mapping-commons · anitacaron · Jun 27, 2023 · Jul 18, 2023 · Jul 21, 2023 · Aug 9, 2023
diff --git a/.gitignore b/.gitignore
@@ -1,7 +1,5 @@
 .vscode
 __pycache__
 .env
-/data/mappings.ttl
-/data/mappings.jsonld
-/data/registry.yml
+/data/*
 poetry.lock
diff --git a/Makefile b/Makefile
@@ -6,7 +6,7 @@ REGISTRY_URL = https://raw.githubusercontent.com/mapping-commons/mh_mapping_init
 $(PWD)/data/registry.yml:
 	wget $(REGISTRY_URL) -O $@
 
-jsonld_from_registry: $(PWD)/data/registry.yml
+ttl_from_registry: $(PWD)/data/registry.yml
 	cd src && python3 registry_parser.py $<
 
 deploy_api:
@@ -19,3 +19,7 @@ rebuild-%:
 build-sssom-api:
 	docker-compose up --build
 
+OBO_CONTEXT_URL = https://raw.githubusercontent.com/biopragmatics/bioregistry/main/exports/contexts/obo.context.jsonld
+.PHONY: update_obo_context
+update_obo_context:
+	wget $(OBO_CONTEXT_URL) -O resources/obo.context.jsonld
diff --git a/api.Dockerfile b/api.Dockerfile
@@ -13,6 +13,4 @@ RUN pip install poetry
 
