source: smart/trunk/p/C0SLAB.m@ 1767

Last change on this file since 1767 was 1591, checked in by Sam Habiel, 12 years ago

Updated license for routines
File size: 10.6 KB
Line 
1C0SLAB ; GPL - Smart Lab Processing ;4/15/12 17:05
2 ;;1.0;VISTA SMART CONTAINER;;Sep 26, 2012;Build 5
3 ;Copyright 2012 George Lilly.
4 ;
5 ; This program is free software: you can redistribute it and/or modify
6 ; it under the terms of the GNU Affero General Public License as
7 ; published by the Free Software Foundation, either version 3 of the
8 ; License, or (at your option) any later version.
9 ;
10 ; This program is distributed in the hope that it will be useful,
11 ; but WITHOUT ANY WARRANTY; without even the implied warranty of
12 ; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 ; GNU Affero General Public License for more details.
14 ;
15 ; You should have received a copy of the GNU Affero General Public License
16 ; along with this program. If not, see <http://www.gnu.org/licenses/>.
17 ;
18 Q
19 ;
20 ; sample VistA NHIN lab result
21 ;
22 ;^TMP("C0STBL",32,"lab",8,"collected@value")=3110626.16
23 ;^TMP("C0STBL",32,"lab",8,"comment")="Report Released Date/Time: Jun 26, 2011@19:00"
24 ;^TMP("C0STBL",32,"lab",8,"comment@xml:space")="preserve"
25 ;^TMP("C0STBL",32,"lab",8,"facility@code")=100
26 ;^TMP("C0STBL",32,"lab",8,"facility@name")="VOE OFFICE INSTITUTION"
27 ;^TMP("C0STBL",32,"lab",8,"groupName@value")="CH 0626 47"
28 ;^TMP("C0STBL",32,"lab",8,"high@value")=" 101"
29 ;^TMP("C0STBL",32,"lab",8,"id@value")="CH;6889372.84;67003"
30 ;^TMP("C0STBL",32,"lab",8,"interpretation@value")="H"
31 ;^TMP("C0STBL",32,"lab",8,"labOrderID@value")=336
32 ;^TMP("C0STBL",32,"lab",8,"localName@value")="FBLDGLU"
33 ;^TMP("C0STBL",32,"lab",8,"loinc@value")="14771-0"
34 ;^TMP("C0STBL",32,"lab",8,"low@value")="69 "
35 ;^TMP("C0STBL",32,"lab",8,"orderID@value")=807
36 ;^TMP("C0STBL",32,"lab",8,"result@value")=178
37 ;^TMP("C0STBL",32,"lab",8,"resulted@value")=3110626.190006
38 ;^TMP("C0STBL",32,"lab",8,"sample@value")="SERUM"
39 ;^TMP("C0STBL",32,"lab",8,"specimen@code")="0X500"
40 ;^TMP("C0STBL",32,"lab",8,"specimen@name")="SERUM"
41 ;^TMP("C0STBL",32,"lab",8,"status@value")="completed"
42 ;^TMP("C0STBL",32,"lab",8,"test@value")="FASTING BLOOD GLUCOSE"
43 ;^TMP("C0STBL",32,"lab",8,"type@value")="CH"
44 ;^TMP("C0STBL",32,"lab",8,"units@value")="MG/DL"
45 ;^TMP("C0STBL",32,"lab",8,"vuid@value")=4656342
46 ;
47 ; sample Smart lab result triples
48 ;
49 ;G("loinc:29571-7","dcterms:identifier")="29571-7"
50 ;G("loinc:29571-7","dcterms:title")="Phe DBS Ql"
51 ;G("loinc:29571-7","rdf:type")="sp:Code"
52 ;G("loinc:29571-7","sp:system")="http://loinc.org/codes/"
53 ;G("loinc:38478-4","dcterms:identifier")="38478-4"
54 ;G("loinc:38478-4","dcterms:title")="Biotinidase DBS Ql"
55 ;G("loinc:38478-4","rdf:type")="sp:Code"
56 ;G("loinc:38478-4","sp:system")="http://loinc.org/codes/"
57 ;G("qqWZZIew993","rdf:type")="sp:Attribution"
