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Merged
merged 7 commits into from
May 24, 2024
Merged

Update imports.yml #3984

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34a00ce
Update imports.yml
sbello May 23, 2024
b9d8b25
Update imports.yml
sbello May 23, 2024
a9c6175
Update imports.yml
sbello May 23, 2024
d034eed
Update imports.yml
sbello May 23, 2024
07cf845
Update imports and components
sbello May 23, 2024
3a79607
Merge pull request #3983 from mgijax/create-pull-request/patch
sbello May 23, 2024
f616c32
Update deploy.yml
sbello May 23, 2024
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16 changes: 6 additions & 10 deletions .github/workflows/deploy.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,16 +6,12 @@ on:

jobs:
deploy:
runs-on: macos-latest
runs-on: ubuntu-latest
container: obolibrary/odkfull:v1.4
strategy:
max-parallel: 1

steps:
- uses: docker-practice/actions-setup-docker@master
- run: |
set -x
docker version

- name: Install ODK
run: docker pull obolibrary/odkfull

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

Expand All @@ -27,7 +23,7 @@ jobs:
run: echo "::set-output name=date::$(date +'%Y-%m-%d')"

- name: Update release files
run: cd src/ontology/ && docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx10G' -e JAVA_OPTS='-Xmx10G' --rm obolibrary/odkfull make GITHUB_ACTION=true prepare_release_fast
run: cd src/ontology/ && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx10G' GITHUB_ACTION=true prepare_release_fast
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@anitacaron do you understand why it says

ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx10G'

instead of

ROBOT_JAVA_ARGS=-Xmx10G

? I can see this also exists in other pipelines but I cannot remember putting this anywhere.

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I don't remember this either. I've checked the commit history and couldn't find anything.


- name: Run release
uses: gaoDean/action-gh-release@6b61bb5648ddc1241deb73ea6b72c3a1e1f9e445
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7 changes: 4 additions & 3 deletions .github/workflows/imports.yml
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Expand Up @@ -7,6 +7,7 @@ jobs:
imports:
runs-on: ubuntu-latest
container: obolibrary/odkfull:v1.4


steps:
# Checks-out current branch
Expand All @@ -18,13 +19,13 @@ jobs:
run: git config --global --add safe.directory "$GITHUB_WORKSPACE"

- name: Refreshing imports
run: cd src/ontology/ && docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx10G' -e JAVA_OPTS='-Xmx10G' --rm obolibrary/odklite make GITHUB_ACTION=true refresh-imports
run: cd src/ontology/ && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx10G' GITHUB_ACTION=true refresh-imports

- name: Refreshing components
run: cd src/ontology/ && docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx10G' -e JAVA_OPTS='-Xmx10G' --rm obolibrary/odklite make IMP=false IMP_LARGE=false GITHUB_ACTION=true ../patterns/definitions.owl
run: cd src/ontology/ && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx10G' GITHUB_ACTION=true ../patterns/definitions.owl

- name: Remove patternized classes
run: cd src/ontology/ && docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx10G' -e JAVA_OPTS='-Xmx10G' --rm obolibrary/odklite make GITHUB_ACTION=true remove_patternised_classes
run: cd src/ontology/ && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx10G' GITHUB_ACTION=true remove_patternised_classes

- name: Create Pull Request
uses: peter-evans/create-pull-request@v3
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6 changes: 3 additions & 3 deletions src/ontology/imports/chebi_import.owl
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Expand Up @@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/mp/imports/chebi_import.owl>
<http://purl.obolibrary.org/obo/mp/releases/2024-04-18/imports/chebi_import.owl>
Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/chebi/obophenotype/releases/2024-04-11/chebi_slim.owl>)
Annotation(owl:versionInfo "2024-04-18")
<http://purl.obolibrary.org/obo/mp/releases/2024-05-23/imports/chebi_import.owl>
Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/chebi/obophenotype/releases/2024-05-05/chebi_slim.owl>)
Annotation(owl:versionInfo "2024-05-23")

Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_10545>))
Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_11955>))
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381 changes: 347 additions & 34 deletions src/ontology/imports/cl_import.owl
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475 changes: 161 additions & 314 deletions src/ontology/imports/go_import.owl
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4 changes: 2 additions & 2 deletions src/ontology/imports/mpath_import.owl
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Expand Up @@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/mp/imports/mpath_import.owl>
<http://purl.obolibrary.org/obo/mp/releases/2024-04-18/imports/mpath_import.owl>
<http://purl.obolibrary.org/obo/mp/releases/2024-05-23/imports/mpath_import.owl>
Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/mpath/2020-05-19/mpath.owl>)
Annotation(owl:versionInfo "2024-04-18")
Annotation(owl:versionInfo "2024-05-23")

Declaration(Class(<http://purl.obolibrary.org/obo/MPATH_0>))
Declaration(Class(<http://purl.obolibrary.org/obo/MPATH_1>))
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4 changes: 2 additions & 2 deletions src/ontology/imports/nbo_import.owl
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Expand Up @@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/mp/imports/nbo_import.owl>
<http://purl.obolibrary.org/obo/mp/releases/2024-04-18/imports/nbo_import.owl>
<http://purl.obolibrary.org/obo/mp/releases/2024-05-23/imports/nbo_import.owl>
Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/nbo/releases/2023-07-04/nbo.owl>)
Annotation(owl:versionInfo "2024-04-18")
Annotation(owl:versionInfo "2024-05-23")

Declaration(Class(<http://purl.obolibrary.org/obo/GO_0007601>))
Declaration(Class(<http://purl.obolibrary.org/obo/GO_0007610>))
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4 changes: 2 additions & 2 deletions src/ontology/imports/pato_import.owl
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Expand Up @@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/mp/imports/pato_import.owl>
<http://purl.obolibrary.org/obo/mp/releases/2024-04-18/imports/pato_import.owl>
<http://purl.obolibrary.org/obo/mp/releases/2024-05-23/imports/pato_import.owl>
Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/pato/releases/2024-03-28/pato.owl>)
Annotation(owl:versionInfo "2024-04-18")
Annotation(owl:versionInfo "2024-05-23")

Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000020>))
Declaration(Class(<http://purl.obolibrary.org/obo/CL_0000000>))
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