for (row_no, row) in enumerate(graph.query(select_query_object)):
+    for (row_no, row) in enumerate(_graph.query(select_query_object)):
         tally = row_no + 1
         record = []
         for (column_no, column) in enumerate(row):
@@ -131,7 +101,7 @@ def main() -> None:
                 # .decode() is because hexlify returns bytes.
                 column_value = binascii.hexlify(column.toPython()).decode()
             elif isinstance(column, rdflib.URIRef):
-                if args.use_prefixes:
+                if use_prefixes:
                     column_value = graph.namespace_manager.qname(column.toPython())
                 else:
                     column_value = column.toPython()
@@ -141,39 +111,128 @@ def main() -> None:
                 _logger.debug("row[0]column[%d] = %r." % (column_no, column_value))
             record.append(column_value)
         records.append(record)
+
     if tally == 0:
-        if args.disallow_empty_results:
+        if disallow_empty_results:
             raise ValueError("Failed to return any results.")
 
     df = pd.DataFrame(records, columns=variables)
+    return df
+
 
+def data_frame_to_table_text(
+    df: pd.DataFrame,
+    *args: typing.Any,
+    output_mode: str,
+    **kwargs: typing.Any,
+) -> str:
     table_text: typing.Optional[str] = None
-    if args.out_table.endswith(".csv") or args.out_table.endswith(".tsv"):
-        # https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.to_csv.html
+
+    if output_mode in {"csv", "tsv"}:
         sep: str
-        if args.out_table.endswith(".csv"):
+        if output_mode == "csv":
             sep = ","
-        elif args.out_table.endswith(".tsv"):
+        elif output_mode == "tsv":
             sep = "\t"
         else:
             raise NotImplementedError(
                 "Output extension not implemented in CSV-style output."
             )
         table_text = df.to_csv(sep=sep)
-    elif args.out_table.endswith(".html"):
+    elif output_mode == "html":
         # https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.to_html.html
         # Add CSS classes for CASE website Bootstrap support.
         table_text = df.to_html(classes=("table", "table-bordered", "table-condensed"))
-    elif args.out_table.endswith(".md"):
+    elif output_mode == "md":
         # https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.to_markdown.html
         # https://pypi.org/project/tabulate/
         # Assume Github-flavored Markdown.
+
         table_text = df.to_markdown(tablefmt="github")
-    if table_text is None:
-        raise NotImplementedError(
-            "Unsupported output extension for output filename %r.", args.out_table
-        )
+    else:
+        if table_text is None:
+            raise NotImplementedError("Unimplemented output mode: %r." % output_mode)
+    assert table_text is not None
+
+    return table_text
+
+
+def main() -> None:
+    parser = argparse.ArgumentParser()
+
+    # Configure debug logging before running parse_args, because there could be an error raised before the construction of the argument parser.
+    logging.basicConfig(
+        level=logging.DEBUG
+        if ("--debug" in sys.argv or "-d" in sys.argv)
+        else logging.INFO
+    )
+
+    parser.add_argument("-d", "--debug", action="store_true")
+    parser.add_argument(
+        "--built-version",
+        choices=tuple(built_version_choices_list),
+        default="case-" + CURRENT_CASE_VERSION,
+        help="Ontology version to use to supplement query, such as for subclass querying.  Does not require networking to use.  Default is most recent CASE release.  Passing 'none' will mean no pre-built CASE ontology versions accompanying this tool will be included in the analysis.",
+    )
+    parser.add_argument(
+        "--disallow-empty-results",
+        action="store_true",
+        help="Raise error if no results are returned for query.",
+    )
+    parser.add_argument(
+        "--use-prefixes",
+        action="store_true",
+        help="Abbreviate node IDs according to graph's encoded prefixes.  (This will use prefixes in the graph, not the query.)",
+    )
+    parser.add_argument(
+        "out_table",
+        help="Expected extensions are .html for HTML tables, .md for Markdown tables, .csv for comma-separated values, and .tsv for tab-separated values.",
+    )
+    parser.add_argument(
+        "in_sparql",
+        help="File containing a SPARQL SELECT query.  Note that prefixes not mapped with a PREFIX statement will be mapped according to their first occurrence among input graphs.",
+    )
+
+    parser.add_argument("in_graph", nargs="+")
+    args = parser.parse_args()
 
+    output_mode: str
+    if args.out_table.endswith(".csv"):
+        output_mode = "csv"
+    elif args.out_table.endswith(".html"):
+        output_mode = "html"
+    elif args.out_table.endswith(".json"):
+        output_mode = "json"
+    elif args.out_table.endswith(".md"):
+        output_mode = "md"
+    elif args.out_table.endswith(".tsv"):
+        output_mode = "tsv"
+    else:
+        raise NotImplementedError("Output file extension not implemented.")
+
+    graph = rdflib.Graph()
+    for in_graph_filename in args.in_graph:
+        graph.parse(in_graph_filename)
+
+    select_query_text: typing.Optional[str] = None
+    with open(args.in_sparql, "r") as in_fh:
+        select_query_text = in_fh.read().strip()
+    if select_query_text is None:
+        raise ValueError("Failed to load query.")
+    _logger.debug("select_query_text = %r." % select_query_text)
+
+    df = graph_and_query_to_data_frame(
+        graph,
+        select_query_text,
+        built_version=args.built_version,
+        disallow_empty_results=args.disallow_empty_results is True,
+        use_prefixes=args.use_prefixes is True,
+    )
+
+    table_text = data_frame_to_table_text(
+        df,
+        output_mode=output_mode,
+    )
     with open(args.out_table, "w") as out_fh:
         out_fh.write(table_text)
         if table_text[-1] != "\n":

From e69959272993d009bc9983724a7b8a162359f8c3 Mon Sep 17 00:00:00 2001
From: Alex Nelson <alexander.nelson@nist.gov>
Date: Wed, 7 Dec 2022 16:36:32 -0500
Subject: [PATCH 13/19] Add case_sparql_select CSV and TSV output

No effects were observed on Make-managed files.

Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
---
 case_utils/case_sparql_select/__init__.py     | 23 ++++++-
 .../.check-prefixed_results-indented.json     |  6 ++
 .../.check-prefixed_results.json              |  1 +
 .../.check-w3-output-indented.json            | 10 +++
 .../case_sparql_select/.check-w3-output.json  |  1 +
 .../case_utils/case_sparql_select/.gitignore  |  2 +-
 tests/case_utils/case_sparql_select/Makefile  | 68 +++++++++++++++++++
 7 files changed, 109 insertions(+), 2 deletions(-)
 create mode 100644 tests/case_utils/case_sparql_select/.check-prefixed_results-indented.json
 create mode 100644 tests/case_utils/case_sparql_select/.check-prefixed_results.json
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-indented.json
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output.json

