[Notebook] Biovia notebook 2023 risk assessment

Owned by Niraj Khaitan
Last updated: Jul 24, 2023
5 min read

Description :

  • A risk assessment on the latest update to Biovia. After reading the "BIOVIA_2023.BIOVIA_Notebook_2023_Product_Release_Document", User have some questions what some of the fields actually mean, and if that change will have an impact on the functionality or effect how we use Biovia. Unfortunately, user is not that familiar with the computer language. User have listed the changes they do not understand here:

    • ACL endpoints are now included in the Notebook API help page. The ACL endpoints in the lookuptype resource are marked as deprecated. Object type validation has been added to the ACL endpoints.

    • Functionality for managing projects and project ACLs has been added to the REST interface. There is a new endpoint, GET v1/projects/{id}/members. In addition, all POST, PUT, GET, and DELETE ACL (and VACL) endpoints support a new Project object type.

    • Notebook web applications and Windows services now use common assemblies from a single location, instead of deploying multiple copies of the same files. ElnUpgrader now stops and starts IIS when upgrading binaries, as needed.

    • A spurious ArgumentNullException" warning message is no longer written to the Notebook log when the API endpoint to show recent experiments is called, and Notebook is connected to Foundation Hub.

    • The getAppNameFromURL functions of the Notebook and Data Archive web clients that determine application scope, and specify the content of the web page, now handle request URLs containing query parameters adequately.

    • It is now possible to import old submitted experiments when their content does not comply with all requirements of new experiments.

    • The logic of image storage has been improved. If the PNG file is smaller than the original file, the PNG file is used. If the PNG file is larger than the original file, a JPEG file is also generated, and the smaller of the PNG and JPEG files is used. - is it possible to manually change this if you want the PNG file?

    • The SQL server script InsertaAclsForAdminGroup.sql now runs without errors.

    • The RecreateAsciiContentIndex procedure in the Oracle upgrade script now executes successfully, without throwing exceptions.

    • The OData filter expressions "substringof" or "endswith" can now be used with the GET v1/templates endpoint. This capability was temporarily removed in Notebook 2022 SP1.

    • When an experiment is deleted using the DELETE v1/experiment endpoint, or when the PURGEDOCUMENT stored procedure is executed, related records in the EXPERIMENTSHARING table are now also removed.

    • A new endpoint, api/v1/groups/id/privileges, allows privileges to be set for groups. It is no longer necessary to use the api/v1/users/id/privileges endpoint for groups.

    • If upgraded from a version showing the wrong entry in the control panel, the entry is not fully updated.

    • ElnDirectorySyncService takes a long time to get data from AD.

    • A submitted invalid experiment does not display in the "Waiting for Co- Signer" section in the witness's Notebook web client.

    • The co-signer receives a “Could not load experiment” error when attempting to sign an experiment.

    • If it is possible an explanation what these points mean or if these changes impact our use of Biovia would be great.

Solutions: DS have categorized the List of Issues you provided into the four categories below. The replies are in parentheses are at the top of each section and for each time in the Known Issue section.

  • API fixes/enhancements:

    • (These are all REST API backend changes and enhancemnts. Only useful if you speciafilly work with the Notebook API or are intergrating Notebook with other BIOVIA applications like Pipeline Pilot. None of these wil affect your existing userbase)

    • ACL endpoints are now included in the Notebook API help page. The ACL endpoints in the lookuptype resource are marked as deprecated. Object type validation has been added to the ACL endpoints.

    • Functionality for managing projects and project ACLs has been added to the REST interface. There is a new endpoint, GET v1/projects/{id}/members. In addition, all POST, PUT, GET, and DELETE ACL (and VACL) endpoints support a new Project object type.

    • A spurious ArgumentNullException" warning message is no longer written to the Notebook log when the API endpoint to show recent experiments is called, and Notebook is connected to Foundation Hub.

    • It is now possible to import old submitted experiments when their content does not comply with all requirements of new experiments.

    • When an experiment is deleted using the DELETE v1/experiment endpoint, or when the PURGEDOCUMENT stored procedure is executed, related records in the EXPERIMENTSHARING table are now also removed.

    • A new endpoint, api/v1/groups/id/privileges, allows privileges to be set for groups. It is no longer necessary to use the api/v1/users/id/privileges endpoint for groups.

  • Installation and Upgrade fixes/enhancements:

    • (These are enhancements to the Notebook upgrader and installer. These will not affect your existing userbase.)

    • The SQL server script InsertaAclsForAdminGroup.sql now runs without errors.

    • Notebook web applications and Windows services now use common assemblies from a single location, instead of deploying multiple copies of the same files. ElnUpgrader now stops and starts IIS when upgrading binaries, as needed.

    • The RecreateAsciiContentIndex procedure in the Oracle upgrade script now executes successfully, without throwing exceptions.

  • Notebook Server Fixes and Enhancements:

    • (These are Notebook Fixes These should will not affect your existing userbase in most cases).

    • The getAppNameFromURL functions of the Notebook and Data Archive web clients that determine application scope, and specify the content of the web page, now handle request URLs containing query parameters adequately.

    • The logic of image storage has been improved. If the PNG file is smaller than the original file, the PNG file is used. If the PNG file is larger than the original file, a JPEG file is also generated, and the smaller of the PNG and JPEG files is used. - is it possible to manually change this if you want the PNG file? (No, it currenlty is not possible to change the behavior image storage process)

  • Known Issues:

    • If upgraded from a version showing the wrong entry in the control panel, the entry is not fully updated. (If Notebook had been updated from previous versions and if the control panel is showing the wrong name and/or the version in control panel, upgrading to a version above 2021sp1, the version is correct but the name still appears as the wrong name.)

    • ElnDirectorySyncService takes a long time to get data from AD. (The time it takes for the winodws service ElnDirectorySyncService to communicate with the sites defined AD Server needs to improve)

    • A submitted invalid experiment does not display in the "Waiting for Co- Signer" section in the witness's Notebook web client. (If the Errata Secction type is added to an experiment with the value Invalid the the experiment will not display in the "waiting for co-signer" section of the witnesses Notebook web client.)

    • The co-signer receives a “Could not load experiment” error when attempting to sign an experiment. (“Could not load experiment” mesaage only appears if the user only has the co-sign permission for the experiment. Co-sign user is still able to sign the experiment.)

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