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Merge pull request #798 from samply/release-v0.18.0
Release v0.18.0
2 parents 40c0939 + c8a8078 commit 867d3e1

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‎.github/scripts/batch-metadata.sh

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#!/bin/bash -e
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#
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# This script fetches the CapabilityStatement through a batch request.
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#
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BASE="http://localhost:8080/fhir"
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bundle() {
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cat <<END
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{
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"resourceType": "Bundle",
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"type": "batch",
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"entry": [
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{
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"request": {
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"method": "GET",
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"url": "metadata"
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}
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}
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]
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}
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END
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}
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RESULT=$(curl -sH "Content-Type: application/fhir+json" -d "$(bundle)" "$BASE")
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RESOURCE_TYPE="$(echo "$RESULT" | jq -r .resourceType)"
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if [ "$RESOURCE_TYPE" = "Bundle" ]; then
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echo "OK: the resource type is Bundle"
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else
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echo "Fail: the resource type is $RESOURCE_TYPE, expected Bundle"
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exit 1
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fi
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BUNDLE_TYPE="$(echo "$RESULT" | jq -r .type)"
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if [ "$BUNDLE_TYPE" = "batch-response" ]; then
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echo "OK: the bundle type is batch-response"
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else
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echo "Fail: the bundle type is $BUNDLE_TYPE, expected batch-response"
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exit 1
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fi
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RESPONSE_STATUS="$(echo "$RESULT" | jq -r .entry[].response.status)"
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if [ "$RESPONSE_STATUS" = "200" ]; then
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echo "OK: the response status is 200"
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else
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echo "Fail: the response status is $RESPONSE_STATUS, expected 200"
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exit 1
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fi
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RESPONSE_RESOURCE_TYPE="$(echo "$RESULT" | jq -r .entry[].resource.resourceType)"
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if [ "$RESPONSE_RESOURCE_TYPE" = "CapabilityStatement" ]; then
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echo "OK: resource type is CapabilityStatement"
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else
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echo "Fail: resource type was $RESPONSE_RESOURCE_TYPE but should be CapabilityStatement"
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exit 1
57+
fi

‎.github/scripts/batch.sh

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@@ -55,6 +55,6 @@ RESPONSE_PATIENT_ID="$(echo "$RESULT" | jq -r .entry[].resource.id)"
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if [ "$RESPONSE_PATIENT_ID" = "$PATIENT_ID" ]; then
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echo "OK: patient id's match"
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else
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echo "Fail: response patient id was $RESPONSE_PATIENT_ID but should be $RESPONSE_PATIENT_ID"
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echo "Fail: response patient id was $RESPONSE_PATIENT_ID but should be $PATIENT_ID"
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exit 1
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fi

‎.github/scripts/download-resources-query-sort.sh

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#!/bin/bash -e
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BASE="http://localhost:8080/fhir"
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TYPE=$1
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QUERY=$2
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SORT=$3
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EXPECTED_SIZE=$4
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FILE_NAME_PREFIX="$(uuidgen)"
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blazectl --server "$BASE" download "$TYPE" -q "_sort=$SORT&$QUERY" -o "$FILE_NAME_PREFIX-get".ndjson
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SIZE=$(wc -l "$FILE_NAME_PREFIX-get".ndjson | xargs | cut -d ' ' -f1)
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if [ "$EXPECTED_SIZE" = "$SIZE" ]; then
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echo "Success: download size matches for GET request"
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else
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echo "Fail: download size was ${SIZE} but should be ${EXPECTED_SIZE} for GET request"
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exit 1
18+
fi
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blazectl --server "$BASE" download "$TYPE" -p -q "_sort=$SORT&$QUERY" -o "$FILE_NAME_PREFIX-post".ndjson
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SIZE=$(wc -l "$FILE_NAME_PREFIX-post".ndjson | xargs | cut -d ' ' -f1)
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if [ "$EXPECTED_SIZE" = "$SIZE" ]; then
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echo "Success: download size matches for POST request"
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else
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echo "Fail: download size was ${SIZE} but should be ${EXPECTED_SIZE} for POST request"
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exit 1
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fi
29+
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if [ "$(diff "$FILE_NAME_PREFIX-get.ndjson" "$FILE_NAME_PREFIX-post.ndjson")" = "" ]; then
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echo "Success: both downloads are identical"
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else
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echo "Fail: the GET and the POST download differ"
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exit 1
35+
fi
36+
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# test sorting, ignoring the milliseconds because Blaze strips them in the index
38+
LAST_UPDATED=$(cat "$FILE_NAME_PREFIX-get.ndjson" | jq -r '.meta.lastUpdated' | cut -d'.' -f1 | uniq)
39+
if [[ "$SORT" == -* ]]; then
40+
LAST_UPDATED_SORT=$(echo "$LAST_UPDATED" | sort -r)
41+
else
42+
LAST_UPDATED_SORT=$(echo "$LAST_UPDATED" | sort)
43+
fi
44+
if [ "$LAST_UPDATED" = "$LAST_UPDATED_SORT" ]; then
45+
echo "Success: resources are sorted"
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else
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echo "Fail: resources are not sorted"
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exit 1
49+
fi

