T43-2020 Notification regarding BIOVIA Pipeline Pilot 2020

Minor

The Administration Portal will no longer import a data source whose name ends with a trailing whitespace character. Leading and trailing whitespace characters will now be trimmed on import and the data source will be stored without them.

PPP-43321

Minor

Fixed the description of the actions available to the Administrator for editable package-defined tasks.

PPP-43693

Minor

Fixed an issue where the Administration Portal's 'Scheduled Tasks' page could not handle scheduled tasks with invalid xml definition files (empty files for example). Additionally, administrators can also delete those files from the Administration Portal.

PPP-43695

Minor

Updated Tagged Resources to be compliant with the deployed JavaScript visual grid library version.

For resource access rights, the Deny option was removed as an option for the "Everybody" entity.

PPP-43715

Minor

Fixed an issue where connecting to the admin portal of a Load Balanced Pipeline Pilot server through the Load Balancer would show the option for displaying "Installed Collections", but selecting the page would show a message indicating the page is disabled due to the Load Balanced configuration.

PPP-43824

Minor

Fixed an issue in configutil where file path settings could not be set correctly due to folder slash direction. The configuration requires forward slashes for many settings while configutil required back slashes.

PPP-44055

Minor

Fixed search failure with ACL users/groups containing UTF-8 characters.

PPP-44131

Minor

Usage Report: Fixed incorrect count of users in User Seats table; fixed inconsistency in Pro User collections table; fixed Logfile summary table showing the same version of logs twice.

PPP-44180

Minor

Fixed an issue where Admin and Client search were not working in servers configured with non-default Shared Public Directory values. The underlying protocols affected have been updated. 

PPP-44464

Minor

Fixed an issue with the NCBI Eukaryota Taxonomy Tree example protocol when run on Pipeline Pilot HTTPS servers. The example now retrieves data from NCBI using the HTTPS protocol. 

PPP-43600

Minor

Reformatted several examples to make the sticky notes easier to spot.

PPP-43635

Minor

Updated the Run Program (on Server) component to convert arguments in the command line that contain URI file paths to the applicable absolute paths. Other "Run Program ..." components  (for example, Run Program (on Grid) or Run Program (on Remote Server)) were not updated because the environment the program is running in (such as Grid or Remote Server) may not have access to the absolute paths of the Pipeline Pilot server. 

When using URI file paths in command line it is important that the URI argument is quoted so that URI file paths with spaces are appropriately handled.

For example, the command line for listing the files in a selected directory should be:

ls '$(DirToUse)'

instead of:

ls $(DirToUse)

PPC-9320

Minor

Updated the Run Program (on Server) component to convert arguments in the command line that contain URI file paths to the applicable absolute paths. Other "Run Program ..." components  (for example, Run Program (on Grid) or Run Program (on Remote Server)) were not updated because the environment the program is running in (such as Grid or Remote Server) may not have access to the absolute paths of the Pipeline Pilot server. 

When using URI file paths in command line it is important that the URI argument is quoted so that URI file paths with spaces are appropriately handled.

For example, the command line for listing the files in a selected directory should be:

ls '$(DirToUse)'

instead of:

ls $(DirToUse)

PPC-9320

Minor

The full path values generated by the List Files components now use the secure URI format for file locations.

PPP-42599

Minor

Fixed an issue where transferring large (> 2GB) files via the SCP component would fail.

PPP-43767

Minor

Fixed an issue where the SMTP Mail Writer did not work with file URI filenames (for example, userdata:/, job:/, etc) when processing the attachments list. Also fixed an issue where reader components would fail with file URI filenames (for example, userdata:/, job:/, and so on) when the administrator had restricted component file access.

PPP-44026

Major

For Pipeline Pilot grid deployments, increased the default time for removing jobs that remained in a queued state for longer than 1 day to 14 days, and made this value configurable.

PPC-9288

Minor

Fixed an issue with difficulties in debugging unknown grid options specified in the Grid Options parameter.  Additionally, properly formatted Grid Options can now be transferred to the submission scripts as environment variables.

PPC-9267

Minor

The HTTP Connector component now supports HTTP PATCH requests, which may be required to apply partial modifications to a resource.

https://en.wikipedia.org/wiki/Patch_verb

PPP-43792

Minor

Updated the HTTP Connector component to support NTLMSSP authentication to remote HTTP/HTTPS services via the Http Negotiate authentication protocol. Previously, Http Negotiate supported only Kerberos token authentication, while NTLM username/password based authentication was restricted to the Http NTLM protocol. To use NTLMSSP, configure the server with Impersonation and set the HTTP Connector's Authentication Method parameter to "Use Pipeline Pilot Credentials".

