Changeset 1569 for smart/trunk/p/C0SLAB.m
- Timestamp:
- Oct 11, 2012, 1:42:56 PM (13 years ago)
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- 1 edited
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smart/trunk/p/C0SLAB.m (modified) (1 diff)
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smart/trunk/p/C0SLAB.m
r1540 r1569 1 C0SLAB 2 ;;1.0;VISTA SMART CONTAINER;;Sep 26, 2012;Build 23 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 LAB(GRTN,C0SARY) 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 . I ZR("sp:unit")="" S ZR("sp:unit")=$G(@LRN@("test@value"))236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 SAMPLE 271 272 273 274 275 1 C0SLAB ; GPL - Smart Lab Processing ;4/15/12 17:05 2 ;;0.1;C0S;nopatch;noreleasedate;Build 2 3 ;Copyright 2012 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 ; sample VistA NHIN lab result 23 ; 24 ;^TMP("C0STBL",32,"lab",8,"collected@value")=3110626.16 25 ;^TMP("C0STBL",32,"lab",8,"comment")="Report Released Date/Time: Jun 26, 2011@19:00" 26 ;^TMP("C0STBL",32,"lab",8,"comment@xml:space")="preserve" 27 ;^TMP("C0STBL",32,"lab",8,"facility@code")=100 28 ;^TMP("C0STBL",32,"lab",8,"facility@name")="VOE OFFICE INSTITUTION" 29 ;^TMP("C0STBL",32,"lab",8,"groupName@value")="CH 0626 47" 30 ;^TMP("C0STBL",32,"lab",8,"high@value")=" 101" 31 ;^TMP("C0STBL",32,"lab",8,"id@value")="CH;6889372.84;67003" 32 ;^TMP("C0STBL",32,"lab",8,"interpretation@value")="H" 33 ;^TMP("C0STBL",32,"lab",8,"labOrderID@value")=336 34 ;^TMP("C0STBL",32,"lab",8,"localName@value")="FBLDGLU" 35 ;^TMP("C0STBL",32,"lab",8,"loinc@value")="14771-0" 36 ;^TMP("C0STBL",32,"lab",8,"low@value")="69 " 37 ;^TMP("C0STBL",32,"lab",8,"orderID@value")=807 38 ;^TMP("C0STBL",32,"lab",8,"result@value")=178 39 ;^TMP("C0STBL",32,"lab",8,"resulted@value")=3110626.190006 40 ;^TMP("C0STBL",32,"lab",8,"sample@value")="SERUM" 41 ;^TMP("C0STBL",32,"lab",8,"specimen@code")="0X500" 42 ;^TMP("C0STBL",32,"lab",8,"specimen@name")="SERUM" 43 ;^TMP("C0STBL",32,"lab",8,"status@value")="completed" 44 ;^TMP("C0STBL",32,"lab",8,"test@value")="FASTING BLOOD GLUCOSE" 45 ;^TMP("C0STBL",32,"lab",8,"type@value")="CH" 46 ;^TMP("C0STBL",32,"lab",8,"units@value")="MG/DL" 47 ;^TMP("C0STBL",32,"lab",8,"vuid@value")=4656342 48 ; 49 ; sample Smart lab result triples 50 ; 51 ;G("loinc:29571-7","dcterms:identifier")="29571-7" 52 ;G("loinc:29571-7","dcterms:title")="Phe DBS Ql" 53 ;G("loinc:29571-7","rdf:type")="sp:Code" 54 ;G("loinc:29571-7","sp:system")="http://loinc.org/codes/" 55 ;G("loinc:38478-4","dcterms:identifier")="38478-4" 56 ;G("loinc:38478-4","dcterms:title")="Biotinidase DBS Ql" 57 ;G("loinc:38478-4","rdf:type")="sp:Code" 58 ;G("loinc:38478-4","sp:system")="http://loinc.org/codes/" 59 ;G("qqWZZIew993","rdf:type")="sp:Attribution" 60 ;G("qqWZZIew993","sp:startDate")="2007-04-21" 61 ;G("qqWZZIew994","rdf:type")="sp:NarrativeResult" 62 ;G("qqWZZIew994","sp:value")="Normal" 