Merge pull request #554 from samply/release-v0.13.4

Release v0.13.4
samply · Nov 30, 2021 · 18a66eb · 18a66eb
2 parents fd53506 + 43badb0
commit 18a66eb
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Showing 26 changed files with 191 additions and 64 deletions.
diff --git a/.github/scripts/batch.sh b/.github/scripts/batch.sh
@@ -4,9 +4,10 @@
 # This script creates a patient and tries to retrieve it through a batch request.
 #
 
+BASE="http://localhost:8080/fhir"
 PATIENT_ID=$(curl -sH "Content-Type: application/fhir+json" \
   -d '{"resourceType": "Patient"}' \
-  "http://localhost:8080/fhir/Patient" | jq -r .id)
+  "$BASE/Patient" | jq -r .id)
 
 bundle() {
 cat <<END
@@ -24,8 +25,7 @@ cat <<END
 }
 END
 }
-RESULT=$(curl -sH "Content-Type: application/fhir+json" -d "$(bundle)" \
-  "http://localhost:8080/fhir")
+RESULT=$(curl -sH "Content-Type: application/fhir+json" -d "$(bundle)" "$BASE")
 
 RESOURCE_TYPE="$(echo "$RESULT" | jq -r .resourceType)"
 if [ "$RESOURCE_TYPE" = "Bundle" ]; then

diff --git a/.github/scripts/conditional-create.sh b/.github/scripts/conditional-create.sh
@@ -0,0 +1,51 @@
+#!/bin/bash -e
+
+BASE="http://localhost:8080/fhir"
+
+bundle() {
+cat <<END
+{
+  "resourceType": "Bundle",
+  "type": "transaction",
+  "entry": [
+    {
+      "fullUrl": "Organization/foo",
+      "resource": {
+        "resourceType": "Organization",
+        "identifier": [
+          {
+            "system": "https://example.com/fhir/NamingSystem/organization",
+            "value": "190723"
+          }
+        ]
+      },
+      "request": {
+        "method": "POST",
+        "url": "Organization",
+        "ifNoneExist": "identifier=https://example.com/fhir/NamingSystem/organization|190723"
+      }
+    }
+  ]
+}
+END
+}
+
+STATUS=$(curl -sH "Content-Type: application/fhir+json" \
+  -d "$(bundle)" "$BASE" | jq -r '.entry[].response.status')
+
+if [ "$STATUS" = "201" ]; then
+  echo "OK: first atempt created the Organization"
+else
+  echo "Fail: status was ${STATUS} but should be 201"
+  exit 1
+fi
+
+STATUS=$(curl -sH "Content-Type: application/fhir+json" \
+  -d "$(bundle)" "$BASE" | jq -r '.entry[].response.status')
+
+if [ "$STATUS" = "200" ]; then
+  echo "OK: second atempt returned the already created Organization"
+else
+  echo "Fail: status was ${STATUS} but should be 200"
+  exit 1
+fi
diff --git a/.github/scripts/delete.sh b/.github/scripts/delete.sh
@@ -1,9 +1,10 @@
 #!/bin/bash -e
 
+BASE="http://localhost:8080/fhir"
 PATIENT_ID=$(uuidgen | tr '[:upper:]' '[:lower:]')
-curl -sfXDELETE "http://localhost:8080/fhir/Patient/$PATIENT_ID"
+curl -sfXDELETE "$BASE/Patient/$PATIENT_ID"
 
-PATIENT_HISTORY=$(curl -s "http://localhost:8080/fhir/Patient/$PATIENT_ID/_history")
+PATIENT_HISTORY=$(curl -s "$BASE/Patient/$PATIENT_ID/_history")
 
 TOTAL=$(echo "$PATIENT_HISTORY" | jq .total)
 if [ "$TOTAL" = "1" ]; then
@@ -29,15 +30,15 @@ else
   exit 1
 fi
 
-PATIENT_STATUS=$(curl -is "http://localhost:8080/fhir/Patient/$PATIENT_ID" | grep HTTP | tr -d '\r\n')
+PATIENT_STATUS=$(curl -is "$BASE/Patient/$PATIENT_ID" | grep HTTP | tr -d '\r\n')
 if [ "$PATIENT_STATUS" = "HTTP/1.1 410 Gone" ]; then
   echo "OK: patient status is HTTP/1.1 410 Gone"
 else
   echo "Fail: patient status is $PATIENT_STATUS"
   exit 1
 fi
 
