JChem Microservices History of Changes

    Long Term Supported Release - September 16th, 2024: JChem Microservices Platinum.1 (24.4.1)

    Feature set is equal to: 24.3.1

    Known issues

    • The Swagger documentation of some endpoints is incomplete, certain properties are missing. This bug only affects the documentation, the endpoints accept and return all properties as before. For the full list of the affected endpoints, see the "Known issues" section for 24.3.0.
    • Security tools may report CVE-2024-38816 in JChem Microservices, but this vulnerability cannot be exploited in the product.

    August 29th, 2024: JChem Microservices 24.3.1

    Bugfixes

    • help/about endpoint fixed and contains version details

    Known issues

    • The Swagger documentation of some endpoints is incomplete, certain properties are missing. This bug only affects the documentation, the endpoints accept and return all properties as before. For the full list of the affected endpoints, see the "Known issues" section for 24.3.0.
    • Security tools may report CVE-2024-38816 in JChem Microservices, but this vulnerability cannot be exploited in the product.

    July 24th, 2024: JChem Microservices 24.3.0

    Improvements

    • Default value of fingerprint parameter fpEdges has been changed from 7 to 6.
    • Homology groups in query structures are handled differently from now on. Documentation
    • Atom-type dependent aromatic rings with query atoms in the appropriate positions can find both aromatic and aliphatic substitutions.
    • Spring-boot framework is updated to 3.3.1.
    • Hazelcast has been upgraded to version 5.4.0.
    • H2 has been updated to version 2.3.230.
      • DB Web Services instruction
      • In Task manager case H2 DB should be dropped and recreated for new version
    • PostgreSQL jdbc driver has been upgraded to version 42.7.3.
    • Molecule escaping and unescaping is available in all services via rest-v1/json-converter/text-to-json and /rest-v1/json-converter/json-to-text endpoints
    • New endpoint (rest-v1/molconvert/append-with-properties) in IO service to convert multiple molecules with properties in a multimolecule
    • rest-v1/molconvert/split-with-properties endpoint removes title attribute of structure and include it in title field of response

    Bugfixes

    • Vulnerability CVE-2024-34750 has been fixed
    • Reindex is needed; see updateMode

    Known issues

    • help/about does not contain version details
    • The Swagger documentation of some endpoints is incomplete, certain properties are missing. This bug only affects the documentation, the endpoints accept and return all properties as before. Affected endpoints:
      • Calculations:
        • In case of the requests of all /rest-v1/calculator/calculate/* endpoints (except the general one), the documentation only includes the inputFormat and structure parameters, and not those that are specific to each calculation. These calculation-specific parameters are the same as the ones in the requests of /rest-v1/calculator/calculate and /rest-v1/calculator/batch/calculate (where they are correctly documented). E.g. /rest-v1/calculator/calculate/charge accepts the ph parameter, as well as inputFormat and structure.
        • In case of the response of the /rest-v1/calculator/calculate and /rest-v1/calculator/batch/calculate endpoints, the documentation only includes the error property for each calculation, and not those that are specific to each calculation. These calculation-specific result properties are the same as the ones in the responses of /rest-v1/calculator/calculate/* endpoints (where they are correctly documented). E.g. on /rest-v1/calculator/calculate, if a charge calculation is requested, the charge.formalCharge, charge.formalChargeByAtom and charge.totalChargeByAtom properties describe a successful result, and the charge.error a failed one.
      • Checker-Fixer:
        • In case of the responses of the three /rest-v1/checker-fixer/* endpoints, for the steps, the documentation only includes the four properties related to the structure fixers (fixState, fixerDescription, fixerName, result) and not the ones related to the structure checkers (atomIds, bondIds, checkerName, checkerTriggered, description, errorType and also some checker-specific ones), but the latter are also returned.
      • Task Manager:
        • The /rest-v1/work-queue/reactor/task/{taskId}/results also returns these properties (along with products or results): pageNumber, totalPages, totalResults and taskStatus.

    June 25th, 2024: JChem Microservices 24.1.5

    Bugfixes

    • Substructure search could result false hit with tautomer handling mode NORMAL_CANONIC_NORMAL_GENERIC_HYBRID
    • Reindex is needed; see updateMode

    Known issues

    • Due molecule type configuration changes manual DB export is needed with the previously used version and import the json with the newly installed version

    June 18th, 2024: JChem Microservices 24.1.4

    Improvements

    • New endpoints in Task Manager to work with Reactor module (only in combinatorial mode)
    • New optional filters on additional data when searching in the DB module
    • New PAUSE option on the /rest-v1/work-queue/db/task/{taskId}/manage endpoint in Task Manager. Tasks can be continued with START after a pause.
    • New rest-v1/reactor/react/combinatorial endpoint in the Reactor module.
    • The endpoints of Task Manager which allow the user to upload structures to a task now all support additional data.