diff --git a/case_utils/case_sparql_select/__init__.py b/case_utils/case_sparql_select/__init__.py
index 8b25f30..16d3c67 100644
--- a/case_utils/case_sparql_select/__init__.py
+++ b/case_utils/case_sparql_select/__init__.py
@@ -123,6 +123,8 @@ def graph_and_query_to_data_frame(
 def data_frame_to_table_text(
     df: pd.DataFrame,
     *args: typing.Any,
+    json_indent: typing.Optional[int] = None,
+    json_orient: str,
     output_mode: str,
     **kwargs: typing.Any,
 ) -> str:
@@ -143,6 +145,12 @@ def data_frame_to_table_text(
         # https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.to_html.html
         # Add CSS classes for CASE website Bootstrap support.
         table_text = df.to_html(classes=("table", "table-bordered", "table-condensed"))
+    elif output_mode == "json":
+        # https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.to_json.html
+
+        table_text = df.to_json(
+            indent=json_indent, orient=json_orient, date_format="iso"
+        )
     elif output_mode == "md":
         # https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.to_markdown.html
         # https://pypi.org/project/tabulate/
@@ -179,6 +187,17 @@ def main() -> None:
         action="store_true",
         help="Raise error if no results are returned for query.",
     )
+    parser.add_argument(
+        "--json-indent",
+        type=int,
+        help="Number of whitespace characters to use for indentation.  Only applicable for JSON output.",
+    )
+    parser.add_argument(
+        "--json-orient",
+        default="columns",
+        choices=("columns", "index", "records", "split", "table", "values"),
+        help="Orientation to use for Pandas DataFrame JSON output.  Only applicable for JSON output.",
+    )
     parser.add_argument(
         "--use-prefixes",
         action="store_true",
@@ -186,7 +205,7 @@ def main() -> None:
     )
     parser.add_argument(
         "out_table",
-        help="Expected extensions are .html for HTML tables, .md for Markdown tables, .csv for comma-separated values, and .tsv for tab-separated values.",
+        help="Expected extensions are .html for HTML tables, .json for JSON tables, .md for Markdown tables, .csv for comma-separated values, and .tsv for tab-separated values.  Note that JSON is a Pandas output JSON format (chosen by '--json-orient'), and not JSON-LD.",
     )
     parser.add_argument(
         "in_sparql",
@@ -231,6 +250,8 @@ def main() -> None:
 
     table_text = data_frame_to_table_text(
         df,
+        json_indent=args.json_indent,
+        json_orient=args.json_orient,
         output_mode=output_mode,
     )
     with open(args.out_table, "w") as out_fh:
diff --git a/tests/case_utils/case_sparql_select/.check-prefixed_results-indented.json b/tests/case_utils/case_sparql_select/.check-prefixed_results-indented.json
new file mode 100644
index 0000000..c356eca
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-prefixed_results-indented.json
@@ -0,0 +1,6 @@
+{
+    "?nFile":{
+        "0":"kb:file-1",
+        "1":"kb:file-2"
+    }
+}
diff --git a/tests/case_utils/case_sparql_select/.check-prefixed_results.json b/tests/case_utils/case_sparql_select/.check-prefixed_results.json
new file mode 100644
index 0000000..63a9d7f
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-prefixed_results.json
@@ -0,0 +1 @@
+{"?nFile":{"0":"kb:file-1","1":"kb:file-2"}}
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-indented.json b/tests/case_utils/case_sparql_select/.check-w3-output-indented.json
new file mode 100644
index 0000000..8f426c6
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-indented.json
@@ -0,0 +1,10 @@
+{
+    "?name":{
+        "0":"Johnny Lee Outlaw",
+        "1":"Peter Goodguy"
+    },
+    "?mbox":{
+        "0":"mailto:jlow@example.com",
+        "1":"mailto:peter@example.org"
+    }
+}
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output.json b/tests/case_utils/case_sparql_select/.check-w3-output.json
new file mode 100644
index 0000000..840035b
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output.json
@@ -0,0 +1 @@
+{"?name":{"0":"Johnny Lee Outlaw","1":"Peter Goodguy"},"?mbox":{"0":"mailto:jlow@example.com","1":"mailto:peter@example.org"}}
diff --git a/tests/case_utils/case_sparql_select/.gitignore b/tests/case_utils/case_sparql_select/.gitignore
index 9d94989..122f73b 100644
--- a/tests/case_utils/case_sparql_select/.gitignore
+++ b/tests/case_utils/case_sparql_select/.gitignore
@@ -1,3 +1,3 @@
 prefixed*
 subclass-*.md
-w3-output.*
+w3-output*
diff --git a/tests/case_utils/case_sparql_select/Makefile b/tests/case_utils/case_sparql_select/Makefile
index 68f11ec..70bb0ec 100644
--- a/tests/case_utils/case_sparql_select/Makefile
+++ b/tests/case_utils/case_sparql_select/Makefile
@@ -20,12 +20,16 @@ tests_srcdir := $(top_srcdir)/tests
 all: \
   prefixed_results.csv \
   prefixed_results.html \
+  prefixed_results.json \
+  prefixed_results-indented.json \
   prefixed_results.md \
   prefixed_results.tsv \
   subclass-explicit-none.md \
   subclass-implicit-any.md \
   w3-output.csv \
   w3-output.html \
+  w3-output.json \
+  w3-output-indented.json \
   w3-output.md \
   w3-output.tsv
 
@@ -35,6 +39,8 @@ all: \
   check-subclass-implicit-any \
   check-w3-csv \
   check-w3-html \
+  check-w3-json \
+  check-w3-json-indented \
   check-w3-markdown \
   check-w3-tsv
 
@@ -46,6 +52,7 @@ all: \
 check: \
   check-w3-csv \
   check-w3-html \
+  check-w3-json \
   check-w3-markdown \
   check-w3-tsv \
   check-prefixed_results \
@@ -54,6 +61,7 @@ check: \
 check-prefixed_results: \
   check-prefixed_results-csv \
   check-prefixed_results-html \
+  check-prefixed_results-json \
   check-prefixed_results-md \
   check-prefixed_results-tsv
 
@@ -67,6 +75,19 @@ check-prefixed_results-html: \
   prefixed_results.html
 	diff $^
 
+check-prefixed_results-json: \
+  check-prefixed_results-json-indented \
+  .check-prefixed_results.json \
+  prefixed_results.json
+	diff \
+	  .check-prefixed_results.json \
+	  prefixed_results.json
+
+check-prefixed_results-json-indented: \
+  .check-prefixed_results-indented.json \
+  prefixed_results-indented.json
+	diff $^
+
 check-prefixed_results-md: \
   .check-prefixed_results.md \
   prefixed_results.md
@@ -101,6 +122,19 @@ check-w3-html: \
   w3-output.html
 	diff $^
 
+check-w3-json: \
+  .check-w3-output.json \
+  check-w3-json-indented \
+  w3-output.json
+	diff \
+	  .check-w3-output.json \
+	  w3-output.json
+
+check-w3-json-indented: \
+  .check-w3-output-indented.json \
+  w3-output-indented.json
+	diff $^
+
 check-w3-markdown: \
   .check-w3-output.md \
   w3-output.md
@@ -119,6 +153,7 @@ clean:
 	  *.html \
 	  *.md \
 	  *.tsv \
+	  *output*.json \
 	  _*
 
 prefixed_results.%: \
@@ -136,6 +171,22 @@ prefixed_results.%: \
 	    subclass.json
 	mv _$@ $@
 
