DO NOT MERGE - Just for comparison of latest updates

.dockerignore

@@ -0,0 +1,13 @@
+.git
+.idea
+properties
+OLS_logo_and_family
+*.rtf
+*.iml
+*.md
+!ols-web/src/main/resources/application.properties
+!ols-web/target/ols-boot.war
+!ols-apps/ols-config-importer/target/ols-config-importer.jar
+!ols-apps/ols-loading-app/target/ols-indexer.jar
+!ols-solr/src/main/solr-5-config
+data

.gitignore

@@ -8,4 +8,11 @@ ols-loader/src/test/resources/tmp
 ols-solr/src/main/resources/solr-conf/ontology/data
 ols-mongo/src/main/resources/mongodb
 ols-web/src/main/resources/static/documents/*
-properties
+properties
+.classpath
+.settings
+.project
+*.log
+new_ols.css
+new_ols.css.map
+.factorypath

.gitlab-ci.yml

@@ -0,0 +1,25 @@
+
+build:
+  image: docker:18-git
+  stage: build
+  only:
+    - dev
+    - test
+    - stable
+  services:
+    - docker:18-dind
+  script:
+    - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
+    - docker build -t ${OLS_IMAGE_PREFIX}/ols-config-importer:$CI_COMMIT_REF_NAME-$CI_BUILD_ID -f  ./ols-apps/ols-config-importer/Dockerfile .
+    - docker build -t ${OLS_IMAGE_PREFIX}/ols-indexer:$CI_COMMIT_REF_NAME-$CI_BUILD_ID -f  ./ols-apps/ols-indexer/Dockerfile .
+    - docker build -t ${OLS_IMAGE_PREFIX}/ols-web:$CI_COMMIT_REF_NAME-$CI_BUILD_ID -f  ./ols-web/Dockerfile .
+    - docker tag ${OLS_IMAGE_PREFIX}/ols-config-importer:$CI_COMMIT_REF_NAME-$CI_BUILD_ID ${OLS_IMAGE_PREFIX}/ols-config-importer:$CI_COMMIT_REF_NAME
+    - docker tag ${OLS_IMAGE_PREFIX}/ols-indexer:$CI_COMMIT_REF_NAME-$CI_BUILD_ID ${OLS_IMAGE_PREFIX}/ols-indexer:$CI_COMMIT_REF_NAME
+    - docker tag ${OLS_IMAGE_PREFIX}/ols-web:$CI_COMMIT_REF_NAME-$CI_BUILD_ID ${OLS_IMAGE_PREFIX}/ols-web:$CI_COMMIT_REF_NAME
+    - docker push ${OLS_IMAGE_PREFIX}/ols-config-importer:$CI_COMMIT_REF_NAME-$CI_BUILD_ID
+    - docker push ${OLS_IMAGE_PREFIX}/ols-config-importer:$CI_COMMIT_REF_NAME
+    - docker push ${OLS_IMAGE_PREFIX}/ols-indexer:$CI_COMMIT_REF_NAME-$CI_BUILD_ID
+    - docker push ${OLS_IMAGE_PREFIX}/ols-indexer:$CI_COMMIT_REF_NAME
+    - docker push ${OLS_IMAGE_PREFIX}/ols-web:$CI_COMMIT_REF_NAME-$CI_BUILD_ID
+    - docker push ${OLS_IMAGE_PREFIX}/ols-web:$CI_COMMIT_REF_NAME
+

README.md

@@ -1,27 +1,139 @@
 # OLS
-Ontology Lookup Service from SPOT at EBI. 
+
+Ontology Lookup Service from SPOT at EBI.
 
 * OLS is currently live at the EBI here http://www.ebi.ac.uk/ols
 * A REST API for OLS is described here http://www.ebi.ac.uk/ols/docs/api
-* Instruction on how to build a local OLS installation are here http://www.ebi.ac.uk/ols/docs/installation-guide
-  * Run OLS with docker here https://github.com/MaastrichtUniversity/ols-docker
-* Further OLS documentation can be found here http://www.ebi.ac.uk/ols/docs
+* Instructions on how to build a local OLS installation are here
+  http://www.ebi.ac.uk/ols/docs/installation-guide
+* Run OLS with docker here
+  https://github.com/MaastrichtUniversity/ols-docker
+* Further OLS documentation can be found here
+  http://www.ebi.ac.uk/ols/docs
 
