added fileman output transform using namespaces
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george
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cecde026df
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14
p/C0XF2N.m
14
p/C0XF2N.m
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@ -37,7 +37,7 @@ INITFARY(ZFARY) ; INITIALIZE FILE NUMBERS AND OTHER USEFUL THINGS
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S @ZFARY@("C0XSFN")=172.201 ; TRIPLES STRINGS FILE NUMBER
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S @ZFARY@("C0XTN")=$NA(^C0X(101)) ; TRIPLES GLOBAL NAME
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S @ZFARY@("C0XSN")=$NA(^C0X(201)) ; STRING FILE GLOBAL NAME
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S @ZFARY@("C0XDIR")="/home/glilly/fmts/trunk/samples/"
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S @ZFARY@("C0XDIR")="/home/glilly/snomed/"
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S @ZFARY@("BLKLOAD")=1 ; this file supports block load
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S @ZFARY@("FMTSSTYLE")="F2N" ; fileman style
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D USEFARY(ZFARY)
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@ -103,7 +103,7 @@ IMPORT(FNAME,INDIR,INURL,FARY) ; EXTRINSIC THAT READS A FILE FROM THE STANDARD
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D INSRDF(ZRDF,INURL,FARY) ; IMPORT AND PROCESS THE RDF
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K INURL
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K C0XFDA
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K ^TMP("MXMLDOM",$J)
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;K ^TMP("MXMLDOM",$J)
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Q
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;
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WGET(ZURL,FARY) ; GET FROM THE INTERNET AN RDF FILE AND INSERT IT
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@ -220,6 +220,7 @@ PROCESS(ZRTN,ZRDF,ZGRF,ZMETA,FARY) ; PROCESS AN INCOMING RDF FILE
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;S C0XDOCID=$$PARSE^C0CNHIN(ZRDF,"C0XARRAY") ; PARSE WITH MXML
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S C0XDLC2=$$NOW^XLFDT ; START OF PARSE
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S C0XDOCID=$$EN^MXMLDOM(ZRDF,"W")
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;B
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K @ZRDF ; DON'T NEED INPUT BUFFER ANYMORE
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; -- assign the MXLM dom global name to ZDOM
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S ZDOM=$NA(^TMP("MXMLDOM",$J,C0XDOCID))
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@ -251,13 +252,16 @@ PROCESS(ZRTN,ZRDF,ZGRF,ZMETA,FARY) ; PROCESS AN INCOMING RDF FILE
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F S ZI=$O(@ZDOM@(1,"A",ZI)) Q:ZI="" D ; FOR EACH xmlns
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. S ZVOC=$P(ZI,"xmlns:",2)
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. I ZVOC'="" S C0XVOC(ZVOC)=$G(@ZDOM@(1,"A",ZI))
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;W !,"VOCABS:" ZWR C0XVOC
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W !,"VOCABS:" ZWR C0XVOC
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;
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; -- look for children called rdf:Description. quit if none. not an rdf file
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;
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S C0XTYPE("rdf:Description")=1
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S C0XTYPE("owl:ObjectProperty")=1
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S ZI=$O(@ZDOM@(1,"C",""))
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I $G(@ZDOM@(1,"C",ZI))'="rdf:Description" D Q ; not an rdf file
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I '$G(C0XTYPE(@ZDOM@(1,"C",ZI))) D Q ; not an rdf file
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. W !,"Error. Not an RDF file. Cannot process."