-PATIENT_OUTCOME=$(curl -s "http://localhost:8080/fhir/Patient/$PATIENT_ID")
+PATIENT_OUTCOME=$(curl -s "$BASE/Patient/$PATIENT_ID")
 
 CODE=$(echo "$PATIENT_OUTCOME" | jq -r .issue[].code)
 if [ "$CODE" = "deleted" ]; then

diff --git a/.github/scripts/download-resources-query.sh b/.github/scripts/download-resources-query.sh
@@ -1,6 +1,6 @@
 #!/bin/bash -e
 
-BASE=http://localhost:8080/fhir
+BASE="http://localhost:8080/fhir"
 TYPE=$1
 QUERY=$2
 EXPECTED_SIZE=$(curl -s "$BASE/$TYPE?$QUERY&_summary=count" | jq -r .total)

diff --git a/.github/scripts/download-resources.sh b/.github/scripts/download-resources.sh
@@ -1,8 +1,8 @@
 #!/bin/bash -e
 
-BASE=http://localhost:8080/fhir
+BASE="http://localhost:8080/fhir"
 TYPE=$1
-EXPECTED_SIZE=$(curl -s "${BASE}/${TYPE}?_summary=count" | jq -r .total)
+EXPECTED_SIZE=$(curl -s "$BASE/${TYPE}?_summary=count" | jq -r .total)
 
 FILE_NAME=$(uuidgen)
 blazectl --server $BASE download "$TYPE" -o "$FILE_NAME".ndjson

diff --git a/.github/scripts/evaluate-measure-subject-list.sh b/.github/scripts/evaluate-measure-subject-list.sh
@@ -95,28 +95,29 @@ create-measure() {
 }
 
 post() {
-  curl -sH "Content-Type: application/fhir+json" -d @- "http://localhost:8080/fhir/$1"
+  curl -sH "Content-Type: application/fhir+json" -d @- "$1/$2"
 }
 
 evaluate-measure() {
-  parameters | curl -sH "Content-Type: application/fhir+json" -d @- "http://localhost:8080/fhir/Measure/$1/\$evaluate-measure"
+  parameters | curl -sH "Content-Type: application/fhir+json" -d @- "$1/Measure/$2/\$evaluate-measure"
 }
 
 fetch-patients() {
-  curl -s "http://localhost:8080/fhir/Patient?_list=$1&_count=100"
+  curl -s "$1/Patient?_list=$2&_count=100"
 }
 
+BASE="http://localhost:8080/fhir"
 FILE=$1
 EXPECTED_COUNT=$2
 
 DATA=$(base64 "$FILE" | tr -d '\n')
 LIBRARY_URI=$(uuidgen | tr '[:upper:]' '[:lower:]')
 MEASURE_URI=$(uuidgen | tr '[:upper:]' '[:lower:]')
 
-create-library "$LIBRARY_URI" "$DATA" | post "Library" > /dev/null
+create-library "$LIBRARY_URI" "$DATA" | post "$BASE" "Library" > /dev/null
 
-MEASURE_ID=$(create-measure "$MEASURE_URI" "$LIBRARY_URI" | post "Measure" | jq -r .id)
-REPORT=$(evaluate-measure "$MEASURE_ID")
+MEASURE_ID=$(create-measure "$MEASURE_URI" "$LIBRARY_URI" | post "$BASE" "Measure" | jq -r .id)
+REPORT=$(evaluate-measure "$BASE" "$MEASURE_ID")
 COUNT=$(echo "$REPORT" | jq -r ".group[0].population[0].count")
 
 if [ "$COUNT" = "$EXPECTED_COUNT" ]; then
@@ -129,7 +130,7 @@ else
 fi
 
 LIST_ID=$(echo "$REPORT" | jq -r '.group[0].population[0].subjectResults.reference | split("/")[1]')
-PATIENT_BUNDLE=$(fetch-patients "$LIST_ID")
+PATIENT_BUNDLE=$(fetch-patients "$BASE" "$LIST_ID")
 ID_COUNT=$(echo "$PATIENT_BUNDLE" | jq -r ".entry[].resource.id" | sort -u | wc -l | xargs | cut -d ' ' -f1)
 
 if [ "$ID_COUNT" = "$EXPECTED_COUNT" ]; then

diff --git a/.github/scripts/evaluate-measure.sh b/.github/scripts/evaluate-measure.sh
@@ -73,24 +73,25 @@ create-measure() {
 }
 
 post() {
-  curl -sH "Content-Type: application/fhir+json" -d @- "http://localhost:8080/fhir/$1"
+  curl -sH "Content-Type: application/fhir+json" -d @- "$1/$2"
 }
 
 evaluate-measure() {
-  curl -s "http://localhost:8080/fhir/Measure/$1/\$evaluate-measure?periodStart=2000&periodEnd=2030"
+  curl -s "$1/Measure/$2/\$evaluate-measure?periodStart=2000&periodEnd=2030"
 }
 
