211 lines
8.6 KiB
Mathematica
211 lines
8.6 KiB
Mathematica
KBAICSNA ; CCDCCR/GPL - SNOMED CT ANALYSIS ROUTINES; 10/14/08
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;;0.1;CCDCCR;nopatch;noreleasedate
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;Copyright 2008 WorldVistA. Licensed under the terms of the GNU
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;General Public License See attached copy of the License.
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;
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;This program is free software; you can redistribute it and/or modify
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;it under the terms of the GNU General Public License as published by
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;the Free Software Foundation; either version 2 of the License, or
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;(at your option) any later version.
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;
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;This program is distributed in the hope that it will be useful,
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;but WITHOUT ANY WARRANTY; without even the implied warranty of
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;MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;GNU General Public License for more details.
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;
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;You should have received a copy of the GNU General Public License along
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;with this program; if not, write to the Free Software Foundation, Inc.,
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;51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
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;
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; THESE ROUTINES ANALYZE THE POTENTIAL RETRIEVAL OF SNOMED CT CODES
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; FOR PATIENT DRUG ALLERGIES FOR INCLUSION IN THE CCR OR CCD
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; USING THE VISTA LEXICON ^LEX
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;
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ANALYZE(BEGIEN,IENCNT) ; SNOMED RETRIEVAL ANALYSIS ROUTINE
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; BEGINS AT BEGIEN AND GOES FOR IENCNT DRUGS IN GMRD
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; TO RESUME AT NEXT DRUG, USE BEGIEN=""
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; USE RESET^KBAICSNA TO RESET TO TOP OF DRUG LIST
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;
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N SNOARY,SNOTMP,SNOI,SNOIEN,RATTR
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N CCRGLO
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D ASETUP ; SET UP VARIABLES AND GLOBALS
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D AINIT ; INITIALIZE ATTRIBUTE VALUE TABLE
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I '$D(@SNOBASE@("RESUME")) S @SNOBASE@("RESUME")=$O(@GMRBASE@(1)) ;1ST TME
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S RESUME=@SNOBASE@("RESUME") ; WHERE WE LEFT OFF LAST RUN
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S SNOIEN=BEGIEN ; BEGIN WITH THE BEGIEN RECORD
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I SNOIEN="" S SNOIEN=RESUME
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I +SNOIEN=0 D Q ; AT THE END OF THE ALLERGY LIST
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. W "END OF DRUG LIST, CALL RESET^KBAICSNA",!
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F SNOI=1:1:IENCNT D Q:+SNOIEN=0 ; FOR IENCNT NUMBER OF PATIENTS OR END
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. ;D CCRRPC^GPLCCR(.CCRGLO,SNOIEN,"CCR","","","") ;PROCESS THE CCR
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. W SNOIEN,@GMRBASE@(SNOIEN,0),!
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. N SNORTN,TTERM ; RETURN ARRAY
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. S TTERM=$P(@GMRBASE@(SNOIEN,0),"^",1)_" ALLERGY"
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. D TEXTRPC(.SNORTN,TTERM)
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. I '$D(SNORTN) Q ;
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. S TVUID=$$GET1^DIQ(120.82,SNOIEN,"VUID")
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. W "VUID:",VUID,!
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. K @SNOBASE@("VARS",SNOIEN) ; CLEAR OUT OLD VARS
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. I $P(TTMP,"^",1)=1 S @SNOBASE@("VARS",SNOIEN)=TTERM_"^"_TTMP_"^"_SNORTN(0)
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. ;
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. ; EVALUATE THE VARIABLES AND CREATE AN ATTRIBUTE MAP
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. ;
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. S RATTR=$$SETATTR(SNOIEN) ; SET THE ATTRIBUTE STRING BASED ON THE VARS
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. S @SNOBASE@("ATTR",SNOIEN)=RATTR ; SAVE THE ATRIBUTES FOR THIS DRUG
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. ;
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. N CATNAME,CATTBL
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. S CATNAME=""
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. D CPUSH(.CATNAME,SNOBASE,"SNOTBL",SNOIEN,RATTR) ; ADD TO CATEGORY
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. ; W "CATEGORY NAME: ",CATNAME,!
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. ;
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. S SNOIEN=$O(@GMRBASE@(SNOIEN)) ; NEXT RECORD
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. S @SNOBASE@("RESUME")=SNOIEN ; WHERE WE ARE LEAVING OFF THIS RUN
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; D PARY^GPLXPATH(@SNOBASE@("ATTRTBL"))
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Q
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;
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TEXTRPC(ORTN,ITEXT) ; CALL THE LEXICON WITH ITEXT AND RETURN RESULTS IN ORTN
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;
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;N TTMP
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W ITEXT,!
