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Merge branch 'master' into pr/jmwhorton/778
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anitacaron committed Mar 13, 2024
2 parents 66d82ea + a389e11 commit 56cf433
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79 changes: 79 additions & 0 deletions .github/workflows/ontobot.yml
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name: Create new pull request

on:
workflow_dispatch:
issues:
types: [ opened, edited ]

jobs:
build:
runs-on: ${{ matrix.os }}
container: obolibrary/odkfull:v1.4.3
strategy:
matrix:
python-version: ["3.9"]
os: [ ubuntu-latest ]

steps:
- name: Checkout main branch
uses: actions/checkout@v3

- name: Return issue number
id: gh-script-issue
uses: actions/github-script@v6
with:
# github-token: ${{ secrets.GH_TOKEN }}
script: |
const issue_number = context.issue.number
const repo = context.repo.owner+"/"+context.repo.repo
return issue_number
- name: Return repository name
id: gh-script-repo
uses: actions/github-script@v6
with:
# github-token: ${{ secrets.GH_TOKEN }}
script: |
const repo = context.repo.owner+"/"+context.repo.repo
return repo
- name: Set branch name
id: vars
run: |
echo "resource=src/ontology/ro-edit.owl" >> $GITHUB_ENV
echo "branch-name=kgcl_automation_"${{ steps.gh-script-issue.outputs.result }} >> $GITHUB_ENV
- name: Get jar & enable plugin.
run: |
mkdir -p robot-plugins
wget https://github.com/gouttegd/kgcl-java/releases/download/kgcl-0.2.0/kgcl-robot-plugin-0.2.0.jar -O robot-plugins/kgcl.jar
echo "ROBOT_PLUGINS_DIRECTORY=$(pwd)/robot-plugins/" >> "$GITHUB_ENV"
- name: Install dependencies
run: |
pip install ontobot-change-agent
- name: Run ochange
id: ochange
run: |
ochange process-issue ${{ env.resource }} \
-r ${{ steps.gh-script-repo.outputs.result }} \
-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}}
with:
token: ${{ secrets.GH_TOKEN }}
branch-suffix: short-commit-hash
labels: Automated
author: ${{ env.ISSUE_CREATOR }} <${{ env.ISSUE_CREATOR }}@users.noreply.github.com>
committer: ${{ env.ISSUE_CREATOR }} <${{ env.ISSUE_CREATOR }}@users.noreply.github.com>
body: ${{ env.PR_BODY }}
title: ${{ env.PR_TITLE }}
base: ${{ github.head_ref }}
branch: ${{ env.branch-name }}
4 changes: 2 additions & 2 deletions .github/workflows/qc.yml
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Expand Up @@ -19,12 +19,12 @@ jobs:
ontology_qc:
# The type of runner that the job will run on
runs-on: ubuntu-latest
container: obolibrary/odkfull:v1.4
container: obolibrary/odkfull:v1.5

# Steps represent a sequence of tasks that will be executed as part of the job
steps:
# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
- uses: actions/checkout@v2
- uses: actions/checkout@v3

- name: Run ontology QC checks
env:
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2 changes: 1 addition & 1 deletion .github/workflows/stale-issues-and-prs.yml
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Expand Up @@ -14,7 +14,7 @@ jobs:
steps:
- uses: actions/stale@v7
with:
days-before-issue-stale: 630
days-before-issue-stale: 730
days-before-issue-close: 60
close-issue-label: 'autoclosed-unfixed'
close-issue-reason: 'not_planned'
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4 changes: 2 additions & 2 deletions core.json
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Expand Up @@ -7,12 +7,12 @@
"val" : "https://creativecommons.org/publicdomain/zero/1.0/"
}, {
"pred" : "http://www.w3.org/2002/07/owl#versionInfo",
"val" : "2023-08-18"
"val" : "2024-02-13"
}, {
"pred" : "http://xmlns.com/foaf/0.1/homepage",
"val" : "https://github.com/oborel/obo-relations/wiki/ROCore"
} ],
"version" : "http://purl.obolibrary.org/obo/ro/releases/2023-08-18/core.json"
"version" : "http://purl.obolibrary.org/obo/ro/releases/2024-02-13/core.json"
},
"nodes" : [ {
"id" : "http://purl.obolibrary.org/obo/BFO_0000002",
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8 changes: 4 additions & 4 deletions core.obo
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@@ -1,9 +1,9 @@
format-version: 1.2
data-version: ro/releases/2023-08-18/core.owl
data-version: ro/releases/2024-02-13/core.owl
ontology: ro/core
property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/
property_value: http://xmlns.com/foaf/0.1/homepage "https://github.com/oborel/obo-relations/wiki/ROCore" xsd:anyURI
property_value: owl:versionInfo "2023-08-18" xsd:string
property_value: owl:versionInfo "2024-02-13" xsd:string

[Term]
id: BFO:0000002
Expand Down Expand Up @@ -381,8 +381,8 @@ property_value: IAO:0000116 "Location as a relation between instances: The primi
property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string
property_value: IAO:0000118 "located_in" xsd:string
property_value: RO:0001900 RO:0001901
domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant
range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant
domain: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant
range: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant
is_transitive: true

[Typedef]
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6 changes: 3 additions & 3 deletions core.owl
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Expand Up @@ -13,9 +13,9 @@
xmlns:terms="http://purl.org/dc/terms/"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/ro/core.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/ro/releases/2023-08-18/core.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/ro/releases/2024-02-13/core.owl"/>
<terms:license rdf:resource="https://creativecommons.org/publicdomain/zero/1.0/"/>
<owl:versionInfo>2023-08-18</owl:versionInfo>
<owl:versionInfo>2024-02-13</owl:versionInfo>
<foaf:homepage rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/oborel/obo-relations/wiki/ROCore</foaf:homepage>
</owl:Ontology>

Expand Down Expand Up @@ -985,5 +985,5 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.



<!-- Generated by the OWL API (version 4.5.25) https://github.com/owlcs/owlapi -->
<!-- Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi -->

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