63 ;G("qqWZZIew995","dcterms:title")="Biotinidase DBS Ql" 64 ;G("qqWZZIew995","rdf:type")="sp:CodedValue" 65 ;G("qqWZZIew995","sp:code")="loinc:38478-4" 66 ;G("qqWZZIew997","rdf:type")="sp:Attribution" 67 ;G("qqWZZIew997","sp:startDate")="2007-09-08" 68 ;G("qqWZZIew998","rdf:type")="sp:NarrativeResult" 69 ;G("qqWZZIew998","sp:value")="Normal" 70 ;G("qqWZZIew999","dcterms:title")="Phe DBS Ql" 71 ;G("qqWZZIew999","rdf:type")="sp:CodedValue" 72 ;G("qqWZZIew999","sp:code")="loinc:29571-7" 73 ;G("smart:99912345/lab_results/3d9b39249193","rdf:type")="sp:LabResult" 74 ;G("smart:99912345/lab_results/3d9b39249193","sp:belongsTo")="smart:99912345" 75 ;G("smart:99912345/lab_results/3d9b39249193","sp:labName")="qqWZZIew995" 76 ;G("smart:99912345/lab_results/3d9b39249193","sp:narrativeResult")="qqWZZIew994" 77 ;G("smart:99912345/lab_results/3d9b39249193","sp:specimenCollected")="qqWZZIew993" 78 ;G("smart:99912345/lab_results/426c7adc4f54","rdf:type")="sp:LabResult" 79 ;G("smart:99912345/lab_results/426c7adc4f54","sp:belongsTo")="smart:99912345" 80 ;G("smart:99912345/lab_results/426c7adc4f54","sp:labName")="qqWZZIew999" 81 ;G("smart:99912345/lab_results/426c7adc4f54","sp:narrativeResult")="qqWZZIew998" 82 ;G("smart:99912345/lab_results/426c7adc4f54","sp:specimenCollected")="qqWZZIew997" 83 ; 84 ; 85 ; another Smart example, this one with sp:quantitativeResult 86 ; 87 ;G("loinc:786-4","dcterms:identifier")="786-4" 88 ;G("loinc:786-4","dcterms:title")="MCHC RBC Auto-mCnc" 89 ;G("loinc:786-4","rdf:type")="sp:Code" 90 ;G("loinc:786-4","sp:system")="http://loinc.org/codes/" 91 ;G("nodeID:4439","rdf:type")="sp:ValueAndUnit" 92 ;G("nodeID:4439","sp:unit")="g/dL" 93 ;G("nodeID:4439","sp:value")=36.6 94 ;G("nodeID:4613","rdf:type")="sp:ValueAndUnit" 95 ;G("nodeID:4613","sp:unit")="g/dL" 96 ;G("nodeID:4613","sp:value")=32 97 ;G("nodeID:4672","rdf:type")="sp:Attribution" 98 ;G("nodeID:4672","sp:startDate")="2005-03-10" 99 ;G("nodeID:4866","rdf:type")="sp:ValueAndUnit" 100 ;G("nodeID:4866","sp:unit")="g/dL" 101 ;G("nodeID:4866","sp:value")=36 102 ;G("nodeID:4871","dcterms:title")="MCHC RBC Auto-mCnc" 103 ;G("nodeID:4871","rdf:type")="sp:CodedValue" 104 ;G("nodeID:4871","sp:code")="loinc:786-4" 105 ;G("nodeID:5221","rdf:type")="sp:QuantitativeResult" 106 ;G("nodeID:5221","sp:normalRange")="nodeID:5282" 107 ;G("nodeID:5221","sp:valueAndUnit")="nodeID:4439" 108 ;G("nodeID:5282","rdf:type")="sp:ValueRange" 109 ;G("nodeID:5282","sp:maximum")="nodeID:4866" 110 ;G("nodeID:5282","sp:minimum")="nodeID:4613" 111 ;G("smart:1540505/lab_results/2fc100850766","rdf:type")="sp:LabResult" 112 ;G("smart:1540505/lab_results/2fc100850766","sp:belongsTo")="smart:1540505" 113 ;G("smart:1540505/lab_results/2fc100850766","sp:labName")="nodeID:4871" 114 ;G("smart:1540505/lab_results/2fc100850766","sp:quantitativeResult")="nodeID:5221" 115 ;G("smart:1540505/lab_results/2fc100850766","sp:specimenCollected")="nodeID:4672" 