3^rd party upgrades:

OpenSSL library  - version 1.1.1o

Apache HTTPD  - version 2.4.53

Apache Tomcat  - version 8.5.78

Zlib – version 1.2.12

Expat – version 2.4.7 (upgraded in Pipeline Pilot 2022 HF3)

PPC-10532

PPC-10007

PPC-10679

PPC-10685

PPC-10636

3^rd party upgrades for Profesional Client:

WinMerge – version 2.16.20

CEF (Chromium Embedded Framework) – version 102

OpenSSL library  - version 1.1.1o

Zlib – version 1.2.12

Expat – version 2.4.7

PPP-48243          

PPP-48268

PPC-10532

PPC-10685

PPC-10636

The file extension .aspx was added to the list of blocked file extensions for upload.

PPP-48306

Description

Areas Affected

Risk Level

 User Story

Added seven optional parameters to the BIOVIA SCSR Template and HELM Monomer definition.

The following new SCSR Template optional keywords are included in the SCSR Template line of the .mol file:

1. FULLNAME
2. CATEGORY
3. UNIQUEID
4. COMMENT
5. CASNUMBER
6. COLLABORATOR
7. PROTECTION

The following corresponding SCSR template parameters are in the centralized library:

1. TemplateFullName
2. TemplateCategory
3. TemplateUniqueID
4. TemplateComment
5. TemplateCasNumber
6. TemplateCollaborator
7. TemplateProtection

Corresponding HELM Monomer properties in SD file as property and in centralized library:

1. MonomerFullName (can be the same as Name property if it exists in file)
2. MonomerCategory
3. MonomerUniqueID
4. MonomerComment
5. MonomerCasNumber
6. MonomerCollaborator
7. MonomerProtection

The value of these optional parameters is string type. If the value of a parameter is empty, the keyword/value pair will not be written into the SCSR template .mol file.

Global Configuration files are modified with these additional parameters, while the coordinates of the SCSR Template and HELM Monomers are not changed.

All Pipeline Pilot Components, Protocols, and Webport applications are modified to work with these additional properties to create, modify, search, and create configuration files from the PLP- and HUB-based Centralized library.

In this release, the SCSR sequence .mol file with local template will not have these optional parameters for backward compatability.

Biologics, Centralized Monomer Libraries

Low

PCHE-8414

Pipette Sketcher is updated to version 3.6.3. This version has enhancements to the Pipette Biosketcher, including support for new fields in HELM monomers and SCSR templates (Category, Unique Id, Comment, CAS Number, Collaborator, and Protection.)

Pipette

Low

PCHE-8505

Updated the Desktop Connector Client. The Hostprocess (Legacy) mode in Chemistry Sketcher is removed, and the default mode is now Messaging Service.

Sketchers

Medium

PCHE-8572

Chemistry Sketcher is updated to support ChemDraw version 21.

Sketchers

Low

PCHE-8577

Minor

When setting values from configutil that start with '-' on Linux or Windows or with '/' on Windows, you can now precede the value with a single backslash character '\' to allow setting the value, such as "configutil <admin login info> -set -r MyKey -v \/some/value" or "configutil <admin login info> -set -r MyKey -v -100".

PPP-48291

Minor

Fixed an issue in the Administration Portal, so that Backup, Restore, and Purge operations on the Protocol database now correctly show a running log of the requested operation, instead of a blank page.

PPP-48311

Major

Depictions for reactions that include SCSR sequences now include reactant and product labels (defined by SMMX:RXNMOLLABEL DAT Sgroups).

Chemistry Depiction

Low

PCHE-8559

Minor

Fixed an issue that resulted in extra pairs of brackets being depicted for some molecules with polymer Sgroups.

Chemistry Depiction

Low

PCHE-8564

Minor

Fixed a bug in the Reporting collection's File Chooser component where a successful file upload would result in an ambiguous message implying both failure and success.

PPP-47600

Minor

Corrections have been made to the regular expression generator for CORS origin matching to fix some issues related to repeated name patterns and optional port specifications.

PPP-48174

Minor

Fixed an issue where files written to S3 had a WebDav path as content instead of the expected content.

PPP-47797

Updated the Pipeline Pilot 2022 installer to enable the installation of the Chemistry SDK package as part of the server installation when the PP Chemistry SDK feature is included in the license file.

PPChem API

Low

PCHE-8462

Minor

Fixed an issue where the Admin Portal Setup/Server Configuration and Security/Security Configuration pages would not notify the administrator when settings that require a restart of the Apache and Tomcat PLP services are changed.

PPP-47526

Minor

Fixed the Security/Authentication page to work correctly when logged into the Admin Portal as an external account (such as a Windows Domain or Linux Local user).

PPP-47618

Major

Fixed an issue where setting the parameter "Use Absolute Urls" to true would create invalid JavaScript within HTML reports written to locations outside the job folder if the report included interactive charts. 

"Use Absolute Urls" is a new parameter for Pipeline Pilot 2022 that restores version 2021 and earlier behavior of writing absolute HTTP URLs within reports.  The default behavior of reports in v2022 is now to use relative server paths for internal HTML links (see the Release Notes for v2022), but there are use cases where the absolute paths must still be used.

PPP-47592

Minor

Browsers with existing valid session cookies from prior versions of Pipeline Pilot (version 2021 and earlier) would not be able to authenticate to a 2022 server. The server home page and web port portals would become inoperative and the login page would not work correctly. The server error logs would indicate that the session had expired.

This would most often occur immediately following an upgrade of an existing Pipeline Pilot server.

Such valid sessions are now converted to the new format.

PPC-10539

Minor

It was observed that large numbers of API HMAC /auth/serverstatus log messages would appear in the scitegicerror_apache.log when Professional Clients would connect to the server from hosts with large latency to the server, such as from a separate continent. The messages were innocuous and generally did not affect the client's behavior. The messages will now only appear if multiple API HMAC failures occur on the server in rapid succession.

PPC-10536

Major

Guidance and installer update to ensure a Windows server has the latest VS2017 redistributable required by the Qt library used in the chemistry collection.

PPD-2881