58 ;G("qqWZZIew993","sp:startDate")="2007-04-21"
59 ;G("qqWZZIew994","rdf:type")="sp:NarrativeResult"
60 ;G("qqWZZIew994","sp:value")="Normal"
61 ;G("qqWZZIew995","dcterms:title")="Biotinidase DBS Ql"
62 ;G("qqWZZIew995","rdf:type")="sp:CodedValue"
63 ;G("qqWZZIew995","sp:code")="loinc:38478-4"
64 ;G("qqWZZIew997","rdf:type")="sp:Attribution"
65 ;G("qqWZZIew997","sp:startDate")="2007-09-08"
66 ;G("qqWZZIew998","rdf:type")="sp:NarrativeResult"
67 ;G("qqWZZIew998","sp:value")="Normal"
68 ;G("qqWZZIew999","dcterms:title")="Phe DBS Ql"
69 ;G("qqWZZIew999","rdf:type")="sp:CodedValue"
70 ;G("qqWZZIew999","sp:code")="loinc:29571-7"
71 ;G("smart:99912345/lab_results/3d9b39249193","rdf:type")="sp:LabResult"
72 ;G("smart:99912345/lab_results/3d9b39249193","sp:belongsTo")="smart:99912345"
73 ;G("smart:99912345/lab_results/3d9b39249193","sp:labName")="qqWZZIew995"
74 ;G("smart:99912345/lab_results/3d9b39249193","sp:narrativeResult")="qqWZZIew994"
75 ;G("smart:99912345/lab_results/3d9b39249193","sp:specimenCollected")="qqWZZIew993"
76 ;G("smart:99912345/lab_results/426c7adc4f54","rdf:type")="sp:LabResult"
77 ;G("smart:99912345/lab_results/426c7adc4f54","sp:belongsTo")="smart:99912345"
78 ;G("smart:99912345/lab_results/426c7adc4f54","sp:labName")="qqWZZIew999"
79 ;G("smart:99912345/lab_results/426c7adc4f54","sp:narrativeResult")="qqWZZIew998"
80 ;G("smart:99912345/lab_results/426c7adc4f54","sp:specimenCollected")="qqWZZIew997"
81 ;
82 ;
83 ; another Smart example, this one with sp:quantitativeResult
84 ;
85 ;G("loinc:786-4","dcterms:identifier")="786-4"
86 ;G("loinc:786-4","dcterms:title")="MCHC RBC Auto-mCnc"
87 ;G("loinc:786-4","rdf:type")="sp:Code"
88 ;G("loinc:786-4","sp:system")="http://loinc.org/codes/"
89 ;G("nodeID:4439","rdf:type")="sp:ValueAndUnit"
90 ;G("nodeID:4439","sp:unit")="g/dL"
91 ;G("nodeID:4439","sp:value")=36.6
92 ;G("nodeID:4613","rdf:type")="sp:ValueAndUnit"
93 ;G("nodeID:4613","sp:unit")="g/dL"
94 ;G("nodeID:4613","sp:value")=32
95 ;G("nodeID:4672","rdf:type")="sp:Attribution"
96 ;G("nodeID:4672","sp:startDate")="2005-03-10"
97 ;G("nodeID:4866","rdf:type")="sp:ValueAndUnit"
98 ;G("nodeID:4866","sp:unit")="g/dL"
99 ;G("nodeID:4866","sp:value")=36
100 ;G("nodeID:4871","dcterms:title")="MCHC RBC Auto-mCnc"
101 ;G("nodeID:4871","rdf:type")="sp:CodedValue"
102 ;G("nodeID:4871","sp:code")="loinc:786-4"
103 ;G("nodeID:5221","rdf:type")="sp:QuantitativeResult"
104 ;G("nodeID:5221","sp:normalRange")="nodeID:5282"
105 ;G("nodeID:5221","sp:valueAndUnit")="nodeID:4439"
106 ;G("nodeID:5282","rdf:type")="sp:ValueRange"
107 ;G("nodeID:5282","sp:maximum")="nodeID:4866"
108 ;G("nodeID:5282","sp:minimum")="nodeID:4613"
109 ;G("smart:1540505/lab_results/2fc100850766","rdf:type")="sp:LabResult"
110 ;G("smart:1540505/lab_results/2fc100850766","sp:belongsTo")="smart:1540505"
111 ;G("smart:1540505/lab_results/2fc100850766","sp:labName")="nodeID:4871"
112 ;G("smart:1540505/lab_results/2fc100850766","sp:quantitativeResult")="nodeID:5221"
