Implement Operation ValueSet $expand

Closes: #2213

.clj-kondo/root/config.edn

@@ -80,6 +80,7 @@
     blaze.middleware.fhir.db db
     blaze.rest-api.header header
     blaze.scheduler sched
+    blaze.terminology-service ts
     blaze.test-util tu
     blaze.util u
     buddy.auth auth

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

@@ -6,9 +6,15 @@ SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
 BASE="http://localhost:8080/fhir"
 CAPABILITY_STATEMENT=$(curl -sH 'Accept: application/fhir+json' "$BASE/metadata")
 
+test "status" "$(echo "$CAPABILITY_STATEMENT" | jq -r .status)" "active"
+test "kind" "$(echo "$CAPABILITY_STATEMENT" | jq -r .kind)" "instance"
 test "software name" "$(echo "$CAPABILITY_STATEMENT" | jq -r .software.name)" "Blaze"
 test "URL" "$(echo "$CAPABILITY_STATEMENT" | jq -r .implementation.url)" "http://localhost:8080/fhir"
+test "FHIR version" "$(echo "$CAPABILITY_STATEMENT" | jq -r .fhirVersion)" "4.0.1"
+test "format" "$(echo "$CAPABILITY_STATEMENT" | jq -r '.format | join(",")')" "application/fhir+json,application/fhir+xml"
 
 test "Operation Measure \$evaluate-measure Definition" "$(echo "$CAPABILITY_STATEMENT" | jq -r '.rest[0].resource[] | select(.type == "Measure") .operation[] | select(.name == "evaluate-measure") | .definition')" "http://hl7.org/fhir/OperationDefinition/Measure-evaluate-measure"
 test "Operation Patient \$everything Definition" "$(echo "$CAPABILITY_STATEMENT" | jq -r '.rest[0].resource[] | select(.type == "Patient") .operation[] | select(.name == "everything") | .definition')" "http://hl7.org/fhir/OperationDefinition/Patient-everything"
 test "Operation Patient \$everything Documentation" "$(echo "$CAPABILITY_STATEMENT" | jq -r '.rest[0].resource[] | select(.type == "Patient") .operation[] | select(.name == "everything") | .documentation')" "Returns all resources from the patient compartment of one concrete patient including the patient. Has a fix limit of 10,000 resources if paging isn't used. Paging is supported when the _count parameter is used. No other params are supported."
+test "Operation ValueSet \$expand Definition" "$(echo "$CAPABILITY_STATEMENT" | jq -r '.rest[0].resource[] | select(.type == "ValueSet") .operation[] | select(.name == "expand") | .definition')" "http://hl7.org/fhir/OperationDefinition/ValueSet-expand"
+test "Operation ValueSet \$expand Documentation" "$(echo "$CAPABILITY_STATEMENT" | jq -r '.rest[0].resource[] | select(.type == "ValueSet") .operation[] | select(.name == "expand") | .documentation')" "The \$expand operation can be used to expand all codes of a ValueSet."

.github/value-set-expand/.gitignore

@@ -0,0 +1 @@
+node_modules

.github/value-set-expand/AbrechnungsDiagnoseProzedur.csv

@@ -0,0 +1,3 @@
+"http://fhir.de/CodeSystem/KontaktDiagnoseProzedur","hospital-main-diagnosis"
+"http://fhir.de/CodeSystem/KontaktDiagnoseProzedur","principle-DRG"
+"http://fhir.de/CodeSystem/KontaktDiagnoseProzedur","secondary-DRG"

