Install Scripts: Documentation updates, fix group permissions

Add note concerning how to connect using SFTP and the user required to
do so.

Change prompt to new default of "OSEHRA>". Add note that it is based on
$instance

Fix group permissions by adding a chown command at the end of
autoInstaller.sh

OSEHRA-Id: http://issues.osehra.org/browse/VAF-166
OSEHRA-Id: http://issues.osehra.org/browse/VAF-165
Change-Id: I1b8e45fc24db436fb5bec9e6d4e87e1300c62101
Install Scripts: Add 2 assumed dependencies, Fix EWD.js restart

Python and curl were assumed to be installed by default, add them to the
apt-get install line for bootstrapping the system

EWD.js when restarted can take a few extra seconds to stop. Add a 5
second sleep to ensure the main EWD.js process has stopped.

Change-Id: I0e3e8679d05a40fca64ddc513ca6daa1d8efbb9b
Add MySQL and Java dev packages to Vagrant

Add MySql JDK7 and Maven to the list of packages that are installed during
the boostrapUbuntuServer.sh file.  These packages are added in response to
some inquiries by the OpenInfoButton developers, but will be useful for
others.

Change-Id: I87b94a896a844a37b97580a66c14d43393c09e2a
OSEHRA-Id: http://issues.osehra.org/browse/OAT-135
OTJTestDrive.cmake.in: Fix CommonFunction include path

"Include(CommonFunction)" statement won't work for file that needs
configuration first, change to use the full path from the source tree.

Change-Id: I6206f2de08e4669bdf85168704891df3ffb6210b
Change Sikuli test to prepare for CPRS V29

Change the problem creation code to prepare for the different process that
is required to create a problem with the 799.9 ICD code.  CPRS v29 has
more steps to enter that data.

Change the step after entering the signature code for the strep test and
the first signature to hit "Enter", rather than clicking on the "OK"
button, as CPRSv29 changes the button to read "Sign"

Change the images used to select the problems.  CPRSv29 doesn't display
the ICD code with the name in the search parameter, it resides in a
separate column.  Take a new screenshot with only the Problem's string.

OSEHRA-Id: http://issues.osehra.org/browse/OAT-131
Change-Id: I87f122a127cff84d9b2c95b889821ae0142749ee
VistAInitFileMan.py: Increase Caché routine Deletion timeout

Increase the timeout value from the default 30 seconds to 120 seconds.

The new timeout value is carefully picked based on the worst case scenario
I tried with numerous tests by a safety factor of 2.

Change-Id: I25aa99c793f3d25b03279595c3c298c956b54152
Add Lab Service Execeptions

Add a set of exceptions in the Lab Services package where calls are being
made into the Imaging package.  The errors expressed
here are found on lines where the routine existence is being checked.  The
errors were found in the March 2014 FOIA release.

Checking the return of the $TEXT function acts as a code guard to ensure
that the calls to the Imaging package will not be executed if the routine
isn't present.

OSEHRA-Id: http://issues.osehra.org/browse/VAF-169
Change-Id: I44530fc1405378148d55bcaff4ae7fbe8e1279df
Update Exceptions for first 3 VAEE increments

Update the exception lists for packages from the first three VAEE
increments that have errors in the March 2014 FOIA release.

Waivers can be found attached to the Jira Issue from exploration of
previous FOIAs and are still in the March 2014 FOIA.

OSEHRA-Id: http://issues.osehra.org/browse/VAF-169
Change-Id: I62027073ee797d20586af3519a2fdd04a9a93010
Fix Problem List MUnit test for Mar 2014 FOIA

With the SNOMED code additions, the stored names of the Problems has been
changed to have the ICD9 code in the string.  Adjust the problem list to
check the result for everything but that additional ICD9 string.

Also, change references to the TESTMASTER,USER or other users names to be
more generic, due to the renaming of certain users in a recent FOIA
release.

