From 38df8b5162037b60dc1f2057083b0ae798289217 Mon Sep 17 00:00:00 2001 From: "James A. Overton" Date: Tue, 12 Nov 2024 15:30:19 -0500 Subject: [PATCH 1/4] Exclude deprecated terms from lowercase_definition check --- .../src/main/resources/report_queries/lowercase_definition.rq | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/robot-core/src/main/resources/report_queries/lowercase_definition.rq b/robot-core/src/main/resources/report_queries/lowercase_definition.rq index cc0c9ae2b..b2aa452f3 100644 --- a/robot-core/src/main/resources/report_queries/lowercase_definition.rq +++ b/robot-core/src/main/resources/report_queries/lowercase_definition.rq @@ -12,7 +12,8 @@ SELECT DISTINCT ?entity ?property ?value WHERE { VALUES ?property { obo:IAO_0000115 obo:IAO_0000600 } ?entity ?property ?value . - FILTER (!regex(?value, "^[A-Z0-9]")) + FILTER NOT EXISTS { ?entity owl:deprecated true } FILTER (!isBlank(?entity)) + FILTER (!regex(?value, "^[A-Z0-9]")) } ORDER BY ?entity From 74bfb1daf284ef1dbf1678b05494809dc778eb6f Mon Sep 17 00:00:00 2001 From: "James A. Overton" Date: Tue, 12 Nov 2024 15:30:34 -0500 Subject: [PATCH 2/4] Update lowercase_definition doc --- docs/report_queries/lowercase_definition.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/report_queries/lowercase_definition.md b/docs/report_queries/lowercase_definition.md index 2911b8885..70918ba05 100644 --- a/docs/report_queries/lowercase_definition.md +++ b/docs/report_queries/lowercase_definition.md @@ -13,8 +13,9 @@ SELECT DISTINCT ?entity ?property ?value WHERE { VALUES ?property { obo:IAO_0000115 obo:IAO_0000600 } ?entity ?property ?value . - FILTER (!regex(?value, "^[A-Z0-9]")) + FILTER NOT EXISTS { ?entity owl:deprecated true } FILTER (!isBlank(?entity)) + FILTER (!regex(?value, "^[A-Z0-9]")) } ORDER BY ?entity ``` From 8b91ae702d949622a3be544bee2049da4f53bab1 Mon Sep 17 00:00:00 2001 From: "James A. Overton" Date: Tue, 12 Nov 2024 15:30:52 -0500 Subject: [PATCH 3/4] Update changelog, with fix --- CHANGELOG.md | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index adfd17655..6eb45d137 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,11 +7,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [Unreleased] +## Fixed +- Add missing filter for deprecated in lowercase_definition check [#1220] +- Bug was fixed that caused logical axioms with axiom annotations not to be processed correctly when merging axiom annotations [#1223] + ## [1.9.7] - 2024-10-30 ### Fixed - Output inferred object property assertions using Whelk reasoner, by updating to Whelk 1.1.3. [#1121] -- Bug was fixed that caused logical axioms with axiom annotations not to be processed correctly when merging axiom annotations [#1223] ### Changed - Update Whelk to 1.2.1 [#1221] @@ -413,7 +416,9 @@ First official release of ROBOT! [`validate`]: http://robot.obolibrary.org/validate [`verify`]: http://robot.obolibrary.org/verify +[#1223]: https://github.com/ontodev/robot/pull/1223 [#1221]: https://github.com/ontodev/robot/pull/1221 +[#1220]: https://github.com/ontodev/robot/issues/1220 [#1211]: https://github.com/ontodev/robot/pull/1211 [#1194]: https://github.com/ontodev/robot/pull/1194 [#1193]: https://github.com/ontodev/robot/pull/1193 From b5f9c05c175b0b76ade1d4207680e08e6b07eb91 Mon Sep 17 00:00:00 2001 From: "James A. Overton" Date: Tue, 12 Nov 2024 16:01:45 -0500 Subject: [PATCH 4/4] Add missing owl prefix --- docs/report_queries/lowercase_definition.md | 1 + .../src/main/resources/report_queries/lowercase_definition.rq | 1 + 2 files changed, 2 insertions(+) diff --git a/docs/report_queries/lowercase_definition.md b/docs/report_queries/lowercase_definition.md index 70918ba05..edd3ffb32 100644 --- a/docs/report_queries/lowercase_definition.md +++ b/docs/report_queries/lowercase_definition.md @@ -7,6 +7,7 @@ **Solution:** Capitalize the first letter of the definition, or disregard this INFO. ```sparql +PREFIX owl: PREFIX obo: SELECT DISTINCT ?entity ?property ?value WHERE { diff --git a/robot-core/src/main/resources/report_queries/lowercase_definition.rq b/robot-core/src/main/resources/report_queries/lowercase_definition.rq index b2aa452f3..b4331fe67 100644 --- a/robot-core/src/main/resources/report_queries/lowercase_definition.rq +++ b/robot-core/src/main/resources/report_queries/lowercase_definition.rq @@ -6,6 +6,7 @@ # # **Solution:** Capitalize the first letter of the definition, or disregard this INFO. +PREFIX owl: PREFIX obo: SELECT DISTINCT ?entity ?property ?value WHERE {