improvements to RNF format routines. FILE2CSV^C0CRNF to export files to csv
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george
parent
68fc454a17
commit
ef1ec0a366
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@ -121,7 +121,7 @@ INIT ; INITIALIZE CCR DICTIONARY BASED ON VARIABLE NAMES
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F S C0CZX=$O(^C0CDIC(170,C0CZX)) Q:+C0CZX=0 D ; FOR EACH DICT ENTRY
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. ;W C0CZX,!
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. K C0CA,C0CN ; CLEAR OUT THE LAST ONE
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. D GETN^C0CRNF("C0CA",170,C0CZX,"ALL") ; GET VARIABLE HASH
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. D GETN1^C0CRNF("C0CA",170,C0CZX,"","ALL") ; GET VARIABLE HASH
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. ;ZWR C0CA B ;
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. S C0CN=$$ZVALUE("VARIABLE") ;NAME OF THE VARIABLE
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. W "VARIABLE: ",C0CN,!
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101
p/C0CRNF.m
101
p/C0CRNF.m
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@ -42,7 +42,7 @@ FIELDS(C0CFRTN,C0CF) ; RETURNS AN ARRAY OF THE FIELDS IN FILE C0CF,
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. S C0CFJ=$O(^DD(C0CFJ)) ; NEXT SUBFILE
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Q
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;
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GETN(GRTN,GFILE,GIEN,GNN) ; GET FIELDS FOR ACCESS BY NAME
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GETNOLD(GRTN,GFILE,GIEN,GNN) ; GET FIELDS FOR ACCESS BY NAME
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; GRTN IS PASSED BY NAME
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;
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N C0CTMP,C0CI,C0CJ,C0CREF,C0CNAME
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@ -68,7 +68,7 @@ GETN(GRTN,GFILE,GIEN,GNN) ; GET FIELDS FOR ACCESS BY NAME
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. . I $P(@GRTN@(C0CI),"^",3)="" K @GRTN@(C0CI) ; KILL THE NULL ENTRIES
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Q
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;
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GETN2(GRTN,GFILE,GREF,GNDX,GNN) ; NEW GET ;GPL ; RETURN A FIELD VALUE MAP
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GETN1(GRTN,GFILE,GREF,GNDX,GNN) ; NEW GET ;GPL ; RETURN A FIELD VALUE MAP
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; GETN IS AN EXTRINSIC WHICH RETURNS THE NEXT IEN AFTER THE CURRENT GIEN
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; GRTN, PASSED BY NAME, RETURNS A FIELD MAP AND A VALUE MAP
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; .. FIELD MAP @GRTN@("F","FIELDNAME^FILE^FIELD#")=""
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@ -120,28 +120,114 @@ GETN2(GRTN,GFILE,GREF,GNDX,GNN) ; NEW GET ;GPL ; RETURN A FIELD VALUE MAP
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. . I $P(@GRTN@(C0CI),"^",3)="" K @GRTN@(C0CI) ; KILL THE NULL ENTRIES
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Q
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;
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GETALL(GARTN,GAFILE,GACNT,GASTRT,GANN) ; RETURN FIELD MAP AND VALUES
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GETN2(GARTN,GAFILE,GAIDX,GACNT,GASTRT,GANN) ; RETURN FIELD MAP AND VALUES
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; GARTN, PASSED BY NAME, RETURNS A FIELD MAP AND A VALUE MAP
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; .. FIELD MAP @GARTN@("F","FIELDNAME^FILE^FIELD#")=""
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; .. FIELD MAP @GARTN@("F","FIELDNAME")="FILE;FIELD#"
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; ... ANY FIELD USED BY ANY RECORD PROCESSED IS IN THE FIELD MAP
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; .. VALUE MAP @GARTN@("V","IEN","FIELDNAME")=VALUE
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; .. VALUE MAP @GARTN@("V","IEN","FIELDNAME","N")=VALUE
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; .. WHERE N IS THE INDEX FOR MULTIPLES.. 1 FOR SINGLE VALUES
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; .. GARTN IS NOT INITIALIZED, SO MULTIPLE CALLS ARE CUMULATIVE
