feat(bbmri-miabis): add MIABIS-on-FHIR + BBMRI.de mixed-node E2E test

bbmri-miabis/README.md

@@ -0,0 +1,64 @@
+## MIABIS-on-FHIR + BBMRI.de mixed-node Locator
+
+Tests a federated search across two nodes: one running MIABIS-on-FHIR data (focus with `CQL_FLAVOUR=miabis`) and one running BBMRI.de data (focus with default flavour).
+
+```bash
+# Local mode (manual UI testing at http://localhost:3000/search/)
+docker compose -f bbmri-miabis/compose.local.yaml up --pull always
+
+# Local mode with automated tests
+docker compose -f bbmri-miabis/compose.local.yaml up -d
+docker compose -f bbmri-miabis/compose.local.yaml wait tester && echo success
+```
+
+### What this tests
+
+Eight scenarios across a 2-node federation (MIABIS-on-FHIR node + BBMRI.de node). Counts are totals across both sites.
+
+**Test data summary:**
+- MIABIS node (`proxy2`, `CQL_FLAVOUR=miabis`): p1 (female, C34) — Plasma/LN + TissueFixed/RT; p2 (male, C18) — WholeBlood/LN
+- BBMRI.de node (`proxy3`, default CQL flavour): bbmri-p1 (female, C50) — blood-plasma/LN; bbmri-p2 (male, C61) — whole-blood/RT
+
+**Mixed-node scenarios (validate totals across both sites):**
+
+| Criterion | MIABIS | BBMRI.de | Total |
+|---|---|---|---|
+| *(empty AST)* | 2 | 2 | 4 |
+| `storage_temperature = temperatureRoom` | 1 (p1, RT specimen) | 1 (bbmri-p2, Room) | 2 |
+| `storage_temperature = temperatureLN` | 2 (p1 + p2, LN specimens) | 1 (bbmri-p1, LN) | 3 |
+| `sample_kind = blood-plasma` | 1 (p1, Plasma) | 1 (bbmri-p1) | 2 |
+| `sample_kind = whole-blood` | 1 (p2, WholeBlood) | 1 (bbmri-p2) | 2 |
+
+**Diagnosis scenarios (validate BBMRI.de node is unaffected by MIABIS workarounds):**
+
+| Criterion | MIABIS | BBMRI.de | Total |
+|---|---|---|---|
+| `diagnosis = C34` | 1 (p1) | 0 | 1 |
+| `diagnosis = C50` | 0 | 1 (bbmri-p1) | 1 |
+| `diagnosis = C61` | 0 | 1 (bbmri-p2) | 1 |
+
+### Key design points
+
+**`CQL_FLAVOUR=miabis` (per-site focus config):** Selects the MIABIS-on-FHIR CQL template in focus. Spot continues to send `PROJECT=bbmri` unchanged — only the per-site focus environment variable differs. The BBMRI.de focus instance runs without `CQL_FLAVOUR` and uses the default BBMRI template.
+
+**`CODE_WORKAROUNDS` translation:** Without it, Lens codes (`temperatureRoom`, `blood-plasma`, etc.) do not exist in MIABIS FHIR data and all filter queries silently return 0. The mixed-node temperature and sample_kind scenarios validate that translation works correctly on the MIABIS node while leaving the BBMRI.de node unaffected.
+
+### Test data
+
+`test-bundle.json` — MIABIS-on-FHIR FHIR transaction bundle:
+- Patient p1 (female, dx C34): Specimen Plasma/LN, Specimen TissueFixed/RT
+- Patient p2 (male, dx C18): Specimen WholeBlood/LN
+
+`test-bundle-bbmri.json` — BBMRI.de FHIR transaction bundle:
+- Patient bbmri-p1 (female, dx C50): Specimen blood-plasma/LN
+- Patient bbmri-p2 (male, dx C61): Specimen whole-blood/RT
+
+### Troubleshooting
+
+**`--exit-code-from tester` kills the stack immediately (Docker Compose v5):** `--exit-code-from` implies `--abort-on-container-exit`, so `pki-setup` exiting normally after PKI initialisation terminates the entire stack before Blaze becomes healthy. Use `up -d` and run `test.sh` directly instead (see commands above).
+
+**All scenarios return `got=` on second run:** Spot does not re-stream results for a task ID it has already processed. Run `docker compose -f bbmri-miabis/compose.local.yaml down -v` before re-running tests to get a clean stack with fresh task IDs.
+
+**Spot rejects non-UUID query IDs:** IDs must be in `xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx` hex format. Shorthand forms like `test-0001-0000-...` are silently rejected.
+
+**BBMRI.de filter queries silently return 0:** BBMRI.de focus CQL uses `fhir.bbmri.de` URLs for the StorageTemperature extension and SampleMaterialType CodeSystem. If `test-bundle-bbmri.json` is modified and the wrong namespace (`fhir.bbmri-eric.eu`) is used instead, all filter queries on the BBMRI.de node return 0 with no error.

