Update ODK 1.4

monarch-initiative · Feb 19, 2023 · 5a4c064 · 5a4c064
1 parent 630a86e
commit 5a4c064
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Showing 8 changed files with 167 additions and 54 deletions.
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
diff --git a/src/ontology/run.sh b/src/ontology/run.sh
@@ -8,10 +8,36 @@
 # The assumption is that you are working in the src/ontology folder;
 # we therefore map the whole repo (../..) to a docker volume.
 #
+# To use singularity instead of docker, please issue
+# export USE_SINGULARITY=<any-value>
+# before running this script.
+#
 # See README-editors.md for more details.
 
-IMAGE=${IMAGE:-odkfull}
-ODK_JAVA_OPTS=-Xmx8G
+if [ -f run.sh.conf ]; then
+    . ./run.sh.conf
+fi
+
+# Look for a GitHub token
+if [ -n "$GH_TOKEN" ]; then
+    :
+elif [ -f ../../.github/token.txt ]; then
+    GH_TOKEN=$(cat ../../.github/token.txt)
+elif [ -f $XDG_CONFIG_HOME/ontology-development-kit/github/token ]; then
+    GH_TOKEN=$(cat $XDG_CONFIG_HOME/ontology-development-kit/github/token)
+elif [ -f "$HOME/Library/Application Support/ontology-development-kit/github/token" ]; then
+    GH_TOKEN=$(cat "$HOME/Library/Application Support/ontology-development-kit/github/token")
+fi
+
+ODK_IMAGE=${ODK_IMAGE:-odkfull}
+TAG_IN_IMAGE=$(echo $ODK_IMAGE | awk -F':' '{ print $2 }')
+if [ -n "$TAG_IN_IMAGE" ]; then
+  # Override ODK_TAG env var if IMAGE already includes a tag
+  ODK_TAG=$TAG_IN_IMAGE
+  ODK_IMAGE=$(echo $ODK_IMAGE | awk -F':' '{ print $1 }')
+fi
+ODK_TAG=${ODK_TAG:-latest}
+ODK_JAVA_OPTS=${ODK_JAVA_OPTS:--Xmx8G}
 ODK_DEBUG=${ODK_DEBUG:-no}
 
 TIMECMD=
@@ -23,7 +49,26 @@ if [ x$ODK_DEBUG = xyes ]; then
     TIMECMD="/usr/bin/time -f ### DEBUG STATS ###\nElapsed time: %E\nPeak memory: %M kb"
 fi
 
-docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS="$ODK_JAVA_OPTS" -e JAVA_OPTS="$ODK_JAVA_OPTS" --rm -ti obolibrary/$IMAGE $TIMECMD "$@"
+VOLUME_BIND=$PWD/../../:/work
+WORK_DIR=/work/src/ontology
+
+if [ -n "$ODK_BINDS" ]; then
+    VOLUME_BIND="$VOLUME_BIND,$ODK_BINDS"
+fi
+
+if [ -n "$USE_SINGULARITY" ]; then
+
+    singularity exec --cleanenv $ODK_SINGULARITY_OPTIONS \
+        --env "ROBOT_JAVA_ARGS=$ODK_JAVA_OPTS,JAVA_OPTS=$ODK_JAVA_OPTS" \
+        --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="$ODK_JAVA_OPTS" \
+        --rm -ti obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@"
+fi
 
 case "$@" in
 *update_repo*|*release*)

diff --git a/src/sparql/edges.sparql b/src/sparql/edges.sparql
@@ -1,4 +1,3 @@
-prefix obo: <http://purl.obolibrary.org/obo/> 
 prefix owl: <http://www.w3.org/2002/07/owl#>
 prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>

diff --git a/src/sparql/inject-subset-declaration.ru b/src/sparql/inject-subset-declaration.ru
@@ -7,5 +7,5 @@ INSERT { ?y rdfs:subPropertyOf <http://www.geneontology.org/formats/oboInOwl#Sub
 WHERE {
   ?x <http://www.geneontology.org/formats/oboInOwl#inSubset>  ?y .
   FILTER(isIRI(?y))
-  FILTER(regex(str(?y),"^(http://purl.obolibrary.org/obo/)") || regex(str(?y),"^(http://www.ebi.ac.uk/efo/)") || regex(str(?y),"^(https://w3id.org/biolink/)"))
+  FILTER(regex(str(?y),"^(http://purl.obolibrary.org/obo/)") || regex(str(?y),"^(http://www.ebi.ac.uk/efo/)") || regex(str(?y),"^(https://w3id.org/biolink/)") || regex(str(?y),"^(http://purl.obolibrary.org/obo)"))
 }
diff --git a/src/sparql/inject-synonymtype-declaration.ru b/src/sparql/inject-synonymtype-declaration.ru
@@ -7,5 +7,5 @@ INSERT { ?y rdfs:subPropertyOf <http://www.geneontology.org/formats/oboInOwl#Syn
 WHERE {
   ?x <http://www.geneontology.org/formats/oboInOwl#hasSynonymType>  ?y .
   FILTER(isIRI(?y))
-  FILTER(regex(str(?y),"^(http://purl.obolibrary.org/obo/)") || regex(str(?y),"^(http://www.ebi.ac.uk/efo/)") || regex(str(?y),"^(https://w3id.org/biolink/)"))
+  FILTER(regex(str(?y),"^(http://purl.obolibrary.org/obo/)") || regex(str(?y),"^(http://www.ebi.ac.uk/efo/)") || regex(str(?y),"^(https://w3id.org/biolink/)") || regex(str(?y),"^(http://purl.obolibrary.org/obo)"))
 }
diff --git a/src/sparql/multiple-replaced_by-violation.sparql b/src/sparql/multiple-replaced_by-violation.sparql
@@ -0,0 +1,12 @@
+PREFIX replaced_by: <http://purl.obolibrary.org/obo/IAO_0100001>
+
+SELECT DISTINCT ?entity ?property ?value WHERE {
+  VALUES ?property {
+    replaced_by:
+  }
+  ?entity ?property ?value1 .
+  ?entity ?property ?value2 .
+  FILTER(?value1!=?value2)
+  BIND(CONCAT(str(?value1), CONCAT("|", str(?value2))) as ?value)
+}
+
diff --git a/src/sparql/simple-seed.sparql b/src/sparql/simple-seed.sparql
@@ -1,5 +1,4 @@
 prefix owl: <http://www.w3.org/2002/07/owl#>
-prefix obo: <http://purl.obolibrary.org/obo/>
 
 SELECT DISTINCT ?cls WHERE
 {

diff --git a/src/sparql/subsets-labeled.sparql b/src/sparql/subsets-labeled.sparql
@@ -1,5 +1,4 @@
 prefix oio: <http://www.geneontology.org/formats/oboInOwl#>
-prefix def: <http://purl.obolibrary.org/obo/IAO_0000115>
 prefix owl: <http://www.w3.org/2002/07/owl#>
 prefix inSubset: <http://www.geneontology.org/formats/oboInOwl#inSubset>
 prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>