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; .. IF GANN="ALL" THEN ALL FIELDS FOR THE FILE ARE IN THE FIELD MAP
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; .. EVEN IF GANN="ALL" ONLY POPULATED FIELDS ARE RETURNED IN THE VALUE MAP
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; .. NUL FIELDS CAN BE DETERMINED BY CHECKING FIELD MAP - THIS SAVES SPACE
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; GAFILE IS THE FILE NUMBER TO BE PROCESSED. IT IS PASSED BY VALUE
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; GAIDX IS THE OPTIONAL INDEX TO USE IN THE FILE. IF GAIDX IS "" THE IEN
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; .. OF THE FILE WILL BE USED
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; GACNT IS THE NUMBER OF RECORDS TO PROCESS. IT IS PASSED BY VALUE
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; .. IF GARCNT IS NULL, ALL RECORDS ARE PROCESSED
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; GASTRT IS THE IEN OF THE FIRST RECORD TO PROCESS. IT IS PASSED BY VALUE
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; .. IF GARSTART IS NULL, PROCESSING STARTS AT THE FIRST RECORD
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; GANN= NOT NULL - IF GANN IS "ALL" THEN EVEN NULL FIELDS WILL BE RETURNED
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; OTHERWISE, ONLY POPULATED FIELDS ARE RETURNED IN GARFLD AND GARVAL
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N GATMP,GAI,GAF
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;N GATMP,GAI,GAF
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S GAF=$$FILEREF(GAFILE) ; GET CLOSED ROOT FOR THE FILE NUMBER GAFILE
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I '$D(GAIDX) S GAIDX="" ;DEFAULT
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I '$D(GANN) S GANN="" ;DEFAULT ONLY POPULATED FIELDS RETURNED
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I GAIDX'="" S GAF=$NA(@GAF@(GAIDX)) ; IF WE ARE USING AN INDEX
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W GAF,!
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W $O(@GAF@(0)) ;
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S GAI=0 ;ITERATOR
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; F S GAI=$O(@GAF@
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F S GAI=$O(@GAF@(GAI)) Q:GAI="" D ;
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. D GETN1("GATMP",GAFILE,GAI,GAIDX,GANN) ;GET ONE RECORD
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. N GAX S GAX=0
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. F S GAX=$O(GATMP(GAX)) Q:GAX="" D ;PULL OUT THE FIELDS
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. . D ADDNV(GARTN,GAI,GAX,GATMP(GAX)) ;INSERT THE NAME/VALUE INTO GARTN
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Q
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;
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ADDNV(GNV,GNVN,GNVF,GNVV) ; CREATE AN ELEMENT OF THE MATRIX
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;
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S @GNV@("F",GNVF)=$P(GNVV,"^",1)_"^"_$P(GNVV,"^",2) ;NAME=FILE^FIELD#
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S @GNV@("V",GNVN,GNVF,1)=$P(GNVV,"^",3) ;SET THE VALUE
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Q
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;
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RNF2CSV(RNRTN,RNIN,RNSTY) ;CONVERTS AN RFN2 GLOBAL TO A CSV FORMAT
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; READY TO WRITE FOR USE WITH EXCEL @RNRTN@(0) IS NUMBER OF LINES
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; RNSTY IS STYLE OF THE OUTPUT -
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; .. "NV"= ROWS ARE NAMES, COLUMNS ARE VALUES
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; .. "VN"= ROWS ARE VALUES, COLUMNS ARE NAMES
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; .. DEFAULT IS "NV" BECAUSE MANY MATRICES HAVE MORE FIELDS THAN VALUES
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N RNR,RNC ;ROW ROOT,COL ROOT
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N RNI,RNJ,RNX
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I '$D(RNSTY) S RNSTY="NV" ;DEFAULT
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I RNSTY="NV" D NV(RNRTN,RNIN) ; INTERNAL SUBROUTINES DEPENDING ON ORIENTATION