OSEHRA-Id: http://issues.osehra.org/browse/VAF-171
Change-Id: Idbffc951d4d5ba0d3f2b05c26916057850635b6e
Add instructions to execute Code Coverage

Add instructions to the RunningandUploadingTest.rst file on how to execute
the code coverage calculation from the command line.

Fix the line width to be <80 characters for non-literal text.

OSEHRA-Id: http://issues.osehra.org/browse/OAT-138'
Change-Id: I61df255fcd94e13edbd63b8d99a7da545a41c493
Merge "Add Lab Service Execeptions"
FOIAExcel2Csv: Python Script to convert FOIA Excel to csv

Read the FOIA excel spreadsheet using python xlrd library, and convert
the excel spreadsheet to csv format.

Change-Id: If918adda737be0ee108080aa2e15318052b824a2
Add VA VistA FOIA patch 2014 spreadsheet

Follow the instructions in 'Scripts/HowtoUpdateSpreadsheets.rst' to
add VA VistA FOIA patch 2014 spreadsheet corresponding to:

 https://downloads.va.gov/files/FOIA/Software/DBA_VistA_FOIA_System_Files/Listing_of_Released_VistA_Patches_2014.xls

Remove extra rows from the bottom.

Change-Id: I790a1d9a3434950d309e5961e933354373fb2b7e
Merge "Add instructions to execute Code Coverage"
Add VA VistA patches from Dec 2013 to Mar 2014

Follow the instructions in 'Scripts/HowtoDownloadPatches.rst' to
download patches from the VA FOIA site.  Use the following shell code to
produce the URL list and pipe it to wget:
{
for f in \
 "2013/December 2013" \
 "2014/January 2014" \
 "2014/February 2014" \
 "2014/March 2014" \
; do
  echo "https://downloads.va.gov/files/FOIA/Software/Patches by Year and Month Released/$f/"
done
}

Retrieve .TXT/.KID files posted as of 2014-04-29.

OSEHRA-Id: http://issues.osehra.org/browse/VAF-175
Change-Id: Ib4a599347dcc7875ca50167c54237fba0c78c069
Merge "Change Sikuli test to prepare for CPRS V29"
Prepare to organize Dec 2013, Jan-Mar 2014 FOIA patch files

Update Packages.csv to include a new package named
"Medication Order Check Healthcare Application" with prefix PREM
and VDL id 201, add VDL ID 202 for package "Pharmacy Product System - National"

Update Scripts/KIDSAssociatedFilesMapping.py to place files with
patches.  Place "LEX_2_94.GBLs" with patch "LEX*2*94".
Place "LEX_2_95.GBLs" with patch "LEX*2*95".
Place "IBRC1401[A-F].TXT" with patch "IB*2*520".

"IBRC1401*.TXT" files in the "February 2014" directory all exist
in the "March 2014" directory too, and are identical.
Remove them.

Remove "December 2013/FB-3P5_SEQ-123_PAT-146.KIDS", "December 2013/IB-2_SEQ-462_PAT-499.KIDS"
and "December 2013/DG-5P3_SEQ-770_PAT-867.KIDS", as those KIDS builds are part of MultiBuilds
"December 2013/NEWBORN_1_2_DG_FB_IB.KIDs".

OSEHRA-Id: http://issues.osehra.org/browse/VAF-175
Change-Id: Iefb251bfa9216e870555008a68ba249c09d334ac
Move patches from FOIA/ to populate Packages/

Follow the instructions in 'Scripts/HowtoPopulatePackages.rst' to move
VA patches out of 'FOIA/' and organize them in the 'Packages/' directory
structure.

OSEHRA-Id: http://issues.osehra.org/browse/VAF-175
Change-Id: Id37a227ae7846d8958170e54f606e126bf4356d2
Merge "Add VA VistA patches from Dec 2013 to Mar 2014"
Merge "Prepare to organize Dec 2013, Jan-Mar 2014 FOIA patch files"