October 24, 2024, Compound Registration 24.3.2 Released (version: 24.3.2-2410211122)

Breaking changes

• The following endpoints changed:
  • GET /projects - response is now containing project id too
  • GET /projects/{offset}/{limit} - response is now containing project id too
  • GET /projects/{projectName}/{offset}/{limit} - response is now containing project id too
  • DELETE /projects/{projectName} -> /projects/{projectId}
  • POST /projects - response is now containing project id too
  • GET /projects/{projectName}/members -> /projects/{projectId}/members
  • DELETE /projects/{projectName}/member/{userId} -> /projects/{projectId}/member/{userId}
  • POST /projects/{projectName}/member -> /projects/{projectId}/member
  • POST /projects/{projectName}/members -> /projects/{projectId}/members
  • PUT /projects/{projectName}/members -> /projects/{projectId}/members

Improvements

• Upgrade spring-webmvc to address CVE-2024-38816 vulnerability.
• The JavaScript runtime Node.js was upgraded to the v20 version.
• Upgrade apache-tomcat to address CVE-2024-34750 vulnerability.
• The bulk upload report of the registered entities can be downloaded now in configurable SDF and CSV format from the Upload summary page.
• System fields like "Restricted" and "Molweight" can be modified using Bulk update operations.
• The "Default" source cannot be selected anymore in a fresh installation. If the "Default" source was already used, after migration, the "Default" source will be added automatically to the list of valid sources, to the list of sources for forms and fields, structure checkers, and registration options configurations.
• During the registration process, the source name is not capitalized anymore. "Default" can be a valid source name.
• Spaces are removed when adding new Projects to the Administration/Projects list if the space is present at the beginning or the end of the Project name.

Bugfixes

• After upgrading to a version higher than 24.3 an error was received when trying to open the uploads from the upload list.
• Access was denied for project names containing white spaces.
• Reactions were registered successfully using the "auto registration" but failed using the upload.
• Salt name generation failed for salts stored in the database in other formats than mol.
• Available ID generators are no longer duplicated on the admin page when loaded as Jar extensions.
• After a quick search for an empty parent no result was returned.
• No error message was displayed in the case of an unsuccessful additional data field configuration change.
• The bulk upload failed with an error when no value but empty lines were provided for additional data fields in the SDF.
• The bulk upload process might get stuck in an 'In progress' state and incomplete when using Oracle DB.
• ​After registering a lot or using the ‘bulk add’ feature the multi-line and select fields had empty values.
• An error was received during registration/upload when a source-based substructure checker was configured.
• In the case of duplicated LnbRef when the LnbRefValidator workflow step was excluded from the registration workflow, the error message was not user-friendly.
• After using the bulk upload collection values might be mixed up.

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August 16, 2024, Compound Registration 24.3.1 Released (version: 24.3.1-2408160857)

Improvement

• The "V9_0_2024_0722\_update_submission_entry.sql" file that caused the migration error was deleted.

{info} When upgrading from version 24.3.0 and the following error is seen during database upgrade: "Validate failed: Migrations have failed validation Detected applied migration not resolved locally: 9.0.2024.07.22. If you removed this migration intentionally, run repair to mark the migration as deleted." Then please run the "-migrateSchema" command again to fix the issue.

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August 7, 2024, Compound Registration 24.3.0 Released (version: 24.3.0-2408061451)

Improvements

• JChem and Marvin JS versions are upgraded to 24.3.0, JChem table: 24030000.
• Registering by providing a version ID option is available among "More actions" on the Submission page.
• The originally assigned ID stored as additional data for the lot, version, and parent can be fetched retrospectively from the Browse page and using the API as well.
• The parent-level amendment of compounds that are part of multi-component compounds is allowed and the change is cascaded to all the involved components of the multi-component compounds (cascade effect).
• The bulk recalculation of additional data for an ID set is possible using the Bulk Regenerate Fields For IDs API endpoint. For more info please check the Browse card page.
• Additional data can be bulk (add, overwrite, delete) updated by uploading a CSV file.
• A proper error message is received during the bulk upload of compounds using an SDF, in which the data item is terminated without a blank line.
• Multiple collection value pairs using delimiters can be provided during the bulk upload of compounds.
• Compound retrieval performance is significantly improved when using project-based access.
• The compound tree retrieval on the Browse page is faster.
• A new administration extension: "Post identification steps" is added. More info is available here.
• Secure Sockets Layer (SSL) protocol was implemented for both Active Directory and LDAP authentication providers.
• Embedded ActiveMQ were removed, Compreg now connects and sends messages to an external ActiveMQ broker

{info} The configuration options from the downstream administration page were moved to registry.properties file. If you are using downstream integration, please note that this is a breaking change and the two new properties 'RegDownstreamPublishEnabled' and 'RegDownstreamFusedImageFormat' need to be set up. For more info, please check the downstream configuration page.

Bugfixes

• The ISOMER flag was not present on the search page structure images nor in the downloaded SDF.
• The Original structure was empty in the History when compounds were registered using the 'Register All' button from the Upload summary page.
• Data was not generated for a compound tree without a lot.
• The maximum 5-minute cache for dictionary values was not kept, the user had to wait longer to update the values.
• It was not possible to add space in the Project field value.
• Uploading a file with an empty project value was failing using Oracle DB.
• During the amendment of a single structure to a multi-component compound on the parent level when there was a match an incorrect lot was created.
• The salt name was not mappable if it was part of another salt name in the salt dictionary.
• Bulk upload might get stuck in 'In progress' state and not complete.
• Bulk upload failed when the upload configuration exceeded 2000 characters.
• The link to the compounds on the Suggestion list did not work in the case of SAML authentication.
• Bulk upload returned an error message when an empty data item was present in the SDF file.
• Bulk upload returned an error message when multiple empty lines or salt info without a value were present in the SDF file.
• Project items from the Administration/Projects list were not successfully deleted if the name contained a space at the beginning or the end of the Project name (instead the other Project having no space in the name was deleted).
• The parent-level amendment of compounds that were part of multi-component compounds was not possible even if the multi-component compound was deleted.
• Having the lot number (LN) configured with a prefix constant (instead of the PCN) and also stored for the LnbRef value, the system was detecting wrongly the duplicate LnbRef after lot movement followed by single lot registration or upload.

Known issue

• Migration can fail during DB upgrade with the following error message: "org.flywaydb.core.internal.sqlscript.FlywaySqlScriptException: Migration V9_0_2024_0722\_update_submission_entry.sql failed"

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May 23, 2024, Compound Registration 24.1.1 Released (version: 24.1.1-2405220834)

Improvements

• A Markush structure can be amended on the parent level to multi-component compounds.
• The salt splitting functionality was redesigned to have better performance during registrations.

Bugfixes

• A core structure search query had slow performance on PostgreSQL with large set of structure data.
• The search page displayed projects for which the user didn't have permission.
• Fields like Molecular Formula and Mol Weight with empty values did not appear on the Browse page header.

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April 25, 2024, Compound Registration 24.1.0 Released (version: 24.1.0-2404241807)

Improvements

• JChem version is upgraded to 24.1.2, JChem table: 24010200.
• Marvin JS version is upgraded to 24.1.0.
• Upgraded the postgresql jdbc driver to address CVE-2024-1597.
• Upgraded spring-web to address CVE-2024-22259, CVE-2024-22243, CVE-2024-22262.
• Upgraded spring-security to address CVE-2022-40152, CVE-2024-22257, CVE-2024-22234.
• Removed submission workspace from API endpoint.
• The file processing in bulk upload was redesigned to fix several issues and to improve performance. For more info please check the Bulk upload page.
• New status "Paused" is introduced for bulk uploads. Paused uploads can be continued by using the "Resume" button.
• Upload errors are more talkative now, instead of "Check the server logs for more information" the number of the problematic line from the uploaded SDF is displayed.
• While uploading compounds salt names from the SDF can be also considered (not just IDs).
• Virtual compound registration is enabled from the Submission page.
• A message is displayed that Markush structures cannot be registered as virtual compounds.
• A proper error message is received when trying to register a No structures without CST as a virtual compound.
• A single structure can be amended on the parent level to multi-component compounds.
• Markush structures can be amended to regular single structures on the parent level.
• Component IDs, percentages, CSTs, and compounds CSTs are displayed now in the Audit/History window for multi-component compounds after amendments.
• The originally assigned ID for the lot, version, and parent can be stored within an additional data field and are kept after amendments.
• The downstream message is consistent now for regular and deleted trees.
• Additional data from parent, version, and lot levels are present in the downstream message.

Bugfixes

• Moving lots was not working in case of No structures.
• Lot level additional data was not kept if it was added at lot level followed by a version level structure amendment.
• When registering using the API multi-component compounds providing component structures with CST and also component IDs, NullPointerException was received on the Search page.
• Additional data update workflows were missing from the Administration page Workflow list.
• After successfully regenerating a value for the second attempt while it was not successful for the first time, an empty value was also present for the field value list.
• New isomers were not properly registered when a CST was also used. PCN mapping failed with two-step Register All function from bulk upload summary page
• The amendment confirmation window showed LN instead of LnbRef when LnbRef is set as the primary lot identifier.
• The component navigation bar for multi-component compounds did not have a fixed width.
• The field list scrollbar on the Form editor of the Administration page was not working properly.
• The previously entered LnbRef was kept although the compound was registered as a virtual one.
• The progress indicator was not visible on the upload page when a large file upload was in progress.
• The uploaded file name overlapped the center panel.
• When changing between the levels of the Additional Data sections on the Browse page next to the loading spinner, there was an extra double prime symbol.
• When changing salts on the version level the Project was also present in the Summary/Audit/History.
• When numbers or dots were used as additional data field identifiers the registration/submission/amendment was blocked.
• When uploading compounds using the default ID generator while parent and version IDs are mapped, the registered version might get a timestamp containing a numeric suffix instead of just the letter increment as configured in ID settings.
• With the new UX design, the error messages were not properly aligned.
• With the new UX design, the structure checkers on the Upload page were not properly aligned.
• With the new UX design, the fields in the Search for salts/solvates panel were not well aligned.
• The original structure images from the Audit/History could not be enlarged.
• The position of the quick search field was not fixed.
• The field selector on the upload page overlapped the application header.
• ‘Unable to search for salts/solvates’ text was visible in the Search for salt/solvates panel.

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February 21, 2024, Compound Registration 23.16.0 Released (version: 23.16.0-2402191324)

Bugfixes

• After amendment, the collection values were mixed when empty values were present.
• Appended Dictionary values were not kept during the bulk upload.
• The application wrote DEBUG log events to the container's log file by default.

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February 6, 2024, Compound Registration 23.16.0 Released (version: 23.16.0-2402021427)

Improvements

• Compound Registration system is available now with a new UX design.
• Multi-component compounds can be amended on the parent level.
• Summary/Audit/History header shows LN instead of LnbRef when LnbRef is set as the primary lot identifier.
• Additional data of registered compounds can be regenerated in bulk using the Bulk Regenerate Fields API endpoint. For more info please check the Browse card page.
• A new error message is received when one cannot undelete a version since the structure already exists under another version.
• Source info is now present in the downstream message.
• Salt solvate analyzer functionality can be applied successfully now for version and lot level from the Browse page Edit mode.
• Compression is used within the application to deliver UI components to prevent unnecessary overhead to the download size.
• The browser JSESSIONID cookie is now using Strict directive in Local mode.

{info} Compound Registration is now PostgreSQL compatible. More info is available in the database setup page.

Bugfixes

• The calculated 'exactmass' property was incorrect on the parent level when the salt was drawn and not loaded from the salt dictionary instead.
• When salt was added by drawing next to the structure during a lot-level amendment and was moved to a new version, the salt was not kept.
• After registering a structure with CST the API response contained the CST in a form that was not any more recognizable by the system.
• The name of the salt was written in capital letters in the Summary/Audit/History.
• The user session was not closed properly after expiration: multiple warning dialogs were generated and the application was still usable without the need to re-login.