‎.github/scripts/install-blazectl.sh

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#!/bin/bash -e
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VERSION=0.8.5
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VERSION=0.9.0
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curl -sLO https://github.com/samply/blazectl/releases/download/v${VERSION}/blazectl-${VERSION}-linux-amd64.tar.gz
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tar xzf blazectl-${VERSION}-linux-amd64.tar.gz

‎.github/scripts/search-patient-last-updated.sh

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@@ -10,7 +10,7 @@ BASE="http://localhost:8080/fhir"
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NOW=$(date +%Y-%m-%dT%H:%M:%S)
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PATIENT_COUNT=$(curl -sH 'Prefer: handling=strict' "$BASE/Patient?_lastUpdated=gt$NOW&_summary=count" | jq -r .total)
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13-
if [ $PATIENT_COUNT -eq 0 ]; then
13+
if [ "$PATIENT_COUNT" -eq 0 ]; then
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echo "Success: no patents are updated after $NOW"
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else
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echo "Fail: $PATIENT_COUNT patents are updated after $NOW"

‎.github/workflows/build.yml

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@@ -22,7 +22,7 @@ jobs:
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- name: Setup clj-kondo
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uses: DeLaGuardo/setup-clj-kondo@master
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with:
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version: '2022.06.22'
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version: '2022.09.08'
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- name: Check out Git repository
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uses: actions/checkout@v3
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- name: Setup Clojure
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uses: DeLaGuardo/setup-clojure@master
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with:
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cli: '1.11.1.1149'
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cli: '1.11.1.1165'
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- name: Check out Git repository
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uses: actions/checkout@v3
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- name: Setup Clojure
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uses: DeLaGuardo/setup-clojure@master
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with:
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cli: '1.11.1.1149'
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cli: '1.11.1.1165'
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- name: Check out Git repository
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uses: actions/checkout@v3
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- name: Setup Clojure
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uses: DeLaGuardo/setup-clojure@master
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with:
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cli: '1.11.1.1149'
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cli: '1.11.1.1165'
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- name: Check out Git repository
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uses: actions/checkout@v3
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- name: Setup Clojure
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uses: DeLaGuardo/setup-clojure@master
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with:
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cli: '1.11.1.1149'
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cli: '1.11.1.1165'
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- name: Check out Git repository
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uses: actions/checkout@v3
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- name: Download Observation Resources of male Patients
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run: .github/scripts/download-resources-query.sh Observation "patient.gender=male" 20466
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- name: Download Observation Resources of male Patients Sorted Ascending
329+
run: .github/scripts/download-resources-query-sort.sh Observation "patient.gender=male" "_lastUpdated" 20466
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- name: Download Observation Resources of male Patients Sorted Descending
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run: .github/scripts/download-resources-query-sort.sh Observation "patient.gender=male" "-_lastUpdated" 20466
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- name: Download Observation Resources of female Patients
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run: .github/scripts/download-resources-query.sh Observation "patient.gender=female" 22463
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- name: Download Observation Resources of female Patients Sorted Ascending
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run: .github/scripts/download-resources-query-sort.sh Observation "patient.gender=female" "_lastUpdated" 22463
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- name: Download Observation Resources of female Patients Sorted Descending
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run: .github/scripts/download-resources-query-sort.sh Observation "patient.gender=female" "-_lastUpdated" 22463
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- name: Download Observation Resources - Including Patients
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run: blazectl --no-progress --server http://localhost:8080/fhir download Observation -q '_include=Observation:patient' -o Observation-Patient.ndjson
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- name: Download MedicationRequest Resources of Medications with code 854235
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run: .github/scripts/download-resources-query.sh MedicationRequest "medication.code=1736854" 112
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- name: Download MedicationRequest Resources of Medications with code 854235 Sorted Ascending
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run: .github/scripts/download-resources-query-sort.sh MedicationRequest "medication.code=1736854" "_lastUpdated" 112
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- name: Download MedicationRequest Resources of Medications with code 854235 Sorted Descending
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run: .github/scripts/download-resources-query-sort.sh MedicationRequest "medication.code=1736854" "-_lastUpdated" 112
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- name: Download MedicationRequest Resources - Including Medications
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run: blazectl --no-progress --server http://localhost:8080/fhir download MedicationRequest -q '_include=MedicationRequest:medication' -o MedicationRequest.ndjson
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- name: Batch
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run: .github/scripts/batch.sh
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- name: Batch Metadata
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run: .github/scripts/batch-metadata.sh
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- name: Transaction
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run: .github/scripts/transaction.sh
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- name: Setup Clojure
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uses: DeLaGuardo/setup-clojure@master
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with:
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cli: '1.11.1.1149'
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cli: '1.11.1.1165'
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- name: Check out Git repository
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uses: actions/checkout@v3
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- name: Download Observation Resources of male Patients
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run: .github/scripts/download-resources-query.sh Observation "patient.gender=male" 20466
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- name: Download Observation Resources of male Patients Sorted Ascending
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run: .github/scripts/download-resources-query-sort.sh Observation "patient.gender=male" "_lastUpdated" 20466
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- name: Download Observation Resources of male Patients Sorted Descending
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run: .github/scripts/download-resources-query-sort.sh Observation "patient.gender=male" "-_lastUpdated" 20466
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- name: Download Observation Resources of female Patients
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run: .github/scripts/download-resources-query.sh Observation "patient.gender=female" 22463
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- name: Download Observation Resources of female Patients Sorted Ascending
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run: .github/scripts/download-resources-query-sort.sh Observation "patient.gender=female" "_lastUpdated" 22463
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- name: Download Observation Resources of female Patients Sorted Descending
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run: .github/scripts/download-resources-query-sort.sh Observation "patient.gender=female" "-_lastUpdated" 22463
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- name: Download Observation Resources - Including Patients
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run: blazectl --no-progress --server http://localhost:8080/fhir download Observation -q '_include=Observation:patient' -o Observation-Patient.ndjson
753786