    Bugfixes

    • Vulnerability CVE-2024-21634 has been fixed
    • Vulnerability CVE-2024-22262 has been fixed
    • Vulnerability CVE-2024-22257 has been fixed
    • Vulnerability CVE-2024-22259 has been fixed
    • The /rest-v1/moleculeType endpoint of the DB module now correctly returns all supported tautomer modes.
    • The /rest-v1/work-queue/db/task/{taskId}/manage endpoint of Task Manager responded very slowly when a task with many structures was started. Now it returns quickly, regardless of the number of structures.
    • In HA mode, the cluster of DB services were sometimes unable to stabilize itself after multiple instances have restarted.
    • Tasks started in Task Manager could sometimes wait indefinitely to be scheduled. This is now much less likely to happen, but to guarantee that it does not, the com.chemaxon.taskmanager.scheduler.enabled property should be set to true in the DB module configuration.
    • /rest-v1/db/additional/upload endpoint of DB Service and /rest-v1/work-queue/db/task endpoint of Task Manager accept "structureReference" and "idProperty" parameter as well for same purpose.

    Long Term Supported Release - June 18th, 2024: JChem Microservices Osmium.2 (24.2.2)

    Bugfixes

    • Vulnerability CVE-2024-22262 has been fixed
    • Vulnerability CVE-2024-21634 has been fixed
    • /rest-v1/db/additional/upload endpoint of DB Service and /rest-v1/work-queue/db/task endpoint of Task Manager accept "structureReference" and "idProperty" parameter as well for same purpose.

    Long Term Supported Release - April 18th, 2024: JChem Microservices Osmium.1 (24.2.1)

    Feature set is equal to: 24.1.3

    Bugfixes

    • Vulnerability CVE-2024-22257 has been fixed
    • Vulnerability CVE-2024-22259 has been fixed

    Known issues

    • /rest-v1/db/additional/upload endpoint of DB Service and /rest-v1/work-queue/db/task endpoint of Task Manager accept "structureReference" parameter instead of "idProperty".

    April 11th, 2024: JChem Microservices 24.1.3

    Improvements

    • Following filtering parameters added to /rest-v1/db/additional/{tableName}/duplicate and /rest-v1/db/additional/{tableName}/ids/duplicate endpoints
      • ignoreCharge
      • ignoreIsotope
      • stereoSearchIgnoreTetrahedralStereo

    Bugfixes

    • Task manager service does not start automatically in Debian installer

    Known issues

    • /rest-v1/db/additional/upload endpoint of DB Service and /rest-v1/work-queue/db/task endpoint of Task Manager accept "structureReference" parameter instead of "idProperty".

    April 9th, 2024: JChem Microservices 24.1.2

    Breaking changes

    • The API of the recently introduced Task Manager has been revised:
      • Renamed endpoints from /rest-v1/work-queue/task/... to /rest-v1/work-queue/db/task/....
        • Specifically, renamed /rest-v1/work-queue/db/task/{taskId}/importFile/{fileName} to /rest-v1/work-queue/db/task/{taskId}/import-file/{fileName}.
      • The service property in the input of the /rest-v1/work-queue/db/task endpoint has been removed.
      • Clarified the difference between the two identifiers of uploaded structures:
        • the automatically generated, Task-Manager-specific identifier is now called key (previously structureId or id),
        • the names id and structureId now always refer to the user-given identifiers.
      • The output of the /rest-v1/work-queue/db/task/{taskId}/results endpoint has been changed to always return both kinds of identifiers.

    Bugfixes

    • /molconvert/file-to-file endpoint of IO Service generated invalid images (e.g. PNG file).

    Known issues

    • /rest-v1/db/additional/upload endpoint of DB Service and /rest-v1/work-queue/db/task endpoint of Task Manager accept "structureReference" parameter instead of "idProperty".

    March 11th, 2024: JChem Microservices 24.1.1

    Bugfixes

    • Duplicate search didn't find molecule in a table created with tautomer handling mode NORMAL_CANONIC_NORMAL_GENERIC_HYBRID
    • Duplicate search didn't find molecule containing double bond in a small ring

    March 1st, 2024: JChem Microservices 24.1

    Improvements

    • New module is introduced: Task Manager
    • Database module
      • "shareEurekaClientWithHazelast" property with typo is removed. Use "shareEurekaClientWithHazelcast" instead.
      • Import/export to S3 bucket feature is improved: com.amazonaws:aws-java-sdk-sts:1.12.261 is on the path from now, so it is not necessary to add it manualy.

    Bugfixes

    • Vulnerability CVE-2024-1597 has been fixed
    • Vulnerability CVE-2024-22234 has been fixed
    • Vulnerability CVE-2024-22243 has been fixed
    • Database module:
      • java.lang.InterruptedException was thrown in some cases of limited search.

    Known issues

    • Database module
      • Automatic reindexing with H2 backend from 22.6.0 not working above 5 million records. See more.

