Improve developer setup (#68)

* Add availability json

* Update gitinogre

* Add omop-lite

* Add contributing

* Update gitignore

* Add main method and VSCode debug configurations

* Add distribution query test configuration

* Improve launch json

.gitignore

@@ -169,3 +169,5 @@ cython_debug/
 
 # PyPI configuration file
 .pypirc
+
+output.json

.vscode/launch.json

@@ -0,0 +1,40 @@
+{
+  // Use IntelliSense to learn about possible attributes.
+  // Hover to view descriptions of existing attributes.
+  // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+  "version": "0.2.0",
+  "configurations": [
+    {
+      "name": "Bunny Daemon",
+      "type": "debugpy",
+      "request": "launch",
+      "module": "hutch_bunny.daemon",
+      "justMyCode": true,
+      "console": "integratedTerminal"
+    },
+    {
+      "name": "Bunny CLI Availability",
+      "type": "debugpy",
+      "request": "launch",
+      "module": "hutch_bunny.cli",
+      "args": [
+        "--body",
+        "tests/queries/availability.json",
+      ],
+      "justMyCode": true,
+      "console": "integratedTerminal"
+    },
+    {
+      "name": "Bunny CLI Distribution",
+      "type": "debugpy",
+      "request": "launch",
+      "module": "hutch_bunny.cli",
+      "args": [
+        "--body",
+        "tests/queries/distribution.json",
+      ],
+      "justMyCode": true,
+      "console": "integratedTerminal"
+    }
+  ]
+}

CONTRIBUTING.md

@@ -0,0 +1,5 @@
+# Contributing
+
+Thanks for your interest in contributing!
+
+Please find guidance to contributing to Bunny in our [documentation](https://health-informatics-uon.github.io/hutch/contributing).

dev.compose.yml

@@ -8,6 +8,16 @@ services:
       - 5432:5432
     environment:
       POSTGRES_PASSWORD: postgres
+      POSTGRES_DB: omop
+
+  omop-lite:
+    image: ghcr.io/health-informatics-uon/omop-lite
+    depends_on:
+      - db
+    environment:
+      DB_PASSWORD: postgres
+      DB_NAME: omop
+      SYNTHETIC: true
 
   adminer:
     image: wodby/adminer

src/hutch_bunny/cli.py

@@ -43,3 +43,7 @@ def main() -> None:
     )
     save_to_output(result, args.output)
     logger.info(f"Saved results to {args.output}")
+
+
+if __name__ == "__main__":
+    main()

src/hutch_bunny/daemon.py

@@ -7,6 +7,7 @@
 from hutch_bunny.core.logger import logger
 from hutch_bunny.core.setting_database import setting_database
 
+
 def main() -> None:
     settings.log_settings()
     # Setting database connection
@@ -74,3 +75,7 @@ def main() -> None:
             logger.info("Got http status code: %s", response.status_code)
 
         time.sleep(settings.POLLING_INTERVAL)
+
+
+if __name__ == "__main__":
+    main()

tests/queries/availability.json

@@ -0,0 +1,26 @@
+{
+  "task_id": "job-2023-01-13-14: 20: 38-project",
+  "project": "project_id",
+  "owner": "user1",
+  "cohort": {
+    "groups": [
+      {
+        "rules": [
+          {
+            "varname": "OMOP",
+            "varcat": "Person",
+            "type": "TEXT",
+            "oper": "=",
+            "value": "8507"
+          }
+        ],
+        "rules_oper": "AND"
+      }
+    ],
+    "groups_oper": "OR"
+  },
+  "collection": "collection_id",
+  "protocol_version": "v2",
+  "char_salt": "salt",
+  "uuid": "unique_id"
+}

tests/queries/distribution.json

@@ -0,0 +1,7 @@
+{
+  "code": "GENERIC",
+  "analysis": "DISTRIBUTION",
+  "uuid": "59952952-c187-432a-981a-b3d35e1a7087",
+  "collection": "RQ-CC-xuihj7ll-kjlj-3989-b201-587934a89797",
+  "owner": "user1"
+}