-
Notifications
You must be signed in to change notification settings - Fork 14
/
Copy pathFHIRCommon.cql
278 lines (246 loc) · 14.4 KB
/
FHIRCommon.cql
1
2
3
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
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
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
271
272
273
274
275
276
277
278
library FHIRCommon version '4.1.000'
using FHIR version '4.0.1'
include FHIRHelpers version '4.1.000'
codesystem "LOINC": 'http://loinc.org'
codesystem "SNOMEDCT": 'http://snomed.info/sct'
codesystem "RoleCode": 'http://terminology.hl7.org/CodeSystem/v3-RoleCode'
codesystem "Diagnosis Role": 'http://terminology.hl7.org/CodeSystem/diagnosis-role'
codesystem "RequestIntent": 'http://terminology.hl7.org/CodeSystem/request-intent'
codesystem "MedicationRequestCategory": 'http://terminology.hl7.org/CodeSystem/medicationrequest-category'
codesystem "ConditionClinicalStatusCodes": 'http://terminology.hl7.org/CodeSystem/condition-clinical'
codesystem "ConditionVerificationStatusCodes": 'http://terminology.hl7.org/CodeSystem/condition-ver-status'
codesystem "AllergyIntoleranceClinicalStatusCodes": 'http://terminology.hl7.org/CodeSystem/allergyintolerance-clinical'
codesystem "AllergyIntoleranceVerificationStatusCodes": 'http://terminology.hl7.org/CodeSystem/allergyintolerance-verification'
//Currently unresolveable in VSAC:
//valueset "Active Condition": 'http://fhir.org/guides/cqf/common/ValueSet/active-condition'
//valueset "Inactive Condition": 'http://fhir.org/guides/cqf/common/ValueSet/inactive-condition'
code "Birthdate": '21112-8' from "LOINC" display 'Birth date'
code "Dead": '419099009' from "SNOMEDCT" display 'Dead'
code "ER": 'ER' from "RoleCode" display 'Emergency room'
code "ICU": 'ICU' from "RoleCode" display 'Intensive care unit'
code "Billing": 'billing' from "Diagnosis Role" display 'Billing'
// Condition Clinical Status Codes - Consider value sets for these
code "active": 'active' from "ConditionClinicalStatusCodes"
code "recurrence": 'recurrence' from "ConditionClinicalStatusCodes"
code "relapse": 'relapse' from "ConditionClinicalStatusCodes"
code "inactive": 'inactive' from "ConditionClinicalStatusCodes"
code "remission": 'remission' from "ConditionClinicalStatusCodes"
code "resolved": 'resolved' from "ConditionClinicalStatusCodes"
// Condition Verification Status Codes - Consider value sets for these
code "unconfirmed": 'unconfirmed' from ConditionVerificationStatusCodes
code "provisional": 'provisional' from ConditionVerificationStatusCodes
code "differential": 'differential' from ConditionVerificationStatusCodes
code "confirmed": 'confirmed' from ConditionVerificationStatusCodes
code "refuted": 'refuted' from ConditionVerificationStatusCodes
code "entered-in-error": 'entered-in-error' from ConditionVerificationStatusCodes
code "allergy-active": 'active' from "AllergyIntoleranceClinicalStatusCodes"
code "allergy-inactive": 'inactive' from "AllergyIntoleranceClinicalStatusCodes"
code "allergy-resolved": 'resolved' from "AllergyIntoleranceClinicalStatusCodes"
// Allergy/Intolerance Verification Status Codes - Consider value sets for these
code "allergy-unconfirmed": 'unconfirmed' from AllergyIntoleranceVerificationStatusCodes
code "allergy-confirmed": 'confirmed' from AllergyIntoleranceVerificationStatusCodes
code "allergy-refuted": 'refuted' from AllergyIntoleranceVerificationStatusCodes
// MedicationRequest Category Codes
code "Community": 'community' from "MedicationRequestCategory" display 'Community'
code "Discharge": 'discharge' from "MedicationRequestCategory" display 'Discharge'
// Diagnosis Role Codes
code "AD": 'AD' from "Diagnosis Role" display 'Admission diagnosis'
code "DD": 'DD' from "Diagnosis Role" display 'Discharge diagnosis'
code "CC": 'CC' from "Diagnosis Role" display 'Chief complaint'
code "CM": 'CM' from "Diagnosis Role" display 'Comorbidity diagnosis'
code "pre-op": 'pre-op' from "Diagnosis Role" display 'pre-op diagnosis'
code "post-op": 'post-op' from "Diagnosis Role" display 'post-op diagnosis'
code "billing": 'billing' from "Diagnosis Role" display 'billing diagnosis'
context Patient
/*
@description: Normalizes a value that is a choice of timing-valued types to an equivalent interval
@comment: Normalizes a choice type of FHIR.dateTime, FHIR.Period, FHIR.Timing, FHIR.instance, FHIR.string, FHIR.Age, or FHIR.Range types
to an equivalent interval. This selection of choice types is a superset of the majority of choice types that are used as possible
representations for timing-valued elements in FHIR, allowing this function to be used across any resource. NOTE: Due to the
complexity of determining a single interval from a Timing or String type, this function will throw a run-time exception if it is used
with a Timing or String.
