WIP V2

.github/workflows/build.yaml

@@ -27,6 +27,8 @@ jobs:
     - name: Upgrade pip
       run: |
         python -m pip install --upgrade pip
+    - name: Create deps dir
+      run: mkdir -p zenproject/zen-packages && chmod 0777 zenproject/zen-packages
     - name: Run tests
       run: ./run_test.sh
       shell: bash

.gitignore

@@ -9,4 +9,5 @@ venv
 aidbox_python_sdk.egg-info/
 .python-version
 .vscode
-dist
+dist
+zenproject/zen-packages

docker-compose.yaml → compose.yaml

@@ -1,42 +1,42 @@
 version: '3.1'
 services:
-  devbox-db:
-    image: "healthsamurai/aidboxdb:14.5"
+  aidbox-db:
+    image: "healthsamurai/aidboxdb:14.9"
     ports:
       - "5434:5432"
     environment:
       POSTGRES_USER:     postgres
       POSTGRES_PASSWORD: postgres
-      POSTGRES_DB:       devbox
-  devbox:
-    image: "healthsamurai/aidboxone:latest"
+      POSTGRES_DB:       aidbox
+  aidbox:
+    image: "healthsamurai/aidboxone:edge"
     depends_on:
-      - devbox-db
+      - aidbox-db
     links:
-      - "devbox-db:database"
+      - "aidbox-db:database"
     ports:
       - "8080:8080"
     env_file:
     - env_tests
     environment:
       PGHOST: database
-      PGDATABASE: devbox
+      PGDATABASE: aidbox
       PGPORT: 5432
       PGUSER: postgres
       PGPASSWORD: postgres
       AIDBOX_CONFIG: /var/config/config.edn
       AIDBOX_LICENSE: ${AIDBOX_LICENSE}
     volumes:
-      - ./config:/var/config
-  devbox-healthcheck:
+      - ./zenproject:/zenproject
+  aidbox-healthcheck:
     image: curlimages/curl
     entrypoint: /bin/sleep 10000
     links:
-      - devbox
+      - aidbox
     depends_on:
-      - devbox
+      - aidbox
     healthcheck:
-      test: curl --fail http://devbox:8080/__healthcheck || exit 1
+      test: curl --fail http://aidbox:8080/__healthcheck || exit 1
       interval: 1s
       timeout: 20s
       retries: 100
@@ -47,11 +47,11 @@ services:
         PYTHON_VERSION: ${PYTHON:-3.11}
     command: ["pipenv", "run", "pytest"]
     depends_on:
-      devbox-healthcheck:
+      aidbox-healthcheck:
         condition:
           service_healthy
     links:
-     - devbox
+     - aidbox
     env_file:
      - env_tests
     ports:

env_tests

@@ -1,13 +1,18 @@
 AIDBOX_CLIENT_ID=root
 AIDBOX_CLIENT_SECRET=secret
-AIDBOX_BASE_URL=http://devbox:8080
+AIDBOX_BASE_URL=http://aidbox:8080
+
+AIDBOX_ZEN_DEV_MODE=enable
+AIDBOX_ZEN_ENTRYPOINT=system/box
+BOX_PROJECT_GIT_TARGET__PATH=/zenproject
+AIDBOX_ZEN_PROJECT=/zenproject
 
 AIDBOX_PORT=8080
-AIDBOX_FHIR_VERSION=3.0.1
+AIDBOX_FHIR_VERSION=4.3.0
 
 APP_INIT_CLIENT_ID=root
 APP_INIT_CLIENT_SECRET=secret
-APP_INIT_URL=http://devbox:8080
+APP_INIT_URL=http://aidbox:8080
 
 APP_ID=app-py-example
 APP_SECRET=secret
@@ -17,7 +22,4 @@ AIO_PORT=8081
 AIO_HOST=0.0.0.0
 AIO_APP_PATH=.
 
