Refresh ODK (includes 1.5.2 migration)

.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:v1.3.0
+    container: obolibrary/odkfull:v1.5.2
 
     # 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 ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false
+        run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false MIR=false
 

docs/odk-workflows/ManageDocumentation.md

@@ -44,3 +44,4 @@ The documentation is _not_ automatically updated from the Markdown, and needs to
    Just make sure you give GitHub 2-5 minutes to build the pages!
 
 
+

docs/odk-workflows/RepoManagement.md

@@ -2,7 +2,7 @@
 
 ## Updating your ODK repository
 
-Your ODK repositories configuration is managed in `src/ontology/pato-odk.yaml`. Once you have made your changes, you can run the following to apply your changes to the repository:
+Your ODK repositories configuration is managed in `src/ontology/pato-odk.yaml`. The [ODK Project Configuration Schema](https://github.com/INCATools/ontology-development-kit/blob/master/docs/project-schema.md) defines all possible parameters that can be used in this config YAML. Once you have made your changes, you can run the following to apply your changes to the repository:
 
 
 ```

src/ontology/run.sh

@@ -14,6 +14,8 @@
 #
 # See README-editors.md for more details.
 
+set -e
+
 if [ -f run.sh.conf ]; then
     . ./run.sh.conf
 fi
@@ -29,6 +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
@@ -40,16 +58,28 @@ ODK_TAG=${ODK_TAG:-latest}
 ODK_JAVA_OPTS=${ODK_JAVA_OPTS:--Xmx12G}
 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 "$ODK_BINDS" ]; then
@@ -59,14 +89,14 @@ fi
 if [ -n "$USE_SINGULARITY" ]; then
 
     singularity exec --cleanenv $ODK_SINGULARITY_OPTIONS \
-        --env "ROBOT_JAVA_ARGS=$ODK_JAVA_OPTS,JAVA_OPTS=$ODK_JAVA_OPTS" \
+        --env "ROBOT_JAVA_ARGS=$ODK_JAVA_OPTS,JAVA_OPTS=$ODK_JAVA_OPTS,SSH_AUTH_SOCK=/run/host-services/ssh-auth.sock,ODK_USER_ID=$ODK_USER_ID,ODK_GROUP_ID=$ODK_GROUP_ID,ODK_DEBUG=$ODK_DEBUG" \
         --bind $VOLUME_BIND \
         -W $WORK_DIR \
         docker://obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@"
 else
     BIND_OPTIONS="-v $(echo $VOLUME_BIND | sed 's/,/ -v /')"
     docker run $ODK_DOCKER_OPTIONS $BIND_OPTIONS -w $WORK_DIR \
-        -e ROBOT_JAVA_ARGS="$ODK_JAVA_OPTS" -e JAVA_OPTS="$ODK_JAVA_OPTS" \
+        -e ROBOT_JAVA_ARGS="$ODK_JAVA_OPTS" -e JAVA_OPTS="$ODK_JAVA_OPTS" -e SSH_AUTH_SOCK=/run/host-services/ssh-auth.sock -e ODK_USER_ID=$ODK_USER_ID -e ODK_GROUP_ID=$ODK_GROUP_ID -e ODK_DEBUG=$ODK_DEBUG \
         --rm -ti obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@"
 fi
 

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

@@ -26,7 +26,8 @@ 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
+
 
 
 cp target/$OID/.github/workflows/docs.yml $ROOTDIR/.github/workflows/docs.yml
@@ -35,5 +36,5 @@ cp target/$OID/.github/workflows/docs.yml $ROOTDIR/.github/workflows/docs.yml
 cp -n target/$OID/mkdocs.yaml $ROOTDIR/
 
 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/class-count-by-prefix.sparql

@@ -7,4 +7,4 @@ SELECT ?prefix (COUNT(DISTINCT ?cls) AS ?numberOfClasses) WHERE
   FILTER (!isBlank(?cls))
   BIND( STRBEFORE(STRAFTER(str(?cls),"http://purl.obolibrary.org/obo/"), "_") AS ?prefix)
 }
-GROUP BY ?prefix
+GROUP BY ?prefix