+prefixed_results-indented.json: \
+  $(tests_srcdir)/.venv.done.log \
+  $(top_srcdir)/case_utils/case_sparql_select/__init__.py \
+  $(top_srcdir)/case_utils/ontology/__init__.py \
+  $(top_srcdir)/case_utils/ontology/version_info.py \
+  subclass.json \
+  subclass.sparql
+	source $(tests_srcdir)/venv/bin/activate \
+	  && case_sparql_select \
+	    --json-indent 4 \
+	    --use-prefixes \
+	    _$@ \
+	    subclass.sparql \
+	    subclass.json
+	mv _$@ $@
+
 subclass-explicit-none.md: \
   $(tests_srcdir)/.venv.done.log \
   $(top_srcdir)/case_utils/case_sparql_select/__init__.py \
@@ -180,3 +231,20 @@ w3-output.%: \
 	    w3-input-2.ttl \
 	    w3-input-3.json
 	mv _$@ $@
+
+w3-output-indented.json: \
+  $(tests_srcdir)/.venv.done.log \
+  $(top_srcdir)/case_utils/case_sparql_select/__init__.py \
+  $(top_srcdir)/case_utils/ontology/__init__.py \
+  $(top_srcdir)/case_utils/ontology/version_info.py \
+  w3-input-1.sparql \
+  w3-input-2.ttl \
+  w3-input-3.json
+	source $(tests_srcdir)/venv/bin/activate \
+	  && case_sparql_select \
+	    --json-indent 4 \
+	    _$@ \
+	    w3-input-1.sparql \
+	    w3-input-2.ttl \
+	    w3-input-3.json
+	mv _$@ $@

From b1bcad32ec2aa8939f38272d3252e8f642706f43 Mon Sep 17 00:00:00 2001
From: Alex Nelson <alexander.nelson@nist.gov>
Date: Wed, 7 Dec 2022 17:13:45 -0500
Subject: [PATCH 14/19] Add options to case_sparql_select to disable headers
 and index numbers

The test pattern for these features encourages an enumerative approach,
so a `pytest` script exercising the freshly broken-out functions is now
included.

No effects were observed on Make-managed files.

Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
---
 case_utils/case_sparql_select/__init__.py     | 70 ++++++++++++++++-
 tests/case_utils/Makefile                     |  1 +
 ...check-w3-output-with_header-with_index.csv |  3 +
 ...heck-w3-output-with_header-with_index.html | 21 ++++++
 ....check-w3-output-with_header-with_index.md |  4 +
 ...check-w3-output-with_header-with_index.tsv |  3 +
 ...ck-w3-output-with_header-without_index.csv |  3 +
 ...k-w3-output-with_header-without_index.html | 18 +++++
 ...eck-w3-output-with_header-without_index.md |  4 +
 ...ck-w3-output-with_header-without_index.tsv |  3 +
 ...ck-w3-output-without_header-with_index.csv |  2 +
 ...k-w3-output-without_header-with_index.html | 14 ++++
 ...eck-w3-output-without_header-with_index.md |  3 +
 ...ck-w3-output-without_header-with_index.tsv |  2 +
 ...w3-output-without_header-without_index.csv |  2 +
 ...3-output-without_header-without_index.html | 12 +++
 ...-w3-output-without_header-without_index.md |  3 +
 ...w3-output-without_header-without_index.tsv |  2 +
 tests/case_utils/case_sparql_select/Makefile  |  3 +
 .../test_data_frame_to_table_text_json.py     | 75 +++++++++++++++++++
 20 files changed, 245 insertions(+), 3 deletions(-)
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index.csv
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index.html
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index.md
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index.tsv
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-with_header-without_index.csv
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-with_header-without_index.html
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-with_header-without_index.md
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-with_header-without_index.tsv
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index.csv
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index.html
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index.md
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index.tsv
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-without_header-without_index.csv
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-without_header-without_index.html
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-without_header-without_index.md
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-without_header-without_index.tsv
 create mode 100644 tests/case_utils/case_sparql_select/test_data_frame_to_table_text_json.py

diff --git a/case_utils/case_sparql_select/__init__.py b/case_utils/case_sparql_select/__init__.py
index 8b25f30..2d8581c 100644
--- a/case_utils/case_sparql_select/__init__.py
+++ b/case_utils/case_sparql_select/__init__.py
@@ -124,10 +124,25 @@ def data_frame_to_table_text(
     df: pd.DataFrame,
     *args: typing.Any,
     output_mode: str,
+    use_header: bool,
+    use_index: bool,
     **kwargs: typing.Any,
 ) -> str:
     table_text: typing.Optional[str] = None
 
+    # Set up kwargs dicts.  One kwarg behaves slightly differently for Markdown vs. other formats.
+    general_kwargs: typing.Dict[str, typing.Any] = dict()
+    md_kwargs: typing.Dict[str, typing.Any] = dict()
+
+    # Note some output modes will drop 'header' from general_kwargs, due to alternate support or lack of support.
+    if use_header:
+        general_kwargs["header"] = True
+    else:
+        general_kwargs["header"] = False
+        md_kwargs["headers"] = tuple()
+
+    general_kwargs["index"] = use_index
+
     if output_mode in {"csv", "tsv"}:
         sep: str
         if output_mode == "csv":
@@ -138,17 +153,22 @@ def data_frame_to_table_text(
             raise NotImplementedError(
                 "Output extension not implemented in CSV-style output."
             )
-        table_text = df.to_csv(sep=sep)
+        table_text = df.to_csv(sep=sep, **general_kwargs)
     elif output_mode == "html":
         # https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.to_html.html
         # Add CSS classes for CASE website Bootstrap support.
-        table_text = df.to_html(classes=("table", "table-bordered", "table-condensed"))
+        table_text = df.to_html(
+            classes=("table", "table-bordered", "table-condensed"), **general_kwargs
+        )
     elif output_mode == "md":
         # https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.to_markdown.html
         # https://pypi.org/project/tabulate/
         # Assume Github-flavored Markdown.
 
-        table_text = df.to_markdown(tablefmt="github")
+        # Drop unsupported kwarg.
+        del general_kwargs["header"]
+
+        table_text = df.to_markdown(tablefmt="github", **general_kwargs, **md_kwargs)
     else:
         if table_text is None:
             raise NotImplementedError("Unimplemented output mode: %r." % output_mode)
@@ -193,6 +213,30 @@ def main() -> None:
         help="File containing a SPARQL SELECT query.  Note that prefixes not mapped with a PREFIX statement will be mapped according to their first occurrence among input graphs.",
     )
 
+    parser_header_group = parser.add_mutually_exclusive_group(required=False)
+    parser_header_group.add_argument(
+        "--header",
+        action="store_true",
+        help="Print column labels.  This is the default behavior.",
+    )
+    parser_header_group.add_argument(
+        "--no-header",
+        action="store_true",
+        help="Do not print column labels.",
+    )
+
+    parser_index_group = parser.add_mutually_exclusive_group(required=False)
+    parser_index_group.add_argument(
+        "--index",
+        action="store_true",
+        help="Print index (auto-incrementing row labels as left untitled column).  This is the default behavior.",
+    )
+    parser_index_group.add_argument(
+        "--no-index",
+        action="store_true",
+        help="Do not print index.",
+    )
+
     parser.add_argument("in_graph", nargs="+")
     args = parser.parse_args()
 
@@ -221,6 +265,24 @@ def main() -> None:
         raise ValueError("Failed to load query.")
     _logger.debug("select_query_text = %r." % select_query_text)
 
