VistA-fmts/p/C0XMAIN.m

378 lines
12 KiB
Mathematica

C0XMAIN ; GPL - Fileman Triples entry point routine ;10/13/11 17:05
;;0.1;C0X;nopatch;noreleasedate;Build 7
;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
;
INITFARY(ZFARY) ; INITIALIZE FILE NUMBERS AND OTHER USEFUL THINGS
; FOR THE DEFAULT TRIPLE STORE. USE OTHER VALUES FOR SUPPORTING ADDITIONAL
; TRIPLE STORES
S @ZFARY@("C0XTFN")=172.101 ; TRIPLES FILE NUMBER
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/all_smart_patient_data/smart-rdf/"
S @ZFARY@("C0XDIR")="/home/george/fmts/trunk/samples/"
D USEFARY(ZFARY)
Q
;
USEFARY(ZFARY) ; INITIALIZES VARIABLES SAVED IN ARRAY ZFARY
N ZI S ZI=""
F S ZI=$O(@ZFARY@(ZI)) Q:ZI="" D
. ;N ZX
. S ZX="S "_ZI_"="""_@ZFARY@(ZI)_""""
. ;W !,ZX
. X ZX
Q
;
IMPORT(FNAME,FDIR,FURL,FARY) ; EXTRINSIC THAT READS A FILE FROM THE STANDARD
; DIRECTORY, LOADS IT INTO THE TRIPLESTORE AS TEXT, AND RETURNS THE
; NODE NAME OF THE TEXT TRIPLE
; FDIR IS THE OPTIONAL DIRECTORY (DEFAUTS TO STANDARD DIR)
; FURL IS THE OPTIONAL URI FOR ACCESSING THE FILE FROM THE TRIPLE STORE
; FARY IS THE OPTIONAL FILE ARRAY OF THE TRIPLE STORE TO USE
I '$D(FARY) D ;
. D INITFARY("C0XFARY")
. S FARY="C0XFARY"
D USEFARY(FARY)
N ZD,ZTMP
I '$D(FDIR) S FDIR=C0XDIR ; DIRECTORY OF THE RDF FILE
I '$D(FURL) D ;
. N ZN2 S ZN2=$TR(FNAME,".","_") ; REMOVE THE DOT FROM THE NAME
. S FURL=FDIR_ZN2
N ZTMP
S ZTMP=$NA(^TMP("C0X",$J,"FILEIN",1)) ; WHERE TO PUT THE INCOMING FILE
K @ZTMP ; MAKE SURE IT'S CLEAR
S C0XSTART=$$NOW^XLFDT
W !,"STARTED: ",C0XSTART
W !,"READING IN: ",FNAME
I '$$FILEIN(ZTMP,FDIR,FNAME,4) D Q ; QUIT IF NO SUCCESS
. W !,"ERROR READING FILE: ",FDIR,FNAME
S ZRDF=$NA(^TMP("C0X",$J,"FILEIN")) ; WITHOUT THE SUBSCRIPT
W !,$O(@ZRDF@(""),-1)," LINES READ"
D INSRDF(ZRDF,FURL,FARY) ; IMPORT AND PROCESS THE RDF
Q
;
WGET(ZURL,FARY) ; GET FROM THE INTERNET AN RDF FILE AND INSERT IT
;
I '$D(FARY) D ;
. D INITFARY("C0XFARY")
. S FARY="C0XFARY"
D USEFARY(FARY)
;N ZLOC,ZTMP
K ZTMP
S ZLOC=$NA(^TMP("C0X","WGET",$J))
S C0XSTART=$$NOW^XLFDT
W !,"STARTED: ",C0XSTART
W !,"DOWNLOADING: ",ZURL
S OK=$$httpGET^%zewdGTM(ZURL,.ZTMP)
M @ZLOC=ZTMP
W !,$O(@ZLOC@(""),-1)," LINES READ"
D INSRDF(ZLOC,ZURL,FARY)
Q
;
INSRDF(ZRDF,ZNAME,FARY) ; INSERT AN RDF FILE INTO THE STORE AND PROCESS
