#!/bin/bash #there are many reads and comments in this document for debugging #This scipt requires a provider organization file for each provider to be in the directory, and AllM1EncounterCodes.txt, #First fix all of the Measures sections in all of the files #The following files must be in the same directory as the QRDA files being processed: #MeasuresAndReportingParametersWithVariables.xml #MEASURES-BY-PATIENT.txt #This script which is FixMeasuresSection.sh #PAT_*_QRDA_V1_0_0-11-08-2010_19.xml is assumged to be the file #TEMPORARY #bash FixMeasuresSection.sh #Find out which files to edit and assign them to the variable "MyFile". As you can see, here I loop through particular files in the same directory with this script for MyFile in $(ls PAT_*_QRDA_V1_0_0-11-10-2010_16.xml) do #Process the problem section by calling the function FunctionProcessProblemSection #You will need the following files # LineNumberDownFunction # AllI9ProblemCodes.txt # LineNumberUpDownFunction # This file FunctionProcessProblemSection #echo "MyFile is $MyFile" #source FunctionProcessProblemSection #FunctionProcessProblemSection $MyFile #cp $MyFile $MyFile"BU" #Replace where is just says SSN for the patient with the SSN ID HL7 number #since this is a medicare patient, no privacy violation as that will also appear in the Payer's section echo "xml files are in the directory" pwd #read #replace the @@@UUID-DOC@@@,@@@UUID-SET@@@ and @@@UUID-PAYER@@@ with UUIDs #should probably do that in the problem section as well with WV HL7 ID as root and UUID as an extension for now VerNum=$(grep versionNumber "$MyFile"|awk -F\" '{print $2}') echo "$VerNum" if [ "1" = "$VerNum" ] then #uuid is a Linux command that generates a new uuid u=$(uuid) sed -i s/'@@@UUID-DOC@@@'/$u/ $MyFile sed -i s/'@@@UUID-SET@@@'/$u/ $MyFile sed -i s/'@@@UUID-PAYER@@@'/$u/ $MyFile else echo "UUIDs should remain unchanged because this is not the first version of this document" fi echo "replace UUID site markers" u="" VerNum="" #read #make sure is no longer than two echo "Fix the state line length" sed -i 's/Alabama/AL/gI' $MyFile sed -i 's/Alaska/AK/gI' $MyFile sed -i 's/Arizona/AZ/gI' $MyFile sed -i 's/Arkansas/AR/gI' $MyFile sed -i 's/California/CA/gI' $MyFile sed -i 's/Colorado/CO/gI' $MyFile sed -i 's/Connecticut/CT/gI' $MyFile sed -i 's/Delaware/DE/gI' $MyFile sed -i 's/District of Columbia/DC/gI' $MyFile sed -i 's/Florida/FL/gI' $MyFile sed -i 's/Georgia/GA/gI' $MyFile sed -i 's/Hawaii/HI/gI' $MyFile sed -i 's/Idaho/ID/gI' $MyFile sed -i 's/Illinois/IL/gI' $MyFile sed -i 's/Indiana/IN/gI' $MyFile sed -i 's/Iowa/IA/gI' $MyFile sed -i 's/Kansas/KS/gI' $MyFile sed -i 's/Kentucky/KY/gI' $MyFile sed -i 's/Louisiana/LA/gI' $MyFile sed -i 's/Maine/ME/gI' $MyFile sed -i 's/Maryland/MD/gI' $MyFile sed -i 's/Massachusetts/MA/gI' $MyFile sed -i 's/Michigan/MI/gI' $MyFile sed -i 's/Minnesota/MN/gI' $MyFile sed -i 's/Mississippi/MS/gI' $MyFile sed -i 's/Missouri/MO/gI' $MyFile sed -i 's/Montana/MT/gI' $MyFile sed -i 's/Nebraska/NE/gI' $MyFile sed -i 's/Nevada/NV/gI' $MyFile sed -i 's/New Hampshire/NH/gI' $MyFile sed -i 's/New Jersey/NJ/gI' $MyFile sed -i 's/New Mexico/NM/gI' $MyFile sed -i 's/New York/NY/gI' $MyFile sed -i 's/North Carolina/NC/gI' $MyFile sed -i 's/North Dakota/ND/gI' $MyFile sed -i 's/Ohio/OH/gI' $MyFile sed -i 's/Oklahoma/OK/gI' $MyFile sed -i 's/Oregon/OR/gI' $MyFile sed -i 's/Pennsylvania/PA/gI' $MyFile sed -i 's/Rhode Island/RI/gI' $MyFile sed -i 's/South Carolina/SC/gI' $MyFile sed -i 's/South Dakota/SD/gI' $MyFile sed -i 's/Tennessee/TN/gI' $MyFile sed -i 's/Texas/TX/gI' $MyFile sed -i 's/Utah/UT/gI' $MyFile sed -i 's/Vermont/VT/gI' $MyFile sed -i 's/Virginia/VA/gI' $MyFile sed -i 's/Washington/WA/gI' $MyFile sed -i 's/West Virginia/WV/'gI $MyFile sed -i 's/Wisconsin/WI/gI' $MyFile sed -i 's/Wyoming/WY/gI' $MyFile sed -i 's/American Samoa/AS/gI' $MyFile sed -i 's/Guam/GU/gI' $MyFile sed -i 's/Northern Mariana Islands/MP/gI' $MyFile sed -i 's/Puerto Rico/PR/gI' $MyFile sed -i 's/Virgin Islands/VI/gI' $MyFile sed -i 's/West VA/WV/gI' $MyFile sed -i 's/N Carolina/NC/gI' $MyFile sed -i 's/N Dakota/ND/gI' $MyFile sed -i 's/S Carolina/SC/gI' $MyFile sed -i 's/S Dakota/SD/gI' $MyFile sed -i 's/Puerto Rico/PR/gI' $MyFile sed -i 's/Virgin Islands/VI/gI' $MyFile sed -i 's/"W. VA"/WV/gI' $MyFile sed -i 's/"N. Carolina"/NC/gI' $MyFile sed -i 's/"N. Dakota"/ND/gI' $MyFile sed -i 's/"S. Carolina"/SC/gI' $MyFile sed -i 's/"S. Dakota"/SD/gI' $MyFile sed -i 's/"R.I."/RI/gI' $MyFile #Fix the state entries (grep -n '' $MyFile |awk -F\: '{print $1}') >> statetags.txt for i in $(cat statetags.txt); do StateLineLength=$(sed -n "$i"p "$MyFile" | sed 's/^[ \t]*//' |awk '{print length}') echo "StateLineLength is $StateLineLength" if [ ! "17" = "$StateLineLength" ] then cat -n $MyFile | grep '';echo "$MyFile" echo "Urgent there is a problem with the tag in $MyFile" #read fi done StateLineLength="" rm -rf statetags.txt #UNCOMMENT THIS!!! echo "$MyFile" a1=$(grep -n \"SSN\" $MyFile | awk -F\" '{print $2}'); echo "$a1" echo "$a1 is the line with SSN on it" sed -i s/@@SSN@@/"$a1"/ $MyFile sed -i 's/SSN/2.16.840.1.113883.4.1/' $MyFile a1="" echo "SSN code added" echo "About to start fixing the problem section" #read #PROBLEM SECTION FUNCTION REMOVED #PROBLEM SECTION 1 FIX - TEMPLATE #Add the added template line after 2.16.840.1.113883.10.20.1.50 sed -in /"2.16.840.1.113883.10.20.1.50"/s/$/"\\n"/ "$MyFile" cat -n "$MyFile" | grep "3.249.11.100.12" #read #PROBLEM FIX 2 - TABLE #Remove the table in the beginning of the section if grep -q "11450-4" "$MyFile" >>/dev/null then ProblemSectionKey=$(grep -n "11450-4" "$MyFile" | awk -F: '{print $1}') grep -n "2.16.840.1.113883.10.20.1.27" "$MyFile" | awk -F: '{print $1}' >> Problem27TemplateLines.txt #read startline="$ProblemSectionKey" endline="$(head -1 Problem27TemplateLines.txt)" echo "$startline is startline" echo "$endline is endline" cat -n "$MyFile" | grep '' #Remove the table at the beginning of the problem section but leaves sed -in "$startline,$endline{ s//\n/ }" "$MyFile" sed -in "$startline,$endline{ //,/<\/text>/d }" "$MyFile" # this in an example of one that works #sed -in "$startline,$endline{ /