+    # Process --header and --no-header.
+    use_header: bool
+    if args.header is True:
+        use_header = True
+    if args.no_header is True:
+        use_header = False
+    else:
+        use_header = True
+
+    # Process --index and --no-index.
+    use_index: bool
+    if args.index is True:
+        use_index = True
+    if args.no_index is True:
+        use_index = False
+    else:
+        use_index = True
+
     df = graph_and_query_to_data_frame(
         graph,
         select_query_text,
@@ -232,6 +294,8 @@ def main() -> None:
     table_text = data_frame_to_table_text(
         df,
         output_mode=output_mode,
+        use_header=use_header,
+        use_index=use_index,
     )
     with open(args.out_table, "w") as out_fh:
         out_fh.write(table_text)
diff --git a/tests/case_utils/Makefile b/tests/case_utils/Makefile
index e77c927..3c65a40 100644
--- a/tests/case_utils/Makefile
+++ b/tests/case_utils/Makefile
@@ -65,6 +65,7 @@ check: \
 	  && pytest \
 	    --ignore case_file \
 	    --ignore case_sparql_construct \
+	    --ignore case_sparql_select \
 	    --ignore case_validate \
 	    --log-level=DEBUG
 
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index.csv b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index.csv
new file mode 100644
index 0000000..063e950
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index.csv
@@ -0,0 +1,3 @@
+,?name,?mbox
+0,Johnny Lee Outlaw,mailto:jlow@example.com
+1,Peter Goodguy,mailto:peter@example.org
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index.html b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index.html
new file mode 100644
index 0000000..bee5944
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index.html
@@ -0,0 +1,21 @@
+<table border="1" class="dataframe table table-bordered table-condensed">
+  <thead>
+    <tr style="text-align: right;">
+      <th></th>
+      <th>?name</th>
+      <th>?mbox</th>
+    </tr>
+  </thead>
+  <tbody>
+    <tr>
+      <th>0</th>
+      <td>Johnny Lee Outlaw</td>
+      <td>mailto:jlow@example.com</td>
+    </tr>
+    <tr>
+      <th>1</th>
+      <td>Peter Goodguy</td>
+      <td>mailto:peter@example.org</td>
+    </tr>
+  </tbody>
+</table>
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index.md b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index.md
new file mode 100644
index 0000000..af68b84
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index.md
@@ -0,0 +1,4 @@
+|    | ?name             | ?mbox                    |
+|----|-------------------|--------------------------|
+|  0 | Johnny Lee Outlaw | mailto:jlow@example.com  |
+|  1 | Peter Goodguy     | mailto:peter@example.org |
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index.tsv b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index.tsv
new file mode 100644
index 0000000..a4fdfca
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index.tsv
@@ -0,0 +1,3 @@
+	?name	?mbox
+0	Johnny Lee Outlaw	mailto:jlow@example.com
+1	Peter Goodguy	mailto:peter@example.org
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-with_header-without_index.csv b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-without_index.csv
new file mode 100644
index 0000000..6bd60fb
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-without_index.csv
@@ -0,0 +1,3 @@
+?name,?mbox
+Johnny Lee Outlaw,mailto:jlow@example.com
+Peter Goodguy,mailto:peter@example.org
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-with_header-without_index.html b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-without_index.html
new file mode 100644
index 0000000..041fd3b
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-without_index.html
@@ -0,0 +1,18 @@
+<table border="1" class="dataframe table table-bordered table-condensed">
+  <thead>
+    <tr style="text-align: right;">
+      <th>?name</th>
+      <th>?mbox</th>
+    </tr>
+  </thead>
+  <tbody>
+    <tr>
+      <td>Johnny Lee Outlaw</td>
+      <td>mailto:jlow@example.com</td>
+    </tr>
+    <tr>
+      <td>Peter Goodguy</td>
+      <td>mailto:peter@example.org</td>
+    </tr>
+  </tbody>
+</table>
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-with_header-without_index.md b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-without_index.md
new file mode 100644
index 0000000..3aa8a01
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-without_index.md
@@ -0,0 +1,4 @@
+| ?name             | ?mbox                    |
+|-------------------|--------------------------|
+| Johnny Lee Outlaw | mailto:jlow@example.com  |
+| Peter Goodguy     | mailto:peter@example.org |
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-with_header-without_index.tsv b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-without_index.tsv
new file mode 100644
index 0000000..dd1e81d
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-without_index.tsv
@@ -0,0 +1,3 @@
+?name	?mbox
+Johnny Lee Outlaw	mailto:jlow@example.com
+Peter Goodguy	mailto:peter@example.org
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index.csv b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index.csv
new file mode 100644
index 0000000..7933d39
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index.csv
@@ -0,0 +1,2 @@
+0,Johnny Lee Outlaw,mailto:jlow@example.com
+1,Peter Goodguy,mailto:peter@example.org
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index.html b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index.html
new file mode 100644
index 0000000..b6a842b
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index.html
@@ -0,0 +1,14 @@
+<table border="1" class="dataframe table table-bordered table-condensed">
+  <tbody>
+    <tr>
+      <th>0</th>
+      <td>Johnny Lee Outlaw</td>
+      <td>mailto:jlow@example.com</td>
+    </tr>
+    <tr>
+      <th>1</th>
+      <td>Peter Goodguy</td>
+      <td>mailto:peter@example.org</td>
+    </tr>
+  </tbody>
+</table>
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index.md b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index.md
new file mode 100644
index 0000000..c5ee8c8
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index.md
@@ -0,0 +1,3 @@
+|---|-------------------|--------------------------|
+| 0 | Johnny Lee Outlaw | mailto:jlow@example.com  |
+| 1 | Peter Goodguy     | mailto:peter@example.org |
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index.tsv b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index.tsv
new file mode 100644
index 0000000..992efe2
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index.tsv
@@ -0,0 +1,2 @@
+0	Johnny Lee Outlaw	mailto:jlow@example.com
+1	Peter Goodguy	mailto:peter@example.org
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-without_header-without_index.csv b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-without_index.csv
new file mode 100644
index 0000000..a4c2c82
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-without_index.csv
@@ -0,0 +1,2 @@
+Johnny Lee Outlaw,mailto:jlow@example.com
+Peter Goodguy,mailto:peter@example.org
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-without_header-without_index.html b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-without_index.html
new file mode 100644
index 0000000..6dbc7c3
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-without_index.html
@@ -0,0 +1,12 @@
+<table border="1" class="dataframe table table-bordered table-condensed">
+  <tbody>
+    <tr>
+      <td>Johnny Lee Outlaw</td>
+      <td>mailto:jlow@example.com</td>
+    </tr>
+    <tr>
+      <td>Peter Goodguy</td>
+      <td>mailto:peter@example.org</td>
+    </tr>
+  </tbody>
+</table>
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-without_header-without_index.md b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-without_index.md
new file mode 100644
index 0000000..6ad505c
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-without_index.md
@@ -0,0 +1,3 @@
+|-------------------|--------------------------|
+| Johnny Lee Outlaw | mailto:jlow@example.com  |
+| Peter Goodguy     | mailto:peter@example.org |
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-without_header-without_index.tsv b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-without_index.tsv
new file mode 100644
index 0000000..833da47
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-without_index.tsv
@@ -0,0 +1,2 @@
+Johnny Lee Outlaw	mailto:jlow@example.com
+Peter Goodguy	mailto:peter@example.org
diff --git a/tests/case_utils/case_sparql_select/Makefile b/tests/case_utils/case_sparql_select/Makefile
index 68f11ec..0523c8a 100644
--- a/tests/case_utils/case_sparql_select/Makefile
+++ b/tests/case_utils/case_sparql_select/Makefile
@@ -50,6 +50,9 @@ check: \
   check-w3-tsv \
   check-prefixed_results \
   check-subclass
+	source $(tests_srcdir)/venv/bin/activate \
+	  && pytest \
+	    --log-level=DEBUG
 