-OPENID_RSA=/var/config/jwtRS256.key
-OPENID_RSA_PUB=/var/config/jwtRS256.key.pub
-
-AIDBOX_STDOUT_PRETTY=debug
+AIDBOX_STDOUT_PRETTY=debug

run_test.sh

@@ -1,3 +1,3 @@
 #!/bin/bash
 
-docker compose -f docker-compose.yaml up --exit-code-from app app
+docker compose up --exit-code-from app app

zenproject/zen-package.edn

@@ -0,0 +1,3 @@
+{:deps
+ {fhir.topic-based-subscription
+  "https://github.com/zen-fhir/hl7-fhir-uv-subscriptions-backport-r4b.git"}}

zenproject/zrc/system.edn

@@ -0,0 +1,71 @@
+{ns system
+ import #{aidbox
+          fhir.topic-based-subscription
+          hl7-fhir-uv-subscriptions-backport-r4b}
+
+ observation-topic
+ {:zen/tags #{fhir.topic-based-subscription/topic-definition}
+  ;; SubscriptionTopic url should be an absolute URI (globally unique)
+  :url "urn:aidbox-python-sdk:SubscriptionTopic:observations"
+  :resourceTrigger [
+                    ;; an SubscriptionTopic may consist 
+                    ;; of any number of resources
+                    {:resource "Observation"
+                     :fhirPathCriteria "%current.value.ofType(Quantity).value > 10"}]
+  :canFilterBy [{:resource        "Observation"
+                 :filterParameter "value"
+                 ;; _fhirPath specifies how to calculate value for the filter
+                 :_fhirPath       "%current.value.ofType(Quantity).value"
+                 :modifier        ["eq" "gt" "lt" "ge" "le"]}
+
+                {:resource        "Observation"
+                 :filterParameter "value-increase"
+                 ;; both %current and %previous state of the 
+                 ;; resource are available
+                 :_fhirPath       "%current.value.ofType(Quantity).value > %previous.value.ofType(Quantity).value"
+                 :modifier        ["eq"]}]}
+
+
+ postgres-observation-topic-storage
+ {:zen/tags #{fhir.topic-based-subscription/topic-storage}
+  ;; At the moment only PostgreSQL is available as a storage
+  :storage-type fhir.topic-based-subscription/postgres
+  ;; The name of the table which will be created to store topic events:
+  :table-name "observation_topic"
+  ;; Possible value for maxContent are: "empty" | "id-only" | "full-resource"
+  ;; The actual Resource is only stored in queue when "full-resource" value 
+  ;; are specified. When deciding which payload type to request, 
+  ;; systems SHOULD consider both ease of processing and security of PHI. 
+  ;; To mitigate the risk of information leakage, systems SHOULD use the 
+  ;; minimum level of detail consistent with the use case. 
+  ;; In practice, id-only provides a good balance between security 
+  ;; and performance for many real-world scenarios.
+  :maxContent "full-resource"
+  ;; The period, in seconds, during which events from the replication slot 
+  ;; will be buffered before being written to storage:
+  :timeout  10
+  ;; The maximum number of events the replication slot will buffer before
+  ;; writing to storage:
+  :maxCount 100
+  ;; Interval in seconds periodic heartbeat record generation 
+  ;; in cdc_topic_heartbeat_table, to reclaim the WAL space:
+  :heartbeat-rate 120
+  ;; The number of workers responsible for notification delivery. 
+  ;; min number 4 is advised. One worker can handle up to 1024 subsrciptions:
+  :senders-number 4}
+
+
+ ;; Service which binds storage with topic definition
+ observation-topic-srv
+ {:zen/tags #{aidbox/service}
+  :engine fhir.topic-based-subscription/change-data-capture-service-engine
+  :topic-definition observation-topic
+  :topic-storage postgres-observation-topic-storage}
+
+
+ ;; Entrypoint for the instance with corresponding service
+
+ box
+ {:zen/tags #{aidbox/system}
+  :services {:observation-topic-srv observation-topic-srv}
+  :zen/desc "Test python sdk"}}