Structure Checker Web Services

• Microservices system mode

• Standalone web application mode

• Download

• Software requirements

• Installation

• Licenses

• Logging

• Configuration

• Running the server

• API documentation

• Demo site

• How to write custom structure checker / structure fixer

• Usage

  • Checker descriptor

  • Checker-fixer

  • General checker

  • Single checker

{info} Structure Checker Web Services provide methods for

• structure checking

• structure fixing

This documentation describes installation, administration and usage of Structure Checker Web Services.

Structure Checker Web Services make possible to reach the chemical functionality provided by Chemaxon's product Structure Checker.

Structure Checker Web Services application is available in two modes:

1. As part of a microservices system

2. As a standalone web application

Microservices system mode

In microservices system mode the Structure Checker Web Service runs together with Config service, Discovery service and Gateway service. These three services are mandatory and optionally other services can also be part of the system. All configuration must be done in the Config module.

The default configuration applies to the microservices system mode.

The web application runs on host <server-host> and listens on port <gateway-server-port>.

Standalone web application mode

In standalone web application mode the Structure Checker Web Service runs alone, without the Config service, Discovery service and Gateway service (however the installer installs them, as well).

The default configuration must be changed according to the standalone web application mode; set

eureka.client.enabled=false in application.properties file, and

up to version 22.2.0

spring.cloud.config.failFast=false and spring.cloud.config.enabled=false in bootstrap.properties file

from version 22.9.0

set spring.cloud.config.enabled=false and comment out line spring.config.import= in application.properties file.

All configuration must be done in the Structure Checker module.

The web application runs on host <server-host> and listens on port <server-port>.

Download

See here.

Software requirements

See here

Installation

See here.

Module is installed into folder: jws/jws-structurechecker

Licenses

See here.

Additionally, IUPAC naming plugin license is required for the usage of Name file format.

Logging

See here.

Configuration

Default configuration:

application.properties
server.port=8066
logging.file.name=../logs/jws-structurechecker.log
spring.config.import=configserver:${CONFIG_SERVER_URI:http\://localhost\:8888}?fail-fast=true&max-attempts=100&max-interval=60000&multiplier=1.2&initial-interval=3000	Added in version 22.6.0.
eureka.client.enabled=true	set eureka.client.enabled=false to switch to standalone Structure Checker Web Services application mode

bootstrap.properties

spring.cloud.config.failFast=true #Removed in version 22.6.0. spring.cloud.config.uri=${CONFIG_SERVER_URI:http\://localhost\:8888/} #Removed in version 22.6.0. spring.cloud.config.retry.initialInterval=3000 #Removed in version 22.6.0. spring.cloud.config.retry.multiplier=1.2 #Removed in version 22.6.0. #Removed in version 22.6.0. spring.cloud.config.retry.maxInterval=60000 #Removed in version 22.6.0. spring.cloud.config.retry.maxAttempts=100 #Removed in version 22.6.0.

For more settings possibilities see spring documentation page.

Running the server

Prerequisites in case of microservices system mode:

1. Config service is running

2. Discovery service is running

3. Gateway service is running

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

jws-structurechecker-service.exe --install
jws-structurechecker-service.exe --start (on Windows in administrator's terminal)

jws-structurechecker-service start (on Linux)

or

run-jws-structurechecker.exe (on Windows)

run-jws-structurechecker (on Linux)

API documentation

Find and try out the API on the Swagger UI.

Mode	URL of Swagger UI	Default URL of Swagger UI
microservices system	<serverhost>:<gateway-port>/jws-checker-fixer/API/	localhost:8080/jws-checker-fixer/API/
standalone web application mode	<serverhost>:server-port>/API/	localhost:8066/API/

Demo site

For detailed description check out the JWS Structure Checker demo site:

https://jchem-microservices.chemaxon.com/jws-checker-fixer/api/index.html

How to write custom structure checker / structure fixer

Here you find an example.

The above example shows how to send custom structurechecker/fixer request when using json format structurechecker/fixer configuration.

Here we document the requirements of sending custom structurechecker/fixer request when using xml format structurechecker/fixer configuration.

• Place the custom created jar file in <jws-home>/extra-libs/.

• Create externalcheckersfixers.xml and place it in <jws-home>/extra-libs/ or in any other folder but jws-user must have the right to read it. Example externalcheckersfixers.xml when it is also in <jws-home>/extra-libs/:

  <?xml version="1.0" encoding="UTF-8"?> 
  <configuration> 
  <checker-list>   
    <checker class="com.checkers.MyChecker" editor-class="" id="MyChecker" jar="custom-checkers.jar"/> 
  </checker-list> 
  <fixer-list>   
    <fixer class="com.checkers.MyFixer" id="MyFixer" jar="custom-checkers.jar"/> 
  </fixer-list> </configuration>

  If externalcheckersfixers.xml is placed in another folder you have to reference to the jar file as:

  ...
  <checker class="com.checkers.MyChecker" editor-class="" id="MyChecker" jar="file:///home/somebody/custom-checkers.jar"/>
  ...
  <fixer class="com.checkers.MyFixer" id="MyFixer" jar="file:///home/somebody/custom-checkers.jar"/>
  ...

• Add the following line to the .vmoptions file of run-jws-structurechecker and/or jws-structurechecker-service:

  -Dchemaxon.structurechecker.factory.ExternalCheckerFixerConfiguration=../extra-libs/externalcheckersfixers.xml

  or

  -Dchemaxon.structurechecker.factory.ExternalCheckerFixerConfiguration=/<dir>/externalcheckersfixers.xml 

  where <dir> is the absolute path of the xml file.

• Start the service jws-structurechecker

• Use the /rest-v1/checker-fixer/xml-based endpoint

Usage

The guidelines, examples on the Demo siteor on the Swagger UI API documentation of your installed module display the methods and syntax implemented for reaching the functionalities of Structure Checker product.

Checker descriptor

Lists the available checkers, fixers, the checkers with their corresponding fixers and the stored checker-fixer configurations.

Checker-fixer

Provides endpoints for structure checking and fixing together.

Here is an endpoint provided for executing previously stored checker-fixer actions: /rest-v1/checker-fixer/stored/{presetName}

The checker-fixer configurations can be stored in xml or in json format in the application.properties file of the jws-srtucturechecker module and also in the application.properties file of the jws-config module.

Examples:

com.chemaxon.structurechecker.presets.exampleXML=<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<checkers>\n  <AbbreviatedGroupChecker contracted=\"true\" excluded=\"\" expanded=\"true\" fixMode=\"fix\" fixerClassName=\"chemaxon.fixers.ContractGroupFixer\"/>\n</checkers>
com.chemaxon.structurechecker.presets.exampleJSON=[{"checkerSettings": {"checkerClass": "MissingAtomMapChecker","displayName": "MyStructureChecker"},"fixerSettings": {"displayName": "MyStructureFixer","exportFormat": "mrv","fixerClass": "MapMoleculeFixer"}},{"checkerSettings": {"checkerClass": "AtomMapChecker","displayName": "MyStructureChecker"}}]

General checker

Provides endpoint for executing multiple structure checkers simultaneously.

Single checker

Provides endpoints for detecting errors by structure checkers one-by-one.