worldvista/vista

OSEHRA VistA

OSEHRA VistA

This source tree contains patches, tests, and tools for VistA, the Veterans Health Information Systems and Technology Architecture. It is maintained by OSEHRA, the Open Source Electronic Health Record Alliance.

This version of VistA includes Open Source Community contributions accepted by OSEHRA.

Purpose

The OSEHRA VistA-M Source Tree contains a static representation of VistA. VistA is built on a database platform that houses both code and data so it requires programmatic operations to apply changes while maintaining consistency. Patches in this source tree may be applied to a running VistA instance to keep it up to date.

Layout

The source tree is organized as follows:

• Packages.csv: A spreadsheet recording VistA packages. For each package it has a name, namespaces, file numbers and names, and a directory name for this source tree.
• CMake: CMake build system modules.
• Documentation: OSEHRA VistA documentation pages.
• Scripts: Contains scripts to process VistA patch files, populate the Packages/ directory layout, analyze dependencies, and compute an order for patch installation.
• Packages/<package>/Patches/<patch>/: Holds distribution files for one patch. The <package> directory name matches that in Packages.csv. The <patch> directory name is derived from the patch build name. For example, directory Packages/Kernel/Patches/XU_8.0_431 holds files for KERNEL patch XU*8.0*431.
• Packages/Order Entry Results Reporting/CPRS: Delphi sources for the "Computerized Patient Record System".
• Packages/RPC Broker/BDK: Delphi sources for the "Broker Development Kit".
• Packages/MultiBuilds: Holds distribution files for multi-build patches. Since these may contain builds from multiple packages we do not keep them under a specific package directory.
• Packages/Uncategorized: Holds files with no clear package category. In addition, it contains *.csv spreadsheets derived from the VA FOIA Spreadsheets. See Scripts/HowtoUpdateSpreadsheets.rst to update them.

Links

• OSEHRA Homepage: http://osehra.org
• OSEHRA Repositories: http://code.osehra.org
• OSEHRA Github: https://github.com/OSEHRA
• VA VistA Document Library: http://www.va.gov/vdl

vista's Issues

Explore deprecation warnings in REGEX for repository

Via @shabiel

/home/sam/workspace/repo/VistA/Python/vista/OSEHRAHelper.py:124: DeprecationWarning: invalid escape sequence \s
match = self.wait_re(volume + ':.+\s', None)
/home/sam/workspace/repo/VistA/Python/vista/OSEHRAHelper.py:131: DeprecationWarning: invalid escape sequence \s
self.wait_re(volume + ':.+\s', None)
/home/sam/workspace/repo/VistA/Python/vista/OSEHRAHelper.py:668: DeprecationWarning: invalid escape sequence ?
"""
/home/sam/workspace/repo/VistA/Python/vista/OSEHRAHelper.py:670: DeprecationWarning: invalid escape sequence (
re_chars = '?*.+-|^$()[]{}'

Remove reference to OSEHRA in documentation; replace with WorldVista

Request to drop references to OSEHRA as this organization does not exist,
and none of the URLS work.

Going forward, these Vista artifacts are managed by WorldVista.

Python 3: Convert RAS Testing and Data scripts

Convert the RAS testing scripts, both the test generation and the data files used in them, to be ready for a python3 environment

Remove "date" line from ZWR header

As part of ZGO

Python 3: Convert OSEHRA Helper python files

Convert the OSEHRAHelper, OSEHRASetup, and other files in the python/vista subdirectory to be ready for a Python 3 environment

Set parameter XU522 to disable during set-up

Functional Testing patients DOB are in US format

For plan 6 versions of VistA, they won't load..

Update MenuTraversalTest and MenuTraversalSmokeTest

They currently do not pass.

They need to be updated to pass in Python2 and then made Python3 compatible.

XINDEX tests are failing in Python 2

   All Routines? No => No
161:
161:
161:
161:   Routine:
161:
161:   Traceback (most recent call last):
161:
161:     File "C:/Users/betsy.mcphail/development/VistA-Build/Testing/XINDEX/SurgeryTest.py", line 47, in <module>
161:       VistA.write(prefix + '*')
161:     File "C:/Users/betsy.mcphail/development/VistA/Python/vista\OSEHRAHelper.py", line 199, in write
161:       self.connection.write(encode(command) + encode('\r'))
161:     File "C:\Python27\lib\telnetlib.py", line 280, in write
161:       if IAC in buffer:
161:     File "C:\Users\betsy.mcphail\AppData\Roaming\Python\Python27\site-packages\future\types\newstr.py", line 127, in __contains__
161:       newkey = newstr(key)
161:     File "C:\Users\betsy.mcphail\AppData\Roaming\Python\Python27\site-packages\future\types\newstr.py", line 102, in __new__
161:       return super(newstr, cls).__new__(cls, value)
161:
161:   UnicodeDecodeError: 'ascii' codec can't decode byte 0xff in position 0:
161:   ordinal not in range(128)

Links on PackageComponent list pages are broken

All objects on "PackageComponent.html" in the DOX pages are marked as routines. This is not correct and should link to the "Option_...." or "List_..."