    January 5th, 2024: JChem Microservices 23.17.0

    Improvements

    • Database module
      • New endpoint for pre-filtering duplicate structures in batch
    • Reactor module
      • Chemaxon Reaction Library is provided by new endpoints
    • Structure Manipulation module
      • Beta version of r-group decomposition, with limited parameter set

    Bugfixes

    • Spring-boot framework is updated to 3.1.6
    • Hazelcast is updated to 5.3.6
    • Vulnerability CVE-2023-6378 has been fixed
    • Vulnerability CVE-2023-33265 has been fixed
    • Vulnerability CVE-2023-34062 has been fixed

    Long Term Supported Release - June 12th, 2024: JChem Microservices Neon.4 (23.15.4)

    Bugfixes

    • Spring-boot framework is updated to 3.2.5
    • Vulnerability CVE-2024-22262 has been fixed
    • Vulnerability CVE-2024-21634 has been fixed

    Long Term Supported Release - April 25th, 2024: JChem Microservices Neon.3 (23.15.3)

    Bugfixes

    • Spring-boot framework is updated to 3.2.4
    • PostgreSQL is updated to 42.5.5
    • Vulnerability CVE-2024-22257 has been fixed
    • Vulnerability CVE-2024-22259 has been fixed
    • Vulnerability CVE-2024-22234 has been fixed
    • Vulnerability CVE-2024-1597 has been fixed

    Long Term Supported Release - February 2nd, 2024: JChem Microservices Neon.2 (23.15.2)

    Bugfixes

    • Spring-boot framework is updated to 3.2.1
    • Hazelcast is updated to 5.3.6
    • Vulnerability CVE-2023-33265 has been fixed
    • Vulnerability CVE-2023-34062 has been fixed
    • Vulnerability CVE-2023-6378 has been fixed

    Long Term Supported Release - November 13, 2023: JChem Microservices Neon.1 (23.15.1)

    No changes.

    October 24th, 2023: JChem Microservices 23.14.0

    Bugfixes

    • Configuration service

      • Common configuration could not be accessed from authenticated CodeCommit repository.

    • Spring-boot framework is updated to 3.1.5

    • Vulnerability CVE-2023-4759 has been fixed

    August 29th, 2023: JChem Microservices 23.12.0

    Bugfixes

    • Database module
      • Structure containing enhanced stereo ABS flag hasn't found itself in some rare cases.
      • Structure containing double bond stereo info hasn't found itself in some rare cases.

    Known issues

    • Mac installer screen may be invisible. Compressed (tar.gz) format can be used instead.

    July 12th, 2023: JChem Microservices 23.9.0

    Improvements

    • Chemical Calculations module:

      • The molecular formula can be specified as input format in the elemental-analysis endpoint.

    June 5th, 2023: JChem Microservices 23.8.0

    Improvements

    • Chemical Calculations module
      • Change in error handling related to chemical calculation APIs: from now on if a calculation request fails due to invalid molecule input, the HTTP status code of the response will be Bad Request (400), instead of an Internal Server Error (500).

    Bugfixes

    • Spring-boot framework has been upgraded to 3.0.7 fixing
      • CVE-2023-20883 Spring Boot autoconfigure vulnerability

    Long Term Supported Release - March 8th, 2024: JChem Microservices Mercury.5 (23.6.5)

    Bugfixes

    • Vulnerability CVE-2024-1597 has been fixed
    • Vulnerability CVE-2024-22234 has been fixed
    • Vulnerability CVE-2024-22243 has been fixed

    Long Term Supported Release - January 29th, 2024: JChem Microservices Mercury.4 (23.6.4)

    Bugfixes

    • Spring-boot framework is updated to 3.2.1
    • Hazelcast is updated to 5.3.6
    • Vulnerability CVE-2023-4759 has been fixed
    • Vulnerability CVE-2023-44487 has been fixed
    • Vulnerability CVE-2023-34062 has been fixed
    • Vulnerability CVE-2023-6378 has been fixed
    • Vulnerability CVE-2023-33265 has been fixed

    Long Term Supported Release - September 28th, 2023: JChem Microservices Mercury.3 (23.6.3)

    Bugfixes

    • CVE-2023-34034 (Spring Security) vulnerability has been fixed.
    • "Invisible Mac installer screen" issue has been fixed.

    Long Term Supported Release - July 28th, 2023: JChem Microservices Mercury.2 (23.6.2)

    Bugfixes

    • CVE-2023-20883 (Spring MVC) vulnerability has been fixed.

    Known issues

    • Mac installer screen may be invisible. Compressed (tar.gz) format can be used instead.

    Long Term Supported Release - May 30th, 2023: JChem Microservices Mercury.1 (23.6.1)

    No changes.

    May 9th, 2023: JChem Microservices 23.5.1

    Bugfixes

    • "/rest-v1/db/additional/{tableName}/exportToFile endpoint cannot save to S3 bucket" issue fixed

    April 19th, 2023: JChem Microservices 23.5.0

    No changes

    March 31st, 2023: JChem Microservices 23.4.0

    Improvements

    • Structure Manipulation module

      • New endpoint /rest-v1/structure/standardize/changes added for returning the list of the applied standardizer actions.

    Bugfixes

    • Spring-boot framework has been upgraded to 3.0.5 fixing
      • CVE-2023-20860 Spring webmvc vulnerability
      • CVE-2022-1471 SnakeYaml vulnerability
      • CVE-2023-1436 Jettison vulnerability
      • CVE-2022-45143 Tomcat-embed vulnerability
    • Similarity search could result missing hits.

    Known Issue

    • /rest-v1/db/additional/{tableName}/exportToFile endpoint cannot save to S3 bucket

    January 27th 2023: JChem Microservices 23.1.0

    Bugfixes

    • CVE-2022-0084 (xnio) vulnerability has been fixed.
    • CVE-2022-36437 (hazelcast) vulnerability has been fixed.
    • CVE-2022-40151 and CVE-2022-41966 (xstream) vulnerability has been fixed.
    • Filter ids were not working for any search type except substructure search.

