added fileman output transform using namespaces

p/C0XF2N.m

@@ -37,7 +37,7 @@ INITFARY(ZFARY) ; INITIALIZE FILE NUMBERS AND OTHER USEFUL THINGS
  S @ZFARY@("C0XSFN")=172.201 ; TRIPLES STRINGS FILE NUMBER
  S @ZFARY@("C0XTN")=$NA(^C0X(101)) ; TRIPLES GLOBAL NAME
  S @ZFARY@("C0XSN")=$NA(^C0X(201)) ; STRING FILE GLOBAL NAME
- S @ZFARY@("C0XDIR")="/home/glilly/fmts/trunk/samples/"
+ S @ZFARY@("C0XDIR")="/home/glilly/snomed/"
  S @ZFARY@("BLKLOAD")=1 ; this file supports block load
  S @ZFARY@("FMTSSTYLE")="F2N" ; fileman style
  D USEFARY(ZFARY)
@@ -103,7 +103,7 @@ IMPORT(FNAME,INDIR,INURL,FARY) ; EXTRINSIC THAT READS A FILE FROM THE STANDARD
  D INSRDF(ZRDF,INURL,FARY) ; IMPORT AND PROCESS THE RDF
  K INURL
  K C0XFDA
- K ^TMP("MXMLDOM",$J)
+ ;K ^TMP("MXMLDOM",$J)
  Q
  ;
 WGET(ZURL,FARY) ; GET FROM THE INTERNET AN RDF FILE AND INSERT IT
@@ -220,6 +220,7 @@ PROCESS(ZRTN,ZRDF,ZGRF,ZMETA,FARY) ; PROCESS AN INCOMING RDF FILE
  ;S C0XDOCID=$$PARSE^C0CNHIN(ZRDF,"C0XARRAY") ; PARSE WITH MXML
  S C0XDLC2=$$NOW^XLFDT ; START OF PARSE
  S C0XDOCID=$$EN^MXMLDOM(ZRDF,"W")
+ ;B
  K @ZRDF ; DON'T NEED INPUT BUFFER ANYMORE
  ; -- assign the MXLM dom global name to ZDOM
  S ZDOM=$NA(^TMP("MXMLDOM",$J,C0XDOCID))
@@ -251,13 +252,16 @@ PROCESS(ZRTN,ZRDF,ZGRF,ZMETA,FARY) ; PROCESS AN INCOMING RDF FILE
  F  S ZI=$O(@ZDOM@(1,"A",ZI)) Q:ZI=""  D  ; FOR EACH xmlns
  . S ZVOC=$P(ZI,"xmlns:",2)
  . I ZVOC'="" S C0XVOC(ZVOC)=$G(@ZDOM@(1,"A",ZI))
- ;W !,"VOCABS:" ZWR C0XVOC
+ W !,"VOCABS:" ZWR C0XVOC
  ;
  ; -- look for children called rdf:Description. quit if none. not an rdf file
  ;
+ S C0XTYPE("rdf:Description")=1
+ S C0XTYPE("owl:ObjectProperty")=1
  S ZI=$O(@ZDOM@(1,"C",""))
- I $G(@ZDOM@(1,"C",ZI))'="rdf:Description" D  Q  ; not an rdf file
+ I '$G(C0XTYPE(@ZDOM@(1,"C",ZI))) D  Q  ; not an rdf file
  . W !,"Error. Not an RDF file. Cannot process."
+ . zwr ^TMP("MXMLDOM",$J,*)
  ;
  ; -- now process the rdf description children
  ;
@@ -267,7 +271,7 @@ PROCESS(ZRTN,ZRDF,ZGRF,ZMETA,FARY) ; PROCESS AN INCOMING RDF FILE
  . ; -- we are skipping any child that is not rdf:Description
  . ; -- TODO: check to see if this is right in general
  . ;
- . IF $G(@ZDOM@(1,"C",ZI))'="rdf:Description" D  Q  ;
+ . IF '$G(C0XTYPE(@ZDOM@(1,"C",ZI))) D  Q  ;
  . . W !,"SKIPPING NODE: ",ZI
  . ; -- now looking for the subject for the triples
  . S ZX=$G(@ZDOM@(ZI,"A","rdf:about"))