 RUN poetry config virtualenvs.create false
 
-RUN poetry install
-
-# CMD ["uvicorn", "app.main:app", "--host", "0.0.0.0", "--port", "80"]
+RUN poetry install
diff --git a/blazegraph.Dockerfile b/blazegraph.Dockerfile
@@ -0,0 +1,22 @@
+FROM ubuntu:20.04
+WORKDIR /tools
+
+# Install base tools from Ubuntu.
+RUN apt-get update && \
+    DEBIAN_FRONTEND="noninteractive" apt-get install -y --no-install-recommends \
+        wget \
+        curl \
+        openjdk-11-jdk \
+        ca-certificates \
+        ca-certificates-java
+
+ENV JAVA_HOME /usr/lib/jvm/java-11-openjdk-amd64/
+RUN export JAVA_HOME
+
+###### Blazegraph #####
+ENV JAVA_OPTS -Xmx16G
+RUN wget -nv https://github.com/blazegraph/database/releases/download/BLAZEGRAPH_2_1_6_RC/blazegraph.jar
+
+CMD java -server $JAVA_OPTS -Dcom.bigdata.rdf.sail.webapp.ConfigParams.propertyFile=/RWStore.properties -Dcom.bigdata.util.config.LogUtil=/log4.properties -jar blazegraph.jar
+
+
diff --git a/config/RWStore.properties b/config/RWStore.properties
@@ -0,0 +1,45 @@
+#
+# Note: These options are applied when the journal and the triple store are
+# first created.
+
+##
+## Journal options.
+##
+
+# The backing file. This contains all your data.  You want to put this someplace
+# safe.  The default locator will wind up in the directory from which you start
+# your servlet container.
+com.bigdata.journal.AbstractJournal.file=blazegraph-mappings.jnl
+
+# The persistence engine.  Use 'Disk' for the WORM or 'DiskRW' for the RWStore.
+com.bigdata.journal.AbstractJournal.bufferMode=DiskRW
+
+# Setup for the RWStore recycler rather than session protection.
+com.bigdata.service.AbstractTransactionService.minReleaseAge=1
+
+com.bigdata.btree.writeRetentionQueue.capacity=4000
+com.bigdata.btree.BTree.branchingFactor=128
+
+# 200M initial extent.
+com.bigdata.journal.AbstractJournal.initialExtent=209715200
+com.bigdata.journal.AbstractJournal.maximumExtent=209715200
+
+##
+## Setup for triples mode without the full text index.
+##
+com.bigdata.rdf.sail.truthMaintenance=false
+com.bigdata.rdf.store.AbstractTripleStore.quads=false
+com.bigdata.rdf.store.AbstractTripleStore.statementIdentifiers=false
+com.bigdata.rdf.store.AbstractTripleStore.textIndex=false
+com.bigdata.rdf.store.AbstractTripleStore.axiomsClass=com.bigdata.rdf.axioms.NoAxioms
+
+# Bump up the branching factor for the lexicon indices on the default kb.
+com.bigdata.namespace.kb.lex.com.bigdata.btree.BTree.branchingFactor=400
+
+# Bump up the branching factor for the statement indices on the default kb.
+com.bigdata.namespace.kb.spo.com.bigdata.btree.BTree.branchingFactor=1024
+
+com.bigdata.search.FullTextIndex.analyzerFactoryClass=com.bigdata.search.ConfigurableAnalyzerFactory
+com.bigdata.search.ConfigurableAnalyzerFactory.analyzer.eng.analyzerClass=org.apache.lucene.analysis.standard.StandardAnalyzer
+com.bigdata.search.ConfigurableAnalyzerFactory.analyzer.eng.stopwords=none
+com.bigdata.search.ConfigurableAnalyzerFactory.analyzer._.like=eng
diff --git a/config/dataloader.xml b/config/dataloader.xml
@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?> 
+<!DOCTYPE properties SYSTEM "http://java.sun.com/dtd/properties.dtd"> 
+	  <properties>
+            <!-- Default Graph URI (Optional - Required for quads mode namespace) --> 
+            <entry key="defaultGraph">kb</entry>
+            <!-- The configuration file for the database instance. It must be readable by the web application. --> 
+            <entry key="propertyFile">/RWStore.properties</entry>
+             <!-- The namespace of the KB instance. Defaults to kb. --> 
+             <entry key="namespace">kb</entry>
+            <!-- Zero or more files or directories containing the data to be loaded. 
+                   This should be a comma delimited list. The files must be readable by the web application. -->
+            <entry key="fileOrDirs">/data</entry>
+            <!-- RDF Format (Default is rdf/xml) --> 
+	        <entry key="format">x-turtle</entry>   
+            <!-- Suppress all stdout messages (Optional) --> 
+            <entry key="quiet">false</entry> 
+            <!-- Show additional messages detailing the load performance. (Optional) --> 
+            <entry key="verbose">100</entry> 
+            <!-- Compute the RDF(S)+ closure. (Optional) --> 
