WebProtégé (with an export feature for Neo4J)

PLEASE NOTE

This webprotege clone is an adaption for ONTIS

This readme has been adapted for this project.

What is WebProtégé?

WebProtégé is a free, open source collaborative ontology development environment.

It provides the following features:

• Support for editing OWL 2 ontologies
• A default simple editing interface, which provides access to commonly used OWL constructs
• Full change tracking and revision history
• Collaboration tools such as, sharing and permissions, threaded notes and discussions, watches and email notifications
• Customizable user interface
• Support for editing OBO ontologies
• Multiple file formats for upload and download of ontologies (supported formats: RDF/XML, Turtle, OWL/XML, OBO, and others)

WebProtégé runs as a Web application. End users access it through their Web browsers. They do not need to download or install any software. We encourage end-users to use

https://webprotege.stanford.edu

If you have downloaded the webprotege war file from GitHub, and would like to deploy it on your own server, please follow the instructions at:

https://github.com/protegeproject/webprotege/wiki/WebProtégé-4.0.0-beta-x-Installation

Build a Docker image for WebProtégé

Minimal Requirements: 8GB RAM, ~15GB free disk space, Docker v20

1. Clone the repository

   git clone https://github.com/woschmid/webprotege-export-neo4j.git
   

2. Change into the cloned folder webprotege-export-neo4j where you will find the Dockerfile.

   cd webprotege-export-neo4j
   

3. The next command creates a local docker image named webprotege-export-neo4j which then can be used to run from Docker (next section). Note: the building process requires 10 - 30 minutes!

   docker build -t webprotege-export-neo4j --build-arg WEBPROTEGE_VERSION=5.0.0-SNAPSHOT .

By default, the host for webprotege is named webprotege and the host for neo4j is named neo4j (defined in the docker-compose.yml and in edu.stanford.bmir.protege.web.server.export.ProjectExportService.java)

Run WebProtégé from Docker

Requirement: A local Docker image named webprotege-export-neo4j exists (see the previous section).

Start WebProtégé, Neo4j, MongoDB, Kafka and Zookeeper:

1. Open a terminal and change into in the root directory of your cloned webprotege-export-neo4j folder in the directory where docker-compose.yml is if not already done.

   cd webprotege-export-neo4j
   

Note: The volume folders .kafka, .neo4j and .protegedata will be created in the current directory. These folders will have root:root file permissions in Linux!

Note: If you deploy on a public host where Kafka shall be accessed from outside, adapt the KAFKA_CFG_ADVERTISED_LISTENERS environment variable according to the comment in docker-compose.yml

2. Enter the following command in the terminal to start the docker container in the background

   docker-compose up -d

3. Check if all containers are running with

   docker stats

   (exit with CTRL+C)

   Note These 5 containers are expected to be running: webprotege, neo4j, webprotege-mongodb, kafka, zookeeper. If one container is not running you can search for error messages in the logs of the container with

   docker logs <containername>

4. Only necessary once: In WebProtege we need to create an admin account with:

   docker exec -it webprotege java -jar /webprotege-cli.jar create-admin-account

   Follow the questions prompted to provide username, email, password.

5. Only necessary once: Next, we must define the settings for WebProtégé

   Browse to the WebProtégé Settings page in a Web browser by navigating to http://localhost:5000/#application/settings (replace localhost with a servername if necessary)

   1. Login with the admin account
   2. Define the System notification email address and application host URL
   3. Enable User creation, Project creation and Project import
   4. Reload the browser and log out
   5. Now you should be able to "Sign up for account" on the top right of http://localhost:5000 to create a standard user account. Note Sign up account creation can be disabled with the admin account (see above).

6. Login into WebProtege at http://localhost:5000/ and login with a standard user to upload and export your ontology.

7. You can open the Neo4j Browser at http://localhost:7474/ and login with neo4j/test

Stop WebProtégé, Neo4j, MongoDB, Kafka and Zookeeper:

docker-compose down

Additional infos

Sharing the volumes used by the WebProtégé app and MongoDB allow to keep persistent data, even when the containers stop. Default shared data storage:

• WebProtégé will store its data in the folder at ./.protegedata/protege where you run docker-compose
• MongoDB will store its data in the folder at ./.protegedata/mongodb where you run docker-compose
• Kafka will store its data in the folder ./.kafka/data where you run docker-compose

Path to the shared volumes can be changed in the docker-compose.yml file.