    December 1st 2022: JChem Microservices 22.22.0

    Bugfixes

    • CVE-2022-40153 woodstocks-core vulnerability has been fixed.

    • Structure manipulation module

      • Components could have been lost during multistep reaction decompose step.

    December 1st 2022: JChem Microservices 22.21.0

    Improvements

    • Inserting of large molecules has been sped up especially in case of hybrid tautomerization strategy.

    Bugfixes

    • CVE-2022-40149 and CVE-2022-40150 (jettison) vulnerability has been fixed.
    • CVE-2022-31692 (spring-security-core) vulnerability has been fixed.
    • Full-fragment and duplicate search missed hits in case of hybrid tautomerization strategy if the query contained explicit Hydrogen.
    • Queries with feasible query properties didn't match corresponding target in tautomer type fullfragment search.

    October 28th 2022: JChem Microservices 22.19.0

    Bugfixes

    • CVE-2022-42004 jackson-databind vulnerability has been fixed.
    • CVE-2022-42889 commons-text vulnerability has been fixed.
    • CVE-2022-41853 hsqldb vulnerability has been fixed.
    • Aromatic query could match aliphatic target in canonic-generic hybrid tautomer mode during full-fragment and duplicate searches.

    Long Term Supported Release - September 28th, 2023: JChem Microservices 22.17.7 (Lithium.7)

    Bugfixes

    • CVE-2023-34034 (Spring Security) vulnerability has been fixed.

    Long Term Supported Release - June 20th, 2023: JChem Microservices 22.17.6 (Lithium.6)

    Bugfixes

    • CVE-2023-20883 (spring mvc) vulnerability has been fixed.
    • CVE-2023-20863 (spring expression) vulnerability has been fixed.

    Long Term Supported Release - April 6th, 2023: JChem Microservices 22.17.5 (Lithium.5)

    Bugfixes

    • CVE-2023-1436 (jettison) vulnerability has been fixed.
    • CVE-2022-1471 (SnakeYaml) vulnerability has been fixed.
    • CVE-2022-45143 (tomcat) vulnerability has been fixed.

    Long Term Supported Release - January 19th, 2023: JChem Microservices 22.17.4 (Lithium.4)

    Bugfixes

    • CVE-2022-0084 (xnio) vulnerability has been fixed.
    • CVE-2022-36437 (hazelcast) vulnerability has been fixed.
    • CVE-2022-40149 and CVE-2022-40150 (jettison) vulnerability has been fixed.
    • CVE-2022-40151 and CVE-2022-41966 (xstream) vulnerability has been fixed.
    • CVE-2022-40153 (woodstox) vulnerability has been fixed.

    Long Term Supported Release - November 29th, 2022: JChem Microservices 22.17.3 (Lithium.3)

    Bugfixes

    • CVE-2022-31692 spring-security-core vulnerability has been fixed.

    Long Term Supported Release - November 9th, 2022: JChem Microservices 22.17.2 (Lithium.2)

    Bugfixes

    • CVE-2022-42004 jackson-databind vulnerability has been fixed.
    • CVE-2022-42889 commons-text vulnerability has been fixed.
    • CVE-2022-41853 hsqldb vulnerability has been fixed.

    Long Term Supported Release - October 19th, 2022: JChem Microservices 22.17.1 (Lithium.1)

    No changes.

    September 12th 2022: JChem Microservices 22.16.0

    Bugfixes

    • Vulnerability CVE-2022-2053 has been fixed: spring-boot framework is updated to 2.7.3.
    • Vulnerability CVE-2022-25857 has been fixed: org.yaml:snakeyaml is updated to 1.31

    August 11th 2022: JChem Microservices 22.15.0

    Improvements

    • DB module
      • There is a 120 sec timeout set in the insert/import/upload processes for the tautomer calculation of each molecules.
      • Any atom doesn't match deuterium or tritium anymore. Speed-up of any atom - and no other query features - containing structures.

    Bugfixes

    • Spring-boot framework has been updated to 2.7.0.
    • Reactions with empty reactant or product component didn't find themselves.

    Known Issues

    June 27th 2022: JChem Microservices 22.12.0

    Bugfixes

    • Vulnerability CVE-2022-22978 has been fixed: spring-boot is updated to 2.5.14.

    May 6th 2022: JChem Microservices 22.11.0

    Bugfixes

    • Vulnerability CVE-2020-36518 has been fixed: jackson-databind is updated to 2.12.6.1.

    • Vulnerability CVE-2022-22965 and CVE-2022-22968 has been fixed: spring-boot is updated to 2.5.13 and xstream to 1.4.19

      • DB module
      • JWS-DB could throw OutOfMemoryError while importing molecules in batch using gcrdb backend (H2, Postgres).

    March 29th 2022: JChem Microservices 22.9.0

    Improvements

    • DB module
      • Duplicate filtering is available - by isDuplicateFiltering parameter - at endpoints
        • /rest-v1/db/additional/upload
        • /rest-v1/db/additional/{tableName}/{id}/molecule
        • /rest-v1/db/additional/{tableName}/batchInsert
        • /rest-v1/db/additional/{tableName}/importFromFile/{fileName}

    Bugfixes

    • The known issue The modules cannot be run in standalone mode has been fixed.