bbmri-miabis/compose.local.yaml

@@ -0,0 +1,123 @@
+services:
+  bbmri-sample-locator:
+    image: samply/bbmri-sample-locator:latest
+    ports:
+      - 3000:3000
+    environment:
+      PUBLIC_SPOT_URL: http://localhost:8055
+
+  spot:
+    image: samply/rustyspot:latest
+    depends_on:
+      - proxy1
+    ports:
+      - 8055:8055
+    extra_hosts:
+      - host.docker.internal:host-gateway
+    environment:
+      BEAM_PROXY_URL: http://host.docker.internal:4001
+      BEAM_APP_ID: spot.proxy1.broker
+      BEAM_SECRET: pass123
+      CORS_ORIGIN: http://localhost:3000
+      PRISM_URL: http://host.docker.internal:8056
+      TRANSFORM: LENS
+      PROJECT: bbmri
+      SITES: &sites "proxy2,proxy3"
+
+  prism:
+    image: samply/prism:main
+    depends_on:
+      test-data-loader-miabis:
+        condition: service_completed_successfully
+      test-data-loader-bbmri:
+        condition: service_completed_successfully
+    ports:
+      - 8056:8056
+    extra_hosts:
+      - host.docker.internal:host-gateway
+    environment:
+      BIND_ADDR: 0.0.0.0:8056
+      BEAM_PROXY_URL: http://host.docker.internal:4001
+      BEAM_APP_ID_LONG: prism.proxy1.broker
+      API_KEY: pass123
+      CORS_ORIGIN: any
+      PROJECT: bbmri
+      SITES: *sites
+
+  focus-miabis:
+    image: samply/focus:develop
+    depends_on:
+      - proxy2
+    extra_hosts:
+      - host.docker.internal:host-gateway
+    environment:
+      BEAM_PROXY_URL: http://host.docker.internal:4002
+      BEAM_APP_ID_LONG: focus.proxy2.broker
+      API_KEY: pass123
+      ENDPOINT_TYPE: blaze
+      BLAZE_URL: http://host.docker.internal:8080/fhir/
+      OBFUSCATE: no
+      CQL_FLAVOUR: miabis
+
+  blaze-miabis:
+    image: samply/blaze:0.32
+    ports:
+      - 8080:8080
+    healthcheck:
+      test: curl -f http://localhost:8080/fhir/metadata
+      start_period: 1m
+
+  test-data-loader-miabis:
+    image: curlimages/curl:latest
+    depends_on:
+      blaze-miabis:
+        condition: service_healthy
+    volumes:
+      - ./test-bundle.json:/test-bundle.json:ro
+    entrypoint: ["curl", "-sf", "-X", "POST", "http://blaze-miabis:8080/fhir", "-H", "Content-Type: application/fhir+json", "-d", "@/test-bundle.json"]
+
+  focus-bbmri:
+    image: samply/focus:develop
+    depends_on:
+      - proxy3
+    extra_hosts:
+      - host.docker.internal:host-gateway
+    environment:
+      BEAM_PROXY_URL: http://host.docker.internal:4003
+      BEAM_APP_ID_LONG: focus.proxy3.broker
+      API_KEY: pass123
+      ENDPOINT_TYPE: blaze
+      BLAZE_URL: http://host.docker.internal:8081/fhir/
+      OBFUSCATE: no
+
+  blaze-bbmri:
+    image: samply/blaze:0.32
+    ports:
+      - 8081:8080
+    healthcheck:
+      test: curl -f http://localhost:8080/fhir/metadata
+      start_period: 1m
+
+  test-data-loader-bbmri:
+    image: curlimages/curl:latest
+    depends_on:
+      blaze-bbmri:
+        condition: service_healthy
+    volumes:
+      - ./test-bundle-bbmri.json:/test-bundle-bbmri.json:ro
+    entrypoint: ["curl", "-sf", "-X", "POST", "http://blaze-bbmri:8080/fhir", "-H", "Content-Type: application/fhir+json", "-d", "@/test-bundle-bbmri.json"]
+
+  tester:
+    image: alpine:latest
+    network_mode: host
+    depends_on:
+      test-data-loader-miabis:
+        condition: service_completed_successfully
+      test-data-loader-bbmri:
+        condition: service_completed_successfully
+    volumes:
+      - ./test.sh:/test.sh:ro
+    command: sh -c 'apk add -q curl jq bash && bash /test.sh'
+
+include:
+  - ../compose.localbeam.yaml