Problem list test failing on CI

e.g. https://code.osehra.org/CDash/testDetails.php?test=2800897&build=40987

Error log:

...............
PXRMOUT^ZZRGUTEX - 150374442,MD+1^ICDEX,%YDB-E-FALLINTOFLST, Fall-through to a label with formallist is not allowed
.............

Ran 1 Routine, 8 Entry Tags
Checked 29 tests, with 0 failures and encountered 1 error.

Note: This is not an issue when using Cache.

HL7 APPLICATION PARAMETER color cannot be found

"violetred" is not a color available in the web browser leading to an unbordered box on the DOX page

change it to "mediumvioletred" or "palevioletred"

See https://code.osehra.org/OSEHRA_dox/Package_Surgery.html for the example

ZGO: Find existing file export doesn't work on GT.M/YDB

Python 3: Convert auto-patching scripts

Convert the PatchSequenceApply and all its dependent files to be prepared for a Python 3 environment

Set Manager Startup Delay in Taskman to be 1 second

Rig

Separate DD.zwr into numberspaced chunks

As part of ZGO, split DD.zwr into file number chunks?

dd.zwr + dic.zwr + 8989.3+<....>.zwr

8989.3+<....>.dd
8989.3+<....>.dic
8989.3+<....>.data

Fix XINDEX_Kernel

This was broken in #139

Set-up MASTER PATIENT INDEX (LOCAL NUMBERS) file

Right now, this crashes patient registration.

Ensure existing global is killed in MFS import

Before importing the new global into the instance, "K" the previous version of that global to ensure that data isn't left behind.

Put pexpect and winpexpect back into Repo

In #128, winexpect and pexpect were removed from the repository and added to a requirements.txt file so that they could be pip installed.

While testing another change, I found that winpexpect fails when running in a virtual environment. It turns out that pip uses this repo while the pexpect that was in the VistA repo was a slightly newer version from here. In particular, this commit is needed to fix the virtual environment issue.

I also noticed that the copies of both winpexpect and pexpect in the VistA repo had been modified. Are these modifications needed?

Python 3: Convert KIDS file custom installers

Convert the Python files that are used for adding custom steps to the Autoinstall process to be python3 ready

Ubuntu autoInstaller breaks

This line does not actually block an installation without one of these 3 DBs.
https://github.com/OSEHRA/VistA/blob/303a301ef30bfc3df6f33f61b1477d4bd2b9430d/Scripts/Install/Ubuntu/autoInstaller.sh#L162

I think the intention of this line is to block execution if one of these 3 DBs is not included. (This is not documented.) For some reason, this line does not work as I would expect either. If it were to work as I expect, then it would block if GT.M is not included because ! $installgtm || ! $cacheinstallerpath is true if $installgtm regardless of whether or not $cacheinstallerpath is included. So, something bash related is wrong here. Then, the logic is not what I would expect. These should be ANDs instead of ORs. If they were ANDs, then if NOT installgtm AND NOT cacheinstallerpath AND NOT installYottaDB would be true and would lead to the next statement running and breaking execution.

This causes issues down the line:

# Install GT.M or YottaDB
if $installgtm; then
    cd GTM
    if $bootstrap; then
        ./install.sh
    else
        ./install.sh -s
    fi
    # Create the VistA instance
    if $bootstrap; then
        ./createVistaInstance.sh -i $instance
    else
        ./createVistaInstance.sh -i $instance -f
    fi
fi

if $installYottaDB; then
    cd GTM
    if $bootstrap; then
        ./install.sh -y
    else
        ./install.sh -s -y
    fi
    # Create the VistA instance
    if $bootstrap; then
        ./createVistaInstance.sh -i $instance -y
    else
        ./createVistaInstance.sh -i $instance -f -y
    fi
fi

# Install Caché if requested
if $cacheinstallerpath; then
    echo "Cache installer path:" $cacheinstallerpath
fi

# Modify the primary user to be able to use the VistA instance
usermod -a -G $instance $primaryuser
chmod g+x /home/$instance

usermod relies on createVistaInstance to have created the instance user
* So, really if cacheinstallerpath is used, then it will also break, I think.

Delete OTJ testing directory within VistA

Determine if 5 year old scripts are sill worth having.

KMPTMP should not be exported from Platinum

A lot of garbage comes out from this temporary file.

Autopatcher documentation still says "No Python3"

Now that the autopatching scripts can utilize Python3, update the documentation to remove the warnings.