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S TTMP=$$TEXT^LEXTRAN(ITEXT,"","","SCT","ORTN")
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Q
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;
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ASETUP ; SET UP GLOBALS AND VARS SNOBASE AND SNOTBL
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I '$D(SNOBASE) S SNOBASE=$NA(^TMP("GPLSNO"))
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I '$D(@SNOBASE) S @SNOBASE=""
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I '$D(GMRBASE) S GMRBASE=$NA(^GMRD(120.82))
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I '$D(SNOTBL) S SNOTBL=$NA(^TMP("GPLSNO","SNOTBL","TABLE")) ; ATTR TABLE
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S ^TMP("GPLSNO","TABLES","SNOTBL")=SNOTBL ; TABLE OF TABLES
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Q
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;
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AINIT ; INITIALIZE ATTRIBUTE TABLE
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I '$D(SNOBASE) D ASETUP ; FOR COMMAND LINE CALLS
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K @SNOTBL
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D APUSH^GPLRIMA(SNOTBL,"CODE")
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D APUSH^GPLRIMA(SNOTBL,"NOCODE")
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D APUSH^GPLRIMA(SNOTBL,"MULTICODE")
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D APUSH^GPLRIMA(SNOTBL,"SUBMULTI")
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D APUSH^GPLRIMA(SNOTBL,"DONE")
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Q
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APOST(PRSLT,PTBL,PVAL) ; POST AN ATTRIBUTE PVAL TO PRSLT USING PTBL
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; PSRLT AND PTBL ARE PASSED BY NAME. PVAL IS A STRING
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; PTBL IS THE NAME OF A TABLE IN @SNOBASE@("TABLES") - "SNOTBL"=ALL VALUES
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; PVAL WILL BE PLACED IN THE STRING PRSLT AT $P(X,U,@PTBL@(PVAL))
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I '$D(SNOBASE) D ASETUP ; FOR COMMANDLINE PROCESSING
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N USETBL
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I '$D(@SNOBASE@("TABLES",PTBL)) D Q ; NO TABLE
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. W "ERROR NO SUCH TABLE",!
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S USETBL=@SNOBASE@("TABLES",PTBL)
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S $P(@PRSLT,U,@USETBL@(PVAL))=PVAL
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Q
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SETATTR(SDFN) ; SET ATTRIBUTES BASED ON VARS
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N SBASE,SATTR
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S SBASE=$NA(@SNOBASE@("VARS",SDFN))
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D APOST("SATTR","SNOTBL","DONE")
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I $P(TTMP,"^",1)=1 D APOST("SATTR","SNOTBL","CODE")
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I $P(TTMP,"^",1)=-1 D APOST("SATTR","SNOTBL","NOCODE")
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Q SATTR ; GPL
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I $D(@SBASE@("PROBLEMS",1)) D ;
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. D APOST("SATTR","SNOTBL","PROBLEMS")
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. ; W "POSTING PROBLEMS",!
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I $D(@SBASE@("VITALS",1)) D APOST("SATTR","SNOTBL","VITALS")
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I $D(@SBASE@("MEDS",1)) D ; IF THE PATIENT HAS MEDS VARIABLES
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. D APOST("SATTR","SNOTBL","MEDS")
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. N ZR,ZI
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. D GETPA^GPLRIMA(.ZR,SDFN,"MEDS","MEDPRODUCTNAMECODEVALUE") ;CHECK FOR MED CODES
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. I ZR(0)>0 D ; VAR LOOKUP WAS GOOD, CHECK FOR NON=NULL RETURN
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. . F ZI=1:1:ZR(0) D ; LOOP THROUGH RETURNED VAR^VALUE PAIRS
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. . . I $P(ZR(ZI),"^",2)'="" D APOST("SATTR","SNOTBL","MEDSCODE") ;CODES
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. ; D PATD^KBAICSNA(2,"MEDS","MEDPRODUCTNAMECODEVALUE") CHECK FOR MED CODES
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D APOST("SATTR","SNOTBL","NOTEXTRACTED") ; OUTPUT NOT YET PRODUCED
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; W "ATTRIBUTES: ",SATTR,!
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Q SATTR
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;
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RESET ; KILL RESUME INDICATOR TO START OVER. ALSO KILL SNO TMP VALUES
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K ^TMP("GPLSNO","RESUME")
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K ^TMP("GPLSNO")
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Q
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;
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CLIST ; LIST THE CATEGORIES
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;
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I '$D(SNOBASE) D ASETUP ; FOR COMMAND LINE CALLS
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N CLBASE,CLNUM,ZI,CLIDX
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S CLBASE=$NA(@SNOBASE@("SNOTBL","CATS"))
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S CLNUM=@CLBASE@(0)
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F ZI=1:1:CLNUM D ; LOOP THROUGH THE CATEGORIES
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. S CLIDX=@CLBASE@(ZI)
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. W "(",$P(@CLBASE@(CLIDX),"^",1)
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. W ":",$P(@CLBASE@(CLIDX),"^",2),") "
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. W CLIDX,!
