Prepare for ODK 1.5

.github/workflows/qc.yml

@@ -19,15 +19,15 @@ jobs:
   ontology_qc:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull
+    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:
           DEFAULT_BRANCH: master
-        run: cd src/ontology && make IMP=false PAT=false prepare_release -B
+        run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false MIR=false
 

src/ontology/fbbt-odk.yaml

@@ -2,6 +2,7 @@ id: fbbt
 title: "Drosophila Anatomy Ontology"
 github_org: FlyBase
 repo: drosophila-anatomy-ontology
+git_main_branch: master
 use_env_file_docker: True
 report_fail_on: none
 use_dosdps: TRUE
@@ -11,6 +12,10 @@ pattern_pipelines_group:
       dosdp_tools_options: "--obo-prefixes=true --restrict-axioms-to=logical"
     - id: all-axioms
       dosdp_tools_options: "--obo-prefixes=true"
+robot_plugins:
+  plugins:
+    - name: flybase
+      mirror_from: https://github.com/FlyBase/flybase-robot-plugin/releases/download/flybase-robot-plugin-0.1.1/flybase.jar
 namespaces: 
   - http://purl.obolibrary.org/obo/FBbt_
   - http://purl.obolibrary.org/obo/fbbt_
@@ -40,6 +45,10 @@ import_group:
   use_base_merging: TRUE
   exclude_iri_patterns:
     - <http://purl.obolibrary.org/obo/UBERON_*>
+  annotation_properties:
+    - RO:0002582
+    - rdfs:label
+    - IAO:0000115
   products:
     - id: go
       make_base: TRUE

src/ontology/fbbt.Makefile

@@ -69,7 +69,6 @@ $(REPORTDIR)/onto_metrics_calc.txt: $(ONT)-simple.obo install_flybase_scripts
 	$(SCRIPTSDIR)/onto_metrics_calc.pl 'fly_anatomy.ontology' $(ONT)-simple.obo > $@
 
 $(REPORTDIR)/chado_load_check_simple.txt: install_flybase_scripts fly_anatomy.obo
-	apt-get install -y --no-install-recommends libbusiness-isbn-perl
 	$(SCRIPTSDIR)/chado_load_checks.pl fly_anatomy.obo > $@
 
 $(REPORTDIR)/obo_qc_%.obo.txt:
@@ -133,13 +132,7 @@ $(ONT)-full.obo: $(ONT)-full.owl
 # special placeholder string to substitute in definitions from external ontologies
 # FBbt only uses DOT definitions - to use SUB, copy code and sparql from FBcv.
 
-export ROBOT_PLUGINS_DIRECTORY = $(TMPDIR)/plugins
-
-$(ROBOT_PLUGINS_DIRECTORY)/flybase.jar:
-	mkdir -p $(ROBOT_PLUGINS_DIRECTORY)
-	curl -L -o $@ https://github.com/FlyBase/flybase-robot-plugin/releases/download/flybase-robot-plugin-0.1.0/flybase.jar
-
-$(EDIT_PREPROCESSED): $(SRC) $(ROBOT_PLUGINS_DIRECTORY)/flybase.jar
+$(EDIT_PREPROCESSED): $(SRC) all_robot_plugins
 	$(ROBOT) flybase:rewrite-def -i $< --dot-definitions --filter-prefix FBbt -o $@
 
 

src/ontology/run.sh

@@ -31,6 +31,22 @@ elif [ -f "$HOME/Library/Application Support/ontology-development-kit/github/tok
     GH_TOKEN=$(cat "$HOME/Library/Application Support/ontology-development-kit/github/token")
 fi
 
+# SSH agent socket
+# On macOS, we cannot use $SSH_AUTH_SOCK directly,
+# we need to use a "magic" socket instead.
+case "$(uname)" in
+Darwin)
+    ODK_SSH_AUTH_SOCKET=/run/host-services/ssh-auth.sock
+    ;;
+*)
+    ODK_SSH_AUTH_SOCKET=$SSH_AUTH_SOCK
+    ;;
+esac
+ODK_SSH_BIND=
+if [ -n "$ODK_SSH_AUTH_SOCKET" ]; then
+    ODK_SSH_BIND=",$ODK_SSH_AUTH_SOCKET:/run/host-services/ssh-auth.sock"
+fi
+
 ODK_IMAGE=${ODK_IMAGE:-odkfull}
 TAG_IN_IMAGE=$(echo $ODK_IMAGE | awk -F':' '{ print $2 }')
 if [ -n "$TAG_IN_IMAGE" ]; then
@@ -42,16 +58,28 @@ ODK_TAG=${ODK_TAG:-latest}
 ODK_JAVA_OPTS=${ODK_JAVA_OPTS:--Xmx8G}
 ODK_DEBUG=${ODK_DEBUG:-no}
 