Python 3: Determine fate of *pexpect files

Determine if we are going to maintain a copy of the pexpect and winpexpect python files in the OSEHRA VistA repository. If so, ready the files for python 3

If not: determine the pip packages that should be installed for the system to work correctly

ZGO: Output from Cache includes quoted numbers

E.g. https://github.com/OSEHRA/VistA-M/blob/master/Packages/Adverse%20Reaction%20Tracking/Globals/120.82%2BGMR%20ALLERGIES.zwr#L346

Python 3: Convert XINDEXExceptionGen

Ensure that the XINDEXExceptionGenerator is python 3 ready

Import script failing in Python 2

$ cmake -P Testing/Setup/ImportRG.cmake
-- Stopping cache instance CACHE
-- Replacing C:/InterSystems/Cache/mgr/VistA/CACHE.DAT
-- Starting cache instance CACHE
-- Preparing M Components...
Looking for routines in subdirectories below C:/Users/betsy.mcphail/development/VistA-M
Looking for globals in subdirectories below C:/Users/betsy.mcphail/development/VistA-M
Looking for routines in subdirectories below C:/Users/betsy.mcphail/development/VistA/Scripts
Looking for globals in subdirectories below C:/Users/betsy.mcphail/development/VistA/Scripts
Packing routines into routines.ro file
Done!
Packing global paths into globals.lst file
Done!
-- Importing VistA Routines...
-- Updating the DPTLK7 routine
-- Importing globals...
-- Initializing VistA...
Traceback (most recent call last):
  File "C:/Users/betsy.mcphail/development/VistA-Build/Testing/Setup/Initialize.py", line 56, in <module>
    OSEHRASetup.addMPILocalNumber(VistA)
  File "C:/Users/betsy.mcphail/development/VistA/Python/vista\OSEHRASetup.py", line 179, in addMPILocalNumber
    VistA.write(localNum)
  File "C:/Users/betsy.mcphail/development/VistA/Python/vista\OSEHRAHelper.py", line 199, in write
    self.connection.write(encode(command) + encode('\r'))
  File "C:\Python27\lib\telnetlib.py", line 280, in write
    if IAC in buffer:
UnicodeDecodeError: 'ascii' codec can't decode byte 0xff in position 0: ordinal not in range(128)
-- Running PostImportSetup script...
Traceback (most recent call last):
  File "C:/Users/betsy.mcphail/development/VistA-Build/Testing/Setup/PostImportSetupScript.py", line 81, in <module>
    OSEHRASetup.setupVistADomain(VistA,"DEMO.OSEHRA.ORG")
  File "C:/Users/betsy.mcphail/development/VistA/Python/vista\OSEHRASetup.py", line 310, in setupVistADomain
    VistA.write('S $P(^XWB(8994.1,1,0),"^")=' + VistA.IENumber)
  File "C:/Users/betsy.mcphail/development/VistA/Python/vista\OSEHRAHelper.py", line 199, in write
    self.connection.write(encode(command) + encode('\r'))
  File "C:\Python27\lib\telnetlib.py", line 280, in write
    if IAC in buffer:
UnicodeDecodeError: 'ascii' codec can't decode byte 0xff in position 0: ordinal not in range(128)
CMake Error at Testing/Setup/ImportRG.cmake:18 (message):
  ERROR: Post Import Setup Failed
Call Stack (most recent call first):
  Testing/Setup/ImportRG.cmake:118 (CheckResult)

Python 3: Convert Non-RAS tests

Convert the rest of the Python scripts used in testing:
XINDEX, Unittest , prefixparsing,and gtm routines parsing python scripts

Test   #1: XINDEX_Accounts_Receivable
..
Test #196: XINDEX_Uncategorized
Test #197: PYTHON_PrefixParser
Test #198: PyUnitTest_TestPatchOrderGenerator
Test #199: PyUnitTest_TestVistATestClient
Test #200: PYTHON_MenuTraversal

Python 3: Convert Post install scripts

Convert the python scripts used to setup a VistA instance after importing the Globals and Routines.

FileManDataToHtml.py: Fix string replacement in _getTableRows()

When this file was converted to be Python 3 compatible in #152 , it was difficult to find a solution that worked in both Python 2 and 3, so the replacement was temporarily removed. This issue is to find a solution that works in both versions of Python.

Before:

dataHtmlLink = "<a href=\"%s/%s/%s\">%s</a>" % (VIV_URL, fileNo.replace(".","_"),
                                                       getDataEntryHtmlFileName(ien, fileNo),
                                                       str(name).replace("\xa0", "")) <<< ----- REIMPLEMENT THIS LINE

After:

dataHtmlLink = "<a href=\"%s/%s/%s\">%s</a>" % (VIV_URL, fileNo.replace(".","_"),
                                                       getDataEntryHtmlFileName(ien, fileNo),
                                                       name)

Vivian Logo does not show-up

https://osehra.org/sites/default/files/vivian.png