 check-prefixed_results: \
   check-prefixed_results-csv \
diff --git a/tests/case_utils/case_sparql_select/test_data_frame_to_table_text_json.py b/tests/case_utils/case_sparql_select/test_data_frame_to_table_text_json.py
new file mode 100644
index 0000000..00d20c3
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/test_data_frame_to_table_text_json.py
@@ -0,0 +1,75 @@
+#!/usr/bin/env python3
+
+# This software was developed at the National Institute of Standards
+# and Technology by employees of the Federal Government in the course
+# of their official duties. Pursuant to title 17 Section 105 of the
+# United States Code this software is not subject to copyright
+# protection and is in the public domain. NIST assumes no
+# responsibility whatsoever for its use by other parties, and makes
+# no guarantees, expressed or implied, about its quality,
+# reliability, or any other characteristic.
+#
+# We would appreciate acknowledgement if the software is used.
+
+import pathlib
+import typing
+
+import pytest
+import rdflib
+
+import case_utils.case_sparql_select
+
+SRCDIR = pathlib.Path(__file__).parent
+
+GRAPH = rdflib.Graph()
+GRAPH.parse(str(SRCDIR / "w3-input-2.ttl"))
+GRAPH.parse(str(SRCDIR / "w3-input-3.json"))
+assert len(GRAPH) > 0
+
+SELECT_QUERY_TEXT: typing.Optional[str] = None
+with (SRCDIR / "w3-input-1.sparql").open("r") as _fh:
+    SELECT_QUERY_TEXT = _fh.read().strip()
+assert SELECT_QUERY_TEXT is not None
+
+DATA_FRAME = case_utils.case_sparql_select.graph_and_query_to_data_frame(
+    GRAPH, SELECT_QUERY_TEXT
+)
+
+
+def make_data_frame_to_json_table_text_parameters() -> typing.Iterator[
+    typing.Tuple[str, bool, bool]
+]:
+    for use_header in [False, True]:
+        for use_index in [False, True]:
+            for output_mode in ["csv", "html", "md", "tsv"]:
+                yield (output_mode, use_header, use_index)
+
+
+@pytest.mark.parametrize(
+    "output_mode, use_header, use_index",
+    make_data_frame_to_json_table_text_parameters(),
+)
+def test_data_frame_to_table_text_json(
+    output_mode: str,
+    use_header: bool,
+    use_index: bool,
+) -> None:
+    table_text = case_utils.case_sparql_select.data_frame_to_table_text(
+        DATA_FRAME,
+        output_mode=output_mode,
+        use_header=use_header,
+        use_index=use_index,
+    )
+
+    output_filename_template = ".check-w3-output-%s_header-%s_index.%s"
+    header_part = "with" if use_header else "without"
+    index_part = "with" if use_index else "without"
+    output_filename = output_filename_template % (
+        header_part,
+        index_part,
+        output_mode,
+    )
+    with (SRCDIR / output_filename).open("w") as out_fh:
+        out_fh.write(table_text)
+        if table_text[-1] != "\n":
+            out_fh.write("\n")

From ed44477f1ae35747b963d40b4ab61087273ac0cc Mon Sep 17 00:00:00 2001
From: Alex Nelson <alexander.nelson@nist.gov>
Date: Wed, 7 Dec 2022 17:26:03 -0500
Subject: [PATCH 15/19] Merge JSON output and --no-(header,index) flag branches

This patch addresses issues with some parameter-values being compatible
with some of the DataFrame table rendering functions, but not with
certain `orient` parameters of the JSON rendering function.  The
incompatible pairings are now caught at parameter-parsing time.

Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
---
 case_utils/case_sparql_select/__init__.py     | 16 +++++++--
 ...with_header-with_index-orient-columns.json |  1 +
 ...t-with_header-with_index-orient-index.json |  1 +
 ...with_header-with_index-orient-records.json |  1 +
 ...t-with_header-with_index-orient-split.json |  1 +
 ...t-with_header-with_index-orient-table.json |  1 +
 ...-with_header-with_index-orient-values.json |  1 +
 ...ith_header-without_index-orient-split.json |  1 +
 ...ith_header-without_index-orient-table.json |  1 +
 ...hout_header-with_index-orient-columns.json |  1 +
 ...ithout_header-with_index-orient-index.json |  1 +
 ...hout_header-with_index-orient-records.json |  1 +
 ...ithout_header-with_index-orient-split.json |  1 +
 ...ithout_header-with_index-orient-table.json |  1 +
 ...thout_header-with_index-orient-values.json |  1 +
 ...out_header-without_index-orient-split.json |  1 +
 ...out_header-without_index-orient-table.json |  1 +
 .../test_data_frame_to_table_text_json.py     | 33 ++++++++++++++++---
 18 files changed, 58 insertions(+), 7 deletions(-)
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index-orient-columns.json
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index-orient-index.json
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index-orient-records.json
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index-orient-split.json
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index-orient-table.json
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index-orient-values.json
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-with_header-without_index-orient-split.json
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-with_header-without_index-orient-table.json
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index-orient-columns.json
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index-orient-index.json
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index-orient-records.json
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index-orient-split.json
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index-orient-table.json
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index-orient-values.json
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-without_header-without_index-orient-split.json
 create mode 100644 tests/case_utils/case_sparql_select/.check-w3-output-without_header-without_index-orient-table.json

diff --git a/case_utils/case_sparql_select/__init__.py b/case_utils/case_sparql_select/__init__.py
index eb41f96..870e44c 100644
--- a/case_utils/case_sparql_select/__init__.py
+++ b/case_utils/case_sparql_select/__init__.py
@@ -165,8 +165,11 @@ def data_frame_to_table_text(
     elif output_mode == "json":
         # https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.to_json.html
 
+        # Drop unsupported kwarg.
+        del general_kwargs["header"]
+
         table_text = df.to_json(
-            indent=json_indent, orient=json_orient, date_format="iso"
+            indent=json_indent, orient=json_orient, date_format="iso", **general_kwargs
         )
     elif output_mode == "md":
         # https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.to_markdown.html
@@ -253,7 +256,7 @@ def main() -> None:
     parser_index_group.add_argument(
         "--no-index",
         action="store_true",
-        help="Do not print index.",
+        help="Do not print index.  If output is JSON, --json-orient must be 'split' or 'table'.",
     )
 
     parser.add_argument("in_graph", nargs="+")
@@ -302,6 +305,15 @@ def main() -> None:
     else:
         use_index = True
 