.github/value-set-expand/Abrechnungsart.csv

@@ -0,0 +1,25 @@
+"http://fhir.de/CodeSystem/dkgev/Abrechnungsart","AOP"
+"http://fhir.de/CodeSystem/dkgev/Abrechnungsart","AP"
+"http://fhir.de/CodeSystem/dkgev/Abrechnungsart","ASV"
+"http://fhir.de/CodeSystem/dkgev/Abrechnungsart","BG"
+"http://fhir.de/CodeSystem/dkgev/Abrechnungsart","DMP"
+"http://fhir.de/CodeSystem/dkgev/Abrechnungsart","DRG"
+"http://fhir.de/CodeSystem/dkgev/Abrechnungsart","HSA"
+"http://fhir.de/CodeSystem/dkgev/Abrechnungsart","IA"
+"http://fhir.de/CodeSystem/dkgev/Abrechnungsart","IV"
+"http://fhir.de/CodeSystem/dkgev/Abrechnungsart","KEK"
+"http://fhir.de/CodeSystem/dkgev/Abrechnungsart","KIA"
+"http://fhir.de/CodeSystem/dkgev/Abrechnungsart","KV"
+"http://fhir.de/CodeSystem/dkgev/Abrechnungsart","MVZ"
+"http://fhir.de/CodeSystem/dkgev/Abrechnungsart","PEPP"
+"http://fhir.de/CodeSystem/dkgev/Abrechnungsart","PIA"
+"http://fhir.de/CodeSystem/dkgev/Abrechnungsart","PS"
+"http://fhir.de/CodeSystem/dkgev/Abrechnungsart","PSY"
+"http://fhir.de/CodeSystem/dkgev/Abrechnungsart","REHA"
+"http://fhir.de/CodeSystem/dkgev/Abrechnungsart","SL"
+"http://fhir.de/CodeSystem/dkgev/Abrechnungsart","SPB"
+"http://fhir.de/CodeSystem/dkgev/Abrechnungsart","SPZ"
+"http://fhir.de/CodeSystem/dkgev/Abrechnungsart","SZ"
+"http://fhir.de/CodeSystem/dkgev/Abrechnungsart","VNSB"
+"http://fhir.de/CodeSystem/dkgev/Abrechnungsart","WLA"
+"http://fhir.de/CodeSystem/dkgev/Abrechnungsart","WLU"

.github/value-set-expand/Diagnosesubtyp.csv

@@ -0,0 +1,6 @@
+"http://fhir.de/CodeSystem/KontaktDiagnoseProzedur","cause-of-death"
+"http://fhir.de/CodeSystem/KontaktDiagnoseProzedur","department-main-diagnosis"
+"http://fhir.de/CodeSystem/KontaktDiagnoseProzedur","infection-control-diagnosis"
+"http://fhir.de/CodeSystem/KontaktDiagnoseProzedur","surgery-diagnosis"
+"http://terminology.hl7.org/CodeSystem/diagnosis-role","AD"
+"http://terminology.hl7.org/CodeSystem/diagnosis-role","DD"

.github/value-set-expand/expand.sh

@@ -0,0 +1,80 @@
+#!/bin/bash -e
+
+SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
+. "$SCRIPT_DIR/../scripts/util.sh"
+
+BASE="http://localhost:8080/fhir"
+
+expand() {
+  curl -sfH "Accept: application/fhir+json" "$BASE/ValueSet/\$expand?url=$1" | jq -r '.expansion.contains[] | [.system, .code] | @csv' | sort
+}
+
+test() {
+  if [ "$2" = "$(cat "$SCRIPT_DIR/$1.csv")" ]; then
+    echo "✅ the $1 matches"
+  else
+    echo "🆘 the $1 is $2, expected $(cat "$SCRIPT_DIR/$1.csv")"
+    exit 1
+  fi
+}
+
+test "Abrechnungsart" "$(expand "http://fhir.de/ValueSet/dkgev/Abrechnungsart")"
+test "AbrechnungsDiagnoseProzedur" "$(expand "http://fhir.de/ValueSet/AbrechnungsDiagnoseProzedur")"
+test "Diagnosesubtyp" "$(expand "http://fhir.de/ValueSet/Diagnosesubtyp")"
+
+test "identifier-type-codes" "$(expand "https://www.medizininformatik-initiative.de/fhir/core/modul-fall/ValueSet/identifier-type-codes")"
+test "location-physical-type" "$(expand "https://www.medizininformatik-initiative.de/fhir/core/modul-fall/ValueSet/location-physical-type")"
+test "mii-vs-consent-answer" "$(expand "https://www.medizininformatik-initiative.de/fhir/modul-consent/ValueSet/mii-vs-consent-answer")"
+test "mii-vs-consent-policy" "$(expand "https://www.medizininformatik-initiative.de/fhir/modul-consent/ValueSet/mii-vs-consent-policy")"
+test "mii-vs-consent-signaturetypes" "$(expand "https://www.medizininformatik-initiative.de/fhir/modul-consent/ValueSet/mii-vs-consent-signaturetypes")"
+
+for url in $(blazectl --server "$BASE" download ValueSet -q "_elements=url&_count=500" 2>/dev/null | jq -r '.url'); do
+  if [[ "$url" == "http://dicom.nema.org/"* ]]; then
+    continue
+  elif [[ "$url" == "http://terminology.hl7.org/ValueSet/"* ]]; then
+    continue
+  elif [[ "$url" == "http://hl7.org/fhir/ValueSet/"* ]]; then
+    continue
+  elif [[ "$url" == "http://loinc.org/"* ]]; then
+    continue
+  elif [[ "$url" == "http://ihe.net/fhir/"* ]]; then
+    continue
+  elif [[ "$url" == "http://ihe-d.de/ValueSets/"* ]]; then
+    continue
+  elif [[ "$url" == "http://hl7.org/fhir/uv/ips/ValueSet/"* ]]; then
+    continue
+  elif [[ "$url" == "http://hl7.org/fhir/uv/genomics-reporting/ValueSet/"* ]]; then
+    continue
+  elif [[ "$url" == "http://cts.nlm.nih.gov/fhir/ValueSet/"* ]]; then
+    continue
+  elif [[ "$url" == "urn:oid:"* ]]; then
+    continue
+  elif [[ "$url" == "https://fhir.kbv.de/ValueSet/"* ]]; then
+    continue
+  elif [[ "$url" == "http://fhir.de/ValueSet/"* ]]; then
+    continue
+  elif [[ "$url" == "http://fhir.de/ConsentManagement/ValueSet/TemplateType" ]]; then
+    continue
+  elif [[ "$url" == "https://www.medizininformatik-initiative.de/fhir/core/modul-diagnose/ValueSet/"* ]]; then
+    continue
+  elif [[ "$url" == "https://www.medizininformatik-initiative.de/fhir/core/modul-labor/ValueSet/"* ]]; then
+    continue
+  elif [[ "$url" == "https://www.medizininformatik-initiative.de/fhir/core/modul-prozedur/ValueSet/"* ]]; then
+    continue
+  elif [[ "$url" == "https://www.medizininformatik-initiative.de/fhir/ext/modul-biobank/ValueSet/"* ]]; then
+    continue
+  elif [[ "$url" == "https://www.medizininformatik-initiative.de/fhir/modul-mikrobio/ValueSet/"* ]]; then
+    continue
+  elif [[ "$url" == "https://www.medizininformatik-initiative.de/fhir/modul-mikrobiologie/ValueSet/"* ]]; then
+    continue
+  elif [[ "$url" == "https://www.medizininformatik-initiative.de/fhir/ext/modul-patho/ValueSet/"* ]]; then
+    continue
+  elif [[ "$url" == "https://www.medizininformatik-initiative.de/fhir/ext/modul-molgen/ValueSet/"* ]]; then
+    continue
+  elif [[ "$url" == "https://www.medizininformatik-initiative.de/fhir/ext/modul-icu/ValueSet/"* ]]; then
+    continue
+  else
+    echo "Expand ValueSet with URL: $url"
+    curl -sfH "Accept: application/fhir+json" -o /dev/null "$BASE/ValueSet/\$expand?url=$url"
+  fi
+done