+            <entry key="closure">false</entry> 
+            <!-- Files will be renamed to either .good or .fail as they are processed. 
+                    The files will remain in the same directory. -->
+            <entry key="durableQueues">true</entry> 
+      </properties>
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diff --git a/data/ols/mpio.ols.sssom.tsv.jsonld.gz b/data/ols/mpio.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/mro.ols.sssom.tsv.jsonld.gz b/data/ols/mro.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/ms.ols.sssom.tsv.jsonld.gz b/data/ols/ms.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/msio.ols.sssom.tsv.jsonld.gz b/data/ols/msio.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/nbo.ols.sssom.tsv.jsonld.gz b/data/ols/nbo.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/ncit.ols.sssom.tsv.jsonld.gz b/data/ols/ncit.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/ncro.ols.sssom.tsv.jsonld.gz b/data/ols/ncro.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/ngbo.ols.sssom.tsv.jsonld.gz b/data/ols/ngbo.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/nmrcv.ols.sssom.tsv.jsonld.gz b/data/ols/nmrcv.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/nomen.ols.sssom.tsv.jsonld.gz b/data/ols/nomen.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/oae.ols.sssom.tsv.jsonld.gz b/data/ols/oae.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/oarcs.ols.sssom.tsv.jsonld.gz b/data/ols/oarcs.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/oba.ols.sssom.tsv.jsonld.gz b/data/ols/oba.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/obcs.ols.sssom.tsv.jsonld.gz b/data/ols/obcs.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/obi.ols.sssom.tsv.jsonld.gz b/data/ols/obi.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/obib.ols.sssom.tsv.jsonld.gz b/data/ols/obib.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/oboinowl.ols.sssom.tsv.jsonld.gz b/data/ols/oboinowl.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/ogg.ols.sssom.tsv.jsonld.gz b/data/ols/ogg.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/ogms.ols.sssom.tsv.jsonld.gz b/data/ols/ogms.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/ogsf.ols.sssom.tsv.jsonld.gz b/data/ols/ogsf.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/ohd.ols.sssom.tsv.jsonld.gz b/data/ols/ohd.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/ohmi.ols.sssom.tsv.jsonld.gz b/data/ols/ohmi.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/ohpi.ols.sssom.tsv.jsonld.gz b/data/ols/ohpi.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/olatdv.ols.sssom.tsv.jsonld.gz b/data/ols/olatdv.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/om.ols.sssom.tsv.jsonld.gz b/data/ols/om.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/omiabis.ols.sssom.tsv.jsonld.gz b/data/ols/omiabis.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/omit.ols.sssom.tsv.jsonld.gz b/data/ols/omit.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/omo.ols.sssom.tsv.jsonld.gz b/data/ols/omo.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/omp.ols.sssom.tsv.jsonld.gz b/data/ols/omp.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/omrse.ols.sssom.tsv.jsonld.gz b/data/ols/omrse.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/one.ols.sssom.tsv.jsonld.gz b/data/ols/one.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/ons.ols.sssom.tsv.jsonld.gz b/data/ols/ons.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/ontoavida.ols.sssom.tsv.jsonld.gz b/data/ols/ontoavida.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/ontoneo.ols.sssom.tsv.jsonld.gz b/data/ols/ontoneo.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/oostt.ols.sssom.tsv.jsonld.gz b/data/ols/oostt.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/opl.ols.sssom.tsv.jsonld.gz b/data/ols/opl.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/opmi.ols.sssom.tsv.jsonld.gz b/data/ols/opmi.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/ordo.ols.sssom.tsv.jsonld.gz b/data/ols/ordo.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/ornaseq.ols.sssom.tsv.jsonld.gz b/data/ols/ornaseq.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/orth.ols.sssom.tsv.jsonld.gz b/data/ols/orth.