| 1 | KBAICSNA ; CCDCCR/GPL - SNOMED CT ANALYSIS ROUTINES; 10/14/08
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| 2 | ;;0.1;CCDCCR;nopatch;noreleasedate
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| 3 | ;Copyright 2008 WorldVistA. Licensed under the terms of the GNU
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| 4 | ;General Public License See attached copy of the License.
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| 5 | ;
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| 6 | ;This program is free software; you can redistribute it and/or modify
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| 7 | ;it under the terms of the GNU General Public License as published by
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| 8 | ;the Free Software Foundation; either version 2 of the License, or
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| 9 | ;(at your option) any later version.
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| 10 | ;
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| 11 | ;This program is distributed in the hope that it will be useful,
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| 12 | ;but WITHOUT ANY WARRANTY; without even the implied warranty of
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| 13 | ;MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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| 14 | ;GNU General Public License for more details.
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| 15 | ;
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| 16 | ;You should have received a copy of the GNU General Public License along
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| 17 | ;with this program; if not, write to the Free Software Foundation, Inc.,
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| 18 | ;51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
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| 19 | ;
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| 20 | ; THESE ROUTINES ANALYZE THE POTENTIAL RETRIEVAL OF SNOMED CT CODES
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| 21 | ; FOR PATIENT DRUG ALLERGIES FOR INCLUSION IN THE CCR OR CCD
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| 22 | ; USING THE VISTA LEXICON ^LEX
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| 23 | ;
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| 24 | ANALYZE(BEGIEN,IENCNT) ; SNOMED RETRIEVAL ANALYSIS ROUTINE
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| 25 | ; BEGINS AT BEGIEN AND GOES FOR IENCNT DRUGS IN GMRD
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| 26 | ; TO RESUME AT NEXT DRUG, USE BEGIEN=""
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| 27 | ; USE RESET^KBAICSNA TO RESET TO TOP OF DRUG LIST
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| 28 | ;
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| 29 | N SNOARY,SNOTMP,SNOI,SNOIEN,RATTR
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| 30 | N CCRGLO
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| 31 | D ASETUP ; SET UP VARIABLES AND GLOBALS
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| 32 | D AINIT ; INITIALIZE ATTRIBUTE VALUE TABLE
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| 33 | I '$D(@SNOBASE@("RESUME")) S @SNOBASE@("RESUME")=$O(@GMRBASE@(1)) ;1ST TME
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| 34 | S RESUME=@SNOBASE@("RESUME") ; WHERE WE LEFT OFF LAST RUN
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| 35 | S SNOIEN=BEGIEN ; BEGIN WITH THE BEGIEN RECORD
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| 36 | I SNOIEN="" S SNOIEN=RESUME
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| 37 | I +SNOIEN=0 D Q ; AT THE END OF THE ALLERGY LIST
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| 38 | . W "END OF DRUG LIST, CALL RESET^KBAICSNA",!
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| 39 | F SNOI=1:1:IENCNT D Q:+SNOIEN=0 ; FOR IENCNT NUMBER OF PATIENTS OR END
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| 40 | . ;D CCRRPC^GPLCCR(.CCRGLO,SNOIEN,"CCR","","","") ;PROCESS THE CCR
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| 41 | . W SNOIEN,@GMRBASE@(SNOIEN,0),!
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| 42 | . N SNORTN,TTERM ; RETURN ARRAY
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| 43 | . S TTERM=$P(@GMRBASE@(SNOIEN,0),"^",1)_" ALLERGY"
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| 44 | . D TEXTRPC(.SNORTN,TTERM)
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| 45 | . I $D(SNORTN) D ;
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| 46 | . . S TVUID=$$GET1^DIQ(120.82,SNOIEN,"VUID")
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| 47 | . . W "VUID:",TVUID,!
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| 48 | . . K @SNOBASE@("VARS",SNOIEN) ; CLEAR OUT OLD VARS
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| 49 | . . I $P(TTMP,"^",1)=1 S @SNOBASE@("VARS",SNOIEN)=TTERM_"^"_TTMP_"^"_SNORTN(0)_"^"_TVUID_"^"_SNORTN("F")
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| 50 | . . ;
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| 51 | . . ; EVALUATE THE VARIABLES AND CREATE AN ATTRIBUTE MAP
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| 52 | . . ;
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| 53 | . . S RATTR=$$SETATTR(SNOIEN) ; SET THE ATTRIBUTE STRING BASED ON THE VARS
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| 54 | . . S @SNOBASE@("ATTR",SNOIEN)=RATTR ; SAVE THE ATRIBUTES FOR THIS DRUG
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| 55 | . . ;
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| 56 | . . N CATNAME,CATTBL
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| 57 | . . S CATNAME=""
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| 58 | . . D CPUSH(.CATNAME,SNOBASE,"SNOTBL",SNOIEN,RATTR) ; ADD TO CATEGORY
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| 59 | . . ; W "CATEGORY NAME: ",CATNAME,!