    Long Term Supported Release - November 9th, 2022: JChem Microservices 22.6.5 (Krypton.5)

    Bugfixes

    • CVE-2022-42004 jackson-databind vulnerability has been fixed.
    • CVE-2022-42889 commons-text vulnerability has been fixed.
    • CVE-2022-41853 hsqldb vulnerability has been fixed.

    Long Term Supported Release - September 13th, 2022: JChem Microservices 22.6.4 (Krypton.4)

    Bugfixes

    • Vulnerability CVE-2022-2053 has been fixed: spring-boot framework is updated to 2.7.3.
    • Vulnerability CVE-2022-25857 has been fixed: org.yaml:snakeyaml is updated to 1.31

    Known Issues

    Long Term Supported Release - June 23rd, 2022: JChem Microservices 22.6.3 (Krypton.3)

    Bugfixes

    • Vulnerability CVE-2022-22978 has been fixed: spring-boot is updated to 2.5.14.

    Long Term Supported Release - May 10th, 2022: JChem Microservices 22.6.2 (Krypton.2)

    Bugfixes

    • Vulnerability CVE-2022-22965 and CVE-2022-22968 has been fixed: spring-boot is updated to 2.5.13

    • Vulnerability CVE-2020-22969 has been fixed.

    • DB module

      • JWS-DB could throw OutOfMemoryError while importing molecules in batch using gcrdb backend (H2, Postgres).

    Long Term Supported Release - April 12th, 2022: JChem Microservices 22.6.1 (Krypton.1)

    Bugfixes

    • The known issue The modules cannot be run in standalone mode has been fixed.
    • Vulnerability CVE-2020-36518 has been fixed: jackson-databind is updated to 2.12.6.1.
    • Vulnerability CVE-2022-22965 has been fixed: spring-boot is updated to 2.5.12.

    March 16th 2022: JChem Microservices 22.6.0

    Improvements

    • DB module
      • Hazelcast has been upgraded to version 5.0.2.
      • H2 has been updated to version 1.4.199. Documentation
      • PostgreSQL jdbc driver has been upgraded to version 42.3.3.

    Bugfixes

    • DB module
      • Superatom sgroups caused IndexOutOfBoundsException in duplicate search.
      • Search could modify the target molecule in the case of duplicate search, if the target contained position variation feature.

    Known Issues

    • The modules cannot be run in standalone mode.

    January 25th 2022: JChem Microservices 22.2.0

    No changes.

    January 18th 2022: JChem Microservices 22.1.0

    No changes.

    January 3rd 2022: JChem Microservices 21.20.0

    • DB module
      • Double bond stereo was not checked in reaction search.

    December 15th 2021: JChem Microservices 21.19.0

    Improvements

    • JChem Microservices runs in Java 11 Environment from now on. Documentation

    Bugfixes

    • DB module
      • The export directory should have been created manually in order to run reindex successfully.
      • Generic tautomer mode of substructure search could result false hits in the case of some overlapping aromatic regions and tautomer regions.
      • Standardizer configuration could not be specified in xml file format.

    November 9th 2021: JChem Microservices 21.18.0

    No changes.

    October 28th 2021: JChem Microservices 21.17.0

    Improvements

    • IO module
      • The /rest-v1/molconvert/split-with-properties endpoint generated 0D output in some cases. These molecules are cleaned in 2D now.

    Bugfixes

    • DB module
      • Normal canonical tautomer search (full-fragment and duplicate) could miss hit in case of aromatic rings with different Kekule format.

    October 18th 2021: JChem Microservices 21.16.0

    Bugfixes

    • DB module
      • Extra "Markush Enumeration" license was necessary due to a bug.

    Long Term Supported Release - November 9th, 2022: JChem Microservices 21.15.6 (Iodine.6)

    Bugfixes

    • CVE-2022-42889 commons-text vulnerability has been fixed.

    Long Term Supported Release - September 13th, 2022: JChem Microservices 21.15.5 (Iodine.5)

    No changes.

    Long Term Supported Release - June 27th, 2022: JChem Microservices 21.15.4 (Iodine.4)

    No changes.
    Vulnerability CVE-2022-22978: Vulnerable dependency is present in jws-gateway service, but the vulnerability does not affect the product since the gateway does not use any of the affected features.

    Long Term Supported Release - May 23th, 2022: JChem Microservices 21.15.3 (Iodine.3)

    Improvements

    • DB module
      • Hazelcast has been upgraded to version 5.0.2.
      • H2 has been updated to version 2.1.210. Documentation
      • PostgreSQL jdbc driver has been upgraded to version 42.3.3.

    Bugfixes

    Long Term Supported Release - January 14th, 2022: JChem Microservices 21.15.2 (Iodine.2)

    Bugfixes

    • DB module
      • Double bond stereo was not checked in reaction search.

    Long Term Supported Release - November 3rd, 2021: JChem Microservices 21.15.1 (Iodine.1)

    No changes.

    September 28th 2021: JChem Microservices 21.15.0

    Improvements

    • DB module
      • Some invalid structures were stopped at inserting. Now it is fixed and the process progresses without errors.

    August 25th 2021: JChem Microservices 21.14.0

    No changes.