If the data volumes are deleted, steps 4. and 5. need to be done again

---

---

This following is an alternative description of how to compile and start WebProtege without Docker

Building (Alternative solution without Docker)

0. By default the installation is set up for Docker. But as an alternatively WebProtege (this instance), Neo4j (desktop app) and MongoDB (desktop app) can be run without Docker too. This however requires some preparation and a modification in the source code.

To build WebProtégé from source

1. Clone the github repository (see Cloning)

2. Use maven to package WebProtégé - skip the tests because they tend to fail because of date problems in some of the tests

   mvn clean package -DskipTests
   

3. The WebProtege .war file will be built into the webprotege-server directory

Running Webprotege from Maven (Alternative solution without Docker)

1. Neo4J is to be run separately as Desktop app and requires the manual installation of the NeoSemantics plugin. Check the online documentation for Neo4J and NeoSemantics.

2. Also install and run a local instance of MongoDB

3. WebProtege requieres an adaption in the source code and a recompilation:

• Change the variables NEO4JHOST and WEBPROTEGEHOST in the class edu.stanford.bmir.protege.web.server.export.ProjectExportService to localhost and then recompile the source code (see Building).

4. Set up the necessary requirements for WebProtege as described in [https://github.com/protegeproject/webprotege/wiki/WebProt%C3%A9g%C3%A9-4.0.0-Installation](the installation instructions) In short:

   • JAVA 11
   • WebProtégé requires a directory, that we call the data directory to store its data in. Create the data directory on your system. We recommend you use the standard location, /srv/webprotege. On a Windows system this corresponds to C:\srv\webprotege
   • Create the directory to hold the WebProtégé configuration files. On Linux/Unix/MacOS this should be /etc/webprotege. On Windows this should be C:\ProgramData\WebProtege (note that the ProgramData directory is a hidden directory).
   • Create a copy of the https://github.com/protegeproject/webprotege/blob/master/webprotege-server-core/src/main/resources/webprotege.properties file inside this configuration directory.
   • In the webprotege.properties file you should adjust the various properties as appropriate for your installation. In particular, you should ensure that the data.directory property is set to point to the WebProtégé data directory for your installation. For example, on Linux/Unix/MacOS, data.directory=/srv/webprotege or on Windows, data.directory=C:\\srv\\webprotege
   • Create a copy of the mail.properties [https://github.com/protegeproject/webprotege/blob/master/webprotege-server-core/src/main/resources/mail.properties]

5. Start the GWT code server in one terminal window

   mvn gwt:codeserver
   

6. In a different terminal window start the tomcat server

   mvn -Denv=dev tomcat7:run
   

7. Bootstrap WebProtégé with an Admin Account (see https://github.com/protegeproject/webprotege/wiki/WebProt%C3%A9g%C3%A9-4.0.0-Installation) HINT: The client jar is located in the webprotege-cli target folder after a successful compilation, therefore just enter the following command into the terminal there: java -jar webprotege-cli-5.0.0-SNAPSHOT.jar create-admin-account

8. Browse to WebProtégé in a Web browser by navigating to http://localhost:8080

9. Sign in with the admin account created before

10. If you get the Error message "WebProtégé is not configured properly" navigate to [http://localhost:8080/#application/settings] and

    1. Specify all required settings such as Application name, Email Address, Scheme (http), Host (localhost) as well as Permission settings. Apply your Settings and the warning should disappear.

11. Start Neo4J separately with your local desktop application

    1. Note that Neo4J version has to support the Neosemantics (n10s) plugin. Last working version at the time of writing this is 4.4.12. No support of this plugin in version 5 yet.
    2. Create a new DB with 4.4.12 and password test (see NEO4JUSER and NEO4JPASS in class edu.stanford.bmir.protege.web.server.export.ProjectExportService)

12. Import an ONTIS ontology and export the ontology into neo4j the projects overview (Export to Neo4j... )