+    if (
+        output_mode == "json"
+        and use_index is False
+        and args.json_orient not in {"split", "table"}
+    ):
+        raise ValueError(
+            "For JSON output, --no-index flag requires --json-orient to be either 'split' or 'table'."
+        )
+
     df = graph_and_query_to_data_frame(
         graph,
         select_query_text,
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index-orient-columns.json b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index-orient-columns.json
new file mode 100644
index 0000000..840035b
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index-orient-columns.json
@@ -0,0 +1 @@
+{"?name":{"0":"Johnny Lee Outlaw","1":"Peter Goodguy"},"?mbox":{"0":"mailto:jlow@example.com","1":"mailto:peter@example.org"}}
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index-orient-index.json b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index-orient-index.json
new file mode 100644
index 0000000..717d3ae
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index-orient-index.json
@@ -0,0 +1 @@
+{"0":{"?name":"Johnny Lee Outlaw","?mbox":"mailto:jlow@example.com"},"1":{"?name":"Peter Goodguy","?mbox":"mailto:peter@example.org"}}
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index-orient-records.json b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index-orient-records.json
new file mode 100644
index 0000000..f053616
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index-orient-records.json
@@ -0,0 +1 @@
+[{"?name":"Johnny Lee Outlaw","?mbox":"mailto:jlow@example.com"},{"?name":"Peter Goodguy","?mbox":"mailto:peter@example.org"}]
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index-orient-split.json b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index-orient-split.json
new file mode 100644
index 0000000..0401af1
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index-orient-split.json
@@ -0,0 +1 @@
+{"columns":["?name","?mbox"],"index":[0,1],"data":[["Johnny Lee Outlaw","mailto:jlow@example.com"],["Peter Goodguy","mailto:peter@example.org"]]}
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index-orient-table.json b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index-orient-table.json
new file mode 100644
index 0000000..92f005c
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index-orient-table.json
@@ -0,0 +1 @@
+{"schema":{"fields":[{"name":"index","type":"integer"},{"name":"?name","type":"string"},{"name":"?mbox","type":"string"}],"primaryKey":["index"],"pandas_version":"1.4.0"},"data":[{"index":0,"?name":"Johnny Lee Outlaw","?mbox":"mailto:jlow@example.com"},{"index":1,"?name":"Peter Goodguy","?mbox":"mailto:peter@example.org"}]}
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index-orient-values.json b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index-orient-values.json
new file mode 100644
index 0000000..e49c3eb
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-with_index-orient-values.json
@@ -0,0 +1 @@
+[["Johnny Lee Outlaw","mailto:jlow@example.com"],["Peter Goodguy","mailto:peter@example.org"]]
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-with_header-without_index-orient-split.json b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-without_index-orient-split.json
new file mode 100644
index 0000000..885bc91
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-without_index-orient-split.json
@@ -0,0 +1 @@
+{"columns":["?name","?mbox"],"data":[["Johnny Lee Outlaw","mailto:jlow@example.com"],["Peter Goodguy","mailto:peter@example.org"]]}
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-with_header-without_index-orient-table.json b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-without_index-orient-table.json
new file mode 100644
index 0000000..c9e7c13
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-with_header-without_index-orient-table.json
@@ -0,0 +1 @@
+{"schema":{"fields":[{"name":"?name","type":"string"},{"name":"?mbox","type":"string"}],"pandas_version":"1.4.0"},"data":[{"?name":"Johnny Lee Outlaw","?mbox":"mailto:jlow@example.com"},{"?name":"Peter Goodguy","?mbox":"mailto:peter@example.org"}]}
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index-orient-columns.json b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index-orient-columns.json
new file mode 100644
index 0000000..840035b
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index-orient-columns.json
@@ -0,0 +1 @@
+{"?name":{"0":"Johnny Lee Outlaw","1":"Peter Goodguy"},"?mbox":{"0":"mailto:jlow@example.com","1":"mailto:peter@example.org"}}
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index-orient-index.json b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index-orient-index.json
new file mode 100644
index 0000000..717d3ae
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index-orient-index.json
@@ -0,0 +1 @@
+{"0":{"?name":"Johnny Lee Outlaw","?mbox":"mailto:jlow@example.com"},"1":{"?name":"Peter Goodguy","?mbox":"mailto:peter@example.org"}}
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index-orient-records.json b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index-orient-records.json
new file mode 100644
index 0000000..f053616
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index-orient-records.json
@@ -0,0 +1 @@
+[{"?name":"Johnny Lee Outlaw","?mbox":"mailto:jlow@example.com"},{"?name":"Peter Goodguy","?mbox":"mailto:peter@example.org"}]
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index-orient-split.json b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index-orient-split.json
new file mode 100644
index 0000000..0401af1
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index-orient-split.json
@@ -0,0 +1 @@
+{"columns":["?name","?mbox"],"index":[0,1],"data":[["Johnny Lee Outlaw","mailto:jlow@example.com"],["Peter Goodguy","mailto:peter@example.org"]]}
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index-orient-table.json b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index-orient-table.json
new file mode 100644
index 0000000..92f005c
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index-orient-table.json
@@ -0,0 +1 @@
+{"schema":{"fields":[{"name":"index","type":"integer"},{"name":"?name","type":"string"},{"name":"?mbox","type":"string"}],"primaryKey":["index"],"pandas_version":"1.4.0"},"data":[{"index":0,"?name":"Johnny Lee Outlaw","?mbox":"mailto:jlow@example.com"},{"index":1,"?name":"Peter Goodguy","?mbox":"mailto:peter@example.org"}]}
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index-orient-values.json b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index-orient-values.json
new file mode 100644
index 0000000..e49c3eb
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-with_index-orient-values.json
@@ -0,0 +1 @@
+[["Johnny Lee Outlaw","mailto:jlow@example.com"],["Peter Goodguy","mailto:peter@example.org"]]
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-without_header-without_index-orient-split.json b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-without_index-orient-split.json
new file mode 100644
index 0000000..885bc91
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-without_index-orient-split.json
@@ -0,0 +1 @@
+{"columns":["?name","?mbox"],"data":[["Johnny Lee Outlaw","mailto:jlow@example.com"],["Peter Goodguy","mailto:peter@example.org"]]}
diff --git a/tests/case_utils/case_sparql_select/.check-w3-output-without_header-without_index-orient-table.json b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-without_index-orient-table.json
new file mode 100644
index 0000000..c9e7c13
--- /dev/null
+++ b/tests/case_utils/case_sparql_select/.check-w3-output-without_header-without_index-orient-table.json
@@ -0,0 +1 @@
+{"schema":{"fields":[{"name":"?name","type":"string"},{"name":"?mbox","type":"string"}],"pandas_version":"1.4.0"},"data":[{"?name":"Johnny Lee Outlaw","?mbox":"mailto:jlow@example.com"},{"?name":"Peter Goodguy","?mbox":"mailto:peter@example.org"}]}
diff --git a/tests/case_utils/case_sparql_select/test_data_frame_to_table_text_json.py b/tests/case_utils/case_sparql_select/test_data_frame_to_table_text_json.py
index 00d20c3..9e5cc24 100644
--- a/tests/case_utils/case_sparql_select/test_data_frame_to_table_text_json.py
+++ b/tests/case_utils/case_sparql_select/test_data_frame_to_table_text_json.py
@@ -37,36 +37,59 @@
 
 
 def make_data_frame_to_json_table_text_parameters() -> typing.Iterator[
-    typing.Tuple[str, bool, bool]
+    typing.Tuple[str, str, bool, bool]
 ]:
     for use_header in [False, True]:
         for use_index in [False, True]:
-            for output_mode in ["csv", "html", "md", "tsv"]:
-                yield (output_mode, use_header, use_index)
+            for output_mode in ["csv", "html", "json", "md", "tsv"]:
+                if output_mode == "json":
+                    for json_orient in [
+                        "columns",
+                        "index",
+                        "records",
+                        "split",
+                        "table",
+                        "values",
+                    ]:
+                        # Handle incompatible parameter pairings for JSON mode.
+                        if use_index is False:
+                            if json_orient not in {"split", "table"}:
+                                continue
+
+                        yield (json_orient, output_mode, use_header, use_index)
+                else:
+                    yield ("columns", output_mode, use_header, use_index)
 