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. zwr ^TMP("MXMLDOM",$J,*)
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;
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; -- now process the rdf description children
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;
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@ -267,7 +271,7 @@ PROCESS(ZRTN,ZRDF,ZGRF,ZMETA,FARY) ; PROCESS AN INCOMING RDF FILE
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. ; -- we are skipping any child that is not rdf:Description
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. ; -- TODO: check to see if this is right in general
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. ;
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. IF $G(@ZDOM@(1,"C",ZI))'="rdf:Description" D Q ;
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. IF '$G(C0XTYPE(@ZDOM@(1,"C",ZI))) D Q ;
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. . W !,"SKIPPING NODE: ",ZI
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. ; -- now looking for the subject for the triples
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. S ZX=$G(@ZDOM@(ZI,"A","rdf:about"))
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@ -0,0 +1,131 @@
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C0XTESTKSB ; GPL - Fileman Triples bulk load tester ;11/6/11 17:05
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; KSB - modified to fix a minor bug and to use
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; high resolution time if routines available ; 11/19/11 1410 EST
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;;0.1;C0X;nopatch;noreleasedate;Build 1
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;Copyright 2011 George Lilly. 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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Q
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;
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EN ; run the test
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;
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k C0XFDA ; clear the node variable
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s U="^" ; initialization - Bhaskar 20111119
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i '$d(^C0X(101,0)) d ; global doesn't exist
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. s ^C0X(101,0)="C0X TRIPLE^172.101^1^1"
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n zg
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S zg="_:G"_$$LKY9 ; all nodes are in the same graph
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n zi
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f zi=1:1:10000 d ; try a test of 10000 nodes
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. s C0XFDA(172.101,zi,.01)="N"_$$LKY17 ; node name
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. s C0XFDA(172.101,zi,.02)=zg
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. s C0XFDA(172.101,zi,.03)=$R(100000)
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. s C0XFDA(172.101,zi,.04)=$R(100000)
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. s C0XFDA(172.101,zi,.05)=$R(100000)
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S C0XST=$$H ; start of the insertion test
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W !,"INSERTION STARTS AT ",$ZDATE(C0XST,"YEAR-MM-DD:24:60:SS"),!
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d BULKLOAD(.C0XFDA)
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s C0XEND=$$H ; end of the insertion test
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W !,"INSERTION ENDS AT ",$ZDATE(C0XEND,"YEAR-MM-DD:24:60:SS")
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S C0XDIFF=(86400*($P(C0XEND,",",1)-$P(C0XST,",",1)))+$P(C0XEND,",",2)-$P(C0XST,",",2)
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W !," ELAPSED TIME: ",C0XDIFF," SECONDS"
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W !
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W:C0XDIFF>0 " APPROXIMATELY ",$FN(10000/C0XDIFF,",",0)," NODES PER SECOND",!
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q
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;
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LKY9() ;EXTRINIC THAT RETURNS A RANDOM 9 DIGIT NUMBER. USED FOR GENERATING
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; UNIQUE NODE AND GRAPH NAMES
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N ZN,ZI
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S ZN=""
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F ZI=1:1:9 D ;
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. S ZN=ZN_$R(10)
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Q ZN
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;
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LKY17() ;EXTRINIC THAT RETURNS A RANDOM 9 DIGIT NUMBER. USED FOR GENERATING
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; UNIQUE NODE AND GRAPH NAMES
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N ZN,ZI
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S ZN=""
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F ZI=1:1:17 D ;
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. S ZN=ZN_$R(10)
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Q ZN
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;
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BULKLOAD(ZBFDA) ; BULK LOADER FOR LOADING TRIPLES INTO FILE 172.101
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; USING GLOBAL SETS INSTEAD OF UPDATE^DIE
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; QUITS IF FILE IS NOT 172.101
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; EXPECTS AN FDA WITHOUT STRINGS FOR THE IENS, STARTING AT 1
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; QUITS IF FIRST ENTRY IS NOT IENS 1
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; ASSUMES THAT THE LAST IENS IS THE COUNT OF ENTRIES
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; ZBFDA IS PASSED BY REFERENCE
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;
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; -- reserves a block of iens from file 172.101 by locking the zero node
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; -- ^C0X(101,0) and adding the count of entries to piece 2 and 3
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; -- then unlocking to minimize the duration of the lock
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;
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W !,"USING BULKLOAD"
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I '$D(ZBFDA) Q ; EMPTY FDA
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I $O(ZBFDA(""))'=172.101 Q ; WRONG FILE
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N ZCNT,ZP3,ZP4
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; -- find the number of nodes to insert
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S ZCNT=$O(ZBFDA(172.101,""),-1)
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I ZCNT="" D Q ;
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. W !,"ERROR IN BULK LOAD - INVALID NODE COUNT"
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. B