{info} A previous migration script has been changed. This might make MySQL migrations to this version fail from previous versions, but re-running the migration will fix the problem.

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December 12, 2023, Compound Registration 23.16.0 Released (version: 23.16.0-2312080842)

Improvements

• JChem and Marvin JS versions are upgraded to 23.16.0, JChem table: 23160000
• Upgrade spring-webmvc to address CVE-2023-34053.
• During the registration salt multiplicity is now considered for the version level data generations when the salt is added from the dictionary.
• The Project Id was added to the /retrieveLots API response.
• The salt formula was added to the /retrieveLots API response.
• Additional data for a registered compound can be regenerated.
• Amendment of Single structures to No structures is allowed.
• Salt modifications in the Summary/Audit/History are represented now as readable data instead of salt fingerprints. The change is present now on the given level where it was performed.

{info} The Flyway version was updated. When upgrading your Compound Registration please consider the latest changes involving database migrations. For more info please check the Upgrade guide page.

Bugfixes

• When moving a lot to another tree with CST an error was received.
• Move lot functionality is available now for Markush-Markush and Single-Markush structures.
• When numbers as additional data field identifiers (deriving from virtual compound registrations) were used the submission registration was blocked.
• Database connection was not released when using retrieve endpoints on MySQL.
• When changing the specified MolWeight from the parent level the Summary/Audit/History was displaying wrongly the change also for the version and lot level.
• When changing the specified MolWeight from lot or version level the Summary/Audit/History was displaying the parent level where actually no change was made.
• Downloading the search results was not successful when the "range" date filtering was used.

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November 2, 2023, Compound Registration 23.14.0 Released (version: 23.14.0-2310301321)

Improvements

• JChem and Marvin JS versions are upgraded to 23.14.0, JChem table: 23100000
• Upgrade spring-security to address CVE-2016-1000027.
• Upgrade SAML library to address CVE-2022-34169.
• Swagger was upgraded to address a potential vulnerability (CVE-2023-34036).
• The structure checker errors are now differentiated on the Registration and Browse pages.
• The status message on the submission page now shows a link that navigates to the structure checker section.
• A new tab on the Staging can be configured for submissions that are left there for more than 24 hours.
• A progress indicator and the result of the process appear when deleting an upload on the Upload summary page.

Bugfixes

• Uploading a larger SD File segment was not successful due to a timeout.
• An info box that no structure was found matching the search criteria was not received.
• Amendment and registration of the same No structure with CST resulted in two different versions of the same parent.
• Deleting more than 1000 compounds on the Upload page was not successful.
• A database error was seen when using the "Register all" for more than 1000 compounds following the two-step registration bulk upload in the case of Oracle DB.
• An empty PDF report was received from the Upload summary page for more than 1000 uploaded compounds when using Oracle DB.
• The fields of a second lot were not refreshed when using collection-type sections.
• During additional data validation on the Browse page Operation failed message was received.
• Adding or removing consecutively a list value (e.g. role) was applied only after page reload.
• When entering a free text input field the first button on the form was automatically triggered.

{info} Since this version only Java 17 is supported.

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July 7, 2023, Compound Registration 23.9.0 Released (version: 23.9.0-2307061855)

Improvements

• JChem and Marvin JS versions are upgraded to 23.9.0, JChem table: 23070000
• Numeric values generated with chemical terms are now using a dot for separating integer and fractional parts and formatted without spaces when the value is over 1000.
• A progress indicator appears when removing the Uncategorized Data on the Browse page.

Bugfixes

• Despite a certain (new) version being chosen in the Similar compounds list, the lot was registered under a new parent compound Id.
• Although the component CST was dropped during the Advanced registration it was still carried over and caused:
  • NullPointerException on the Search page and
  • Unsuccessful additional data change on the Browse page.
• When using the Find button during autoregistration the Registration options were not applied in the Suggestion list.
• The configuration import/export did not retain the field order correctly in some cases.

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June 14, 2023, Compound Registration 23.8.0 Released (version: 23.8.0-2306091339)

Improvements

• JChem and Marvin JS versions are upgraded to 23.8.0, JChem table: 23070000
• Bond angle structure checker corrections were implemented.
• Tautomerize action extension with "canonical" option is available.
• The search in audit service is now part of the public Swagger-based API documentation.
• Listing all the registered compounds through JSON messages in a downstream system is now possible.

Bugfixes

• The loading of the Restored additional data window might be slow.
• The calculation for racemic stereocenters was incorrect when the 'and' enhanced flag was used.
• The calculated IUPAC and SMILES property was missing when salt was loaded from the salt dictionary instead of drawing.
• The generated SMILES and IUPAC names on the parent level contained the version salt multiplied when salt was drawn.
• The import of a previously exported configuration containing an external dictionary was not working.

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May 9, 2023, Compound Registration 23.5.0 Released (version: 23.5.0-2305081137)

Improvements

• JChem and Marvin JS versions are upgraded to 23.5.0, JChem table: 23050000
• Improved performance when loading the Upload and Staging pages and when uploading compounds after the introduction of all structural errors in the submission status.
• The lockout after a certain number of failed login of database users is strengthened.

Bugfixes

• A blank Search page was displayed for users with missing SEARCH_DELETED_STRUCTURES role.
• In the Staging area and on the Upload Summary page an SQL exception was received when hundreds of users were present in the Oracle DB.
• When changing the additional data for isomers, not the amend data endpoint was used, and this caused the appearance of the Suggestion list.
• The status contained also the "null" for uploaded "Ready For Registration" compounds.
• IUPAC name was generated only for the lot level.

Known issues

• The loading of the Restored additional data window might be slow.

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March 31, 2023, Compound Registration 23.2.0 Released (version: 23.2.0-2303302138)

Improvements

• Additional data changes for registered compounds are not involving the Suggestion list anymore.
• In case of only structural errors with no configured automatic fixes:
  • the submissions are now present in each structural error category on the Upload summary page
  • the status on the Submission page will contain all the structural errors

Bugfixes

• When the amend data endpoint was used multiple times, database connections were not released and the system became unusable.
• Changing the Lot level identifier on the Administration/Browse page caused an undefined value on the Browse page.
• Parent level additional data update caused modified date update in lots.

Known issues

• A blank Search page is displayed for users with missing SEARCH_DELETED_STRUCTURES role.
• In the Staging area and on the Upload Summary page an SQL exception is received when hundreds of users were present in the Oracle DB.

API change

• the /openSubmission endpoint for the submission status was extended.

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March 10, 2023, Compound Registration 23.2.0 Released (version: 23.2.0-2303100954)

Improvements

• JChem and Marvin JS versions are upgraded to 23.2.0, JChem table: 22200000
• Non-chiral N atoms are not marked with enhanced stereo flags when the 'Convert to enhanced stereo' Standardizer action is applied.
• The current functionality of the export and import configuration of the system is moved from a command-line script to REST endpoints.
• Upgrade commons-fileupload to address CVE-2023-24998.
• Upgrade spring-security to address CVE-2022-31690.

Bugfixes

• Isomer counting was restarted after parent level amendment.
• The ID generation failed when Additional Data was part of the ID but was not provided.
• Molweight (Structure +Salt) and Version Created by values were missing on the Search page for bulk-moved lots.
• The substructure checker's custom name was not specified in the error message during registration.
• Structure checker errors were listed despite an empty source-based checker configuration when switching between sources during Advanced registration or on the Submission page.
• Loading spinner appeared on the Browse page additional data section when there was no field configured for the given level.

Known issues

• Changing the Lot level identifier on the Administration/Browse page is causing an undefined value on the Browse page.
• A blank Search page is displayed for users with missing SEARCH_DELETED_STRUCTURES role.
• In the Staging area and on the Upload Summary page an SQL exception is received when hundreds of users were present in the Oracle DB.

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November 28, 2022, Compound Registration 22.19.0 Released (version: 22.19.0-2211251056)

Improvements

• JChem and Marvin JS versions are upgraded to 22.19.0, JChem table: 22190000
• A new Standardizer option has been added to enforce enhanced 'abs' stereo notation on all unlabelled stereo centers, where applicable.
• New commands (add-or-update-secret, delete-secret) are added to the migration tool.
• Support for UTF-8 BOM file encoding is added during bulk upload.
• A fix for a potential vulnerability (CVE-2022-42889) was included.

Bugfixes

• Salt was not removed from a compound with CST when a salt atom was the first atom in the molfile.
• Filtering on the "Created by" column in the Staging didn't work when non-exact usernames were provided.
• Few submissions might be kept in the "Ready For Registration" state after using the "Register all" following the two-step registration bulk upload using MySQL database.

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October 5, 2022, Compound Registration 22.16.0 Released (version: 22.16.0-2209271405)

Improvements

• JChem and Marvin JS versions are upgraded to 22.16.0, JChem table: 21200000.
• Xalan library was removed from references to address a potential vulnerability (CVE-2022-34169).

Bugfixes

• When entering a free text multi-value input the cursor might jump to another field on the form.

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September 1, 2022, Compound Registration 22.13.0 Released (version: 22.13.0-2208311155)

Bugfixes

• Parent level structure layout changes were not saved during the Update layout functionality.
• The Registration options were incorrectly initialized if the user lacked the OVERRIDE_SWITCHERS role.
• The default height of the structure editor was too small.

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July 13, 2022, Compound Registration 22.13.0 Released (version: 22.13.0-2207121140)

Improvements

• JChem and Marvin JS versions are upgraded to 22.13.0, JChem table: 21200000.
• Option to configure Secure Sockets Layer (SSL) protocol for SMTP email notification settings is added.

Bugfixes

• Additional data was alternating between deleted and undeleted state in the downstream client if the same tree was published multiple times without modifications.
• Editable system fields from the Submission details section were not stored.
• Tooltips for generated/inherited fields on the Registration page were not displayed properly.

Known issues

• Parent level structure layout changes are not saved during the Update layout functionality.
• The Registration options are incorrectly initialized if the user lacked the OVERRIDE_SWITCHERS role.
• The default height of the structure editor is too small.

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June 10, 2022, Compound Registration 22.11.0 Released (version: 22.11.0-2206091310)

Improvements

• Marvin JS version is upgraded to 22.11.0.
• Version of Spring Framework was upgraded to address a potential vulnerability (CVE-2022-22970, CVE-2022-22978).
• Embedded ActiveMQ was upgraded to 5.16.5.
• Source-based checkers are now automatically pre-selected according to the configuration during advanced or manual registration and bulk upload.
• The expiration time of the SAML authentication statement is now configurable so that it can be harmonized with the session expiration time of your SAML identity provider.
• SMTP email server settings are now stored in the application database. Upgrading from previous versions will migrate existing settings from the application properties file.

Bugfixes

• For additional data fields of type "Checkbox" values were always presented as "yes" in read-only or "ON" when entering Edit mode, regardless of the value stored.
• Deleted submissions were included in abandoned submission notification emails.

Known issues

• Editable system fields from the Submission details section are not stored.
• Parent level structure layout changes are not saved during the Update layout functionality.
• The Registration options are incorrectly initialized if the user lacked the OVERRIDE_SWITCHERS role.

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May 10, 2022, Compound Registration 22.11.0 Released (version: 22.11.0-2205061430)

Improvements

• JChem version is upgraded to 22.11.0, JChem table: 21200000
• Version of Spring Framework was upgraded to address a potential vulnerability (CVE-2022-22965, CVE-2022-22968).
• Jackson-databind library was upgraded to address a potential vulnerability (CVE-2020-36518).
• Health check endpoint now reports "DOWN", in case expected JChem table version is not found.
• When switching from a Single Structure type to any multi-component structure type after using the Load from Database action, the CST of the loaded compound is now kept as a Component CST.

