Merge develop into master DPL317

.release-version

@@ -1 +1 @@
-2.24.0
+2.25.0

README.md

@@ -85,9 +85,11 @@ Various environment variables are set in the docker-compose file.
 ### Running
 
 1. Start the Lighthouse service specified in the `docker-compose.yml` from the
-   root of the repository:
+   root of the repository (this builds the docker image if it does not exist, then starts it up i.e. take care to delete old images or add --build):
 
         docker-compose up
+        or
+        docker-compose up --build
 
    This will keep running continuously in your terminal window, so to execute further commands you'll need
    to open a new terminal window or tab.

lighthouse/classes/beckman.py

@@ -76,7 +76,7 @@ def get_robots() -> Optional[List[Dict[str, str]]]:
     def get_failure_types() -> List[Dict[str, str]]:
         logger.debug("Getting Beckman failure types information from config...")
 
-        failure_types_config = app.config.get("BECKMAN_FAILURE_TYPES")
+        failure_types_config = app.config.get("ROBOT_FAILURE_TYPES")
 
         if failure_types_config is None or not isinstance(failure_types_config, dict):
             message = "no config found or unreadable"

lighthouse/config/defaults.py

@@ -213,13 +213,15 @@
     "BKRB0003": {"name": "Robot 3", "uuid": "90d8bc7a-2f6e-4a5f-8bea-1e8d27a1ac89"},
     "BKRB0004": {"name": "Robot 4", "uuid": "675002fe-f364-47e4-b71f-4fe1bb7b5091"},
 }
-# TODO: make these the generic failure types
-BECKMAN_FAILURE_TYPES = {
+# failure types (shared by Beckman and Biosero fail screens in Lighthouse-UI)
+ROBOT_FAILURE_TYPES = {
+    "plate_too_low_empty": "Plate volumes are too low or empty",
+    "general_software_error": "General software error",
     "robot_crashed": "The robot crashed",
     "sample_contamination": "Sample contamination occurred",
     "power_failure": "Power loss to instrument",
     "network_failure": "Cannot retrieve sample data",
-    "SILAS_error": "Internal communication error in Beckman system",
+    "SILAS_error": "Internal communication error in robot system",
     "instrument_loaded_incorrectly": "Labware has been incorrectly loaded onto instrument",
     "other": "Any other failure",
 }

lighthouse/config/test.py

@@ -80,9 +80,9 @@
 RMQ_LIMS_ID = "LH_TEST"
 
 ###
-# Beckman config
+# Robot config
 ###
-BECKMAN_FAILURE_TYPES = {key: BECKMAN_FAILURE_TYPES[key] for key in ("robot_crashed", "sample_contamination", "other")}
+ROBOT_FAILURE_TYPES = {key: ROBOT_FAILURE_TYPES[key] for key in ("robot_crashed", "sample_contamination", "other")}
 
 ###
 # SS plate creation config (UUID for the plate purpose and study of the plate created)

lighthouse/routes/common/cherrypicked_plates.py

@@ -153,7 +153,7 @@ def fail_plate_from_barcode() -> FlaskResponse:
 
         return bad_request(str(e))
     try:
-        if failure_type not in app.config["BECKMAN_FAILURE_TYPES"]:
+        if failure_type not in app.config["ROBOT_FAILURE_TYPES"]:
             logger.error(f"{ERROR_CHERRYPICKED_FAILURE_RECORD} unknown failure type")
 
             return bad_request(f"'{failure_type}' is not a known cherrypicked plate failure type")

tests/helpers/test_plates_helpers.py

@@ -103,7 +103,7 @@ def mock_event_helpers():
 
 
 def any_failure_type(app):
-    return list(app.config["BECKMAN_FAILURE_TYPES"].keys())[0]
+    return list(app.config["ROBOT_FAILURE_TYPES"].keys())[0]
 
 
 # ---------- tests ----------

tests/routes/v1/test_beckman.py

@@ -70,7 +70,7 @@ def test_get_failure_types_returns_expected_failure_types(app, client, base_url)
 @pytest.mark.parametrize("base_url", FAILURE_TYPES_BASE_URLS)
 def test_get_failure_types_internal_server_error_no_failure_types_config_exists(app, client, base_url):
     with app.app_context():
-        del app.config["BECKMAN_FAILURE_TYPES"]
+        del app.config["ROBOT_FAILURE_TYPES"]
         response = client.get(base_url)
 
         assert response.status_code == HTTPStatus.INTERNAL_SERVER_ERROR
@@ -81,7 +81,7 @@ def test_get_failure_types_internal_server_error_no_failure_types_config_exists(
 @pytest.mark.parametrize("base_url", FAILURE_TYPES_BASE_URLS)
 def test_get_failure_types_internal_server_error_incorrect_format_config(app, client, base_url):
     with app.app_context():
-        app.config["BECKMAN_FAILURE_TYPES"] = ["not the expected dictionary"]
+        app.config["ROBOT_FAILURE_TYPES"] = ["not the expected dictionary"]
         response = client.get(base_url)
 
         assert response.status_code == HTTPStatus.INTERNAL_SERVER_ERROR