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; -- lock the zero node and reserve a block of iens to insert
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W !,"LOCKING ZERO NODE"
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LOCK +^C0X(101,0)
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S ZP3=$P(^C0X(101,0),U,3)
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S ZP4=$P(^C0X(101,0),U,4)
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S $P(^C0X(101,0),U,3)=ZP3+ZCNT+1
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S $P(^C0X(101,0),U,4)=ZP4+ZCNT+1
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LOCK -^C0X(101,0)
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N ZI,ZN,ZG,ZS,ZP,ZO,ZIEN,ZBASE
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S ZBASE=ZP3 ; the last ien in the file
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W !,"ZERO NODE UNLOCKED, IENS RESERVED=",ZCNT
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W !,$ZDATE($$H,"YEAR-MM-DD:24:60:SS")
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S ZI=""
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F S ZI=$O(ZBFDA(172.101,ZI)) Q:ZI="" D ;
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. S ZN=$G(ZBFDA(172.101,ZI,.01)) ; node name
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. I ZN="" D BLKERR Q ;
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. S ZG=$G(ZBFDA(172.101,ZI,.02)) ; graph pointer
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. I ZG="" D BLKERR Q ;
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. S ZS=$G(ZBFDA(172.101,ZI,.03)) ; subject pointer
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. I ZS="" D BLKERR Q ;
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. S ZP=$G(ZBFDA(172.101,ZI,.04)) ; predicate pointer
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. I ZP="" D BLKERR Q ;
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. S ZO=$G(ZBFDA(172.101,ZI,.05)) ; object pointer
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. I ZO="" D BLKERR Q ;
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. S ZIEN=ZI+ZBASE ; the new ien
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. S ^C0X(101,ZIEN,0)=ZN_U_ZG_U_ZS_U_ZP_U_ZO ; set the zero node
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. S ^C0X(101,"B",ZN,ZIEN)="" ; the B index
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. S ^C0X(101,"G",ZG,ZIEN)="" ; the G for Graph index
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. S ^C0X(101,"SPO",ZS,ZP,ZO)=""
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. S ^C0X(101,"SOP",ZS,ZO,ZP)=""
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. S ^C0X(101,"OPS",ZO,ZP,ZS)=""
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. S ^C0X(101,"OSP",ZO,ZS,ZP)=""
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. S ^C0X(101,"GOPS",ZG,ZO,ZP,ZS)=""
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. S ^C0X(101,"GOSP",ZG,ZO,ZS,ZP)=""
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. S ^C0X(101,"GPSO",ZG,ZP,ZS,ZO)=""
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. S ^C0X(101,"GSPO",ZG,ZS,ZP,ZO)=""
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Q
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;
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BLKERR ;
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W !,"ERROR IN BULK LOAD",! ZWR ZBFDA(ZI)
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B
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Q
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;
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H()
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quit:$length($ztrnlnm("GTMXC_posix"))&$length($text(zhorolog^%POSIX)) $$zhorolog^%POSIX quit $horolog
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@ -0,0 +1,55 @@
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C0XUTIL ; GPL - Fileman Triples utilities ;11/07/11 17:05
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;;0.1;C0X;nopatch;noreleasedate;Build 5
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;Copyright 2011 George Lilly. 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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Q
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;
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NSP(ZX) ; OUTPUT TRANSFORM EXTRINSIC
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;
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N ZR
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; I WOULD REALLY LIKE TO NOT HAVE THE FILE NUMBER HARD CODED HERE
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; ANYONE KNOW HOW I COULD DO THAT? :) GPL
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S ZR=$$GET1^DIQ(172.201,ZX_",",.01)
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I '$D(C0XNSP) S C0XNSP=1 ; DEFAULT ON
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I C0XNSP=0 Q ZR ; SWITCHED OFF
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I '$D(C0XVOC) D VOCINIT ; INITIALIZE THE VOCABULARIES
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N ZI,ZJ,ZK S ZI=""
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N DONE S DONE=0
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F S ZI=$O(C0XVOC(ZI)) Q:(DONE=1)!(ZI="") D ;
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. ;W !,ZI
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. S ZJ=C0XVOC(ZI)
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. S ZK=$P(ZR,ZJ,2)
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. ;W !,"ZK=",ZK
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. I ZK'="" D ; BINGO
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. . S ZR=ZI_":"_ZK
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. . S DONE=1
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Q ZR
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;
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VOCINIT ; INITIALIZE VOCABULARIES
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S C0XVOC("dcterms")="http://purl.org/dc/terms/"
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S C0XVOC("rdf")="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
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S C0XVOC("sp")="http://smartplatforms.org/terms#"
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S C0XVOC("qds")="http://cms.gov/pqri/qds/"
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S C0XVOC("smart")="http://sandbox-api.smartplatforms.org/records/"
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S C0XVOC("snomed")="http://www.ihtsdo.org/snomed-ct/concepts/"
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S C0XVOC("rxnorm")="http://rxnav.nlm.nih.gov/REST/rxcui/"
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S C0XVOC("loinc")="http://loinc.org/codes/"
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S C0XVOC("file")="/home/glilly/fmts/trunk/samples/"
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S C0XVOC("foaf")="http://xmlns.com/foaf/0.1/"
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Q
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;
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