Ignore:
Timestamp:
Sep 26, 2012, 12:58:34 PM (12 years ago)
Author:
Sam Habiel
Message:

Proper KIDS build + Routines

File:
1 edited

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Added
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  • fmts/trunk/p/C0XMAIN.m

    r1343 r1539  
    1 C0XMAIN ; GPL - Fileman Triples entry point routine ;10/13/11  17:05
    2  ;;0.1;C0X;nopatch;noreleasedate;Build 7
    3  ;Copyright 2011 George Lilly.  Licensed under the terms of the GNU
    4  ;General Public License See attached copy of the License.
    5  ;
    6  ;This program is free software; you can redistribute it and/or modify
    7  ;it under the terms of the GNU General Public License as published by
    8  ;the Free Software Foundation; either version 2 of the License, or
    9  ;(at your option) any later version.
    10  ;
    11  ;This program is distributed in the hope that it will be useful,
    12  ;but WITHOUT ANY WARRANTY; without even the implied warranty of
    13  ;MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    14  ;GNU General Public License for more details.
    15  ;
    16  ;You should have received a copy of the GNU General Public License along
    17  ;with this program; if not, write to the Free Software Foundation, Inc.,
    18  ;51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
    19  ;
    20  Q
    21  ;
    22 INITFARY(ZFARY) ; INITIALIZE FILE NUMBERS AND OTHER USEFUL THINGS
    23  ; FOR THE DEFAULT TRIPLE STORE. USE OTHER VALUES FOR SUPPORTING ADDITIONAL
    24  ; TRIPLE STORES
    25  S @ZFARY@("C0XTFN")=172.101 ; TRIPLES FILE NUMBER
    26  S @ZFARY@("C0XSFN")=172.201 ; TRIPLES STRINGS FILE NUMBER
    27  S @ZFARY@("C0XTN")=$NA(^C0X(101)) ; TRIPLES GLOBAL NAME
    28  S @ZFARY@("C0XSN")=$NA(^C0X(201)) ; STRING FILE GLOBAL NAME
    29  ;S @ZFARY@("C0XDIR")="/home/glilly/all_smart_patient_data/smart-rdf/"
    30  S @ZFARY@("C0XDIR")="/home/george/fmts/trunk/samples/"
    31  D USEFARY(ZFARY)
    32  Q
    33  ;
    34 USEFARY(ZFARY) ; INITIALIZES VARIABLES SAVED IN ARRAY ZFARY
    35  N ZI S ZI=""
    36  F  S ZI=$O(@ZFARY@(ZI)) Q:ZI=""  D 
    37  . ;N ZX
    38  . S ZX="S "_ZI_"="""_@ZFARY@(ZI)_""""
    39  . ;W !,ZX
    40  . X ZX
    41  Q
    42  ;
    43 IMPORT(FNAME,FDIR,FURL,FARY) ; EXTRINSIC THAT READS A FILE FROM THE STANDARD
    44  ; DIRECTORY, LOADS IT INTO THE TRIPLESTORE AS TEXT, AND RETURNS THE
    45  ; NODE NAME OF THE TEXT TRIPLE
    46  ; FDIR IS THE OPTIONAL DIRECTORY (DEFAUTS TO STANDARD DIR)
    47  ; FURL IS THE OPTIONAL URI FOR ACCESSING THE FILE FROM THE TRIPLE STORE
    48  ; FARY IS THE OPTIONAL FILE ARRAY OF THE TRIPLE STORE TO USE
    49  I '$D(FARY) D  ;
    50  . D INITFARY("C0XFARY")
    51  . S FARY="C0XFARY"
    52  D USEFARY(FARY)
    53  N ZD,ZTMP
    54  I '$D(FDIR) S FDIR=C0XDIR ; DIRECTORY OF THE RDF FILE
    55  I '$D(FURL) D  ;
    56  . N ZN2 S ZN2=$TR(FNAME,".","_") ; REMOVE THE DOT FROM THE NAME
    57  . S FURL=FDIR_ZN2
    58  N ZTMP
    59  S ZTMP=$NA(^TMP("C0X",$J,"FILEIN",1)) ; WHERE TO PUT THE INCOMING FILE
    60  K @ZTMP ; MAKE SURE IT'S CLEAR
    61  S C0XSTART=$$NOW^XLFDT
    62  W !,"STARTED: ",C0XSTART
    63  W !,"READING IN: ",FNAME
    64  I '$$FILEIN(ZTMP,FDIR,FNAME,4) D  Q  ; QUIT IF NO SUCCESS
    65  . W !,"ERROR READING FILE: ",FDIR,FNAME
    66  S ZRDF=$NA(^TMP("C0X",$J,"FILEIN")) ; WITHOUT THE SUBSCRIPT
    67  W !,$O(@ZRDF@(""),-1)," LINES READ"
    68  D INSRDF(ZRDF,FURL,FARY) ; IMPORT AND PROCESS THE RDF
    69  Q
    70  ;
    71 WGET(ZURL,FARY) ; GET FROM THE INTERNET AN RDF FILE AND INSERT IT
    72  ;
    73  I '$D(FARY) D  ;
    74  . D INITFARY("C0XFARY")
    75  . S FARY="C0XFARY"
    76  D USEFARY(FARY)
    77  ;N ZLOC,ZTMP
    78  K ZTMP
    79  S ZLOC=$NA(^TMP("C0X","WGET",$J))
    80  S C0XSTART=$$NOW^XLFDT
    81  W !,"STARTED: ",C0XSTART
    82  W !,"DOWNLOADING: ",ZURL
    83  S OK=$$httpGET^%zewdGTM(ZURL,.ZTMP)
    84  M @ZLOC=ZTMP
    85  W !,$O(@ZLOC@(""),-1)," LINES READ"
    86  D INSRDF(ZLOC,ZURL,FARY)
    87  Q
    88  ;
    89 INSRDF(ZRDF,ZNAME,FARY) ; INSERT AN RDF FILE INTO THE STORE AND PROCESS
    90  ; ZRDF IS PASSED BY NAME
    91  I '$D(FARY) D  ;
    92  . D INITFARY("C0XFARY")
    93  . S FARY="C0XFARY"
    94  D USEFARY(FARY)
    95  N ZGRAPH,ZSUBJECT
    96  S ZGRAPH="_:G"_$$LKY9 ; RANDOM GRAPH NAME
    97  S ZSUBJECT=$$ANONS ; RANDOM ANOYMOUS SUBJECT