 ## Overview
 
-This is the entire codebase for the EBI OLS. OLS has been developed around two key ontology indexes that can be built and used
- independently from the core website. We provide service to build a SOLR index and and a Neo4j index. The SOLR index is used to provide text based queries over the ontologies while the neo4j index is used to query the ontology structure and is the primary driver of the OLS REST API. 
+![OLS Architecture](OLS-Architecture.png)
+
+This is the entire codebase for the EBI OLS. OLS has been developed
+around two key ontology indexes that can be built and used independently
+from the core website. We provide services to build a Solr index and a
+Neo4j index. The Solr index is used to provide text-based queries over
+the ontologies while the Neo4j index is used to query the ontology
+structure and is the primary driver of the OLS REST API.
+
+OLS has been developed with the Spring Data and Spring Boot framework.
+You can build this project with Maven and the following Spring Boot
+applications will be available to run.
 
- OLS has been developed with the Spring data and Spring boot framework. You can build this project with Maven and the following Spring Boot applications will be available to run. 
+All of the apps are available under the ols-apps module.
+
+* [ols-apps/ols-solr-app](ols-apps/ols-solr-app) - Spring Boot
+  application for building a Solr index for one or more ontologies.
+  Requires access to a Solr server.
+* [ols-apps/ols-neo4j-app](ols-apps/ols-neo4j-app) - Spring Boot
+  application for building a Neo4j index for one or more ontologies.
+  Builds an embedded Neo4j database. You can run a Neo4j server that
+  uses the generated Neo4j database.
+
+To run a complete local OLS installation you will need a MongoDB
+database. This is a lightweight database that is used to store all the
+ontology configuration and application state information. See here for
+more information http://www.ebi.ac.uk/ols/docs/installation-guide
+
+* [ols-apps/ols-config-importer](ols-apps/ols-config-importer) - Spring
+  Boot application for loading config files into the MongoDB database.
+  This includes support for reading config files specified using the OBO
+  Foundry YAML format.
+* [ols-apps/ols-indexer](ols-apps/ols-indexer) - Spring Boot
+  application for building the complete OLS indexes. This app fetches
+  ontologies specified in the config files, checks whether they have
+  changed from a previous download, and if they have changed, will
+  create all the necessary Solr and Neo4j indexes.
+* [ols-web](ols-web) - This contains the WAR file that can be deployed
+  in Tomcat to launch the OLS website and REST API. It depends on
+  [ols-term-type-treeview]
+  (https://github.com/EBISPOT/ols-term-type-treeview) and
+  [ols-tabbed-term-treeview]
+  (https://github.com/EBISPOT/ols-tabbed-term-treeview).
+
+
+## Deploying with Docker
+
+The preferred method of deployment for OLS is using Docker.  First, create the
+necessary volumes:
+
+    docker volume create --name=ols-neo4j-data
+    docker volume create --name=ols-mongo-data
+    docker volume create --name=ols-solr-data
+    docker volume create --name=ols-downloads
+
+Then, start solr and mongodb only:
+
+    docker-compose up -d solr mongo
+
+Then, adjust the configuration YAML files in the `config` directory as required,
+and load the configuration into the Mongo database using the config loader:
+
+    docker run --net=host -v $(pwd)/config:/config ebispot/ols-config-importer:stable
+
+Then, run the indexer:
+
+    docker run --net=host -v ols-neo4j-data:/mnt/neo4j -v ols-downloads:/mnt/downloads ebispot/ols-indexer:stable
+
+Finally, start the OLS webserver:
+
+    docker-compose up -d ols-web
+
+You should now be able to access a populated OLS instance at `http://localhost:8080`.
+
+
+### Building the Docker images manually
+
+Rather than using the images from Docker Hub, the Docker images can also be
+built using the Dockerfiles in this repository.
+
+    docker build -f ols-apps/ols-config-importer/Dockerfile -t ols-config-importer .
+    docker build -f ols-apps/ols-indexer/Dockerfile -t ols-indexer .
+
+
+
+## Building OLS manually
+
+To build OLS you will need to use Java 8 and Maven 3.x.
+
+To build OLS, in the root directory of OLS, run:
+`mvn clean package`. Currently this will fail with the following error:
+
+`[ERROR] Failed to execute goal on project ols-neo4j: Could not resolve dependencies for project uk.ac.ebi.spot:ols-neo4j:jar:3.2.1-SNAPSHOT: Failed to collect dependencies at org.springframework.data:spring-data-neo4j:jar:3.4.5.RELEASE -> org.neo4j:neo4j-cypher-dsl:jar:2.0.1: Failed to read artifact descriptor for org.neo4j:neo4j-cypher-dsl:jar:2.0.1: Could not transfer artifact org.neo4j:neo4j-cypher-dsl:pom:2.0.1 from/to maven-neo4j (https://m2.neo4j.org/content/repositories/releases/): Failed to transfer file https://m2.neo4j.org/content/repositories/releases/org/neo4j/neo4j-cypher-dsl/2.0.1/neo4j-cypher-dsl-2.0.1.pom with status code 502 -> [Help 1]`
+
+To correct this, copy the contents of the `build-fix` directory into your Maven 
+repository under `~/.m2/repository`.
+
+Run `mvn clean package` again. OLS should now build successfully. 
+
+### Other build errors
+Other build errors you may come across are the following:
+
+1. Wrong version of Java used:
+
+`[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (default-compile) on project ols-solr: Compilation failure: Compilation failure: 
+ [ERROR] /Users/james/OLS/ols-solr/src/main/java/uk/ac/ebi/spot/ols/config/SolrContext.java:[15,24] package javax.annotation does not exist
+ [ERROR] /Users/james/OLS/ols-solr/src/main/java/uk/ac/ebi/spot/ols/config/SolrContext.java:[25,4] cannot find symbol
+ [ERROR]  symbol:  class Resource
+ [ERROR]  location: class uk.ac.ebi.spot.ols.config.SolrContext
+ [ERROR] -> [Help 1]` 
 
