Merge pull request #560 from samply/release-v0.14.0

Release v0.14.0
samply · Dec 3, 2021 · 6533433 · 6533433
2 parents 4b1cea6 + ecd065c
commit 6533433
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diff --git a/.github/scripts/check-referential-integrity-enforced.sh b/.github/scripts/check-referential-integrity-enforced.sh
@@ -0,0 +1,10 @@
+#!/bin/bash -e
+
+ENFORCED=$(curl -s http://localhost:8080/fhir/metadata | jq -r 'isempty(.rest[].resource[].referencePolicy[] | select(. == "enforced")) | not')
+
+if [ "true" = "$ENFORCED" ]; then
+  echo "Success"
+else
+  echo "Fail"
+  exit 1
+fi
diff --git a/.github/scripts/check-referential-integrity-not-enforced.sh b/.github/scripts/check-referential-integrity-not-enforced.sh
@@ -0,0 +1,10 @@
+#!/bin/bash -e
+
+ENFORCED=$(curl -s http://localhost:8080/fhir/metadata | jq -r 'isempty(.rest[].resource[].referencePolicy[] | select(. == "enforced")) | not')
+
+if [ "false" = "$ENFORCED" ]; then
+  echo "Success"
+else
+  echo "Fail"
+  exit 1
+fi
diff --git a/.github/scripts/check-total-number-of-resources.sh b/.github/scripts/check-total-number-of-resources.sh
@@ -0,0 +1,10 @@
+#!/bin/bash -e
+
+TOTAL=$(curl -s http://localhost:8080/fhir | jq -r .total)
+
+if [ "$1" = "$TOTAL" ]; then
+  echo "Success"
+else
+  echo "Fail: total number of resources was $TOTAL but should be $1"
+  exit 1
+fi
diff --git a/.github/test-data/etl/0-condition.json b/.github/test-data/etl/0-condition.json
@@ -0,0 +1,33 @@
+{
+  "resourceType": "Bundle",
+  "type": "transaction",
+  "entry": [
+    {
+      "fullUrl": "Condition/1-1",
+      "request": {
+        "method": "PUT",
+        "url": "Condition/1-1"
+      },
+      "resource": {
+        "id": "1-1",
+        "meta": {
+          "profile": [
+            "https://fhir.bbmri.de/StructureDefinition/Condition"
+          ]
+        },
+        "resourceType": "Condition",
+        "code": {
+          "coding": [
+            {
+              "system": "http://fhir.de/CodeSystem/dimdi/icd-10-gm",
+              "code": "C34.9"
+            }
+          ]
+        },
+        "subject": {
+          "reference": "Patient/1"
+        }
+      }
+    }
+  ]
+}
diff --git a/.github/test-data/etl/1-specimen.json b/.github/test-data/etl/1-specimen.json
@@ -0,0 +1,111 @@
+{
+  "resourceType": "Bundle",
+  "type": "transaction",
+  "entry": [
+    {
+      "fullUrl": "Specimen/1-1",
+      "request": {
+        "method": "PUT",
+        "url": "Specimen/1-1"
+      },
+      "resource": {
+        "extension": [
+          {
+            "url": "https://fhir.bbmri.de/StructureDefinition/Custodian",
+            "valueReference": {
+              "reference": "Organization/zebanc"
+            }
+          }
+        ],
+        "id": "1-1",
+        "meta": {
+          "profile": [
+            "https://fhir.bbmri.de/StructureDefinition/Specimen"
+          ]
+        },
+        "resourceType": "Specimen",
+        "subject": {
+          "reference": "Patient/1"
+        },
+        "type": {
+          "coding": [
+            {
+              "code": "blood-plasma",
+              "system": "https://fhir.bbmri.de/CodeSystem/SampleMaterialType"
+            }
+          ]
+        }
+      }
+    },
+    {
+      "fullUrl": "Specimen/1-2",
+      "request": {
+        "method": "PUT",
+        "url": "Specimen/1-2"
+      },
+      "resource": {
+        "extension": [
+          {
+            "url": "https://fhir.bbmri.de/StructureDefinition/Custodian",
+            "valueReference": {
+              "reference": "Organization/zebanc"
+            }
+          }
+        ],
+        "id": "1-2",
+        "meta": {
+          "profile": [
+            "https://fhir.bbmri.de/StructureDefinition/Specimen"
+          ]
+        },
+        "resourceType": "Specimen",
+        "subject": {
+          "reference": "Patient/1"
+        },
+        "type": {
+          "coding": [
+            {
+              "code": "peripheral-blood-cells-vital",
+              "system": "https://fhir.bbmri.de/CodeSystem/SampleMaterialType"
+            }
+          ]
+        }
+      }
+    },
+    {
+      "fullUrl": "Specimen/1-3",
+      "request": {
+        "method": "PUT",
+        "url": "Specimen/1-3"
+      },
+      "resource": {
+        "extension": [
+          {
+            "url": "https://fhir.bbmri.de/StructureDefinition/Custodian",
+            "valueReference": {
+              "reference": "Organization/zebanc"
+            }
+          }
+        ],
+        "id": "1-3",
+        "meta": {
+          "profile": [
+            "https://fhir.bbmri.de/StructureDefinition/Specimen"
+          ]
+        },
+        "resourceType": "Specimen",
+        "subject": {
+          "reference": "Patient/1"
+        },
+        "type": {
+          "coding": [
+            {
+              "code": "blood-plasma",
+              "system": "https://fhir.bbmri.de/CodeSystem/SampleMaterialType"
+            }
+          ]
+        }
+      }
+    }
+  ]
+}
diff --git a/.github/test-data/etl/2-patient.json b/.github/test-data/etl/2-patient.json
@@ -0,0 +1,24 @@
+{
+  "resourceType": "Bundle",
+  "type": "transaction",
+  "entry": [
+    {
+      "fullUrl": "Patient/1",
+      "request": {
+        "method": "PUT",
+        "url": "Patient/1"
+      },
+      "resource": {
+        "birthDate": "1989-11-18",
+        "gender": "male",
+        "id": "1",
+        "meta": {
+          "profile": [
+            "https://fhir.bbmri.de/StructureDefinition/Patient"
+          ]
+        },
+        "resourceType": "Patient"
+      }
+    }
+  ]
+}
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diff --git a/...994a-5fec-874c-8452-e45786bcfb0a.json.bz2 → ...994a-5fec-874c-8452-e45786bcfb0a.json.bz2 b/...994a-5fec-874c-8452-e45786bcfb0a.json.bz2 → ...994a-5fec-874c-8452-e45786bcfb0a.json.bz2
diff --git a/.github/test-data/README.md → .github/test-data/synthea/README.md b/.github/test-data/README.md → .github/test-data/synthea/README.md
@@ -1,4 +1,4 @@
-# FHIR Test Data
+# FHIR Synthea Test Data
 
