From d09f3199b5b11579e3c604c43b3684556a3b7d29 Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Wed, 4 Oct 2023 16:32:47 +0100 Subject: [PATCH 01/12] update ODK image in QC --- .github/workflows/qc.yml | 2 +- src/ontology/Makefile | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml index 64342f751e..7f8809b5af 100644 --- a/.github/workflows/qc.yml +++ b/.github/workflows/qc.yml @@ -19,7 +19,7 @@ jobs: ontology_qc: # The type of runner that the job will run on runs-on: ubuntu-latest - container: obolibrary/odkfull:v1.4.1 + container: obolibrary/odkfull:v1.4.3 # Steps represent a sequence of tasks that will be executed as part of the job steps: diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 909913e3ca..3951dcad80 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -1,7 +1,7 @@ # ---------------------------------------- # Makefile for uberon # Generated using ontology-development-kit -# ODK Version: v1.4.2 +# ODK Version: v1.4.3 # ---------------------------------------- # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use uberon.Makefile instead @@ -44,7 +44,7 @@ REPORT_PROFILE_OPTS = --profile $(ROBOT_PROFILE) OBO_FORMAT_OPTIONS = SPARQL_VALIDATION_CHECKS = equivalent-classes owldef-self-reference illegal-annotation-property taxon-range orcid-contributor obsolete-replaced_by xrefs-mesh-pattern label-synonym-polysemy id-format SPARQL_EXPORTS = basic-report -ODK_VERSION_MAKEFILE = v1.4.2 +ODK_VERSION_MAKEFILE = v1.4.3 TODAY ?= $(shell date +%Y-%m-%d) OBODATE ?= $(shell date +'%d:%m:%Y %H:%M') From 8708fd918b18074f1f58f97b5ad80c73f2e3b0d2 Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Wed, 4 Oct 2023 16:58:42 +0100 Subject: [PATCH 02/12] increase ROBOT_JAVA_ARGS in qc --- .github/workflows/qc.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml index 7f8809b5af..c444c8be75 100644 --- a/.github/workflows/qc.yml +++ b/.github/workflows/qc.yml @@ -30,7 +30,7 @@ jobs: env: DEFAULT_BRANCH: master ROBOT_JAVA_ARGS: -Xmx6G - run: cd src/ontology && mkdir -p tmp reports mirror && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' BRI=false MIR=false IMP=false test > TESTLOG.log + run: cd src/ontology && mkdir -p tmp reports mirror && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx8G' BRI=false MIR=false IMP=false test > TESTLOG.log - name: Last rows of QC report if: ${{ failure() }} run: tail -20 src/ontology/TESTLOG.log \ No newline at end of file From 8a6439e77e50b46c23718f5bbc2161c8e0028d7c Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Thu, 5 Oct 2023 10:09:13 +0100 Subject: [PATCH 03/12] change to macos runner and increase memory --- .github/workflows/qc.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml index c444c8be75..b851c843a9 100644 --- a/.github/workflows/qc.yml +++ b/.github/workflows/qc.yml @@ -18,7 +18,7 @@ jobs: # This workflow contains a single job called "ontology_qc" ontology_qc: # The type of runner that the job will run on - runs-on: ubuntu-latest + runs-on: macos-latest container: obolibrary/odkfull:v1.4.3 # Steps represent a sequence of tasks that will be executed as part of the job @@ -30,7 +30,7 @@ jobs: env: DEFAULT_BRANCH: master ROBOT_JAVA_ARGS: -Xmx6G - run: cd src/ontology && mkdir -p tmp reports mirror && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx8G' BRI=false MIR=false IMP=false test > TESTLOG.log + run: cd src/ontology && mkdir -p tmp reports mirror && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx10G' BRI=false MIR=false IMP=false test > TESTLOG.log - name: Last rows of QC report if: ${{ failure() }} run: tail -20 src/ontology/TESTLOG.log \ No newline at end of file From 5115f603cfb26ee786f7491e5a3cb5f1539d5073 Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Thu, 5 Oct 2023 13:58:28 +0100 Subject: [PATCH 04/12] setup macos runner in qc --- .github/workflows/qc.yml | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml index b851c843a9..f1c93c3ad8 100644 --- a/.github/workflows/qc.yml +++ b/.github/workflows/qc.yml @@ -19,18 +19,24 @@ jobs: ontology_qc: # The type of runner that the job will run on runs-on: macos-latest - container: obolibrary/odkfull:v1.4.3 - # 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: docker-practice/actions-setup-docker@master + - run: | + set -x + docker version + - name: Install ODK + run: docker pull obolibrary/odklite + # Checks-out current branch + - uses: actions/checkout@v3 - name: Run ontology QC checks + run: | + cd src/ontology + mkdir -p tmp reports mirror + docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx9G' -e JAVA_OPTS='-Xmx9G' --rm obolibrary/odklite make BRI=false MIR=false IMP=false test > TESTLOG.log env: DEFAULT_BRANCH: master - ROBOT_JAVA_ARGS: -Xmx6G - run: cd src/ontology && mkdir -p tmp reports mirror && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx10G' BRI=false MIR=false IMP=false test > TESTLOG.log - name: Last rows of QC report if: ${{ failure() }} run: tail -20 src/ontology/TESTLOG.log \ No newline at end of file From ccbbe7332d3aa858434e254676d9ea7b8243dd57 Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Thu, 5 Oct 2023 14:40:07 +0100 Subject: [PATCH 05/12] increase memory --- .github/workflows/qc.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml index f1c93c3ad8..08bf4e3acf 100644 --- a/.github/workflows/qc.yml +++ b/.github/workflows/qc.yml @@ -34,7 +34,7 @@ jobs: run: | cd src/ontology mkdir -p tmp reports mirror - docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx9G' -e JAVA_OPTS='-Xmx9G' --rm obolibrary/odklite make BRI=false MIR=false IMP=false test > TESTLOG.log + docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx13G' -e JAVA_OPTS='-Xmx13G' --rm obolibrary/odklite make BRI=false MIR=false IMP=false test > TESTLOG.log env: DEFAULT_BRANCH: master - name: Last rows of QC report From 40d24483658da2173ce912c23c3eeb169714f2b2 Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Thu, 5 Oct 2023 16:48:19 +0100 Subject: [PATCH 06/12] decrease memory --- .github/workflows/qc.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml index 08bf4e3acf..726465bf23 100644 --- a/.github/workflows/qc.yml +++ b/.github/workflows/qc.yml @@ -34,7 +34,7 @@ jobs: run: | cd src/ontology mkdir -p tmp reports mirror - docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx13G' -e JAVA_OPTS='-Xmx13G' --rm obolibrary/odklite make BRI=false MIR=false IMP=false test > TESTLOG.log + docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx11G' -e JAVA_OPTS='-Xmx11G' --rm obolibrary/odklite make BRI=false MIR=false IMP=false test > TESTLOG.log env: DEFAULT_BRANCH: master - name: Last rows of QC report From 5a8d6afabc7e19baae2be529448869839d88e68b Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Thu, 5 Oct 2023 21:28:02 +0100 Subject: [PATCH 07/12] decrease memory --- .github/workflows/qc.