From 86add54f514086962c436bf0b108aeba17b31a51 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Fri, 27 Oct 2023 10:38:36 +0200 Subject: [PATCH 01/19] Standardize ad-hoc definition of plural synonym Part of https://github.com/OBOFoundry/OBOFoundry.github.io/issues/2450 --- src/envo/envo-edit.owl | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/src/envo/envo-edit.owl b/src/envo/envo-edit.owl index ef1bc04a..5c1cd590 100644 --- a/src/envo/envo-edit.owl +++ b/src/envo/envo-edit.owl @@ -4327,8 +4327,8 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -4433,16 +4433,16 @@ AnnotationAssertion(rdfs:label "exp AnnotationAssertion(rdfs:label "term replaced by") +# Annotation Property: (plural form) + +AnnotationAssertion(rdfs:label "plural form") +SubAnnotationPropertyOf( ) + # Annotation Property: () AnnotationAssertion(rdfs:comment "EnvO-Lite-GSC") SubAnnotationPropertyOf( ) -# Annotation Property: (plurals) - -AnnotationAssertion(rdfs:label "plurals") -SubAnnotationPropertyOf( ) - # Annotation Property: (disconnected_from) AnnotationAssertion(Annotation( ) "A is disconnected_from B if they have no parts in common.") @@ -10868,7 +10868,7 @@ AnnotationAssertion(Annotation( "USGS:SDTS") "mount") AnnotationAssertion( "https://en.wikipedia.org/wiki/Pingo") AnnotationAssertion(Annotation( "https://en.wikipedia.org/wiki/Pingo") "hydrolaccolith") -AnnotationAssertion(Annotation( ) "pingos") +AnnotationAssertion(Annotation( ) "pingos") AnnotationAssertion( "bugor") AnnotationAssertion( "bulginniakh") AnnotationAssertion( "envoPolar") @@ -21750,7 +21750,7 @@ SubClassOf( ObjectSomeValuesFrom(< AnnotationAssertion(Annotation( "https://en.wikipedia.org/wiki/Ice_Lens") "An ice mass which is formed when moisture, diffused within soil or rock, accumulates and freezes in a localized zone, wedging soil or rock apart.") AnnotationAssertion( "ORCID:0000-0002-4366-3088") AnnotationAssertion( "2013-10-13T12:20:34Z") -AnnotationAssertion(Annotation( ) "ice lenses") +AnnotationAssertion(Annotation( ) "ice lenses") AnnotationAssertion( "envoPolar") AnnotationAssertion(rdfs:label "ice lens") SubClassOf( ) From ae04982223ad20934fcb47eaf380039bed1a7ebf Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Wed, 1 Nov 2023 15:27:53 -0500 Subject: [PATCH 02/19] update workflow --- .github/workflows/ontobot.yml | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/.github/workflows/ontobot.yml b/.github/workflows/ontobot.yml index 7105b68a..71309e18 100644 --- a/.github/workflows/ontobot.yml +++ b/.github/workflows/ontobot.yml @@ -44,11 +44,13 @@ jobs: echo "branch-name=kgcl_automation_"${{ steps.gh-script-issue.outputs.result }} >> $GITHUB_ENV - name: Get jar & create alias command. - run: wget https://github.com/gouttegd/kgcl-java/releases/download/kgcl-0.2.0/kgcl-robot-standalone-0.2.0.jar -O kgcl-robot.jar + run: | + mkdir -p ~/.robot/plugin + wget https://github.com/gouttegd/kgcl-java/releases/download/kgcl-0.2.0/kgcl-robot-plugin-0.2.0.jar -O ~/.robot/plugin/kgcl.jar - name: Install dependencies run: | - pip install ontobot-change-agent + pip install ontobot-change-agent==0.4.7rc1 - name: Run ochange id: ochange @@ -56,11 +58,7 @@ jobs: ochange process-issue ${{ env.resource }} \ -r ${{ steps.gh-script-repo.outputs.result }} \ -n ${{ steps.gh-script-issue.outputs.result }} \ - -g ${{ secrets.GH_TOKEN }} \ - -j kgcl-robot.jar - - - name: Clean-up - run: rm -f kgcl-robot.jar + -g ${{ secrets.GH_TOKEN }} - name: Create Pull Request uses: peter-evans/create-pull-request@v5 From 274b4f17e288f5c8360ff137276372f3d17d2bf4 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Wed, 1 Nov 2023 15:43:26 -0500 Subject: [PATCH 03/19] install main branch --- .github/workflows/ontobot.yml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ontobot.yml b/.github/workflows/ontobot.yml index 71309e18..1baef4e3 100644 --- a/.github/workflows/ontobot.yml +++ b/.github/workflows/ontobot.yml @@ -44,13 +44,11 @@ jobs: echo "branch-name=kgcl_automation_"${{ steps.gh-script-issue.outputs.result }} >> $GITHUB_ENV - name: Get jar & create alias command. - run: | - mkdir -p ~/.robot/plugin - wget https://github.com/gouttegd/kgcl-java/releases/download/kgcl-0.2.0/kgcl-robot-plugin-0.2.0.jar -O ~/.robot/plugin/kgcl.jar + run: wget https://github.com/gouttegd/kgcl-java/releases/download/kgcl-0.2.0/kgcl-robot-plugin-0.2.0.jar -O kgcl.jar - name: Install dependencies run: | - pip install ontobot-change-agent==0.4.7rc1 + pip install git+https://github.com/hrshdhgd/ontobot-change-agent.git - name: Run ochange id: ochange From ab8f10f2a7da1cb59c93a47980c9a9d4ae2fae21 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Wed, 1 Nov 2023 15:58:34 -0500 Subject: [PATCH 04/19] docker latest --- .github/workflows/ontobot.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ontobot.yml b/.github/workflows/ontobot.yml index 1baef4e3..fe5d0527 100644 --- a/.github/workflows/ontobot.yml +++ b/.github/workflows/ontobot.yml @@ -8,7 +8,7 @@ on: jobs: build: runs-on: ${{ matrix.os }} - container: obolibrary/odkfull:v1.4.1 + container: obolibrary/odkfull:latest strategy: matrix: python-version: ["3.9"] @@ -44,7 +44,9 @@ jobs: echo "branch-name=kgcl_automation_"${{ steps.gh-script-issue.outputs.result }} >> $GITHUB_ENV - name: Get jar & create alias command. - run: wget https://github.com/gouttegd/kgcl-java/releases/download/kgcl-0.2.0/kgcl-robot-plugin-0.2.0.jar -O kgcl.jar + run: | + mkdir -p ~/.robot/plugins + wget https://github.com/gouttegd/kgcl-java/releases/download/kgcl-0.2.0/kgcl-robot-plugin-0.2.0.jar -O ~/.robot/plugins/kgcl.jar - name: Install dependencies run: | From d2aae7011683c68404bfbf1d34db8a57ccb948bf Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Wed, 1 Nov 2023 17:25:39 -0500 Subject: [PATCH 05/19] odk v1.4.3 --- .github/workflows/ontobot.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ontobot.yml b/.github/workflows/ontobot.yml index fe5d0527..d4302498 100644 --- a/.github/workflows/ontobot.yml +++ b/.github/workflows/ontobot.yml @@ -8,7 +8,7 @@ on: jobs: build: runs-on: ${{ matrix.os }} - container: obolibrary/odkfull:latest + container: obolibrary/odkfull:1.4.3 strategy: matrix: python-version: ["3.9"] From d51336f27646423a2abf9228da809dc818a9ce3a Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Wed, 1 Nov 2023 18:06:08 -0500 Subject: [PATCH 06/19] forgot version --- .github/workflows/ontobot.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ontobot.yml b/.github/workflows/ontobot.yml index d4302498..7834e8b5 100644 --- a/.github/workflows/ontobot.yml +++ b/.github/workflows/ontobot.yml @@ -8,7 +8,7 @@ on: jobs: build: runs-on: ${{ matrix.os }} - container: obolibrary/odkfull:1.4.3 + container: obolibrary/odkfull:v1.4.3 strategy: matrix: python-version: ["3.9"] From b09a92a414077132dd13d179f51bb7f9694bd1df Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 2 Nov 2023 09:35:23 -0500 Subject: [PATCH 07/19] updarte env variable --- .github/workflows/ontobot.