 Generates with Synthea v2.7.0 using openjdk 11.
 
@@ -269,4 +269,4 @@ Max Age: 140
 98 -- Billy698 Homenick806 (78 y/o M) Newton, Massachusetts 
 93 -- Karine844 Blanda868 (58 y/o F) Worcester, Massachusetts 
 Records: total=120, alive=100, dead=20
-```
+```
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -303,17 +303,6 @@ jobs:
     - name: Check out Git repository
       uses: actions/checkout@v2
 
-    - name: Setup Java
-      uses: actions/setup-java@v2
-      with:
-        distribution: 'temurin'
-        java-version: '17'
-
-    - name: Setup Clojure
-      uses: DeLaGuardo/setup-clojure@master
-      with:
-        tools-deps: '1.10.3.1029'
-
     - name: Install Blazectl
       run: .github/scripts/install-blazectl.sh
 
@@ -339,8 +328,14 @@ jobs:
     - name: Check Capability Statement
       run: .github/scripts/check-capability-statement.sh
 
+    - name: Check Referential Integrity Enforced
+      run: .github/scripts/check-referential-integrity-enforced.sh
+
     - name: Load Data
-      run: blazectl --server http://localhost:8080/fhir upload .github/test-data
+      run: blazectl --server http://localhost:8080/fhir upload .github/test-data/synthea
+
+    - name: Check Total-Number of Resources are 92114
+      run: .github/scripts/check-total-number-of-resources.sh 92114
 
     - name: Count Resources
       run: blazectl --server http://localhost:8080/fhir count-resources
@@ -459,6 +454,48 @@ jobs:
     - name: Prometheus Metrics
       run: curl -f http://localhost:8081/metrics
 
