Merge pull request #1789 from samply/release/v0.27.0

Release v0.27.0

.github/distributed-test/docker-compose.yml

@@ -108,7 +108,7 @@ services:
   blaze-1:
     image: "blaze:latest"
     environment:
-      JAVA_TOOL_OPTIONS: "-Xmx1g"
+      JAVA_TOOL_OPTIONS: "-Xmx2g"
       STORAGE: "distributed"
       DB_KAFKA_BOOTSTRAP_SERVERS: "kafka:9092"
       DB_KAFKA_MAX_REQUEST_SIZE: "10485760"
@@ -121,9 +121,6 @@ services:
       DB_CASSANDRA_CONTACT_POINTS: "cassandra-1:9042,cassandra-2:9042"
       DB_CASSANDRA_REQUEST_TIMEOUT: "60000"
       DB_CASSANDRA_MAX_CONCURRENT_REQUESTS: "128"
-      DB_RESOURCE_CACHE_SIZE: "100000"
-      ENABLE_ADMIN_API: "true"
-      LOG_LEVEL: "debug"
     ports:
     - "8081:8081"
     volumes:
@@ -138,7 +135,7 @@ services:
   blaze-2:
     image: "blaze:latest"
     environment:
-      JAVA_TOOL_OPTIONS: "-Xmx1g"
+      JAVA_TOOL_OPTIONS: "-Xmx2g"
       STORAGE: "distributed"
       DB_KAFKA_BOOTSTRAP_SERVERS: "kafka:9092"
       DB_KAFKA_MAX_REQUEST_SIZE: "10485760"
@@ -151,9 +148,6 @@ services:
       DB_CASSANDRA_CONTACT_POINTS: "cassandra-1:9042,cassandra-2:9042"
       DB_CASSANDRA_REQUEST_TIMEOUT: "60000"
       DB_CASSANDRA_MAX_CONCURRENT_REQUESTS: "128"
-      DB_RESOURCE_CACHE_SIZE: "100000"
-      ENABLE_ADMIN_API: "true"
-      LOG_LEVEL: "debug"
     ports:
     - "8082:8081"
     volumes:

.github/scripts/admin-api/async-job.sh

@@ -0,0 +1,51 @@
+#!/bin/bash -e
+
+# issues an async request and inspects the resulting job
+
+SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
+. "$SCRIPT_DIR/../util.sh"
+
+if [[ "$OSTYPE" == "darwin"* ]]; then
+  DATE_CMD="gdate"
+else
+  DATE_CMD="date"
+fi
+
+BASE="http://localhost:8080/fhir"
+HEADERS=$(curl -s -H 'Prefer: respond-async' -H 'Accept: application/fhir+json' -o /dev/null -D - "$BASE/Observation?code=http://loinc.org|8310-5&_summary=count")
+JOB_ID=$(echo "$HEADERS" | grep -i content-location | tr -d '\r' | cut -d '/' -f6)
+
+# wait to fetch the completed job
+sleep 1
+JOB=$(curl -s -H 'Accept: application/fhir+json' "$BASE/__admin/Task/$JOB_ID")
+
+test "profile URL" "$(echo "$JOB" | jq -r '.meta.profile[]')" "https://samply.github.io/blaze/fhir/StructureDefinition/AsyncInteractionJob"
+test "status" "$(echo "$JOB" | jq -r '.status')" "completed"
+
+AUTHORED_ON_ISO=$(echo "$JOB" | jq -r '.authoredOn')
+AUTHORED_ON_EPOCH_SECONDS=$($DATE_CMD -d "$AUTHORED_ON_ISO" +%s)
+NOW_EPOCH_SECONDS=$($DATE_CMD +%s)
+if ((NOW_EPOCH_SECONDS - AUTHORED_ON_EPOCH_SECONDS < 10)); then
+  echo "OK 👍: the authoredOn dateTime is set and current"
+else
+  echo "Fail 😞: the authoredOn dateTime is $AUTHORED_ON_ISO, but should be a current dateTime"
+  exit 1
+fi
+
+PARAMETER_URI="https://samply.github.io/blaze/fhir/CodeSystem/AsyncInteractionJobParameter"
+
+input_expr() {
+  echo ".input[] | select(.type.coding[] | select(.system == \"$PARAMETER_URI\" and .code == \"$1\"))"
+}
+
+test "t" "$(echo "$JOB" | jq -r "$(input_expr "t") | .valueUnsignedInt")" "0"
+
+OUTPUT_URI="https://samply.github.io/blaze/fhir/CodeSystem/AsyncInteractionJobOutput"
+
+output_expr() {
+  echo ".output[] | select(.type.coding[] | select(.system == \"$OUTPUT_URI\" and .code == \"$1\"))"
+}
+
+PROCESSING_DURATION="$(echo "$JOB" | jq "$(output_expr "processing-duration") | .valueQuantity")"
+test "processing-duration unit system" "$(echo "$PROCESSING_DURATION" | jq -r .system)" "http://unitsofmeasure.org"
+test "processing-duration unit code" "$(echo "$PROCESSING_DURATION" | jq -r .code)" "s"