/,/<\/table>/d }" M1-PAT_100839_QRDA_V1_0_0.xml cat -n "$MyFile" | grep '
' echo "Done removing the table" startline="" endline="" rm -rf Problem27TemplateLines.txt rm -rf MyValueLinesInProblems.txt fi #PROBLEM SECTION FIX 3 - TEXT TAGS #Remove section near effectiveTime #read index="0" grep -n "2.16.840.1.113883.3.249.11.100.8" $MyFile | awk -F: '{print $1}' >> MyTextLinesKeysProblems.txt for i in $(cat MyTextLinesKeysProblems.txt); do startline="$(($i+$index))" endline="$(($i+$index+10))" sed -in "$startline,$endline{ //,/<\/text>/d }" "$MyFile" index="$((index-3))" done index="" starline="" endline="" rm -rf MyTextLinesKeysProblems.txt echo "done removing " #read #PROBLEM SECTION 4 FIX - REMOVE BAD VALUE LINE #remove the value tags after the 2.16.840.1.113883.10.20.1.50 enty index="0" echo "value Lines in Problems about to be written to the file" #grep -n "2.16.840.1.113883.10.20.1.50" $MyFile | awk -F: '{print $1}' grep -n "2.16.840.1.113883.10.20.1.50" $MyFile | awk -F: '{print $1}' >> MyValueLinesInProblems.txt for i in $(cat MyValueLinesInProblems.txt); do startline="$((i+index))" endline="$(($i+index+8))" #sed -in "$startline,$endline{ //,/<\/value>/d }" "$MyFile" sed -in "$startline,$endline{ //,/<\/value>/d }" "$MyFile" echo "a value line was deleted from the $startline area" index="$((index-3))" done index="" starline="" endline="" cat MyValueLinesInProblems.txt rm -rf MyValueLinesInProblems.txt echo "done removing bad value lines" #read #PROBLEM SECTION 5 FIX - ADD GOOD VALUE LINE #Put in a good value line if there are bad ones cat -n "$MyFile" | grep "55561003"; echo "greped 55561003" cat -n "$MyFile" | grep "2.16.840.1.113883.3.249.11.100.12";echo "grepped 2.16.840.1.113883.3.249.11.100.12" cat -n "$MyFile" | grep "2.16.840.1.113883.10.20.1.50"; echo "grepped 2.16.840.1.113883.10.20.1.50" echo " about to add xsi value lines with sed" #read #sed -in '/"2.16.840.1.113883.10.20.1.50"/{n;n;n;s/$/\n/}' "$MyFile" sed -in '/"2.16.840.1.113883.10.20.1.50"/{N;N;N;s/$/\n/}' "$MyFile" #echo "value Lines in Problems about to be written to screen and then the file" #grep -n "2.16.840.1.113883.10.20.1.50" $MyFile | awk -F: '{print $1}' #grep -n "2.16.840.1.113883.10.20.1.50" $MyFile | awk -F: '{print $1}' >> MyValueLinesInProblems.txt #for i in $(cat MyValueLinesInProblems.txt) #do # sed -in "$i","$((i+6))"p "$MyFile" #done #rm -rf MyValueLinesInProblems.txt echo "done adding good value line" #read #PROBLEM #6 - XSI PROBLEM #Fix the missing xsi:code value lines #Fix any wrong value elements in the problem section #I don't think there are any #cat MyStatusTemplates.txt #echo "above checking the MyStatusTemplates.txt file content" #read echo "issuing the sed command to delete the buffer" sed -e 'd' /home/nancy/CCR-Template/MyFile.txt #read Startline="$(cat "$MyFile" | grep -n "11450-4" | awk -F: '{print $1}')" grep -n "2.16.840.1.113883.10.20.1.50" "$MyFile" | awk -F: '{print $1}' >> MyStatusTemplates.txt Endline="$(tail -1 MyStatusTemplates.txt)" cat -n "$MyFile" | grep '> MyNewFile.xml a="" agc="" #read #the race and ethnicity will eventually come from the CCR Social History #orde needs to be adminGender, birthTIme, race, ethnicity #Now add the administrative gender #now add the race code line to my new file #right now everybody is native Hawaiian until we get this fixed! #Plan to use only the existing VistA codes which match meaningful use echo '' >> MyNewFile.xml echo '' >> MyNewFile.xml echo '' >> MyNewFile.xml tail -6 MyNewFile.xml #the race and ethnicity that will eventually come from the CCR Social History echo "fix administrativeGender, birthTime, raceCode and ethnicGroup" #read #copy the lines with the birthTime and and into the file in tieir proper place #by pulling their locatin from the original file relative to the administrativeGenderCode line #The providerOrganization sectiono is missing entrirely so put it in from these hard coded files for Matt and Nancy #in their proper place right after the > MyNewFile.xml else cat MatthewsProviderOranization.txt >> MyNewFile.xml fi #this just adds a line feed to MyNewFile.xml echo >> MyNewFile.xml echo "read Provider organizaton added" #read #put the document beginning with /patientRole until the tag that is 2 lines after the only incidence of into MyNewFile.xml d=$(grep -n "/patientRole" $MyFile|awk -F: '{print $1}');echo $d e=$(($d+1));echo $e f=$(grep -n "/associatedPerson" $MyFile|awk -F: '{print $1}');echo $f g=$(($f+2));echo $g cat $MyFile | sed -n $d,$g"p" >> MyNewFile.xml #now add in the echo "read /patientRole to /participant Person added" #read #now add the documentation of pulling the data from the encounter procedures later in the document. Searches for Encounters that are #appropriate for the measure which will be in Encounter.txt #!!!!ADD MATT HERE for i in $(cat AllEncounterCodes.txt); do if [ "0" = "$(grep -q "$i" "$MyFile";echo "$?")" ] then echo $(grep -n "$i" "$MyFile" | awk -F: '{print $1}') >> Encounters.txt echo "$i" echo "above code added" fi done cat "Encounters.txt" #read if [ -f Encounters.txt ] then for i in $(cat Encounters.txt); do echo echo "" >> MyNewFile.xml echo "" >> MyNewFile.xml cat $MyFile | sed -n $i"p" >> MyNewFile.xml x=$(($i+5)); echo $x y=$(($i+8)); echo $y #echo "sed -n "$x","$y"p >> MyNewFile.xml" cat "$MyFile" | sed -n "$x","$y"p >> MyNewFile.xml cat EndDocumentationOfSectionNancy.txt >> MyNewFile.xml #added a line feed echo >> MyNewFile.xml #for testing print out the last 10 lines to the screen tail MyNewFile.xml done else echo "$MyFile" >> FilesWithoutEncounters.txt fi tail MyNewFile.xml rm -rf Encounters.txt y="" x="" echo "read documentationOf added and each section of that tailed -10" #read #read #takes the low value date and puts it in the high value if the the is a nullFlavor there