113 ;G("smart:1540505/lab_results/2fc100850766","sp:specimenCollected")="nodeID:4672"
114 ;
115LAB(GRTN,C0SARY) ; GRTN, passed by reference,
116 ; is the return name of the graph created. "" if none
117 ; C0SARY is passed in by reference and is the NHIN array of lab
118 ;
119 I $O(C0SARY("lab",""))="" D Q ;
120 . I $D(DEBUG) W !,"No Labs"
121 S GRTN="" ; default to no labs
122 N C0SGRF
123 S C0SGRF="vistaSmart:"_ZPATID_"/lab_results"
124 I $D(DEBUG) W !,"Processing ",C0SGRF
125 D DELGRAPH^C0XF2N(C0SGRF) ; delete the old graph
126 D INITFARY^C0XF2N("C0XFARY") ; which triple store to use
127 N FARY S FARY="C0XFARY"
128 D USEFARY^C0XF2N(FARY)
129 D VOCINIT^C0XUTIL
130 ;
131 D STARTADD^C0XF2N ; initialize to create triples
132 ;
133 N ZI S ZI=""
134 F S ZI=$O(C0SARY("lab",ZI)) Q:ZI="" D ;
135 . N LRN,ZR ; ZR is the local array for building the new triples
136 . S LRN=$NA(C0SARY("lab",ZI)) ; base for values in this lab result
137 . ;
138 . N RSLTID ; unique Id for this lab result
139 . S RSLTID=C0SGRF_"/"_$$LKY17^C0XF2N ; use a random number
140 . ;
141 . ; i don't like this because the same labs result gets a
142 . ; different ID every time it's reported. Can't trace it back to VistA
143 . ; I'd rather be using id@value ie "id@value")="CH;6889372.84;67003"
144 . ; .. either that or store an OID with the lab result - but that
145 . ; will have to wait for the redesign of file 60.. - gpl 4/16/2012
146 . ;
147 . N LOINC S LOINC=$G(@LRN@("loinc@value"))
148 . I LOINC="" D Q ;
149 . . I $D(DEBUG) W !,"NO LOINC VALUE, SKIPPING"
150 . N LABTST S LABTST=$G(@LRN@("test@value"))
151 . I $D(DEBUG) D ;
152 . . W !,"Processing Lab Result ",RSLTID
153 . . W !,"test: ",LABTST
154 . . W !,"loinc: ",LOINC
155 . ;
156 . ; first do the base result graph
157 . ;
158 . S ZR("rdf:type")="sp:LabResult"
159 . S ZR("sp:belongsTo")=C0SGRF ; the subject for this patient's lab results
160 . ; ie /vista/smart/99912345/lab_results
161 . ;
162 . N LABNAME S LABNAME=$$ANONS^C0XF2N ; new node for lab name
163 . S ZR("sp:labName")=LABNAME
164 . ;
165 . N NARRSLT S NARRSLT=$$ANONS^C0XF2N ; new node for narrative result
166 . S ZR("sp:narrativeResult")=NARRSLT
167 . ;
168 . N QNTRSLT S QNTRSLT=$$ANONS^C0XF2N ; new node for narrative result
169 . S ZR("sp:quantitativeResult")=QNTRSLT
170 . ;
171 . N SPECCOLL S SPECCOLL=$$ANONS^C0XF2N ; new node for specimen collected
172 . S ZR("sp:specimenCollected")=SPECCOLL
173 . ;
174 . D ADDINN^C0XF2N(C0SGRF,RSLTID,.ZR) ; addIfNotNull the triples
175 . K ZR ; clean up
176 . ;
177 . ; create the narrative result graph
178 . ;
179 . N IVAL S IVAL=$G(@LRN@("interpretation@value"))'="" D ; H OR L
180 . I IVAL'=""
181 . . S ZR("rdf:type")="sp:NarrativeResult"
182 . . S ZR("sp:value")=$G(@LRN@("interpretation@value")) ; H or L
183 . . I ZR("sp:value")="L" S ZR("sp:value")="abnormal"
184 . . I ZR("sp:value")="H" S ZR("sp:value")="abnormal"
185 . . I ZR("sp:value")="HH" S ZR("sp:value")="critical"