Bugfixes

• Performing registrations in quick succession could lead to failing submissions with an Unknown error caused by a Java ConcurrentModificationException.
• The Structure checker toggle was missing on the Submission page.

Known issues

• For additional data fields of type "Checkbox", the user interface always shows "yes" in read-only or ON when entering Edit mode, although the desired checkbox state (true or false) was correctly stored in the registration database during registration and amendments.
• The Registration options are incorrectly initialized if the user lacked the OVERRIDE_SWITCHERS role.

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March 23, 2022, Compound Registration 22.6.0 Released (version: 22.6.0-2203171710)

Improvements

• JChem version is upgraded to 22.6.0, JChem table: 21200000
• For SaaS operated Compound Registration, calling the REST API with ClientID and Client secret authentication is now restricted to those endpoints that are explicitly listed in the public Swagger-based API documentation.

{info} ChemDraw and MarvinApplet are no longer supported by Compound Registration. Users who previously selected one of these sketchers on their profile page will be automatically migrated to MarvinJS.

Bugfixes

• Adding or moving lots into a compound tree, where previously at least one lot with mapped LN was registered by a bulk upload, could fail.
• Accessing Dictionary Manager administrative functions required MODIFY_PARAMETERS instead of ROLE_DICTIONARY_MODIFY role.

Known issues

• The Structure checker toggle is missing on the Submission page.
• For additional data fields of type "Checkbox", the user interface always shows "yes" in read-only or ON when entering Edit mode, although the desired checkbox state (true or false) was correctly stored in the registration database during registration and amendments.

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February 1, 2022, Compound Registration 21.20.0 Released (version: 21.20.0-2201311605)

Improvements

• JChem version is upgraded to 21.20.0, JChem table: 21200000
• Global Structure Checkers can now be configured to flag a compound either with an error (as before) or with a warning. Compounds with only warnings may be registered without further changes, though a record of the warning will be kept in the submission history. Warnings are displayed next to structure errors on advanced registration, amendment and submission screens.
• Log4J library version 1.2 has been removed from Compound Registration and downstream client.

Bugfixes

• Could not create Structure checkers for a new source.
• When the "Stereo Comment Check" switcher is ON and the stereo comment is missing, the submission did not fail and did not end up in the Staging area during registration.
• Additional data fields without values were missing from the downstream message.
• "Select" type fields missed background color when set to required in the Form Editor preview.
• "Locate field" would not scroll to the correct field in the Form Editor preview
• Changing a default value for a field was not immediately visible in the Form Editor preview

{info} Since this version only Java 11 is supported.

{info} Since this version Internet Explorer is not supported.

{info} Since this version using ChemDraw directly as structure editor in Compound Registration is no longer supported. Structures drawn with ChemDraw can still be imported to MarvinJS as before.

Known issues

• Accessing Dictionary Manager administrative functions requires MODIFY_PARAMETERS instead of ROLE_DICTIONARY_MODIFY role.
• For additional data fields of type "Checkbox", the user interface always shows "yes" in read-only or ON when entering Edit mode, although the desired checkbox state (true or false) was correctly stored in the registration database during registration and amendments.

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December 20, 2021, Compound Registration 21.18.0 Released (version: 21.18.0-2112161730)

Improvements

• JChem version is upgraded to 21.18.0, JChem table: 21150000
• Improved performance of certain SQL commands during bulk upload.
• The general format of the application logs has been changed to JSON messages. Custom listeners consuming the old log format will have to be changed when upgrading to this version.
• Audit log includes a new property 'clientIdentity' displaying the client id when the API was used with client_credentials.
• The maximum file size for a bulk upload is now configurable from the application properties file. The new default has been increased from 100 to 200 MB.

Bugfixes

• Using the application default value for 'custom user attribute list' when using LDAP or Active Directory prevented the application from starting up.
• Including the Tautomerization action in the Standardizer configuration occasionally caused matching issues during bulk registration.
• After removing a group from a user, it was not possible to immediately re-add the same group without leaving the assignment dialogue.

Known issues

• Cannot create the structure checkers for a new source.
• When the "Stereo Comment Check" switcher is ON and the stereo comment is missing, the submission is not failing and not ending up in the Staging area during registration.
• Additional data fields without values are missing from the downstream message.
• Accessing Dictionary Manager administrative functions requires MODIFY_PARAMETERS instead of ROLE_DICTIONARY_MODIFY role.

#

October 29, 2021, Compound Registration 21.15.0 Released (version: 21.15.0-2110261635)

Improvements

• JChem version is upgraded to 21.15.0, JChem table: 21150000
• Database manipulation through REST API has been modified. Clearing application data, schema recreation and migration endpoints are removed from the application.
• Application properties log level is changed to DEBUG level to prevent sensitive information being logged to Console.
• Search criteria is extended to include "Modified by".
• Health check endpoint response data is extended.
• Field administration now supports default value selection for additional data fields bound to dictionaries or manually provided lists of values.

Bugfixes

• CSTs containing multiple underscore characters and numbers were rendered with an offset to their desired location or not visible at all on the structure image.

Known issues

• When the "Stereo Comment Check" switcher is ON and the stereo comment is missing, the submission is not failing and not ending up in the Staging area during registration.
• Additional data fields without values are missing from the downstream message.

#

September 8, 2021, Compound Registration 21.14.0 Released (version: 21.14.0-2109061125)

Improvements

• JChem version is upgraded to 21.14.0, JChem table: 21140000
• License Manager & About dialog are now displaying the number of licensed users and support expiration date.
• Applied natural ordering for dictionary- and list-based field dropdowns.

Bugfixes

• Selecting an ISOMER from the suggestion list resulted in a new ID during registration when the Remove attached data fixer was included in the configuration.
• Users were able to see projects they have not been assigned to in form drop-downs, though registrations were validated as expected.
• When "Calculate Stereo Comment" switcher was turned on then No Structure could not be registered.
• Polymer transformation error prevented the registration of an existing polymer, which was made up of monomers with at least one alternate kekule form when compared to the monomers of the existing polymer.
• For polymers, Structure Editor actions on the Browse page were partially hidden.
• Automatic submission assignment was failing when registering Multi-component compounds with advanced registration.
• The tooltip on the Search page for non-resolved dictionary values was flickering.
• In the bulk edit summary report the vertical scrollbar was not visible using IE11 web browser.

#

July 28, 2021, Compound Registration 21.11.0 Released (version: 21.11.0-2107261415)

Improvements

• JChem version is upgraded to 21.11.0, JChem table: 21110000
• Support for differentiating syn and anti stereoisomers based on structures drawn without wedge bonds (pseudo 3D representation) has been disabled. It is recommended to use appropriate wedge bond schemes instead.

Bugfixes

• NullPointerException appeared during the first login attempt, when login was initiated from a SAML identity provider.
• Polymer registration was failing when registering under an existing parent compound.
• Polymer matching was not successful when during a new registration one component had a CST and was matched against a similar polymer, where this component was registered without CST.
• New lots of bicyclic molecules were sometimes registered as a new parent when coordinates differed between the registered structures or when applying 2D clean.
• In case of spiro compounds a wedge bond change during parent level amendment caused structure update issues on version and lot levels.
• Selection type multi-value input fields were not displayed properly on the Submission page when the field was empty if Oracle database is used.
• Using custom identifier generators, the option to generate tree-independent identifiers was not working during parent level amendments, thus inadvertently changing lot numbers.
• Removing a remote user from a remote group did not remove the group association in Compound Registration.
• Changed default configurations to fix rare cases, when Tomcat was not able to shut down gracefully.

#

May 28, 2021, Compound Registration 21.9.0 Released (version: 21.9.0-2105250635)

Improvements

• JChem version is upgraded to 21.9.0, JChem table: 21040000.
• The ordering of the additional data elements in the downstream messages is ensured.
• The names of the collections containing additional data fields have been added to the downstream messages.
• The underlying JChem tables are automatically upgraded during the downstream schema migration process.

Bugfixes

• Uncategorized additional data fields were not displayed properly.
• Submission Update required dictionary values in the SDF, which was not compatible with Submission Download.

#

May 7, 2021, Compound Registration 21.8.0 Released (version: 21.8.0-2105051415)

Improvements

• JChem version is upgraded to 21.8.0 (JChem table: 21040000).

Bugfixes

• Critical vulnerability has been eliminated.

#

May 6, 2021, Compound Registration 21.4.1 LTS Helium 1 Released (version: 21.4.1-2105051115)

Improvements

• JChem version is upgraded to 21.4.1 (JChem table: 21040000).

#

May 5, 2021, Compound Registration 21.4.0 Released (version: 21.4.0-2105031420)

Improvements

• JChem version is upgraded to 21.4.0, JChem table: 21040000.

{info} Temporarily removed feature: The improvement 'Searching for IDs is case-insensitive in quick search, bulk move, load by Id actions and on the Search page' has been reverted due to causing performance issues. With that performance is again comparable to version prior to 20.16.0.

Bugfixes

• Assigning a default value or appending values to system fields (CST, LN etc.) during a bulk upload was not possible.
• When no additional data field bound to a dictionary and set to persisting IDs was configured, then adding extra columns to the Search page results would make it impossible to view Search results on the UI.
• When no additional data field bound to a dictionary and set to persisting IDs was configured, the bulk operations for additional data on the Search page would not work correctly.
• The user name related columns (CREATED_BY, MODIFIED_BY, CHEMIST) in the Downstream Client database were not matching the column specification in the Compound Registration database.

#

March 25, 2021, Compound Registration 21.3.0 Released (version: 21.3.0-2103251330)

Improvements

• JChem version is upgraded to 21.3.0, JChem table: 21020000.
• Additional Data database query was optimized. QuickSearch and Opening from Dashboard is now faster.
• Dictionary item identifiers are now optionally stored instead of values in order to directly reflect dictionary changes for all business data.
• There are some changes regarding bulkloader and registration API. Please find more information in the API documentation.
• When using MarvinJS as the default sketcher an option to disable exporting to any of the MDL V2000 formats, and to prevent users from setting the absolute chiral flag was added. By default this option is turned OFF.
• Downstream publishing can now target a different external broker service than the internal bulk upload process. Please find more info here

{info} Search REST API was modified by adding parameters. Existing REST integrations should be compatible with this change. As a consequence older Java API clients are no longer usable with this and newer versions of Compound Registration.

Bugfixes

• User synchronization was not handling transactions correctly, resulting in users not being able to perform successive actions with high frequency.
• Fixed duplicated application properties logging on startup
• Images of the audit history were not showing salt and parent multiplicity information correctly, always the latest salt information showed up in the images.
• The identifier of a polymer component loaded from the database was not shown in case the component had a CST.
• The 'Find' button on the Amendment page for polymers did not show any matches.
• The identifier of a polymer component loaded from the database was not stored for pending submissions in the Staging area.
• Advanced registration of the same polymer with different order of its components was failing.
• Registration of structures with SRU group (eg. n repeating units), and structures that contain a single star atom (but not empty structures) was wrongly creating new trees for each registration with the same structure.
• SRU (Structural Repeating Unit) polymers used to be identified as duplicates (during parent matching and search) of their counterparts with no repeating units.

Known issues

• Parent level amendment of structures with SRU (Structural Repeating Unit) is causing inconsistent compound trees on the Browse page. Workaround: repeat the same amendment on version levels too.

• Uncategorized data that is stored during a bulk upload is not displayed correctly on the UI.

#

December 3, 2020, Compound Registration 20.19.1 LTS Gallium 1 Released (version: 20.19.1-2012031053)

Improvements

• JChem version is upgraded to 20.19.1, JChem table: 20120000.