+  not-enforcing-referential-integrity-test:
+    needs: build
+    runs-on: ubuntu-20.04
+
+    steps:
+    - name: Check out Git repository
+      uses: actions/checkout@v2
+
+    - name: Install Blazectl
+      run: .github/scripts/install-blazectl.sh
+
+    - name: Login to GitHub Container Registry
+      uses: docker/login-action@v1
+      with:
+        registry: ghcr.io
+        username: ${{ github.repository_owner }}
+        password: ${{ secrets.CR_PAT }}
+
+    - name: Pull Docker Image
+      run: docker pull ghcr.io/samply/blaze:sha-${{ github.sha }}
+
+    - name: Run Blaze
+      run: docker run --name blaze -d -e JAVA_TOOL_OPTIONS=-Xmx2g -e ENFORCE_REFERENTIAL_INTEGRITY=false -p 8080:8080 -v blaze-data:/app/data ghcr.io/samply/blaze:sha-${{ github.sha }}
+
+    - name: Sleep 60 Seconds
+      run: sleep 60
+
+    - name: Docker Logs
+      run: docker logs blaze
+
+    - name: Check Capability Statement
+      run: .github/scripts/check-capability-statement.sh
+
+    - name: Check Referential Integrity Not Enforced
+      run: .github/scripts/check-referential-integrity-not-enforced.sh
+
+    - name: Load Data
+      run: blazectl --server http://localhost:8080/fhir upload -c1 .github/test-data/etl
+
+    - name: Check Total-Number of Resources are 5
+      run: .github/scripts/check-total-number-of-resources.sh 5
+
   jepsen-test:
     needs: build
     runs-on: ubuntu-20.04
@@ -556,23 +593,6 @@ jobs:
     - name: Check out Git repository
       uses: actions/checkout@v2
 
-    - name: Setup Java
-      uses: actions/setup-java@v2
-      with:
-        distribution: 'temurin'
-        java-version: '17'
-
-    - name: Setup Clojure
-      uses: DeLaGuardo/setup-clojure@master
-      with:
-        tools-deps: '1.10.3.1029'
-
-    - name: APT Update
-      run: sudo apt-get update
-
-    - name: Install Gnuplot
-      run: sudo apt-get install gnuplot
-
     - name: Install Blazectl
       run: .github/scripts/install-blazectl.sh
 
@@ -613,8 +633,14 @@ jobs:
     - name: Check Capability Statement
       run: .github/scripts/check-capability-statement.sh
 
+    - name: Check Referential Integrity Enforced
+      run: .github/scripts/check-referential-integrity-enforced.sh
+
     - name: Load Data
-      run: blazectl --server http://localhost:8080/fhir upload .github/test-data
+      run: blazectl --server http://localhost:8080/fhir upload .github/test-data/synthea
+
+    - name: Check Total-Number of Resources are 92114
+      run: .github/scripts/check-total-number-of-resources.sh 92114
 
     - name: Count Resources
       run: blazectl --server http://localhost:8080/fhir count-resources

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,13 @@
 # Changelog
 
+## v0.14.0
+
+### New Features
+
+* Allow Disabling Referential Integrity ([#544](https://github.com/samply/blaze/pull/544))
+
+The full changelog can be found [here](https://github.com/samply/blaze/milestone/11?closed=1).
+
 ## v0.13.5
 
 ### 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 0.13.5 in 8.2 seconds
+2021-06-27T11:02:37.836Z ee086ef908c1 main INFO [blaze.core:67] - Successfully started Blaze version 0.14.0 in 8.2 seconds
 ```
 
 In order to test connectivity, query the health endpoint:
@@ -47,7 +47,7 @@ that should return:
 ```json
 {
   "name": "Blaze",
-  "version": "0.13.5"
+  "version": "0.14.0"
 }
 ```
 

diff --git a/docs/deployment/environment-variables.md b/docs/deployment/environment-variables.md
@@ -80,6 +80,7 @@ More information about distributed deployment are available [here](distributed.m
 | JAVA_TOOL_OPTIONS | — |  | JVM options \(Docker only\) |
 | FHIR_OPERATION_EVALUATE_MEASURE_THREADS | 4 | v0.8 | The maximum number of parallel $evaluate-measure executions. Not the same as the number of threads used for measure evaluation which equal to the number of available processors. |
 | OPENID_PROVIDER_URL | - | v0.11 | [OpenID Connect][4] provider URL to enable [authentication][5] |
+| ENFORCE_REFERENTIAL_INTEGRITY | true | v0.14 | Enforce referential integrity on resource create, update and delete. It's enabled by default but can be disabled on proxy/middleware/secondary systems were a primary system ensures referential integrity. |
 
 ### Common JAVA_TOOL_OPTIONS