-All of the apps are available under the ols-apps module. 
+This is the error you get when you compile OLS with Java 11. The fix for this 
+build error is to ensure your Maven installation is indeed using Java 8 for 
+compilation.  
 
- * [ols-apps/ols-solr-app](ols-apps/ols-solr-app) - Spring boot application for building a SOLR index for one of more ontologies. Requires access to a SOLR server. 
- * [ols-apps/ols-neo4j-app](ols-apps/ols-neo4j-app) - Spring boot application for building a Neo4j index for one of more ontologies. Builds an embedded neo4j database. You can run a Neo4j server that uses the generated neo4j database. 
+## Customisation
 
-To run a complete local OLS installation you will need a mongodb database. This is a lightweight database that used to store all the ontology configuration and application state information. See here for more information http://www.ebi.ac.uk/ols/docs/installation-guide 
+It is possible to customise several branding options in `ols-web/src/main/resources/application.properties`:
 
- * [ols-apps/ols-config-importer](ols-apps/ols-config-importer) - Spring boot application for loading config files into the mongodb database. This includes support for reading config files specified using the OBO foundry YAML format. 
- * [ols-apps/ols-loading-app](ols-apps/ols-loading-app) - Spring boot application for that build the complete OLS indexes. This app fetches ontologies specified in the config files, checks if they have changed form a previous download, and if hey have changed it will create all the necessary SOLR and Neo4j indexes. 
+* `ols.customisation.debrand` — If set to true, removes the EBI header and footer, documentation, and about page
+* `ols.customisation.title` — A custom title for your instance, e.g. "My OLS Instance"
+* `ols.customisation.short-title` — A shorter version of the custom title, e.g. "MYOLS"
+* `ols.customisation.org` — The organisation hosting your instance
 
- * [ols-web](ols-web) - This will contain the WAR file that can be deployed in tomcat to launch the OLS website and REST API. 

RELEASE_NOTES.md

@@ -1,3 +1,6 @@
+See https://github.com/EBISPOT/ols/releases for latest releases and notes. 
+
+
 --------------------------------
 OLS 3.1.0 release notes
 --------------------------------

build-fix/org/neo4j/neo4j-cypher-dsl/2.0.1/_remote.repositories

@@ -0,0 +1,4 @@
+#NOTE: This is a Maven Resolver internal implementation file, its format can be changed without prior notice.
+#Fri Jan 17 16:17:27 GMT 2020
+neo4j-cypher-dsl-2.0.1.pom>maven-neo4j=
+neo4j-cypher-dsl-2.0.1.jar>maven-neo4j=

build-fix/org/neo4j/neo4j-cypher-dsl/2.0.1/neo4j-cypher-dsl-2.0.1.jar.sha1

@@ -0,0 +1 @@
+519d317979935773646356ee2f7923090f7d53e8