    98  D ADD(ZGRAPH,ZSUBJECT,"fmts:url",ZNAME,FARY)
    99  N ZTXTNM
    100  S ZTXTNM="_TXT_INCOMING_RDF_FILE_"_ZNAME_"_"_$$LKY9 ; NAME FOR TEXT NODE
    101  D ADD(ZGRAPH,ZSUBJECT,"fmts:rdfSource",ZTXTNM,FARY)
    102  D UPDIE(.C0XFDA) ; TRY IT OUT
    103  K C0XCNT ;RESET FOR NEXT TIME
    104  D STORETXT(ZRDF,ZTXTNM,FARY)
    105  W !,"ADDED: ",ZGRAPH," ",ZSUBJECT," fmts:rdfSource ",ZTXTNM
    106  D PROCESS(.G,ZRDF,ZNAME,ZGRAPH,FARY) ; PARSE AND INSERT THE RDF
    107  Q
    108  ;
    109 STORETXT(ZTXT,ZNAME,FARY) ; STORE TEXT IN THE TRIPLESTORE AT ZNAME
    110  ;
    111  I '$D(FARY) D  ;
    112  . D INITFARY("C0XFARY")
    113  . S FARY="C0XFARY"
    114  D USEFARY(FARY)
    115  N ZIEN
    116  S ZIEN=$$IENOF(ZNAME,FARY) ; GET THE IEN
    117  D CLEAN^DILF
    118  K ZERR
    119  D WP^DIE(C0XSFN,ZIEN_",",1,,ZTXT,"ZERR")
    120  I $D(ZERR) D  ;
    121  . ZWR ZERR
    122  Q
    123  ;
    124 GETTXT(ZRTN,ZNAME,FARY) ; RETURNS RDF SOURCE OR OTHER TEXT
    125  ; ZRTN IS PASSED BY REFERENCE
    126  I '$D(FARY) D  ;
    127  . D INITFARY("C0XFARY")
    128  . S FARY="C0XFARY"
    129  D USEFARY(FARY)
    130  N ZIEN
    131  S ZIEN=$$IENOF(ZNAME)
    132  S OK=$$GET1^DIQ(C0XSFN,ZIEN_",",1,,"ZRTN")
    133  Q
    134  ;
    135 WHERETXT(ZNAME,FARY) ; EXTRINSIC WHICH RETURNS THE NAME OF THE GLOBAL
    136  ; WHERE THE TEXT IS LOCATED. NAME IS THE NAME OF THE STRING
    137  I '$D(FARY) D  ;
    138  . D INITFARY("C0XFARY")
    139  . S FARY="C0XFARY"
    140  D USEFARY(FARY)
    141  N ZIEN
    142  S ZIEN=$$IENOF(ZNAME)
    143  Q $NA(@C0XSN@(ZIEN,1))
    144  ;
    145 FILEIN(ZINTMP,ZDIR,ZFNAME,ZLVL) ; READS A FILE INTO ZINTMP USING FTG^%ZISH
    146  ; ZINTMP IS PASSED BY NAME AND INCLUDES THE NEW SUBSCRIPT
    147  ; IE ^TMP("C0X","FILEIN",1)
    148  ; ZLVL IN THIS CASE WOULD BE 3 INCREMENTING THE 1
    149  ; EXTRINSIC WHICH RETURNS THE RESULT OF FTG^%ZISH
    150  S OK=$$FTG^%ZISH(ZDIR,FNAME,ZINTMP,ZLVL)
    151  Q OK
    152  ;
    153 TESTPROC ; TEST PROCESS WITH EXISTING SMALL RDF FILE
    154  S ZIN=$NA(^TMP("C0X",12226,"FILEIN"))
    155  S ZGRAPH="/test/rdfFile"
    156  S ZM="/test/rdfFile/meta"
    157  D PROCESS(.G,ZIN,ZGRAPH,ZM)
    158  Q
    159  ;
    160 PROCESS(ZRTN,ZRDF,ZGRF,ZMETA,FARY) ; PROCESS AN INCOMING RDF FILE
    161  ; ZRTN IS PASS BY REFERENCE AND RETURNS MESSAGES ABOUT THE PROCESSING
    162  ; ZRDF IS PASSED BY NAME AND IS THE GLOBAL CONTAINING THE RDF FILE
    163  ; ZGRF IS THE NAME OF THE GRAPH TO USE IN THE TRIPLE STORE FOR RESULTS
    164  ; ZMETA IS OPTIONAL AND IS THE NAME OF THE GRAPH TO STORE METADATA
    165  ;
    166  I '$D(FARY) D  ;
    167  . D INITFARY("C0XFARY")
    168  . S FARY="C0XFARY"
    169  D USEFARY(FARY)
    170  ; -- first parse the rdf file with the MXML parser
    171  ;S C0XDOCID=$$PARSE^C0CNHIN(ZRDF,"C0XARRAY") ; PARSE WITH MXML
    172  S C0XDOCID=$$EN^MXMLDOM(ZRDF,"W")
    173  ; -- assign the MXLM dom global name to ZDOM
    174  S ZDOM=$NA(^TMP("MXMLDOM",$J,C0XDOCID))
    175  W !,$O(@ZDOM@(""),-1)," XML NODES PARSED"
    176  ; -- populate the metagraph to point to the graph with status unfinished
    177  S METAS=$$ANONS ; GET AN ANONOMOUS RANDOM SUBJECT
    178  I '$D(ZMETA) S ZMETA="_:G"_$$LKY9 ; RANDOM GRAPH NAME FOR METAGRAPH
    179  D ADD(ZMETA,METAS,"fmts:about",ZGRF,FARY) ; POINT THE META TO THE GRAPH
    180  D ADD(ZMETA,METAS,"fmts:status","unfinished",FARY) ; mark as unfinished
    181  ;S C0XDATE=$$FMDTOUTC^C0CUTIL($$NOW^XLFDT,"DT")
    182  S C0XDATE=$$NOW^XLFDT
    183  D ADD(ZMETA,METAS,"fmts:dateTime",C0XDATE,FARY)
    184  D UPDIE(.C0XFDA) ; commit the metagraph changes to the triple store
    185  ; --
    186  ; -- pull out the vocabularies in the RDF statement. marked with xmlns:
    187  ; -- put them in a local variable for quick reference
    188  ; -- TODO: create a graph for vocabularies and validate incoming against it
    189  ;
    190  S C0XVOC=""
    191  N ZI,ZJ,ZK S ZI=""
    192  F  S ZI=$O(@ZDOM@(1,"A",ZI)) Q:ZI=""  D  ; FOR EACH xmlns
    193  . S ZVOC=$P(ZI,"xmlns:",2)
    194  . I ZVOC'="" S C0XVOC(ZVOC)=$G(@ZDOM@(1,"A",ZI))
    195  ;W !,"VOCABS:" ZWR C0XVOC
    196  ;
    197  ; -- look for children called rdf:Description. quit if none. not an rdf file
    198  ;
    199  S ZI=$O(@ZDOM@(1,"C",""))
    200  I $G(@ZDOM@(1,"C",ZI))'="rdf:Description" D  Q  ; not an rdf file
    201  . W !,"Error. Not an RDF file. Cannot process."
