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$TXT by YAW,LINDA linda.yaw@vistaexpertise.net (KIDS) 2021-12-10t15:57z

Chenoweth’s Patch

SAMI (VAPALS-ELCAP) 18-15

(SAMI*18.0*15 SEQ #15)

George P. Lilly, Domenic DiNatale, Larry G. Carlson & Frederick D. S. Marshall
2021-12-10

‍i. Front matter

App

SAMI (VAPALS-ELCAP)

Version

18-15

Vista ID

SAMI*18.0*15 SEQ #15: Version 18.0, Patch ID #15, Seq #15

Priority

High

Categories

Routine, File

Status

Test Release: SAMI-18-15.zip

Depends on

SAMI 18-1 (SAMI*18.0*1 SEQ #1)
SAMI 18-2 (SAMI*18.0*2 SEQ #2)
SAMI 18-3 (SAMI*18.0*3 SEQ #3)
SAMI 18-4 (SAMI*18.0*4 SEQ #4)
SAMI 18-5 (SAMI*18.0*5 SEQ #5)
SAMI 18-6 (SAMI*18.0*6 SEQ #6)
SAMI 18-8 (SAMI*18.0*8 SEQ #8)
SAMI 18-9 (SAMI*18.0*9 SEQ #9)
SAMI 18-10 (SAMI*18.0*10 SEQ #10)
SAMI 18-11 (SAMI*18.0*11 SEQ #11)
SAMI 18-12 (SAMI*18.0*12 SEQ #12)
SAMI 18-13 (SAMI*18.0*13 SEQ #13)
SAMI 18-14 (SAMI*18.0*14 SEQ #14)

‍ii. Contents

1. Description

SAMI 18-15 adds 18 updates, most of them changes to the CT Evaluation form and the CT report.

The definitive source for the VAPALS-ELCAP application—codebase, package distributions (including this patch), and documentation—is a public GitHub repository.

These instructions are for your Vista environment’s sysadmin. As usual, please capture the complete dialog of your install and send it to your VAPALS-ELCAP support team.

The following list shows changes for:

1.1. CT Evaluation Form: Make lymph-node map a little bigger

Issue 21-149 (medium priority): Make the lymph-node map in the Neck and Mediastinal section bigger if possible.

Solution: Enlarged the lymph-node map.

Reported: 2021-07-25 by Chenoweth.

1.2. CT Evaluation Form: Revert change for nodule status options

Issue 21-128 (medium priority): This partially reverts an earlier request. Current behavior of these two nodule status options is to blank out fields in the nodule table; desired behavior is to keep the information (as maybe later scans will have the nodules). The fields should only be grayed out for Prev seen, resolved or Prev seen, not a nodule, not for other choices.

Solution: Changed to desired behavior.

Reported: 2021-07-13 by Yip.

1.3. CT Evaluation Form: Automates resolution of nodule status

Issue 21-129 (medium priority): Automatically set the nodule status to resolved if the Is it new? option is set to Prev seen, resolved.

Solution: Changed to desired behavior.

Reported: 2021-07-13 by Yip.

1.4. CT Evaluation Form: Comparative and prior scans should be visible for baseline exams

Issue 21-198 (medium priority): Previously, comparative and prior scan fields were not visible when type of exam was baseline.

Solution: Changed to desired behavior.

Reported: 2021-10-25 by Henschke.

1.5. CT Report: Add “Not Provided” option for Emphysema and CAC

Issues 21-192, 21-203 and 21-205 (high priority): In Emphysema (both protocols) and Coronary Artery Calcification (for Lungrads), or CAC Score (for I-ELCAP), add a radio button for Not Provided.

Solution: Changed to desired behavior.

Reported: 2021-10-11, 2021-11-08 by Henschke.

1.6. CT Evaluation Form: CAC should be reported in different ways by protocol

Issue 21-204 (medium priority): Leave Emphysema and Coronary Artery Calcification Line in Lungrads version, remove CAC Score section. Leave Emphysema and CAC Score section in ELCAP version, remove CAC Score section.

Solution: Changed to desired behavior.

Reported: 2021-11-08 by Henschke.

1.7. CT Evaluation Form and CT Report: Add “right” and “left” for lymph nodes N10–N14

Issue 21-170 (high priority): In the Neck and Mediastinal section on the form add “right” and “left” for lymph nodes N10–N14. Extend CT Report to handle new form fields.

Solution: Added form-fields and checkboxes.

Reported: 2021-09-07 by Henschke

1.8. CT Report: The lymph-node station does not carry over to the CT Report

Issue 21-148 (high priority): Lymph-node stations are reported in the Neck and Mediastinal section on the form but that information is not included in the CT Report.

Solution: Add lymph node stations to CT Report.

Reported: 2021-07-25 by Chenoweth.

1.9. CT Report: There is an extra space in front of Description

Issue 21-150 (low priority): There is an extra space in front of Description at the top of the CT Report.

Solution: Removed extra space.

Reported: 2021-07-25 by Chenoweth.

1.10. CT Report: Comparative and prior scans should not include current date

Issue 21-167 (medium priority): Current date should not be included in comparative scans and prior scans in report or CT Evaluation form.