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml index 726465bf23..19b052bb50 100644 --- a/.github/workflows/qc.yml +++ b/.github/workflows/qc.yml @@ -34,9 +34,9 @@ jobs: run: | cd src/ontology mkdir -p tmp reports mirror - docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx11G' -e JAVA_OPTS='-Xmx11G' --rm obolibrary/odklite make BRI=false MIR=false IMP=false test > TESTLOG.log + docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx10G' -e JAVA_OPTS='-Xmx10G' --rm obolibrary/odklite make BRI=false MIR=false IMP=false test > TESTLOG.log env: DEFAULT_BRANCH: master - name: Last rows of QC report if: ${{ failure() }} - run: tail -20 src/ontology/TESTLOG.log \ No newline at end of file + run: tail -20 src/ontology/TESTLOG.log From b9acb3acfb26c8c53b248f3bba0dd27a26dbd9a6 Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Fri, 6 Oct 2023 11:43:25 +0100 Subject: [PATCH 08/12] change image to odkfull --- .github/workflows/qc.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml index 19b052bb50..d85e324c54 100644 --- a/.github/workflows/qc.yml +++ b/.github/workflows/qc.yml @@ -27,14 +27,14 @@ jobs: set -x docker version - name: Install ODK - run: docker pull obolibrary/odklite + run: docker pull obolibrary/odkfull:v1.4.3 # Checks-out current branch - uses: actions/checkout@v3 - name: Run ontology QC checks run: | cd src/ontology mkdir -p tmp reports mirror - docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx10G' -e JAVA_OPTS='-Xmx10G' --rm obolibrary/odklite make BRI=false MIR=false IMP=false test > TESTLOG.log + docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx10G' -e JAVA_OPTS='-Xmx10G' --rm obolibrary/odkfull:v1.4.3 make BRI=false MIR=false IMP=false test > TESTLOG.log env: DEFAULT_BRANCH: master - name: Last rows of QC report From 70cd041a70d3e8fdda51e4cf24e1a4ee0efa0141 Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Fri, 6 Oct 2023 13:49:14 +0100 Subject: [PATCH 09/12] decrease memory --- .github/workflows/qc.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml index d85e324c54..f99b091334 100644 --- a/.github/workflows/qc.yml +++ b/.github/workflows/qc.yml @@ -34,7 +34,7 @@ jobs: run: | cd src/ontology mkdir -p tmp reports mirror - docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx10G' -e JAVA_OPTS='-Xmx10G' --rm obolibrary/odkfull:v1.4.3 make BRI=false MIR=false IMP=false test > TESTLOG.log + docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx9G' -e JAVA_OPTS='-Xmx9G' --rm obolibrary/odkfull:v1.4.3 make BRI=false MIR=false IMP=false test > TESTLOG.log env: DEFAULT_BRANCH: master - name: Last rows of QC report From 5640a26bbd0e2811de3de646efc8d20149d39eb7 Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Tue, 10 Oct 2023 14:33:59 +0100 Subject: [PATCH 10/12] roll back qc to use ubuntu runner --- .github/workflows/qc.yml | 22 ++++++++-------------- 1 file changed, 8 insertions(+), 14 deletions(-) diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml index f99b091334..64342f751e 100644 --- a/.github/workflows/qc.yml +++ b/.github/workflows/qc.yml @@ -18,25 +18,19 @@ jobs: # This workflow contains a single job called "ontology_qc" ontology_qc: # The type of runner that the job will run on - runs-on: macos-latest + runs-on: ubuntu-latest + container: obolibrary/odkfull:v1.4.1 + # 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: docker-practice/actions-setup-docker@master - - run: | - set -x - docker version - - name: Install ODK - run: docker pull obolibrary/odkfull:v1.4.3 - # Checks-out current branch - - uses: actions/checkout@v3 + - uses: actions/checkout@v2 + - name: Run ontology QC checks - run: | - cd src/ontology - mkdir -p tmp reports mirror - docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS='-Xmx9G' -e