Index: ccr2ccd-xslt/trunk/make/FixQRDA-M1Only-TestShortDateReadsVer15.sh =================================================================== --- ccr2ccd-xslt/trunk/make/FixQRDA-M1Only-TestShortDateReadsVer15.sh (revision 1000) +++ ccr2ccd-xslt/trunk/make/FixQRDA-M1Only-TestShortDateReadsVer15.sh (revision 1000) @@ -0,0 +1,537 @@ +#!/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, + + + +#cat PAT_100146_QRDA_V1_0_0.xml|grep SSN +#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 /home/nancy/CCR-Template/M1-*0.xml) +do + +#cp $MyFile $MyFile"BU" +#Replace where is just says SSN for the patient with the SSN ID HL7 number +#since this is a medicare patient, no privacy violation as that will also appear in the Payer's section + +echo "xml files are in the directory" +read + +#replace the @@@UUID-DOC@@@,@@@UUID-SET@@@ and @@@UUID-PAYER@@@ with UUIDs +#should probably do that in the problem section as well with WV HL7 ID as root and UUID as an extension for now + +VerNum=$(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/' $MyFile +a1="" + + +echo "SSN code added" +echo "About to start fixing the problem section" +read + + + + + +#PROBLEM SECTION 1 FIX - TEMPLATE +#Add the added template line after 2.16.840.1.113883.10.20.1.50 +sed -in /"2.16.840.1.113883.10.20.1.50"/s/$/"\\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 +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 +#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 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 $(cat MyValueLinesInProblems.txt); +do +startline="$((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 AllM1EncounterCodes.txt); + do + echo $i + if grep -q $i $MyFile + then + echo $(grep -n $i $MyFile | awk -F: '{print $1}') >> Encounters.txt + fi +done +cat Encounters.txt +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 + tail MyNewFile.xml + + done +rm -rf Encounters.txt +y="" +x="" + +echo "read documentationOf added and each section of that tailed -10" +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\"'/"$o"/ MyNewFile.xml +done +rm -rf NullFlavorTimes.txt + +l="" +m="" +n="" +u="" +v="" +w="" +j="" +o="" +i="" +echo "read NullFlavorTimes Fixed" +# +read + + +#Remove all of the sections that are not for M1 which begin 2 lines before the PQRI-2 entry and end 2 lines before the reporting parameters code entry 55187.9 This section to be developed + + + +#Now remove the Procedures section from the M1 report as the procedures are not in the downloadable resource table. Need to find the code 47519-4 and delete the whole component that begins with and and goes to the immediately after the code line.47519-4 is the code for the procedures section +if grep -q "47519-4" MyNewFile.xml +then +#Sets a to the line number with the code in it +LineNum="$(grep -n "47519-4" MyNewFile.xml|awk -F: '{print $1}')" +echo "$LineNum" + + +#about two lines above line with 47519-4 in it is a line that is just . Go backward one line at a time and find the line number of that line which is set to a1 +#GrepForComponentLineNumber returns $? with 0 is true and 1 is false +#work backwards from LineNum to find the line with in it + +Result="$(sed -n "$LineNum"p MyNewFile.xml | grep -n "";echo $?)" +echo "$Result" +echo "$LineNum" +echo "$(($LineNum-1))" +while [ "1" = "$Result" ]; +do + LineNum="$(($LineNum-1))" + echo "$LineNum" + Result="$(sed -n "$LineNum"p MyNewFile.xml | grep -n "";echo $?)" +done + +BeginLineNum="$LineNum"; echo "BeginLineNum is $BeginLineNum" + +#initialize EndLineNum which will ultimately be the line with the ending component tag, +EndLineNum="$(($LineNum+1))"; echo "EndLineNum is $EndLineNum" + +#This is to check the line and if it does not contain , add 1 to EndLineNum and go to the next line and check that one + +Result2="$(sed -n "$EndLineNum"p MyNewFile.xml | grep -n '';echo "$?")" +echo "Result2 is $Result2" +while [ "$Result2" = "1" ]; +do + EndLineNum="$(($EndLineNum+1))" + echo "EndLineNum is $EndLineNum" + Result2="$(sed -n "$EndLineNum"p MyNewFile.xml | grep -n '';echo "$?")" +done +echo "Beginning line Number of the Procedure Section is $BeginLineNum" +echo "Ending Line Number of the Procedure Section is $EndLineNum" +#Now delete the procedure section + +sed -in "$BeginLineNum","$EndLineNum"d MyNewFile.xml +fi + +echo "read deleted the procedures section" +read + + +#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