Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update ODK image to v1.4.3 in QC #3087

Merged
merged 11 commits into from
Oct 12, 2023
Merged

Update ODK image to v1.4.3 in QC #3087

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
11 commits
Select commit Hold shift + click to select a range
d09f319
update ODK image in QC
anitacaron Oct 4, 2023
8708fd9
increase ROBOT_JAVA_ARGS in qc
anitacaron Oct 4, 2023
8a6439e
change to macos runner and increase memory
anitacaron Oct 5, 2023
5115f60
setup macos runner in qc
anitacaron Oct 5, 2023
ccbbe73
increase memory
anitacaron Oct 5, 2023
40d2448
decrease memory
anitacaron Oct 5, 2023
5a8d6af
decrease memory
Oct 5, 2023
b9acb3a
change image to odkfull
anitacaron Oct 6, 2023
70cd041
decrease memory
anitacaron Oct 6, 2023
5640a26
roll back qc to use ubuntu runner
anitacaron Oct 10, 2023
71b0dd8
add conditional use not to materialize when running qc
anitacaron Oct 10, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions .github/workflows/qc.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand All @@ -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
4 changes: 2 additions & 2 deletions src/ontology/Makefile
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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

Expand Down Expand Up @@ -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')
Expand Down
8 changes: 6 additions & 2 deletions src/ontology/uberon.Makefile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -124,11 +124,15 @@ $(OWLSRC): $(SRC) $(COMPONENTSDIR)/disjoint_union_over.ofn $(REPORTDIR)/$(SRC)-g
# For the temporary injection of property chains, see
# <https://github.com/obophenotype/uberon/issues/2381>
DEVELOPS_FROM_CHAIN=$(COMPONENTSDIR)/develops-from-chains.owl
ifeq ($(GH_ACTION),true)
MATERIALIZE=
else
MATERIALIZE = materialize -T $(CONFIGDIR)/basic_properties.txt -r elk
endif
gouttegd marked this conversation as resolved.
Show resolved Hide resolved
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) \
Expand Down