Merge branch '2.x-dev'

.dockerignore

@@ -0,0 +1,2 @@
+Dockerfile
+docker.Makefile

.gitlab-ci.yml

@@ -0,0 +1,16 @@
+
+build:
+  image: docker:18-git
+  stage: build
+  only:
+    - main
+    - stable
+  services:
+    - docker:18-dind
+  script:
+    - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
+    - docker build -t ${ZOOMA_IMAGE_PREFIX}/zooma:$CI_COMMIT_REF_NAME-$CI_BUILD_ID .
+    - docker tag ${ZOOMA_IMAGE_PREFIX}/zooma:$CI_COMMIT_REF_NAME-$CI_BUILD_ID ${ZOOMA_IMAGE_PREFIX}/zooma:$CI_COMMIT_REF_NAME
+    - docker push ${ZOOMA_IMAGE_PREFIX}/zooma:$CI_COMMIT_REF_NAME-$CI_BUILD_ID
+    - docker push ${ZOOMA_IMAGE_PREFIX}/zooma:$CI_COMMIT_REF_NAME
+

Dockerfile

@@ -0,0 +1,41 @@
+FROM tomcat:9-jdk8-openjdk
+
+# ENV ZOOMA_HOME=/opt/zooma cant set this because hard coded in build-virtuoso-index.sh 
+ENV ZOOMA_OPTS="-Xms1g -Xmx4g"
+
+RUN mkdir /opt/zooma_github /opt/zooma
+RUN apt-get update && apt-get install -y nano maven
+COPY . /opt/zooma_github/
+ENV OJDBC6="https://www.oracle.com/webapps/redirect/signon?nexturl=https://download.oracle.com/otn/utilities_drivers/jdbc/11204/ojdbc6.jar"
+RUN wget $OJDBC6 -O /lib/ojdbc6.jar \
+    && mvn install:install-file -DgroupId=com.oracle -DartifactId=ojdbc6 -Dpackaging=jar -Dversion=11.2.0.4 -Dfile=/lib/ojdbc6.jar \
+    && test /root/.m2/repository/com/oracle/ojdbc6/11.2.0.4/ojdbc6-11.2.0.4.jar
+RUN cd /opt/zooma_github && mvn clean package
+RUN mkdir /opt/tmp && unzip /opt/zooma_github/zooma-builder-app/target/zooma-builder.zip -d /opt/tmp
+RUN cp /opt/zooma_github/zooma-ui/target/zooma.war /usr/local/tomcat/webapps/
+
+ENV VIRTUOSO_VERSION="7.2.5"
+ENV VIRTUOSO_HOME=/opt/virtuoso/virtuoso-opensource
+ENV VIRTUOSO="https://downloads.sourceforge.net/project/virtuoso/virtuoso/${VIRTUOSO_VERSION}/virtuoso-opensource.x86_64-generic_glibc25-linux-gnu.tar.gz"
+# ?r=&ts=1597420967
+RUN mkdir /opt/virtuoso && wget $VIRTUOSO -O /opt/virtuoso/virtuoso-${VIRTUOSO_VERSION}.tar.gz \
+    && tar -xzvf /opt/virtuoso/virtuoso-${VIRTUOSO_VERSION}.tar.gz -C /opt/virtuoso
+
+RUN sed -i 's@base=\${0%\/[*]}/..;@base=..;@g' /opt/tmp/bin/build-labels.sh
+RUN sed -i 's@base=\${0%\/[*]}/..;@base=..;@g' /opt/tmp/bin/build-lucene-index.sh
+RUN sed -i 's@base=\${0%\/[*]};@base=.;@g' /opt/tmp/bin/build-virtuoso-index.sh 
+RUN sed -i 's@base=\${0%\/[*]}/..;@base=..;@g' /opt/tmp/bin/build-rdf.sh
+
+# ERROR: $ZOOMA_DATA_DIR not set - using /root/.zooma/data (build-virtuoso-index.sh )
+ENV ZOOMA_HOME=/root/.zooma
+RUN ls -a /root/
+RUN cp /opt/zooma_github/startup.sh /root/startup.sh
+# The following is a bit of a hack to initialise the zooma directories
+RUN startup.sh && sleep 20 && shutdown.sh 
+
+# Overwriting server.xml is necessary only because of we had to add relaxedQueryChars='^{}[]|"' to the main connector
+COPY server.xml /usr/local/tomcat/conf/server.xml
+#RUN mkdir $ZOOMA_HOME $ZOOMA_HOME/config
+EXPOSE 8080
+CMD ["bash","/root/startup.sh"]
+#CMD ["catalina.sh","run"]