; ZRDF IS PASSED BY NAME
I '$D(FARY) D ;
. D INITFARY("C0XFARY")
. S FARY="C0XFARY"
D USEFARY(FARY)
N ZGRAPH,ZSUBJECT
S ZGRAPH="_:G"_$$LKY9 ; RANDOM GRAPH NAME
S ZSUBJECT=$$ANONS ; RANDOM ANOYMOUS SUBJECT
D ADD(ZGRAPH,ZSUBJECT,"fmts:url",ZNAME,FARY)
N ZTXTNM
S ZTXTNM="_TXT_INCOMING_RDF_FILE_"_ZNAME_"_"_$$LKY9 ; NAME FOR TEXT NODE
D ADD(ZGRAPH,ZSUBJECT,"fmts:rdfSource",ZTXTNM,FARY)
D UPDIE(.C0XFDA) ; TRY IT OUT
K C0XCNT ;RESET FOR NEXT TIME
D STORETXT(ZRDF,ZTXTNM,FARY)
W !,"ADDED: ",ZGRAPH," ",ZSUBJECT," fmts:rdfSource ",ZTXTNM
D PROCESS(.G,ZRDF,ZNAME,ZGRAPH,FARY) ; PARSE AND INSERT THE RDF
Q
;
STORETXT(ZTXT,ZNAME,FARY) ; STORE TEXT IN THE TRIPLESTORE AT ZNAME
;
I '$D(FARY) D ;
. D INITFARY("C0XFARY")
. S FARY="C0XFARY"
D USEFARY(FARY)
N ZIEN
S ZIEN=$$IENOF(ZNAME,FARY) ; GET THE IEN
D CLEAN^DILF
K ZERR
D WP^DIE(C0XSFN,ZIEN_",",1,,ZTXT,"ZERR")
I $D(ZERR) D ;
. ZWR ZERR
Q
;
GETTXT(ZRTN,ZNAME,FARY) ; RETURNS RDF SOURCE OR OTHER TEXT
; ZRTN IS PASSED BY REFERENCE
I '$D(FARY) D ;
. D INITFARY("C0XFARY")
. S FARY="C0XFARY"
D USEFARY(FARY)
N ZIEN
S ZIEN=$$IENOF(ZNAME)
S OK=$$GET1^DIQ(C0XSFN,ZIEN_",",1,,"ZRTN")
Q
;
WHERETXT(ZNAME,FARY) ; EXTRINSIC WHICH RETURNS THE NAME OF THE GLOBAL
; WHERE THE TEXT IS LOCATED. NAME IS THE NAME OF THE STRING
I '$D(FARY) D ;
. D INITFARY("C0XFARY")
. S FARY="C0XFARY"
D USEFARY(FARY)
N ZIEN
S ZIEN=$$IENOF(ZNAME)
Q $NA(@C0XSN@(ZIEN,1))
;
FILEIN(ZINTMP,ZDIR,ZFNAME,ZLVL) ; READS A FILE INTO ZINTMP USING FTG^%ZISH
; ZINTMP IS PASSED BY NAME AND INCLUDES THE NEW SUBSCRIPT
; IE ^TMP("C0X","FILEIN",1)
; ZLVL IN THIS CASE WOULD BE 3 INCREMENTING THE 1
; EXTRINSIC WHICH RETURNS THE RESULT OF FTG^%ZISH
S OK=$$FTG^%ZISH(ZDIR,FNAME,ZINTMP,ZLVL)
Q OK
;
TESTPROC ; TEST PROCESS WITH EXISTING SMALL RDF FILE
S ZIN=$NA(^TMP("C0X",12226,"FILEIN"))
S ZGRAPH="/test/rdfFile"
S ZM="/test/rdfFile/meta"
D PROCESS(.G,ZIN,ZGRAPH,ZM)
Q
;
PROCESS(ZRTN,ZRDF,ZGRF,ZMETA,FARY) ; PROCESS AN INCOMING RDF FILE
; ZRTN IS PASS BY REFERENCE AND RETURNS MESSAGES ABOUT THE PROCESSING
; ZRDF IS PASSED BY NAME AND IS THE GLOBAL CONTAINING THE RDF FILE
; ZGRF IS THE NAME OF THE GRAPH TO USE IN THE TRIPLE STORE FOR RESULTS
; ZMETA IS OPTIONAL AND IS THE NAME OF THE GRAPH TO STORE METADATA
;
I '$D(FARY) D ;
. D INITFARY("C0XFARY")
. S FARY="C0XFARY"