    202  ;
    203  ; -- now process the rdf description children
    204  ;
    205  S ZI=""
    206  S (C0XSUB,C0XPRE,C0XOBJ)="" ; INITIALIZE subject, object and predicate
    207  F  S ZI=$O(@ZDOM@(1,"C",ZI)) Q:ZI=""  D  ;
    208  . ; -- we are skipping any child that is not rdf:Description
    209  . ; -- TODO: check to see if this is right in general
    210  . ;
    211  . IF $G(@ZDOM@(1,"C",ZI))'="rdf:Description" D  Q  ;
    212  . . W !,"SKIPPING NODE: ",ZI
    213  . ; -- now looking for the subject for the triples
    214  . S ZX=$G(@ZDOM@(ZI,"A","rdf:about"))
    215  . I ZX'="" D  ; we have the subject
    216  . . ;W " about: ",ZX
    217  . . S C0XSUB=ZX
    218  . E  D  ;
    219  . . S ZX=$G(@ZDOM@(ZI,"A","rdf:nodeID")) ; node id is another style of subject
    220  . . I ZX'="" D  ;
    221  . . . S C0XSUB=ZX
    222  . I C0XSUB="" S C0XSUB=$$ANONS ; DEFAULT TO BLANK SUBJECT
    223  . ;
    224  . ; -- we now have the subject. the children of this node have the rest
    225  . ;
    226  . S ZJ="" ; for the children of the rdf:Description nodes
    227  . F  S ZJ=$O(@ZDOM@(ZI,"C",ZJ)) Q:ZJ=""  D  ; for each child
    228  . . S C0XPRE=@ZDOM@(ZJ) ; the predicate without a prefix
    229  . . S ZX=$G(@ZDOM@(ZJ,"A","xmlns")) ; name space
    230  . . I ZX'="" S C0XPRE=ZX_C0XPRE ; add the namespace prefix
    231  . . I C0XPRE[":" D  ; expand using vocabulary
    232  . . . N ZB,ZA
    233  . . . S ZB=$P(C0XPRE,":",1)
    234  . . . S ZA=$P(C0XPRE,":",2)
    235  . . . I $G(C0XVOC(ZB))'="" D  ;
    236  . . . . S C0XPRE=C0XVOC(ZB)_ZA ; expanded
    237  . . S ZY=$G(@ZDOM@(ZJ,"A","rdf:resource")) ; potential object
    238  . . I ZY'="" D  Q ;
    239  . . . S C0XOBJ=ZY ; object
    240  . . . D ADD(ZGRF,C0XSUB,C0XPRE,C0XOBJ) ; finally. our first real triple
    241  . . ; -- this is an else because of the quit above
    242  . . S ZX=$G(@ZDOM@(ZJ,"A","rdf:nodeID")) ; fishing for nodeId object
    243  . . I ZX'="" D  Q  ; got one
    244  . . . S C0XOBJ=ZX ; we are using the incoming nodeIDs as object/subject
    245  . . . ; without change... this could be foolish .. look at it again later
    246  . . . D ADD(ZGRF,C0XSUB,C0XPRE,C0XOBJ) ; go for it and add a node
    247  . . S C0XOBJ=$G(@ZDOM@(ZJ,"T",1)) ; hopefully an object is here
    248  . . I C0XOBJ="" D  Q  ; not a happy situation
    249  . . . W !,"ERROR, NO OBJECT FOUND FOR NODE: ",ZJ
    250  . . D ADD(ZGRF,C0XSUB,C0XPRE,C0XOBJ) ; go for it and add a node
    251  W !,"INSERTING ",C0XCNT," TRIPLES"
    252  D UPDIE(.C0XFDA) ; commit the updates to the file
    253  ; next, mark the graph as finished
    254  S C0XEND=$$NOW^XLFDT
    255  W !," ENDED AT: ",C0XEND
    256  S C0XDIFF=$$FMDIFF^XLFDT(C0XEND,C0XSTART,2)
    257  W !," ELAPSED TIME: ",C0XDIFF," SECONDS"
    258  W !," APPROXIMATELY ",$P(C0XCNT/C0XDIFF,".")," TRIPLES PER SECOND"
    259  Q
    260  ;
    261 SHOW(ZN) ;
    262  ZWR ^TMP("MXMLDOM",$J,1,ZN,*)
    263  Q
    264  ;
    265 ANONS() ; RETURNS AN ANONOMOUS SUBJECT
    266  Q "_S:"_$$LKY9
    267  ;
    268 NEWG(NGRAPH,NMETA) ; CREATES A NEW META GRAPH, MARKS IT AS UNFINISHED
    269  ; THEN CREATES A NEW GRAPH AND POINTS THE METAGRAPH TO IT
    270  ; NGRAPH AND NMETA ARE PASSED BY REFERENCE AND ARE THE RETURN
    271  S NGRAPH="G"_$$LKY9
    272  S NMETA=NGRAPH_"A"
    273  Q
    274  ;
    275 ADD(ZG,ZS,ZP,ZO,FARY) ; ADD A TRIPLE TO THE TRIPLESTORE. ALL VALUES ARE TEXT
    276  ; THE FDA IS SET UP BUT THE FILES ARE NOT UPDATED. CALL UPDIE TO COMPLETE
