Create $compaction Operation

Closes: #208

.clj-kondo/root/config.edn

@@ -72,6 +72,8 @@
     blaze.fhir.spec.references fsr
     blaze.fhir.structure-definition-repo sdr
     blaze.job-scheduler js
+    blaze.job.async-interaction job-async
+    blaze.job.compact job-compact
     blaze.middleware.fhir.db db
     blaze.rest-api.header header
     blaze.scheduler sched

.github/scripts/compact-all.sh

@@ -0,0 +1,22 @@
+#!/bin/bash -e
+
+SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
+
+"$SCRIPT_DIR/compact.sh" index search-param-value-index
+"$SCRIPT_DIR/compact.sh" index resource-value-index
+"$SCRIPT_DIR/compact.sh" index compartment-search-param-value-index
+"$SCRIPT_DIR/compact.sh" index compartment-resource-type-index
+"$SCRIPT_DIR/compact.sh" index active-search-params
+"$SCRIPT_DIR/compact.sh" index tx-success-index
+"$SCRIPT_DIR/compact.sh" index tx-error-index
+"$SCRIPT_DIR/compact.sh" index t-by-instant-index
+"$SCRIPT_DIR/compact.sh" index resource-as-of-index
+"$SCRIPT_DIR/compact.sh" index type-as-of-index
+"$SCRIPT_DIR/compact.sh" index system-as-of-index
+"$SCRIPT_DIR/compact.sh" index patient-last-change-index
+"$SCRIPT_DIR/compact.sh" index type-stats-index
+"$SCRIPT_DIR/compact.sh" index system-stats-index
+"$SCRIPT_DIR/compact.sh" index cql-bloom-filter
+"$SCRIPT_DIR/compact.sh" index cql-bloom-filter-by-t
+"$SCRIPT_DIR/compact.sh" transaction default
+"$SCRIPT_DIR/compact.sh" resource default

.github/scripts/compact-unknown-database.sh

@@ -0,0 +1,47 @@
+#!/bin/bash -e
+
+SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
+. "$SCRIPT_DIR/util.sh"
+
+START_EPOCH="$(date +"%s")"
+
+eclipsed() {
+  EPOCH="$(date +"%s")"
+  echo $((EPOCH - START_EPOCH))
+}
+
+BASE="http://localhost:8080/fhir"
+
+parameters() {
+cat <<END
+{
+  "resourceType": "Parameters",
+  "parameter": [
+    {
+      "name": "database",
+      "valueCode": "foo"
+    },
+    {
+      "name": "column-family",
+      "valueCode": "bar"
+    }
+  ]
+}
+END
+}
+
+HEADERS="$(curl -sfH 'Accept: application/fhir+json' -H 'Content-Type: application/fhir+json' -d "$(parameters)" -o /dev/null -D - "$BASE/\$compact")"
+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}' "$STATUS_URL")" != "200") ]]; do
+  sleep 1
+done
+
+BUNDLE=$(curl -sH 'Accept: application/fhir+json' "$STATUS_URL")
+
+test "bundle type" "$(echo "$BUNDLE" | jq -r '.type')" "batch-response"
+test "response status" "$(echo "$BUNDLE" | jq -r '.entry[0].response.status')" "400"
+test "response severity" "$(echo "$BUNDLE" | jq -r '.entry[0].response.outcome.issue[0].severity')" "error"
+test "response code" "$(echo "$BUNDLE" | jq -r '.entry[0].response.outcome.issue[0].code')" "invalid"
+test "response diagnostics" "$(echo "$BUNDLE" | jq -r '.entry[0].response.outcome.issue[0].diagnostics')" "Unknown database \`foo\`."