README.md

@@ -2,15 +2,34 @@
 
 ZOOMA is an application for discovering optimal ontology mappings, developed by the Samples, Phenotypes and Ontologies Team at [EMBL-EBI](http://www.ebi.ac.uk). It can be used to automatically annotate "properties" (plain text, descriptive values about biological entities) with "semantic tags" (ontology classes).
 
-## Links
+* ZOOMA is currently live at the EBI here http://www.ebi.ac.uk/spot/zooma
+* ZOOMA documentation can be found here http://www.ebi.ac.uk/spot/zooma/docs
 
-### ZOOMA homepage
+## Deploying with Docker
 
-http://www.ebi.ac.uk/spot/zooma
+The preferred method of deployment for ZOOMA is using Docker.  First, create the
+necessary volumes:
 
-### ZOOMA documentation
+    docker volume create --name=zooma-config
 
-http://www.ebi.ac.uk/spot/zooma/docs
+Then, start ZOOMA:
+
+    docker run -d --name zooma -p 8009:8080 -v zooma-config:/root/.zooma/config ebispot/zooma:latest
+
+You should now be able to access ZOOMA at `http://localhost:8080`.
+
+To configure ZOOMA, first stop the docker container:
+
+    docker stop zooma
+
+The configuration files will be located in the zooma-config volume on your filesystem. For Ubuntu, this will be located at `/var/lib/docker/volumes/zooma-config/_data`.
+
+Once configured, start ZOOMA again:
+
+    docker start zooma
+
+
+## Building ZOOMA manually
 
