DB Web Services

    {info} DB Web Services provide methods for storing and searching chemical structures in a persistent database, currently in MapDB. MapDB works with collections, but in this documentation the terminology table is used instead of collection .

    There are methods provided for

    • creating / deleting tables
    • inserting / deleting / modifying structures and data in the tables
    • executing duplicate, substructure, full fragment and similarity searches

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

    DB Web Services make possible to reach the chemical searching functionality provided by ChemAxon's products JChem Base, JChem Choral, JChem PostgreSQL Cartridge, JChem Oracle Cartridge.

    DB Web Services application is available in two modes:

    1. As part of a microservices system

    2. As standalone web application

    Microservices system mode

    In microservices system mode the DB 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 DB 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 ,

    spring.cloud.config.enabled=false and

    spring.cloud.config.uri= (so to empty) in bootstrap.properties file.

    All configuration must be done in the DB 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-db

    Licenses

    See here.

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

    Configuration

    Default configuration:

    *application.properties
    server.port=8062
    logging.file.name=../logs/jws-db.log
    eureka.client.enabled=true set eureka.client.enabled=false to switch to standalone DB Web Services application mode
    initOnStart=AUTO initOnStart can be INIT
    updateMode=EXIT updateMode gets in action only if the version number has changed updateMode can be 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].tautomerHandlingMode = OFF com.chemaxon.zetor.types[0].standardizerConfig = 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].tautomerHandlingMode = GENERIC
    com.chemaxon.zetor.types[1].standardizerConfig = aromatize
    Here are the molecule types defined.
    You can delete, modify or add new molecules types.
    version must be 1
    typeName must be unique
    typeID must be unique integer tautomerHandlingMode can be OFF or GENERIC or CANONIC_GENERIC_HYBRID (available from version 20.10)
    standardizerConfig can be made of action strings or the content of a standardizer configuration xml file
    standardizerConfig=aromatize:b..removeExplicitH
    Important:
    Indexing of the types array must always be sequential 0, 1, 2, ....

    All changes take effect only if initOnStart is set to INIT, and the application is re-started. Take care, the existing database will be deleted.
    com.chemaxon.zetor.additional.scheme=mapdb
    com.chemaxon.zetor.additional.indexDir=data/extra-data/

    Performance tuning can be executed by doing some cache related settings. Please use our JChem Engines cache and memory calculator page (take into account that superstructure search is not available) to calculate the appropriate settings.

    All properties calculated by the calculator must be copied into the application.properties file (not into the file specified on the calculator page) like:

    com.chemaxon.zetor.settings.label.cachePolicy=DISABLED com.chemaxon.zetor.settings.label.cachedObjectCount=0 com.chemaxon.zetor.settings.molecule.cachePolicy=DISABLED com.chemaxon.zetor.settings.molecule.cachedObjectCount=0 com.chemaxon.zetor.settings.fingerprint.cachedObjectCount=1320000

    The infix ' .runtime ' in keys was used in version 19.10 and earlier:

    com.chemaxon.zetor.settings.runtime.label.cachePolicy=DISABLED com.chemaxon.zetor.settings.runtime.label.cachedObjectCount=0 com.chemaxon.zetor.settings.runtime.molecule.cachePolicy=DISABLED com.chemaxon.zetor.settings.runtime.molecule.cachedObjectCount=0 com.chemaxon.zetor.settings.runtime.fingerprint.cachedObjectCount=1320000

    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
    spring.cloud.config.retry.maxAttempts=100

    For more settings possibilities see spring documentation page.

    Search logging

    Debug level of search logging can be set in the files configuring the JVM options:

    jws-db-service.vmoptions

    run-jws-db.vmoptions

    by adding line

    -Djchem.debug=true

    High Availability (HA)

    HA and load balancing is provided for DB Web Services, for the only stateful web service in JChem Microservices.

    Running more instances of the db service ensures HA and load balancing.

    In HA mode, Hazelcast is used for distributed caching of the data.

    It can be optionally set that all nodes present in the system have their own cache ('Near' cache). By default, near cache is switched on.

    Features when near cache is switched on:

    • quicker structure search

    • increased memory usage

    • in the case of data update, the system eventually becomes inconsistent; it can take a few seconds to get back again consistent.

    Requirements

    HA mode needs PostgreSQL database installed, user and database created

    Configure HA mode

    HA mode must be configure in /jws-config/common-config/application.properties file

    Example configuration:

    /jws-config/common-config/application.properties
    com.chemaxon.zetor.settings.indexDir=data/chemical-data/store com.chemaxon.zetor.settings.scheme=crdb
    com.chemaxon.zetor.settings.forcePurge=true com.chemaxon.zetor.settings.crdb.sqlBuilderProvider=POSTGRESQL
    com.chemaxon.zetor.settings.crdb.jdbcUrl=jdbc:postgresql://localhost:5432/zetor
    com.chemaxon.zetor.settings.crdb.user=chemaxon com.chemaxon.zetor.settings.crdb.password=chemaxon
    com.chemaxon.zetor.additional.scheme=crdb com.chemaxon.zetor.additional.indexDir=data/extra-data/
    com.chemaxon.zetor.additional.crdb.sqlBuilderProvider=POSTGRESQL
    com.chemaxon.zetor.additional.crdb.jdbcUrl=jdbc:postgresql://localhost:5432/zetor
    com.chemaxon.zetor.additional.crdb.user=chemaxon com.chemaxon.zetor.additional.crdb.password=chemaxon

    Load balanced example

    Here you find a load balanced example application on GitHub.

    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-db/ :

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

    jws- db -service start (on Linux)

    or

    run-jws- db .exe (on Windows)

    run-jws- db (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>/jwsdb/API/ localhost:8080/jwsdb/API/
    standalone web application mode <serverhost>:<server-port>/API/ localhost:8062/API/

    Demo site

    For detailed description check out the JWS DB demo site:

    https://jchem-microservices.chemaxon.com/jwsdb/api/index.html

    Usage

    The guidelines, examples on the Demo site or on the Swagger UI API documentation of your installed module display the methods and syntax implemented for reaching the essential chemical searching functionalities of JChem Base.

    Molecule type information

    DB Web Services provides method for getting the available molecule types.

    Every table has a Molecule type: this is a descriptor that is used by the search engine. It contains information about how structures are handled during search. The application has two very simple built in types called: sample (search with aromatization) and taumol (tautomer search). See the type definitions in the application.properties file.

    Store and search molecules and non-chemical data

    Table operations

    Structure Insert/Delete methods

    Duplicate search methods

    Substructure search methods

    Similarity search methods

    {primary} Timeout From version 19.25 the default timeout ( hystrix.command.default.execution.isolation.thread.timeoutInMilliseconds ) is taken into account during indexing. If an indexing job is started already and timeout occurs, then in the background the indexing continues. and the user is informed in the message of the error response about it: "this process has started already will finish in the background" . If the process was only waiting for other indexing processes to finish, then "this process was cancelled" message appears in the error message. The default timeout is 25000 milliseconds. We stop the process slightly before the end of the timeout (default: 300 milliseconds, can be set with zetor.indexing.timeoutDifferenceInMilliseconds property) so we have a chance to provide the answer correctly.

    Data recovery

    The data apparently stored in tables (collections) are stored in the file system under jws-db/data/ folder. The content of that folder must be stored as backup. Furthermore, the application.properties file(s) also should be saved.