186 . . I ZR("sp:value")="LL" S ZR("sp:value")="critical"
187 . . D ADDINN^C0XF2N(C0SGRF,NARRSLT,.ZR)
188 . . K ZR
189 . ;
190 . ; create the quantitative result graph
191 . ;
192 . S ZR("rdf:type")="sp:QuantitativeResult"
193 . N NORMNM S NORMNM=$$ANONS^C0XF2N ; new node for normal range graph
194 . N VUNM S VUNM=$$ANONS^C0XF2N ; new node for value and unit graph
195 . N HASNORMAL S HASNORMAL=0
196 . I $G(@LRN@("high@value"))'="" S HASNORMAL=1
197 . I HASNORMAL S ZR("sp:normalRange")=NORMNM
198 . S ZR("sp:valueAndUnit")=VUNM
199 . D ADDINN^C0XF2N(C0SGRF,QNTRSLT,.ZR)
200 . K ZR
201 . ;
202 . ; create the normal range graph
203 . ;
204 . I HASNORMAL D ;
205 . . S ZR("rdf:type")="sp:ValueRange"
206 . . N MAXNM S MAXNM=$$ANONS^C0XF2N ; new node for maximum graph
207 . . N MINNM S MINNM=$$ANONS^C0XF2N ; new node for minimum graph
208 . . S ZR("sp:maximum")=MAXNM
209 . . S ZR("sp:minimum")=MINNM
210 . . D ADDINN^C0XF2N(C0SGRF,NORMNM,.ZR)
211 . . K ZR
212 . . ;
213 . . ; create the maximum graph
214 . . ;
215 . . S ZR("rdf:type")="sp:ValueAndUnit"
216 . . S ZR("sp:unit")=$G(@LRN@("units@value"))
217 . . S ZR("sp:value")=$G(@LRN@("high@value"))
218 . . D ADDINN^C0XF2N(C0SGRF,MAXNM,.ZR)
219 . . K ZR
220 . . ;
221 . . ; create the minimum graph
222 . . ;
223 . . S ZR("rdf:type")="sp:ValueAndUnit"
224 . . S ZR("sp:unit")=$G(@LRN@("units@value"))
225 . . S ZR("sp:value")=$G(@LRN@("low@value"))
226 . . D ADDINN^C0XF2N(C0SGRF,MINNM,.ZR)
227 . . K ZR
228 . ;
229 . ; create the value and unit graph
230 . ;
231 . S ZR("rdf:type")="sp:ValueAndUnit"
232 . S ZR("sp:unit")=$G(@LRN@("units@value"))
233 . I ZR("sp:unit")="" S ZR("sp:unit")="{unknown}" ; was $G(@LRN@("test@value")) gpl
234 . S ZR("sp:value")=$G(@LRN@("result@value"))
235 . D ADDINN^C0XF2N(C0SGRF,VUNM,.ZR)
236 . K ZR
237 . ;
238 . ; create specimen collected graph
239 . ;
240 . S ZR("rdf:type")="sp:Attribution"
241 . S ZR("sp:startDate")=$$SPDATE^C0SUTIL($G(@LRN@("collected@value")))
242 . D ADDINN^C0XF2N(C0SGRF,SPECCOLL,.ZR)
243 . K ZR
244 . ;
245 . ; create lab name graph - this contains the test name and code
246 . ;
247 . I LOINC'="" D ;
248 . . S ZR("rdf:type")="sp:CodedValue"
249 . . S ZR("dcterms:title")=LABTST
250 . . N LOINCNM S LOINCNM="loinc:"_LOINC
251 . . S ZR("sp:code")="loinc:"_LOINC
252 . . D ADDINN^C0XF2N(C0SGRF,LABNAME,.ZR)
253 . . K ZR
254 . . S ZR("dcterms:identifier")=LOINC
255 . . S ZR("dcterms:title")=LABTST
256 . . S ZR("rdf:type")="sp:Code"
257 . . S ZR("sp:system")="http://loinc.org/codes/"
258 . . D ADDINN^C0XF2N(C0SGRF,LOINCNM,.ZR)
259 . . K ZR
260 . ;
261 . ; that's all for now folks (there is more to do like reference ranges
262 . ; and result values)
263 . ;
264 D BULKLOAD^C0XF2N(.C0XFDA)
265 S GRTN=C0SGRF
266 Q
267 ;
268SAMPLE ; import sample lab tests to the triplestore
269 N GN
270 S GN=$NA(^rdf("lab_results"))
271 D INSRDF^C0XF2N(GN,"/smart/lab/samples")
272 Q
273 ;
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