Two routines modified: C0CRXNRD and C0CRXNLK.
C0CRXNRD (loader utility): - Can now import RxNorm prescribably subset - Will import public domain by default except if RESTRICTED is passed to IMPORT as 1 (second parameter). C0CRXNLK (lookup utilities): - FDB Unit Tests don't run if FDB from RxNorm isn't loaded. - New API: $$RXN2GCN - Get GCNs from RXNCUI (+UT). - New API: $$VUI2GCN - Get VUIDs from GCN (No UT supplied). - New API: $$RXN2NDC - Get NDCs for a given RxNorm CUI (+UT).
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@ -1,5 +1,5 @@
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C0CRXNAD ; VEN/SMH - Add a drug to VISTA from RxNorm;2013-04-19 5:39 PM
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;;1.0;RX NORM;;Apr 25, 2012;Build 99
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;;2.2;RXNORM FOR VISTA;;Nov 14, 2013;Build 8
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; (C) 2013 Sam Habiel
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; Proprietary Code. Don't use if license terms aren't supplied.
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;
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@ -1,5 +1,5 @@
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C0CRXNLK ; VEN/SMH - RxNorm Lookup Utilities ;2013-04-10 7:01 PM
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;;1.0;RX NORM;;Apr 25, 2012;Build 99
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C0CRXNLK ; VEN/SMH - RxNorm Lookup Utilities ;2013-11-14 2:43 PM
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;;2.2;RXNORM FOR VISTA;;Nov 14, 2013;Build 8
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;(c) Sam Habiel 2013
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; See accompanying license. Don't use otherwise.
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;
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@ -22,6 +22,7 @@ GCN2RXN(GCN) ; $$ Public - Get RxNorm CUI using GCN
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Q ^(IEN)
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;
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GCN2RXNT ; @TEST - Test Get RxNorm CUI using GCN
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Q:'$D(^C0CRXN(176.001,"STC","NDDF"))
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N L F L=1:1 N LN S LN=$T(GCN2RXND+L) Q:LN["<<END>>" Q:LN="" D
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. N GCN S GCN=$P(LN,";",3)
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. N RXN S RXN=$P(LN,";",4)
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@ -38,6 +39,34 @@ GCN2RXND ; @DATA - Data for Tests ;;GCN;EXPECTED RXNCUI
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;
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;
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;
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RXN2GCN(RXNCUI) ; $$ Public - Get GCN(s) given an RxNorm Number
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; Input: RXNCUI by Value
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; Output: Caret delimited Extrinsic
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N GCNS S GCNS=""
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N I S I=""
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F S I=$O(^C0CRXN(176.001,"STX","NDDF","CDC",RXNCUI,I)) Q:I="" S GCNS=GCNS_+^(I)_U ; + b/c we want the GCN w/o leading zeros
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S GCNS=$E(GCNS,1,$L(GCNS)-1) ; remove trailing ^
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Q GCNS
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;
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RXN2GCNT ; @TEST - Test Get GCN from RXNCUI
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Q:'$D(^C0CRXN(176.001,"STX","NDDF"))
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N L F L=1:1 N LN S LN=$T(RXN2GCND+L) Q:LN["<<END>>" Q:LN="" D
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. N RXN S RXN=$P(LN,";",3)
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. N GCN S GCN=$P(LN,";",4)
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. D CHKEQ^XTMUNIT($$RXN2GCN(RXN),GCN,"Translation from RXCUI to GCN failed")
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QUIT
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;
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;
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RXN2GCND ; @DATA - Data for Tests ;;RXNORM CUI;Expected GCN; Human Readable Drug name for dear reader
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;;998689;5145;Acetabulol 200mg tab
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;;745679;5037;Albuterol Inhaler
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;;197320;2536;Allopurinol 300mg tab
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;;993691;3948^46236;Bupropion 75mg tab
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;;197591;3768;Diazepam 5mg tab
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;;<<END>>
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;
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;
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;
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RXN2VUI(RXNCUI) ; $$ Public - Get VUID(s) for given RXNCUI for Clinical Drug
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; Input: RXNCUI by Value
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; Output: Caret delimited extrinsic. Should not be more than 2 entries.
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@ -122,7 +151,7 @@ RXN2MEDS(RXNCUI) ; $$ Public - Convert RxNorm value to currently existing drugs
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N I F I=1:1:$L(VUIDS,U) D Q:DONE
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. N VUID S VUID=$P(VUIDS,U,I)
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. N VAPRODS S VAPRODS=$$VUI2VAP(VUID) ; Get VA Product from VUID (multiple products per VUID)
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. I '$L(VAPRODS) S ^SAM(RXNCUI)="TELL SAM",DONE=1 QUIT ; MUST EXIST. Every VUID must have a product to go with it.
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. I '$L(VAPRODS) S $ECODE=",U-NO-VA-PRODUCT-CORRUPT-NDF," ; MUST EXIST. Every VUID must have a product to go with it.