.github/value-set-expand/identifier-type-codes.csv

@@ -0,0 +1,19 @@
+"http://terminology.hl7.org/CodeSystem/v2-0203","ACSN"
+"http://terminology.hl7.org/CodeSystem/v2-0203","BRN"
+"http://terminology.hl7.org/CodeSystem/v2-0203","DL"
+"http://terminology.hl7.org/CodeSystem/v2-0203","DR"
+"http://terminology.hl7.org/CodeSystem/v2-0203","EN"
+"http://terminology.hl7.org/CodeSystem/v2-0203","FILL"
+"http://terminology.hl7.org/CodeSystem/v2-0203","JHN"
+"http://terminology.hl7.org/CodeSystem/v2-0203","MCN"
+"http://terminology.hl7.org/CodeSystem/v2-0203","MD"
+"http://terminology.hl7.org/CodeSystem/v2-0203","MR"
+"http://terminology.hl7.org/CodeSystem/v2-0203","NIIP"
+"http://terminology.hl7.org/CodeSystem/v2-0203","PLAC"
+"http://terminology.hl7.org/CodeSystem/v2-0203","PPN"
+"http://terminology.hl7.org/CodeSystem/v2-0203","PRN"
+"http://terminology.hl7.org/CodeSystem/v2-0203","SB"
+"http://terminology.hl7.org/CodeSystem/v2-0203","SNO"
+"http://terminology.hl7.org/CodeSystem/v2-0203","TAX"
+"http://terminology.hl7.org/CodeSystem/v2-0203","UDI"
+"http://terminology.hl7.org/CodeSystem/v2-0203","VN"

.github/value-set-expand/location-physical-type.csv

@@ -0,0 +1,3 @@
+"http://terminology.hl7.org/CodeSystem/location-physical-type","bd"
+"http://terminology.hl7.org/CodeSystem/location-physical-type","ro"
+"http://terminology.hl7.org/CodeSystem/location-physical-type","wa"

.github/value-set-expand/mii-vs-consent-answer.csv

@@ -0,0 +1,3 @@
+"urn:oid:2.16.840.1.113883.3.1937.777.24.5.2","2.16.840.1.113883.3.1937.777.24.5.2.1"
+"urn:oid:2.16.840.1.113883.3.1937.777.24.5.2","2.16.840.1.113883.3.1937.777.24.5.2.2"
+"urn:oid:2.16.840.1.113883.3.1937.777.24.5.2","2.16.840.1.113883.3.1937.777.24.5.2.3"

.github/value-set-expand/mii-vs-consent-policy.csv

@@ -0,0 +1,13 @@
+"urn:oid:2.16.840.1.113883.3.1937.777.24.5.3","2.16.840.1.113883.3.1937.777.24.5.3.1"
+"urn:oid:2.16.840.1.113883.3.1937.777.24.5.3","2.16.840.1.113883.3.1937.777.24.5.3.10"
+"urn:oid:2.16.840.1.113883.3.1937.777.24.5.3","2.16.840.1.113883.3.1937.777.24.5.3.14"
+"urn:oid:2.16.840.1.113883.3.1937.777.24.5.3","2.16.840.1.113883.3.1937.777.24.5.3.18"
+"urn:oid:2.16.840.1.113883.3.1937.777.24.5.3","2.16.840.1.113883.3.1937.777.24.5.3.24"
+"urn:oid:2.16.840.1.113883.3.1937.777.24.5.3","2.16.840.1.113883.3.1937.777.24.5.3.26"
+"urn:oid:2.16.840.1.113883.3.1937.777.24.5.3","2.16.840.1.113883.3.1937.777.24.5.3.30"
+"urn:oid:2.16.840.1.113883.3.1937.777.24.5.3","2.16.840.1.113883.3.1937.777.24.5.3.32"
+"urn:oid:2.16.840.1.113883.3.1937.777.24.5.3","2.16.840.1.113883.3.1937.777.24.5.3.35"
+"urn:oid:2.16.840.1.113883.3.1937.777.24.5.3","2.16.840.1.113883.3.1937.777.24.5.3.44"
+"urn:oid:2.16.840.1.113883.3.1937.777.24.5.3","2.16.840.1.113883.3.1937.777.24.5.3.48"
+"urn:oid:2.16.840.1.113883.3.1937.777.24.5.3","2.16.840.1.113883.3.1937.777.24.5.3.50"
+"urn:oid:2.16.840.1.113883.3.1937.777.24.5.3","2.16.840.1.113883.3.1937.777.24.5.3.54"

.github/value-set-expand/mii-vs-consent-signaturetypes.csv

@@ -0,0 +1,2 @@
+"urn:iso-astm:E1762-95:2013","1.2.840.10065.1.12.1.11"
+"urn:iso-astm:E1762-95:2013","1.2.840.10065.1.12.1.7"