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| 60 | . . ;
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| 61 | . S SNOIEN=$O(@GMRBASE@(SNOIEN)) ; NEXT RECORD
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| 62 | . S @SNOBASE@("RESUME")=SNOIEN ; WHERE WE ARE LEAVING OFF THIS RUN
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| 63 | ; D PARY^GPLXPATH(@SNOBASE@("ATTRTBL"))
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| 64 | Q
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| 65 | ;
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| 66 | TEXTRPC(ORTN,ITEXT) ; CALL THE LEXICON WITH ITEXT AND RETURN RESULTS IN ORTN
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| 67 | ;
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| 68 | ;N TTMP
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| 69 | W ITEXT,!
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| 70 | S TTMP=$$TEXT^LEXTRAN(ITEXT,"","","SCT","ORTN")
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| 71 | Q
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| 72 | ;
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| 73 | ASETUP ; SET UP GLOBALS AND VARS SNOBASE AND SNOTBL
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| 74 | I '$D(SNOBASE) S SNOBASE=$NA(^TMP("GPLSNO"))
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| 75 | I '$D(@SNOBASE) S @SNOBASE=""
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| 76 | I '$D(GMRBASE) S GMRBASE=$NA(^GMRD(120.82))
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| 77 | I '$D(SNOTBL) S SNOTBL=$NA(^TMP("GPLSNO","SNOTBL","TABLE")) ; ATTR TABLE
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| 78 | S ^TMP("GPLSNO","TABLES","SNOTBL")=SNOTBL ; TABLE OF TABLES
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| 79 | Q
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| 80 | ;
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| 81 | AINIT ; INITIALIZE ATTRIBUTE TABLE
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| 82 | I '$D(SNOBASE) D ASETUP ; FOR COMMAND LINE CALLS
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| 83 | K @SNOTBL
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| 84 | D APUSH^GPLRIMA(SNOTBL,"CODE")
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| 85 | D APUSH^GPLRIMA(SNOTBL,"NOCODE")
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| 86 | D APUSH^GPLRIMA(SNOTBL,"MULTICODE")
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| 87 | D APUSH^GPLRIMA(SNOTBL,"SUBMULTI")
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| 88 | D APUSH^GPLRIMA(SNOTBL,"DONE")
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| 89 | Q
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| 90 | APOST(PRSLT,PTBL,PVAL) ; POST AN ATTRIBUTE PVAL TO PRSLT USING PTBL
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| 91 | ; PSRLT AND PTBL ARE PASSED BY NAME. PVAL IS A STRING
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| 92 | ; PTBL IS THE NAME OF A TABLE IN @SNOBASE@("TABLES") - "SNOTBL"=ALL VALUES
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| 93 | ; PVAL WILL BE PLACED IN THE STRING PRSLT AT $P(X,U,@PTBL@(PVAL))
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| 94 | I '$D(SNOBASE) D ASETUP ; FOR COMMANDLINE PROCESSING
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| 95 | N USETBL
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| 96 | I '$D(@SNOBASE@("TABLES",PTBL)) D Q ; NO TABLE
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| 97 | . W "ERROR NO SUCH TABLE",!
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| 98 | S USETBL=@SNOBASE@("TABLES",PTBL)
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| 99 | S $P(@PRSLT,U,@USETBL@(PVAL))=PVAL
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| 100 | Q
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| 101 | SETATTR(SDFN) ; SET ATTRIBUTES BASED ON VARS
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| 102 | N SBASE,SATTR
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| 103 | S SBASE=$NA(@SNOBASE@("VARS",SDFN))
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| 104 | D APOST("SATTR","SNOTBL","DONE")
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| 105 | I $P(TTMP,"^",1)=1 D APOST("SATTR","SNOTBL","CODE")
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| 106 | I $P(TTMP,"^",1)=-1 D APOST("SATTR","SNOTBL","NOCODE")
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| 107 | Q SATTR ; GPL
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| 108 | I $D(@SBASE@("PROBLEMS",1)) D ;
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| 109 | . D APOST("SATTR","SNOTBL","PROBLEMS")
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| 110 | . ; W "POSTING PROBLEMS",!