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. N J F J=1:1:$L(VAPRODS,U) D Q:DONE
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. . N VAPROD S VAPROD=$P(VAPRODS,U,J)
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. . S MEDS=$$VAP2MED(VAPROD) ; Get Meds from VA Product
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@ -137,6 +166,7 @@ FDI2RXN(BASE) ; $$ Public - Get RxNorm CUI for FDB Ingredient/Base
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N IEN S IEN=$O(^C0CRXN(176.001,"STC","NDDF","IN",BASE,"")) Q ^(IEN)
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;
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FDI2RXNT ; @TEST - Test Get RxNorm CUI for FDB Ingredient/Base
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Q:'$D(^C0CRXN(176.001,"STC","NDDF"))
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D CHKEQ^XTMUNIT($$FDI2RXN(14739),1362160,"$$FDI2RXN failed")
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QUIT
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;
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@ -201,6 +231,16 @@ VUI2RXN(VUID) ; $$ Public - Get RXNCUI for VUID (any VUID type)
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S RXNS=$E(RXNS,1,$L(RXNS)-1)
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QUIT RXNS
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;
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VUI2GCN(VUID) ; $$ Public - Get GCNs for a given VUID (any VUID type)
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; Input: VUID by Value
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; Output: GCNs delimited by ^
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; TODO: Unit Test
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N RXNS S RXNS=$$VUI2RXN(VUID)
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N GCNS S GCNS=""
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N I F I=1:1:$L(RXNS,U) S GCNS=GCNS_$$RXN2GCN($P(RXNS,U,I))_U
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S GCNS=$E(GCNS,1,$L(GCNS)-1)
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QUIT GCNS
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;
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MED2RXN(DA) ; $$ Public - Get RxNorm CUI for Drug
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; Input: DA - Medication IEN
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; Output: RXNCUIs delimited by ^
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@ -299,3 +339,14 @@ RXN2BNS(RXN) ; $$ Public - Get all Brand Names associated with an RXN
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RXN2BNST ; @TEST - Test Get all Brand Names associated with an RXN
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D CHKTF^XTMUNIT($$RXN2BNS(205535)["Prozac","$$RXN2BNS failed")
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QUIT
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;
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; ---
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;
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RXN2NDC(RXN) ; Get NDC codes for RxNorm code
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N NDCS S NDCS=""
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N I F I=0:0 S I=$O(^C0CRXN(176.002,"ASAR","RXNORM","NDC",RXN,I)) Q:'I S NDCS=NDCS_^(I)_"^"
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S $E(NDCS,$L(NDCS))=""
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QUIT NDCS
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RXN2NDCT ; @TEST - Test Get NDC codes for RxNorm code
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D CHKTF^XTMUNIT($$RXN2NDC(197379)["^"_16714003309,"$$RXN2NDC failed")
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QUIT
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@ -1,14 +1,18 @@
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C0CRXNRD ; VEN/SMH - RxNorm Utilities: Routine to Read RxNorm files;2013-03-06 4:32 PM
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;;2.0;RX NORM;;May 11, 2012;Build 50
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C0CRXNRD ; VEN/SMH - RxNorm Utilities: Routine to Read RxNorm files;2013-11-14 1:23 PM
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;;2.2;RXNORM FOR VISTA;;Nov 14, 2013;Build 8
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; (C) Sam Habiel 2013
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; See license for terms of use.
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;
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W "No entry from top" Q
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IMPORT(PATH) ; PUBLIC ENTRY POINT. Rest are private
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IMPORT(PATH,RESTRICTED) ; PUBLIC ENTRY POINT. Rest are private
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I PATH="" QUIT
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S RESTRICTED=$G(RESTRICTED,0)
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S U="^"
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N STARTTIME S STARTTIME=$P($H,",")*24*60*60+$P($H,",",2)
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D SAB(PATH),CONSO(PATH),SAT(PATH),STY(PATH),REL(PATH),DOC(PATH)
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N SABS
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D SAB(PATH,.SABS) ; Load restriction values into SAB. ; 176.006
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D CONSO(PATH,.SABS,RESTRICTED),SAT(PATH,.SABS,RESTRICTED) ; 176.001,176.002
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D STY(PATH),REL(PATH),DOC(PATH) ; 176.003-5
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N ENDTIME S ENDTIME=$P($H,",")*24*60*60+$P($H,",",2)
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W !,(ENDTIME-STARTTIME)/60_" minutes elapsed"
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QUIT
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@ -24,17 +28,19 @@ DELFILED(FN) ; Delete file data; PEP procedure; only for RxNorm files
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S @ROOT@(0)=ZERO ; It riseth again!