D USEFARY(FARY)
; -- first parse the rdf file with the MXML parser
;S C0XDOCID=$$PARSE^C0CNHIN(ZRDF,"C0XARRAY") ; PARSE WITH MXML
S C0XDOCID=$$EN^MXMLDOM(ZRDF,"W")
; -- assign the MXLM dom global name to ZDOM
S ZDOM=$NA(^TMP("MXMLDOM",$J,C0XDOCID))
W !,$O(@ZDOM@(""),-1)," XML NODES PARSED"
; -- populate the metagraph to point to the graph with status unfinished
S METAS=$$ANONS ; GET AN ANONOMOUS RANDOM SUBJECT
I '$D(ZMETA) S ZMETA="_:G"_$$LKY9 ; RANDOM GRAPH NAME FOR METAGRAPH
D ADD(ZMETA,METAS,"fmts:about",ZGRF,FARY) ; POINT THE META TO THE GRAPH
D ADD(ZMETA,METAS,"fmts:status","unfinished",FARY) ; mark as unfinished
;S C0XDATE=$$FMDTOUTC^C0CUTIL($$NOW^XLFDT,"DT")
S C0XDATE=$$NOW^XLFDT
D ADD(ZMETA,METAS,"fmts:dateTime",C0XDATE,FARY)
D UPDIE(.C0XFDA) ; commit the metagraph changes to the triple store
; --
; -- pull out the vocabularies in the RDF statement. marked with xmlns:
; -- put them in a local variable for quick reference
; -- TODO: create a graph for vocabularies and validate incoming against it
;
S C0XVOC=""
N ZI,ZJ,ZK S ZI=""
F S ZI=$O(@ZDOM@(1,"A",ZI)) Q:ZI="" D ; FOR EACH xmlns
. S ZVOC=$P(ZI,"xmlns:",2)
. I ZVOC'="" S C0XVOC(ZVOC)=$G(@ZDOM@(1,"A",ZI))
;W !,"VOCABS:" ZWR C0XVOC
;
; -- look for children called rdf:Description. quit if none. not an rdf file
;
S ZI=$O(@ZDOM@(1,"C",""))
I $G(@ZDOM@(1,"C",ZI))'="rdf:Description" D Q ; not an rdf file
. W !,"Error. Not an RDF file. Cannot process."
;
; -- now process the rdf description children
;
S ZI=""
S (C0XSUB,C0XPRE,C0XOBJ)="" ; INITIALIZE subject, object and predicate
F S ZI=$O(@ZDOM@(1,"C",ZI)) Q:ZI="" D ;
. ; -- we are skipping any child that is not rdf:Description
. ; -- TODO: check to see if this is right in general
. ;
. IF $G(@ZDOM@(1,"C",ZI))'="rdf:Description" D Q ;
. . W !,"SKIPPING NODE: ",ZI
. ; -- now looking for the subject for the triples
. S ZX=$G(@ZDOM@(ZI,"A","rdf:about"))
. I ZX'="" D ; we have the subject
. . ;W " about: ",ZX
. . S C0XSUB=ZX
. E D ;
. . S ZX=$G(@ZDOM@(ZI,"A","rdf:nodeID")) ; node id is another style of subject
. . I ZX'="" D ;
. . . S C0XSUB=ZX
. I C0XSUB="" S C0XSUB=$$ANONS ; DEFAULT TO BLANK SUBJECT
. ;
. ; -- we now have the subject. the children of this node have the rest
. ;
. S ZJ="" ; for the children of the rdf:Description nodes