+ODK_USER_ID=${ODK_USER_ID:-$(id -u)}
+ODK_GROUP_ID=${ODK_GROUP_ID:-$(id -g)}
+
+# Convert OWLAPI_* environment variables to the OWLAPI as Java options
+# See http://owlcs.github.io/owlapi/apidocs_4/org/semanticweb/owlapi/model/parameters/ConfigurationOptions.html
+# for a list of allowed options
+OWLAPI_OPTIONS_NAMESPACE=org.semanticweb.owlapi.model.parameters.ConfigurationOptions
+for owlapi_var in $(env | sed -n s/^OWLAPI_//p) ; do
+    ODK_JAVA_OPTS="$ODK_JAVA_OPTS -D$OWLAPI_OPTIONS_NAMESPACE.${owlapi_var%=*}=${owlapi_var#*=}"
+done
+
 TIMECMD=
 if [ x$ODK_DEBUG = xyes ]; then
     # If you wish to change the format string, take care of using
     # non-breaking spaces (U+00A0) instead of normal spaces, to
     # prevent the shell from tokenizing the format string.
-    echo "Running ${IMAGE} with ${ODK_JAVA_OPTS} of memory for ROBOT and Java-based pipeline steps."
+    echo "Running obolibrary/${ODK_IMAGE}:${ODK_TAG} with '${ODK_JAVA_OPTS}' as options for ROBOT and other Java-based pipeline steps."
     TIMECMD="/usr/bin/time -f ### DEBUG STATS ###\nElapsed time: %E\nPeak memory: %M kb"
 fi
+rm -f tmp/debug.log
 
-VOLUME_BIND=$PWD/../../:/work
+VOLUME_BIND=$PWD/../../:/work$ODK_SSH_BIND
 WORK_DIR=/work/src/ontology
 
 if [ -n "$ODK_BINDS" ]; then
@@ -66,6 +94,10 @@ cat <<EOF > run.sh.env
 ROBOT_JAVA_ARGS=$ODK_JAVA_OPTS
 JAVA_OPTS=$ODK_JAVA_OPTS
 GH_TOKEN=$GH_TOKEN
+SSH_AUTH_SOCK=/run/host-services/ssh-auth.sock
+ODK_USER_ID=$ODK_USER_ID
+ODK_GROUP_ID=$ODK_GROUP_ID
+ODK_DEBUG=$ODK_DEBUG
 EOF
 
 if [ -n "$USE_SINGULARITY" ]; then

src/ontology/travis.sh

@@ -1,4 +1,4 @@
 # Running the DPO release pipeline for TRAVIS
 set -e
 
-sh run.sh make IMP=false PAT=false prepare_release -B
+sh run.sh make MIR=false IMP=false PAT=false prepare_release -B

src/scripts/run-command.sh

@@ -0,0 +1,4 @@
+#!/bin/sh
+ODK_DEBUG_FILE=${ODK_DEBUG_FILE:-debug.log}
+echo "Command: sh $@" >> $ODK_DEBUG_FILE
+/usr/bin/time -a -o $ODK_DEBUG_FILE -f "Elapsed time: %E\nPeak memory: %M kb" /bin/sh "$@"

src/scripts/update_repo.sh

@@ -21,10 +21,11 @@ cp target/$OID/src/ontology/run.sh $SRCDIR/ontology/
 cp -r target/$OID/src/sparql/* $SRCDIR/sparql/
 mkdir -p $ROOTDIR/.github
 mkdir -p $ROOTDIR/.github/workflows
-cp -n target/$OID/.github/workflows/qc.yml $ROOTDIR/.github/workflows/qc.yml
+cp target/$OID/.github/workflows/qc.yml $ROOTDIR/.github/workflows/qc.yml
+
 
 
 
 echo "WARNING: These files should be manually migrated: mkdocs.yaml, .gitignore, src/ontology/catalog.xml (if you added a new import or component)"
-echo "WARNING: Your QC workflows have not been updated automatically. Please update the ODK version number(s) in .github/workflows/qc.yml."
+
 echo "Ontology repository update successfully completed."

src/sparql/dc-properties-violation.sparql

@@ -0,0 +1,11 @@
+# The purpose of this violation is to make sure people update
+# from using the deprecated DC Elements 1.1 namespace (http://purl.org/dc/elements/1.1/)
+# to using the recommended DC Terms namespace (http://purl.org/dc/terms/)
+# See also discussion on https://github.com/oborel/obo-relations/pull/692
+
+SELECT ?term ?predicate WHERE {
+  ?term ?predicate ?value .
+  FILTER(STRSTARTS(STR(?predicate), "http://purl.org/dc/elements/1.1/"))
+  FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/FBbt_") || STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/fbbt_")))
+}
+