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ontobot.yml b/.github/workflows/ontobot.yml index 7834e8b5..7272a171 100644 --- a/.github/workflows/ontobot.yml +++ b/.github/workflows/ontobot.yml @@ -47,6 +47,7 @@ jobs: run: | mkdir -p ~/.robot/plugins wget https://github.com/gouttegd/kgcl-java/releases/download/kgcl-0.2.0/kgcl-robot-plugin-0.2.0.jar -O ~/.robot/plugins/kgcl.jar + "ROBOT_PLUGINS_DIRECTORY=r~/.robot/plugins" >> "$GITHUB_ENV" - name: Install dependencies run: | From 8219f2497e0e813380397dbe6ec635f05befda88 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 2 Nov 2023 09:38:47 -0500 Subject: [PATCH 08/19] typo --- .github/workflows/ontobot.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ontobot.yml b/.github/workflows/ontobot.yml index 7272a171..ce249b86 100644 --- a/.github/workflows/ontobot.yml +++ b/.github/workflows/ontobot.yml @@ -47,7 +47,7 @@ jobs: run: | mkdir -p ~/.robot/plugins wget https://github.com/gouttegd/kgcl-java/releases/download/kgcl-0.2.0/kgcl-robot-plugin-0.2.0.jar -O ~/.robot/plugins/kgcl.jar - "ROBOT_PLUGINS_DIRECTORY=r~/.robot/plugins" >> "$GITHUB_ENV" + "ROBOT_PLUGINS_DIRECTORY=~/.robot/plugins" >> "$GITHUB_ENV" - name: Install dependencies run: | From cdbaa022e9acc7be89f492d9d120c74b15616bff Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 2 Nov 2023 09:48:31 -0500 Subject: [PATCH 09/19] added quotes --- .github/workflows/ontobot.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ontobot.yml b/.github/workflows/ontobot.yml index ce249b86..ef98b276 100644 --- a/.github/workflows/ontobot.yml +++ b/.github/workflows/ontobot.yml @@ -47,7 +47,7 @@ jobs: run: | mkdir -p ~/.robot/plugins wget https://github.com/gouttegd/kgcl-java/releases/download/kgcl-0.2.0/kgcl-robot-plugin-0.2.0.jar -O ~/.robot/plugins/kgcl.jar - "ROBOT_PLUGINS_DIRECTORY=~/.robot/plugins" >> "$GITHUB_ENV" + "ROBOT_PLUGINS_DIRECTORY='~/.robot/plugins'" >> "$GITHUB_ENV" - name: Install dependencies run: | From 6d4131b214014106321e3dae29376ddddc3167b8 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 2 Nov 2023 09:51:22 -0500 Subject: [PATCH 10/19] full path --- .github/workflows/ontobot.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ontobot.yml b/.github/workflows/ontobot.yml index ef98b276..f1280275 100644 --- a/.github/workflows/ontobot.yml +++ b/.github/workflows/ontobot.yml @@ -47,7 +47,7 @@ jobs: run: | mkdir -p ~/.robot/plugins wget https://github.com/gouttegd/kgcl-java/releases/download/kgcl-0.2.0/kgcl-robot-plugin-0.2.0.jar -O ~/.robot/plugins/kgcl.jar - "ROBOT_PLUGINS_DIRECTORY='~/.robot/plugins'" >> "$GITHUB_ENV" + "ROBOT_PLUGINS_DIRECTORY='/github/home/.robot/plugins/'" >> "$GITHUB_ENV" - name: Install dependencies run: | From 9010f988fafb050ffa83e5ea5fd45384b9d34351 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 2 Nov 2023 09:53:32 -0500 Subject: [PATCH 11/19] removed quotes --- .github/workflows/ontobot.