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772805
- name: Download MedicationRequest Resources of Medications with code 854235
773806
run: .github/scripts/download-resources-query.sh MedicationRequest "medication.code=1736854" 112
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808+
- name: Download MedicationRequest Resources of Medications with code 854235 Sorted Ascending
809+
run: .github/scripts/download-resources-query-sort.sh MedicationRequest "medication.code=1736854" "_lastUpdated" 112
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811+
- name: Download MedicationRequest Resources of Medications with code 854235 Sorted Descending
812+
run: .github/scripts/download-resources-query-sort.sh MedicationRequest "medication.code=1736854" "-_lastUpdated" 112
813+
775814
- name: Download MedicationRequest Resources - Including Medications
776815
run: blazectl --no-progress --server http://localhost:8080/fhir download MedicationRequest -q '_include=MedicationRequest:medication' -o MedicationRequest.ndjson
777816

@@ -853,6 +892,9 @@ jobs:
853892
- name: Batch
854893
run: .github/scripts/batch.sh
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895+
- name: Batch Metadata
896+
run: .github/scripts/batch-metadata.sh
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- name: Transaction
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run: .github/scripts/transaction.sh
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- name: Setup Clojure
895937
uses: DeLaGuardo/setup-clojure@master
896938
with:
897-
cli: '1.11.1.1149'
939+
cli: '1.11.1.1165'
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- name: Check out Git repository
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uses: actions/checkout@v3

‎CHANGELOG.md

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11
# Changelog
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3+
## v0.18.0
4+
5+
### New Features
6+
7+
* Allow Population Basis Differ from Subject in Measures ([#768](https://github.com/samply/blaze/pull/768))
8+
* Implement Sorting by _lastUpdated ([#98](https://github.com/samply/blaze/issues/98))
9+
* Allow Metadata Requests in Batches ([#781](https://github.com/samply/blaze/pull/781))
10+
* Allow to Set Separate RocksDB WAL Dirs ([#791](https://github.com/samply/blaze/pull/791))
11+
12+
The full changelog can be found [here](https://github.com/samply/blaze/milestone/36?closed=1).
13+
314
## v0.17.12
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516
### Security