.github/scripts/compact.sh

@@ -0,0 +1,93 @@
+#!/bin/bash -e
+
+SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
+. "$SCRIPT_DIR/util.sh"
+
+if [[ "$OSTYPE" == "darwin"* ]]; then
+  DATE_CMD="gdate"
+else
+  DATE_CMD="date"
+fi
+
+START_EPOCH="$(date +"%s")"
+
+eclipsed() {
+  EPOCH="$(date +"%s")"
+  echo $((EPOCH - START_EPOCH))
+}
+
+BASE="http://localhost:8080/fhir"
+
+DATABASE="$1"
+COLUMN_FAMILY="$2"
+
+parameters() {
+cat <<END
+{
+  "resourceType": "Parameters",
+  "parameter": [
+    {
+      "name": "database",
+      "valueCode": "$DATABASE"
+    },
+    {
+      "name": "column-family",
+      "valueCode": "$COLUMN_FAMILY"
+    }
+  ]
+}
+END
+}
+
+NOW_EPOCH_SECONDS=$($DATE_CMD +%s)
+HEADERS="$(curl -sfH 'Accept: application/fhir+json' -H 'Content-Type: application/fhir+json' -d "$(parameters)" -o /dev/null -D - "$BASE/\$compact")"
+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}' "$STATUS_URL")" != "200") ]]; do
+  sleep 1
+done
+
+JOB_ID=$(echo "$STATUS_URL" | cut -d '/' -f6)
+JOB=$(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/CompactJob"
+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)
+if ((NOW_EPOCH_SECONDS - AUTHORED_ON_EPOCH_SECONDS < 10)); then
+  echo "✅ the authoredOn dateTime is set and current"
+else
+  echo "🆘 the authoredOn dateTime is $AUTHORED_ON_ISO, but should be a current dateTime"
+  exit 1
+fi
+
+PARAMETER_URI="https://samply.github.io/blaze/fhir/CodeSystem/CompactJobParameter"
+
+input_expr() {
+  echo ".input[] | select(.type.coding[] | select(.system == \"$PARAMETER_URI\" and .code == \"$1\"))"
+}
+
+test "database" "$(echo "$JOB" | jq -r "$(input_expr "database") | .valueCode")" "$DATABASE"
+test "column-family" "$(echo "$JOB" | jq -r "$(input_expr "column-family") | .valueCode")" "$COLUMN_FAMILY"
+
+OUTPUT_URI="https://samply.github.io/blaze/fhir/CodeSystem/CompactJobOutput"
+
+output_expr() {
+  echo ".output[] | select(.type.coding[] | select(.system == \"$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"
+
+# History
+JOB_HISTORY=$(curl -s -H 'Accept: application/fhir+json' "$BASE/__admin/Task/$JOB_ID/_history")
+
+test "history resource type" "$(echo "$JOB_HISTORY" | jq -r '.resourceType')" "Bundle"
+test "history bundle type" "$(echo "$JOB_HISTORY" | jq -r '.type')" "history"
+test "history total" "$(echo "$JOB_HISTORY" | jq -r '.total')" "3"
+test "history 0 status" "$(echo "$JOB_HISTORY" | jq -r '.entry[0].resource.status')" "completed"
+test "history 1 status" "$(echo "$JOB_HISTORY" | jq -r '.entry[1].resource.status')" "in-progress"
+test "history 2 status" "$(echo "$JOB_HISTORY" | jq -r '.entry[2].resource.status')" "ready"

.github/workflows/build.yml

@@ -1116,7 +1116,7 @@ jobs:
       run: docker load --input /tmp/blaze.tar
 
     - name: Run Blaze
-      run: docker run --name blaze -d -e JAVA_TOOL_OPTIONS=-Xmx2g -e DB_BLOCK_CACHE_SIZE=2048 -p 8080:8080 --read-only --tmpfs /tmp:exec -v blaze-data:/app/data blaze:latest
+      run: docker run --name blaze -d -e JAVA_TOOL_OPTIONS=-Xmx2g -e DB_BLOCK_CACHE_SIZE=2048 -e ENABLE_ADMIN_API=true -p 8080:8080 --read-only --tmpfs /tmp:exec -v blaze-data:/app/data blaze:latest
 
     - name: Wait for Blaze
       run: .github/scripts/wait-for-url.sh http://localhost:8080/health
@@ -1142,6 +1142,9 @@ jobs:
     - name: Load Data
       run: blazectl --no-progress --server http://localhost:8080/fhir upload test-data-synthea-1000
 
+    - name: Compact All Column Families
+      run: .github/scripts/compact-all.sh
+
     - name: Check Total-Number of Resources are 1099594
       run: .github/scripts/check-total-number-of-resources.sh 1099594
 
@@ -1298,6 +1301,12 @@ jobs:
     - name: Create Async Job
       run: .github/scripts/admin-api/async-job.sh
 
+    - name: Load Data
+      run: blazectl --no-progress --server http://localhost:8080/fhir upload .github/test-data/synthea
+
+    - name: Compact Unknown Database
+      run: .github/scripts/compact-unknown-database.sh
+
   # This test uploads many small transactions in order to show that Blaze can handle many small requests containing
   # chunked payload blazectl uses. Versions of Blaze from 0.13.2 to 0.15.3, starting with the migration to Jetty, had
   # the problem that the JSON parser did not read the entire inputstream so that terminal chunks could remain, which

Makefile

@@ -31,13 +31,19 @@ clean: $(MODULES) clean-root
 build-frontend:
 	$(MAKE) -C modules/frontend build
 
+build-frontend-image: build-frontend
+	docker build -t blaze-frontend:latest modules/frontend
+
 build-ingress:
 	$(MAKE) -C modules/ingress all
 
 uberjar: prep
 	clojure -T:build uber
 
-build-all: uberjar build-frontend build-ingress
+build-image: uberjar
+	docker build -t blaze:latest .
+
+build-all: build-image build-frontend-image build-ingress
 
 outdated:
 	clojure -M:outdated
@@ -62,5 +68,5 @@ cloc-test-root:
 cloc-test: $(MODULES) cloc-test-root
 