116 ; 117 LAB(GRTN,C0SARY) ; GRTN, passed by reference, 118 ; is the return name of the graph created. "" if none 119 ; C0SARY is passed in by reference and is the NHIN array of lab 120 ; 121 I $O(C0SARY("lab",""))="" D Q ; 122 . I $D(DEBUG) W !,"No Labs" 123 S GRTN="" ; default to no labs 124 N C0SGRF 125 S C0SGRF="vistaSmart:"_ZPATID_"/lab_results" 126 I $D(DEBUG) W !,"Processing ",C0SGRF 127 D DELGRAPH^C0XF2N(C0SGRF) ; delete the old graph 128 D INITFARY^C0XF2N("C0XFARY") ; which triple store to use 129 N FARY S FARY="C0XFARY" 130 D USEFARY^C0XF2N(FARY) 131 D VOCINIT^C0XUTIL 132 ; 133 D STARTADD^C0XF2N ; initialize to create triples 134 ; 135 N ZI S ZI="" 136 F S ZI=$O(C0SARY("lab",ZI)) Q:ZI="" D ; 137 . N LRN,ZR ; ZR is the local array for building the new triples 138 . S LRN=$NA(C0SARY("lab",ZI)) ; base for values in this lab result 139 . ; 140 . N RSLTID ; unique Id for this lab result 141 . S RSLTID=C0SGRF_"/"_$$LKY17^C0XF2N ; use a random number 142 . ; 143 . ; i don't like this because the same labs result gets a 144 . ; different ID every time it's reported. Can't trace it back to VistA 145 . ; I'd rather be using id@value ie "id@value")="CH;6889372.84;67003" 146 . ; .. either that or store an OID with the lab result - but that 147 . ; will have to wait for the redesign of file 60.. - gpl 4/16/2012 148 . ; 149 . N LOINC S LOINC=$G(@LRN@("loinc@value")) 150 . I LOINC="" D Q ; 151 . . I $D(DEBUG) W !,"NO LOINC VALUE, SKIPPING" 152 . N LABTST S LABTST=$G(@LRN@("test@value")) 153 . I $D(DEBUG) D ; 154 . . W !,"Processing Lab Result ",RSLTID 155 . . W !,"test: ",LABTST 156 . . W !,"loinc: ",LOINC 157 . ; 158 . ; first do the base result graph 159 . ; 160 . S ZR("rdf:type")="sp:LabResult" 161 . S ZR("sp:belongsTo")=C0SGRF ; the subject for this patient's lab results 162 . ; ie /vista/smart/99912345/lab_results 163 . ; 164 . N LABNAME S LABNAME=$$ANONS^C0XF2N ; new node for lab name 165 . S ZR("sp:labName")=LABNAME 166 . ; 167 . N NARRSLT S NARRSLT=$$ANONS^C0XF2N ; new node for narrative result 168 . S ZR("sp:narrativeResult")=NARRSLT 169 . ; 170 . N QNTRSLT S QNTRSLT=$$ANONS^C0XF2N ; new node for narrative result 171 . S ZR("sp:quantitativeResult")=QNTRSLT 172 . ; 173 . N SPECCOLL S SPECCOLL=$$ANONS^C0XF2N ; new node for specimen collected 174 . S ZR("sp:specimenCollected")=SPECCOLL 175 . ; 176 . D ADDINN^C0XF2N(C0SGRF,RSLTID,.ZR) ; addIfNotNull the triples 177 . K ZR ; clean up 178 . ; 179 . ; create the narrative result graph 180 . ; 181 . N IVAL S IVAL=$G(@LRN@("interpretation@value"))'="" D ; H OR L 182 . I IVAL'="" 183 . . S ZR("rdf:type")="sp:NarrativeResult" 184 . . S ZR("sp:value")=$G(@LRN@("interpretation@value")) ; H or L 185 . . I ZR("sp:value")="L" S ZR("sp:value")="abnormal" 186 . . I ZR("sp:value")="H" S ZR("sp:value")="abnormal" 187 . . I ZR("sp:value")="HH" S ZR("sp:value")="critical" 188 . . I ZR("sp:value")="LL" S