    277  I '$D(FARY) D  ;
    278  . D INITFARY("C0XFARY")
    279  . S FARY="C0XFARY"
    280  D USEFARY(FARY)
    281  I '$D(C0XCNT) S C0XCNT=0
    282  N ZNODE
    283  S ZNODE="N"_$$LKY17
    284  N ZNARY ; GET READY TO CALL IENOFA
    285  S ZNARY("ZG",ZG)=""
    286  S ZNARY("ZS",ZS)=""
    287  S ZNARY("ZP",ZP)=""
    288  S ZNARY("ZO",ZO)=""
    289  D IENOFA(.ZIENS,.ZNARY,FARY) ; RESOLVE/ADD STRINGS
    290  ;S ZGIEN=$$IENOF(ZG) ; LAYGO TO GET IEN
    291  ;S ZSIEN=$$IENOF(ZS)
    292  ;S ZPIEN=$$IENOF(ZP)
    293  ;S ZOIEN=$$IENOF(ZO)
    294  ;I $D(C0XFDA) D UPDIE ; ADD THE STRINGS IF NEEDED
    295  S C0XCNT=C0XCNT+1
    296  S C0XFDA(C0XTFN,"?+"_C0XCNT_",",.01)=ZNODE
    297  S C0XFDA(C0XTFN,"?+"_C0XCNT_",",.02)=$O(ZIENS("IEN","ZG",""))
    298  S C0XFDA(C0XTFN,"?+"_C0XCNT_",",.03)=$O(ZIENS("IEN","ZS",""))
    299  S C0XFDA(C0XTFN,"?+"_C0XCNT_",",.04)=$O(ZIENS("IEN","ZP",""))
    300  S C0XFDA(C0XTFN,"?+"_C0XCNT_",",.05)=$O(ZIENS("IEN","ZO",""))
    301  ; REMEMBER TO CALL UPDIE WHEN YOU'RE DONE
    302  Q
    303  ;
    304 LKY9() ;EXTRINIC THAT RETURNS A RANDOM 9 DIGIT NUMBER. USED FOR GENERATING
    305  ; UNIQUE NODE AND GRAPH NAMES
    306  N ZN,ZI
    307  S ZN=""
    308  F ZI=1:1:9 D  ;
    309  . S ZN=ZN_$R(10)
    310  Q ZN
    311  ;
    312 LKY17() ;EXTRINIC THAT RETURNS A RANDOM 9 DIGIT NUMBER. USED FOR GENERATING
    313  ; UNIQUE NODE AND GRAPH NAMES
    314  N ZN,ZI
    315  S ZN=""
    316  F ZI=1:1:17 D  ;
    317  . S ZN=ZN_$R(10)
    318  Q ZN
    319  ;
    320 IENOF(ZSTRING,FARY) ; EXTRINSIC WHICH RETURNS THE IEN OF ZS IN THE STRINGS FILE
    321  I '$D(FARY) D  ;
    322  . D INITFARY("C0XFARY")
    323  . S FARY="C0XFARY"
    324  N ZIEN
    325  S ZIEN=$O(@C0XSN@("B",ZSTRING,""))
    326  I ZIEN="" D  ;
    327  . S C0XFDA2(C0XSFN,"+1,",.01)=ZSTRING
    328  . D UPDIE(.C0XFDA2)
    329  . S ZIEN=$O(@C0XSN@("B",ZSTRING,""))
    330  . K C0XFDA2
    331  Q ZIEN
    332  ;
    333 IENOFA(ZOUTARY,ZINARY,FARY) ; RESOLVE STRINGS TO IEN IN STRINGS FILE
    334  ; OR ADD THEM IF
    335  ; MISSING. ZINARY AND ZOUTARY ARE PASSED BY REFERENCE
    336  ; ZINARY LOOKS LIKE ZINARY("VAR","VAL")=""
    337  ; RETURNS IN ZOUTARY OF THE FORM ZOUTARY("IEN","VAR",IEN)=""
    338  I '$D(FARY) D  ;
    339  . D INITFARY("C0XFARY")
    340  . S FARY="C0XFARY"
    341  K ZOUTARY ; START WITH CLEAN RESULTS
    342  K C0XFDA2 ; USE A SEPARATE FDA FOR THIS
    343  N ZI S ZI=""
    344  N ZV,ZIEN
    345  N ZCNT S ZCNT=0
    346  F  S ZI=$O(ZINARY(ZI)) Q:ZI=""  D  ; LOOK FOR MISSING STRINGS
    347  . S ZV=$O(ZINARY(ZI,""))
    348  . I $O(@C0XSN@("B",ZV,""))="" D  ;
    349  . . S ZCNT=ZCNT+1
    350  . . S C0XFDA2(C0XSFN,"+"_ZCNT_",",.01)=ZV
    351  I $D(C0XFDA2) D  ;
    352  . D UPDIE(.C0XFDA2) ; ADD MISSING STRINGS
    353  . K C0XFDA2 ; CLEAN UP
    354  F  S ZI=$O(ZINARY(ZI)) Q:ZI=""  D  ; NOT GET ALL IENS
    355  . S ZV=$O(ZINARY(ZI,""))
    356  . S ZIEN=$O(@C0XSN@("B",ZV,"")) ; THEY SHOULD BE THERE NOW
    357  . I ZIEN="" D  ;
    358  . . W !,"ERROR ADDING STRING: ",ZV
    359  . . B
    360  . S ZOUTARY("IEN",ZI,ZIEN)=""
    361  Q
    362  ;
    363 UPDIE(ZFDA) ; INTERNAL ROUTINE TO CALL UPDATE^DIE AND CHECK FOR ERRORS
    364  ; ZFDA IS PASSED BY REFERENCE
    365  ;ZWR ZFDA
    366  ;B
    367  K ZERR
    368  D CLEAN^DILF
    369  D UPDATE^DIE("","ZFDA","","ZERR")
    370  I $D(ZERR) S ZZERR=ZZERR ; ZZERR DOESN'T EXIST,
    371  ; INVOKE THE ERROR TRAP IF TASKED
    372  ;. W "ERROR",!
