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