#

November 30, 2020, Compound Registration 20.19.0 Released (version: 20.19.0-2011251655)

Improvements

• JChem version is upgraded to 20.19.0, JChem table: 20120000.
• Dictionary entry IDs are displayed next to each entry in the Dictionary Manager UI and in the Edit Dialog for Local Dictionaries on the Administration Page.
• Project list and dictionaries are now cached for 5 min since last access, thus reducing network traffic especially during bulk registration.
• Field identifiers are now displayed either next to field labels or as a tooltip when hovering over the respective field label in all relevant places on the bulk upload and search page. Field identifiers are shown in a tooltip on the Search page above the column names (labels) and are also displayed while configuring new columns. Bulk edit data, and search criteria definition dropdowns show the field identifier alongside with the label.
• Auto-mapping of fields during a bulk upload now tries matching first to the field identifier of currently available fields, and if not found will perform a secondary matching to field display names.
• Calculated fields that are based on structure are now calculated for the appropriate level (parent, version, lot). Previously all values were calculated based on the corresponding version structure.
• During amendment, generated fields will only be stored according to the configured levels (parent, version, lot), and will no longer be stored as uncategorized data on other levels.

Bugfixes

• Cartridge connection profile was not working correctly in the downstream client example.
• When accepting a match for a component during a multi-component compound registration, where the matching component contained a CST, whenever this multi-component compound was part of a search result the Search page would display an error and become unusable.
• With project-based filtering turned on and at least one compound with CST registered for a given project, when using ‘Register lot’ function for this compound from parent level without a project to this lot, lead to creation of a duplicated version.
• It was not possible to register alternates, mixtures or formulations when the structures of the components were the same and just the CSTs were different.
• Different Kekule representation was not always identified as an exact match on the suggestion list.
• On the Browse page, the application could not display trees with more than 500 lots.
• Filtering labels on the Staging area based on group names did not work properly.
• Creating default Registration options (Workflow/Registration options) and Structure checker configuration (Chemistry/Structure checker) was not possible for a freshly created Source.
• Using the 'Register lot' action from the 'More actions' dropdown was blocked in case the parent had a required field.
• Groups were not listed and 'Duplicate key' error message was received on the Administration page when more than 1000 user to group mappings were used.
• Project based filtering on search page returned wrong results.

{info} The bugfix for 'Image was not regenerated when the CST was removed from the submission and it was saved in Staging area.' from version 20.16.0 was reverted due to escalating defects when using the Search page when multi-component compounds were registered.

#

September 4, 2020, Compound Registration 20.16.0 Released (version: 20.16.0-2008281630)

Improvements

• JChem version is upgraded to 20.16.0, JChem table: 20120000.
• Searching for IDs is case-insensitive in quick search, bulk move, load by Id actions and on the Search page.
• User Search Filter for ActiveDirectory-based authentication can now be configured from the Administration page, and from the registry.properties file (parameter name: RegAuthADSearchFilter).

{info} Please note that if you previously had AD enabled and you were using usernames like "user@company.local", then additional configuration might be needed for you. Please refer to the Authentication documentation (RegAuthADSearchFilter).

Bugfixes

• During registration the components were not always published in downstream before the multi-component structure.
• When assigning submissions to users the recent assignee selection showed deactivated users as well.
• Image was not regenerated when the CST was removed from the submission and it was saved in Staging area.

Known issue

• Temporarily you cannot add new Sources to the system. The previously created Sources can be still used and configured.

#

July 8, 2020, Compound Registration 20.13.0 Released (version: 20.13.0-2007060635)

Improvements

• JChem and Marvin versions are upgraded to 20.13, JChem table: 20120000.

Bulk actions

• Bulk Move Lots supports moving lots between no structure compounds.
• Revision of error messages for Bulk Move Lot operations to be more indicative.
• Lots are sorted by creation date on Browse page.

Isomers

• Configuration option has been added to admin page to globally control Isomer label generation in case of OR-flag enhanced molecule registration.
• Isomer flag is not added anymore while submission is not successfully registered.

Atropisomers

• Atropisomers differentiation in the Suggestion list.

UX improvements

• Progress indicator has been added to handle slow connection while MarvinJS is loading.

API change

• Amendment API no longer requires all saved additional data keys for the given compound to be present in the call. While previously failing the amendment in such case, now missing additional data keys will be considered removed on purpose, and will be removed from the compound during amendment.

Bugfixes

• Bulk move lots action did not create downstream update messages.
• Bulk deletion action did not create downstream update messages.
• Bulk move lots failed with empty message when field value generation was not successful.
• Deletion of a bulk upload did not change the modification date and modifier user of the uploaded records.
• Lot deletion saved modification date with wrong timezone in the database.
• During bulk upload of identical structures with OR enhanced stereo flag in the same file, sometimes the same isomer label was assigned to more than one record.
• Fixed Parent level amendment and Lot level amendment in case of atropisomers.
• When a structure with CST was registered and the same structure was registered as a salt, the CST would also be present on the salt.
• “Register all” action on the bulk upload summary page was not working correctly for No structure compounds without CST.
• Manual CST input was ignored when "Load from database" action was used.
• Downloaded SD files from the upload page contained wrong letter case for the project field.
• When both system Project field and an additional data field ‘Project’ were present, the values of the additional data field were duplicated for the system Project field.
• It was not possible to remove the last value from additional data fields with 'multiple input values' during an amendment.
• After accepting a suggested structure from the suggestion list, attempting to further edit the structure with MarvinJS as structure editor was causing an application error.
• When LnbRef was set as the primary identifier, the LN was not displayed for the given lot on the Browse page.
• New compound was registered after adding a version to an already existing compound.

Known issue

• Temporarily you cannot add new Sources to the system. The previously created Sources can be still used and configured.

#

May 19, 2020, Compound Registration 20.8.1 LTS Fermium 1 Released (version: 20.8.1-2005180829)

Improvements

• JChem and Marvin versions are upgraded to 20.8.1, JChem table: 20060000.

Known issue

• Temporarily you cannot add new Sources to the system. The previously created Sources can be still used and configured.
• Parent level amendment of atropisomers may remove atropisomeric wedge bond

May 13, 2020, Compound Registration 20.8.0 Released (version: 20.8.0-2005111440)

Improvements

• JChem and Marvin versions are upgraded to 20.8, JChem table: 20060000. Support for atropisomer M/P stereo flag calculation within MarvinJS is available
• Atropisomers can be distinguished during autoregistration
• Atropisomers can be searched on the Search page
• Add new value bulk action for registered compounds is introduced. Multiple compounds on the search page can be selected to add a new additional data value to them. Additional data field configuration toggle “Enable multi-value input” (previously “Store as list”) is validated for this action.
• Delete value bulk action for registered compounds is introduced. Multiple compounds on the search page can be selected to remove a specified additional data value from them.
• Change value bulk action for registered compounds is introduced. Multiple compounds on the search page can be selected to replace an additional data value with another value.
• New additional data field option is introduced for lot level fields: "Inherit data from parent level". Lots will be presented with additional data values inherited from its parent during searching and viewing as if they were present on lot level. They can however only be changed on parent level. In case of lot movement to another parent, inherited additional data will not travel with the lot, but it will only display the inherited data from the new parent.
• Bulk move lot action is introduced: multiple lots can be selected and moved to a different existing parent. Both source and target parent must be stereoisomers of one another.
• Restore additional data action is available in the compound history. After selecting a state from the current level, a preview is generated for restore. Data will be changed according to the preview. Generated and inherited fields cannot be restored this way.
• All compounds registered during a bulk upload session can be deleted in one operation.
• API to republish downstream messages is added
• Audit history shows state changes of the given compound under previous ids as well
• Changing workflows no longer requires application server restart
• More detailed messages for input files errors during submission update are available
• Public Docker released (https://chemaxon.com/products/compound-registration/download)
• All structures are saved in the database in MolV3000 format
• "Exact" match name is replaced with "Duplicate" match name (in correlation with JChem). "2D match" is replaced with "Stereo matches"
• Support for ChemDraw version 17 and 18 is added
• "Failed submissions" is renamed to "Staging area" on the Dashboard
• New variable introduced for the bulk upload notification email template to refer to a specific upload: \${attemptSummary.uploadId}
• Notification email subject for submissions created in the staging area is changed to reflect their current status
• New variable introduced for the registration email notification template to refer to the corresponding submission: \${id}
• New option to show deleted records on the Search page is available
• Form configuration is simplified. All "select" type inputs have a typeahead filter, to narrow down the selection pool. "Select (typeahead)" is removed as an input type
• Form Editor: additional data configuration has a simplified and more intuitive user interface
• UX improvements: Added progress indicators or loading animations to provide better interactive feedback on slower network connections
• Date format of the compound retrieval service is now expecting the date format according to the application configuration
• Added structure and additional data amendment roles that permit only changes to registered compounds if the user performed the initial registration or was added as the submitter of it. Changes to compounds which this user did not register or is submitter of will not be possible.
• Percentages are added to molecular formula of Formulations
• Structure type names can be customized on the UI
• Single field values of SD files can be split to multiple values by defining a delimiter
• During a bulk upload operation only those fields need to be mapped that are configured for the selected source
• New command-line scripts has been added to export and import the current configuration (only Forms and fields plus parameters are included) of the systems

{info} The migration script has been changed. This makes migrations to this or future versions fail from previous versions, but re-running the migration will fix the problem

Bugfixes

• During migration from: pre 18.03.12-2503 versions to: any 18.x.x. or 19.x.x versions Markush compounds have lost reference to their actual molecules. If Markush and Single type no structures with CST molecules were registered they were all turned into NoStructure molecules.
• Chemical structures could not be viewed on the Search page
• Custom checker/fixers did not work
• Registering more than 1000 submissions with the Register All functionality during two-stage bulk upload was not possible when using Oracle database with more than 1000 users
• Undeletion of version or lot level No Structure type compounds failed if the parent level had also been deleted
• Adding a structure or CST to a No Structure without CST on parent level failed
• Amendment of No Structure type compound versions by adding salts was not possible
• Missing lot issue during downstream publishing was fixed
• Downstream messages for deletions of multi-component structures were not properly generated
• Fixed parent level amendment downstream message sending
• "Assign to submitter" feature honors direct assignment and does not override it
• Not all open dialogs were closed if session expired automatically
• Default (exact) and the selected exact search did not return the same results
• Boron atom was erroneously treated as a stereo center in certain cases (fixed in core chemistry module)
• Structure search with Duplicate search did not always return the correct result
• NullPointerException was thrown while checking "fromList" validator on empty data on Oracle
• Stereochemistry was incorrectly calculated for phosphates in certain cases
• Additional data would not change if an amendment of both the structure and additional data was executed on lot level
• Status text was incorrect for structure checker errors in the submission creation notification email
• Generated data was not being consistent for lots having salts or solvates
• Additional data changes in the audit window were incorrect if a lot was moved under a different tree during lot amendment
• Changes in list Additional Data showed unchanged elements in the audit history
• Searches in metadata did not return records when only deleted metadata matched the query
• Update submission function was present in the Staging area Bulk actions even if the user lacked the IMPORT_SUBMISSIONS role
• Similarity search did not order by similarity correctly
• Non-defined projects were created when the project based access was enabled and the Project field was mapped during bulk upload
• Project audit was different than other audits
• For users that didn't have the OVERRIDE_SWITCHERS role, the list of the used registration options while saving a submission was validated against the REGISTRAR source instead of the actual source
• Clicking on the "Scan More" during bulk upload cleared the previously defined mappings
• When the structure and additional data was modified in the same time on version level and there was a generator among the additional data fields the additional data change was not audited
• "Auto-scrolling to top" issue was present when closing modal dialogs
• Line breaks were not visible on the UI in Text (multi line) fields after registration
• Issues appeared during executing actions on more than 1000 objects while using Oracle database
• Mappable required fields were not considered based on the used source/form during bulk upload
• Amending additional data of an isomer on parent level leaded to a changed isomer
• During bulk upload the label of a field could be matched with the name of another field, and this caused data mapped to only one field (users are now prevented from naming a field with a name that is already occupied by another label)
• When a Project field and a Project additional data field was present, the values were duplicated for the default Project field
• Projects were conflicting with internal dictionaries named "Projects" at field configuration
• All batches were offered for match for No Structure with CST when Project based access was enabled