    373  ;. ZWR ZERR
    374  ;. B
    375  K ZFDA
    376  Q
    377  ;
     1C0XMAIN ; GPL - Fileman Triples entry point routine ;10/13/11  17:05
     2        ;;1.0;FILEMAN TRIPLE STORE;;Sep 26, 2012;Build 10
     3        ;Copyright 2011 George Lilly.  Licensed under the terms of the GNU
     4        ;General Public License See attached copy of the License.
     5        ;
     6        ;This program is free software; you can redistribute it and/or modify
     7        ;it under the terms of the GNU General Public License as published by
     8        ;the Free Software Foundation; either version 2 of the License, or
     9        ;(at your option) any later version.
     10        ;
     11        ;This program is distributed in the hope that it will be useful,
     12        ;but WITHOUT ANY WARRANTY; without even the implied warranty of
     13        ;MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
     14        ;GNU General Public License for more details.
     15        ;
     16        ;You should have received a copy of the GNU General Public License along
     17        ;with this program; if not, write to the Free Software Foundation, Inc.,
     18        ;51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
     19        ;
     20        Q
     21        ;
     22INITFARY(ZFARY) ; INITIALIZE FILE NUMBERS AND OTHER USEFUL THINGS
     23        ; FOR THE DEFAULT TRIPLE STORE. USE OTHER VALUES FOR SUPPORTING ADDITIONAL
     24        ; TRIPLE STORES
     25        S @ZFARY@("C0XTFN")=172.101 ; TRIPLES FILE NUMBER
     26        S @ZFARY@("C0XSFN")=172.201 ; TRIPLES STRINGS FILE NUMBER
     27        S @ZFARY@("C0XTN")=$NA(^C0X(101)) ; TRIPLES GLOBAL NAME
     28        S @ZFARY@("C0XSN")=$NA(^C0X(201)) ; STRING FILE GLOBAL NAME
     29        ;S @ZFARY@("C0XDIR")="/home/glilly/all_smart_patient_data/smart-rdf/"
     30        S @ZFARY@("C0XDIR")="/home/george/fmts/trunk/samples/"
     31        D USEFARY(ZFARY)
     32        Q
     33        ;
     34USEFARY(ZFARY)  ; INITIALIZES VARIABLES SAVED IN ARRAY ZFARY
     35        N ZI S ZI=""
     36        F  S ZI=$O(@ZFARY@(ZI)) Q:ZI=""  D 
     37        . ;N ZX
     38        . S ZX="S "_ZI_"="""_@ZFARY@(ZI)_""""
     39        . ;W !,ZX
     40        . X ZX
     41        Q
     42        ;
     43IMPORT(FNAME,FDIR,FURL,FARY)    ; EXTRINSIC THAT READS A FILE FROM THE STANDARD
     44        ; DIRECTORY, LOADS IT INTO THE TRIPLESTORE AS TEXT, AND RETURNS THE
     45        ; NODE NAME OF THE TEXT TRIPLE
     46        ; FDIR IS THE OPTIONAL DIRECTORY (DEFAUTS TO STANDARD DIR)
     47        ; FURL IS THE OPTIONAL URI FOR ACCESSING THE FILE FROM THE TRIPLE STORE
     48        ; FARY IS THE OPTIONAL FILE ARRAY OF THE TRIPLE STORE TO USE
     49        I '$D(FARY) D  ;
     50        . D INITFARY("C0XFARY")
     51        . S FARY="C0XFARY"
     52        D USEFARY(FARY)
     53        N ZD,ZTMP
     54        I '$D(FDIR) S FDIR=C0XDIR ; DIRECTORY OF THE RDF FILE
     55        I '$D(FURL) D  ;
     56        . N ZN2 S ZN2=$TR(FNAME,".","_") ; REMOVE THE DOT FROM THE NAME
     57        . S FURL=FDIR_ZN2
     58        N ZTMP
     59        S ZTMP=$NA(^TMP("C0X",$J,"FILEIN",1)) ; WHERE TO PUT THE INCOMING FILE
     60        K @ZTMP ; MAKE SURE IT'S CLEAR
     61        S C0XSTART=$$NOW^XLFDT
     62        W !,"STARTED: ",C0XSTART
     63        W !,"READING IN: ",FNAME
     64        I '$$FILEIN(ZTMP,FDIR,FNAME,4) D  Q  ; QUIT IF NO SUCCESS
     65        . W !,"ERROR READING FILE: ",FDIR,FNAME
     66        S ZRDF=$NA(^TMP("C0X",$J,"FILEIN")) ; WITHOUT THE SUBSCRIPT
     67        W !,$O(@ZRDF@(""),-1)," LINES READ"
     68        D INSRDF(ZRDF,FURL,FARY) ; IMPORT AND PROCESS THE RDF
     69        Q
     70        ;
     71WGET(ZURL,FARY) ; GET FROM THE INTERNET AN RDF FILE AND INSERT IT
     72        ;
     73        I '$D(FARY) D  ;
     74        . D INITFARY("C0XFARY")
     75        . S FARY="C0XFARY"
     76        D USEFARY(FARY)
     77        ;N ZLOC,ZTMP
     78        K ZTMP
     79        S ZLOC=$NA(^TMP("C0X","WGET",$J))
     80        S C0XSTART=$$NOW^XLFDT
     81        W !,"STARTED: ",C0XSTART
     82        W !,"DOWNLOADING: ",ZURL
     83        S OK=$$httpGET^%zewdGTM(ZURL,.ZTMP)
     84        M @ZLOC=ZTMP
     85        W !,$O(@ZLOC@(""),-1)," LINES READ"
     86        D INSRDF(ZLOC,ZURL,FARY)
     87        Q
     88        ;
     89INSRDF(ZRDF,ZNAME,FARY) ; INSERT AN RDF FILE INTO THE STORE AND PROCESS
     90        ; ZRDF IS PASSED BY NAME
     91        I '$D(FARY) D  ;
     92        . D INITFARY("C0XFARY")
     93        . S FARY="C0XFARY"
     94        D USEFARY(FARY)
     95        N ZGRAPH,ZSUBJECT
     96        S ZGRAPH="_:G"_$$LKY9 ; RANDOM GRAPH NAME
     97        S ZSUBJECT=$$ANONS ; RANDOM ANOYMOUS SUBJECT
     98        D ADD(ZGRAPH,ZSUBJECT,"fmts:url",ZNAME,FARY)
     99        N ZTXTNM
     100        S ZTXTNM="_TXT_INCOMING_RDF_FILE_"_ZNAME_"_"_$$LKY9 ; NAME FOR TEXT NODE