 .PHONY: $(MODULES) lint-root lint prep test-root test test-coverage clean-root \
-	clean build-frontend build-ingress uberjar build-all outdated deps-tree \
-	deps-list emacs-repl cloc-prod cloc-test
+	clean build-frontend build-frontend-image build-ingress uberjar build-all \
+	outdated deps-tree deps-list emacs-repl cloc-prod cloc-test

deps.edn

@@ -13,6 +13,9 @@
   blaze/interaction
   {:local/root "modules/interaction"}
 
+  blaze.operation/compact
+  {:local/root "modules/operation-compact"}
+
   blaze.operation/graphql
   {:local/root "modules/operation-graphql"}
 

docs/api.md

@@ -188,6 +188,7 @@ The return content is a Bundle with type set to `history` containing the version
 
 The following Operations are implemented:
 
+* [$compact](api/operation-compact.md)
 * [$graphql](http://hl7.org/fhir/resource-operation-graphql.html)
 * [Measure $evaluate-measure](api/operation-measure-evaluate-measure.md)
 * [Patient $everything](api/operation-patient-everything.md)

docs/api/admin.md

@@ -1,5 +1,11 @@
 # Admin API
 
+> [!NOTE]
+> To enable the Admin API, set the environment variable `ENABLE_ADMIN_API` to true. By default, this API is disabled for security.
+
+> [!CAUTION]
+> The Admin API exposes sensitive system information about your Blaze environment. Always enable [authentication](../authentication.md) when using the Admin API to prevent unauthorized access.
+
 ## OpenAPI Spec
 
 ```sh

docs/api/operation-compact.md

@@ -0,0 +1,57 @@
+# Operation \$compact
+
+> [!NOTE]
+> The system level \$compact operation is only activated if the [Admin API](./admin.md) is activated.
+
+The system level \$compact operation is used to compact column families of RocksDB databases. RockDB compaction is done automatically but in certain situations manual compaction can be useful.
+
+```
+POST [base]/$compact
+```
+
+## Parameters
+
+| Use | Name          | Cardinality | Type | Documentation                                                          |
+|-----|---------------|-------------|------|------------------------------------------------------------------------|
+| IN  | database      | 1..1        | code | One of three possible databases: `index`, `transaction` and `resource` |
+| IN  | column-family | 1..1        | code | Name of the column family depending on the database. See below.        |
+
+### Column Families
+
+| Database    | Column Family                        |
+|-------------|--------------------------------------|
+| index       | search-param-value-index             |
+| index       | resource-value-index                 |
+| index       | compartment-search-param-value-index |
+| index       | compartment-resource-type-index      |
+| index       | active-search-params                 |
+| index       | tx-success-index                     |
+| index       | tx-error-index                       |
+| index       | t-by-instant-index                   |
+| index       | resource-as-of-index                 |
+| index       | type-as-of-index                     |
+| index       | system-as-of-index                   |
+| index       | patient-last-change-index            |
+| index       | type-stats-index                     |
+| index       | system-stats-index                   |
+| index       | cql-bloom-filter                     |
+| index       | cql-bloom-filter-by-t                |
+| transaction | default                              |
+| resource    | default                              |
+
+### Response
+
+The response will be always async according the [Asynchronous Interaction Request Pattern][2] from FHIR R5.
+
+## Using blazectl
+
+The \$compact operation can be executed using [blazectl][1].
+
+### Example
+
+```sh
+blazectl --server http://localhost:8080/fhir compact index resource-as-of-index
+```
+
+[1]: <https://github.com/samply/blazectl>
+[2]: <http://hl7.org/fhir/R5/async-bundle.html>

job-ig/Makefile

@@ -10,4 +10,7 @@ validator_cli.jar:
 validate: validator_cli.jar
 	java -jar validator_cli.jar -version 4.0.1 -level error -debug -ig fsh-generated/resources fsh-generated/resources/Task-*.json fsh-generated/resources/Bundle-*.json
 
-.PHONY: install build validate
+clean:
+	rm -r fsh-generated
+
+.PHONY: install build validate clean

job-ig/input/fsh/column-family.fsh

@@ -0,0 +1,27 @@
+CodeSystem: ColumnFamily
+Id: ColumnFamily
+Title: "Column Family"
+* ^status = #active
+* #default
+* #search-param-value-index
+* #resource-value-index
+* #compartment-search-param-value-index 
+* #compartment-resource-type-index 
+* #active-search-params 
+* #tx-success-index 
+* #tx-error-index 
+* #t-by-instant-index 
+* #resource-as-of-index 
+* #type-as-of-index 
+* #system-as-of-index 
+* #patient-last-change-index 
+* #type-stats-index 
+* #system-stats-index 
+* #cql-bloom-filter 
+* #cql-bloom-filter-by-t 
+
+ValueSet: ColumnFamily
+Id: ColumnFamily
+Title: "Column Family Value Set"
+* ^status = #active
+* include codes from system ColumnFamily