+BASE="http://localhost:8080/fhir"
 FILE=$1
 EXPECTED_COUNT=$2
 
 DATA=$(base64 "$FILE" | tr -d '\n')
 LIBRARY_URI=$(uuidgen | tr '[:upper:]' '[:lower:]')
 MEASURE_URI=$(uuidgen | tr '[:upper:]' '[:lower:]')
 
-create-library "$LIBRARY_URI" "$DATA" | post "Library" > /dev/null
+create-library "$LIBRARY_URI" "$DATA" | post "$BASE" "Library" > /dev/null
 
-MEASURE_ID=$(create-measure "$MEASURE_URI" "$LIBRARY_URI" | post "Measure" | jq -r .id)
-REPORT=$(evaluate-measure "$MEASURE_ID")
+MEASURE_ID=$(create-measure "$MEASURE_URI" "$LIBRARY_URI" | post "$BASE" "Measure" | jq -r .id)
+REPORT=$(evaluate-measure "$BASE" "$MEASURE_ID")
 COUNT=$(echo "$REPORT" | jq -r ".group[0].population[0].count")
 
 if [ "$COUNT" = "$EXPECTED_COUNT" ]; then

diff --git a/.github/scripts/evaluate-patient-q1-measure.sh b/.github/scripts/evaluate-patient-q1-measure.sh
@@ -68,33 +68,34 @@ create-measure() {
 }
 
 post() {
-  curl -sH "Content-Type: application/fhir+json" -d @- "http://localhost:8080/fhir/$1"
+  curl -sH "Content-Type: application/fhir+json" -d @- "$1/$2"
 }
 
 evaluate-measure() {
-  curl -s "http://localhost:8080/fhir/Measure/$1/\$evaluate-measure?periodStart=2000&periodEnd=2030&subject=$2"
+  curl -s "$1/Measure/$2/\$evaluate-measure?periodStart=2000&periodEnd=2030&subject=$3"
 }
 
+BASE="http://localhost:8080/fhir"
 FILE="modules/operation-measure-evaluate-measure/test/blaze/fhir/operation/evaluate_measure/q1-query.cql"
 DATA=$(base64 "$FILE" | tr -d '\n')
 LIBRARY_URI=$(uuidgen | tr '[:upper:]' '[:lower:]')
 MEASURE_URI=$(uuidgen | tr '[:upper:]' '[:lower:]')
 
-create-library "$LIBRARY_URI" "$DATA" | post "Library" > /dev/null
+create-library "$LIBRARY_URI" "$DATA" | post "$BASE" "Library" > /dev/null
 
-MEASURE_ID=$(create-measure "$MEASURE_URI" "$LIBRARY_URI" | post "Measure" | jq -r .id)
+MEASURE_ID=$(create-measure "$MEASURE_URI" "$LIBRARY_URI" | post "$BASE" "Measure" | jq -r .id)
 
-MALE_PATIENT_ID=$(curl -s 'http://localhost:8080/fhir/Patient?gender=male&_count=1' | jq -r '.entry[].resource.id')
-COUNT=$(evaluate-measure "$MEASURE_ID" "$MALE_PATIENT_ID" | jq -r ".group[0].population[0].count")
+MALE_PATIENT_ID=$(curl -s "$BASE/Patient?gender=male&_count=1" | jq -r '.entry[].resource.id')
+COUNT=$(evaluate-measure "$BASE" "$MEASURE_ID" "$MALE_PATIENT_ID" | jq -r ".group[0].population[0].count")
 if [ "$COUNT" = "1" ]; then
   echo "Success: count ($COUNT) equals the expected count"
 else
   echo "Fail: count ($COUNT) != 1"
   exit 1
 fi
 