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; D PARY^GPLXPATH(CLBASE)
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Q
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;
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CPUSH(CATRTN,CBASE,CTBL,CDFN,CATTR) ; ADD PATIENTS TO CATEGORIES
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; AND PASS BACK THE NAME OF THE CATEGORY TO WHICH THE PATIENT
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; WAS ADDED IN CATRTN, WHICH IS PASSED BY REFERENCE
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; CBASE IS WHERE TO PUT THE CATEGORIES PASSED BY NAME
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; CTBL IS THE NAME OF THE TABLE USED TO CREATE THE ATTRIBUTES,
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; PASSED BY NAME AND USED TO CREATE CATEGORY NAMES IE "@CTBL_X"
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; WHERE X IS THE CATEGORY NUMBER. CTBL(0) IS THE NUMBER OF CATEGORIES
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; CATBL(X)=CATTR STORES THE ATTRIBUTE IN THE CATEGORY
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; CDFN IS THE PATIENT DFN, CATTR IS THE ATTRIBUTE STRING
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; THE LIST OF PATIENTS IN A CATEGORY IS STORED INDEXED BY CATEGORY
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; NUMBER IE CTBL_X(CDFN)=""
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;
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; N CCTBL,CENTRY,CNUM,CCOUNT,CPATLIST
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S CCTBL=$NA(@CBASE@(CTBL,"CATS"))
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; W "CBASE: ",CCTBL,!
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;
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I '$D(@CCTBL@(CATTR)) D ; FIRST PATIENT IN THIS CATEGORY
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. D PUSH^GPLXPATH(CCTBL,CATTR) ; ADD THE CATEGORY TO THE ARRAY
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. S CNUM=@CCTBL@(0) ; ARRAY ENTRY NUMBER FOR THIS CATEGORY
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. S CENTRY=CTBL_"_"_CNUM_U_0 ; TABLE ENTRY DEFAULT
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. S @CCTBL@(CATTR)=CENTRY ; DEFAULT NON INCREMENTED TABLE ENTRY
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. ; NOTE THAT P1 IS THE CATEGORY NAME MADE UP OF THE TABLE NAME
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. ; AND CATGORY ARRAY NUMBER. P2 IS THE COUNT WHICH IS INITIALLY 0
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;
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S CCOUNT=$P(@CCTBL@(CATTR),U,2) ; COUNT OF PATIENTS IN THIS CATEGORY
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S CCOUNT=CCOUNT+1 ; INCREMENT THE COUNT
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S $P(@CCTBL@(CATTR),U,2)=CCOUNT ; PUT IT BACK
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;
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S CATRTN=$P(@CCTBL@(CATTR),U,1) ; THE CATEGORY NAME WHICH IS RETURNED
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;
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S CPATLIST=$NA(@CBASE@(CTBL,"IENS",CATRTN)) ; BASE OF PAT LIST FOR THIS CAT
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; W "IENS BASE: ",CPATLIST,!
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S @CPATLIST@(CDFN)="" ; ADD THIS PATIENT TO THE CAT PAT LIST
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;
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Q
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;
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REUSE ; GET SAVED VALUES FROM ^TMP("GPLSAV") AND PUT THEM IN A DATABASE
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;
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D ASETUP
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D AINIT
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N SNOI,SNOJ,SNOK,SNOSNO,SNOSEC,SNOIEN,SNOOLD,SNOSRCH
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D DO^KBAICX1 ; INITIALIZE GPLSAV VARIABLES
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S SAVBASE=$NA(^TMP("GPLSAV","VARS"))
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S CSVARY=$NA(^TMP("GPLSNO","CSV"))
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K @CSVARY
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D PUSH^GPLXPATH(CSVARY,"OLDCODE|GMRText|MediationCode|MediationText") ; header for CSV file
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S SNOI=""
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F D Q:$O(@SAVBASE@(SNOI))="" ;THE WHOLE LIST
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. S SNOI=$O(@SAVBASE@(SNOI))
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. S SNOJ=@SAVBASE@(SNOI)
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. S SNOK=$P($P(SNOJ,"^",1)," ALLERGY",1)
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. S SNOSRCH=$P(SNOJ,"^",1) ;SEARCH TERM USED TO OBTAIN SNOMED CODE
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. S SNOIEN=$P(SNOJ,"^",3) ; IEN OF ELEMENT IN LEXICON
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. S SNOSNO=$P(SNOJ,"^",4) ; SNOMED CODE
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. S SNOSEC=$P(SNOJ,"^",5) ; SECTION OF SNOMED FOR THIS CODE
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. S SNOOLD=$P(SNOJ,"^",7) ; OLD NUMBER FOR THIS CODE
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. D PUSH^GPLXPATH(CSVARY,SNOOLD_"|"_$P(SNOSRCH," ALLERGY",1)_"|"_SNOSNO_"|"_SNOSRCH_"("_SNOSEC_")")
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. W "SEARCH:",SNOSRCH," IEN:",SNOIEN," CODE:",SNOSNO," SEC:",SNOSEC," OLD:",SNOOLD,!
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. W SNOK,!
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. W SNOJ,!
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S OARY=$NA(@CSVARY@(1)) ; SETUP FOR OUTPUT ROUTINE
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D PARY^GPLXPATH(CSVARY)
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S OFILE="GMR_ALLERGY_MAPPING_TABLE.csv"
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S ODIR="/home/glilly/"
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S ZY=$$OUTPUT^GPLXPATH(OARY,OFILE,ODIR)
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I ZY W "WROTE ",OFILE," to ",ODIR,!
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Q
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;
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