 
 @pytest.mark.parametrize(
-    "output_mode, use_header, use_index",
+    "json_orient, output_mode, use_header, use_index",
     make_data_frame_to_json_table_text_parameters(),
 )
 def test_data_frame_to_table_text_json(
+    json_orient: str,
     output_mode: str,
     use_header: bool,
     use_index: bool,
 ) -> None:
     table_text = case_utils.case_sparql_select.data_frame_to_table_text(
         DATA_FRAME,
+        json_orient=json_orient,
         output_mode=output_mode,
         use_header=use_header,
         use_index=use_index,
     )
 
-    output_filename_template = ".check-w3-output-%s_header-%s_index.%s"
+    output_filename_template = ".check-w3-output-%s_header-%s_index%s.%s"
     header_part = "with" if use_header else "without"
     index_part = "with" if use_index else "without"
+    if output_mode == "json":
+        json_orient_part = "-orient-" + json_orient
+    else:
+        json_orient_part = ""
     output_filename = output_filename_template % (
         header_part,
         index_part,
+        json_orient_part,
         output_mode,
     )
     with (SRCDIR / output_filename).open("w") as out_fh:

From b7a61fe54952384aa259db52b4ca590253fa3d77 Mon Sep 17 00:00:00 2001
From: Alex Nelson <alexander.nelson@nist.gov>
Date: Thu, 8 Dec 2022 13:21:07 -0500
Subject: [PATCH 16/19] Add SHACL shapes to set of CDO concepts

This patch adds a test to reproduce the discovery of Issue 85.

A follow-on patch will regenerate Make-managed files.

References:
* https://github.com/casework/CASE-Utilities-Python/issues/85

Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
---
 case_utils/case_validate/__init__.py          |  4 ++
 tests/case_utils/case_validate/Makefile       | 20 ++++++-
 .../case_validate/shape_disabling/Makefile    | 52 +++++++++++++++++++
 .../shape_disabling/disable_shape.ttl         | 11 ++++
 .../case_validate/shape_disabling/example.ttl | 11 ++++
 5 files changed, 96 insertions(+), 2 deletions(-)
 create mode 100644 tests/case_utils/case_validate/shape_disabling/Makefile
 create mode 100644 tests/case_utils/case_validate/shape_disabling/disable_shape.ttl
 create mode 100644 tests/case_utils/case_validate/shape_disabling/example.ttl

diff --git a/case_utils/case_validate/__init__.py b/case_utils/case_validate/__init__.py
index a97e0ff..34a317d 100644
--- a/case_utils/case_validate/__init__.py
+++ b/case_utils/case_validate/__init__.py
@@ -51,6 +51,7 @@
 NS_OWL = rdflib.OWL
 NS_RDF = rdflib.RDF
 NS_RDFS = rdflib.RDFS
+NS_SH = rdflib.SH
 
 _logger = logging.getLogger(os.path.basename(__file__))
 
@@ -189,6 +190,9 @@ def main() -> None:
         NS_OWL.DatatypeProperty,
         NS_OWL.ObjectProperty,
         NS_RDFS.Datatype,
+        NS_SH.NodeShape,
+        NS_SH.PropertyShape,
+        NS_SH.Shape,
     ]:
         for ontology_triple in ontology_graph.triples(
             (None, NS_RDF.type, n_structural_class)
diff --git a/tests/case_utils/case_validate/Makefile b/tests/case_utils/case_validate/Makefile
index b6bf821..aa5a489 100644
--- a/tests/case_utils/case_validate/Makefile
+++ b/tests/case_utils/case_validate/Makefile
@@ -27,14 +27,17 @@ tests_srcdir := $(top_srcdir)/tests
 all: \
   all-cli \
   all-case_test_examples \
-  all-uco_test_examples
+  all-uco_test_examples \
+  all-shape_disabling
 
 .PHONY: \
   all-case_test_examples \
   all-cli \
+  all-shape_disabling \
   all-uco_test_examples \
   check-case_test_examples \
   check-cli \
+  check-shape_disabling \
   check-uco_test_examples
 
 all-case_test_examples:
@@ -45,6 +48,10 @@ all-cli:
 	$(MAKE) \
 	  --directory cli
 
+all-shape_disabling:
+	$(MAKE) \
+	  --directory shape_disabling
+
 all-uco_test_examples:
 	$(MAKE) \
 	  --directory uco_test_examples
@@ -52,7 +59,8 @@ all-uco_test_examples:
 check: \
   check-cli \
   check-case_test_examples \
-  check-uco_test_examples
+  check-uco_test_examples \
+  check-shape_disabling
 
 check-case_test_examples:
 	$(MAKE) \
@@ -64,6 +72,11 @@ check-cli:
 	  --directory cli \
 	  check
 
+check-shape_disabling:
+	$(MAKE) \
+	  --directory shape_disabling \
+	  check
+
 check-uco_test_examples: \
   uco_monolithic.ttl
 	$(MAKE) \
@@ -71,6 +84,9 @@ check-uco_test_examples: \
 	  check
 
 clean:
+	@$(MAKE) \
+	  --directory shape_disabling \
+	  clean
 	@$(MAKE) \
 	  --directory case_test_examples \
 	  clean
diff --git a/tests/case_utils/case_validate/shape_disabling/Makefile b/tests/case_utils/case_validate/shape_disabling/Makefile
new file mode 100644
index 0000000..b9603ac
--- /dev/null
+++ b/tests/case_utils/case_validate/shape_disabling/Makefile
@@ -0,0 +1,52 @@
+#!/usr/bin/make -f
+
+# This software was developed at the National Institute of Standards
+# and Technology by employees of the Federal Government in the course
+# of their official duties. Pursuant to title 17 Section 105 of the
+# United States Code this software is not subject to copyright
+# protection and is in the public domain. NIST assumes no
+# responsibility whatsoever for its use by other parties, and makes
+# no guarantees, expressed or implied, about its quality,
+# reliability, or any other characteristic.
+#
+# We would appreciate acknowledgement if the software is used.
+
+SHELL := /bin/bash
+
+top_srcdir := $(shell cd ../../../.. ; pwd)
+
+tests_srcdir := $(top_srcdir)/tests
+
+all: \
+  validation_with_uuid_shape_disabled.txt \
+  validation_with_uuid_shape_enabled.txt
+
+check: \
+  validation_with_uuid_shape_disabled.txt \
+  validation_with_uuid_shape_enabled.txt
+
+clean:
+	@rm -f \
+	  *.txt \
+	  _*
+
+validation_with_uuid_shape_disabled.txt: \
+  $(tests_srcdir)/.venv.done.log \
+  disable_shape.ttl \
+  example.ttl
+	source $(tests_srcdir)/venv/bin/activate \
+	  && case_validate \
+	    --ontology disable_shape.ttl \
+	    example.ttl \
+	    > _$@
+	mv _$@ $@
+
+validation_with_uuid_shape_enabled.txt: \
+  $(tests_srcdir)/.venv.done.log \
+  example.ttl
+	source $(tests_srcdir)/venv/bin/activate \
+	  && case_validate \
+	    --allow-infos \
+	    example.ttl \
+	    > _$@
+	mv _$@ $@
diff --git a/tests/case_utils/case_validate/shape_disabling/disable_shape.ttl b/tests/case_utils/case_validate/shape_disabling/disable_shape.ttl
new file mode 100644
index 0000000..e9e9bf7
--- /dev/null
+++ b/tests/case_utils/case_validate/shape_disabling/disable_shape.ttl
@@ -0,0 +1,11 @@
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix sh: <http://www.w3.org/ns/shacl#> .
+@prefix uco-core: <https://ontology.unifiedcyberontology.org/uco/core/> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+uco-core:UcoThing-identifier-regex-shape
+	sh:deactivated "true"^^xsd:boolean ;
+	.
+
diff --git a/tests/case_utils/case_validate/shape_disabling/example.ttl b/tests/case_utils/case_validate/shape_disabling/example.ttl
new file mode 100644
index 0000000..9f7a89c
--- /dev/null
+++ b/tests/case_utils/case_validate/shape_disabling/example.ttl
@@ -0,0 +1,11 @@
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix uco-core: <https://ontology.unifiedcyberontology.org/uco/core/> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+<urn:example:thing-1>
+	a uco-core:UcoThing ;
+	rdfs:comment "This node's IRI is designed to trigger a UUID review shape."@en ;
+	.
+