. F S ZJ=$O(@ZDOM@(ZI,"C",ZJ)) Q:ZJ="" D ; for each child
. . S C0XPRE=@ZDOM@(ZJ) ; the predicate without a prefix
. . S ZX=$G(@ZDOM@(ZJ,"A","xmlns")) ; name space
. . I ZX'="" S C0XPRE=ZX_C0XPRE ; add the namespace prefix
. . I C0XPRE[":" D ; expand using vocabulary
. . . N ZB,ZA
. . . S ZB=$P(C0XPRE,":",1)
. . . S ZA=$P(C0XPRE,":",2)
. . . I $G(C0XVOC(ZB))'="" D ;
. . . . S C0XPRE=C0XVOC(ZB)_ZA ; expanded
. . S ZY=$G(@ZDOM@(ZJ,"A","rdf:resource")) ; potential object
. . I ZY'="" D Q ;
. . . S C0XOBJ=ZY ; object
. . . D ADD(ZGRF,C0XSUB,C0XPRE,C0XOBJ) ; finally. our first real triple
. . ; -- this is an else because of the quit above
. . S ZX=$G(@ZDOM@(ZJ,"A","rdf:nodeID")) ; fishing for nodeId object
. . I ZX'="" D Q ; got one
. . . S C0XOBJ=ZX ; we are using the incoming nodeIDs as object/subject
. . . ; without change... this could be foolish .. look at it again later
. . . D ADD(ZGRF,C0XSUB,C0XPRE,C0XOBJ) ; go for it and add a node
. . S C0XOBJ=$G(@ZDOM@(ZJ,"T",1)) ; hopefully an object is here
. . I C0XOBJ="" D Q ; not a happy situation
. . . W !,"ERROR, NO OBJECT FOUND FOR NODE: ",ZJ
. . D ADD(ZGRF,C0XSUB,C0XPRE,C0XOBJ) ; go for it and add a node
W !,"INSERTING ",C0XCNT," TRIPLES"
D UPDIE(.C0XFDA) ; commit the updates to the file
; next, mark the graph as finished
S C0XEND=$$NOW^XLFDT
W !," ENDED AT: ",C0XEND
S C0XDIFF=$$FMDIFF^XLFDT(C0XEND,C0XSTART,2)
W !," ELAPSED TIME: ",C0XDIFF," SECONDS"
W !," APPROXIMATELY ",$P(C0XCNT/C0XDIFF,".")," TRIPLES PER SECOND"
Q
;
SHOW(ZN) ;
ZWR ^TMP("MXMLDOM",$J,1,ZN,*)
Q
;
ANONS() ; RETURNS AN ANONOMOUS SUBJECT
Q "_S:"_$$LKY9
;
NEWG(NGRAPH,NMETA) ; CREATES A NEW META GRAPH, MARKS IT AS UNFINISHED
; THEN CREATES A NEW GRAPH AND POINTS THE METAGRAPH TO IT
; NGRAPH AND NMETA ARE PASSED BY REFERENCE AND ARE THE RETURN
S NGRAPH="G"_$$LKY9
S NMETA=NGRAPH_"A"
Q
;
ADD(ZG,ZS,ZP,ZO,FARY) ; ADD A TRIPLE TO THE TRIPLESTORE. ALL VALUES ARE TEXT
; THE FDA IS SET UP BUT THE FILES ARE NOT UPDATED. CALL UPDIE TO COMPLETE
I '$D(FARY) D ;
. D INITFARY("C0XFARY")
. S FARY="C0XFARY"
D USEFARY(FARY)
I '$D(C0XCNT) S C0XCNT=0
N ZNODE
S ZNODE="N"_$$LKY17
N ZNARY ; GET READY TO CALL IENOFA
S ZNARY("ZG",ZG)=""
S ZNARY("ZS",ZS)=""
S ZNARY("ZP",ZP)=""
S ZNARY("ZO",ZO)=""