.github/scripts/admin-api/create-invalid-jobs.sh

@@ -16,10 +16,11 @@ cat <<END
     "profile": [
       "https://samply.github.io/blaze/fhir/StructureDefinition/ReIndexJob"
     ]
-  }
+  },
+  "status": "on-hold"
 }
 END
 }
 
 ERROR_MESSAGE="$(curl -s -H 'Content-Type: application/fhir+json' -H 'Accept: application/fhir+json' -d "$(re-index-job)" "$BASE/__admin/Task" | jq -r '.issue[0].diagnostics')"
-test "error message" "$ERROR_MESSAGE" "Task.status: minimum required = 1, but only found 0 (from https://samply.github.io/blaze/fhir/StructureDefinition/ReIndexJob)"
+test "error message" "$ERROR_MESSAGE" "Rule status-reason-on-hold: 'Assigns possible reasons to the 'on-hold' status.' Failed"

.github/scripts/cancel-async.sh

@@ -0,0 +1,20 @@
+#!/bin/bash -e
+
+SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
+. "$SCRIPT_DIR/util.sh"
+
+BASE="http://localhost:8080/fhir"
+HEADERS=$(curl -s -H 'Prefer: respond-async' -H 'Accept: application/fhir+json' -o /dev/null -D - "$BASE/Observation?date=lt2100&_summary=count")
+STATUS_URL=$(echo "$HEADERS" | grep -i content-location | tr -d '\r' | cut -d: -f2- | xargs)
+
+STATUS_CODE=$(curl -s -XDELETE -o /dev/null -w '%{response_code}' "$STATUS_URL")
+test "cancel status code" "$STATUS_CODE" "202"
+
+test "status code after cancel" "$(curl -s -o /dev/null -w '%{response_code}' "$STATUS_URL")" "404"
+
+DIAGNOSTICS="$(curl -s -H 'Accept: application/fhir+json' "$STATUS_URL" | jq -r '.issue[0].diagnostics')"
+if [[ "$DIAGNOSTICS" =~ The\ asynchronous\ request\ with\ id\ \`[A-Z0-9]+\`\ is\ cancelled. ]]; then
+    echo "OK 👍: the diagnostics message is right"
+else
+    echo "Fail 😞: the diagnostics message is $DIAGNOSTICS, expected /The asynchronous request with id \`[A-Z0-9]\+\` is cancelled./"
+fi

.github/scripts/count-async.sh

@@ -0,0 +1,31 @@
+#!/bin/bash -e
+
+SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
+. "$SCRIPT_DIR/util.sh"
+
+START_EPOCH="$(date +"%s")"
+
+eclipsed() {
+  EPOCH="$(date +"%s")"
+  echo $((EPOCH - START_EPOCH))
+}
+
+BASE="http://localhost:8080/fhir"
+CODE="$1"
+COUNT="$2"
+HEADERS=$(curl -s -H 'Prefer: respond-async' -H 'Accept: application/fhir+json' -o /dev/null -D - "$BASE/Observation?code=http://loinc.org|$CODE&_summary=count")
+STATUS_URL=$(echo "$HEADERS" | grep -i content-location | tr -d '\r' | cut -d: -f2- | xargs)
+
+# wait for response available
+while [[ ($(eclipsed) -lt 120) && ("$(curl -s -o /dev/null -w '%{response_code}' "$STATUS_URL")" != "200") ]]; do
+  sleep 1
+done
+
+RESPONSE_BUNDLE="$(curl -s -H 'Accept: application/fhir+json' "$STATUS_URL")"
+
+test "response bundle type" "$(echo "$RESPONSE_BUNDLE" | jq -r .type)" "batch-response"
+
+RESULT_BUNDLE="$(echo "$RESPONSE_BUNDLE" | jq '.entry[0].resource')"
+
+test "result bundle type" "$(echo "$RESULT_BUNDLE" | jq -r .type)" "searchset"
+test "result total" "$(echo "$RESULT_BUNDLE" | jq -r .total)" "$COUNT"

.github/scripts/cql/stratifier-condition-code.cql

@@ -0,0 +1,11 @@
+library "stratifier-condition-code"
+using FHIR version '4.0.0'
+include FHIRHelpers version '4.0.0'
+
+context Patient
+
+define InInitialPopulation:
+  [Condition]
+
+define function Code(condition FHIR.Condition):
+  condition.code