    August 3rd 2021: JChem Microservices 21.13.0

    Improvements

    • DB module
      • New search parameters implemented: ignoreCharge, ignoreIsotope

    July 16th 2021: JChem Microservices 21.12.0

    No changes.

    June 23rd 2021: JChem Microservices 21.11.0

    Improvements

    • DB module
      • /rest-v1/db/additional/upload endpoint:
        • Can now use import options from inputFormat
        • Does not add new line after one-line structures

    Bugfixes

    • DB module
      • Searching any bond on aromatic bond missed hit in substructure search in the case of molecule types with tautomerHandlingMode=GENERIC parameter.

    June 9th 2021: JChem Microservices 21.10.0

    No changes.

    May 18th 2021: JChem Microservices 21.9.0

    Bugfixes

    • False similarity search results were given in the case of molecule types with tautomerHandlingMode=GENERIC parameter.

    April 27th 2021: JChem Microservices 21.8.0

    Bugfixes

    • Critical vulnerability has been eliminated.

    April 21st 2021: JChem Microservices 21.7.0

    Bugfixes

    • DB module
      • The known issue relating the idProperty has been fixed.
      • Structures with multicenter bonds - in tables with molecule types with tautomer handling mode GENERIC - throw java.lang.RuntimeException: contract violation!
      • Standardized molecule search (rest-v1/db/substructure/ endpoint) could give false hits when the query structure contained specific combination of query bonds because query tetrahedral stereo configuration beside bondlists was not checked when matching on target tetrahedral configurations.

    JChem Microservices 21.6.0

    Not released.

    JChem Microservices 21.5.0

    Not released.

    Long Term Supported Release - January 19th, 2022: JChem Microservices 21.4.6 (Helium.6)

    Bugfixes

    • DB module
      • Double bond stereo was not checked in reaction search.

    Long Term Supported Release - November 2nd, 2021: JChem Microservices 21.4.5 (Helium.5)

    No changes.

    Long Term Supported Release - August 31st, 2021: JChem Microservices 21.4.4 (Helium.4)

    No changes.

    Long Term Supported Release - June 15th, 2021: JChem Microservices 21.4.3 (Helium.3)

    No changes.

    Long Term Supported Release - April 28th, 2021: JChem Microservices 21.4.2 (Helium.2)

    Bugfixes

    • Critical vulnerability has been eliminated.

    Long Term Supported Release - April 21st, 2021: JChem Microservices 21.4.1 (Helium.1)

    Bugfixes

    • DB module
      • The known issue relating the idProperty has been fixed.

    March 24th 2021: JChem Microservices 21.4.0

    Bugfixes

    • DB module

      • Duplicate search could result missing hit in case of structures with repeating units.
      • The known issue relating the gcrdb schema has been fixed

    Known Issues

    • DB module
      • /rest-v1/db/additional/ upload endpoint can throw exception com.chemaxon.webservices.db.exception.BadChemicalDataInRequestException if idProperty is autogenerated in the case of tables with those molecule types which have tautomer handling mode different than OFF. The relevant parameter of the molecule type is specified in the application.properties file as com.chemaxon.zetor.types[n].tautomerHandlingMode.

    February 23rd 2021: JChem Microservices 21.3.0

    Bugfixes

    • DB module
      • Duplicate and full fragment search failed with some query structures if the molecule type had generic tautomerization method and some custom transformation set in its standaridzer configuration.

    Known Issues

    • DB module
      • If the default schema gcrdb is set in the application.properties file, the additional parameters - taken from JChem Engines cache and memory calculator like com.chemaxon.zetor.settings.molecule.cachedObjectCount are not taken into account. If you want to set these additional parameters, please set com.chemaxon.zetor.settings.scheme= mapdb
      • /rest-v1/db/additional/ upload endpoint can throw exception com.chemaxon.webservices.db.exception.BadChemicalDataInRequestException if idProperty is autogenerated in the case of tables with those molecule types which have tautomer handling mode different than OFF. The relevant parameter of the molecule type is specified in the application.properties file as com.chemaxon.zetor.types[n].tautomerHandlingMode.

    February 1st 2021: JChem Microservices 21.2.0

    Improvements

    • DB module

      • First search after restarting service on each table with each search type was very slow on large databases.
      • Significant speedup at similarity search with low or zero similarity threshold. Decreasing the threshold still slows down searches, but the effect on speed is decreased.

    Bugfixes

    • Structure checker module

      • StructureChecker custom name was not used when parsing from XML and checker was triggered.

    Known Issues

    • DB module

      • If the default schema gcrdb is set in the application.properties file, the additional parameters - taken from JChem Engines cache and memory calculator like com.chemaxon.zetor.settings.molecule.cachedObjectCount are not taken into account. If you want to set these additional parameters, please set com.chemaxon.zetor.settings.scheme= mapdb
      • /rest-v1/db/additional/ upload endpoint can throw exception com.chemaxon.webservices.db.exception.BadChemicalDataInRequestException if idProperty is autogenerated in the case of tables with those molecule types which have tautomer handling mode different than OFF. The relevant parameter of the molecule type is specified in the application.properties file as com.chemaxon.zetor.types[n].tautomerHandlingMode.