ZR("sp:value")="critical" 189 . . D ADDINN^C0XF2N(C0SGRF,NARRSLT,.ZR) 190 . . K ZR 191 . ; 192 . ; create the quantitative result graph 193 . ; 194 . S ZR("rdf:type")="sp:QuantitativeResult" 195 . N NORMNM S NORMNM=$$ANONS^C0XF2N ; new node for normal range graph 196 . N VUNM S VUNM=$$ANONS^C0XF2N ; new node for value and unit graph 197 . N HASNORMAL S HASNORMAL=0 198 . I $G(@LRN@("high@value"))'="" S HASNORMAL=1 199 . I HASNORMAL S ZR("sp:normalRange")=NORMNM 200 . S ZR("sp:valueAndUnit")=VUNM 201 . D ADDINN^C0XF2N(C0SGRF,QNTRSLT,.ZR) 202 . K ZR 203 . ; 204 . ; create the normal range graph 205 . ; 206 . I HASNORMAL D ; 207 . . S ZR("rdf:type")="sp:ValueRange" 208 . . N MAXNM S MAXNM=$$ANONS^C0XF2N ; new node for maximum graph 209 . . N MINNM S MINNM=$$ANONS^C0XF2N ; new node for minimum graph 210 . . S ZR("sp:maximum")=MAXNM 211 . . S ZR("sp:minimum")=MINNM 212 . . D ADDINN^C0XF2N(C0SGRF,NORMNM,.ZR) 213 . . K ZR 214 . . ; 215 . . ; create the maximum graph 216 . . ; 217 . . S ZR("rdf:type")="sp:ValueAndUnit" 218 . . S ZR("sp:unit")=$G(@LRN@("units@value")) 219 . . S ZR("sp:value")=$G(@LRN@("high@value")) 220 . . D ADDINN^C0XF2N(C0SGRF,MAXNM,.ZR) 221 . . K ZR 222 . . ; 223 . . ; create the minimum graph 224 . . ; 225 . . S ZR("rdf:type")="sp:ValueAndUnit" 226 . . S ZR("sp:unit")=$G(@LRN@("units@value")) 227 . . S ZR("sp:value")=$G(@LRN@("low@value")) 228 . . D ADDINN^C0XF2N(C0SGRF,MINNM,.ZR) 229 . . K ZR 230 . ; 231 . ; create the value and unit graph 232 . ; 233 . S ZR("rdf:type")="sp:ValueAndUnit" 234 . S ZR("sp:unit")=$G(@LRN@("units@value")) 235 . I ZR("sp:unit")="" S ZR("sp:unit")="{unknown}" ;$G(@LRN@("test@value")) 236 . S ZR("sp:value")=$G(@LRN@("result@value")) 237 . D ADDINN^C0XF2N(C0SGRF,VUNM,.ZR) 238 . K ZR 239 . ; 240 . ; create specimen collected graph 241 . ; 242 . S ZR("rdf:type")="sp:Attribution" 243 . S ZR("sp:startDate")=$$SPDATE^C0SUTIL($G(@LRN@("collected@value"))) 244 . D ADDINN^C0XF2N(C0SGRF,SPECCOLL,.ZR) 245 . K ZR 246 . ; 247 . ; create lab name graph - this contains the test name and code 248 . ; 249 . I LOINC'="" D ; 250 . . S ZR("rdf:type")="sp:CodedValue" 251 . . S ZR("dcterms:title")=LABTST 252 . . N LOINCNM S LOINCNM="loinc:"_LOINC 253 . . S ZR("sp:code")="loinc:"_LOINC 254 . . D ADDINN^C0XF2N(C0SGRF,LABNAME,.ZR) 255 . . K ZR 256 . . S ZR("dcterms:identifier")=LOINC 257 . . S ZR("dcterms:title")=LABTST 258 . . S ZR("rdf:type")="sp:Code" 259 . . S ZR("sp:system")="http://loinc.org/codes/" 260 . . D ADDINN^C0XF2N(C0SGRF,LOINCNM,.ZR) 261 . . K ZR 262 . ; 263 . ; that's all for now folks (there is more to do like reference ranges 264 . ; and result values) 265 . ; 266 D BULKLOAD^C0XF2N(.C0XFDA) 267 S GRTN=C0SGRF 268 Q 269 ; 270 SAMPLE ; import sample lab tests to the triplestore 271 N GN 272 S GN=$NA(^rdf("lab_results")) 273 D INSRDF^C0XF2N(GN,"/smart/lab/samples") 274 Q 275 ;
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