{info} Temporarily removed features

• Bulk register selected submissions from Staging

• Automatic search is removed from the Search page

Known issue

• Temporarily you cannot add new Sources to the system. The previously created Sources can be still used and configured.
• Parent level amendment of atropisomers may remove atropisomeric wedge bond

May 4, 2020, Compound Registration 19.21.4 LTS Europium 4 Released (version: 19.21.4-2004301238)

Improvements

• JChem and Marvin versions have been upgraded to 19.21.4 (JChem table: 19210000)

Bugfixes

• Changes to rest/configurationService/forms and rest/configurationService/fields responses for dictionaries were reverted and harmonized with /rest/dictionaryManagement/dictionaries/{DICTIONARY_ID}/items

• SELECT fields configured with a Dictionary (local, remote)

possess a property "valuesUrl" with an url relative to /rest path, from where possible values for this field can be fetched

• Amending additional data of an isomer on parent level could cause an unwanted change of the isomer number
• When both structure and additional data was modified at the same time on version level and there was a generator among the additional data fields, the additional data change was not audited
• If compounds of type Markush and Single type no structures with CST were present in the database at the same time with versions prior to 18.03.12-2503, all Markush structures would lose reference to their actual molecule structures when migrating to any 18.x.x. or 19.x.x versions
• Downstream messages for deletions of multi-component structures (alternates, mixtures, formulations, polymers) were not properly generated

March 5, 2020, Compound Registration 19.21.3 LTS Europium 3 Released (version: 19.21.3-2002251526)

Improvements

• JChem and Marvin versions have been upgraded to 19.21.3 (JChem table: 19210000)
• API has been added to republish downstream messages.

Bugfixes

• Fixed an issue where lots might not get published downstream.
• Fixed an issue where new projects could be created during a bulk upload outside of regular project administration.
• A database migration step for changing the configuration format failed.

{info} A previous migration script has been changed. This will make migrations to this or future versions fail from previous versions, but re-running the migration will fix the problem.

Known issue

• During migration from: pre 18.03.12-2503 versions to: any 18.x.x. or 19.x.x versions Markush compounds have lost reference to their actual molecules. If Markush and Single type no structures with CST molecules were registered they were all turned into NoStructure molecules.

February 3, 2020, Compound Registration 19.21.2 LTS Europium 2 Released (version: 19.21.2-2001241202)

Improvements

• Notification email subject for submissions created in the staging area is changed to reflect their current status.
• New variable available to be used in the bulk upload notification email template: \${attemptSummary.uploadId}.
• The Submission ID is available to be used in the email notification template for individual registrations as a variable: \${id}.
• More detailed messages for input file errors during submission update.
• JChem and Marvin version: 19.21.2 (JChem table 19210000)

Bugfixes

• Status text was incorrect for structure checker errors in the submission creation notification email.
• Calculation of certain generated fields was not executed if one field generator had failed with an error.
• Additional data changes in the audit window were incorrect if a lot was moved under a different tree during lot amendment.
• Additional data would not change if an amendment of both the structure and additional data was executed on lot level.
• NullPointerException was thrown while checking "fromList" validator on empty data on Oracle.
• Listing more than 1000 users was not possible with Oracle database.
• Fixed a problem with data in generated fields not being consistent for lots having salts or solvates.
• Date format of the compound retrieval service was changed to the application default format "yyyy-MM-dd HH:mm:ss".
• Registering more than 1000 submissions with the Register All functionality during two-stage bulk upload was not possible when using Oracle database.
• Undeletion of version or lot level No Structure type compounds failed if the parent level had also been deleted.
• Adding a structure or CST to a No Structure type compound without CST on parent level failed.
• Amending No Structure type compound versions by adding salts was not possible.
• Fixed error in case of moving a second lot in the same tree.
• Structure image CSS property was updated to work with the newest Chrome.

{info} By default the Search page will return no search results. You need to add the search criteria in order to have the registered items displayed. You can just hit the Search button even without setting search criteria, but note that the search response might take a longer time.

October 18, 2019, Compound Registration 19.21.1 LTS Europium Released (version: 19.21.1-1910181313)

Improvements

• JChem version: 19.21.1 (JChem table 19210000)

Bugfixes

• The migration tool could not be used with the MySQL JDBC driver.

October 7, 2019, Compound Registration 19.20.0-1910071220

Improvements

• New command-line script has been added to update the roles of an existing group.
• User assignment: username, e-mail address and full name properties of a user is now searchable. These properties are also displayed in the user selector dropdown.
• Unused salts or solvates can be deleted from the system.
• The creation of a local user with the same name as a deleted one has now failed with an error message "Username already exists", instead of re-activating the deleted user.
• Auto-resolve user conflict during SSO login when using the same local and remote username.
• The default salt or solvate multiplicity is set to one when adding salt/solvate through the structure editor.
• SSO user's groups are respected after upgrading to this version from 19.7 and earlier.
• Inactive users are shown in the Administration Zone > Access Control > Users page.
• Inactive local users can be re-activated in their User Details page in Administration Zone > Access Control > Users.
• A shortcut is added to the submission assignment to easily assign submissions back to the original creator.
• User search has been improved when selecting assignees.
  • Typeahead search has been introduced to all user properties
  • Fuzzy search (approximate string matching) has been introduced to match users even if the query is misspelled
• The suggestion list doesn't display version level IDs if the version level is hidden.
• User list filter property for Active Directory configuration.
• Group list filter property for LDAP and Active Directory configuration.
• Standardizer steps applied to the structure during registration are available in the submission history.
• Structure Checker fixers applied to the structure during registration are available in the submission history.
• Submissions are auto-saved when clicking on the "Register" button. Temporarily removed feature: Bulk register selected submission from staging.
• Changed database structure to increase the performance of submission handling.
• New option to see the history of a given Submission on the Submission page in the Staging. Reachable from the More Actions menu. Structure Checker, Standardizer reports and Drawn Structure are also shown here.
• New roles to configure who has access to Submission History, or Restore functions.
• Structure Checker "Fall to staging" has been renamed to "Do not fix".

Bugfixes

• "Assign to submitter" function did not respect direct assignment and overrided it.
• Synchronized user groups didn't appear on the User Details page.
• The Dashboard piechart overflowed the other panels.
• Some structures were not saved in MolV3000 format in the database.

{info} "Submission opened by" was replaced with "Submission assigned to" in the downloaded submissions .sdf. Because of this, previously downloaded submissions .sdf are incompatible with the current version for submission update.

{info} The order on the submissions in the Restore page has been changed so that the newest state appears on the top, while the oldest one on the bottom.

{info} The JDBC Driver for MySQL is not distributed with the Migration tool any more. For details please check the Upgrade Guide.

Known issue

• Chemical structures cannot be viewed on the Search page using latest Chrome browser, affecting all versions from 18.7.9 until 19.20.0, including current LTS versions. The issue will be fixed in the next release version of Compound Registration.
  • Workaround1: use a supported web browser other than Chrome or use an older Chrome version.
  • Workaround2: use a third party Chrome Plugin to manipulate the application CSS on the fly, though be advised that you do so at your own risk. Steps to follow:
  • Install a chrome extension from the Chrome Webstore that can manipulate the CSS of a website on the fly, for example the "User JavaScript and CSS" extension: https://chrome.google.com/webstore/detail/user-javascript-and-css/nbhcbdghjpllgmfilhnhkllmkecfmpld?hl=en-GB
  • Navigate to your Compound Registration search page and click on the extension icon, then the "Add new" button to add a new rule
  • Copy the following code to the CSS panel (right side): .cxn .cxnStructureImage .structureImageContainer svg { height:inherit}
  • Hit "Save".
  • Reload the Search page. Once these steps have been followed the application should display structure thumbnails on the search page again as expected.

July 15, 2019, Compound Registration 19.13.0-1907171250

Improvements

• JChem version: 19.13.0 (JChem table 19100000)
• Suggestion list dialog layout improvements.
• The database structure is changed to increase the performance of submission handling.
• EULA update.
• Possible configuration is added to capture user email and name properties as additional data during registration.
• Compound retrieval REST API documentation is added to swagger-ui.
• When a user selects a different assignee as previously when assigning, the default assignee of that user will be updated.
• Assigning submissions to users has been incorporated in the suggestion list.
• Submission auto-assign feature change:
  • A toggle called "Auto-assign submissions" has been added to the administration zone.
  • If this toggle is ON, the submission will be automatically assigned to the logged-in user upon opening. Auto-assign is happening only when the submission has no assignee. Previous assignees are not overwritten.
  • On the submission details page, the "assignee" of the submission is clearly visible now.
• "Copy structure" action is added to suggestion list thumbnails. By pressing this button the actual structure will be copied to clipboard in MolV3000 format.
• Command Line Tool command: create-group has been extended with an optional source argument allowing to create remote groups.
• Assignee selection: user list is searchable through a typeahead filter. A "Recent selection" section is added to display the last 5 users.
• Upon assigning a submission to a user, an e-mail is sent to inform the new assignee if email notifications are turned on.
• User property field generator can handle custom LDAP and Active Directory user attributes.
• Admin > Access Control > Users and Groups pages have been improved to fully support remote user handling.
• First name, Last name and Full name attributes are stored upon user synchronization.
• Custom user attributes can be synchronized from LDAP or Active Directory.
• Username conflict resolver. Compound Registration provides a web interface based tool to solve the problem of conflicting usernames after an LDAP or AD synchronization.
• Button has been added to the users' page and group page to do the synchronization of users and groups. Upon synchronization a report will be shown to the administrator, that shows the number of created/updated/deleted users. These numbers can be expanded to see the related users.
• User details are stored in the database upon login process.
• A dedicated page is added to the Administration zone to manage external dictionaries.
  • External dictionaries now support adding custom headers when querying an external URL.
  • Additional data field improvements: "select" input types can be configured to use the new external dictionaries.
  • Additional data field improvements: a new validator has been introduced to check if the value of the additional data is amongst the dictionary items. If the value is not present the compound falls to the staging area. This is useful for example to enforce the input of a valid "Project" field.
• A new command-line script has been added to update roles of an existing group.

Bugfixes

• Field value was set for the first record instead of the last on the Upload page mapping section.

• Lot registration from the parent level was published downstream.

• An exception was fixed while bulk registering No Structure compounds from Staging.

• Date format validator was added to additional data fields.

• Parent additional data was replaced when a lot is moved after amendment.

• An incomplete display of CSTs was fixed when all caps CST contains a number.

• Analyze Salt/Solvate was not running on the structure without CST.

• After multiple amendments 'The selected CN was not found anymore in the database' error message appeared.

• IDs were not refreshed on the Dashboard after modifying or moving the related lot.

• Fix for deleted compounds that were offered as a match in the case of multi-component compounds.

• Fix for the original structure which contained "ISOMER #" in the History.

• Downloading a Bulk upload report created a corrupt PDF file.

• CST and percentage data were displayed not in the correct location.

• Removed legacy jsr250-API dependency, that could cause dependency clash issues on Java 11

• Polymer and monomer CSTs are displayed for registered polymers.

• Using Template-based 2D clean action from Compound Registration during bulk upload failed with MolSearch error.

• Fixed salt/solvate multiplicity rounding on the Submission page (solvate multiplicity was saved for submission).

• Bulk Uploaded NoStructures with mapped PCN fell to staging with ReadyForRegistration when two-step registration was used.

• Specified mol weight couldn't be added for No Structures without CST.

