Technical Updates

Onboarding Outreach: Production Exceptions

Sometimes, sites send data to the Production environment before the facilities have passed NSSP’s validation review. When this occurs, the messages are routed to the Production Exceptions table and annotated with one of two reason codes: “04” to indicate C_Facility_ID was not found on the Operational Crosswalk or “05” to indicate C_Facility_ID was not an active facility at time of message processing.

When the NSSP onboarding team conducts its monthly site review of the Production Exceptions tables and finds 04 or 05 exceptions, a team member will email the site administrator(s) and ask them to review the list of facilities and respond as described below.

►  04    C_Facility_ID was not found on the Operational Crosswalk*

The 04 exception indicates a facility identifier is NOT associated with an “Onboarding” or “Active” status.

To correct, take one of the following actions:

1. If the facility does NOT exist on the Master Facility Table (MFT), add the facility to the MFT and set the facility status to “Onboarding.” Add the provided Treating or Sending Facility ID as the Primary FacilityID_UUID.
2. If the facility exists, update the entry in the MFT to include the provided Treating or Sending Facility ID as the Primary FacilityID_UUID.

►  05    C_Facility_ID was not an active facility at time of message processing

The 05 exception indicates a facility is recognized (listed on the MFT), but the MFT facility status is not “Active” with a Review Status of “Complete.”

To correct, take one of the following actions:

1. If the facility’s data are of good enough quality,** update the MFT facility status to “Active.”
   1. An “Active” status will notify the NSSP onboarding team that the facility data are ready to validate (before activation in production).
   2. Once the data validity is confirmed, the activation will be approved. Data will begin flowing to the Processed table and then to ESSENCE.
2. If the facility’s data do NOT meet minimum NSSP validation requirements . . .
   1. Make sure the MFT facility status is set to “Onboarding” with a Review Status of “Complete.”
   2. Send data from this facility to the Onboarding environment, if possible.

This guidance does NOT replace the onboarding activities that individual sites use; instead, this guidance supplements or enhances those activities. The NSSP onboarding team supports all onboarding and data flow activities in support of individual site administrator(s) after reviewing the 04 and 05 Production Exceptions.

If you have questions about the Exceptions table or want to enlist the onboarding team’s help, please submit a ticket to the NSSP Service Desk (an account is required).

Did you find this article useful? If so, two more articles about onboarding outreach are available: “Onboarding Outreach: 90-Day Inactivation Follow Up” and “Onboarding Outreach: Moving Data Into Production.”

Announcing Online Documentation for Rnssp R Markdown Templates

Now you can access, tailor, and distribute reports from within the Rnssp R Markdown package. In June 2021, NSSP developers released a catalog of report templates for the use by the NSSP Community of Practice. The catalog includes report templates for developing “Text Analysis Dashboard,” “ESSENCE CCDD Categories,” “Syndrome Definition Evaluation,” and more. After testing and refining the templates, the Rnssp R Markdown v0.02 documentation is available online to benefit all community members: https://cdcgov.github.io/Rnssp-rmd-templates. The online documentation serves as a repository of support material for NSSP CoP members by providing:

• instructions on how to add, use, and remove a template from an existing Rnssp R package installation;
• detailed descriptions of each template; and
• blog posts on various topics related to R Markdown templates.

Importantly, the online documentation is designed to promote collaboration and encourage outreach.

To use the Rnssp R Markdown Templates, remember to install the Rnssp R package first. Then, after you’ve sampled one of the templates, we look forward to receiving your feedback.

How to Contribute to the Online Documentation  

To contribute to this project, please email your request to gazondekon@cdc.gov. You may also submit an edit to the documentation on pages where the “Edit this page” icon is visible, if you have a Github user account.

Getting Help  

If you encounter a bug using the templates, please email the authors at gazondekon@cdc.gov or file an issue. If possible, include a reproducible example.

Additional Resources  

• Rnssp R Markdown Templates Github Repository: https://github.com/CDCgov/Rnssp-rmd-templates
• Rnssp R Package Online Documentation: https://cdcgov.github.io/Rnssp
• Rnssp R Package Github Repository: https://github.com/CDCgov/Rnssp

Maintenance Updates to AMC Resolve Issues and Improve Functionality

The BioSense Platform Access & Management Center (AMC) version 1.5.5.2 was installed on November 18, 2021. This maintenance release focused on resolving several issues summarized below:

• A special character that was invalidating temporarily reset passwords was removed from the AMC password generator.
• In the Master Facility Table (MFT), three issues were resolved:
  • If the “Cancel” action on the edit page resulted in an error, it was not reported on the screen. Errors are now reported on the screen and navigation will remain on the edit page. Any changes made will revert to their previous values.
  • When creating a facility, the latitude and longitude are recorded exactly as presented either when entered manually in the AMC or when uploaded using the batch add process.
  • The fields will now auto-populate when selecting the “Copy Primary Facility” checkbox. In addition, the facility will be added to the table upon selecting the “Add” button, and the associated facility will be saved.
• When editing a data access rule for a site with numerous users and selecting the Save Draft button, the rule will be saved, and the user will be redirected to the Data Access page instead of the “Return to AMC” page.
• On the “Forgot Username” dialog box, the text label on the action button was changed from “Save” to “Submit” for consistency.
• A “sortable column” indicator was added to table column headers in the “Data Access,” “Manage Users,” “MFT,” “MFT Review,” and “Reports” tabs to show that clicking on the table header will sort the column.
• When creating or editing a User Profile, the “R Studio” checkbox will no longer be displayed.

Laboratory User Tables Now Available

To support the Commercial Lab Data Dictionary, an Excel file containing a set of Laboratory User Tables has been developed and posted on the NSSP Technical Resource Center. The file contains three tables:

1. Lab by Result Data Dictionary—This lists the basic fields available inside the Laboratory by Result table, located within ESSENCE. This tab describes the fields for analytic use. For more information on all fields available, including technical descriptions, please see the larger NSSP Data Dictionary.
2. Lab Test Standard—This describes the lookup table of laboratory tests for a “test category.” This table categorizes all NSSP laboratory tests (C_Result_Test_Description) into level 1 and level 2 categories for query purposes. The lookup table maps the raw values from C_Result_Test_Description into Lab Result Category 1 and Lab Result Category 2. Use this table to investigate the results available for a given test or test category. (This table is generated and maintained by NSSP.)
3. Lab Result Standard (Laboratory result categorizations)—This lookup table lists which raw laboratory test results are being placed into standard result categories. The values in C_Result_Description are all raw values sent by Laboratory A, which are then categorized into C_Result_Test_Category. For ease of use, the Lab Result Category 1 and 2 fields are duplicated from the Lab Test Standard lookup table. Use the Lab Result Standard table to investigate what test results are available for a given test or test category.

For more information about available fields, including technical descriptions, please see the NSSP Data Dictionary, which is also available in the NSSP Technical Resource Center.

CDC Statistician Stephanie Dietz presented on how to use the new Laboratory User Tables during the Annual Syndromic Surveillance Symposium, held November 2021. The symposium presentations will be posted in the NSSP CoP Knowledge Repository.

Changes in Licensing Affects Use of RStudio Workbench

Under RStudio’s new licensing scheme, NSSP’s licensing changed from unlimited users to a limited number of user licenses, requiring NSSP to adopt a new, more rigidly structured license assignment policy. NSSP assigns new licenses on a first-come, first-served basis and has introduced a wait list to prioritize new license requests. For detailed information, please see the NSSP announcement email dated November 15, 2021, or contact your site administrator.