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| 111 | I $D(@SBASE@("VITALS",1)) D APOST("SATTR","SNOTBL","VITALS")
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| 112 | I $D(@SBASE@("MEDS",1)) D ; IF THE PATIENT HAS MEDS VARIABLES
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| 113 | . D APOST("SATTR","SNOTBL","MEDS")
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| 114 | . N ZR,ZI
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| 115 | . D GETPA^GPLRIMA(.ZR,SDFN,"MEDS","MEDPRODUCTNAMECODEVALUE") ;CHECK FOR MED CODES
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| 116 | . I ZR(0)>0 D ; VAR LOOKUP WAS GOOD, CHECK FOR NON=NULL RETURN
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| 117 | . . F ZI=1:1:ZR(0) D ; LOOP THROUGH RETURNED VAR^VALUE PAIRS
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| 118 | . . . I $P(ZR(ZI),"^",2)'="" D APOST("SATTR","SNOTBL","MEDSCODE") ;CODES
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| 119 | . ; D PATD^KBAICSNA(2,"MEDS","MEDPRODUCTNAMECODEVALUE") CHECK FOR MED CODES
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| 120 | D APOST("SATTR","SNOTBL","NOTEXTRACTED") ; OUTPUT NOT YET PRODUCED
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| 121 | ; W "ATTRIBUTES: ",SATTR,!
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| 122 | Q SATTR
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| 123 | ;
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| 124 | RESET ; KILL RESUME INDICATOR TO START OVER. ALSO KILL SNO TMP VALUES
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| 125 | K ^TMP("GPLSNO","RESUME")
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| 126 | K ^TMP("GPLSNO")
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| 127 | Q
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| 128 | ;
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| 129 | CLIST ; LIST THE CATEGORIES
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| 130 | ;
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| 131 | I '$D(SNOBASE) D ASETUP ; FOR COMMAND LINE CALLS
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| 132 | N CLBASE,CLNUM,ZI,CLIDX
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| 133 | S CLBASE=$NA(@SNOBASE@("SNOTBL","CATS"))
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| 134 | S CLNUM=@CLBASE@(0)
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| 135 | F ZI=1:1:CLNUM D ; LOOP THROUGH THE CATEGORIES
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| 136 | . S CLIDX=@CLBASE@(ZI)
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| 137 | . W "(",$P(@CLBASE@(CLIDX),"^",1)
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| 138 | . W ":",$P(@CLBASE@(CLIDX),"^",2),") "
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| 139 | . W CLIDX,!
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| 140 | ; D PARY^GPLXPATH(CLBASE)
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| 141 | Q
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| 142 | ;
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| 143 | CPUSH(CATRTN,CBASE,CTBL,CDFN,CATTR) ; ADD PATIENTS TO CATEGORIES
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| 144 | ; AND PASS BACK THE NAME OF THE CATEGORY TO WHICH THE PATIENT
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| 145 | ; WAS ADDED IN CATRTN, WHICH IS PASSED BY REFERENCE
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| 146 | ; CBASE IS WHERE TO PUT THE CATEGORIES PASSED BY NAME
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| 147 | ; CTBL IS THE NAME OF THE TABLE USED TO CREATE THE ATTRIBUTES,
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| 148 | ; PASSED BY NAME AND USED TO CREATE CATEGORY NAMES IE "@CTBL_X"
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| 149 | ; WHERE X IS THE CATEGORY NUMBER. CTBL(0) IS THE NUMBER OF CATEGORIES
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| 150 | ; CATBL(X)=CATTR STORES THE ATTRIBUTE IN THE CATEGORY
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| 151 | ; CDFN IS THE PATIENT DFN, CATTR IS THE ATTRIBUTE STRING
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| 152 | ; THE LIST OF PATIENTS IN A CATEGORY IS STORED INDEXED BY CATEGORY
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| 153 | ; NUMBER IE CTBL_X(CDFN)=""
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| 154 | ;
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| 155 | ; N CCTBL,CENTRY,CNUM,CCOUNT,CPATLIST
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| 156 | S CCTBL=$NA(@CBASE@(CTBL,"CATS"))
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| 157 | ; W "CBASE: ",CCTBL,!