• Notification emails about successful, and failed registration showed incorrect data ( like $pcn $cn ) instead of the data itself. From now the real data is shown. However in case of failed registration PCN and CN data will be blank, because they are only available after a successful registration. To fix the bulk upload notification an administrator must change the email template "E-mail template for bulk upload report" in the Administration>Notifications>E-mail. The (${attemptSummary. attemptId}) has to be changed to: (${attemptSummary.library})) )

• Assigning was restricted to active users.

• Fixed image structure display in the Restore submission dialog.

• Search based on LN failed when a No Structure with salt was included in the search results.

• Fixed ordering of search results by MolWeight (Parent) and Restricted columns.

• CSTs with underscore characters were displayed not properly in case of some structure types.

If you experience issues with login, please find information here about how to resolve conflicting usernames, resolve administrator lock-out and granting administrator privileges for SAML users: Users and groups, Conflicting users

February 8, 2019, Compound Registration 19.2.0-1902051635

Improvements

• JChem version: 19.2.0 (JChem table 18180000)
• Navigation bar responds to the screen size in a more clever manner.
• New improved Suggestion list during registration and amendments for single structures.
• Longer Project names (up to 200 characters) can be used. Asian characters can be set for Projects.
• Register to Staging using REST API and API Client
• Structure checkers will not run on "No structure" type compounds.
• Downstream message API changed. Components added to the multi-component compounds.
• Scan more button on the Upload page displays the number of scanned records from the SDF
• Embedded ActiveMQ version upgraded to 5.15.8

Bugfixes

• Accepting a matching compound during a parent level amendment of no structures with CST leads to duplicate entries.
• SQL Upgrade is extremely slow – the migration script has been changed.
• Delete lot message in the downstream system does not contain full additional data.
• Parent additional data is replaced when a lot is moved after amendment.
• Field value set for the first record instead of the last on Upload page mapping section.
• Exception while bulk registering No Structure compounds from Staging
• Bulk upload mapping: fixed display for cases when the mapping fields are too long (no more overflows or distorted text).
• Bulk upload summary: error categories are not refreshed properly while watching the upload progresses.

Known issues

• Inconsistency between the generated messages for deleted and not-deleted entries.
• The composition percentages are placed wrongly on the registered polymer images
• ActiveMQ 5.15.8 message serialization in the persistence layer is not compatible with the previous version. Make sure your ACTIVEMQ_MSGS table is empty before starting the application.

December 7, 2018, Compound Registration 18.27.0-1812061612

Improvements

• Users are now notified five minutes before their login session would expire, giving a chance to prolong their session
• The drawn structure is saved even when the user selects a suggestion to be registered instead. Amendment saves drawn structure as well, and when the user amend a No Structure Without CST to a Single Structure, the new structure will have the amendment drawn structure as drawn structure.

Bugfixes

• Existing mixture component replace creates a new unique component
• No fused image is created when at least one component of the AMF is CST only
• No structure registration: the additional data field value is duplicated on parent/version level

Known issues

• SQL Upgrade is extremely slow – we changed the representation of the original structure in database level, but the migration script for that performs extremely bad. We will remove this script in the next version. If you do a new deployment on an empty database it runs fine.
• Accepting a matching compound during a parent level amendment of no structures with CST leads to duplicate entries.

November 16, 2018, Compound Registration 18.23.0-1811150945

Improvements

• Improved performance of certain SQL commands during registration
• To protect sensitive information, the application will automatically navigate to the login screen after the authentication session is expired
• Detailed compound list on the bulk upload summary page
• Downloadable PDF report added to Bulk Upload Summary page

Bugfixes

• Required lists fields have a light yellow background
• Register All function does not work if two step registration has been used for uploading
• Boolean type additional data conversion is fixed. Falsy values won't be interpreted as true any more
• From the Java API (version 18.5.14-1805110920) duplicate IDs are not rejected

Known issues

• Ordering issues with MySQL (Search page):
  • order by the Restricted column and by the Molweight (Parent) column (lot, version level) does not work
  • order the Markush structures

October 4, 2018, Compound Registration 18.22.0-1810031627

Improvements

• Json validation

• Before/After structure images are clickable/magnified in the Audit window

• Focus stays on Register button after registration is complete

• Improved visibility when fields in forms are non-editable

• Staging: filtering is performed both in short and detailed status messages

• Upload: import of mapping files (.map) now clears the auto-mapped fields before applying the map

• Registration page: multi-component compound preview is generated when no structure but CST is available

• Round parent multiplicity replaced by Round salt multiplicity in the Administration panel

Bugfixes

• Downstream Client with Additional data is not working
• Additional data group is displayed even if it does not contain any field
• Uploading non existing project causes silent failure
• Submissions are lost during SDF upload when undefined Project is mapped
• Upload hangs when additional data is too large to fit in database
• No Structure with CST registration updated parent fields with latest data
• Parent level amendment breaks No structure with CST matching
• The order of forms is not reflected on the UI
• "undefined" appears for "Link" type fields with "null" content, when appending collections
• Long text is out of field during Upload mapping
• Original query structure is not shown when hitting on "Back to last search"
• Inconsistent behaviour in case of percentage field of FORMULATION (and POLYMERS)
• Audit field length too short
• Validation failed error message during amendment process after using Esc in the Audit
• In Staging filtering "Current status" column does not work
• Submission export is terribly slow
• Install wizard messes up with invalid license
• Registering a virtual compound: View Details leads to an empty Tree Browser
• Spring context doesn't start without DB connection
• Too many users are out of the box in IE11
• Submissions with "InProgress" status thrown NullPointerException at server restart
• No fused image is created and registration is prohibited from the Staging area/Submission page in case of Alternates, Mixtures and Formulations using Oracle DB
• Polymer matching fails upon modification

Known issues

• The structures within the multi-component compound fused images might be covered by the percentage.

August 23, 2018, Compound Registration 18.20.0-1808230810

Improvements

• Added ChemDraw 16 support
• Modal dialogs became adaptive, considering the screen size and its content
• Drag & drop functionality to bulk upload files
• Performance improvements during submission handling
• JChem version updated to 18.20.0

Bugfixes

• Project info cannot be set on the Registration/Submission/Browse page if Projects are not added from the Administration page
• Scrollbar missing in certain modal dialogs in IE11
• Too long additional data appears out of the box during bulk upload
• Required field validation is ignored during bulk upload
• Search export might get stuck in 'In progress' state and not complete
• Additional data not being captured during bulk upload when the molfile is invalid
• Migration issues with MySQL

Known issues

• Downstream Client with Additional data is not working

July 10, 2018, Compound Registration 18.7.9-1807061344

Improvements

• Search speed improvement:
  • by adding indexes to the additional data table
  • by requesting only structure images for visible entries on the Search page
• Add cursor navigation to select, combobox and typeahead input elements (by using the arrow keys)

Bugfixes

• SAML workflow:
  • After a certain period of inactivity, you get redirected to a user/password page rather than SAML workflow
  • Everything after the hash gets dropped after going through the SAML login workflow
• Migration failing with timeout for "No structure"
• "No structure" and "No CST" compounds are not sent to the downstream system
• Downstream client misses lots
• Sorting of search results might not work using Oracle
• Loading more results is not always present when scrolling down the search results
• Search criteria dropdown is not positioned correctly
• Search page criteria selectors are shifting
• Structure column is overlapping the Formula on the Search page
• Uploading "No structures": PCN mapping is not considered when the PCN of an already registered "No structure" is used
• Uploading "No structures" should fail when mapping the PCN of an already registered structure
• Browse, Viewing Collections appear in an Edit window with Apply option
• Pressing Esc button on the Form config's Level selection dialog leaves the overlay on the page
• Cannot delete a user with long name from the Group using Internet Explorer 11 as web browse
• Staging filter does not validate the input
• Not possible to leave the Search for Salts/Solvates field without selecting something
• Empty Upload page displays for a few seconds when user switches from the Bulk Upload Summary page
• File upload: when browsing twice the same file, the upload becomes inactive
• Form render issue when using \${currentDate} as Default value for Date field

Known issues

• "To Be Reviewed" functionality has been temporary removed from the Registration process (instead a "Two-step-registration" can be used during bulk upload)

• Database migration to this version fails on MySQL with certain configurations (ToBeReviewedValidator step is wrongly present in some workflows)

• Cannot set a Project info if Projects are not added on the Administration page

June 13, 2018, Compound Registration 18.6.11-1806081557

New features and improvements

• New improved form configurator

• Configurable Advanced mode registration option

• Mappable fields are sorted during bulk upload

• Type-ahead selection of fields for mapping during bulk upload is available

• User group membership info can be extracted from the authentication token

• Message extension

Bugfixes

• Fix for downloading/deleting submissions from the Upload Summary page
• Fix for login after using wrong AD settings
• Fix for placeholder text not visible for date field
• Fix for bulk upload containing no-structure but having CST (Invalid Structure Type validation error was received)

Known issues

• Migration failing with timeout for "No structure"
• Cannot set a Project info if Projects are not added on the Administration page

May 11, 2018, Compound Registration 18.5.14-1805110920

New features and improvements

• CompReg license can be uploaded from the UI: Administration/Tools/License Manager

• Expired license notification and warning that a license is about to expire appears on the toolbar

• The E-mail server configuration is available on the UI: Administration/Notification/E-mail

• LotId "unique" switch is removed. LotId "required" switch is kept. Administration/Integration/Identifiers/LnbRef and LotId

• Bulk upload page layout improvements

• Form arrangement improvements

• Admin user can have access to all uploads made by other users

• Register all is available from Upload Summary page

• Structures with error can be downloaded from the Upload Summary page

• Structures (ready, erroneous or all) can be deleted from the Upload Summary page

• Update structures is available from the Upload Summary page

• Long salt name are displayed on selection

• A filtered Staging area can be viewed using the error cards from the Upload Summary page

• Human readable status messages are displayed in the Staging area and Submission page

• Detailed structure checker errors are displayed on the cards of the Upload Summary page

API changes

• SOAP API has been modified: submission Status XML serialization changed

Bugfixes

• Fix the case of submissions with "Unknown error" in the Staging area caused by duplicate LotIds
• Fix for the not working LotId "unique" validation when the LotId "required" switch was off
• Fix for disappearing molecules during the upload
• Fix for not overwriting a valid license by an invalid one
• Fix for SQL exposure in exception message from installer wizard
• Fix for Upload Summary page IE11 layout issues
• Fix for Register lot page when no error message is displayed if the user enters an LnbRef instead of CN or PCN

Limitations

• If you use version 18.1.22 or earlier and the "required" LotId is off (which is the default setting), then your Identifier table can contain LotId(5) duplications, and 0 values. From now we do not allow duplications in that table. The data auto migration cannot be made, since data might be lost. Therefore, we strongly recommend to contact our Consultancy Team to do the upgrade.

Known issues

• Submissions cannot be downloaded/deleted from the Upload Summary page
• Cannot login after using wrong AD settings
• Migration failing with timeout for "No structure"

April 5, 2018, Compound Registration 18.04.09-2578

New features and improvements

• Two-step registration is available on the Upload page: submissions are not registered, but flagged with "Ready for Registration" and found in the Staging area
• Recent uploads are displayed on the Upload page
• Detailed summary report is available for each bulk upload session
• Selected/all submissions can be deleted from the Upload summary page

Known issues

• Migration failing with timeout for "No structure"

March 23, 2018, Compound Registration 18.03.26-2532

New features and improvements

• New statistic page created for each bulk registartion session with detailed summary report collected during the upload: successful and unsuccessful processes, errors, error categories etc..