p/C0XTKSB.m

@@ -0,0 +1,131 @@
+C0XTESTKSB ; GPL - Fileman Triples bulk load tester ;11/6/11  17:05
+ ; KSB - modified to fix a minor bug and to use
+ ;       high resolution time if routines available ; 11/19/11 1410 EST
+ ;;0.1;C0X;nopatch;noreleasedate;Build 1
+ ;Copyright 2011 George Lilly.  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.
+ ;
+ Q
+ ;
+EN ; run the test
+ ;
+ k C0XFDA ; clear the node variable
+ s U="^"  ; initialization - Bhaskar 20111119
+ i '$d(^C0X(101,0)) d  ; global doesn't exist
+ . s ^C0X(101,0)="C0X TRIPLE^172.101^1^1"
+ n zg
+ S zg="_:G"_$$LKY9 ; all nodes are in the same graph
+ n zi
+ f zi=1:1:10000 d  ; try a test of 10000 nodes
+ . s C0XFDA(172.101,zi,.01)="N"_$$LKY17 ; node name
+ . s C0XFDA(172.101,zi,.02)=zg
+ . s C0XFDA(172.101,zi,.03)=$R(100000)
+ . s C0XFDA(172.101,zi,.04)=$R(100000)
+ . s C0XFDA(172.101,zi,.05)=$R(100000)
+ S C0XST=$$H    ; start of the insertion test
+ W !,"INSERTION STARTS AT ",$ZDATE(C0XST,"YEAR-MM-DD:24:60:SS"),!
+ d BULKLOAD(.C0XFDA)
+ s C0XEND=$$H    ; end of the insertion test
+ W !,"INSERTION ENDS AT ",$ZDATE(C0XEND,"YEAR-MM-DD:24:60:SS")
+ S C0XDIFF=(86400*($P(C0XEND,",",1)-$P(C0XST,",",1)))+$P(C0XEND,",",2)-$P(C0XST,",",2)
+ W !," ELAPSED TIME: ",C0XDIFF," SECONDS"
+ W !
+ W:C0XDIFF>0 " APPROXIMATELY ",$FN(10000/C0XDIFF,",",0)," NODES PER SECOND",!
+ q
+ ;
+LKY9() ;EXTRINIC THAT RETURNS A RANDOM 9 DIGIT NUMBER. USED FOR GENERATING
+ ; UNIQUE NODE AND GRAPH NAMES
+ N ZN,ZI
+ S ZN=""
+ F ZI=1:1:9 D  ;
+ . S ZN=ZN_$R(10)
+ Q ZN
+ ;
+LKY17() ;EXTRINIC THAT RETURNS A RANDOM 9 DIGIT NUMBER. USED FOR GENERATING
+ ; UNIQUE NODE AND GRAPH NAMES
+ N ZN,ZI
+ S ZN=""
+ F ZI=1:1:17 D  ;
+ . S ZN=ZN_$R(10)
+ Q ZN
+ ;
+BULKLOAD(ZBFDA) ; BULK LOADER FOR LOADING TRIPLES INTO FILE 172.101
+ ; USING GLOBAL SETS INSTEAD OF UPDATE^DIE
+ ; QUITS IF FILE IS NOT 172.101
+ ; EXPECTS AN FDA WITHOUT STRINGS FOR THE IENS, STARTING AT 1
+ ; QUITS IF FIRST ENTRY IS NOT IENS 1
+ ; ASSUMES THAT THE LAST IENS IS THE COUNT OF ENTRIES
+ ; ZBFDA IS PASSED BY REFERENCE
+ ;
+ ; -- reserves a block of iens from file 172.101 by locking the zero node
+ ; -- ^C0X(101,0) and adding the count of entries to piece 2 and 3
+ ; -- then unlocking to minimize the duration of the lock
+ ;
+ W !,"USING BULKLOAD"
+ I '$D(ZBFDA) Q  ; EMPTY FDA
+ I $O(ZBFDA(""))'=172.101 Q  ; WRONG FILE
+ N ZCNT,ZP3,ZP4
+ ; -- find the number of nodes to insert
+ S ZCNT=$O(ZBFDA(172.101,""),-1)
+ I ZCNT="" D  Q  ;
+ . W !,"ERROR IN BULK LOAD - INVALID NODE COUNT"
+ . B
+ ; -- lock the zero node and reserve a block of iens to insert
+ W !,"LOCKING ZERO NODE"
+ LOCK +^C0X(101,0)
+ S ZP3=$P(^C0X(101,0),U,3)
+ S ZP4=$P(^C0X(101,0),U,4)
+ S $P(^C0X(101,0),U,3)=ZP3+ZCNT+1
+ S $P(^C0X(101,0),U,4)=ZP4+ZCNT+1
+ LOCK -^C0X(101,0)
+ N ZI,ZN,ZG,ZS,ZP,ZO,ZIEN,ZBASE
+ S ZBASE=ZP3 ; the last ien in the file
+ W !,"ZERO NODE UNLOCKED, IENS RESERVED=",ZCNT
+ W !,$ZDATE($$H,"YEAR-MM-DD:24:60:SS")
+ S ZI=""
+ F  S ZI=$O(ZBFDA(172.101,ZI)) Q:ZI=""  D  ;
+ . S ZN=$G(ZBFDA(172.101,ZI,.01)) ; node name
+ . I ZN="" D BLKERR Q  ; 
+ . S ZG=$G(ZBFDA(172.101,ZI,.02)) ; graph pointer
+ . I ZG="" D BLKERR Q  ; 
+ . S ZS=$G(ZBFDA(172.101,ZI,.03)) ; subject pointer
+ . I ZS="" D BLKERR Q  ; 
+ . S ZP=$G(ZBFDA(172.101,ZI,.04)) ; predicate pointer
+ . I ZP="" D BLKERR Q  ; 
+ . S ZO=$G(ZBFDA(172.101,ZI,.05)) ; object pointer
+ . I ZO="" D BLKERR Q  ; 
+ . S ZIEN=ZI+ZBASE ; the new ien
+ . S ^C0X(101,ZIEN,0)=ZN_U_ZG_U_ZS_U_ZP_U_ZO ; set the zero node
+ . S ^C0X(101,"B",ZN,ZIEN)="" ; the B index
+ . S ^C0X(101,"G",ZG,ZIEN)="" ; the G for Graph index
+ . S ^C0X(101,"SPO",ZS,ZP,ZO)=""
+ . S ^C0X(101,"SOP",ZS,ZO,ZP)=""
+ . S ^C0X(101,"OPS",ZO,ZP,ZS)=""
+ . S ^C0X(101,"OSP",ZO,ZS,ZP)=""
+ . S ^C0X(101,"GOPS",ZG,ZO,ZP,ZS)=""
+ . S ^C0X(101,"GOSP",ZG,ZO,ZS,ZP)=""
+ . S ^C0X(101,"GPSO",ZG,ZP,ZS,ZO)=""
+ . S ^C0X(101,"GSPO",ZG,ZS,ZP,ZO)=""
+ Q
+ ;
+BLKERR ; 
+ W !,"ERROR IN BULK LOAD",! ZWR ZBFDA(ZI)
+ B
+ Q
+ ;
+H()
+ quit:$length($ztrnlnm("GTMXC_posix"))&$length($text(zhorolog^%POSIX)) $$zhorolog^%POSIX quit $horolog