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/ovae.ols.sssom.tsv.jsonld.gz b/data/ols/ovae.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/owl.ols.sssom.tsv.jsonld.gz b/data/ols/owl.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/pato.ols.sssom.tsv.jsonld.gz b/data/ols/pato.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/pcl.ols.sssom.tsv.jsonld.gz b/data/ols/pcl.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/pco.ols.sssom.tsv.jsonld.gz b/data/ols/pco.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/pdro.ols.sssom.tsv.jsonld.gz b/data/ols/pdro.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/pdumdv.ols.sssom.tsv.jsonld.gz b/data/ols/pdumdv.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/peco.ols.sssom.tsv.jsonld.gz b/data/ols/peco.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/phipo.ols.sssom.tsv.jsonld.gz b/data/ols/phipo.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/plana.ols.sssom.tsv.jsonld.gz b/data/ols/plana.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/planp.ols.sssom.tsv.jsonld.gz b/data/ols/planp.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/po.ols.sssom.tsv.jsonld.gz b/data/ols/po.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/poro.ols.sssom.tsv.jsonld.gz b/data/ols/poro.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/ppo.ols.sssom.tsv.jsonld.gz b/data/ols/ppo.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/pr.ols.sssom.tsv.jsonld.gz b/data/ols/pr.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/proco.ols.sssom.tsv.jsonld.gz b/data/ols/proco.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/prov.ols.sssom.tsv.jsonld.gz b/data/ols/prov.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/psdo.ols.sssom.tsv.jsonld.gz b/data/ols/psdo.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/pso.ols.sssom.tsv.jsonld.gz b/data/ols/pso.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/pw.ols.sssom.tsv.jsonld.gz b/data/ols/pw.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/rbo.ols.sssom.tsv.jsonld.gz b/data/ols/rbo.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/rdfs.ols.sssom.tsv.jsonld.gz b/data/ols/rdfs.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/reproduceme.ols.sssom.tsv.jsonld.gz b/data/ols/reproduceme.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/reto.ols.sssom.tsv.jsonld.gz b/data/ols/reto.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/rex.ols.sssom.tsv.jsonld.gz b/data/ols/rex.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/rexo.ols.sssom.tsv.jsonld.gz b/data/ols/rexo.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/ro.ols.sssom.tsv.jsonld.gz b/data/ols/ro.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/rs.ols.sssom.tsv.jsonld.gz b/data/ols/rs.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/rxno.ols.sssom.tsv.jsonld.gz b/data/ols/rxno.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/sbo.ols.sssom.tsv.jsonld.gz b/data/ols/sbo.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/scdo.ols.sssom.tsv.jsonld.gz b/data/ols/scdo.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/schemaorg_http.ols.sssom.tsv.jsonld.gz b/data/ols/schemaorg_http.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/schemaorg_https.ols.sssom.tsv.jsonld.gz b/data/ols/schemaorg_https.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/sdgio.ols.sssom.tsv.jsonld.gz b/data/ols/sdgio.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/sepio.ols.sssom.tsv.jsonld.gz b/data/ols/sepio.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/shareloc.ols.sssom.tsv.jsonld.gz b/data/ols/shareloc.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/sibo.ols.sssom.tsv.jsonld.gz b/data/ols/sibo.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/sio.ols.sssom.tsv.jsonld.gz b/data/ols/sio.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/skos.ols.sssom.tsv.jsonld.gz b/data/ols/skos.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/snomed.ols.sssom.tsv.jsonld.gz b/data/ols/snomed.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/so.ols.sssom.tsv.jsonld.gz b/data/ols/so.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/spd.ols.sssom.tsv.jsonld.gz b/data/ols/spd.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/srao.ols.sssom.tsv.jsonld.gz b/data/ols/srao.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/stato.ols.sssom.tsv.jsonld.gz b/data/ols/stato.