Add oxigraph load step.

INCATools · Aug 3, 2023 · 5685ae6 · 5685ae6
1 parent cf1db12
commit 5685ae6
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Showing 2 changed files with 13 additions and 2 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -9,6 +9,12 @@ FROM obolibrary/odkfull:v1.4.1
 ###### Souffle ######
 #RUN curl -s https://packagecloud.io/install/repositories/souffle-lang/souffle/script.deb.sh | bash && apt-get install -y souffle
 
+###### oxigraph ######
+ENV OXIGRAPH=0.3.18
+RUN if [ "$TARGETPLATFORM" = "linux/amd64" ]; then ARCHITECTURE=x86_64; elif [ "$TARGETPLATFORM" = "linux/arm64" ]; then ARCHITECTURE=aarch64; else ARCHITECTURE=x86_64; fi \
+&& wget -nv https://github.com/oxigraph/oxigraph/releases/download/v$OXIGRAPH/oxigraph_server_v${OXIGRAPH}_${ARCHITECTURE}_linux_gnu \
+&& mv oxigraph_server_v${OXIGRAPH}_${ARCHITECTURE}_linux_gnu /tools/oxigraph_server
+
 ###### blazegraph-runner #####
 ENV BR=1.7
 ENV PATH "/tools/blazegraph-runner/bin:$PATH"

diff --git a/Makefile b/Makefile
@@ -9,7 +9,7 @@ BIOLINK=3.0.0
 
 NONBASE_ONTOLOGIES := $(shell cat "ontologies.txt")
 
-all: ubergraph.jnl.gz ubergraph.nq.gz redundant-graph-table.tgz nonredundant-graph-table.tgz ontologies-merged.ofn.gz
+all: ubergraph.jnl.gz ubergraph.nq.gz redundant-graph-table.tgz nonredundant-graph-table.tgz ontologies-merged.ofn.gz ubergraph-oxigraph.tgz
 
 mirror: ontologies.txt pr-base.owl po-base.owl ppo-base.owl apo-base.owl mmusdv-base.owl foodon-base.owl to-base.owl peco-base.owl mro-base.owl hao-base.owl clao-base.owl oarcs-base.owl ubergraph-axioms.ofn
 	mkdir -p $@ && cd $@ &&\
@@ -276,6 +276,11 @@ ubergraph-tdb.tgz: ubergraph.nq.gz
 	mv stats.opt ubergraph-tdb/Data-0001/stats.opt &&\
 	tar -zcf $@ ubergraph-tdb
 
+ubergraph-oxigraph.tgz: ubergraph.nq.gz
+	rm -rf ubergraph-oxigraph && mkdir ubergraph-oxigraph &&\
+	oxigraph_server --location ubergraph-oxigraph load --file $< &&\
+	tar -zcf $@ ubergraph-oxigraph
+
 kgx/nodes.tsv: ubergraph.jnl build-sparql/kgx-nodes.rq
 	mkdir -p kgx
 	$(BG_RUNNER) select --journal=$< --outformat=tsv build-sparql/kgx-nodes.rq kgx/nodes.tsv
@@ -288,7 +293,7 @@ kgx/edges.tsv: kgx/nodes.tsv
 #### Commands for building the Docker image ####
 ################################################
 
-VERSION = "1.6"
+VERSION = "1.7"
 IM=monarchinitiative/ubergraph
 
 docker-build-no-cache: