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Support FHIR R6
Closes: #2892
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+1518
-558714
lines changed

‎.github/scripts/check-capability-statement-terminology-service.sh‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -10,7 +10,7 @@ test "status" "$(echo "$CAPABILITY_STATEMENT" | jq -r .status)" "active"
1010
test "kind" "$(echo "$CAPABILITY_STATEMENT" | jq -r .kind)" "instance"
1111
test "software name" "$(echo "$CAPABILITY_STATEMENT" | jq -r .software.name)" "Blaze"
1212
test "URL" "$(echo "$CAPABILITY_STATEMENT" | jq -r .implementation.url)" "http://localhost:8080/fhir"
13-
test "FHIR version" "$(echo "$CAPABILITY_STATEMENT" | jq -r .fhirVersion)" "4.0.1"
13+
test "FHIR version" "$(echo "$CAPABILITY_STATEMENT" | jq -r .fhirVersion)" "6.0.0-ballot3"
1414
test "format" "$(echo "$CAPABILITY_STATEMENT" | jq -r '.format | join(",")')" "application/fhir+json,application/fhir+xml"
1515

1616
test "Operation CodeSystem \$validate-code Definition" "$(echo "$CAPABILITY_STATEMENT" | jq -r '.rest[0].resource[] | select(.type == "CodeSystem") .operation[] | select(.name == "validate-code") | .definition')" "http://hl7.org/fhir/OperationDefinition/CodeSystem-validate-code"

‎.github/scripts/check-capability-statement.sh‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -10,7 +10,7 @@ test "status" "$(echo "$CAPABILITY_STATEMENT" | jq -r .status)" "active"
1010
test "kind" "$(echo "$CAPABILITY_STATEMENT" | jq -r .kind)" "instance"
1111
test "software name" "$(echo "$CAPABILITY_STATEMENT" | jq -r .software.name)" "Blaze"
1212
test "URL" "$(echo "$CAPABILITY_STATEMENT" | jq -r .implementation.url)" "http://localhost:8080/fhir"
13-
test "FHIR version" "$(echo "$CAPABILITY_STATEMENT" | jq -r .fhirVersion)" "4.0.1"
13+
test "FHIR version" "$(echo "$CAPABILITY_STATEMENT" | jq -r .fhirVersion)" "6.0.0-ballot3"
1414
test "format" "$(echo "$CAPABILITY_STATEMENT" | jq -r '.format | join(",")')" "application/fhir+json,application/fhir+xml"
1515

1616
test "Patient Profile" "$(echo "$CAPABILITY_STATEMENT" | jq -r '.rest[0].resource[] | select(.type == "Patient") .profile')" "http://hl7.org/fhir/StructureDefinition/Patient"

‎.github/scripts/check-resource-totals-after-patient-purge.sh‎

Lines changed: 1 addition & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -6,30 +6,12 @@ SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
66
BASE="http://localhost:8080/fhir"
77
ACTUAL_TOTALS="$(curl -sH 'Accept: application/fhir+json' "$BASE/\$totals" | jq -r '.parameter[] | [.name, .valueUnsignedInt] | @csv')"
88
EXPECTED_TOTALS="$(cat <<END
9-
"AllergyIntolerance",2
10-
"CarePlan",33
11-
"CareTeam",33
12-
"Claim",1053
13-
"Condition",157
14-
"Device",28
15-
"DiagnosticReport",1113
16-
"DocumentReference",407
17-
"Encounter",407
18-
"ExplanationOfBenefit",407
19-
"Immunization",104
209
"Location",194
2110
"Medication",326
22-
"MedicationAdministration",26
23-
"MedicationRequest",646
24-
"Observation",6944
2511
"Organization",194
26-
"Patient",8
2712
"Practitioner",195
2813
"PractitionerRole",195
29-
"Procedure",307
30-
"Provenance",8
31-
"StructureDefinition",185
32-
"SupplyDelivery",571
14+
"StructureDefinition",204
3315
END
3416
)"
3517

‎.github/scripts/check-resource-totals.sh‎

Lines changed: 1 addition & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -11,16 +11,13 @@ EXPECTED_TOTALS="$(cat <<END
1111
"CareTeam",540
1212
"Claim",9856
1313
"Condition",1597
14-
"Device",28
1514
"DiagnosticReport",8229
1615
"DocumentReference",4769
1716
"Encounter",4769
1817
"ExplanationOfBenefit",4769
19-
"ImagingStudy",145
2018
"Immunization",1616
2119
"Location",194
2220
"Medication",326
23-
"MedicationAdministration",326
2421
"MedicationRequest",5087
2522
"Observation",42929
2623
"Organization",194
@@ -29,7 +26,7 @@ EXPECTED_TOTALS="$(cat <<END
2926
"PractitionerRole",195
3027
"Procedure",3608
3128
"Provenance",120
32-
"StructureDefinition",185
29+
"StructureDefinition",204
3330
"SupplyDelivery",1886
3431
END
3532
)"

‎.github/scripts/graph.sh‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -14,7 +14,7 @@ BUNDLE=$(curl -sH 'Accept: application/fhir+json' "$BASE/Patient/$PATIENT_ID/\$g
1414
ACTUAL_SIZE=$(echo "$BUNDLE" | jq -r .total)
1515
IDS="$(echo "$BUNDLE" | jq -r '.entry[].resource.id')"
1616

17-
test "size" "$ACTUAL_SIZE" "195"
17+
test "size" "$ACTUAL_SIZE" "150"
1818

1919
test "no duplicates" "$(echo "$IDS" | sort -u | wc -l | xargs)" "$(echo "$IDS" | wc -l | xargs)"
2020

‎.github/scripts/graph/GraphDefinition-patient-observation-encounter.json‎

Lines changed: 46 additions & 204 deletions
Original file line numberDiff line numberDiff line change
@@ -1,242 +1,84 @@
11
{
22
"resourceType": "GraphDefinition",
3-
"extension": [
4-
{
5-
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.start",
6-
"valueId": "patient"
7-
},
3+
"url": "patient-observation-encounter",
4+
"name": "patient-observation-encounter",
5+
"status": "active",
6+
"start": "patient",
7+
"node": [
88
{
9-
"extension": [
10-
{
11-
"url": "nodeId",
12-
"valueId": "patient"
13-
},
14-
{
15-
"url": "type",
16-
"valueCode": "Patient"
17-
}
18-
],
19-
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.node"
9+
"nodeId": "patient",
10+
"type": "Patient"
2011
},
2112
{
22-
"extension": [
23-
{
24-
"url": "nodeId",
25-
"valueId": "viral-sinusitis"
26-
},
27-
{
28-
"url": "type",
29-
"valueCode": "Condition"
30-
}
31-
],
32-
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.node"
13+
"nodeId": "viral-sinusitis",
14+
"type": "Condition"
3315
},
3416
{
35-
"extension": [
36-
{
37-
"url": "nodeId",
38-
"valueId": "cisplatin-reason"
39-
},
40-
{
41-
"url": "type",
42-
"valueCode": "Condition"
43-
}
44-
],
45-
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.node"
17+
"nodeId": "cisplatin-reason",
18+
"type": "Condition"
4619
},
4720
{
48-
"extension": [
49-
{
50-
"url": "nodeId",
51-
"valueId": "leukocytes"
52-
},
53-
{
54-
"url": "type",
55-
"valueCode": "Observation"
56-
}
57-
],
58-
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.node"
21+
"nodeId": "leukocytes",
22+
"type": "Observation"
5923
},
6024
{
61-
"extension": [
62-
{
63-
"url": "nodeId",
64-
"valueId": "erythrocytes"
65-
},
66-
{
67-
"url": "type",
68-
"valueCode": "Observation"
69-
}
70-
],
71-
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.node"
25+
"nodeId": "erythrocytes",
26+
"type": "Observation"
7227
},
7328
{
74-
"extension": [
75-
{
76-
"url": "nodeId",
77-
"valueId": "cisplatin"
78-
},
79-
{
80-
"url": "type",
81-
"valueCode": "MedicationAdministration"
82-
}
83-
],
84-
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.node"
29+
"nodeId": "cisplatin",
30+
"type": "MedicationAdministration"
8531
},
8632
{
87-
"extension": [
88-
{
89-
"url": "nodeId",
90-
"valueId": "encounter"
91-
},
92-
{
93-
"url": "type",
94-
"valueCode": "Encounter"
95-
}
96-
],
97-
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.node"
33+
"nodeId": "encounter",
34+
"type": "Encounter"
9835
}
9936
],
100-
"url": "patient-observation-encounter",
101-
"name": "patient-observation-encounter",
102-
"status": "active",
103-
"_start": {
104-
"extension": [
105-
{
106-
"url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
107-
"valueCode": "unsupported"
108-
}
109-
]
110-
},
11137
"link": [
11238
{
113-
"extension": [
114-
{
115-
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.sourceId",
116-
"valueId": "patient"
117-
},
118-
{
119-
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.targetId",
120-
"valueId": "viral-sinusitis"
121-
},
122-
{
123-
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.params",
124-
"valueString": "patient={ref}&code=http://snomed.info/sct|444814009"
125-
}
126-
]
39+
"sourceId": "patient",
40+
"targetId": "viral-sinusitis",
41+
"params": "patient={ref}&code=http://snomed.info/sct|444814009"
12742
},
12843
{
129-
"extension": [
130-
{
131-
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.sourceId",
132-
"valueId": "patient"
133-
},
134-
{
135-
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.targetId",
136-
"valueId": "leukocytes"
137-
},
138-
{
139-
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.params",
140-
"valueString": "patient={ref}&code=http://loinc.org|6690-2"
141-
}
142-
]
44+
"sourceId": "patient",
45+
"targetId": "leukocytes",
46+
"params": "patient={ref}&code=http://loinc.org|6690-2"
14347
},
14448
{
145-
"extension": [
146-
{
147-
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.sourceId",
148-
"valueId": "patient"
149-
},
150-
{
151-
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.targetId",
152-
"valueId": "erythrocytes"
153-
},
154-
{
155-
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.params",
156-
"valueString": "patient={ref}&code=http://loinc.org|789-8"
157-
}
158-
]
49+
"sourceId": "patient",
50+
"targetId": "erythrocytes",
51+
"params": "patient={ref}&code=http://loinc.org|789-8"
15952
},
16053
{
161-
"extension": [
162-
{
163-
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.sourceId",
164-
"valueId": "patient"
165-
},
166-
{
167-
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.targetId",
168-
"valueId": "cisplatin"
169-
},
170-
{
171-
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.params",
172-
"valueString": "patient={ref}&code=http://www.nlm.nih.gov/research/umls/rxnorm|1736854"
173-
}
174-
]
54+
"sourceId": "patient",
55+
"targetId": "cisplatin",
56+
"params": "patient={ref}&code=http://www.nlm.nih.gov/research/umls/rxnorm|1736854"
17557
},
17658
{
177-
"extension": [
178-
{
179-
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.sourceId",
180-
"valueId": "viral-sinusitis"
181-
},
182-
{
183-
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.targetId",
184-
"valueId": "encounter"
185-
}
186-
],
187-
"path": "encounter"
59+
"sourceId": "viral-sinusitis",
60+
"path": "encounter",
61+
"targetId": "encounter"
18862
},
18963
{
190-
"extension": [
191-
{
192-
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.sourceId",
193-
"valueId": "leukocytes"
194-
},
195-
{
196-
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.targetId",
197-
"valueId": "encounter"
198-
}
199-
],
200-
"path": "encounter"
64+
"sourceId": "leukocytes",
65+
"path": "encounter",
66+
"targetId": "encounter"
20167
},
20268
{
203-
"extension": [
204-
{
205-
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.sourceId",
206-
"valueId": "erythrocytes"
207-
},
208-
{
209-
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.targetId",
210-
"valueId": "encounter"
211-
}
212-
],
213-
"path": "encounter"
69+
"sourceId": "erythrocytes",
70+
"path": "encounter",
71+
"targetId": "encounter"
21472
},
21573
{
216-
"extension": [
217-
{
218-
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.sourceId",
219-
"valueId": "cisplatin"
220-
},
221-
{
222-
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.targetId",
223-
"valueId": "encounter"
224-
}
225-
],
226-
"path": "context"
74+
"sourceId": "cisplatin",
75+
"path": "context",
76+
"targetId": "encounter"
22777
},
22878
{
229-
"extension": [
230-
{
231-
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.sourceId",
232-
"valueId": "cisplatin"
233-
},
234-
{
235-
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.targetId",
236-
"valueId": "cisplatin-reason"
237-
}
238-
],
239-
"path": "reason"
79+
"sourceId": "cisplatin",
80+
"path": "reason",
81+
"targetId": "cisplatin-reason"
24082
}
24183
]
24284
}

‎.github/scripts/graph/X79746011X-patient-observation-encounter-type-counts.csv‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,4 @@
11
"Condition",4
22
"Encounter",51
3-
"MedicationAdministration",45
43
"Observation",94
54
"Patient",1

‎.github/scripts/patient-everything-date-range.sh‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -10,7 +10,7 @@ BUNDLE=$(curl -s "$BASE/Patient/$PATIENT_ID/\$everything?start=2013&end=2014")
1010
ACTUAL_SIZE=$(echo "$BUNDLE" | jq -r .total)
1111
IDS="$(echo "$BUNDLE" | jq -r '.entry[].resource.id')"
1212

13-
test "size" "$ACTUAL_SIZE" "1997"
13+
test "size" "$ACTUAL_SIZE" "1806"
1414

1515
test "no duplicates" "$(echo "$IDS" | sort -u | wc -l | xargs)" "$(echo "$IDS" | wc -l | xargs)"
1616

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