Bugfixes

• LnbRef field appears again when the Virtual Compound button switched off
• Register lot functionality is not allowed in the Submission page
• Lots are moved to a new tree after version and lot level amendment using Oracle DB
• No Structure with CST as a component of an Alternate, Mixture, Formulation, or a Polymer is registered as No Structure instead of Single Structure
• Broken Register lot page in case of long additional data
• Wrong error message when bulk registering no structures by mapping existing PCNs

Known issues

• Migration failing with timeout for "No structure"

March 6, 2018, Compound Registration 18.03.12-2503

New features and improvements

• "No Structure" structure type is available, and it must be used to register compounds without structure
• "No Structure" compounds can be registered without providing CST
• Parent Ids (PCNs) can be mapped during the upload of "No Structures"
• Suggestion list is shown when amending structures
• Suggestion list displays all matches (e.g. Stereoisomer-Different CST)
• "Original structure" is stored also when amending a structure on parent level
• The list of previously uploaded files is shown on the Upload page
• New Administration page is created for Pages (Registration, Browse, Submission, Staging), Workflow, Notification and Navigation settings. Administration/Configuration page has been removed.
• Staging area and Search page have new table looks

Bugfixes

• New lot can be registered under an existing stereoismer with "ISOMER #" attached data
• Markush table contains all non-Markush results
• BrokerService error, memory allocation
• Lock fails because it's persisted
• Thumbnail image on the search page should reflect the same structure view
• Install wizard does not start for fresh instance
• Bulk upload stops working (ActiveMQ, JMS Connection is unable to recover)
• After registering a Markush structure a star atom is displayed on the lot level

Limitations

• The old match list is used for multi-component compounds during registrations and amendments

API changes

• SOAP API has been modified. "amendStructure" does not need source as parameter, it is already included in the structure

Known issues

• Suggestion list also be displayed if only additional data is changed
• When MySQL database is used and there are multiple Compound Registration schemas on the same server, please make sure that the configured database user has privileges only on the configured database schema
• Migration failing with timeout for "No structure"

January 15, 2018, Compound Registration 18.01.22-2339

New features and improvements

• JChem and Marvin JS upgrade. JChem: 18.1.0 (JChem table: 17290000), Marvin JS: 17.30.0

Bugfixes

• An underscore within a CST results in the subscript of the following character
• Active MQ does not persist messages

Known issues

• Installer wizard is broken, registry.properties should be configured manually.

December 12, 2017, Compound Registration 17.12.18-2275

New features and improvements

• The original (drawn or uploaded) structure is stored for the registered structure within the Compound History.
• Ability to amend a virtual compound (on parent and version level).
• Improved Registration option (formerly system switchers) configuration: Administration/Registration options
• Improved search: search is run only on the compounds for which the user has access
• Polymer generation: explicit Hydrogens can be considered as leaving groups (if the Remove Explicit Hydrogen standardizer action is not present in the configuration)
• Improved Identifiers configuration page: Administration/Integration/Identifiers
• Improved Structure checker configuration page: Administration/Chemistry/Structure Checkers
• Registered compounds can be linked to a 3rd party inventory: Administration/Integration/Links

October 25, 2017, Compound Registration 17.10.30-2159

New features and improvements

• New match (suggestions) list is used during registration.
• Additional data can be saved on parent level for multi-component compounds
• DB password is encrypted during command line or via web-interface installation.
• A script is available for clearing all the structures from the database while keeping the configuration, users, groups and projects in the system.
• JChem and Marvin JS upgrade. JChem: 17.25.0 (JChem table: 17240000), Marvin JS: 17.24.0
• Possibility to set license URL via the environment variable CHEMAXON_LICENSE_URL
• Security changes: Strong password is enforced; After a certain number of failed login attempts the user is locked out.
• Administration page changes:
  • New hierarchical navigation
  • New categories: Menu and Advanced. Menu : Access Control, Forms, Chemistry, Chemical structures, General settings. Advanced : Configuration, Sources, Integration, Tools.
  • Access Control includes: Users, Groups, Projects. Projects includes the formerly Configuration/SecurityConfig.
  • Forms: Forms and Fields, Dictionary Manager
  • Chemistry: General (Allow isotopic parent, Check for positive charges, Check for balanced charge); Salts and solvates (including also the salt/solvate related settings formerly from the Configuration/ValidationConfig); Standardizer (formerly Configuration/StandardizerConfig); Stereo Analyzer (formerly Configuration/StereoAnalyzer)
  • Chemical structures: Structure types (formerly Tools) including also the Polymer and Mixture settings (formerly Configuration/PolymerConfig and Configuration/ValidationConfig); Image options (formerly Configuration/StructureDisplayConfig)
  • General settings page is created includes: Date format, Show version level and Virtual compound registration
  • Sources: Source settings formerly from the Configuration/ValidationConfig
  • Integration: Downstream (formerly Configuration/DownstreamConfig); Identifiers including LnbRef and LotID settings (formerly Configuration/ValidationConfig) and General ID settings (formerly Configuration/IDConfig).

Bugfixes

• Cannot modify the Source on parent level
• Link from Search Results doesn't navigate to the correct record (when the same number is used as a PCN and LnbRef/LN)
• Submission is empty if Register lot is used with an invalid LnbRef
• Empty list items are listed when appending fields of forms
• Search performance issue when for a user that have no project based access to a lots of compounds present in the DB
• IE11, Mozilla FF: the ID field is empty on the Register lot page
• Dashboard is empty after logging in with case-insensitive username
• Changed source is not applied when using the Register lot functionality
• Cannot upload Markush or structures having OR1 flag
• LnbRefs should be trimmed during bulk upload
• Registration fails for Register lot if no LnbRef is provided
• Structure image generation fails due to corrupted additional data
• Using "chemicalterms" and FieldGenerator: name is changed also for the original structure
• Project based access on: tree is not visible
• Cancelled structural change is still applied
• Registration is not prevented when uploading an SDF that does not have the required fields

August 28, 2017, Compound Registration 17.08.28-1996

New features and improvements

• Ability to edit metadata of a lot when the lot is part of a multi-component compound.
• Structure types (e.g. Mixture) accessible from the structure editor can be hidden.
• Project assignment is made for case insensitive LDAP usernames.
• Email addresses as usenames and long usernames are allowed.
• Search button is disabled while a search is in progress.

Bugfixes

• Fix for Failing registration if name generation (via chemical terms) is used in case of empty structures.
• Fix for Load mapping file on the Upload page.
• Fix for Source change does not refresh additional data inputs on the Browse page.
• Fix for Unable to register with empty Project field using MySQL DB when using Project based access.
• Fix for No results are displayed when changing the search level (all the search criteria all deleted when changing the search level).
• Fix for Molecular formula overlaps the Molweight value using Internet Explorer.

Known issues

• Markush structures cannot be registered at all. Structures having "or1" flags can be automatically registered but cannot be registered using advanced registration mode or from the Staging area. Already registered Markush structures or structures with "or1" flags cannot be successfully changed/amended.
• Workaround: remove the StructureTypeValidator from all workflows (Administration/Configuration/WorkflowConfig) and restart the server.

August 9, 2017, Compound Registration 17.08.14-1931

• Suggestion list improvements.
• Adding primary key to the MULTI_COMPONENTS table.
• Fix for polymer publishing to downstream when associating projects.
• Fix for NPE when "chemicalterms" was used (Oracle).
• Fix for Active Directory authentication issue.

July 21, 2017, Compound Registration 17.07.24-1889

• New navigation bar.
• New layout of the Registration, Submission and Browse pages.
• The registration of compounds having Unknown CSTs can be controlled by a switcher, CSTs are not automatically added to the CST Dictionary.
• Formerly "Check" option is renamed to "Find" (near to the structure editor).
• Suggestion list improvements: the formerly "2D match" type is replaced with "stereoisomer" and "CST different" match types.
• LDAP usernames can be used case-insensitive during login.
• Fix for the constant flashing error (There is no configuration for "") received on the Browse page.
• Fix for the failing polymer publishing to downstream when using projects.
• Fix for the SOAP authentication issue.

July 03, 2017, Compound Registration 17.07.10-1844

Bug fixes related to:

• Basic authentication
• JChem version dependency clash

June 23, 2017, Compound Registration 17.06.26-1828

• Registration of virtual compounds (compounds without lots) is available on the Registration and Upload pages.
• New "Check" window (Suggestion list) for suggested structures based on the database matches is available on the Registration, Submission and Browse pages.
• Fix for the successful saving of the mapping file on the Upload page.
• Fix for the SDF file import of submissions in the Staging area.

June 7, 2017, Compound Registration 17.06.12-1738

Resource handling of Compound Registration has been changed!

External resources of the registration system will be loaded from the home directory from now on. More details can be found here.

The installation wizard is available. Includes the followings:

• License configuration page
• Database configuration page
• Creating the admin user
• Welcome page for missing properties

The login.html was removed and the login page is put in the angular application.

Improved polymer handling.

Fix for: Cannot use any type of LnbRef when loading components from the DB

Fix for: Substructure search won't find every eligible structure

Fix for: Applet is not loading in IE

Fix for: Project info is displayed twice on the Browse page if the Project based access is enabled

Fix for: The project list has an empty item when a submission without project is in staging (Oracle)

May 16, 2017, Compound Registration 17.05.22-1687

• New login page and login.html has been removed.
• New REST API documentation
• Exchange webservices2 with custom MarvinJs services (integrated to a custom controller).
• The application can run without authentication properties.
• Project lists can be stored/displayed for a lot.
• Back to search results remembers the exact position in the Search result list.
• Improved polymer representation.
• JChem version upgraded to 17.2.27.
• KahaDB was eliminated, temporary files are not created.
• "Update layout" info can be delivered in the downstream system.
• New salt/solvate import.
• Fix the substructure search in order to display all the matches.
• Fix the applet not loading issue in IE.
• Fix for Register lot not successful if providing the LnbRef is not required.

April 3, 2017, Compound Registration 17.04.10-1606

• Components can be loaded by providing the LnbRef.
• The full name and email of the user can be saved.
• Search page: select all option is available.
• Search page: sorting is remembered.
• UI is adapting to the screen size.
• Fix for "Created on" field is not populated on the UI.
• Fix for preventing registering Mixtures containing two identical components.

March 9, 2017, Compound Registration 17.03.13-1525

• The search field is added to the navigation bar, left side Browse is removed.
• New style Search page: more intuitive "More columns" dropdown, more intelligent row clicking, remembering column configuration.
• New improved Forms and Field configuration page.
• Administration menu order change.
• New style Dictionary Manager.

February 21, 2017, Compound Registration 17.02.27-1504

• New Salt and Solvate page.
• Improved Forms and Fields Configuration.
• REST API documentation available.

February 9, 2017, Compound Registration 17.02.13-1447

• System requirements have been changed to Java JDK: 1.8 and Apache Tomcat 8.
• Improved Access Control: new Users & Groups and Projects pages.
• Fix "Register All" issue from the Staging area in case of compounds having no structure just CST.
• Fix the bulk upload issue for large SD Files containing compounds having no structure just CST.
• Fix for Oracle issue, when adding additional data resulted in a list.
• Fix for Register lot functionality used from the Submission page.
• Fix for the shifted table columns on the Staging and Search page.
• Fix for advanced registration in the case when Id providing (LnbRef) is not needed.
• Fix for bulk upload when invalid format characters where used for salt fields.

January 24, 2017, Compound Registration 17.01.30-1410

• Improved the handling of multi-component compounds. Store components at version level.
• Introduce handling of Polymers. Polymers can be created and stored from registered monomers.
• Project info can be amended.
• Fix the bulk upload issue when "Auto-generated" was set for the Library identifier.
• The "matchId" property has been removed from the API calls and its functionality was merged into the "compId" property.

November 18, 2016, Compound Registration 16.11.21-1195

• Field generator (e.g. Chemical Terms) implemented.

November 7, 2016, Compound Registration 16.11.07-1164

• Ability to register a lot from the Browse page.
• Ability to navigate back to the Search page from the Browse page.
• Improved field configuration.
• Storing the "source" also for parent and version level and "source" changes can be saved on each level.

October 11, 2016, Compound Registration 16.10.17-1095

• Fixing Internet Explorer 11 Registration page issue.
• Structure Editor: salts and solvates are listed with their names and IDs.