Solution: Changed to desired behavior.

Reported: 2021-09-02 by Phoenix Team.

1.11. CT Report: Pleural effusion bug in CT report

Issue 21-135 (high priority): Pleural effusions information was translating incorrectly into the CT report.

Solution: Corrected translation.

Reported: 2021-08-03 by Slaughter.

1.12. CT Report: Wording change

Issue 21-176 (low priority): Remove the word "above" from Impression section.

Solution: Removed word from CT Report. Must run INIT2GPH^SAMICTD2 to get the fix which will be in the Post-install. No extra action required by system administrator.

Reported: 2021-09-16 by Murphy.

1.13. Intake Form: Informed decision making is required but not marked so

Issue 21-200 (low priority): Informed decision making is required but does not have a red star.

Solution: Red star added.

Reported: 2021-11-04 by Yaw.

1.14. Intake-but-no-CT Report: Include patients who had CTs, but none since enrollment

Issue 21-160 (high priority): To make sure all participants have a CT scan in the program those who had CT scans before enrollment need to be on this report.

Solution: Add active patients who have not had a CT scan since enrollment.

Reported: 2021-08-23 by Henschke.

1.15. Infrastructure: Improve support for parameterization by system and site

Issue 21-194 (high priority): Some sites or organizations will need different wording or other differences from the default (for example, ELCAP protocols vs. Lung-Rads).

Solution: Developed new parameters to customize VAPALS.

Parameter Value

Non VA (1)

socialSecurityNumber

Patient ID

socialSecurityNumber.short

PID

socialSecurityNumber.mask

socialSecurityNumber.regex

matchingReportEnabled

true

ruralUrbanChartEnabled

false

lungradsOrElcapCTtemplate

elcap

username

User Name

password

Password

veteransAffairsSite

false

 

VHA (2)

socialSecurityNumber

Social Security Number

socialSecurityNumber.short

SSN

socialSecurityNumber.mask

000-00-0000

socialSecurityNumber.regex

(?!(000|666|9(?!99)))\d{3}-(?!00)\d{2}-(?!0000)\d{4}$

matchingReportEnabled

true

ruralUrbanChartEnabled

true

lungradsOrElcapCTtemplate

lungrads

username

Access

password

Verify

veteransAffairsSite

true

 

SYS (3)

systemDemoOnly

false

systemDemoUseDUZ

username

User Name

password

Password

Reported: 2021-02-24 by Avila.

1.16. Infrastructure: Default site of SYS causes undesired behavior

Issue 21-201 (high priority): Fix an error where SYS is used as a site code and it shouldn’t be.

Solution: Intercept site=SYS and make it null.

Reported: 2021-11-04 by Lilly.

1.17. Infrastructure: If the siteid field is added to the URL, signon is bypassed

Issue 21-202 (critical priority): Important security fix needed.

Solution: Remove ability to bypass signon.

Reported: 2021-11-08 by Jirapatnakul.

1.18. Infrastructure: Add an About page to the menu bar at the top of the page

Issue 21-206 (medium priority): The team would like an about page, which describes the application and the software version.

Solution: Add link to menu bar.

Reported: 2021-11-02 by DiNatale.

2. Package elements

Fileman File Number Change

SAMI PARAMETER DEFAULTS

311.14

modified (data)

3. Prepare for installation

This involves creating a directory to work in, running a script to back up certain datafiles and web-application files, and then going through steps to back up M routines that will be replaced by the patch.

3.1. Assume the identity of your osehra Unix user

This step assumes you use a dzdo or sudo command to do this; here, the symbol $DEMAND will stand for whichever command you use. (Also, in all the command-line examples below, $ simply means your command-line prompt.) If your configuration is different, please adjust this step to match your configuration:

$ $DEMAND su - osehra
$ _

3.2. Prepare install directory

If this is your first time installling this, execute the following commands. They create a shell variable, and then creates the work directory and sets it as your current directory.

$ INDIR=~/run/in/sami/18-15
$ mkdir -p $INDIR
$ cd $INDIR

If you’ve already tried installing this before, you can use the following commands instead:

$ INDIR=~/run/in/sami/18-15
$ cd $INDIR
$ rm -rf ./sami*.{txt,kid} ./auxfiles

3.3. Download and prepare the archive file

You may safely download the archive file (sami-18-15.zip) in advance of the actual install.

Then unzip the archive file with the following command.

3.4. Install web-application files

At this point, the web-application files must be installed. This is done with a script that backs up the affected directories before installing anything, then upgrades the web-application files. The output looks like this (where [x] represents a number).

$ ./upgrade-auxfiles
Backing up files to ./.aux-backup:
[... lists of files backed up ...]
Compressing the backup:
[... list of files being compressed ...]
Cleaning up.
Done with backup of auxiliary files.

Updating from ./auxfiles
[... list of files being updated ...]
Done with install.

You may now proceed with the KIDS installation.
$ _

Outside the VA firewall, VAPALS-ELCAP systems maintain up-to-date clones of the official GitHub repository, and this script will have different output.