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/swo.ols.sssom.tsv.jsonld.gz b/data/ols/swo.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/symp.ols.sssom.tsv.jsonld.gz b/data/ols/symp.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/t4fs.ols.sssom.tsv.jsonld.gz b/data/ols/t4fs.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/tads.ols.sssom.tsv.jsonld.gz b/data/ols/tads.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/tao.ols.sssom.tsv.jsonld.gz b/data/ols/tao.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/taxrank.ols.sssom.tsv.jsonld.gz b/data/ols/taxrank.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/tgma.ols.sssom.tsv.jsonld.gz b/data/ols/tgma.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/to.ols.sssom.tsv.jsonld.gz b/data/ols/to.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/trans.ols.sssom.tsv.jsonld.gz b/data/ols/trans.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/tto.ols.sssom.tsv.jsonld.gz b/data/ols/tto.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/txpo.ols.sssom.tsv.jsonld.gz b/data/ols/txpo.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/uberon.ols.sssom.tsv.jsonld.gz b/data/ols/uberon.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/uo.ols.sssom.tsv.jsonld.gz b/data/ols/uo.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/upa.ols.sssom.tsv.jsonld.gz b/data/ols/upa.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/vbo.ols.sssom.tsv.jsonld.gz b/data/ols/vbo.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/vo.ols.sssom.tsv.jsonld.gz b/data/ols/vo.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/vsao.ols.sssom.tsv.jsonld.gz b/data/ols/vsao.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/vt.ols.sssom.tsv.jsonld.gz b/data/ols/vt.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/vto.ols.sssom.tsv.jsonld.gz b/data/ols/vto.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/wbbt.ols.sssom.tsv.jsonld.gz b/data/ols/wbbt.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/wbls.ols.sssom.tsv.jsonld.gz b/data/ols/wbls.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/wbphenotype.ols.sssom.tsv.jsonld.gz b/data/ols/wbphenotype.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/xao.ols.sssom.tsv.jsonld.gz b/data/ols/xao.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/xco.ols.sssom.tsv.jsonld.gz b/data/ols/xco.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/xlmod.ols.sssom.tsv.jsonld.gz b/data/ols/xlmod.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/xpo.ols.sssom.tsv.jsonld.gz b/data/ols/xpo.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/zeco.ols.sssom.tsv.jsonld.gz b/data/ols/zeco.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/zfa.ols.sssom.tsv.jsonld.gz b/data/ols/zfa.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/zfs.ols.sssom.tsv.jsonld.gz b/data/ols/zfs.ols.sssom.tsv.jsonld.gz
diff --git a/data/ols/zp.ols.sssom.tsv.jsonld.gz b/data/ols/zp.ols.sssom.tsv.jsonld.gz
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -15,14 +15,22 @@ services:
       - triplestore
       - upload-triplestore
     environment:
-      - SPARQL_ENDPOINT=http://triplestore:8080/rdf4j-server/repositories/sssom
+      - SPARQL_ENDPOINT=http://triplestore:9999/blazegraph/namespace/kb/sparql
   triplestore:
-    image: eclipse/rdf4j-workbench:latest
+    image: anitacaron/blazegraph:v0.4
     environment:
-      - JAVA_OPTS=-Xms10g -Xmx20g
-      - RDF4J_DATA=/data 
+      - JAVA_OPTS=-Xmx10G
     ports:
-      - 8080:8080
+      - 9999:9999
+    volumes:
+      - ./data:/data
+      - ./config/RWStore.properties:/RWStore.properties
+      - ./config/log4j.properties:/log4j.properties
+    healthcheck:
+      test: ["CMD", "curl", "-f", "http://triplestore:9999/"]
+      interval: 3s
+      timeout: 5s
+      retries: 3
   upload-triplestore:
     build:
       context: .
@@ -32,6 +40,7 @@ services:
     links:
       - triplestore
     environment:
-      - SERVER=http://triplestore:8080
+      - SERVER=http://triplestore:9999/blazegraph
     volumes:
-      - ./data:/data
+      - ./data:/data
+      - ./config/RWStore.properties:/RWStore.properties
diff --git a/process.sh b/process.sh
@@ -7,45 +7,54 @@ echo "Start: upload-triplestore"
 echo "TIME:"
 date
 
