Connect Troubleshooting & FAQs

Matt
Matt
  • Updated

Purpose

This article will help you troubleshoot your Benchling Gateway and answer many common questions about the set-up process. It is recommended to CMD + F and search on key words relevant to you issue rather than reading through the whole doc

 

Troubleshooting Errors

 

1. Error Type: Benchling Gateway Setup Wizard Ended Prematurely

  • You may receive this error if the Setup Wizard quits unexpectedly. There are some clean-up steps you should do before trying to reinstall the Gateway again:
    • Delete the local bench_gw user. This use might have been created even though the installer didn’t fully complete. 
      • You can do this by opening the powershell and running: net user /delete benchgw_user
      • Note: in certain cases, the machine may have multiple domains and benchgw_user may be a user in multiple domains; it may be worth checking that the user has been deleted from all domains present. If you are installing while generating the logfile (see below), if this is the case, you might see some errors immediately after a line similar to this:
        • Executing: C:\Windows\SysWOW64\wbem\wmic.exe UserAccount where "Name='benchgw_user'" set PasswordExpires=False
    • Delete Benchling Gateway folder in Program Files on failure
      • A reboot may be necessary before doing this
  • After following those instructions you can try installing again. 
    • Make sure you use a different name for your Gateway than the one you previously had.

 

2. Error Type: The Benchling Gateway Setup Wizard is erroring out after multiple attempts. 

  • If this occurs, you will need to reach out to the Benchling Support team for assistance. Before doing so, be sure to follow the instructions below and send over the logfile generated by the Powershell command. 

When running Powershell as an admin, run the following command:

msiexec.exe /i 
"C:\replace\this\with\the\path\to\the\installer\file\BenchlingGateway.msi" /l*v 
"C:\replace\this\with\the\desired\path\to\installerlog.txt"
  • The first file path should be the path to where the MSI installer file is located (enclosed in quotation marks) and the second file path should be a specific location that the user wants to place the resulting log file (also enclosed in quotation marks) 

 

3. Error Type: The user ‘benchgw_user’ already exists

  • Run this command: 
    • net user /delete benchgw_user


4. Error Type: Pending validation; The default timezone is added to timestamps in a vendor file if they are not already set

  • The pending validation on default_timezone is not actually an issue.
  • This is due to us not having implemented a check for this kind of field, it does not signify a problem. This is not blocking to actually ingesting the file.

 

5. Error Type: The installation package could not be opened. Verify that the package exists and that you can access it.

  • 2 suggestions on the internet which could help unblock, neither of these will guarantee a fix; they are only suggested actions.:
    • Check that Windows Installer service is up and running.

  • Re-register msiexec by calling following commands as administrator and reboot the PC.

 

msiexec /unregister
msiexec /regserver

 

6. Error Type: No adapters have been installed. Last deployment status: Failed.

  • benchgw_user on their computer needs to have "Allow local log on" enabled

  • Context: benchgw_user is a local account, created by the Gateway installer -- the Gateway background service runs as the LocalSystem user and runs subprocesses as the less-privileged benchgw_user , our installer saves the password for benchgw_user to LocalSystem's credential manager. If you see this error the Gateway cannot start the subprocesses that run under that user. For customers that have run into this, it's been because a Group Policy is disallowing "Allow log on locally" for local accounts
  • After resolving the “Allow local log on” you may need to archive and unarchive any Connections associated with that gateway and create a new to make the Gateway retry to establish a connection.

 

7. Error Type: Benchling Gateway Setup Wizard ended prematurely

  • To troubleshoot, if you could run the installer manually with this command in powershell, this will write verbose logging to installerlog.txt (or you can change the filename as you see fit), and then review the verbose logging file with Connect engineering
msiexec.exe /i 
"C:\replace\this\with\the\path\to\the\installer\file\BenchlingGateway.msi" /l*v 
"C:\replace\this\with\the\desired\path\to\installerlog.txt"

The first file path should be the path to where the MSI installer file is located (enclosed in quotation marks) and the second file path should be a specific location that the user wants to place the resulting log file (also enclosed in quotation marks)

  • Often a failed install will end up creating a local benchgw_user and not clean it up correctly, so the next attempt will fail and log an error about the user already existing, instead of the original cause. In this case, it is recommended to check for benchgw_user first and delete it before running it again with logging OR run net user /delete benchgw_user in a powershell as admin.

8. Error Type: "The contents of the configured directory are too large to poll"

  • In this case, this limit error would be the result of too many files being added to the directory
  • To resolve this error, clear any legacy files that were not intended to be imported into Benchling

Common Questions * FAQs

  1. After the laptop gets back up from hibernated state or restart, sometimes the gateway status stays in error and is not updated. How often does the gateway sync with the server?
    • This will be updated within a 15 minute time period. 
  2. The gateway can connect to maximum 3 tenants, named Development, Test, and Production. What is the upgrade procedure so the new version of Gateway can be tested in dev and test environments before deploying it to production? 
    • You can use the same installer to deploy the gateway into the other tenants. You will need to make sure to have the installer token from each tenant downloaded. Instructions on how you can accomplish this can be found in the gateway installation guide. 
  3. Java related questions:
  • Which Java provider is installed with Connect?
    • Amazon Corretto 17  (specifically amazon-corretto-17.0.4.8.1 )
  • Is Java included within the Benchling Gateway installation or a separately installed package?
    • Java is included within the Gateway installation and does require installing separately
  • Where is Java installed ( on the gateway or on the lab endpoint)?
    • Whichever folder was chosen during the gateway installation, by default this is installed at Program Files/Benchling Gateway/jdk
  • How is Java updated (with updates to Connect or can it be updated separately by IT?
    • The lab endpoint version will be updated automatically as needed via AWS greengrass
  •  

       4. Are there minimum hardware specs for Connect?

        5. Are there permissions to enable/disable a Connection schema?

  • Only users with WRITE or ADMIN access can only enable/disable a Connection. This permission can be managed from the Connection Setting. This can be found by navigating to a Connection and clicking the gear icon in the top right corner
  1. During the Gateway installation what is the difference between the “Will be installed on local hard drive” and “Entire feature will be installed on local hard drive” options?
    • Due to limitations in the Windows Installer software, the “Will be installed on local hard drive” and “Entire feature will be installed on local hard drive” options are identical. 
    • “Entire feature will be unavailable” means that gateway will not be installed, or it will be uninstalled if it previously existed.

 

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