‎README.md

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@@ -14,7 +14,7 @@ The goal of this project is to provide a FHIR® Store with an internal CQL Evalu
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Blaze passes all [Touchstone FHIR 4.0.1 Basic Tests][12] and almost all [CQL Tests][3]. Please refer to the [Conformance](docs/conformance.md) section and report any issues you encounter during evaluation.
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17-
Latest release: [v0.17.12][5]
17+
Latest release: [v0.18.0][5]
1818

1919
## Quick Start
2020

@@ -24,7 +24,7 @@ In order to run Blaze just execute the following:
2424

2525
```sh
2626
docker volume create blaze-data
27-
docker run -p 8080:8080 -v blaze-data:/app/data samply/blaze:0.17
27+
docker run -p 8080:8080 -v blaze-data:/app/data samply/blaze:0.18
2828
```
2929

3030
Blaze will create multiple directories inside the `blaze-data` volume on its first start and use the same directories on subsequent starts.
@@ -72,7 +72,7 @@ Unless required by applicable law or agreed to in writing, software distributed
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[3]: <https://cql.hl7.org/tests.html>
7474
[4]: <https://alexanderkiel.gitbook.io/blaze/deployment>
75-
[5]: <https://github.com/samply/blaze/releases/tag/v0.17.12>
75+
[5]: <https://github.com/samply/blaze/releases/tag/v0.18.0>
7676
[6]: <https://www.yourkit.com/java/profiler/>
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[7]: <https://www.yourkit.com/.net/profiler/>
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[8]: <https://www.yourkit.com/youmonitor/>

‎deps.edn

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{:mvn/version "1.3.6"}
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4343
org.slf4j/slf4j-nop
44-
{:mvn/version "1.7.36"}}
44+
{:mvn/version "2.0.2"}}
4545

4646
:aliases
4747
{:depstar
@@ -66,7 +66,7 @@
6666
:kaocha
6767
{:extra-deps
6868
{lambdaisland/kaocha
69-
{:mvn/version "1.68.1059"}}
69+
{:mvn/version "1.70.1086"}}
7070

7171
:main-opts ["-m" "kaocha.runner"]}
7272

@@ -80,10 +80,10 @@
8080
:outdated
8181
{:replace-deps
8282
{com.github.liquidz/antq
83-
{:mvn/version "1.9.863"}
83+
{:mvn/version "2.1.927"}
8484

8585
org.slf4j/slf4j-nop
86-
{:mvn/version "1.7.36"}}
86+
{:mvn/version "2.0.2"}}
8787

8888
:main-opts
8989
["-m" "antq.core"

‎docker-compose.yml

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@@ -1,7 +1,7 @@
11
version: '3.2'
22
services:
33
blaze:
4-
image: "samply/blaze:0.17"
4+
image: "samply/blaze:0.18"
55
environment:
66
BASE_URL: "http://localhost:8080"
77
JAVA_TOOL_OPTIONS: "-Xmx2g"

‎docs/README.md

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# Documentation
2+
3+
* [Deployment](deployment/README.md)
4+
* [FHIR RESTful API](api.md)
5+
* [Importing Data](importing-data.md)
6+
* [Sync Data](data-sync.md)
7+
* [Conformance](conformance.md)
8+
* [Performance](performance.md)
9+
* [Tuning Guide](tuning-guide.md)
10+
* [Tooling](tooling.md)
11+
* [CQL Queries](cql-queries.md)
12+
* [Authentication](authentication.md)
13+
* [Architecture](architecture.md)
14+
* [Implementation](implementation/README.md)

‎docs/cql-queries.md

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@@ -17,7 +17,7 @@ The most accessible way to create and execute CQL queries is to use the Quality
1717
If you don't already have Blaze running, you can read about how to do it in [Deployment](deployment/README.md). If you have Docker available just run:
1818

1919
```
20-
docker run -p 8080:8080 -v blaze-data:/app/data samply/blaze:0.17
20+
docker run -p 8080:8080 -v blaze-data:/app/data samply/blaze:0.18
2121
```
2222

2323
Start the Quality Reporting UI. You should see an empty measure list.

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