Update web-and-data dockerfile for core module removal

docker/web-and-data/Dockerfile

@@ -18,11 +18,7 @@ COPY pom.xml                                        /cbioportal/
 COPY version.sh                                     /cbioportal/
 WORKDIR /cbioportal
 
-# Download and explore core jar
-RUN wget https://github.com/cBioPortal/cbioportal-core/releases/download/1.0.1/core-1.0.1.jar -P cbioportal-core/
-RUN cd cbioportal-core; jar -xf core-1.0.1.jar
-
-RUN for subproject in */.; do cp version.sh "$subproject"; cd "$subproject"; mvn dependency:go-offline --fail-never; cd ..; done
+# RUN for subproject in */.; do cp version.sh "$subproject"; cd "$subproject"; mvn dependency:go-offline --fail-never; cd ..; done
 
 RUN mvn dependency:go-offline --fail-never
 
@@ -47,17 +43,24 @@ RUN apt-get update; apt-get install -y --no-install-recommends \
 
 # copy over core files and data-related scripts
 RUN mkdir -p /cbioportal
-COPY --from=build /cbioportal-core /cbioportal/core
-COPY --from=build /cbioportal-core/scripts /cbioportal/scripts
-COPY --from=build /cbioportal/db-scripts /cbioportal/db-scripts
+
+#Download core files
+RUN wget https://github.com/cBioPortal/cbioportal-core/releases/download/1.0.1/core-1.0.1.jar -P core/
+RUN cd core; jar -xf core-1.0.1.jar; cd ..;
+
+
+
+#COPY --from=build /cbioportal/core /cbioportal/core
+#COPY --from=build /cbioportal/scripts /cbioportal/scripts
+COPY --from=build /cbioportal/src/main/resources/db-scripts /cbioportal/db-scripts
 COPY --from=build /cbioportal/requirements.txt /cbioportal/requirements.txt
 
 # install build and runtime dependencies
 # ignore update failure980[1298[01 w2308s
 RUN  pip3 install -r /cbioportal/requirements.txt
 
 # add importer scripts to PATH for easy running in containers
-RUN find /cbioportal/core/src/main/scripts/ -type f -executable \! -name '*.pl'  -print0 | xargs -0 -- ln -st /usr/local/bin
+RUN find /core/scripts/ -type f -name '*.pl' -print0 | xargs -0 -- ln -st /usr/local/bin
 
 # put config files in this folder if you want to override config
 ENV PORTAL_WEB_HOME=/cbioportal-webapp
@@ -67,13 +70,13 @@ ENV WEBAPP_OPTS=
 
 # add exploded Spring Boot jar contents to image
 # See: https://spring.io/guides/topicals/spring-boot-docker/
-ARG DEPENDENCY=/cbioportal/target/dependency
+ARG DEPENDENCY=/cbioportal/target/
 RUN mkdir -p $PORTAL_WEB_HOME
-COPY --from=build ${DEPENDENCY}/BOOT-INF/lib        $PORTAL_WEB_HOME/lib/
-COPY --from=build ${DEPENDENCY}/META-INF            $PORTAL_WEB_HOME/META-INF/
-COPY --from=build ${DEPENDENCY}/BOOT-INF/classes    $PORTAL_WEB_HOME/
+# COPY --from=build ${DEPENDENCY}/BOOT-INF/lib        $PORTAL_WEB_HOME/lib/
+#COPY --from=build ${DEPENDENCY}/classes/META-INF            $PORTAL_WEB_HOME/META-INF/
+COPY --from=build ${DEPENDENCY}/classes    $PORTAL_WEB_HOME/
 
 # add entrypoint
 COPY --from=build /cbioportal/docker/web-and-data/docker-entrypoint.sh /usr/local/bin/
 ENTRYPOINT ["docker-entrypoint.sh"]
-CMD ["sh", "-c", "java $(echo $JAVA_OPTS) -cp /cbioportal-webapp:/cbioportal-webapp/lib/* org.cbioportal.PortalApplication $(echo $WEBAPP_OPTS)"]
+CMD ["sh", "-c", "java $(echo $JAVA_OPTS) -cp /cbioportal-webapp:/cbioportal-webapp/lib/* org.cbioportal.PortalApplication $(echo $WEBAPP_OPTS)"]