October 10, 2016, Compound Registration 16.10.10-1092

• The new layout of the Registration, Submission and Browse pages.
• Browsing page with two different looks: View and Edit mode.
• Forms and fields validations are available.
• Measurement data can be registered within a collection type group.
• Salts and solvates can be added from one single button.

August 31, 2016, Compound Registration 16.09.05-917

• Expanding the Register lot functionality.
• Simplifying the storing of multi-component compounds.
• A prototype for measurement data is available.

August 22, 2016, Compound Registration 16.08.29-897

• Date filtering is available on the Search page.

August 15, 2016, Compound Registration 16.08.22-870

• Publicly accessible download site for the Compound Registration was created.

July 25, 2016, Compound Registration 16.07.25-806

• Monitoring that checks the availability of CompReg test servers was added.

July 18, 2016, Compound Registration 16.07.18-795

• Changes in the REST API to enable requests of structures based on any ID.

January, 2014: Compound Registration 6.2.0

New Features and Improvements

Registration Web Client

• An administration interface is available for the new general dictionary handling module
• New stereo and geometric isomerism sample dictionaries are available that can be used e.g. in the configurable dropdown fields
• New staging table user interface was created that features dynamic filtering and pagination free navigation
• Staging area user interface can now have different configurations for different user groups (if a user is part of multiple groups then the union of the items defined for the groups will be available for the user)

Registration Back-end Services

• A standardized server-side parameter management solution is implemented that helps the easy configuration of the back-end business rules
• A refactored packaging is provided with a single war file for easier deployment
• External data reader service is now fully integrated into the application
• A command line tool can be provided to help the MySQL-to-Oracle migration
• On parent and version level the submitter is also calculated from the preparation level data
• A general dictionary handling module is provided on server side
• A new Spring based authentication solution is provided that supports authentication against local DB, LDAP, AD
• Submission source based StuctureChecker configurations of the system are now exposed to the client application(s)

Integration, Export-Import

• The VERSION_SALT_SOLVATE table is populaterd during the downstream data transfer

Bugfixes

Registration Web Client

• A parent-only record could not be displayed when the system was configured to hide the version level
• Event triggering and synchronization issues are fixed when using the structure editor in Mozilla Firefox
• The fused image is the default view and all the necessary buttons are enabled on the amendment page even if using MarvinJS as a structure editor

Registration Back-end Services

• LLA: twig optimization was performed when two lots were present but the user had permission only for one of those lots
• Users having only "read", "read_own" or "write_own" permissions within a project could undelete lots which belonged to other users
• The submitter ID of a newly created version was enherited from the parent instead of the lot
• After accepting a match the newly created version would not inherit the submitter of its own preparation

November, 2013: Compound Registration 6.1.3

Improvements

Registration Web Client

• An additional button is available on the registration confirmation dialog that redirects to an external page
• Customizable dropdowns can be created optionally on the free-text input fields of the registration page
• It is possible to include the logged in user ID in the validation query of the fields on registration page
• The content of the "Registration successful" is now configurable

Registration Back-end Services

• A refactored packaging is provided with a single war file for easier deployment
• LotID is now populated with the autoincremented ID of the PREPARATION DB table if the incoming LotID is 0 and LotID validations are turned off

Integration, Export-Import

• The VERSION table of the downstream DB contains a fused structure image of the version (besides the structure and salt fingerprint)

Bugfixes

Registration Web Client

• Salt import issues fixed on certain combinations of Internet Explorer 10 - Java 7 runtime - https connection
• No results were displayed on the search page if the user had no permission to view the first 5 preparations
• Long text entries were not visible in the dropdown fields
• Using Internet Exploer 10 project access control window was empty
• Once Marvin JS was loaded, parent multiplicity could not be modified
• CST dropdown on Registration/Submission/Amendment pages was hidden behind the structure editor
• Close button had to be clicked several times in order to close a structure opened from a search query list

Integration, Export-Import

• Records having parent multiplicity were not going downstream
• Submissions registered by the Bulkloader are now properly transferred downstream

September, 2013: Compound Registration 6.1.0

New Features and Improvements

Registration Web Client

• Hiding the Version level on the Amendment page is configurable
• Hiding the Version level on the Search page is configurable
• It is possible to bulk register saved/restored submissions
• Salts and/or solvates can be imported from an SD file
• Marvin for JavaScript as available as a structure editor
• The displayed columns on the Search page are customizable
• The 'Assign to specified user' functionality is available on the Submission page
• Project data can be searched and filtered on the Search page
• Project info storage and basic administration GUI page

Registration Back-end Services

• A new service method is available that returns and also reserves the next available PCN(s)
• Project based restrictions are applied for registration, staging, amendment and search procedures
• Hiding the Version level on the Amendment page is configurable
• Hiding the Version level on the Search page is configurable
• The autoversionfix code is updated with the new MCES algorithm
• Project data can be searched and filtered on the Search page
• Configurable corporate ID can be generated for the Lot level

Bugfixes

Registration Web Client

• It was not possible to bulk register submissions with edited structures, the records were registered with their original structures, not with the modified ones
• On the Search page a part of the search query and results were greyed out
• On the Amendment page it was not possible to change the parent multiplicity if the salt/solvate info was not modified
• Structure type was empty for registered records with "unknown=isomer #" data
• Bulkloader was not working and it was not possible to successfully import salt/solvates from an SD file using IE10 browser

Registration Back-end Services

• It was not possible to continue a registration that involved manual version fix if an inconsistent tree was caused

Integration, Export-Import

• Exported search results containing "or#" flags and "and1" flags with "Range 56-79%" were not displayed in MarvinView

July, 2013: Compound Registration 6.0.2

Bugfixes

Registration Web Client

• Staging table was empty when running Oracle on certain localizations

June, 2013: Compound Registration 6.0.1

Improvements on the Registration Web Client

• Apply common Chemaxon style to the User administration table
• Salt search table cleanup, styling and usability changes

Bugfixes

Registration Web Client

• The "No salts and solvates found" message was not received when searching for non-existing salt/solvate Id
• The registration/amendment of records with the salts/solvates was not possible using the "Open salt admin page" button in the "No salts and solvates found" window
• On the Amendment page when changing the structure type or added/modified a component CST, there was no Amend option unless you click in the structure area or in the CST field
• It was not possible to register a CST only record using ChemDraw as structure editor if you clicked on the structure area
• Mixtures with ranges [21-44% and 45-55%] / [56-79% and 45-55% ] were not client validated and they fell to the Staging area
• On the Submission page there was no response when clicking on Register after correcting the LnbRef

Registration Back-end Services

• When using the register with CN option the lot level additional data were not stored
• Inconsistent tree was caused after amending a single compound to a multi-component compound when the components are newly created and further amendment is performed on the multi-component compound while the parent and version Ids are kept
• Two PCN's are reserved for the same component when registering a multi-component compound with two components having the same component (with isotope or with charge)
• It was possible to register salts/solvates without name
• The RejectId system switcher set to "true" had no effect on "No structure" submissions since these were still visible in the Staging area

May, 2013: Compound Registration 6.0.0

New Features and Improvements

Registration Web Client

• Ability to use ChemDraw as a structure editor instead of MarvinSketch applet
• Internet Explorer compatibility (v9 or higher)
• Configurable data input fields on the Registration page (mandatory/optional fields, data validation rules)
• Chemically Significant Text dictionary, ability to select CSTs from a predefined list
• Specify custom molecular formula during registration, store in the database
• Enter project data for submissions, configure data validation on project input
• View project data for parent, version and lot levels on the Amendment page
• Real-time validation of input fields on the Registration page

Registration Back-end Services

• LotID validation configurability – mandatory/optional, uniqueness check
• Storage of project data in the registry database
• Return project data for parent, version and lot levels
• E-mail feedback to the submitter about the status of a submission

Integration, Export-Import

• Active Directory integration
• Support Oracle 11g as a back-end DBMS
• Downstream service – ability to send all structure data modifications of the registry to a JMS messaging server, create a default implementation of the message consumer

Bugfixes

Registration Web Client

• Version level amendment issues of multi-component structures when components also exist as singles
• “Show all” button did not work on the Search page
• Accept and Replace buttons were available even if there was an exact match in the database
• Structure/CST amendment was allowed even if the level to be changed had no lots
• Delete structure window did not disappear after deleting a PCN
• Amendment of multi-component structured was not successful if component removal and structural changes happened at the same time
• “Open salt admin page” button did not work
• Register button in the Staging area / Submission page was not active after a structurechecker error
• When amending a CST-only single to a multi-component compound the CST was also added to the first component
• “Analyze salt/solvate” switch did not work in the Staging area
• Complex PCN-separation cases did not work
• LotID validation allowed non-numeric entries
• Submissions with InvalidSalt status could not be registered anymore
• Audit of parent level amendment showed version structure on the target side
• Salts and solvates could not be searched by ID in the “Add new salt/solvate” window
• List of recent salts and solvates contained the same entry multiple times
• Search page showed ‘results 1-5’ in the status line even if there were less than 5 results
• User supplied molecular weights were not considered when searching
• Version molecular weights were shown only without salts/solvates
• Single to multi-component amendment was enabled and failed on parent level
• No warning message and login dialog came when the session expired
• Fixed to use “:” instead of “-” before salt multiplicities
• Match list did not show “Accept” and “Replace” buttons for tautomer matches
• “Similar to” option was missing from CST search on Search page
• Rename LnbRef to an invalid one showed a summary of the unsuccessful modification and redirected the user to the non-existent invalid ID
• Molecular weight and CST were not editable after the “components used elsewhere” warning dialog
• Salt/solvate removal in version level or lot level amendment of singles was unsuccessful
• Submission was not assigned to the user when opened up from the Registration page
• In Mozilla Firefox the “Register”, “Amend” and “Add Salt/Solvate” buttons had to be clicked twice in order to perform the operation
• Editable additional info on Submission page could not be added after once deleted
• Could not add a salt or solvate to the dictionary if first navigated to another tab of the administration page
• Staging area showed an empty page when having more than 8000 entries
• Salt search page did not work properly
• Manage database dialogs on the Administration page did not return proper error message if the provided password was incorrect
• After hitting Enter instead of clicking on the “Deploy database” button (Administration page - Manage database tab) the password was displayed in the URL field of the browser and the requested operation was not performed

Registration Back-end Services

• Parent multiplicity validation problems, values other than 1 accepted even if there were no salts/solvates
• Undelete of a version returned a NullPointerException when the lot under the deleted version was moved to another tree
• No results were returned by the GetNextDirtyTree service call if the tree had no lots
• Could not register/amend a multi-component structure if a component had isotopes on explicit hydrogens
• Version level amendment issues of multi-component structures when components also exist as singles
• Structure/CST amendment was allowed even if the level to be changed had no lots
• Version level amendment was unsuccessful if previously a lot was deleted and a new lot registered to the same version
• Complex PCN-separation cases did not work
• Isotopes were lost in manual version fix cases that involved explicit hydrogens
• Analyze salt/solvate method fixed to return a proper submission status
• Amendment of isotopic/charged single to multi-component (on version or lot level) resulted in 2 parents created for the same component and an unsuccessful amendment
• CST modification involving manual version fix could not be performed
• Changing structure (CST) and salt/solvate info at the same time in twig optimization cases showed no salt/solvate modification in the audit
• Bulkloader could not register without lot ID even if lot ID validation was switched off
• New version was created after registration from Submission page involving manual version fix
• Specified molecular weight was not saved during autoregistration
• Molecular weight (structure and salt) condition did not work together with substructure search

Integration, Export-Import

• Superfluous characters appeared in the result of the SD file Export, SD file was unreadable
• Downstream systems did not reflect move lot and manual version fix changes
• Exported SD file was empty if any of the search results had a null molecular weight