    JChem Microservices 21.1.0

    Not released.

    December 3rd 2020: JChem Microservices 20.21.0

    No changes.

    October 29th 2020: JChem Microservices 20.20.0

    Bugfixes

    • DB module

      • Fix known issue present since version 20.16.0.

    Long Term Supported Release - September 10th, 2021: JChem Microservices 20.19.5 (Gallium.5)

    No changes.

    Long Term Supported Release - June 11th, 2021: JChem Microservices 20.19.4 (Gallium.4)

    No changes.

    Long Term Supported Release - May 10th, 2021: JChem Microservices 20.19.3 (Gallium.3)

    Bugfixes

    • Critical vulnerability has been eliminated.

    Long Term Supported Release - February 18th, 2021: JChem Microservices 20.19.2 (Gallium.2)

    No changes.

    Long Term Supported Release - October 28th, 2020: JChem Microservices 20.19.1 (Gallium.1)

    September 17th 2020: JChem Microservices 20.19.0

    Bugfixes

    • Structure checker module

      • When using json as preset then exportFormat for final result did not work.

    Known Issues

    • DB module

      • Database cannot be reindexed if upgraded from version less than 20.16. In that case, export the data before the upgrade, and create new table(s) and import the data after the upgrade.

    September 2nd 2020: JChem Microservices 20.18.0

    Improvements

    • DB module

      • Autogenerated IDs are returned.

    Bugfixes

    • DB module

      • Double bond stereo information was sometimes also ignored in case of search parameter stereoSearchIgnoreTetrahedralStereo set to true .

    Known Issues

    • DB module

      • Database cannot be reindexed if upgraded from version less than 20.16. In that case, export the data before the upgrade, and create new table(s) and import the data after the upgrade.

    August 12th 2020: JChem Microservices 20.17.0

    Improvements

    • DB module

      • Import from and export to Amazone S3 buckets is supported from now on.

      • Highlight endpoint has been improved. It is able to export to different formats including images with all image options.

      • Version of Hazelcast backend has been increased to 4.

    Bugfixes

    • DB module

      • Queries with explicit H and any or notlist atoms didn't match the appropriate target in generic tautomer substructure search.

    • IO module

      • Arrow and structures were mispositioned at image generation for reactions.

    Known Issues

    • DB module

      • Database cannot be reindexed if upgraded from version less than 20.16. In that case, export the data before the upgrade, and create new table(s) and import the data after the upgrade.

    July 20th 2020: JChem Microservices 20.16.0

    Improvements

    • All modules

      • The configuration parameters specified in the jws-config/common-config/application.properties file can also be received from a table. Documentation

    • Structure manipulation module

      • CIP Stereo Calculator endpoint is added

      • Reaction Converter endpoint is added

    • DB module

      • Tautomer hits are also displayed at Hit highlight

      • Endpoints added for Standardized molecule search

    Bugfixes

    • Structure checker module

      • SubstructureChecker could throw AIOOBE in case of structures with explicit Hydrogen atoms.

    Known Issues

    • DB module

      • Database cannot be reindexed. Export the data before the upgrade, and create new table(s) and import the data after the upgrade.

    June 30th 2020: JChem Microservices 20.15.0

    Improvements

    • Structure manipulation module

      • Automapper endpoint is added.

      • Aromatization/Dearomatization endpoints are added.

    • DB module

      • Hit highlight endpoint is added.

      • Query transformations stereoSearchIgnoreTetrahedralStereo and stereoSearchOnMarkedDoubleBondOnly are available for refining stereo searches.

    June 18th 2020: JChem Microservices 20.14.0

    Improvements

    • Calculation module

      • New operations are added to TopologyAnalyser: possibleCTBondCount and possibleCTBonds

    Bugfixes

    • Calculation module

      • IllegalArgumentException was thrown in BatchCalculations because of missing pH property.

    May 22nd 2020: JChem Microservices 20.13.0

    Improvements

    • Calculation module

      • Properties can be separately requested in Topology analyzer..

    • DB module

      • Standard reindex process does not work when upgrading from previous version to this version. The stored data must be exported and re-imported.

    May 4th 2020: JChem Microservices 20.12.0

    Improvements

    • DB module

      • Consideration of chiral flag can be set by com.chemaxon.zetor.types[n].stereoAssumption=RELATIVE in the application.properties file of jws-config and of jws-db.

    April 16th 2020: JChem Microservices 20.11.0

    Bugfixes

    • DB module

      • AIOBE could have been thrown in case of some standardizer configuration.

    April 6th 2020: JChem Microservices 20.10.0

    No changes.

    March 23th 2020: JChem Microservices 20.9.0

    No changes.

    Long Term Supported Release - September 17th, 2020: JChem Microservices 20.8.5 (Fermium.5)

    No changes.

    Long Term Supported Release - August 12th, 2020: JChem Microservices 20.8.4 (Fermium.4)

    No changes.

    Long Term Supported Release - June 5th, 2020: JChem Microservices 20.8.3 (Fermium.3)

    Bugfixes

    • DB module

      • Database export/import did not work.

      Long Term Supported Release - May 14th, 2020: JChem Microservices 20.8.2 (Fermium.2)

    No changes.