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ontobot.yml b/.github/workflows/ontobot.yml index f1280275..430b56fb 100644 --- a/.github/workflows/ontobot.yml +++ b/.github/workflows/ontobot.yml @@ -47,7 +47,7 @@ jobs: run: | mkdir -p ~/.robot/plugins wget https://github.com/gouttegd/kgcl-java/releases/download/kgcl-0.2.0/kgcl-robot-plugin-0.2.0.jar -O ~/.robot/plugins/kgcl.jar - "ROBOT_PLUGINS_DIRECTORY='/github/home/.robot/plugins/'" >> "$GITHUB_ENV" + "ROBOT_PLUGINS_DIRECTORY=/github/home/.robot/plugins/" >> "$GITHUB_ENV" - name: Install dependencies run: | From c0457a444b0ff7f1d1c4c18ebf5cc049756d2ab8 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 2 Nov 2023 09:55:10 -0500 Subject: [PATCH 12/19] changed the path entirely --- .github/workflows/ontobot.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ontobot.yml b/.github/workflows/ontobot.yml index 430b56fb..ae598e53 100644 --- a/.github/workflows/ontobot.yml +++ b/.github/workflows/ontobot.yml @@ -45,9 +45,9 @@ jobs: - name: Get jar & create alias command. run: | - mkdir -p ~/.robot/plugins - wget https://github.com/gouttegd/kgcl-java/releases/download/kgcl-0.2.0/kgcl-robot-plugin-0.2.0.jar -O ~/.robot/plugins/kgcl.jar - "ROBOT_PLUGINS_DIRECTORY=/github/home/.robot/plugins/" >> "$GITHUB_ENV" + mkdir -p robot-plugins + wget https://github.com/gouttegd/kgcl-java/releases/download/kgcl-0.2.0/kgcl-robot-plugin-0.2.0.jar -O robot-plugins/kgcl.jar + "ROBOT_PLUGINS_DIRECTORY=robot-plugins/" >> "$GITHUB_ENV" - name: Install dependencies run: | From 6ca1d0815419988722761186884f711897e345eb Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 2 Nov 2023 09:57:45 -0500 Subject: [PATCH 13/19] added pwd --- .github/workflows/ontobot.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ontobot.yml b/.github/workflows/ontobot.yml index ae598e53..5f5b78df 100644 --- a/.github/workflows/ontobot.yml +++ b/.github/workflows/ontobot.yml @@ -47,7 +47,7 @@ jobs: run: | mkdir -p robot-plugins wget https://github.com/gouttegd/kgcl-java/releases/download/kgcl-0.2.0/kgcl-robot-plugin-0.2.0.jar -O robot-plugins/kgcl.jar - "ROBOT_PLUGINS_DIRECTORY=robot-plugins/" >> "$GITHUB_ENV" + "ROBOT_PLUGINS_DIRECTORY=${{pwd}}/robot-plugins/" >> "$GITHUB_ENV" - name: Install dependencies run: | From cb7f1127ac117c5f5a818929f26aaf266b1a027b Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 2 Nov 2023 10:00:08 -0500 Subject: [PATCH 14/19] corrected line to set env var --- .github/workflows/ontobot.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ontobot.yml b/.github/workflows/ontobot.yml index 5f5b78df..95a21814 100644 --- a/.github/workflows/ontobot.yml +++ b/.github/workflows/ontobot.yml @@ -47,7 +47,7 @@ jobs: run: | mkdir -p robot-plugins wget https://github.com/gouttegd/kgcl-java/releases/download/kgcl-0.2.0/kgcl-robot-plugin-0.2.0.jar -O robot-plugins/kgcl.jar - "ROBOT_PLUGINS_DIRECTORY=${{pwd}}/robot-plugins/" >> "$GITHUB_ENV" + echo "ROBOT_PLUGINS_DIRECTORY=$(pwd)/robot-plugins/" >> "$GITHUB_ENV" - name: Install dependencies run: | From 79ef0dd1377c2bf47708d097e4e14b2b73e607ba Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 2 Nov 2023 10:51:48 -0500 Subject: [PATCH 15/19] cleanup code --- .github/workflows/ontobot.