$TXT by MARSHALL,RICK DS@vapalsyotta.fiscientific.org (KIDS) 2021-08-24T18:35Z
CT Report Fix
SAMI (VAPALS-ELCAP) 18-13
(SAMI*18.0*13 SEQ #13)
George P. Lilly,
Domenic DiNatale,
Larry G. Carlson
& Frederick D. S. Marshall
2021-08-24
i. Front matter
App |
SAMI (VAPALS-ELCAP) |
Revision |
SAMI*18.0*13 SEQ #13: Version 18.0, Patch ID #13, Seq #13 |
Priority |
Critical |
Categories |
Routine, File |
Status |
Test Patch: sami-18-13.zip |
Depends on |
SAMI 18-1 (SAMI*18.0*1 SEQ #1) |
ii. Contents
1. Description
SAMI 18-13 adds 1 update, correcting an error in translating CAC scores from the CT Evaluation form to the CT Evaluation 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:
-
Critical bugfixes (1)
1.1. CT Report: Correcting CAC score field
Issues 21-142 and 21-143: The CAC score is sometimes different between the CT Eval form and the report. Circumflex value is always none in report, but CAC score is correct on first view. First view seems to reset the circumflex to none, causing subsequent views to be incorrect.
Solution: Found typo of field name in routine and corrected.
Reported: 2021-08-11 by Murphy.
2. Package elements
| File | Change |
|---|---|
sami-18-13-recipe.txt |
new |
sami-18-13.txt |
new |
sami-18-13.kid |
new |
www/* |
modified |
step1-backup |
new |
step1a-vasites |
new |
step2-install |
new |
sami-18-13.zip |
new |
| Routine | Change |
|---|---|
SAMICTT3 |
modified |
SAMICTUL |
modified |
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. If your configuration is different, please adjust this step to match your configuration:
$ $DEMAND su - osehra
3.2. Prepare install directory
Execute the following commands ($ simply means your command-line prompt). They create a shell variable, and then creates the directory or, if it already exists, removes previous installation files before proceeding.
$ INDIR=~/run/in/sami/18-13
$ mkdir -p $INDIR || rm -rf $INDIR/sami-*.{kid,txt} $INDIR/{form-fields,www}
$ cd $INDIR
3.3. Download and prepare the archive file
You may safely download the archive file (sami-18-13.zip) in advance of the actual install. In the following text, [now] represents a time stamp representing your current time, and [bits/sec] is a data rate and [time] is how long the file took to transfer (both of which vary based on the user’s network conditions).
$ wget 'http://vistaexpertise.net/newsite/project/vapals-elcap/sami-18-13.zip' --[now]-- http://vistaexpertise.net/newsite/project/vapals-elcap/sami-18-13.zip Resolving vistaexpertise.net (vistaexpertise.net)... 208.113.153.6 Connecting to vistaexpertise.net (vistaexpertise.net)|208.113.153.6|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 2585153 (2.5M) [application/zip] Saving to: ‘sami-18-13.zip’ 100%[================================>] 2.47M [bits/sec] in [time] [now] ([bits/sec]) - ‘sami-18.13.zip’ saved [2585153/2585153] $ unzip sami-18-13.zip Archive: sami-18-13.zip [... 539 files in archive, about 9.0 Mb ...] $ _
3.4. Back up files
Several files will be overwritten by this install. This step backs those up as a safety measure to your working directory.
$ ./step1-backup Backing up files ... done. $ _
3.4.1. IMPORTANT NOTE for VA VAPALS-ELCAP sites
Installations within the VA firewall may not access the VAPALS-ELCAP Git repository; they maintain a static copy which is occasionally updated. VAPALS-ELCAP scripts, however, have no reliable way of telling the difference, but need to in order to update files properly.
If you are certain you are on such a site, please run the following script now. It marks your Git repository as isolated by putting an additional file within it; scripts will use this to operate properly for your installation.
$ ./step1a-vasites If you are within the VA firewall, you cannot update your Git repository automatically. The software update scripts provided with VAPALS-ELCAP patches have no reliable way to determine this, but this script will place an additional file in the repository marking it as 'isolated' so that the installation script below will perform the correct actions. Are you sure you want to do this [yes/no] ? y Marking as 'isolated' ... done. $ _
Note that if this isn’t done, the following step (and future patches) will not work properly.
3.5. Install web-application files
At this point in the install process, the VAPALS-ELCAP routines have been updated, but the corresponding web-application files have not; these must first be installed. On VA VAPALS-ELCAP systems, the output will look like this:
$ ./step2-install Updating files ... done. $ _
Outside the VA firewall, VAPALS-ELCAP systems maintain up-to-date clones of the official GitHub repository, and this script will have different output.
$ ./step2-install [... output varies ...] Done. $ _
3.6. 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.
3.6.1. 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 >_
3.6.2. 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: >_
3.6.3. 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.
SAMICTT3 SAMICTUL
3.6.4. 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 it). 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:
>do ^%RO
Routine output (please use %ROMF for object code output)
Routines(s): SAMICTT3
Routines(s): SAMICTUL
Routines(s):
Description: SAMI 18-13 routine backup
Output routines to
Device: /home/osehra/run/in/sami/18-13/back/sami-18-13-back.ro
Parameters? ("WNS") =>
Printer Format? No => No
SAMICTT3.INT SAMICTUL.INT
>_
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:
>do ^%RO Routine Output - Save selected routines into RO file. Routines: SAMICTT3 SAMICTT3 Current total of 1 routines. Routines: SAMICTUL SAMICTUL Current total of 2 routines. Routine: Output device <terminal>: /home/osehra/run/in/sami/18-13/back/sami-18-13-back.ro Header Label: SAMI 18-13 routine backup Strip comments <No>?: SAMICTT3 SAMICTUL Total of 694 in 2 routines. >_
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.