    Long Term Supported Release - March 30th, 2020: JChem Microservices 20.8.1 (Fermium.1)

    March 13th 2020: JChem Microservices 20.8.0

    Bugfixes

    • DB module

      • Duplicate search in tables of molecule type with tautomerHandlingMode = GENERIC parameter didn't find hits for some structures with tetrahedral stereo information.

    March 3rd 2020: JChem Microservices 20.7.0

    No changes.

    February 26th 2020: JChem Microservices 20.6.0

    Improvements

    • Calculation module

      • Atom count and isotope count is added to elemental analysis.

    Bugfixes

    • DB module

      • Non-polymer query was not found in polymer targets if it was matching on end groups.

    February 21st 2020: JChem Microservices 20.5.0

    No changes.

    February 7th 2020: JChem Microservices 20.4.0

    Bugfixes

    • DB module

      • Large structures with stereo configuration could be incorrectly handled.

    January 24th 2020: JChem Microservices 20.3.0

    Improvements

    • DB module

      • Searching with ignored tetrahedral stereo information has been introduced.

    January 21st 2020: JChem Microservices 20.2.0

    No changes.

    January 13th 2020: JChem Microservices 20.1.0

    Improvements

    • DB module

      • Technical improvements were made on the search process. Reindex is needed; see updateMode.

      • New endpoint /rest-v1/db/additional/upload added for importing molecule files.

    December 19th 2019: JChem Microservices 19.27.0

    No changes.

    December 12th 2019: JChem Microservices 19.26.0

    No changes.

    November 29th 2019: JChem Microservices 19.25.0

    Improvements

    • DB module

      • Duplicate search takes also higher order stereo information (like axial stereo information) into account.

    November 15th 2019: JChem Microservices 19.24.0

    No changes.

    November 8th 2019: JChem Microservices 19.23.0

    Improvements

    • New module - Structure Checker - has been implemented providing structure checker and fixer functionalities.

    October 21th 2019: JChem Microservices 19.22.0

    Improvements

    • DB module

      • Cache size decreased by 20%.

      • 15% import speed improvement.

      • 20-50% search speedup for frequent queries

    Bugfixes

    October 7th 2019: JChem Microservices 19.21.0

    Improvements

    • DB module

      • Memory need decreases in case of datasets with explicit Hydrogens.

    Bugfixes

    • DB module

      • Sometimes searches did not stop if search wall time limit was reached.

    September 18th 2019: JChem Microservices 19.20.0

    No changes.

    September 2nd 2019: JChem Microservices 19.19.0

    Improvements

    • DB module

      • Double bond stereo information can be ignored during substructure search.

    August 3rd, 2019: JChem Microservices 19.18.0

    No changes.

    July 16th, 2019: JChem Microservices 19.17.0

    No changes.

    July 4th, 2019: JChem Microservices 19.16.0

    No changes.

    June 27th, 2019: JChem Microservices 19.15.0

    Improvements

    • Default timeout is lowered to 30 seconds.

    June 24th, 2019: JChem Microservices 19.14.0

    No changes.

    June 17th, 2019: JChem Microservices 19.13.0

    No changes.

    June 3rd, 2019: JChem Microservices 19.12.0

    Improvements

    • DB module

      • New endpoint added: substructureHitCountEstimate

    May 21st, 2019: JChem Microservices 19.11.0

    Bugfixes

    • Config server was not visible in Eureka.

    • Calculations module

      • API provided superfluous fields for structure input.

    May 7th, 2019: JChem Microservices 19.10.0

    Improvements

    • Calculations module has been extended by

      • Batch calculations

    March 18th, 2019: JChem Microservices 19.8.0 (removed from the downloadables)

    No changes.

    Long Term Supported Release - July 30th, 2019: JChem Microservices 19.7.3 (Deuterium.3)

    Long Term Supported Release - June 3rd, 2019: JChem Microservices 19.7.2 (Deuterium.2)

    Long Term Supported Release - April 11th, 2019: JChem Microservices 19.7.1 (Deuterium.1)

    March 8th, 2019: JChem Microservices 19.7.0

    No changes.

    February 28th, 2019: JChem Microservices 19.6.0

    Improvements

    • New module - Markush (Markush Enumeration) - has been implemented.

    • Structure manipulation module has been extended by

      • Extractor

      • Fragmenter

      • Molecule cleaner

    Bugfixes

    • Substructure search returned NaN if similarity value was requested but could not be calculated. From now on, fingerprint bit distance is returned instead of similarity value.

    February 13th, 2019: JChem Microservices 19.4.0

    Improvements

    • Calculations module has been extended by

      • Topology analyser

      • Polar surface area

      • Major microspecies

    February 4th, 2019: JChem Microservices 19.3.0

    Improvements

    • Calculations module has been extended by

      • HBDA

      • logD

      • pKa distribution

      • Canonical tautomerization

      • Dominant tautomerization

    January 23rd, 2019: JChem Microservices 19.2.0

    No changes.

    January 11th, 2019: JChem Microservices 19.1.0

    Improvements

    • Calculations module has been extended by

      • Elemental analysis

      • HLB

      • Isoelectric point

      • logP

      • pKa

      • Solubitility

      • Stereoisomer

    December 14th, 2018: JChem Microservices 18.30.0

    Improvements.

    • New module - Calculations - has been implemented