 ### Dependencies
 1. Java - Tested on Oracle JDK version 1.8

server.xml

@@ -0,0 +1,171 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+  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.
+-->
+<!-- Note:  A "Server" is not itself a "Container", so you may not
+     define subcomponents such as "Valves" at this level.
+     Documentation at /docs/config/server.html
+ -->
+<Server port="8005" shutdown="SHUTDOWN">
+  <Listener className="org.apache.catalina.startup.VersionLoggerListener" />
+  <!-- Security listener. Documentation at /docs/config/listeners.html
+  <Listener className="org.apache.catalina.security.SecurityListener" />
+  -->
+  <!--APR library loader. Documentation at /docs/apr.html -->
+  <Listener className="org.apache.catalina.core.AprLifecycleListener" SSLEngine="on" />
+  <!-- Prevent memory leaks due to use of particular java/javax APIs-->
+  <Listener className="org.apache.catalina.core.JreMemoryLeakPreventionListener" />
+  <Listener className="org.apache.catalina.mbeans.GlobalResourcesLifecycleListener" />
+  <Listener className="org.apache.catalina.core.ThreadLocalLeakPreventionListener" />
+
+  <!-- Global JNDI resources
+       Documentation at /docs/jndi-resources-howto.html
+  -->
+  <GlobalNamingResources>
+    <!-- Editable user database that can also be used by
+         UserDatabaseRealm to authenticate users
+    -->
+    <Resource name="UserDatabase" auth="Container"
+              type="org.apache.catalina.UserDatabase"
+              description="User database that can be updated and saved"
+              factory="org.apache.catalina.users.MemoryUserDatabaseFactory"
+              pathname="conf/tomcat-users.xml" />
+  </GlobalNamingResources>
+
+  <!-- A "Service" is a collection of one or more "Connectors" that share
+       a single "Container" Note:  A "Service" is not itself a "Container",
+       so you may not define subcomponents such as "Valves" at this level.
+       Documentation at /docs/config/service.html
+   -->
+  <Service name="Catalina">
+
+    <!--The connectors can use a shared executor, you can define one or more named thread pools-->
+    <!--
+    <Executor name="tomcatThreadPool" namePrefix="catalina-exec-"
+        maxThreads="150" minSpareThreads="4"/>
+    -->
+
+
+    <!-- A "Connector" represents an endpoint by which requests are received
+         and responses are returned. Documentation at :
+         Java HTTP Connector: /docs/config/http.html
+         Java AJP  Connector: /docs/config/ajp.html
+         APR (HTTP/AJP) Connector: /docs/apr.html
+         Define a non-SSL/TLS HTTP/1.1 Connector on port 8080
+    -->
+    <Connector port="8080" protocol="HTTP/1.1"
+               connectionTimeout="20000"
+               redirectPort="8443" relaxedQueryChars='^{}[]|&quot;' />
+    <!-- A "Connector" using the shared thread pool-->
+    <!--
+    <Connector executor="tomcatThreadPool"
+               port="8080" protocol="HTTP/1.1"
+               connectionTimeout="20000"
+               redirectPort="8443" />
+    -->
+    <!-- Define an SSL/TLS HTTP/1.1 Connector on port 8443
+         This connector uses the NIO implementation. The default
+         SSLImplementation will depend on the presence of the APR/native
+         library and the useOpenSSL attribute of the
+         AprLifecycleListener.
+         Either JSSE or OpenSSL style configuration may be used regardless of
+         the SSLImplementation selected. JSSE style configuration is used below.
+    -->
+    <!--
+    <Connector port="8443" protocol="org.apache.coyote.http11.Http11NioProtocol"
+               maxThreads="150" SSLEnabled="true">
+        <SSLHostConfig>
+            <Certificate certificateKeystoreFile="conf/localhost-rsa.jks"
+                         type="RSA" />
+        </SSLHostConfig>
+    </Connector>
+    -->
+    <!-- Define an SSL/TLS HTTP/1.1 Connector on port 8443 with HTTP/2
+         This connector uses the APR/native implementation which always uses
+         OpenSSL for TLS.
+         Either JSSE or OpenSSL style configuration may be used. OpenSSL style
+         configuration is used below.
+    -->
+    <!--
+    <Connector port="8443" protocol="org.apache.coyote.http11.Http11AprProtocol"
+               maxThreads="150" SSLEnabled="true" >
+        <UpgradeProtocol className="org.apache.coyote.http2.Http2Protocol" />
+        <SSLHostConfig>
+            <Certificate certificateKeyFile="conf/localhost-rsa-key.pem"
+                         certificateFile="conf/localhost-rsa-cert.pem"
+                         certificateChainFile="conf/localhost-rsa-chain.pem"
+                         type="RSA" />
+        </SSLHostConfig>
+    </Connector>
+    -->
+
+    <!-- Define an AJP 1.3 Connector on port 8009 -->
+    <!--
+    <Connector protocol="AJP/1.3"
+               address="::1"
+               port="8009"
+               redirectPort="8443" />
+    -->
+
+    <!-- An Engine represents the entry point (within Catalina) that processes
+         every request.  The Engine implementation for Tomcat stand alone
+         analyzes the HTTP headers included with the request, and passes them
+         on to the appropriate Host (virtual host).
+         Documentation at /docs/config/engine.html -->
+
+    <!-- You should set jvmRoute to support load-balancing via AJP ie :
+    <Engine name="Catalina" defaultHost="localhost" jvmRoute="jvm1">
+    -->
+    <Engine name="Catalina" defaultHost="localhost">
+
+      <!--For clustering, please take a look at documentation at:
+          /docs/cluster-howto.html  (simple how to)
+          /docs/config/cluster.html (reference documentation) -->
+      <!--
+      <Cluster className="org.apache.catalina.ha.tcp.SimpleTcpCluster"/>
+      -->
+
+      <!-- Use the LockOutRealm to prevent attempts to guess user passwords
+           via a brute-force attack -->
+      <Realm className="org.apache.catalina.realm.LockOutRealm">
+        <!-- This Realm uses the UserDatabase configured in the global JNDI
+             resources under the key "UserDatabase".  Any edits
+             that are performed against this UserDatabase are immediately
+             available for use by the Realm.  -->
+        <Realm className="org.apache.catalina.realm.UserDatabaseRealm"
+               resourceName="UserDatabase"/>
+      </Realm>
+
+      <Host name="localhost"  appBase="webapps"
+            unpackWARs="true" autoDeploy="true">
+
+        <!-- SingleSignOn valve, share authentication between web applications
+             Documentation at: /docs/config/valve.html -->
+        <!--
+        <Valve className="org.apache.catalina.authenticator.SingleSignOn" />
+        -->
+
+        <!-- Access log processes all example.
+             Documentation at: /docs/config/valve.html
+             Note: The pattern used is equivalent to using pattern="common" -->
+        <Valve className="org.apache.catalina.valves.AccessLogValve" directory="logs"
+               prefix="localhost_access_log" suffix=".txt"
+               pattern="%h %l %u %t &quot;%r&quot; %s %b" />
+
+      </Host>
+    </Engine>
+  </Service>
+</Server>

