Structure Checker Web Services¶

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 and listens on 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

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

All configuration must be done in the Structure Checker module.

The web application runs on host and listens on 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
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 spring.cloud.config.uri=${CONFIG_SERVER_URI:http://localhost:8888/} spring.cloud.config.retry.initialInterval=3000 spring.cloud.config.retry.multiplier=1.2 spring.cloud.config.retry.maxInterval=60000 pring.cloud.config.retry.maxAttempts=100

For more settings possibilities see spring documentation page.

Running the server¶

Prerequisites in case of microservices system mode:

Config service is running
Discovery service is running
Gateway service is running

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

jws-structurechecker-service start (on Windows)

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.

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:

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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.