and it also corrects the dates by adding a 0 #in the 5th digit position if the date is 7 long instead of 8 and a zero in the 5th and next to the last position if the date is 6 long (ie,too short in either the low or high value) The latter is fixed now so it can be trimmed out - soon All dates and times are 8 or more echo "" >> MyNewFile.xml p=$(grep -n '' $MyFile | awk -F: '{print $1}') q=$(grep -n '' $MyFile | awk -F: '{print $1}') cat "$MyFile" | sed -n "$p","$q"p >> MyNewFile.xml # take out and replace it with the same value that is in low value everywhere it appears grep -n '' MyNewFile.xml | awk -F: '{print $1}' >> NullFlavorTimes.txt #NullFlavorTimes.txt has the line numbers for i in $(cat NullFlavorTimes.txt); do #low value is one line above the high value with the nullFlavor, so get the date as it is l=$(($i-1));echo $l m=$(sed -n "$l"p MyNewFile.xml) n=$(echo "$m" | awk -F\" '{print $2}') u=$(echo "${#n}") #fixes the date in low value if it is 7 long if [ $u = 7 ] then v=$(echo $n |cut -c1-4) w=$(echo $n |cut -c5-7) j=$(echo $v"0"$w);echo $n sed -i "$l"s/"$n"/"$j"/ MyNewFile.xml n="$j" #fixes the date if it is 6 long elif [ $u = 6 ] then v=$(echo $n |cut -c1-4) w=$(echo $n |cut -c5) x=$(echo $n |cut -c6) j=$(echo $v"0"$w"0"$x);echo $n sed -i "$l"s/"$n"/"$j"/ MyNewFile.xml n="$j" fi #now puts the low value corrected date in the high value o="value="\""$n"\""" echo $o echo $i #echo "sed -i "$i"s/nullFlavor=\"UNK\"/$o/ MyNewFile.xml" sed -i "$i"s/'nullFlavor=\"UNK\"'/"$o"/ MyNewFile.xml done rm -rf NullFlavorTimes.txt l="" m="" n="" u="" v="" w="" j="" o="" i="" echo "read NullFlavorTimes Fixed" # #read #THIS NEEDS TO BE REPLACED WITH CUTTING OUT PROCEDURES NOT IN THE DOWNLOADABLE RESOURCE TABLE #CODE FOR DELETING PROCEDURES WAS HERE AND IS NOW IN CodeForDeletingProcedures.txt #Replace anything with SNOMED or SNOMED-CT with SNM and replace anything with ICD9CM with I9 and and replace where it says codeSystem="" in the problem list with codeSysetm="2.16.840.1.113883.6.103" #in lines that contain ICD9CM, replace codeSystem="" with codeSystem="2.16.840.1.113883.6.103" sed -i '/ICD9CM/s/codeSystem=\"\"/codeSystem=\"2.16.840.1.113883.6.103\"/' MyNewFile.xml sed -i 's/SNOMED-CT/SNM/' MyNewFile.xml sed -i 's/ICD9CM/I9/' MyNewFile.xml sed -i 's/ICD9/I9/' MyNewFile.xml sed -i 's/SNOMED/SNM/' MyNewFile.xml #Now put out a new file that has the same name as the original with Ver2 at the end which will contain the corrected header echo "replace the codes with their proper names" #read cp MyNewFile.xml $(echo $MyFile | echo $(awk -F. '{print $1}')"Ver2.xml") #mv MyNewFile.xml $(echo $MyFile | echo $(awk -F. '{print $1}')"Ver2.xml") if grep -q 30954-2 MyNewFile.xml then echo "$MyFile contains results" >> FilesWithResults.txt echo "$MyFile contains results" fi rm -rf MyNewFile.xml rm -rf MyNewFile.xmln echo "this is the end" #read echo "end $MyFile" done echo "read FilesWithResults.txt has the names of files for running the results script" #read exit