Merge pull request #42 from InformaticsMatters/issue38_update_keycloak

#38 update keycloak and fix search container to use rdkit correctly

Author: alanbchristie

README.md

@@ -26,6 +26,7 @@ For more information see:
 
 * [Talk at 2018 RDKit UGM](https://github.com/rdkit/UGM_2018/blob/master/Lightning/tim_dudgeon_fragment-network.pdf).
 * [Informatics Matters website](https://www.informaticsmatters.com/pages/fragment_network.html)
+* [Fragnet Search application](https://fragnet.informaticsmatters.com/)
 
 ## Building (CI)
 The project containers are built automatically using GitHub Actions
@@ -45,9 +46,9 @@ web app.
 Test the container using the [docker-compose.yml](docker-compose.yml)
 file:
 
-    docker-compose -f docker-compose-test.yml up
+    docker-compose up
 
-This uses a sample Neo4j database with a small amount of data.
+This uses a sample Neo4j database with a small amount of data. It takes a short time to initialise.
 
 ## Official deployments
 Official deployments (to Kubernetes) use AWX and our [fragnet-ansible]

docker-compose.yml

@@ -25,8 +25,8 @@ services:
   # This container runs the REST API that queries the test database.
   # Some useful queries are:
   # export FRAGNET_SERVER=http://localhost
-  # curl $FRAGNET_SERVER:8080/fragnet-search/rest/v2/search/suppliers
   # curl $FRAGNET_SERVER:8080/fragnet-search/rest/ping
+  # curl $FRAGNET_SERVER:8080/fragnet-search/rest/v2/search/suppliers
   # curl "$FRAGNET_SERVER:8080/fragnet-search/rest/v2/search/neighbourhood/OC(Cn1ccnn1)C1CC1?hac=3&rac=1&hops=2"
   # curl "$FRAGNET_SERVER:8080/fragnet-search/rest/v2/search/availability/OC(Cn1ccnn1)C1CC1"
   # curl "$FRAGNET_SERVER:8080/fragnet-search/rest/v2/search/expand/OC(Cn1ccnn1)C1CC1?hacMin=5&hacMax=10&racMin=3&racMax=3&hops=2"

fragnet-search/build.gradle

@@ -118,30 +118,27 @@ test {
 tasks.test.dependsOn("startNeoContainer")
 tasks.test.finalizedBy("stopNeoContainer")
 
-task copyKeycloakJars(type: Copy) {
-    from "../lib/keycloak-2.1.0-jars-tomcat8"
-    into "build/libs/keycloak-2.1.0-jars-tomcat8/"
-    include "*.jar"
-}
 
 task buildDockerFile(type: Dockerfile) {
 
     dependsOn = [
-            war,
-            copyKeycloakJars
+            war
     ]
 
     destFile = project.file('build/Dockerfile')
     from "informaticsmatters/rdkit-tomcat-debian:Release_2019_09"
     label(['maintainer': 'Tim Dudgeon "[email protected]"'])
 
     // include the keycloak adapters
-    runCommand('''mkdir keycloak && cd keycloak && curl -s -o keycloak.tar.gz\
- https://downloads.jboss.org/keycloak/3.4.3.Final/adapters/keycloak-oidc/keycloak-tomcat8-adapter-dist-3.4.3.Final.tar.gz &&\
+    runCommand('''mkdir keycloak &&\
+ cd keycloak &&\
+ curl -s -o keycloak.tar.gz\
+ https://downloads.jboss.org/keycloak/10.0.2/adapters/keycloak-oidc/keycloak-tomcat-adapter-dist-10.0.2.tar.gz &&\
  tar xfz keycloak.tar.gz &&\
  rm keycloak.tar.gz &&\
  mv *.jar $CATALINA_HOME/lib &&\
- cd $CATALINA_HOME && rm -rf keycloak''')
+ cd $CATALINA_HOME &&\
+ rm -rf keycloak''')
 
     addFile('./libs/fragnet-search*.war', "/usr/local/tomcat/webapps/")
     // need to unpack the zip as we need to mess with the keycloak related jars