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https://github.com/EBISPOT/OLS

Ontology Lookup Service from SPOT at EBI
https://github.com/EBISPOT/OLS

java neo4j obofoundry owl owl-api

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Ontology Lookup Service from SPOT at EBI

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README 

        
# We are currently developing a new version of OLS. This repository is no longer maintained.



Check out https://github.com/EBISPOT/ols4 for updates on the new version!



---



Legacy 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

* 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/EBISPOT/ontotools-docker-config

* Further OLS documentation can be found here

  http://www.ebi.ac.uk/ols/docs



## Overview



![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.

 

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. If you would like to deploy **the entire OntoTools stack** (OLS, OxO, and ZOOMA), check out the [OntoTools Docker Config](https://github.com/EBISPOT/ontotools-docker-config) repository. If you would like to deploy **OLS only**, read on.



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]` 

 

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.  



## Customisation



It is possible to customise several branding options in `ols-web/src/main/resources/application.properties`:



* `ols.customisation.debrand` — If set to true, removes header and footer, documentation, and about page

* `ols.customisation.ebiInfo` — If set to true, EBI specific banners are enabled

* `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.description` — A description of the instance

* `ols.customisation.org` — The organisation hosting your instance

* `ols.customisation.hideGraphView` — Set to true to hide the graph view 

* `ols.customisation.errorMessage` — Message to show on error pages

* `ols.customisation.ontologyAlias` — A custom word or phrase to use instead of "Ontology", e.g. "Data Dictionary"

* `ols.customisation.ontologyAliasPlural` — As `ontologyAlias` but plural, e.g. "Data Dictionaries"

* `ols.customisation.oxoUrl` — The URL of an OxO instance to link to with a trailing slash e.g. `https://www.ebi.ac.uk/spot/oxo/`