-FEMALE_PATIENT_ID=$(curl -s 'http://localhost:8080/fhir/Patient?gender=female&_count=1' | jq -r '.entry[].resource.id')
-COUNT=$(evaluate-measure "$MEASURE_ID" "$FEMALE_PATIENT_ID" | jq -r ".group[0].population[0].count")
+FEMALE_PATIENT_ID=$(curl -s "$BASE/Patient?gender=female&_count=1" | jq -r ".entry[].resource.id")
+COUNT=$(evaluate-measure "$BASE" "$MEASURE_ID" "$FEMALE_PATIENT_ID" | jq -r ".group[0].population[0].count")
 if [ "$COUNT" = "0" ]; then
   echo "Success: count ($COUNT) equals the expected count"
 else

diff --git a/.github/scripts/revinclude.sh b/.github/scripts/revinclude.sh
@@ -1,11 +1,11 @@
 #!/bin/bash -e
 
-BASE=http://localhost:8080/fhir
-EXPECTED_NUM_PATIENTS=$(curl -s "${BASE}/Patient?_summary=count" | jq -r .total)
-EXPECTED_NUM_OBSERVATIONS=$(curl -s "${BASE}/Observation?_summary=count" | jq -r .total)
-EXPECTED_NUM_CONDITIONS=$(curl -s "${BASE}/Condition?_summary=count" | jq -r .total)
-EXPECTED_NUM_ENCOUNTERS=$(curl -s "${BASE}/Encounter?_summary=count" | jq -r .total)
-EXPECTED_NUM_PROCEDURES=$(curl -s "${BASE}/Procedure?_summary=count" | jq -r .total)
+BASE="http://localhost:8080/fhir"
+EXPECTED_NUM_PATIENTS=$(curl -s "$BASE/Patient?_summary=count" | jq -r .total)
+EXPECTED_NUM_OBSERVATIONS=$(curl -s "$BASE/Observation?_summary=count" | jq -r .total)
+EXPECTED_NUM_CONDITIONS=$(curl -s "$BASE/Condition?_summary=count" | jq -r .total)
+EXPECTED_NUM_ENCOUNTERS=$(curl -s "$BASE/Encounter?_summary=count" | jq -r .total)
+EXPECTED_NUM_PROCEDURES=$(curl -s "$BASE/Procedure?_summary=count" | jq -r .total)
 
 blazectl --server $BASE download Patient -q '_revinclude=Observation:subject&_revinclude=Condition:subject&_revinclude=Procedure:subject&_revinclude=Encounter:subject' -o output.ndjson
 

diff --git a/.github/scripts/search-compartment.sh b/.github/scripts/search-compartment.sh
@@ -1,6 +1,6 @@
 #!/bin/bash -e
 
-BASE=http://localhost:8080/fhir
+BASE="http://localhost:8080/fhir"
 PATIENT_ID=$(curl -s "$BASE/Patient?identifier=http://hl7.org/fhir/sid/us-ssn|999-82-5655" | jq -r '.entry[].resource.id')
 OBSERVATION_COUNT=$(curl -s "$BASE/Patient/$PATIENT_ID/Observation?_summary=count" | jq .total)
 

diff --git a/.github/scripts/search-observation-profile.sh b/.github/scripts/search-observation-profile.sh
@@ -1,6 +1,6 @@
 #!/bin/bash -e
 
-BASE=http://localhost:8080/fhir
+BASE="http://localhost:8080/fhir"
 LAB_COUNT=$(curl -s "$BASE/Observation?_profile=http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-lab&_summary=count" | jq -r .total)
 
 if [ "$LAB_COUNT" = "27218" ]; then

diff --git a/.github/scripts/search-patient-last-updated.sh b/.github/scripts/search-patient-last-updated.sh
@@ -6,9 +6,9 @@
 # The script assumes that Blaze contains at least some patients that were
 # imported before this script runs.
 
