Marvin JS Web Services

Marvin JS Web Services is a small, simple web service application embedding Marvin JS and providing tools for transforming, exporting, and converting chemical structures. It contains the latest webjar release of Marvin JS.

This documentation describes installation, administration and usage of Marvin JS Web Services.

• Software Requirements
• Installation
  • Licenses
• Configuration
  • Configuring Cross Origin Policy
  • Forbid CORS
  • Allow CORS on Two Origins
  • Enabling HTTPS
• Running the Server
• Usage
  • Functionalities Available on the Canvas of Marvin JS
  • Functionalities Available from API
• Docker Image Example

Software Requirements

• Windows, Linux, or Mac OS
• Java 17 (from version 23.10.0) is needed. We support AdoptOpenJDK 17 as well. In the case of AdoptOpenJDK, libfontconfig package must be included.

Installation

The operating system dependent mjs-webservice (mjsws) installers (.exe, .sh, .deb, .rpm, .dmg) must be run or the independent installers must be extracted (.zip, .tar.gz).

Licenses

Required license: Marvin JS license

Put the Marvin JS license file under <userhome>/chemaxon/licenses/ (on Windows) or <userhome>/.chemaxon/licenses/ (on Linux) folder or apply any of the options listed in Installing to Servers page.

Configuration

Configuration file application.properties is available under the installed mjs-webservice/config/ folder. In application.properties file you can set the followings:

Option name	Default value
server.port	8080
logging.file.name	./logs/mjs-webservice.log
spring.application.name	mjs-webservice

For more settings possibilities, see the spring documentation page.

Configuring Cross Origin Policy

By default it is allowed to access the web services from every origin. If you want to limit which JavaScript applications can access the web services, configure the following default values in application.properties accordingly:

endpoints.cors.allowed-headers=*
endpoints.cors.allowed-methods=*
endpoints.cors.allowed-origin-patterns=*
endpoints.cors.max-age=1800

You can set a list of values by separating the individual values with a comma. For more information, see CORS.

Forbid CORS

The following setting accepts same-origin requests only.

endpoints.cors.allowed-headers=
endpoints.cors.allowed-methods=
endpoints.cors.allowed-origin-patterns=

Allow CORS on Two Origins

To enable cross origin calls from specific domains only, like origin1.com and origin2.example.com:

endpoints.cors.allowed-headers=*
endpoints.cors.allowed-methods=*
endpoints.cors.allowed-origin-patterns=http://origin1.com, http://origin2.example.com
endpoints.cors.max-age=1800

Enabling HTTPS

By default, the REST endpoints use plain HTTP as a transport. You can switch to HTTPS easily, by adding a certificate to your configuration. You can either create a new file, that contains the SSL configuration, for example, skipper.yml, or amend your application.properties file with the same information.

{info} You can reference the SSL configuration file as well as the original application.properties file together by using the following parameter: --spring.config.location=skipper.yml,application.properties

server:
  port: 8443                                         (1)
  ssl:
    key-alias: yourKeyAlias                          (2)
    key-store: path/to/keystore                      (3)
    key-store-password: yourKeyStorePassword         (4)
    key-password: yourKeyPassword                    (5)
    trust-store: path/to/trust-store                 (6)
    trust-store-password: yourTrustStorePassword     (7)

Alternatively, the same information can be appended to the application.properties configuration file:

server.port=8443                                        (1)
server.ssl.key-alias=yourKeyAlias                       (2)
server.ssl.key-store=path/to/keystore                   (3)
server.ssl.key-store-password=yourKeyStorePassword      (4)
server.ssl.key-password=yourKeyPassword                 (5)
server.ssl.trust-store=path/to/trust-store              (6)
server.ssl.trust-store-password=yourTrustStorePassword  (7)

1. As the default port is 7577, you may choose to change the port to a more common HTTPS-typical port.
2. The alias (or name) under which the key is stored in the keystore.
3. The path to the keystore file. Classpath resources may also be specified, by using the classpath prefix: classpath:path/to/keystore.
4. The password of the keystore.
5. The password of the key.
6. The path to the trust store file. Classpath resources may also be specified, by using the classpath prefix: classpath:path/to/trust-store.
7. The password of the trust store.

For more details, see spring configuration-security.

Running the server

Start the service application by either running run-mjs-webservice.exe or run-mjs-webservice.sh. The service application (mjs-webservice.exe or mjs-webservice.sh) can also be set as a service, and started or stopped by the operating system. For installing as a service in Windows, run mjs-webservice/mjs-webservice.exe --install.

Usage

Open Marvin JS on <serverhost>:<port>. Default: localhost:8080. See below how to work with the provided web service functions.

Functionalities available on the canvas of Marvin JS

The red labeled icons below on the top toolbar of Marvin JS serve for executing structure transformations.

• 2D Clean
• 3D Clean
• Auto Map
• Calculate Stereo
• Add-Remove Explicit Hydrogen

Functionalities available from API

Click on the WebServices API icon on the right bottom corner of Marvin JS.

The opening Marvin JS Web Services page contains API examples and a link to the API documentation.

• calculate-controller
  • cipStereoInfo
  • elementalAnalysis
  • molExport
  • reactionExport
• convert-controller
  • clean
  • formats
  • hydrogenizer
  • reactionConverter
• license-controller
  • grant

Docker Image Example

We created an example page to help you get started with Marvin JS in a container with its backend services. For more information, see the example page.