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E D VN(RNRTN,RNIN) ;
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Q
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;
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NV(RNRTN,RNIN) ;
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S RNR=$NA(@RNIN@("F"))
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S RNC=$NA(@RNIN@("V"))
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;S RNY=$P(@RNIN@(0),"^",1) ; FILE NUMBER
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S RNX="""FILE"""_"," ; FIRST COLUMN NAME IS "FIELD"
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S RNI=""
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F S RNI=$O(@RNC@(RNI)) Q:RNI="" D ; FOR EACH COLUMN
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. S RNX=RNX_RNI_"," ;ADD THE COLUMM ELEMENT AND A COMMA
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S RNX=$E(RNX,1,$L(RNX)-1) ; STRIP OFF THE LAST COMMA
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D PUSH^GPLXPATH(RNRTN,RNX) ; FIRST LINE CONTAINS COLUMN HEADINGS
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S RNI=""
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F S RNI=$O(@RNR@(RNI)) Q:RNI="" D ; FOR EACH ROW
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. S RNX=""""_RNI_""""_"," ; FIRST ELEMENT ON ROW IS THE FIELD
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. S RNJ=""
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. F S RNJ=$O(@RNC@(RNJ)) Q:RNJ="" D ; FOR EACH COL
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. . I $D(@RNC@(RNJ,RNI,1)) D ; THIS ROW HAS THIS COLUMN
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. . . S RNX=RNX_""""_@RNC@(RNJ,RNI,1)_""""_"," ; ADD THE ELEMENT PLUS A COMMA
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. . E S RNX=RNX_"," ; NUL COLUMN
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. S RNX=$E(RNX,1,$L(RNX)-1) ; STRIP OFF THE LAST COMMA
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. D PUSH^GPLXPATH(RNRTN,RNX)
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Q
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;
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VN(RNRTN,RNIN) ;
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S RNR=$NA(@RNIN@("V"))
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S RNC=$NA(@RNIN@("F"))
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;S RNY=$P(@RNIN@(0),"^",1) ; FILE NUMBER
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S RNX="""FILE"""_"," ; FIRST COLUMN NAME IS "FIELD"
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S RNI=""
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F S RNI=$O(@RNC@(RNI)) Q:RNI="" D ; FOR EACH COLUMN
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. S RNX=RNX_RNI_"," ;ADD THE COLUMM ELEMENT AND A COMMA
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S RNX=$E(RNX,1,$L(RNX)-1) ; STRIP OFF THE LAST COMMA
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D PUSH^GPLXPATH(RNRTN,RNX) ; FIRST LINE CONTAINS COLUMN HEADINGS
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S RNI=""
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F S RNI=$O(@RNR@(RNI)) Q:RNI="" D ; FOR EACH ROW
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. S RNX=""""_RNI_""""_"," ; FIRST ELEMENT ON ROW IS THE FIELD
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. S RNJ=""
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. F S RNJ=$O(@RNC@(RNJ)) Q:RNJ="" D ; FOR EACH COL
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. . I $D(@RNR@(RNI,RNJ,1)) D ; THIS ROW HAS THIS COLUMN
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. . . S RNX=RNX_""""_@RNR@(RNI,RNJ,1)_""""_"," ; ADD THE ELEMENT PLUS A COMMA
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. . E S RNX=RNX_"," ; NUL COLUMN
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. S RNX=$E(RNX,1,$L(RNX)-1) ; STRIP OFF THE LAST COMMA
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. D PUSH^GPLXPATH(RNRTN,RNX)
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Q
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;
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FILE2CSV(FNUM,FVN) ; WRITES OUT A FILEMAN FILE TO CSV
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;
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;N G1,G2