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QUIT
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GETLINES(PATH,FILENAME) ; Get number of lines in a file
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N POP
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D OPEN^%ZISH("FILE",PATH,FILENAME,"R")
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Q:POP
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U IO
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N I,LINE
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F I=1:1 R LINE:0 Q:$$STATUS^%ZISH
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D CLOSE^%ZISH("FILE")
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Q I-1
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CONSO(PATH,INCRES) ; Open and read concepts file: RXNCONSO.RRF
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CONSO(PATH,SABS,RESTRICTED) ; Open and read concepts file: RXNCONSO.RRF
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; PATH ByVal, path of RxNorm files
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; INCRES ByVal, include restricted sources. 1 for yes, 0 for no
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; SABS ByRef, arrays of SABS(SAB)=restriction level
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; RESTRICTED ByVal, include restricted sources. 1 for yes, 0 for no
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I PATH="" QUIT
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S INCRES=+$G(INCRES) ; if not passed, becomes zero.
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N FILENAME S FILENAME="RXNCONSO.RRF"
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D DELFILED(176.001) ; delete data
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N LINES S LINES=$$GETLINES(PATH,FILENAME)
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@ -47,20 +53,22 @@ CONSO(PATH,INCRES) ; Open and read concepts file: RXNCONSO.RRF
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. N LINE R LINE:0
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. IF $$STATUS^%ZISH QUIT
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. I '(C0CCOUNT#1000) U $P W C0CCOUNT," of ",LINES," read ",! U IO ; update every 1000
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. ;
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. ; Deal with restriction level
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. N SAB S SAB=$P(LINE,"|",12)
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. I 'RESTRICTED,SABS(SAB) QUIT ; If not include restricted, and SABS(SAB) is not zero, quit
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. ;
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. ; Save data
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. S ^C0CRXN(176.001,C0CCOUNT,0)=$TR(LINE,"|^","^|")
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. ; TODO Implement Filtering:
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. ; If the source is a restricted source, decide what to do based on what's asked.
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. ; N SRCIEN S SRCIEN=$$FIND1^DIC(176.003,"","QX",SAB,"B") ; SrcIEN in RXNORM SOURCES file
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. ; N RESTRIC S RESTRIC=$$GET1^DIQ(176.003,SRCIEN,14,"I") ; 14 is restriction field; values 0-4
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. ; If RESTRIC is zero, then it's unrestricted. Everything else is restricted.
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. ; If user didn't ask to include restricted sources, and the source is restricted, then quit
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. ; I 'INCRES,RESTRIC QUIT
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EX D CLOSE^%ZISH("FILE")
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N DIK S DIK="^C0CRXN(176.001," D IXALL^DIK
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QUIT
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;
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;
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SAT(PATH) ; Open and read Concept and Atom attributes: RXNSAT.RRF
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SAT(PATH,SABS,RESTRICTED) ; Open and read Concept and Atom attributes: RXNSAT.RRF
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; PATH ByVal, path of RxNorm files
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; SABS ByRef, arrays of SABS(SAB)=restriction level
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; RESTRICTED ByVal, include restricted sources. 1 for yes, 0 for no
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I PATH="" QUIT
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N FILENAME S FILENAME="RXNSAT.RRF"
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D DELFILED(176.002) ; delete data
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@ -81,6 +89,10 @@ SAT(PATH) ; Open and read Concept and Atom attributes: RXNSAT.RRF
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. S $P(LINE,"|",1)=ATN9
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. S $P(LINE,"|",9)=RXCUI1
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. ;
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. ; Deal with restricted sources
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. N SAB S SAB=$P(LINE,"|",10)
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. I 'RESTRICTED,SABS(SAB) QUIT ; If not include restricted, and SABS(SAB) is not zero, quit
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. ;
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. ; Save off
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. S ^C0CRXN(176.002,C0CCOUNT,0)=$TR(LINE,"|^","^|")
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EX2 D CLOSE^%ZISH("FILE")
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@ -88,7 +100,7 @@ EX2 D CLOSE^%ZISH("FILE")
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QUIT
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;
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;
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SAB(PATH) ; Open the read RxNorm Sources file: RXNSAB.RRF
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SAB(PATH,SABS) ; Open the read RxNorm Sources file: RXNSAB.RRF
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I PATH="" QUIT
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N FILENAME S FILENAME="RXNSAB.RRF"
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D DELFILED(176.003) ; delete data
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@ -108,6 +120,8 @@ SAB(PATH) ; Open the read RxNorm Sources file: RXNSAB.RRF
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. S ^C0CRXN(176.003,I,0)=$TR(LINE,"^|","|^")
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EX3 D CLOSE^%ZISH("FILE")
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N DIK S DIK="^C0CRXN(176.003," D IXALL^DIK
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N C0CI F C0CI=0:0 S C0CI=$O(^C0CRXN(176.003,C0CI)) Q:'C0CI D
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. S SABS($$GET1^DIQ(176.003,C0CI,.01))=$$GET1^DIQ(176.003,C0CI,"SRL")
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QUIT
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STY(PATH) ; Open and read RxNorm Semantic types file: RXNSTY.RRF
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I PATH="" QUIT
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