     101        D ADD(ZGRAPH,ZSUBJECT,"fmts:rdfSource",ZTXTNM,FARY)
     102        D UPDIE(.C0XFDA) ; TRY IT OUT
     103        K C0XCNT ;RESET FOR NEXT TIME
     104        D STORETXT(ZRDF,ZTXTNM,FARY)
     105        W !,"ADDED: ",ZGRAPH," ",ZSUBJECT," fmts:rdfSource ",ZTXTNM
     106        D PROCESS(.G,ZRDF,ZNAME,ZGRAPH,FARY) ; PARSE AND INSERT THE RDF
     107        Q
     108        ;
     109STORETXT(ZTXT,ZNAME,FARY)       ; STORE TEXT IN THE TRIPLESTORE AT ZNAME
     110        ;
     111        I '$D(FARY) D  ;
     112        . D INITFARY("C0XFARY")
     113        . S FARY="C0XFARY"
     114        D USEFARY(FARY)
     115        N ZIEN
     116        S ZIEN=$$IENOF(ZNAME,FARY) ; GET THE IEN
     117        D CLEAN^DILF
     118        K ZERR
     119        D WP^DIE(C0XSFN,ZIEN_",",1,,ZTXT,"ZERR")
     120        I $D(ZERR) D  ;
     121        . ZWR ZERR
     122        Q
     123        ;
     124GETTXT(ZRTN,ZNAME,FARY) ; RETURNS RDF SOURCE OR OTHER TEXT
     125        ; ZRTN IS PASSED BY REFERENCE
     126        I '$D(FARY) D  ;
     127        . D INITFARY("C0XFARY")
     128        . S FARY="C0XFARY"
     129        D USEFARY(FARY)
     130        N ZIEN
     131        S ZIEN=$$IENOF(ZNAME)
     132        S OK=$$GET1^DIQ(C0XSFN,ZIEN_",",1,,"ZRTN")
     133        Q
     134        ;
     135WHERETXT(ZNAME,FARY)    ; EXTRINSIC WHICH RETURNS THE NAME OF THE GLOBAL
     136        ; WHERE THE TEXT IS LOCATED. NAME IS THE NAME OF THE STRING
     137        I '$D(FARY) D  ;
     138        . D INITFARY("C0XFARY")
     139        . S FARY="C0XFARY"
     140        D USEFARY(FARY)
     141        N ZIEN
     142        S ZIEN=$$IENOF(ZNAME)
     143        Q $NA(@C0XSN@(ZIEN,1))
     144        ;
     145FILEIN(ZINTMP,ZDIR,ZFNAME,ZLVL) ; READS A FILE INTO ZINTMP USING FTG^%ZISH
     146        ; ZINTMP IS PASSED BY NAME AND INCLUDES THE NEW SUBSCRIPT
     147        ; IE ^TMP("C0X","FILEIN",1)
     148        ; ZLVL IN THIS CASE WOULD BE 3 INCREMENTING THE 1
     149        ; EXTRINSIC WHICH RETURNS THE RESULT OF FTG^%ZISH
     150        S OK=$$FTG^%ZISH(ZDIR,FNAME,ZINTMP,ZLVL)
     151        Q OK
     152        ;
     153TESTPROC        ; TEST PROCESS WITH EXISTING SMALL RDF FILE
     154        S ZIN=$NA(^TMP("C0X",12226,"FILEIN"))
     155        S ZGRAPH="/test/rdfFile"
     156        S ZM="/test/rdfFile/meta"
     157        D PROCESS(.G,ZIN,ZGRAPH,ZM)
     158        Q
     159        ;
     160PROCESS(ZRTN,ZRDF,ZGRF,ZMETA,FARY)      ; PROCESS AN INCOMING RDF FILE
     161        ; ZRTN IS PASS BY REFERENCE AND RETURNS MESSAGES ABOUT THE PROCESSING
     162        ; ZRDF IS PASSED BY NAME AND IS THE GLOBAL CONTAINING THE RDF FILE
     163        ; ZGRF IS THE NAME OF THE GRAPH TO USE IN THE TRIPLE STORE FOR RESULTS
     164        ; ZMETA IS OPTIONAL AND IS THE NAME OF THE GRAPH TO STORE METADATA
     165        ;
     166        I '$D(FARY) D  ;
     167        . D INITFARY("C0XFARY")
     168        . S FARY="C0XFARY"
     169        D USEFARY(FARY)
     170        ; -- first parse the rdf file with the MXML parser
     171        ;S C0XDOCID=$$PARSE^C0CNHIN(ZRDF,"C0XARRAY") ; PARSE WITH MXML
     172        S C0XDOCID=$$EN^MXMLDOM(ZRDF,"W")
     173        ; -- assign the MXLM dom global name to ZDOM
     174        S ZDOM=$NA(^TMP("MXMLDOM",$J,C0XDOCID))
     175        W !,$O(@ZDOM@(""),-1)," XML NODES PARSED"
     176        ; -- populate the metagraph to point to the graph with status unfinished
     177        S METAS=$$ANONS ; GET AN ANONOMOUS RANDOM SUBJECT
     178        I '$D(ZMETA) S ZMETA="_:G"_$$LKY9 ; RANDOM GRAPH NAME FOR METAGRAPH
     179        D ADD(ZMETA,METAS,"fmts:about",ZGRF,FARY) ; POINT THE META TO THE GRAPH
     180        D ADD(ZMETA,METAS,"fmts:status","unfinished",FARY) ; mark as unfinished
     181        ;S C0XDATE=$$FMDTOUTC^C0CUTIL($$NOW^XLFDT,"DT")
     182        S C0XDATE=$$NOW^XLFDT
     183        D ADD(ZMETA,METAS,"fmts:dateTime",C0XDATE,FARY)
     184        D UPDIE(.C0XFDA) ; commit the metagraph changes to the triple store
     185        ; --
     186        ; -- pull out the vocabularies in the RDF statement. marked with xmlns:
     187        ; -- put them in a local variable for quick reference
     188        ; -- TODO: create a graph for vocabularies and validate incoming against it
     189        ;
     190        S C0XVOC=""
     191        N ZI,ZJ,ZK S ZI=""
     192        F  S ZI=$O(@ZDOM@(1,"A",ZI)) Q:ZI=""  D  ; FOR EACH xmlns
     193        . S ZVOC=$P(ZI,"xmlns:",2)
     194        . I ZVOC'="" S C0XVOC(ZVOC)=$G(@ZDOM@(1,"A",ZI))
     195        ;W !,"VOCABS:" ZWR C0XVOC
     196        ;
     197        ; -- look for children called rdf:Description. quit if none. not an rdf file
     198        ;
     199        S ZI=$O(@ZDOM@(1,"C",""))
     200        I $G(@ZDOM@(1,"C",ZI))'="rdf:Description" D  Q  ; not an rdf file
     201        . W !,"Error. Not an RDF file. Cannot process."