.github/scripts/cql/stratifier-condition-code.csv

@@ -0,0 +1,203 @@
+"Acquired coagulation disorder (disorder)",1
+"Acute Cholecystitis",3
+"Acute allergic reaction",12
+"Acute bacterial sinusitis (disorder)",70
+"Acute bronchitis (disorder)",527
+"Acute deep venous thrombosis (disorder)",9
+"Acute myeloid leukemia, disease (disorder)",103
+"Acute pulmonary embolism (disorder)",6
+"Acute respiratory distress syndrome (disorder)",2
+"Acute respiratory failure (disorder)",2
+"Acute viral pharyngitis (disorder)",598
+"Alcoholism",8
+"Alzheimer's disease (disorder)",50
+"Anemia (disorder)",382
+"Antepartum eclampsia",18
+"Appendicitis",54
+"Asthma",1
+"Atopic dermatitis",13
+"Atrial Fibrillation",95
+"Bacteremia (finding)",22
+"Bleeding from anus",1
+"Blighted ovum",16
+"Blindness due to type 2 diabetes mellitus (disorder)",1
+"Body mass index 30+ - obesity (finding)",528
+"Body mass index 40+ - severely obese (finding)",8
+"Brain damage - traumatic",10
+"Bullet wound",1
+"COVID-19",83
+"Carcinoma in situ of prostate (disorder)",29
+"Cardiac Arrest",44
+"Child attention deficit disorder",20
+"Childhood asthma",18
+"Chill (finding)",15
+"Cholelithiasis",3
+"Chronic congestive heart failure (disorder)",9
+"Chronic intractable migraine without aura",49
+"Chronic kidney disease stage 1 (disorder)",148
+"Chronic kidney disease stage 2 (disorder)",137
+"Chronic kidney disease stage 3 (disorder)",96
+"Chronic kidney disease stage 4 (disorder)",18
+"Chronic low back pain (finding)",199
+"Chronic neck pain (finding)",131
+"Chronic obstructive bronchitis (disorder)",12
+"Chronic pain",52
+"Chronic paralysis due to lesion of spinal cord",2
+"Chronic sinusitis (disorder)",257
+"Chronic type B viral hepatitis (disorder)",1
+"Closed fracture of hip",16
+"Concussion injury of brain",4
+"Concussion with loss of consciousness",14
+"Concussion with no loss of consciousness",49
+"Contact dermatitis",4
+"Coronary Heart Disease",90
+"Cough (finding)",52
+"Cystitis",21
+"Diabetes",96
+"Diabetic renal disease (disorder)",157
+"Diabetic retinopathy associated with type II diabetes mellitus (disorder)",25
+"Diarrhea symptom (finding)",3
+"Drug overdose",62
+"Dyspnea (finding)",24
+"Epilepsy",13
+"Escherichia coli urinary tract infection",25
+"Facial laceration",36
+"Familial Alzheimer's disease of early onset (disorder)",5
+"Fatigue (finding)",40
+"Febrile neutropenia (disorder)",79
+"Fetus with unknown complication",26
+"Fever (finding)",77
+"Fibromyalgia (disorder)",22
+"First degree burn",26
+"Fracture of ankle",32
+"Fracture of clavicle",39
+"Fracture of forearm",60
+"Fracture of rib",20
+"Fracture of vertebral column without spinal cord injury",2
+"Fracture subluxation of wrist",44
+"Full-time employment (finding)",20900
+"Gout",9
+"Has a criminal record (finding)",312
+"Headache (finding)",14
+"History of amputation of foot (situation)",1
+"History of appendectomy",54
+"History of cardiac arrest (situation)",44
+"History of disarticulation at wrist (situation)",1
+"History of lower limb amputation (situation)",2
+"History of myocardial infarction (situation)",5
+"History of single seizure (situation)",25
+"Homeless (finding)",7
+"Housing unsatisfactory (finding)",113
+"Human immunodeficiency virus infection (disorder)",2
+"Hyperglycemia (disorder)",42
+"Hyperlipidemia",158
+"Hypertension",466
+"Hypertriglyceridemia (disorder)",97
+"Hypoxemia (disorder)",15
+"Idiopathic atrophic hypothyroidism",13
+"Impacted molars",55
+"Injury of anterior cruciate ligament",3
+"Injury of medial collateral ligament of knee",16
+"Injury of tendon of the rotator cuff of shoulder",11
+"Joint pain (finding)",17
+"Laceration of foot",43
+"Laceration of forearm",28
+"Laceration of hand",20
+"Laceration of thigh",31
+"Lack of access to transportation (finding)",96
