Merge branch 'uce-biofid-demo-12/24' into develop

.gitignore

@@ -48,4 +48,4 @@ build/
 /rag/env
 /rag/src/cBERT/data
 /rag/src/cBERT/models
-__pycache__
+__pycache__

database/createGinIndexes.sql

@@ -1,3 +1,6 @@
+CREATE EXTENSION IF NOT EXISTS pg_trgm;
+CREATE EXTENSION IF NOT EXISTS btree_gin;
+
 -- Some standard indexes on title and such
 CREATE INDEX IF NOT EXISTS idx_metadatatitleinfo_title ON metadatatitleinfo (title);
 CREATE INDEX IF NOT EXISTS idx_metadatatitleinfo_published ON metadatatitleinfo (published);

docker-compose.yaml

@@ -1,6 +1,22 @@
 # version: '3.8'
 
 services:
+
+  uce-fuseki-sparql:
+    build:
+      context: ./sparql
+      dockerfile: ./Dockerfile
+      args:
+        JENA_VERSION: 5.2.0
+    image: fuseki
+    ports:
+      - "8030:5430"
+    volumes:
+      - ./../sparql/run/databases/biofid-search:/fuseki/databases/biofid-search
+    command: --update --tdb2 --port 5430 --loc /fuseki/databases/biofid-search /biofid-search
+    networks:
+      - app_net
+
   uce-rag-service:
     build:
       context: .
@@ -9,6 +25,8 @@ services:
       - "8080:5678" 
     depends_on:
       - uce-postgresql-db 
+    networks:
+      - app_net
 
   uce-web:
     build:
@@ -18,17 +36,26 @@ services:
       - "8008:4567"
     depends_on:
       - uce-postgresql-db
+    networks:
+      - app_net
+    volumes:
+      - "./../releases/uceConfig.json:/app/config/uceConfig.json"
+    command: ["java", "-jar", "./target/webportal-jar-with-dependencies.jar", "-cf", "/app/config/uceConfig.json"]
 
   uce-postgresql-db:
     image: pgvector/pgvector:pg16
     environment:
-      POSTGRES_DB: uce-gerparcor
+      POSTGRES_DB: uce
       POSTGRES_USER: postgres
       POSTGRES_PASSWORD: 1234 
     ports:
       - "8002:5432"
-    #volumes:
-    #  - pgdata:/var/lib/uce-gerparcor-eval/data 
+    networks:
+      - app_net
+
+networks:
+  app_net:
+    driver: bridge
 
 volumes:
   pgdata:

rag/src/webserver.py

@@ -284,6 +284,10 @@ def rag_complete():
         print(ex)
     return jsonify(result)
 
+@app.route('/', methods=['GET'])
+def hello():
+    return 'RAGServer running.'
+
 def get_embedding_model():
     '''Gets the embedding model from the app's cache'''
     if 'embedding_model' not in current_app.config:

sparql/Dockerfile

@@ -0,0 +1,124 @@
+## Licensed to the Apache Software Foundation (ASF) under one or more
+## contributor license agreements.  See the NOTICE file distributed with
+## this work for additional information regarding copyright ownership.
+## The ASF licenses this file to You under the Apache License, Version 2.0
+## (the "License"); you may not use this file except in compliance with
+## the License.  You may obtain a copy of the License at
+##
+##     http://www.apache.org/licenses/LICENSE-2.0
+##
+## Unless required by applicable law or agreed to in writing, software
+## distributed under the License is distributed on an "AS IS" BASIS,
+## WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+## See the License for the specific language governing permissions and
+## limitations under the License.
+
+## Apache Jena Fuseki server Dockerfile.
+
+## This Dockefile builds a reduced footprint container.
+
+ARG JAVA_VERSION=21
+
+ARG ALPINE_VERSION=3.20.3
+ARG JENA_VERSION=""
+
+# Internal, passed between stages.
+ARG FUSEKI_DIR=/fuseki
+ARG FUSEKI_JAR=jena-fuseki-server-${JENA_VERSION}.jar
+ARG JAVA_MINIMAL=/opt/java-minimal
+
+## ---- Stage: Download and build java.
+FROM eclipse-temurin:${JAVA_VERSION}-alpine AS base
+
+ARG JAVA_MINIMAL
+ARG JENA_VERSION
+ARG FUSEKI_DIR
+ARG FUSEKI_JAR
+ARG REPO=https://repo1.maven.org/maven2
+ARG JAR_URL=${REPO}/org/apache/jena/jena-fuseki-server/${JENA_VERSION}/${FUSEKI_JAR}
+
+RUN [ "${JENA_VERSION}" != "" ] || { echo -e '\n**** Set JENA_VERSION ****\n' ; exit 1 ; }
+RUN echo && echo "==== Docker build for Apache Jena Fuseki ${JENA_VERSION} ====" && echo
+
+# Alpine: For objcopy used in jlink
+RUN apk add --no-cache curl binutils
+
+## -- Fuseki installed and runs in /fuseki.
+WORKDIR $FUSEKI_DIR
+
+## -- Download the jar file.
+COPY download.sh .
+RUN chmod a+x download.sh
+
+# Download, with check of the SHA1 checksum.
+RUN ./download.sh --chksum sha1 "$JAR_URL"
+
+## -- Alternatives to download : copy already downloaded.
+## COPY ${FUSEKI_JAR} .
+
+## Use Docker ADD - does not retry, does not check checksum, and may run every build.
+## ADD "$JAR_URL"
+
+## -- Make reduced Java JDK
+
+ARG JDEPS_EXTRA="jdk.crypto.cryptoki,jdk.crypto.ec"
+RUN \
+  JDEPS="$(jdeps --multi-release base --print-module-deps --ignore-missing-deps ${FUSEKI_JAR})"  && \
+  jlink \
+        --compress 2 --strip-debug --no-header-files --no-man-pages \
+        --output "${JAVA_MINIMAL}" \
+        --add-modules "${JDEPS},${JDEPS_EXTRA}"
+
+ADD entrypoint.sh .
+ADD log4j2.properties .
+
+## ---- Stage: Build runtime
+FROM alpine:${ALPINE_VERSION}
+
+## Import ARGs
+ARG JENA_VERSION
+ARG JAVA_MINIMAL
+ARG FUSEKI_DIR
+ARG FUSEKI_JAR
+
+COPY --from=base /opt/java-minimal /opt/java-minimal
+COPY --from=base /fuseki /fuseki
+
+WORKDIR $FUSEKI_DIR
+
+ARG LOGS=${FUSEKI_DIR}/logs
+ARG DATA=${FUSEKI_DIR}/databases
+
+ARG JENA_USER=fuseki
+ARG JENA_GROUP=$JENA_USER
+ARG JENA_GID=1000
+ARG JENA_UID=1000
+
+# Run as this user
+# -H : no home directory
+# -D : no password
+RUN addgroup -g "${JENA_GID}" "${JENA_GROUP}" && \
+    adduser "${JENA_USER}" -G "${JENA_GROUP}" -s /bin/ash -u "${JENA_UID}" -H -D
+
+RUN mkdir --parents "${FUSEKI_DIR}" && \
+    chown -R $JENA_USER ${FUSEKI_DIR}
+
+USER $JENA_USER
+
+RUN \
+    mkdir -p $LOGS && \
+    mkdir -p $DATA && \
+    chmod a+x entrypoint.sh
+
+## Default environment variables.
+ENV \
+    JAVA_HOME=${JAVA_MINIMAL}           \
+    JAVA_OPTIONS="-Xmx2048m -Xms2048m"  \
+    JENA_VERSION=${JENA_VERSION}        \
+    FUSEKI_JAR="${FUSEKI_JAR}"          \
+    FUSEKI_DIR="${FUSEKI_DIR}"
+
+EXPOSE 5430
+
+ENTRYPOINT ["./entrypoint.sh" ]
+CMD []