bbmri-miabis/test-bundle-bbmri.json

@@ -0,0 +1,114 @@
+{
+  "resourceType": "Bundle",
+  "type": "transaction",
+  "entry": [
+    {
+      "fullUrl": "urn:uuid:bbmri-patient-1",
+      "resource": {
+        "resourceType": "Patient",
+        "id": "bbmri-patient-1",
+        "gender": "female",
+        "birthDate": "1972-05-10"
+      },
+      "request": { "method": "PUT", "url": "Patient/bbmri-patient-1" }
+    },
+    {
+      "fullUrl": "urn:uuid:bbmri-patient-2",
+      "resource": {
+        "resourceType": "Patient",
+        "id": "bbmri-patient-2",
+        "gender": "male",
+        "birthDate": "1968-11-03"
+      },
+      "request": { "method": "PUT", "url": "Patient/bbmri-patient-2" }
+    },
+    {
+      "fullUrl": "urn:uuid:bbmri-condition-1",
+      "resource": {
+        "resourceType": "Condition",
+        "id": "bbmri-condition-1",
+        "subject": { "reference": "Patient/bbmri-patient-1" },
+        "code": {
+          "coding": [
+            { "system": "http://hl7.org/fhir/sid/icd-10", "code": "C50" }
+          ]
+        }
+      },
+      "request": { "method": "PUT", "url": "Condition/bbmri-condition-1" }
+    },
+    {
+      "fullUrl": "urn:uuid:bbmri-condition-2",
+      "resource": {
+        "resourceType": "Condition",
+        "id": "bbmri-condition-2",
+        "subject": { "reference": "Patient/bbmri-patient-2" },
+        "code": {
+          "coding": [
+            { "system": "http://hl7.org/fhir/sid/icd-10", "code": "C61" }
+          ]
+        }
+      },
+      "request": { "method": "PUT", "url": "Condition/bbmri-condition-2" }
+    },
+    {
+      "fullUrl": "urn:uuid:bbmri-specimen-1",
+      "resource": {
+        "resourceType": "Specimen",
+        "id": "bbmri-specimen-1",
+        "subject": { "reference": "Patient/bbmri-patient-1" },
+        "type": {
+          "coding": [
+            {
+              "system": "https://fhir.bbmri.de/CodeSystem/SampleMaterialType",
+              "code": "blood-plasma"
+            }
+          ]
+        },
+        "extension": [
+          {
+            "url": "https://fhir.bbmri.de/StructureDefinition/StorageTemperature",
+            "valueCodeableConcept": {
+              "coding": [
+                {
+                  "system": "https://fhir.bbmri.de/CodeSystem/StorageTemperature",
+                  "code": "temperatureLN"
+                }
+              ]
+            }
+          }
+        ]
+      },
+      "request": { "method": "PUT", "url": "Specimen/bbmri-specimen-1" }
+    },
+    {
+      "fullUrl": "urn:uuid:bbmri-specimen-2",
+      "resource": {
+        "resourceType": "Specimen",
+        "id": "bbmri-specimen-2",
+        "subject": { "reference": "Patient/bbmri-patient-2" },
+        "type": {
+          "coding": [
+            {
+              "system": "https://fhir.bbmri.de/CodeSystem/SampleMaterialType",
+              "code": "whole-blood"
+            }
+          ]
+        },
+        "extension": [
+          {
+            "url": "https://fhir.bbmri.de/StructureDefinition/StorageTemperature",
+            "valueCodeableConcept": {
+              "coding": [
+                {
+                  "system": "https://fhir.bbmri.de/CodeSystem/StorageTemperature",
+                  "code": "temperatureRoom"
+                }
+              ]
+            }
+          }
+        ]
+      },
+      "request": { "method": "PUT", "url": "Specimen/bbmri-specimen-2" }
+    }
+  ]
+}