*/
define function ToInterval(choice Choice<FHIR.dateTime, FHIR.Period, FHIR.Timing, FHIR.instant, FHIR.string, FHIR.Age, FHIR.Range>):
case
when choice is FHIR.dateTime then
Interval[FHIRHelpers.ToDateTime(choice as FHIR.dateTime), FHIRHelpers.ToDateTime(choice as FHIR.dateTime)]
when choice is FHIR.Period then
FHIRHelpers.ToInterval(choice as FHIR.Period)
when choice is FHIR.instant then
Interval[FHIRHelpers.ToDateTime(choice as FHIR.instant), FHIRHelpers.ToDateTime(choice as FHIR.instant)]
when choice is FHIR.Age then
Interval[FHIRHelpers.ToDate(Patient.birthDate) + FHIRHelpers.ToQuantity(choice as FHIR.Age),
FHIRHelpers.ToDate(Patient.birthDate) + FHIRHelpers.ToQuantity(choice as FHIR.Age) + 1 year)
when choice is FHIR.Range then
Interval[FHIRHelpers.ToDate(Patient.birthDate) + FHIRHelpers.ToQuantity((choice as FHIR.Range).low),
FHIRHelpers.ToDate(Patient.birthDate) + FHIRHelpers.ToQuantity((choice as FHIR.Range).high) + 1 year)
when choice is FHIR.Timing then
Message(null as Interval<DateTime>, true, '1', 'Error', 'Cannot compute a single interval from a Timing type')
when choice is FHIR.string then
Message(null as Interval<DateTime>, true, '1', 'Error', 'Cannot compute an interval from a String value')
else
null as Interval<DateTime>
end
/*
@description: Returns an interval representing the normalized Abatement of a given Condition resource.
@comment: NOTE: Due to the complexity of determining an interval from a String, this function will throw
a run-time exception if used with a Condition instance that has a String as the abatement value.
*/
define function ToAbatementInterval(condition Condition):
if condition.abatement is FHIR.dateTime then
Interval[FHIRHelpers.ToDateTime(condition.abatement as FHIR.dateTime), FHIRHelpers.ToDateTime(condition.abatement as FHIR.dateTime)]
else if condition.abatement is FHIR.Period then
FHIRHelpers.ToInterval(condition.abatement as FHIR.Period)
else if condition.abatement is FHIR.string then
Message(null as Interval<DateTime>, true, '1', 'Error', 'Cannot compute an interval from a String value')
else if condition.abatement is FHIR.Age then
Interval[FHIRHelpers.ToDate(Patient.birthDate) + FHIRHelpers.ToQuantity(condition.abatement as FHIR.Age),
FHIRHelpers.ToDate(Patient.birthDate) + FHIRHelpers.ToQuantity(condition.abatement as FHIR.Age) + 1 year)
else if condition.abatement is FHIR.Range then
Interval[FHIRHelpers.ToDate(Patient.birthDate) + FHIRHelpers.ToQuantity((condition.abatement as FHIR.Range).low),
FHIRHelpers.ToDate(Patient.birthDate) + FHIRHelpers.ToQuantity((condition.abatement as FHIR.Range).high) + 1 year)
else if condition.abatement is FHIR.boolean then
Interval[end of ToInterval(condition.onset), condition.recordedDate)
else null
/*
@description: Returns an interval representing the normalized prevalence period of a given Condition resource.
@comment: Uses the ToInterval and ToAbatementInterval functions to determine the widest potential interval from
onset to abatement as specified in the given Condition.
*/
define function ToPrevalenceInterval(condition Condition):
if condition.clinicalStatus ~ "active"
or condition.clinicalStatus ~ "recurrence"
or condition.clinicalStatus ~ "relapse" then
Interval[start of ToInterval(condition.onset), end of ToAbatementInterval(condition)]
else
Interval[start of ToInterval(condition.onset), end of ToAbatementInterval(condition))
/*
@description: Returns any extensions defined on the given resource with the specified url.
@comment: NOTE: Extensions are not the preferred approach, but are used as a way to access
content that is defined by extensions but not yet surfaced in the
CQL model info.
*/
define function Extensions(domainResource DomainResource, url String):
domainResource.extension E
where E.url = url
return E
/*
@description: Returns the single extension (if present) on the given resource with the specified url.
@comment: This function uses singleton from to ensure that a run-time exception is thrown if there
is more than one extension on the given resource with the specified url.