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/ontobot.yml b/.github/workflows/ontobot.yml index 95a21814..a99fca93 100644 --- a/.github/workflows/ontobot.yml +++ b/.github/workflows/ontobot.yml @@ -61,6 +61,9 @@ jobs: -n ${{ steps.gh-script-issue.outputs.result }} \ -g ${{ secrets.GH_TOKEN }} + - name: Clean-up + run: rm -rf robot-plugins + - name: Create Pull Request uses: peter-evans/create-pull-request@v5 if: ${{ env.PR_TITLE}} From 5d83054b37d11b87926aee08d0eb3cddd0284874 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 2 Nov 2023 12:26:36 -0500 Subject: [PATCH 16/19] comment change --- .github/workflows/ontobot.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ontobot.yml b/.github/workflows/ontobot.yml index a99fca93..5d5e990f 100644 --- a/.github/workflows/ontobot.yml +++ b/.github/workflows/ontobot.yml @@ -43,7 +43,7 @@ jobs: echo "resource=src/envo/envo-edit.owl" >> $GITHUB_ENV echo "branch-name=kgcl_automation_"${{ steps.gh-script-issue.outputs.result }} >> $GITHUB_ENV - - name: Get jar & create alias command. + - name: Get jar & enable plugin. run: | mkdir -p robot-plugins wget https://github.com/gouttegd/kgcl-java/releases/download/kgcl-0.2.0/kgcl-robot-plugin-0.2.0.jar -O robot-plugins/kgcl.jar From 5fca1626119ee1436adde45b4cfbfc3cca71c45a Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Thu, 2 Nov 2023 12:27:26 -0500 Subject: [PATCH 17/19] install package directly rather than github repo --- .github/workflows/ontobot.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ontobot.yml b/.github/workflows/ontobot.yml index 5d5e990f..d0396344 100644 --- a/.github/workflows/ontobot.yml +++ b/.github/workflows/ontobot.yml @@ -51,7 +51,7 @@ jobs: - name: Install dependencies run: | - pip install git+https://github.com/hrshdhgd/ontobot-change-agent.git + pip install ontobot-change-agent - name: Run ochange id: ochange From 3ab210f85c26bec4cf9b6b3b431ab81fb0b61713 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 17 Nov 2023 14:37:03 -0600 Subject: [PATCH 18/19] Preliminary check for the phrase hey ontobot --- .github/workflows/ontobot.yml | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/.github/workflows/ontobot.yml b/.github/workflows/ontobot.yml index d0396344..8d0ff9d7 100644 --- a/.github/workflows/ontobot.yml +++ b/.github/workflows/ontobot.yml @@ -6,7 +6,30 @@ on: types: [ opened, edited ] jobs: + check: + runs-on: ubuntu-latest + outputs: + phraseExists: ${{ steps.check-body.outputs.result }} + steps: + - name: Check if issue body contains 'Hey ontobot' + id: check-body + uses: actions/github-script@v6 + with: + script: | + const issue = await github.rest.issues.get({ + owner: context.repo.owner, + repo: context.repo.repo, + issue_number: context.issue.number + }); + if (!issue.data.body) { + console.log('Issue body is empty or null'); + return false; + } + return issue.data.body.includes('Hey ontobot'); + build: + needs: check + if: needs.check.outputs.phraseExists == 'true' runs-on: ${{ matrix.os }} container: obolibrary/odkfull:v1.4.3 strategy: From 47b34a482159c12f9049766db2a889190ccd9cfb Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Fri, 17 Nov 2023 14:47:36 -0600 Subject: [PATCH 19/19] case insensitive --- .github/workflows/ontobot.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ontobot.yml b/.github/workflows/ontobot.yml index 8d0ff9d7..7eaef88a 100644 --- a/.github/workflows/ontobot.yml +++ b/.github/workflows/ontobot.yml @@ -25,7 +25,7 @@ jobs: console.log('Issue body is empty or null'); return false; } - return issue.data.body.includes('Hey ontobot'); + return issue.data.body.toLowerCase().includes('hey ontobot'); build: needs: check