-BASE=http://localhost:8080/fhir
+BASE="http://localhost:8080/fhir"
 NOW=$(date +%Y-%m-%dT%H:%M:%S)
-PATIENT_COUNT=$(curl -sH 'Prefer: handling=strict' "${BASE}/Patient?_lastUpdated=gt$NOW&_summary=count" | jq -r .total)
+PATIENT_COUNT=$(curl -sH 'Prefer: handling=strict' "$BASE/Patient?_lastUpdated=gt$NOW&_summary=count" | jq -r .total)
 
 if [ $PATIENT_COUNT -eq 0 ]; then
   echo "Success: no patents are updated after $NOW"

diff --git a/.github/scripts/transaction-rw.sh b/.github/scripts/transaction-rw.sh
@@ -4,6 +4,7 @@
 # This script creates and reads a patient in a single transaction.
 #
 
+BASE="http://localhost:8080/fhir"
 PATIENT_ID="e42a47bb-a371-4cf5-9f17-51e59c1f612a"
 
 bundle() {
@@ -32,8 +33,7 @@ cat <<END
 }
 END
 }
-RESULT=$(curl -sH "Content-Type: application/fhir+json" -d "$(bundle)" \
-  "http://localhost:8080/fhir")
+RESULT=$(curl -sH "Content-Type: application/fhir+json" -d "$(bundle)" "$BASE")
 
 RESOURCE_TYPE="$(echo "$RESULT" | jq -r .resourceType)"
 if [ "$RESOURCE_TYPE" = "Bundle" ]; then

diff --git a/.github/scripts/transaction.sh b/.github/scripts/transaction.sh
@@ -5,9 +5,9 @@
 # request.
 #
 
+BASE="http://localhost:8080/fhir"
 PATIENT_ID=$(curl -sH "Content-Type: application/fhir+json" \
-  -d '{"resourceType": "Patient"}' \
-  "http://localhost:8080/fhir/Patient" | jq -r .id)
+  -d '{"resourceType": "Patient"}' "$BASE/Patient" | jq -r .id)
 
 bundle() {
 cat <<END
@@ -25,8 +25,7 @@ cat <<END
 }
 END
 }
-RESULT=$(curl -sH "Content-Type: application/fhir+json" -d "$(bundle)" \
-  "http://localhost:8080/fhir")
+RESULT=$(curl -sH "Content-Type: application/fhir+json" -d "$(bundle)" "$BASE")
 
 RESOURCE_TYPE="$(echo "$RESULT" | jq -r .resourceType)"
 if [ "$RESOURCE_TYPE" = "Bundle" ]; then

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -450,6 +450,12 @@ jobs:
     - name: OPTIONS
       run: curl -f -XOPTIONS http://localhost:8080/fhir/metadata
 
+    - name: Health
+      run: curl -f http://localhost:8080/health
+
+    - name: Health - HEAD
+      run: curl -f --head http://localhost:8080/health
+
     - name: Prometheus Metrics
       run: curl -f http://localhost:8081/metrics
 
@@ -718,6 +724,12 @@ jobs:
     - name: OPTIONS
       run: curl -f -XOPTIONS http://localhost:8080/fhir/metadata
 
+    - name: Health
+      run: curl -f http://localhost:8080/health
+
+    - name: Health - HEAD
+      run: curl -f --head http://localhost:8080/health
+
     - name: Prometheus Metrics - Blaze 1
       run: curl -f http://localhost:8081/metrics
 

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,13 @@
 # Changelog
 
+## v0.13.4
+
+### Bugfixes
+
+* Fix Health Handler ([#553](https://github.com/samply/blaze/pull/553))
+
+The full changelog can be found [here](https://github.com/samply/blaze/milestone/19?closed=1).
+
 ## v0.13.3
 
 ### Bugfixes

diff --git a/docs/deployment/docker-deployment.md b/docs/deployment/docker-deployment.md
@@ -27,7 +27,7 @@ Blaze should log something like this:
 2021-06-27T11:02:37.834Z ee086ef908c1 main INFO [blaze.core:64] - JVM version: 16.0.2
 2021-06-27T11:02:37.834Z ee086ef908c1 main INFO [blaze.core:65] - Maximum available memory: 1738 MiB
 2021-06-27T11:02:37.835Z ee086ef908c1 main INFO [blaze.core:66] - Number of available processors: 8
-2021-06-27T11:02:37.836Z ee086ef908c1 main INFO [blaze.core:67] - Successfully started Blaze version 0.13.3 in 8.2 seconds
+2021-06-27T11:02:37.836Z ee086ef908c1 main INFO [blaze.core:67] - Successfully started Blaze version 0.13.4 in 8.2 seconds
 ```
 
 In order to test connectivity, query the health endpoint:
@@ -47,7 +47,7 @@ that should return:
 ```json
 {
   "name": "Blaze",
-  "version": "0.13.3"
+  "version": "0.13.4"
 }
 ```