     202        ;
     203        ; -- now process the rdf description children
     204        ;
     205        S ZI=""
     206        S (C0XSUB,C0XPRE,C0XOBJ)="" ; INITIALIZE subject, object and predicate
     207        F  S ZI=$O(@ZDOM@(1,"C",ZI)) Q:ZI=""  D  ;
     208        . ; -- we are skipping any child that is not rdf:Description
     209        . ; -- TODO: check to see if this is right in general
     210        . ;
     211        . IF $G(@ZDOM@(1,"C",ZI))'="rdf:Description" D  Q  ;
     212        . . W !,"SKIPPING NODE: ",ZI
     213        . ; -- now looking for the subject for the triples
     214        . S ZX=$G(@ZDOM@(ZI,"A","rdf:about"))
     215        . I ZX'="" D  ; we have the subject
     216        . . ;W " about: ",ZX
     217        . . S C0XSUB=ZX
     218        . E  D  ;
     219        . . S ZX=$G(@ZDOM@(ZI,"A","rdf:nodeID")) ; node id is another style of subject
     220        . . I ZX'="" D  ;
     221        . . . S C0XSUB=ZX
     222        . I C0XSUB="" S C0XSUB=$$ANONS ; DEFAULT TO BLANK SUBJECT
     223        . ;
     224        . ; -- we now have the subject. the children of this node have the rest
     225        . ;
     226        . S ZJ="" ; for the children of the rdf:Description nodes
     227        . F  S ZJ=$O(@ZDOM@(ZI,"C",ZJ)) Q:ZJ=""  D  ; for each child
     228        . . S C0XPRE=@ZDOM@(ZJ) ; the predicate without a prefix
     229        . . S ZX=$G(@ZDOM@(ZJ,"A","xmlns")) ; name space
     230        . . I ZX'="" S C0XPRE=ZX_C0XPRE ; add the namespace prefix
     231        . . I C0XPRE[":" D  ; expand using vocabulary
     232        . . . N ZB,ZA
     233        . . . S ZB=$P(C0XPRE,":",1)
     234        . . . S ZA=$P(C0XPRE,":",2)
     235        . . . I $G(C0XVOC(ZB))'="" D  ;
     236        . . . . S C0XPRE=C0XVOC(ZB)_ZA ; expanded
     237        . . S ZY=$G(@ZDOM@(ZJ,"A","rdf:resource")) ; potential object
     238        . . I ZY'="" D  Q ;
     239        . . . S C0XOBJ=ZY ; object
     240        . . . D ADD(ZGRF,C0XSUB,C0XPRE,C0XOBJ) ; finally. our first real triple
     241        . . ; -- this is an else because of the quit above
     242        . . S ZX=$G(@ZDOM@(ZJ,"A","rdf:nodeID")) ; fishing for nodeId object
     243        . . I ZX'="" D  Q  ; got one
     244        . . . S C0XOBJ=ZX ; we are using the incoming nodeIDs as object/subject
     245        . . . ; without change... this could be foolish .. look at it again later
     246        . . . D ADD(ZGRF,C0XSUB,C0XPRE,C0XOBJ) ; go for it and add a node
     247        . . S C0XOBJ=$G(@ZDOM@(ZJ,"T",1)) ; hopefully an object is here
     248        . . I C0XOBJ="" D  Q  ; not a happy situation
     249        . . . W !,"ERROR, NO OBJECT FOUND FOR NODE: ",ZJ
     250        . . D ADD(ZGRF,C0XSUB,C0XPRE,C0XOBJ) ; go for it and add a node
     251        W !,"INSERTING ",C0XCNT," TRIPLES"
     252        D UPDIE(.C0XFDA) ; commit the updates to the file
     253        ; next, mark the graph as finished
     254        S C0XEND=$$NOW^XLFDT
     255        W !," ENDED AT: ",C0XEND
     256        S C0XDIFF=$$FMDIFF^XLFDT(C0XEND,C0XSTART,2)
     257        W !," ELAPSED TIME: ",C0XDIFF," SECONDS"
     258        W !," APPROXIMATELY ",$P(C0XCNT/C0XDIFF,".")," TRIPLES PER SECOND"
     259        Q
     260        ;
     261SHOW(ZN)        ;
     262        ZWR ^TMP("MXMLDOM",$J,1,ZN,*)
     263        Q
     264        ;
     265ANONS() ; RETURNS AN ANONOMOUS SUBJECT
     266        Q "_S:"_$$LKY9
     267        ;
     268NEWG(NGRAPH,NMETA)      ; CREATES A NEW META GRAPH, MARKS IT AS UNFINISHED
     269        ; THEN CREATES A NEW GRAPH AND POINTS THE METAGRAPH TO IT
     270        ; NGRAPH AND NMETA ARE PASSED BY REFERENCE AND ARE THE RETURN
     271        S NGRAPH="G"_$$LKY9
     272        S NMETA=NGRAPH_"A"
     273        Q
     274        ;
     275ADD(ZG,ZS,ZP,ZO,FARY)   ; ADD A TRIPLE TO THE TRIPLESTORE. ALL VALUES ARE TEXT
     276        ; THE FDA IS SET UP BUT THE FILES ARE NOT UPDATED. CALL UPDIE TO COMPLETE
     277        I '$D(FARY) D  ;
     278        . D INITFARY("C0XFARY")
     279        . S FARY="C0XFARY"
     280        D USEFARY(FARY)