p/C0XUTIL.m

@@ -0,0 +1,55 @@
+C0XUTIL ; GPL - Fileman Triples utilities ;11/07/11  17:05
+ ;;0.1;C0X;nopatch;noreleasedate;Build 5
+ ;Copyright 2011 George Lilly.  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.
+ ;
+ Q
+ ;
+NSP(ZX) ; OUTPUT TRANSFORM EXTRINSIC
+ ;
+ N ZR
+ ; I WOULD REALLY LIKE TO NOT HAVE THE FILE NUMBER HARD CODED HERE
+ ; ANYONE KNOW HOW I COULD DO THAT?  :) GPL
+ S ZR=$$GET1^DIQ(172.201,ZX_",",.01)
+ I '$D(C0XNSP) S C0XNSP=1 ; DEFAULT ON
+ I C0XNSP=0 Q ZR ; SWITCHED OFF
+ I '$D(C0XVOC) D VOCINIT ; INITIALIZE THE VOCABULARIES
+ N ZI,ZJ,ZK S ZI=""
+ N DONE S DONE=0
+ F  S ZI=$O(C0XVOC(ZI)) Q:(DONE=1)!(ZI="")  D  ;
+ . ;W !,ZI
+ . S ZJ=C0XVOC(ZI)
+ . S ZK=$P(ZR,ZJ,2)
+ . ;W !,"ZK=",ZK
+ . I ZK'="" D  ; BINGO
+ . . S ZR=ZI_":"_ZK
+ . . S DONE=1
+ Q ZR
+ ;
+VOCINIT ; INITIALIZE VOCABULARIES
+ S C0XVOC("dcterms")="http://purl.org/dc/terms/"
+ S C0XVOC("rdf")="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ S C0XVOC("sp")="http://smartplatforms.org/terms#"
+ S C0XVOC("qds")="http://cms.gov/pqri/qds/"
+ S C0XVOC("smart")="http://sandbox-api.smartplatforms.org/records/"
+ S C0XVOC("snomed")="http://www.ihtsdo.org/snomed-ct/concepts/"
+ S C0XVOC("rxnorm")="http://rxnav.nlm.nih.gov/REST/rxcui/"
+ S C0XVOC("loinc")="http://loinc.org/codes/"
+ S C0XVOC("file")="/home/glilly/fmts/trunk/samples/"
+ S C0XVOC("foaf")="http://xmlns.com/foaf/0.1/"
+ Q
+ ;