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| 158 | ;
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| 159 | I '$D(@CCTBL@(CATTR)) D ; FIRST PATIENT IN THIS CATEGORY
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| 160 | . D PUSH^GPLXPATH(CCTBL,CATTR) ; ADD THE CATEGORY TO THE ARRAY
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| 161 | . S CNUM=@CCTBL@(0) ; ARRAY ENTRY NUMBER FOR THIS CATEGORY
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| 162 | . S CENTRY=CTBL_"_"_CNUM_U_0 ; TABLE ENTRY DEFAULT
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| 163 | . S @CCTBL@(CATTR)=CENTRY ; DEFAULT NON INCREMENTED TABLE ENTRY
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| 164 | . ; NOTE THAT P1 IS THE CATEGORY NAME MADE UP OF THE TABLE NAME
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| 165 | . ; AND CATGORY ARRAY NUMBER. P2 IS THE COUNT WHICH IS INITIALLY 0
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| 166 | ;
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| 167 | S CCOUNT=$P(@CCTBL@(CATTR),U,2) ; COUNT OF PATIENTS IN THIS CATEGORY
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| 168 | S CCOUNT=CCOUNT+1 ; INCREMENT THE COUNT
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| 169 | S $P(@CCTBL@(CATTR),U,2)=CCOUNT ; PUT IT BACK
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| 170 | ;
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| 171 | S CATRTN=$P(@CCTBL@(CATTR),U,1) ; THE CATEGORY NAME WHICH IS RETURNED
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| 172 | ;
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| 173 | S CPATLIST=$NA(@CBASE@(CTBL,"IENS",CATRTN)) ; BASE OF PAT LIST FOR THIS CAT
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| 174 | ; W "IENS BASE: ",CPATLIST,!
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| 175 | S @CPATLIST@(CDFN)="" ; ADD THIS PATIENT TO THE CAT PAT LIST
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| 176 | ;
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| 177 | Q
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| 178 | ;
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| 179 | REUSE ; GET SAVED VALUES FROM ^TMP("GPLSAV") AND PUT THEM IN A DATABASE
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| 180 | ;
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| 181 | D ASETUP
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| 182 | D AINIT
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| 183 | N SNOI,SNOJ,SNOK,SNOSNO,SNOSEC,SNOIEN,SNOOLD,SNOSRCH
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| 184 | D DO^KBAICX1 ; INITIALIZE GPLSAV VARIABLES
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| 185 | ;S SAVBASE=$NA(^TMP("GPLSAV","VARS"))
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| 186 | S SAVBASE=$NA(@SNOBASE@("VARS"))
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| 187 | S CSVARY=$NA(^TMP("GPLSNO","CSV"))
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| 188 | K @CSVARY
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| 189 | D PUSH^GPLXPATH(CSVARY,"VUID|VUIDText|MediationCode|MediationText") ; header for CSV file
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| 190 | S SNOI=""
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| 191 | F D Q:$O(@SAVBASE@(SNOI))="" ;THE WHOLE LIST
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| 192 | . S SNOI=$O(@SAVBASE@(SNOI))
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| 193 | . S SNOJ=@SAVBASE@(SNOI)
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| 194 | . S SNOK=$P($P(SNOJ,"^",1)," ALLERGY",1)
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| 195 | . S SNOSRCH=$P(SNOJ,"^",1) ;SEARCH TERM USED TO OBTAIN SNOMED CODE
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| 196 | . S SNOIEN=$P(SNOJ,"^",3) ; IEN OF ELEMENT IN LEXICON
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| 197 | . S SNOSNO=$P(SNOJ,"^",4) ; SNOMED CODE
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| 198 | . S SNOSEC=$P(SNOJ,"^",5) ; SECTION OF SNOMED FOR THIS CODE
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| 199 | . S SNOOLD=$P(SNOJ,"^",7) ; OLD NUMBER FOR THIS CODE
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| 200 | . S SNOVUID=$P(SNOJ,"^",9) ; VUID FOR THIS RECORD
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| 201 | . S SNOTXT=$P(SNOJ,"^",10) ; NOMED TEXT FOR CODE
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| 202 | . D PUSH^GPLXPATH(CSVARY,SNOVUID_"|"_$P(SNOSRCH," ALLERGY",1)_"|"_SNOSNO_"|"_SNOTXT)
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| 203 | . W "SEARCH:",SNOSRCH," IEN:",SNOIEN," CODE:",SNOSNO," SEC:",SNOSEC," OLD:",SNOOLD,!
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| 204 | . W SNOK,!
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| 205 | . W SNOJ,!
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| 206 | S OARY=$NA(@CSVARY@(1)) ; SETUP FOR OUTPUT ROUTINE
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| 207 | D PARY^GPLXPATH(CSVARY)
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| 208 | S OFILE="GMR_ALLERGY_MAPPING_TABLE.csv"
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| 209 | S ODIR="/home/vademo2/"
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| 210 | S ZY=$$OUTPUT^GPLXPATH(OARY,OFILE,ODIR)
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| 211 | I ZY W "WROTE ",OFILE," to ",ODIR,!
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| 212 | Q
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| 213 | ;
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