Marvin JS Web Services

Installation, Administration and User Guide

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

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

• Installation, Administration and User Guide

• Software requirements

• Installation

  • Licenses

• Configuration

  • Configuring Cross Origin Policy:

    • Example: forbid CORS

    • Example: allow CORS on two origins

• Running the server

• Usage

  • Functionalities available on the canvas of Marvin JS

  • Functionalities available from API

Software requirements

Windows, Linux, or Mac OS

Java 8 is needed. Beside Oracle JDK, Marvin JS Web Services is also tested against AdoptOpenJDK 8. Note: 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 on the 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:

• server.port

default: 8080

• logging.file

default: ./logs/mjs-webservice.log

• spring.application.name

default: mjs-webservice

For more settings possibilities see 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, then you should set the following values in application.properties accordingly: default CORS in application.properties endpoints.cors.allowed-headers=*

endpoints.cors.allowed-methods=*

endpoints.cors.allowed-origins=*

endpoints.cors.max-age=1800

You can find more information here: https://developer.mozilla.org/en-US/docs/Web/HTTP/CORS

You can set a list of values by separating the individual values with a comma.

Example: forbid CORS

how to disable cross origin endpoints.cors.allowed-headers=

endpoints.cors.allowed-methods=

endpoints.cors.allowed-origins=

This setting accepts same-origin requests only.

Example: allow CORS on two origins

Enable Cross origin calls from origin1.com and origin2.example.com endpoints.cors.allowed-headers=*

endpoints.cors.allowed-methods=*

endpoints.cors.allowed-origins=http://origin1.com, http://origin2.example.com

endpoints.cors.max-age=1800

Running the server

Start the service application by

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/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 mapping

• stereo calculation

• 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