D IENOFA(.ZIENS,.ZNARY,FARY) ; RESOLVE/ADD STRINGS
;S ZGIEN=$$IENOF(ZG) ; LAYGO TO GET IEN
;S ZSIEN=$$IENOF(ZS)
;S ZPIEN=$$IENOF(ZP)
;S ZOIEN=$$IENOF(ZO)
;I $D(C0XFDA) D UPDIE ; ADD THE STRINGS IF NEEDED
S C0XCNT=C0XCNT+1
S C0XFDA(C0XTFN,"?+"_C0XCNT_",",.01)=ZNODE
S C0XFDA(C0XTFN,"?+"_C0XCNT_",",.02)=$O(ZIENS("IEN","ZG",""))
S C0XFDA(C0XTFN,"?+"_C0XCNT_",",.03)=$O(ZIENS("IEN","ZS",""))
S C0XFDA(C0XTFN,"?+"_C0XCNT_",",.04)=$O(ZIENS("IEN","ZP",""))
S C0XFDA(C0XTFN,"?+"_C0XCNT_",",.05)=$O(ZIENS("IEN","ZO",""))
; REMEMBER TO CALL UPDIE WHEN YOU'RE DONE
Q
;
LKY9() ;EXTRINIC THAT RETURNS A RANDOM 9 DIGIT NUMBER. USED FOR GENERATING
; UNIQUE NODE AND GRAPH NAMES
N ZN,ZI
S ZN=""
F ZI=1:1:9 D ;
. S ZN=ZN_$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_$R(10)
Q ZN
;
IENOF(ZSTRING,FARY) ; EXTRINSIC WHICH RETURNS THE IEN OF ZS IN THE STRINGS FILE
I '$D(FARY) D ;
. D INITFARY("C0XFARY")
. S FARY="C0XFARY"
N ZIEN
S ZIEN=$O(@C0XSN@("B",ZSTRING,""))
I ZIEN="" D ;
. S C0XFDA2(C0XSFN,"+1,",.01)=ZSTRING
. D UPDIE(.C0XFDA2)
. S ZIEN=$O(@C0XSN@("B",ZSTRING,""))
. K C0XFDA2
Q ZIEN
;
IENOFA(ZOUTARY,ZINARY,FARY) ; RESOLVE STRINGS TO IEN IN STRINGS FILE
; OR ADD THEM IF
; MISSING. ZINARY AND ZOUTARY ARE PASSED BY REFERENCE
; ZINARY LOOKS LIKE ZINARY("VAR","VAL")=""
; RETURNS IN ZOUTARY OF THE FORM ZOUTARY("IEN","VAR",IEN)=""
I '$D(FARY) D ;
. D INITFARY("C0XFARY")
. S FARY="C0XFARY"
K ZOUTARY ; START WITH CLEAN RESULTS
K C0XFDA2 ; USE A SEPARATE FDA FOR THIS
N ZI S ZI=""
N ZV,ZIEN
N ZCNT S ZCNT=0
F S ZI=$O(ZINARY(ZI)) Q:ZI="" D ; LOOK FOR MISSING STRINGS
. S ZV=$O(ZINARY(ZI,""))
. I $O(@C0XSN@("B",ZV,""))="" D ;
. . S ZCNT=ZCNT+1
. . S C0XFDA2(C0XSFN,"+"_ZCNT_",",.01)=ZV
I $D(C0XFDA2) D ;
. D UPDIE(.C0XFDA2) ; ADD MISSING STRINGS
. K C0XFDA2 ; CLEAN UP
F S ZI=$O(ZINARY(ZI)) Q:ZI="" D ; NOT GET ALL IENS
. S ZV=$O(ZINARY(ZI,""))
. S ZIEN=$O(@C0XSN@("B",ZV,"")) ; THEY SHOULD BE THERE NOW
. I ZIEN="" D ;
. . W !,"ERROR ADDING STRING: ",ZV
. . B
. S ZOUTARY("IEN",ZI,ZIEN)=""
Q
;
UPDIE(ZFDA) ; INTERNAL ROUTINE TO CALL UPDATE^DIE AND CHECK FOR ERRORS
; ZFDA IS PASSED BY REFERENCE
;ZWR ZFDA
;B
K ZERR
D CLEAN^DILF
D UPDATE^DIE("","ZFDA","","ZERR")
I $D(ZERR) S ZZERR=ZZERR ; ZZERR DOESN'T EXIST,
; INVOKE THE ERROR TRAP IF TASKED
;. W "ERROR",!
;. ZWR ZERR
;. B
K ZFDA
Q
;