VistA-ccr/p/KBAICSNA.m

211 lines
8.6 KiB
Mathematica

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