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I '$D(FVN) S FVN="NV" ; DEFAULT ORIENTATION OF CVS FILE
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S G1=$NA(^TMP($J,"C0CCSV",1))
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S G2=$NA(^TMP($J,"C0CCSV",2))
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D GETN2(G1,FNUM) ; GET THE MATRIX
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D RNF2CSV(G2,G1,FVN) ; PREPARE THE CVS FILE
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K @G1
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W $$OUTPUT^GPLXPATH(@G2@(1),"FILE_"_FNUM_".csv",^TMP("GPLCCR","ODIR"))
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K @G2
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Q
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;
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FILEREF(FNUM) ; EXTRINSIC THAT RETURNS A CLOSED ROOT FOR FILE NUMBER FNUM
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@ -149,6 +235,7 @@ FILEREF(FNUM) ; EXTRINSIC THAT RETURNS A CLOSED ROOT FOR FILE NUMBER FNUM
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N C0CF
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S C0CF=^DIC(FNUM,0,"GL") ;OPEN ROOT TO FILE
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S C0CF=$P(C0CF,",",1)_")" ; CLOSE THE ROOT
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I C0CF["()" S C0CF=$P(C0CF,"()",1)
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Q C0CF
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;
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ZFILE(ZFN,ZTAB) ; EXTRINSIC TO RETURN FILE NUMBER FOR FIELD NAME PASSED
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18
p/C0CRXN.m
18
p/C0CRXN.m
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@ -42,7 +42,7 @@ EXPAND ; MAIN ROUTINE TO CREATE THE C0C RXNORM VUID EXPANSION FILE (176.112)
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F S C0CZX=$O(^C0CCODES(176.111,C0CZX)) Q:+C0CZX=0 D ; FOR EVERY RECORD
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. K C0CA,C0CB,C0CC ; CLEAR ARRAYS
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. D FIELDS^C0CRNF("C0CC",176.112) ;GET FIELD NAMES FOR OUTPUT FILE
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. D GETN2^C0CRNF("C0CA",176.111,C0CZX,"","ALL") ;GET THE FIELDS
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. D GETN1^C0CRNF("C0CA",176.111,C0CZX,"","ALL") ;GET THE FIELDS
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. I $$ZVALUE("MEDIATION CODE")="" D
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. . S NORXN=NORXN+1 ;
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. E D ; PROCESS MEDIATION CODE
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@ -53,7 +53,7 @@ EXPAND ; MAIN ROUTINE TO CREATE THE C0C RXNORM VUID EXPANSION FILE (176.112)
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. . ;D SETFDA("VUID",$$ZVALUE("VUID"))
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. E D SETFDA("VUID TEXT",$$ZVALUE("VUID TEXT"))
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. . ;ZWR C0CA
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. D GETN2^C0CRNF("C0CB",176.001,$$ZVALUE("VUID"),"VUID","ALL")
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. D GETN1^C0CRNF("C0CB",176.001,$$ZVALUE("VUID"),"VUID","ALL")
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. I $$ZVALUE("RXCUI","C0CB")'="" D ; RXNORM FOUND
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. . S RXFOUND=RXFOUND+1
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. . I $$ZVALUE("MEDIATION CODE")="" D ; THIS IS A NEW CODE
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@ -111,9 +111,9 @@ EXP2 ; ROUTINE TO CREATE 176.113 C0C RXNORM VUID MAPPING DISCREPANCIES FILE
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F S C0CZX=$O(^C0CRXN(176.001,"VUID",C0CZX)) Q:+C0CZX=0 D ; FOR EVERY VUID
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. K C0CA,C0CB,C0CC,C0CD ; CLEAR ARRAYS
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. D FIELDS^C0CRNF("C0CC",176.113) ;GET FIELD NAMES FOR OUTPUT FILE
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. D GETN2^C0CRNF("C0CA",176.001,C0CZX,"VUID","ALL") ;GET FROM RXNORM FILE
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. D GETN2^C0CRNF("C0CB",176.111,C0CZX,"B","ALL") ;GET FROM VA MAPPING FILE
