Importing patient intake data to VAPALS-ELCAP

For new VAPALS-ELCAP installations, the VAPALS-ELCAP project provides an intake spreadsheet which is intended to collect intake data on patients enrolled in your lung-screening program in advance of your institution’s rollout of the system. This document describes this process, which comes in two parts:

Converting and importing the Excel data, then
verifying the data before form submission.

For this process, we refer to a “VAPALS user,” who is the person overseeing the collection of intake data via the spreadsheet, and ensuring that what’s in the VAPALS system is correct, and the “VAPALS system administrator,” who is responsible for importing the intake data and making it available for review by the VAPALS User before it actually gets submitted to the system.

1. Prior to the import

The VAPALS system administrator may wish to familiarize themselves with the import process prior to importing the actual data. If so, you are strongly encouraged to do this on a test server.

2. For the VAPALS user

When the VAPALS User is ready to have the spreadsheet imported, it should be made available to the VAPALS system administrator.

3. For the VAPALS system administrator

‍NOTE: If there are issues, please contact your VAPALS-ELCAP development team with as much data as possible for instruction and fixes.

3.1. Export the data from Excel

Open the spreadsheet in Excel, and export it in tab-delimited text format. (This will be referred to below as the “TSV file,” even if Excel wants to name it with a file extension of .txt.)

(Note: If you are testing the import process on a test server, but don’t have the import data yet, you may use the pre-exported data at intake-test-data-tab-del.txt to experiment with.)

3.2. Copy it to the correct location

The VAPALS system administrator should then copy the TSV file to the www directory at the top layer of the osehra directory on the VAPALS-ELCAP server. (In other words, it should be a file in the /home/osehra/www directory.)

3.3. Check the environment

Make sure the site is configured. If you aren’t sure, check with the system administrator. If you are the system administrator, and you don’t know, see the instructions for configuring a new site.

3.4. Enter M

Type mumps -dir at the Unix prompt to enter the M programmer’s environment.

3.5. Start the conversion program

Type DO LOAD^SAMILD2 at the M prompt to start the conversion program.

3.6. Enter site code

Enter your three-letter site code. (If you don’t have one, see How to add a VAPALS site.)

For this example, we will be using a dummy site, but you are expected to be using your own site or a test site.

Select SAMI SITE: XXX  VISTA HEALTH CARE     XXX      6100

3.7. Specify the correct directory

Hit enter to accept the default directory (unless you had to put the TSV file somewhere else):

File Directory: /home/osehra/www/// _

3.8. Begin conversion

After Replace, enter three periods (...) to accept replacing the whole file name, after "With" enter the file you want to use. Hit enter after the second "Replace" to let it know that you don’t want to replace anything else.

Example:

Enter filename to load.: LCSV2_DATA_2021-06-29_REDCAP.tsv
  Replace ... With intake-test-data-tab-del.txt  Replace
   intake-test-data-tab-del.txt

Note: If you didn’t put the TSV file in the right place, or something is misspelled, you’ll see a error that looks something like this:

%YDB-E-SETECODE, Non-empty value assigned to $ECODE (user-defined error trap)

The output you should see begins with something similar to this:

keyrow is 3 ROW=saminame        ssn     last5   sigi    sex     sbdob ...

The output could spout out for many pages and several minutes depending on how many lines of data you have in the TSV file. Don’t worry if you see ******** exception **********—it’s not a bad thing.

3.9. Exit M

Once the output stops, type halt at the prompt to go back out to the Unix level.

The data should now be converted.

4. For the VAPALS user

Start the VAPALS application using your web browser. (Check with your system administrator if you haven’t been given the web address and your login credentials.)

4.1. Reviewing the Intake forms before submitting changes

The IT team and the medical expert team recommends that you review Intake Forms the first time you encounter the patient after moving the data over to VAPALS-ELCAP, instead of trying to do them all at once.

For each patient, check these fields in particular:

Eligible based on chart review?
Was a pre-enrollment discussion held?
Primary address verified?

If you find a discrepancy on the patient’s intake form, please check the spreadsheet to see if it was entered correctly there. If it was correct on the spreadsheet, but incorrect on the Intake Form, please let your VAPALS-ELCAP system administrator team know which field was incorrect, and as long as it isn’t the name or MRN, let us know what the value was on the spreadsheet and on the intake form, and describe what the difference was as specifically as possible.

If there is not a selection, please fill it in. It is most likely to be a No but could have been missed in the process of entering data in the spreadsheet.

When everything looks good, hit Submit at the bottom of the form. You can choose Save for Later if you aren’t ready to submit the form.