-SETUP=${WORKSPACE}/rdf4j_sssom.txt
-RDF4J=/opt/eclipse-rdf4j-${RDF4J_VERSION}
-RDF4JSERVER=${SERVER}/rdf4j-server
-DATA=/data/ols
+# SETUP=${WORKSPACE}/rdf4j_sssom.txt
+#BLAZEGRAPH_UID=/opt/eclipse-rdf4j-${RDF4J_VERSION}
+BLAZEGRAPHSERVER=${SERVER}/dataloader
+DATA=/data
+DATALOADER=/opt/SSSOM/
 
-if [ `ls $DATA/*.jsonld.gz | wc -l` -lt 1 ]; then echo "ERROR: No data in data directory! Aborting.. " && exit 1; fi
+#if [ `ls $DATA/*.jsonld.gz | wc -l` -lt 1 ]; then echo "ERROR: No data in data directory! Aborting.. " && exit 1; fi
 
-echo 'Waiting for RDF4J server..'
-until $(curl --output /dev/null --silent --head --fail ${RDF4JSERVER}); do
+echo 'Waiting for BLAZEGRAPH WORKBENCH..'
+until $(curl --output /dev/null --silent --head --fail ${SERVER}); do
     printf '.'
     sleep 5
 done
 
-echo "connect "${RDF4JSERVER}|cat - ${SETUP} > /tmp/out && mv /tmp/out ${SETUP}
-cat ${SETUP}
-cat ${SETUP} | sh ${RDF4J}/bin/console.sh
+# echo "connect "${RDF4JSERVER}|cat - ${SETUP} > /tmp/out && mv /tmp/out ${SETUP}
+# cat ${SETUP}
+# cat ${SETUP} | sh ${RDF4J}/bin/console.sh
 
 ls -lh $DATA
 
 
 echo "TIME:"
 date
 
-cd $DATA
+cd $DATALOADER
+echo $BLAZEGRAPHSERVER
+
+echo "curl -X POST --data-binary @dataloader.xml --header 'Content-Type:application/xml' http://localhost:9999/blazegraph/dataloader"
+curl POST -v --data-binary @dataloader.xml --header 'Content-Type:application/xml' ${BLAZEGRAPHSERVER}
+
+
 
 # The following for loop writes the load commands into the RDF4J setup script
-for i in *.jsonld.gz; do
-    [ -f "$i" ] || break
-    #arg="load "$DATA/$i" into ns:"$i
-    echo $i
+# for i in *.jsonld.gz; do
+#     [ -f "$i" ] || break
+#     #arg="load "$DATA/$i" into ns:"$i
+#     echo $i
     #awk -v line="$arg" '/open vfb/ { print; print line; next }1' $WS/rdf4j.txt > $WS/tmp.txt
     #cp $WS/tmp.txt $WS/rdf4j.txt
     # URI="%3Chttp%3A%2F%2Fvirtualflybrain.org%2Fdata%2FVFB%2FOWL%2F${i}%3E"
-    echo "curl -v --retry 5 --retry-delay 10 -X POST -H \"Content-type: application/ld+json\" --data-binary @$i ${RDF4JSERVER}/repositories/sssom/statements?context=null"
-    curl -v --retry 5 --retry-delay 10 -X POST -H "Content-type: application/ld+json" --data-binary @$i ${RDF4JSERVER}/repositories/sssom/statements?context=null || exit 1
-    echo "TIME:"
-    date
-    sleep 5
-done
+    # echo "curl -v --retry 5 --retry-delay 10 -X POST -H \"Content-type: application/ld+json\" --data-binary @$i ${RDF4JSERVER}/repositories/sssom/statements?context=null"
+    # echo "curl -X POST --data-binary @dataloader.xml --header 'Content-Type:application/xml' http://localhost:9999/bigdata/dataloader"
+    # curl -v --retry 5 --retry-delay 10 -X POST -H "Content-type: application/ld+json" --data-binary @$i ${RDF4JSERVER}/repositories/sssom/statements?context=null || exit 1
+    # curl -X POST --data-binary @dataloader.xml --header 'Content-Type:application/xml' ${BLAZEGRAPHSERVER}
+    # echo "TIME:"
+    # date
+    # sleep 5
+# done
 
 
 echo "End: upload-triplestore"

diff --git a/pyproject.toml b/pyproject.toml
@@ -11,10 +11,11 @@ python = "^3.9"
 fastapi = "^0.95.0"
 uvicorn = {extras = ["standard"], version = "^0.21.1"}
 pydantic = {extras = ["dotenv"], version = "^1.10.7"}
-oaklib = "0.1.71"
-sssom-schema = "^v0.9.4"
-sssom = "^0.3.26"
+sssom-schema = "^0.15.0"
+sssom = "0.4.10"
 toolz = "^0.12.0"
+pyld = "^2.0.3"
+oaklib = "^0.5.21"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.2.2"

diff --git a/rdf4j_sssom.txt b/rdf4j_sssom.txt