JChem Microservices

    JChem Microservices provide microservices in small separate modules for different areas of ChemAxon functionalities like chemical dataset searching, conversion between chemical file formats.

    JChem Microservices contain common microservice modules and modules providing ChemAxon functionalities.

    Common modules:

    • config

    • discovery

    • gateway

    JChem modules:

    • DB Web Services

    • IO Web Services

    • Structure Manipulation

    • Calculations Web Services

    • etc.


    Download jws-installer - appropriate for your operating system - from


    Software requirements

    • Windows (64-bit), Linux, Mac OS

    • Java 8



    • unzip jws_windowsx64<version_number>. zip or

    • run jws_windowsx64<version_number>.exe as Adminstrator


    run jws_unix_<version-number>.sh


    On Debian, Ubuntu

    sudo dpkg -i jws_linux_<version-number>.deb

    On Redhat, Centos

    sudo yum install jws_linux_<version-number>.rpm

    Mac OS

    run jws_macos_<version-number>.dmg


    Upgrade is the same process as installation.

    The content of the config folders and the data folder of the DB Web Services module will not be overwritten.

    However, special care must be taken in case of DB Web Services.

    If the data structure version number of the new DB Web Services is higher than that of the existing old DB Web Services, the updateMode configuration parameter controls how the upgrade will be performed when DB Web Services service is started:

    updateMode: EXIT|DROP|REINDEX

    The available options are as follows.

    EXIT: the service start process exits if any change is detected. Afterwards updateMode parameter must be set to DROP or REINDEX to start, or you should migrate back to the previous version.

    DROP: the existing table and index data will be dropped.

    REINDEX: the existing tables will be reindexed.


    Depends on the operating system and on the installation mode you applied.


    run C:\Program Files\ChemAxon\JChem Micro Services\uninstall.exe


    run <Installation folder>/ChemAxon/JChem Micro Services/uninstall


    On Debian, Ubuntu

    sudo dpkg -r jws

    On Redhat, Centos

    sudo yum erase jws


    Put the license file under jws/license/ folder with name: license.cxl or apply any of the options listed on the Installing to servers page.

    • For using DB Web Services , " JChem Microservices DB " license is required.

    • For using IO Web Services , " JChem Microservices IO " license is required.

    • For using Structure Manipulation , " JChem Microservices Structure Manipulation "license is required.

    • For using Calculations Web Services , " JChem Microservices Calculations " license is required.

    • For using Markush Web Services , " JChem Microservices Markush Enumeration " license is required.


    By default, the log files of all the modules are separately stored in jws/logs/ folder. The place of log files and the logging level can be modified in the application.properties file of each service.

    Health status

    /actuator/health endpoint on the gateway reports the health status of the whole microservices system. It reports Status 2xx if all services are alive and work well.

    The individual health status of the modules can be seen on the <module_name>/actuator/health endpoint.

    Why does JChem Microservices have so many modules?

    The idea behind JChem Microservices is to provide a solution with High-Availability, Robust and modern Web Service where highly used parts can be scaled up and rarely used parts can be switched down. For this we provide the opportunity to set up different arts of the software on many machines. All of the services can be configured by a central configuration service, they all register into a discovery service and have a common entry point, which should be the only visible service in your network.

    Description of the modules


    Spring Cloud Configuration service is provided.

    Run the service in command line in folder jws/jws-config/

    jws-config-service --start (on Windows)

    jws-config-service start(on Linux)


    run-jws-config.exe (on Windows)

    run-jws-config(on Linux)

    Default configuration

    # You can set all settings here for all applications
    # LOG config: logging.level.root=WARN logging.level.com.chemaxon.webservices.license=INFO
    # DB config: initOnStart=AUTO updateMode=EXIT search.wallTimeLimitSeconds=3600 com.chemaxon.zetor.settings.indexDir=data/chemical-data/store com.chemaxon.zetor.settings.scheme=mapdb com.chemaxon.zetor.settings.forcePurge=true com.chemaxon.zetor.types[0].version = 1 com.chemaxon.zetor.types[0].typeName = sample com.chemaxon.zetor.types[0].typeId = 1 com.chemaxon.zetor.types[0].tautomer = OFF com.chemaxon.zetor.types[0].standardizerAction = aromatize com.chemaxon.zetor.types[1].version = 1 com.chemaxon.zetor.types[1].typeName = taumol com.chemaxon.zetor.types[1].typeId = 2 com.chemaxon.zetor.types[1].tautomer = GENERIC com.chemaxon.zetor.types[1].standardizerAction = aromatize com.chemaxon.zetor.additional.scheme=mapdb com.chemaxon.zetor.additional.indexDir=data/extra-data/ > {warning} If DB Web Services are run as part of a microservices system, specify here its configuration parameters.If DB Web Services are run as standalone web application, specify its configurations in its own module's application.properties file. > {info} See explanations here
    # Communication settings of gateway:ribbon.ReadTimeout=30000hystrix.command.default.execution.isolation.thread.timeoutInMilliseconds=25000000 You can set up various timeouts in JChem MicroServices. We use the Spring Cloud Stack with solutions from Netflix. Ribbon load balancer is responsible for the communication between the services. You can set up its timeout settings with the ribbon prefix, like: ribbon.ReadTimeout. This property controls when to interrupt waiting for an answer between ChemAxon services. You can also setup a guard with Hystrix circuit breaker with properties like: execution.isolation.thread.timeoutInMilliseconds which will interrupt your request if it does not get an answer during the timeout.


    Eureka, the Netflix Service Discovery Server and Client is provided.

    Run the service in command line in folder jws/jws-discovery/ :

    jws-discovery-service --start (on Windows)

    jws-discovery-service start (on Linux)


    run-jws-discovery.exe (on Windows)

    run-jws-discovery(on Linux)

    Default configuration



    Spring Cloud Gateway is provided.

    Run the service in command line in folder jws/jws-gateway/ :

    jws-gateway-service --start (on Windows)

    jws-gateway-service start (on Linux)


    run-jws-gateway.exe (on Windows)

    run-jws- gateway(on Linux)

    Default configuration:


    Message limitations in Gateway

    Our Gateway is a simple Zuul Proxy (https://github.com/Netflix/zuul), developed by Netflix. By default it has a smart algorithm to retry failed requests on different backend instances. For this it keeps each request in memory until it is answered successfully or it cannot be retried on any other servers. This leads us to a limitation where the sent message is kept in memory so if we want to send lots of data at once (like indexing a large batch of molecules), we have to grant enough memory for Zuul to keep our whole request in memory during the process. You can set Gateway's maximum memory as any Java process in the appropriate .vmoptions file. (If you execute the service with jws-gateway-servcie, then use jws-gateway-service.vmoptions; if you execute the service with run-jws-gateway, then use run-jws-gateway.vmoptions.) The default setting is -Xmx256m, which means maximum 256 MB memory.

    To protect Gateway from overloading its memory, we have introduced a filter to reject every message where Content-Length header is greater than 1/3 of the available maximum memory. With default memory settings this will lead you to reject every request with body greater than 85 MB.

    You can also specify directly how many bytes do you allow in a request. For this set gateway.max-message-size=<number_of_bytes_to_allow> to the number of bytes you want to allow in a request. (Set this as any other property in Config server.)

    If a request is too large, then a HTTP 413 error will be returned by the Gateway server.

    Calculations Web Services

    DB Web Services

    IO Web Services

    Markush Web Services

    Structure Manipulation

    Docker image example

    A docker image of JChem Microservices is provided as an example.