JAVA_OPTS='-Xmx9G' --rm obolibrary/odkfull:v1.4.3 make BRI=false MIR=false IMP=false test > TESTLOG.log env: DEFAULT_BRANCH: master + ROBOT_JAVA_ARGS: -Xmx6G + run: cd src/ontology && mkdir -p tmp reports mirror && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' BRI=false MIR=false IMP=false test > TESTLOG.log - name: Last rows of QC report if: ${{ failure() }} - run: tail -20 src/ontology/TESTLOG.log + run: tail -20 src/ontology/TESTLOG.log \ No newline at end of file From 71b0dd8ee853d00c8259e34a085f1db0c04c0064 Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Tue, 10 Oct 2023 15:17:53 +0100 Subject: [PATCH 11/12] add conditional use not to materialize when running qc --- .github/workflows/qc.yml | 4 ++-- src/ontology/uberon.Makefile | 8 ++++++-- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml index 64342f751e..257dad319d 100644 --- a/.github/workflows/qc.yml +++ b/.github/workflows/qc.yml @@ -19,7 +19,7 @@ jobs: ontology_qc: # The type of runner that the job will run on runs-on: ubuntu-latest - container: obolibrary/odkfull:v1.4.1 + container: obolibrary/odkfull:v1.4.3 # Steps represent a sequence of tasks that will be executed as part of the job steps: @@ -30,7 +30,7 @@ jobs: env: DEFAULT_BRANCH: master ROBOT_JAVA_ARGS: -Xmx6G - run: cd src/ontology && mkdir -p tmp reports mirror && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' BRI=false MIR=false IMP=false test > TESTLOG.log + run: cd src/ontology && mkdir -p tmp reports mirror && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' GH_ACTION=true BRI=false MIR=false IMP=false test > TESTLOG.log - name: Last rows of QC report if: ${{ failure() }} run: tail -20 src/ontology/TESTLOG.log \ No newline at end of file diff --git a/src/ontology/uberon.Makefile b/src/ontology/uberon.Makefile index 803292caac..502c9c140a 100644 --- a/src/ontology/uberon.Makefile +++ b/src/ontology/uberon.Makefile @@ -124,11 +124,15 @@ $(OWLSRC): $(SRC) $(COMPONENTSDIR)/disjoint_union_over.ofn $(REPORTDIR)/$(SRC)-g # For the temporary injection of property chains, see # DEVELOPS_FROM_CHAIN=$(COMPONENTSDIR)/develops-from-chains.owl +ifeq ($(GH_ACTION),true) +MATERIALIZE= +else +MATERIALIZE = materialize -T $(CONFIGDIR)/basic_properties.txt -r elk +endif uberon.owl: $(OWLSRC) $(BRIDGEDIR)/uberon-bridge-to-bfo.owl $(DEVELOPS_FROM_CHAIN) $(ROBOT) merge -i $(OWLSRC) -i $(BRIDGEDIR)/uberon-bridge-to-bfo.owl \ -i $(DEVELOPS_FROM_CHAIN) \ - relax \ - materialize -T $(CONFIGDIR)/basic_properties.txt -r elk \ + relax $(MATERIALIZE) \ reason -r elk --exclude-duplicate-axioms true \ --equivalent-classes-allowed asserted-only \ unmerge -i $(DEVELOPS_FROM_CHAIN) \ From b3602faa4e5fefc3a1c582780c6d07730ae2d017 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Thu, 12 Oct 2023 13:47:45 +0100 Subject: [PATCH 12/12] Add comment and link to explain MATERIALIZE. --- src/ontology/uberon.Makefile | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/ontology/uberon.Makefile b/src/ontology/uberon.Makefile index 502c9c140a..e311be5a8f 100644 --- a/src/ontology/uberon.Makefile +++ b/src/ontology/uberon.Makefile @@ -124,6 +124,9 @@ $(OWLSRC): $(SRC) $(COMPONENTSDIR)/disjoint_union_over.ofn $(REPORTDIR)/$(SRC)-g # For the temporary injection of property chains, see # DEVELOPS_FROM_CHAIN=$(COMPONENTSDIR)/develops-from-chains.owl +# The 'materialize' step is too resource-intensive for the GitHub +# Action runners, so we leave it out when running online QC checks, see +# ifeq ($(GH_ACTION),true) MATERIALIZE= else