     281        I '$D(C0XCNT) S C0XCNT=0
     282        N ZNODE
     283        S ZNODE="N"_$$LKY17
     284        N ZNARY ; GET READY TO CALL IENOFA
     285        S ZNARY("ZG",ZG)=""
     286        S ZNARY("ZS",ZS)=""
     287        S ZNARY("ZP",ZP)=""
     288        S ZNARY("ZO",ZO)=""
     289        D IENOFA(.ZIENS,.ZNARY,FARY) ; RESOLVE/ADD STRINGS
     290        ;S ZGIEN=$$IENOF(ZG) ; LAYGO TO GET IEN
     291        ;S ZSIEN=$$IENOF(ZS)
     292        ;S ZPIEN=$$IENOF(ZP)
     293        ;S ZOIEN=$$IENOF(ZO)
     294        ;I $D(C0XFDA) D UPDIE ; ADD THE STRINGS IF NEEDED
     295        S C0XCNT=C0XCNT+1
     296        S C0XFDA(C0XTFN,"?+"_C0XCNT_",",.01)=ZNODE
     297        S C0XFDA(C0XTFN,"?+"_C0XCNT_",",.02)=$O(ZIENS("IEN","ZG",""))
     298        S C0XFDA(C0XTFN,"?+"_C0XCNT_",",.03)=$O(ZIENS("IEN","ZS",""))
     299        S C0XFDA(C0XTFN,"?+"_C0XCNT_",",.04)=$O(ZIENS("IEN","ZP",""))
     300        S C0XFDA(C0XTFN,"?+"_C0XCNT_",",.05)=$O(ZIENS("IEN","ZO",""))
     301        ; REMEMBER TO CALL UPDIE WHEN YOU'RE DONE
     302        Q
     303        ;
     304LKY9()  ;EXTRINIC THAT RETURNS A RANDOM 9 DIGIT NUMBER. USED FOR GENERATING
     305        ; UNIQUE NODE AND GRAPH NAMES
     306        N ZN,ZI
     307        S ZN=""
     308        F ZI=1:1:9 D  ;
     309        . S ZN=ZN_$R(10)
     310        Q ZN
     311        ;
     312LKY17() ;EXTRINIC THAT RETURNS A RANDOM 9 DIGIT NUMBER. USED FOR GENERATING
     313        ; UNIQUE NODE AND GRAPH NAMES
     314        N ZN,ZI
     315        S ZN=""
     316        F ZI=1:1:17 D  ;
     317        . S ZN=ZN_$R(10)
     318        Q ZN
     319        ;
     320IENOF(ZSTRING,FARY)     ; EXTRINSIC WHICH RETURNS THE IEN OF ZS IN THE STRINGS FILE
     321        I '$D(FARY) D  ;
     322        . D INITFARY("C0XFARY")
     323        . S FARY="C0XFARY"
     324        N ZIEN
     325        S ZIEN=$O(@C0XSN@("B",ZSTRING,""))
     326        I ZIEN="" D  ;
     327        . S C0XFDA2(C0XSFN,"+1,",.01)=ZSTRING
     328        . D UPDIE(.C0XFDA2)
     329        . S ZIEN=$O(@C0XSN@("B",ZSTRING,""))
     330        . K C0XFDA2
     331        Q ZIEN
     332        ;
     333IENOFA(ZOUTARY,ZINARY,FARY)     ; RESOLVE STRINGS TO IEN IN STRINGS FILE
     334        ; OR ADD THEM IF
     335        ; MISSING. ZINARY AND ZOUTARY ARE PASSED BY REFERENCE
     336        ; ZINARY LOOKS LIKE ZINARY("VAR","VAL")=""
     337        ; RETURNS IN ZOUTARY OF THE FORM ZOUTARY("IEN","VAR",IEN)=""
     338        I '$D(FARY) D  ;
     339        . D INITFARY("C0XFARY")
     340        . S FARY="C0XFARY"
     341        K ZOUTARY ; START WITH CLEAN RESULTS
     342        K C0XFDA2 ; USE A SEPARATE FDA FOR THIS
     343        N ZI S ZI=""
     344        N ZV,ZIEN
     345        N ZCNT S ZCNT=0
     346        F  S ZI=$O(ZINARY(ZI)) Q:ZI=""  D  ; LOOK FOR MISSING STRINGS
     347        . S ZV=$O(ZINARY(ZI,""))
     348        . I $O(@C0XSN@("B",ZV,""))="" D  ;
     349        . . S ZCNT=ZCNT+1
     350        . . S C0XFDA2(C0XSFN,"+"_ZCNT_",",.01)=ZV
     351        I $D(C0XFDA2) D  ;
     352        . D UPDIE(.C0XFDA2) ; ADD MISSING STRINGS
     353        . K C0XFDA2 ; CLEAN UP
     354        F  S ZI=$O(ZINARY(ZI)) Q:ZI=""  D  ; NOT GET ALL IENS
     355        . S ZV=$O(ZINARY(ZI,""))
     356        . S ZIEN=$O(@C0XSN@("B",ZV,"")) ; THEY SHOULD BE THERE NOW
     357        . I ZIEN="" D  ;
     358        . . W !,"ERROR ADDING STRING: ",ZV
     359        . . B
     360        . S ZOUTARY("IEN",ZI,ZIEN)=""
     361        Q
     362        ;
     363UPDIE(ZFDA)     ; INTERNAL ROUTINE TO CALL UPDATE^DIE AND CHECK FOR ERRORS
     364        ; ZFDA IS PASSED BY REFERENCE
     365        ;ZWR ZFDA
     366        ;B
     367        K ZERR
     368        D CLEAN^DILF
     369        D UPDATE^DIE("","ZFDA","","ZERR")
     370        I $D(ZERR) S ZZERR=ZZERR ; ZZERR DOESN'T EXIST,
     371        ; INVOKE THE ERROR TRAP IF TASKED
     372        ;. W "ERROR",!
     373        ;. ZWR ZERR
     374        ;. B
     375        K ZFDA
     376        Q
     377        ;
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