startup.sh

@@ -0,0 +1,14 @@
+set -e
+
+echo "Data dir:"
+ls $ZOOMA_DATA_DIR
+
+SCRIPT_DIR=/opt/tmp/bin/
+cd $SCRIPT_DIR
+bash build-rdf.sh
+bash build-virtuoso-index.sh
+bash virtuoso-start.sh
+bash build-labels.sh
+bash build-lucene-index.sh
+
+catalina.sh run

zooma-builder-app/src/main/java/uk/ac/ebi/fgpt/zooma/ZOOMA2BackingUpDriver.java

@@ -37,29 +37,28 @@ protected void backupFiles(Path path, Path backupPath, PrintStream out) throws I
         if (!Files.exists(backupPath)) {
             out.print(
                     "Backing up " + path.toString() + " to " + backupPath.toString() + "...");
-            Files.move(path,
+            Files.copy(path,
                        backupPath,
-                       StandardCopyOption.REPLACE_EXISTING,
-                       StandardCopyOption.ATOMIC_MOVE);
+                       StandardCopyOption.REPLACE_EXISTING);
             out.println("ok!");
         }
         else {
             out.print(
                     "Backup already exists for today, clearing " + path.toString() + "...");
-            Files.walkFileTree(path, new SimpleFileVisitor<Path>() {
-                @Override
-                public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
-                    Files.delete(file);
-                    return FileVisitResult.CONTINUE;
-                }
-
-                @Override
-                public FileVisitResult postVisitDirectory(Path dir, IOException exc) throws IOException {
-                    Files.delete(dir);
-                    return FileVisitResult.CONTINUE;
-                }
-            });
-            out.println("ok!");
         }
+        Files.walkFileTree(path, new SimpleFileVisitor<Path>() {
+            @Override
+            public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
+                Files.delete(file);
+                return FileVisitResult.CONTINUE;
+            }
+
+            @Override
+            public FileVisitResult postVisitDirectory(Path dir, IOException exc) throws IOException {
+                Files.delete(dir);
+                return FileVisitResult.CONTINUE;
+            }
+        });
+        out.println("ok!");
     }
 }