*/
define function Extension(domainResource DomainResource, url String):
singleton from "Extensions"(domainResource, url)
/*
@description: Returns any extensions defined on the given element with the specified url.
@comment: NOTE: Extensions are not the preferred approach, but are used as a way to access
content that is defined by extensions but not yet surfaced in the CQL model info.
*/
define function Extensions(element Element, url String):
element.extension E
where E.url = url
return E
/*
@description: Returns the single extension (if present) on the given element with the specified url.
@comment: This function uses singleton from to ensure that a run-time exception is thrown if there
is more than one extension on the given resource with the specified url.
*/
define function Extension(element Element, url String):
singleton from Extensions(element, url)
/*
@description: Returns any modifier extensions defined on the given resource with the specified url.
@comment: NOTE: Extensions are not the preferred approach, but are used as a way to access
content that is defined by extensions but not yet surfaced in the
CQL model info.
*/
define function ModifierExtensions(domainResource DomainResource, url String):
domainResource.modifierExtension E
where E.url = url
return E
/*
@description: Returns the single modifier extension (if present) on the given resource with the specified url.
@comment: This function uses singleton from to ensure that a run-time exception is thrown if there
is more than one extension on the given resource with the specified url.
*/
define function ModifierExtension(domainResource DomainResource, url String):
singleton from ModifierExtensions(domainResource, url)
/*
@description: Returns any modifier extensions defined on the given element with the specified url.
@comment: NOTE: Extensions are not the preferred approach, but are used as a way to access
content that is defined by extensions but not yet surfaced in the CQL model info.
*/
define function ModifierExtensions(element BackboneElement, url String):
element.modifierExtension E
where E.url = url
return E
/*
@description: Returns the single modifier extension (if present) on the given element with the specified url.
@comment: This function uses singleton from to ensure that a run-time exception is thrown if there
is more than one extension on the given resource with the specified url.
*/
define function ModifierExtension(element BackboneElement, url String):
singleton from ModifierExtensions(element, url)
/*
@description: Returns any base-FHIR extensions defined on the given resource with the specified id.
@comment: NOTE: Extensions are not the preferred approach, but are used as a way to access
content that is defined by extensions but not yet surfaced in the CQL model info.
*/
define function BaseExtensions(domainResource DomainResource, id String):
domainResource.extension E
where E.url = ('http://hl7.org/fhir/StructureDefinition/' + id)
return E
/*
@description: Returns the single base-FHIR extension (if present) on the given resource with the specified id.
@comment: This function uses singleton from to ensure that a run-time exception is thrown if there
is more than one extension on the given resource with the specified url.
*/
define function BaseExtension(domainResource DomainResource, id String):
singleton from BaseExtensions(domainResource, id)
/*
@description: Returns any base-FHIR extensions defined on the given element with the specified id.
@comment: NOTE: Extensions are not the preferred approach, but are used as a way to access
content that is defined by extensions but not yet surfaced in the CQL model info.
*/
define function BaseExtensions(element Element, id String):
element.extension E
where E.url = ('http://hl7.org/fhir/StructureDefinition/' + id)
return E
/*
@description: Returns the single base-FHIR extension (if present) on the given element with the specified id.
@comment: This function uses singleton from to ensure that a run-time exception is thrown if there
is more than one extension on the given resource with the specified url.
*/
define function BaseExtension(element Element, id String):
singleton from BaseExtensions(element, id)
/*
@description: Returns any base-FHIR modifier extensions defined on the given resource with the specified id.
@comment: NOTE: Extensions are not the preferred approach, but are used as a way to access
content that is defined by extensions but not yet surfaced in the CQL model info.
*/
define function BaseModifierExtensions(domainResource DomainResource, id String):
domainResource.modifierExtension E
where E.url = ('http://hl7.org/fhir/StructureDefinition/' + id)
return E
/*
@description: Returns the single base-FHIR modifier extension (if present) on the given resource with the specified id.
@comment: This function uses singleton from to ensure that a run-time exception is thrown if there
is more than one extension on the given resource with the specified url.
*/
define function BaseModifierExtension(domainResource DomainResource, id String):
singleton from BaseModifierExtensions(domainResource, id)
/*
@description: Returns any base-FHIR modifier extensions defined on the given element with the specified id.
@comment: NOTE: Extensions are not the preferred approach, but are used as a way to access
content that is defined by extensions but not yet surfaced in the CQL model info.
*/
define function BaseModifierExtensions(element BackboneElement, id String):
element.modifierExtension E
where E.url = ('http://hl7.org/fhir/StructureDefinition/' + id)
return E
/*
@description: Returns the single base-FHIR extension (if present) on the given element with the specified id.
@comment: This function uses singleton from to ensure that a run-time exception is thrown if there
is more than one extension on the given resource with the specified url.
*/
define function BaseModifierExtension(element BackboneElement, id String):
singleton from BaseModifierExtensions(element, id)