PPP-44025

Minor

The GEMS package (with its scheduled tasks) component is no longer installed by default. It is now only installed with applications that  require it.

PPP-42667

Minor

Restored Apache Tomcat server logging on Linux.

PPP-43946

Minor

Restored Apache Tomcat application logging to a single log file from daily logs.

PPP-44132

Minor

WARNING: This can affect the behavior of existing protocols.
 Updated the Pipeline Pilot "is whitespace" detection to include Unicode space characters. This brings Pipeline Pilot's internal isspace() function in line with the Microsoft implementation of iswspace() which includes the POSIX standard whitespace characters described in https://en.cppreference.com/w/c/string/wide/iswspace, but also includes non-breaking whitespace and ellipsis characters (0x0085, 0x00A0, 0x2007, 0x202F).

This affects a number of different sections of Pipeline Pilot including the Pilotscript "trim()" function and JSON processing. In most cases, there should be no change of behavior as this primarily changes the state of extended Unicode white space characters.

PPP-43621

Minor

Fixed an issue where the PilotScript function "doesfileexist()" would fail with an error for shortcuts that did not exist such as "shortcut:/does_not_exist/mypath/myfile.txt" and other paths where the format of the path was invalid in some way such as "htttttp:/myserver.com". The function now returns "false". This also may affect the error messages created when passing in invalid source parameters for readers and other file path based components.

PPP-44081

Minor

Fixed an issue that occurred when renaming subfolders and subfiles in the Server File Explorer.

PPC-9321

Minor

Fixed an issue with the Server File Browser within the Professional Client where attempting to create or rename a subfolder would result in the folder appearing instead at the top level with a corrupted name.

PPP-43774

Minor

Fixed an issue where the Data Record Tree Viewer and Global Data Tree Viewers would not appear if a snapshot window from a prior Global Data Tree Viewer component was still visible.

PPP-43838

Minor

Fixed an issue with the Professional Client where the dialog for editing array parameters would show an extra blank line when editing an empty parameter. Additionally, when the dialog appears, the edit box window is now active by default.

PPP-44104

Minor

Fixed an issue with display of invalid error messages within the Server File Browser when a selected file path does not exist.

PPP-44205

Major

Fixed an issue where the Pipeline Pilot Client would sometimes shut down if a browser-based window within the main view, such as the Client Welcome Window or Protocol Search Window, was closed. This often happened with the Window/Close All command.

PPP-44472

Minor

Fixed sorting of files and folders by Date Modified in the Server File Browser of the Professional Client.

PPP-43786

Minor

Fixed an issue where creating or deleting folders within the Protocol database from usernames containing dots (e.g. "jane.doe") would cause invalid folders to exist within the Protocol Database containing a URL encoded form "%2e".

PPC-8725

Minor

The Python component can now handle unicode characters in comments.

PPP-44214

Minor

Changed the behavior of the Python (on Server) component for DateTimeValues.
 The changed code will now generate a Python datetime.time or datetime.datetime object out of a DateTimeValue, even if the seconds field was not set. In such a case, seconds will be set to 0. Previously, None was returned.

PPP-44228

Minor

The Python component now supports the sqlite3 module on Linux.

PPP-43733

Minor

Fixed a minor issue in the Python on Server component that led to duplicate entries being added to the PythonPath .

PPP-43807

Minor

Panning and zoom operations now work as expected when one or more chart axes are inverted.

PPC-9286

PPP-41074

Minor

The Link and Actions/Link Options parameter is now hidden for the Pipeline Pilot Link component because it is not relevant.

PPP-37409

Minor

The external link in the Heat Map component's help text now opens to a new tab in the default web browser.

PPP-42267

Minor

With the deprecation of Flash support in modern web browsers, all references to Flash have been removed from the Canvas component.

Note that the ongoing deprecation of Flash support in web browsers may cause existing protocols to stop working as designed, if they depend on Flash capabilities in some way.

Also, the administrator can block the use of Flash entirely by setting off the "AllowFlashInCanvas" global setting for the Reporting package. In future releases, all ability to run Flash-based rendering will be removed.

PPP-43176

PPP-44432

Minor

Fixed a defect where under some configurations, the clickable example charts did not return data when clicked on.

PPP-43617

Minor

HTML5 Table: Fixed a defect where only properties defined on the first data record appear as columns.

PPP-43709

Major

Suppressed a cross origin error pop-up message that opened when launching the installation page of Desktop Connector from the Pipeline Pilot Web port using Chrome.

PPP-43866

Major

Fixed an issue in the Web Port file browser dialog where re-adding multiple files to the selected file list could leave some items marked as 'undefined'.

PPP-44076