Select Installation <TEST ACCOUNT> Option: 1 Load a Distribution
Enter a Host File: /home/osehra/run/in/sami/18-13/sami-18-13.kid
KIDS Distribution saved on Aug 24, 2021@11:12:43
Comment: SAMI 18-13
This Distribution contains Transport Globals for the following Package(s):
SAMI*18.0*13
Distribution OK!
Want to Continue with Load? YES//
Loading Distribution...
SAMI*18.0*13
Use INSTALL NAME: SAMI*18.0*13 to install this Distribution.
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:_
4.1.3. 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.
Select Installation <TEST ACCOUNT> Option: 6 Install Packages(s)
Select INSTALL NAME: SAMI*18.0*13 Loaded from Distribution [now]
=> SAMI 18-13 ;Created on Aug 24, 2021@11:12:43
This Distribution was loaded on [now] with header of
SAMI 18-13 ;Created on Aug 24, 2021@11:12:43
It consisted of the following Install(s):
SAMI*18.0*13
Checking Install for Package SAMI*18.0*13
Install Questions for SAMI*18.0*13
Incoming Files:
Want KIDS to INHIBIT LOGONs during the install? NO//
Want to DISABLE Scheduled Options, Menu Options, and Protocols? NO//
Enter the Device you want to print the Install messages.
You can queue the install by enter a 'Q' at the device prompt.
Enter a '^' to abort the install.
DEVICE: HOME// VMS
Install Started for SAMI*18.0*13 :
[now]
Build Distribution Date: Aug 24, 2021
Installing Routines:.
[now]
Installing Data Dictionaries: .
[now]
Installing Data:
[now]
Updating Routine file
Updating KIDS files.......
SAMI*18.0*13 Installed.
[now]
NO Install Message sent
Install Completed
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:_
4.2. Activating web-application files
Both the VAPALS-ELCAP routines and web-application files have been updated at this point, but the routines are using cached copies of the web-application files; this step refreshes those copies.
4.2.1. Refresh web-application cache
To improve performance, M-Web maintains cached copies of the data dictionaries for the fields on all the VAPALS-ELCAP forms, and of the HTML templates used by its services. Every time we update those files in Unix, we must also direct M-Web to update its cache.
To do so, exit the Installation menu by hitting carriage return (possibly more than once) to get to a direct-mode prompt, and then copy and paste the following list of commands into that prompt:
set SAMIDIR="/home/osehra/lib/silver/a-sami-vapals-elcap--vo-osehra-github/docs/form-fields/" do PRSTSV^SAMIFF(SAMIDIR,"background.tsv","form fields - background") do PRSTSV^SAMIFF(SAMIDIR,"biopsy.tsv","form fields - biopsy") do PRSTSV^SAMIFF(SAMIDIR,"ct-evaluation.tsv","form fields - ct evaluation") do PRSTSV^SAMIFF(SAMIDIR,"follow-up.tsv","form fields - follow up") do PRSTSV^SAMIFF(SAMIDIR,"intake.tsv","form fields - intake") do PRSTSV^SAMIFF(SAMIDIR,"intervention.tsv","form fields - intervention") do PRSTSV^SAMIFF(SAMIDIR,"pet-evaluation.tsv","form fields - pet evaluation") do PRSTSV^SAMIFF(SAMIDIR,"register.tsv","form fields - register") do CLRWEB^SAMIADMN do INIT2GPH^SAMICTD2
The output is shown below (where [job] is a job number displayed by the PRSTSV routine):
Select Installation <TEST ACCOUNT> Option: > set SAMIDIR="/home/osehra/lib/silver/a-sami-vapals-elcap--vo-osehra-github/docs/form-fields/" > do PRSTSV^SAMIFF(SAMIDIR,"background.tsv","form fields - background") [job] > do PRSTSV^SAMIFF(SAMIDIR,"biopsy.tsv","form fields - biopsy") [job] > do PRSTSV^SAMIFF(SAMIDIR,"ct-evaluation.tsv","form fields - ct evaluation") [job] > do PRSTSV^SAMIFF(SAMIDIR,"follow-up.tsv","form fields - follow up") [job] > do PRSTSV^SAMIFF(SAMIDIR,"intake.tsv","form fields - intake") [job] > do PRSTSV^SAMIFF(SAMIDIR,"intervention.tsv","form fields - intervention") [job] > do PRSTSV^SAMIFF(SAMIDIR,"pet-evaluation.tsv","form fields - pet evaluation") [job] > do PRSTSV^SAMIFF(SAMIDIR,"register.tsv","form fields - register") [job] > do CLRWEB^SAMIADMN > do INIT2GPH^SAMICTD2 >_
You now have VAPALS-ELCAP 18-13 (SAMI*18.0*13 SEQ #13) 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:
;;18.0;SAMI;[Patch List];2020-01;[optional build #] ;;18.13
The checksums below are Vista Type B checksums (do CHECK1^XTSUMBLD).
| Name | Checksum before | Checksum after | Patch list |
|---|---|---|---|
SAMICTT3 |
B222224982 |
B222214559 |
*4,10,13* |
SAMICTUL |
B100661 |
B101132 |
*10,11,12,13* |
7. Authors
| Dates | By | |
|---|---|---|
Developed |
2021-08-16 |
George P. Lilly (VEN) |
Tested |
2021-08-16/18 |
George P. Lilly (VEN) |
Released |
2021-08-24 |
Frederick D. S. Marshall (VEN) |
$END TXT