$ ./upgrade-auxfiles
Backing up files to ./.aux-backup
[... lists of files backed up ...]
Compressing the backup:
[... list of files being compressed ...]
Cleaning up.
Done with backup of auxiliary files.

Found a valid Git repository; pulling updates ...
[... output varies ...]
Done with install.
$ _

3.5. Back up M routines

Before the installation, we also need to back up existing VAPALS-ELCAP routines that will be overwritten by this install. To do this, you will have to start a Caché or YottaDB session (depending on your particular installation), sign in to Vista, and then call the direct-mode interface ^%RO (“routine out”).

We have made efforts to display accurate instructions, but there are likely to be minor differences between implementations. Be sure to follow the correct dialog for your implementation.

3.5.1. Enter M

At the Unix prompt, enter the M environment in direct mode, using the csession command on Caché or the mumps command on YottaDB/GT.M:

On Caché

$ csession vapals

Node: vapalscache, Instance: VAPALS

>_

On YottaDB/GT.M

$ mumps -dir

>_

3.5.2. Sign into Vista

At the M prompt, call Vista’s direct-mode interface, enter your access code, and then just press return at the OPTION NAME prompt to return to direct mode. This sets up your authentication variables. Here’s a sample capture of this step:

>do ^XUP

Setting up programmer environment
This is a TEST account.

Access Code: *******
Terminal Type set to: C-VT100

Select OPTION NAME:
>_

3.5.3. List of routines

The routine names to save are listed below; you may copy the list and paste it at the appropriate Routine prompt. At the final Routine prompt, press return to indicate the list of routines is done.

3.5.4. Run the backup

Creating the routine backup file differs by implementation.

On Caché

Note that routines that don’t currently exist will result in a warning message (specifically, the routine name will have [???] after it, and the line [does not exist] after that). These messages can be safely disregarded.

In addition to naming the routines and routine-out file, we also provide a Description and press return at the Parameters and Printer Format prompts to accept the defaults of WNS and No, respectively:

On YottaDB/GT.M

Note that routines that don’t currently exist will result in the routine name not appearing under the input line, and won’t count towards the number of routines. These can be safely disregarded.

In addition to naming the routines and routine-out file, we also provide a Header Label and press return at the Strip comments prompt to accept the default of no:

You’ll remain in the M environment for the next section.

4. Main install instructions

This consists of loading and installing the KIDS package, and activating the new web-application files.

4.1. Installing the KIDS package

This installs the various M assets required by the application.

4.1.1. Enter the KIDS Installation menu

At the OPTION NAME prompt select XPD MAIN to enter the Kernel Installation & Distribution System main menu, and at the Select ... Option prompt select Installation:

>do ^XUP

Select OPTION NAME: XPD MAIN       Kernel Installation & Distribution System


      Edits and Distribution ...
      Utilities ...
      Installation ...
      Patch Monitor Main Menu ...

Select Kernel Installation & Distribution System <TEST ACCOUNT> Option: installation


   1      Load a Distribution
   2      Verify Checksums in Transport Global
   3      Print Transport Global
   4      Compare Transport Global to Current System
   5      Backup a Transport Global
   6      Install Package(s)
          Restart Install of Package(s)
          Unload a Distribution

Select Installation <TEST ACCOUNT> Option:_

4.1.2. Load KIDS package

Select option 1 and press return at the Continue prompt.

4.1.3. Install KIDS package

Select option 6, enter the space bar at the INSTALL NAME prompt, and press return at the next three prompts. Note that [now] denotes the current time when you’re doing the install.

You now have VAPALS-ELCAP 18-15 (SAMI*18.0*15 SEQ #15) installed in your M environment. The install is now complete. We recommend running tests of your VAPALS-ELCAP application to confirm the environment is operational and bug-free, before notifying users that VAPALS-ELCAP is ready for their use.

5. Optional backout instructions

Should errors or other problems result from installing this package, contact the VAPALS-ELCAP development team for package-backout instructions.

6. Routines

Lines 2 and 3 of each of these routines now look like:

The checksums below are Vista Type B checksums (do CHECK1^XTSUMBLD).

7. Authors

Dates By

Developed

2021-10-20/11-14

George P. Lilly (VEN)
Dominic DiNatale (PAR)
Larry G. Carlson (VEN)
Frederick D. S. Marshall (VEN)
Kenneth W. McGlothlen (VEN)
Linda M. R. Yaw (VEN)

Tested

2021-10-25/12-09

George P. Lilly (VEN)
Dominic DiNatale (PAR)
Larry G. Carlson (VEN)
Claudia Henschke (VA-PHO)
Artit Jirapatnakul (VA-PHO)
Providencia Morales (VA-PHO)
Lorenza A. Murphy (VA-PHO)
Martha A. Rukavena (VA-PHO)
Frederick D. S. Marshall (VEN)
Kenneth W. McGlothlen (VEN)
Linda M. R. Yaw (VEN)

Released

2021-12-10

Frederick D. S. Marshall (VEN)
Kenneth W. McGlothlen (VEN)
Linda M. R. Yaw (VEN)

 
$END TXT