Critical eXtyles patch for PubMed Linking modules

Update: The grace period given to eXtyles users for HTTP-support for PubMed Reference Checking has been disabled. PubMed Reference Checking now requires the the HTTPS patch available in this news post. (updated Jan. 20, 2017)  

Update: NCBI will be testing HTTPS on public web servers on the following two days:

  • Wednesday, November 2, from 1:00pm to 4:00pm EDT
  • Friday, November 4, from 10:00am to 2:00pm EDT

Please contact us at [email protected] with any questions or concerns (updated Nov. 1, 2016)

Update: NCBI has informed us that their transition to HTTPS for eUtils services will be delayed until November 9, 2016. This means the deadline for applying patches for PubMed Linking, NCBI Linking, and PubMed XML Export features is likewise extended to November 9. Please contact us at [email protected] with any questions or concerns (updated Sept. 30, 2016)

On September 30, 2016, NCBI will completely transition their web services from HTTP to HTTPS. This is in response to a U.S. federal mandate that all publicly accessible federal websites and web services only provide service through a secure HTTPS connection.

eXtyles PubMed reference linking tools use API services provided by NCBI and are affected by this change. We now have a patch available to make eXtyles compatible with the new HTTPS requirement.

This patch must be installed by all eXtyles customers who use PubMed reference linking tools by September 30, 2016. After this date, NCBI will turn off HTTP access, and the existing eXtyles PubMed feature will cease to function unless this critical patch is installed.

We appreciate your cooperation as we strive to ensure a smooth transition to the updated NCBI service. Please feel free to contact us with any questions or concerns.


To install this update, please follow the instructions below.

  1. If you have not already done so, update all eXtyles users in your organization to your most recent release of eXtyles. If you are unsure of the build number or date of your most recent release, please contact us.
  2. Download the patch package from the following URL*:* Note that this package is freely available and no login credentials are required.
  3. Quit Microsoft Word. You will not be able to apply the patch files while Word is running.
  4. Unzip the patch package and copy the three files therein (Characters.xml, LinkRefs.xvc, and XprocLib.dll) to the following location*:if you use 64-bit Windows: c:\Program Files (x86)\eXtyles\OMServerif you use 32-bit Windows: c:\Program Files\eXtyles\OMServer* Note that you must have Write and Modify permissions for the eXtyles directory and OMServer directory to successfully copy/paste these patch files. The eXtyles directory and OMServer directories must not be set to “Read-Only.”
  5. You should not see any change in behavior when running PubMed linking tools. However, if you would like to confirm that the patch files have been successfully applied, please see the instructions below.

Please note that this update will be fully incorporated into your next full release of eXtyles, and you will not need to reinstall these patch files for future builds 3500 or higher.

Note: This update requires that you are running eXtyles or eXtyles SI on Windows 7 (Windows Server 2008) or later.

For organizations with more restrictive IT requirements

If your IT policies restrict the installation of patches, we are happy to provide a full build release of eXtyles that incorporates this update. Please contact us no later than Friday September 16, 2016 if you need a full update instead of patches so we can ensure delivery at least one week before NCBI’s September 30 cutoff.

For organizations with customized network protocols

While this change should be transparent, some IT departments have made special exceptions in their network protocols to allow eXtyles access to PubMed, and these exceptions may require an update.

Your IT department may have set up a network exception for the “User Agent” used by eXtyles. The old user agent was “OmniMark OMHTTP/1.1.3”. If your IT department has set up an exception for this agent, the new code requires an additional user agent, “eXtyles WinINet 1.0”. Your IT department should set up exceptions for both user agents, not just the newer one.

For organizations with proxy servers

(updated Sept. 30, 2016)

Previously, eXtyles was able to access proxy servers by either reading the proxy server settings in the Windows registry or reading the proxy server settings defined in your eXtyles configuration. However, this update has changed the way eXtyles interacts with proxy servers.

The update required that we switch to using WinINet functionality, which reads Windows proxy settings from the Windows registry. We no longer have the ability to set up proxy server values or overrides for specific settings in any eXtyles configuration. This means that the settings we had previously set up in certain eXtyles configurations will no longer work for any Internet-dependent eXtyles modules, such as PubMed Linking, Crossref Linking, and URL Checking.

Your proxy server must be set up according to Microsoft’s standard format described in the eXtyles IT documentation (see page 20).

Confirming the installation

After applying the patch files, you should not see any change in behavior when running eXtyles. If the patches have not been applied correctly, you may not see any errors until NCBI switches to HTTPS at the end of September.

To confirm that the patch files have been successfully applied, first check the “Date Modified” property for each of the three files. In most Windows environments, the Date Modified reflects the date on which the files were pasted into the OMServer folder. However, in some environments, the Date Modified reflects the date on which the contents of the files were modified. If your environment uses this latter setting, the Date Modified for each of the patch files should match the following:

  • Characters.xml: 12/22/2015
  • LinkRefs.xvc: 9/10/2016
  • XprocLib.dll: 9/8/2016

It is also possible to test the patch by following the instructions below to trigger an updated error message:

  1. Disable your computer’s connection to the Internet.
  2. Run your configuration’s PubMed reference linking module.
  3. Review the resulting error dialog:If the error says, Error 12007: ERROR_INTERNET_NAME_NOT_RESOLVED, the patch has been applied successfully!If the error says, HOST_NOT_FOUND Socket Error – Authoritive: Host not found, the patch has NOT been applied successfully. Please check that you have Read/Write permissions before copying the patch files to the eXtyles/OMServer directory. If you are unable to apply the patch files successfully, please contact us.

For those who are interested, NCBI provides technical details of this change on their website.