+"Limited social contact (finding)",1514
+"Localized, primary osteoarthritis of the hand",37
+"Loss of taste (finding)",43
+"Lupus erythematosus",1
+"Macular edema and retinopathy due to type 2 diabetes mellitus (disorder)",6
+"Major depression disorder",3
+"Malignant neoplasm of breast (disorder)",25
+"Malignant tumor of colon",3
+"Metabolic syndrome X (disorder)",244
+"Metastasis from malignant tumor of prostate (disorder)",2
+"Microalbuminuria due to type 2 diabetes mellitus (disorder)",138
+"Miscarriage in first trimester",220
+"Misuses drugs (finding)",60
+"Muscle pain (finding)",17
+"Myocardial Infarction",5
+"Nausea (finding)",5
+"Neoplasm of prostate",31
+"Neuropathy due to type 2 diabetes mellitus (disorder)",37
+"Neutropenia (disorder)",24
+"Nonproliferative diabetic retinopathy due to type 2 diabetes mellitus (disorder)",10
+"Normal pregnancy",370
+"Not in labor force (finding)",1513
+"Obstructive sleep apnea syndrome (disorder)",38
+"Only received primary school education (finding)",85
+"Opioid abuse (disorder)",11
+"Osteoarthritis of hip",30
+"Osteoarthritis of knee",58
+"Osteoporosis (disorder)",129
+"Otitis media",145
+"Overlapping malignant neoplasm of colon",5
+"Part-time employment (finding)",3496
+"Passive conjunctival congestion (finding)",3
+"Pathological fracture due to osteoporosis (disorder)",61
+"Perennial allergic rhinitis with seasonal variation",16
+"Perennial allergic rhinitis",17
+"Pneumonia (disorder)",15
+"Polyp of colon",101
+"Posttraumatic stress disorder",1
+"Prediabetes",444
+"Preeclampsia",19
+"Primary fibromyalgia syndrome",7
+"Primary malignant neoplasm of colon",4
+"Proliferative diabetic retinopathy due to type II diabetes mellitus (disorder)",4
+"Proteinuria due to type 2 diabetes mellitus (disorder)",96
+"Protracted diarrhea",1
+"Pulmonary emphysema (disorder)",9
+"Received certificate of high school equivalency (finding)",260
+"Received higher education (finding)",490
+"Recurrent rectal polyp",28
+"Recurrent urinary tract infection",13
+"Refugee (person)",53
+"Reports of violence in the environment (finding)",756
+"Respiratory distress (finding)",15
+"Rheumatoid arthritis",1
+"Risk activity involvement (finding)",333
+"Rupture of appendix",20
+"Rupture of patellar tendon",8
+"Seasonal allergic rhinitis",5
+"Second degree burn",16
+"Secondary malignant neoplasm of colon",1
+"Seizure disorder",25
+"Sepsis (disorder)",27
+"Sepsis caused by virus (disorder)",2
+"Septic shock (disorder)",2
+"Served in armed forces (finding)",52
+"Severe anxiety (panic) (finding",181
+"Shock (disorder)",1
+"Sinusitis (disorder)",64
+"Sleep apnea (disorder)",10
+"Sleep disorder (disorder)",48
+"Smokes tobacco daily",12
+"Social isolation (finding)",1677
+"Social migrant (finding)",2
+"Sore throat symptom (finding)",11
+"Sprain of ankle",109
+"Sprain of wrist",49
+"Sputum finding (finding)",27
+"Streptococcal sore throat (disorder)",161
+"Stress (finding)",7477
+"Stroke",110
+"Suspected COVID-19",84
+"Suspected lung cancer (situation)",1
+"Tear of meniscus of knee",6
+"Third degree burn",2
+"Toxoplasma gondii antibody positive (finding)",1
+"Transformed migraine (disorder)",14
+"Transport problems (finding)",95
+"Traumatic brain injury (disorder)",1
+"Tubal pregnancy",36
+"Unemployed (finding)",76
+"Unhealthy alcohol drinking behavior (finding)",169
+"Victim of intimate partner abuse (finding)",1184
+"Viral sinusitis (disorder)",1083
+"Vomiting symptom (finding)",5
+"Wheezing (finding)",24
+"Whiplash injury to neck",42

.github/scripts/cql/stratifier-condition-code.yml

@@ -0,0 +1,8 @@
+library: .github/scripts/cql/stratifier-condition-code.cql
+group:
+- type: Condition
+  population:
+  - expression: InInitialPopulation
+  stratifier:
+  - code: code
+    expression: Code