From 8534c13b9c29bca8ffbfd29681593f531521e35a Mon Sep 17 00:00:00 2001
From: Alex Nelson <alexander.nelson@nist.gov>
Date: Thu, 8 Dec 2022 13:29:26 -0500
Subject: [PATCH 17/19] Regenerate Make-managed files

References:
* https://github.com/casework/CASE-Utilities-Python/issues/85

Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
---
 .../validation_with_uuid_shape_disabled.txt   |  2 ++
 .../validation_with_uuid_shape_enabled.txt    | 23 +++++++++++++++++++
 2 files changed, 25 insertions(+)
 create mode 100644 tests/case_utils/case_validate/shape_disabling/validation_with_uuid_shape_disabled.txt
 create mode 100644 tests/case_utils/case_validate/shape_disabling/validation_with_uuid_shape_enabled.txt

diff --git a/tests/case_utils/case_validate/shape_disabling/validation_with_uuid_shape_disabled.txt b/tests/case_utils/case_validate/shape_disabling/validation_with_uuid_shape_disabled.txt
new file mode 100644
index 0000000..0c16da6
--- /dev/null
+++ b/tests/case_utils/case_validate/shape_disabling/validation_with_uuid_shape_disabled.txt
@@ -0,0 +1,2 @@
+Validation Report
+Conforms: True
diff --git a/tests/case_utils/case_validate/shape_disabling/validation_with_uuid_shape_enabled.txt b/tests/case_utils/case_validate/shape_disabling/validation_with_uuid_shape_enabled.txt
new file mode 100644
index 0000000..1e6b23f
--- /dev/null
+++ b/tests/case_utils/case_validate/shape_disabling/validation_with_uuid_shape_enabled.txt
@@ -0,0 +1,23 @@
+Validation Report
+Conforms: True
+Results (1):
+Validation Result in SPARQLConstraintComponent (http://www.w3.org/ns/shacl#SPARQLConstraintComponent):
+	Severity: sh:Info
+	Source Shape: core:UcoThing-identifier-regex-shape
+	Focus Node: <urn:example:thing-1>
+	Value Node: <urn:example:thing-1>
+	Source Constraint: [ rdf:type sh:SPARQLConstraint ; rdfs:seeAlso <https://datatracker.ietf.org/doc/html/rfc4122#section-4.1.3> ; sh:message Literal("UcoThings are suggested to end with a UUID.", lang=en) ; sh:select Literal("
+			PREFIX uco-core: <https://ontology.unifiedcyberontology.org/uco/core/>
+			SELECT $this
+			WHERE {
+			        $this a/rdfs:subClassOf* uco-core:UcoThing .
+			        FILTER (
+			                ! REGEX (
+			                        STR($this),
+			                        "[0-9a-f]{8}-[0-9a-f]{4}-[0-5][0-9a-f]{3}-[0-9a-f]{4}-[0-9a-f]{12}$",
+			                        "i"
+			                )
+			        )
+			}
+		") ]
+	Message: UcoThings are suggested to end with a UUID.

From fa77296ab70f2b17925fcd3245c19acecc1ae19b Mon Sep 17 00:00:00 2001
From: Alex Nelson <alexander.nelson@nist.gov>
Date: Thu, 8 Dec 2022 13:40:59 -0500
Subject: [PATCH 18/19] Add CODEOWNERS file

References:
* https://github.com/usnistgov/opensource-repo/#codeowners

Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
---
 .github/CODEOWNERS | 10 ++++++++++
 1 file changed, 10 insertions(+)
 create mode 100644 .github/CODEOWNERS

diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
new file mode 100644
index 0000000..b6a76fb
--- /dev/null
+++ b/.github/CODEOWNERS
@@ -0,0 +1,10 @@
+# This file lists the contributors responsible for the
+# repository content. They will also be automatically
+# asked to review any pull request made in this repository.
+
+# Each line is a file pattern followed by one or more owners.
+# The sequence matters: later patterns take precedence.
+
+# FILES  OWNERS
+*        @casework/maintainers-global
+*        @casework/maintainers-case-python-utilities

From be829b18306b553bc82131e2aa6b9be073b08a59 Mon Sep 17 00:00:00 2001
From: Alex Nelson <alexander.nelson@nist.gov>
Date: Thu, 8 Dec 2022 17:10:30 -0500
Subject: [PATCH 19/19] Bump versions

Signed-off-by: Alex Nelson <alexander.nelson@nist.gov>
---
 case_utils/__init__.py                    | 2 +-
 case_utils/case_sparql_select/__init__.py | 2 +-
 case_utils/case_validate/__init__.py      | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/case_utils/__init__.py b/case_utils/__init__.py
index 99dc0f8..2af6aa1 100644
--- a/case_utils/__init__.py
+++ b/case_utils/__init__.py
@@ -11,6 +11,6 @@
 #
 # We would appreciate acknowledgement if the software is used.
 
-__version__ = "0.8.0"
+__version__ = "0.9.0"
 
 from . import local_uuid  # noqa: F401
diff --git a/case_utils/case_sparql_select/__init__.py b/case_utils/case_sparql_select/__init__.py
index 870e44c..1e94265 100644
--- a/case_utils/case_sparql_select/__init__.py
+++ b/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__ = "0.4.4"
+__version__ = "0.5.0"
 
 import argparse
 import binascii
diff --git a/case_utils/case_validate/__init__.py b/case_utils/case_validate/__init__.py
index 34a317d..5ef2952 100644
--- a/case_utils/case_validate/__init__.py
+++ b/case_utils/case_validate/__init__.py
@@ -29,7 +29,7 @@
 details.)
 """
 
-__version__ = "0.2.0"
+__version__ = "0.3.0"
 
 import argparse
 import importlib.resources