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. D GETN2^C0CRNF("C0CD",50.68,C0CZX,"AVUID","ALL") ;GET FROM NDF
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. D GETN1^C0CRNF("C0CA",176.001,C0CZX,"VUID","ALL") ;GET FROM RXNORM FILE
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. D GETN1^C0CRNF("C0CB",176.111,C0CZX,"B","ALL") ;GET FROM VA MAPPING FILE
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. D GETN1^C0CRNF("C0CD",50.68,C0CZX,"AVUID","ALL") ;GET FROM NDF
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. ;D SETFDA("VUID",$$ZVALUE("CODE")) ;SET THE VUID CODE
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. D SETFDA("RXNORM",$$ZVALUE("RXCUI")) ;SET THE RXNORM CODE
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. D SETFDA("RXNORM TEXT",$$ZVALUE("STR")) ;SET THE RXNORM TEXT
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@ -172,11 +172,11 @@ CHKNDF ; ROUTINE TO CHECK THE NATIONAL DRUG FILE WITH THE UMLS RXNORM DB
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F S C0CZX=$O(^PSNDF(50.68,"AVUID",C0CZX)) Q:+C0CZX=0 D ; FOR EVERY VUID
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. K C0CA,C0CB,C0CC,C0CD ; CLEAR ARRAYS
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. ;D FIELDS^C0CRNF("C0CC",176.113) ;GET FIELD NAMES FOR OUTPUT FILE
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. D GETN2^C0CRNF("C0CA",50.68,C0CZX,"AVUID","ALL") ;GET THE FIELDS
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. D GETN1^C0CRNF("C0CA",50.68,C0CZX,"AVUID","ALL") ;GET THE FIELDS
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. I $$ZVALUE("VUID")="" D ; ERROR, SHOULD NOT HAPPEN
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. . S NOVUID=NOVUID+1 ; FLAG THE ERROR
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. . D PUSH^GPLXPATH("NOVUID",C0CZX) ; RECORD THE VUID
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. D GETN2^C0CRNF("C0CD",176.001,C0CZX,"VUID","ALL") ;TRY RXNORM DB
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. D GETN1^C0CRNF("C0CD",176.001,C0CZX,"VUID","ALL") ;TRY RXNORM DB
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. I $$ZVALUE("CODE","C0CD")=C0CZX D ; FOUND IN RXNORM
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. . S VMATCH=VMATCH+1 ; COUNT OF PSNDF VUIDS FOUND IN RXNORM
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. . I $$ZVALUE("NAME")=$$ZVALUE("STR","C0CD") D ;TEXT MATCHES
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@ -187,7 +187,7 @@ CHKNDF ; ROUTINE TO CHECK THE NATIONAL DRUG FILE WITH THE UMLS RXNORM DB
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. . . W ZV,!
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. . . D PUSH^GPLXPATH("TXTNM",ZV) ; RECORD THE TXT MISMATCH
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. E S NOMATCH=NOMATCH+1 ; NOT FOUND IN RXNORM
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. D GETN2^C0CRNF("C0CB",176.111,C0CZX,"B","ALL") ;TRY TO GET FROM 176.111
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. D GETN1^C0CRNF("C0CB",176.111,C0CZX,"B","ALL") ;TRY TO GET FROM 176.111
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. I $$ZVALUE("VUID","C0CB")="" D ; VUID NOT FOUND
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. . ;W "NOT FOUND: ",C0CZX," ",$$ZVALUE("STR")," ",$$ZVALUE("RXCUI"),!
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. . S MISSING=MISSING+1
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@ -216,7 +216,7 @@ CHKNDF ; ROUTINE TO CHECK THE NATIONAL DRUG FILE WITH THE UMLS RXNORM DB
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. . ;D SETFDA("VUID",$$ZVALUE("VUID"))
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. E D SETFDA("VUID TEXT",$$ZVALUE("VUID TEXT"))
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. . ;ZWR C0CA
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. D GETN2^C0CRNF("C0CB",176.001,$$ZVALUE("VUID"),"VUID","ALL")
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. D GETN1^C0CRNF("C0CB",176.001,$$ZVALUE("VUID"),"VUID","ALL")
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. I $$ZVALUE("RXCUI","C0CB")'="" D ; RXNORM FOUND
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. . S RXFOUND=RXFOUND+1
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. . I $$ZVALUE("MEDIATION CODE")="" D ; THIS IS A NEW CODE
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