minor improvements to substrate app

applications/NIDHI/src/substrate_app.py

@@ -0,0 +1,56 @@
+#!/usr/bin/env python3
+"""Experiment application for Chris and Nidhi's substrate experiment"""
+
+from pathlib import Path
+
+from wei import ExperimentClient
+
+
+def main() -> None:
+    """Runs the Substrate Experiment Application"""
+
+    # Define the Experiment object that will communicate with the WEI server
+    exp = ExperimentClient("localhost", "8000", "Substrate_Experiment")
+
+    # Specify the paths to the Workflow definition yaml file
+    app_directory = Path(__file__).parent.parent
+    wf_directory = app_directory / "workflows"
+    protocol_directory = app_directory / "protocols"
+
+    run_ot2_workflow = wf_directory / "run_ot2_protocol.yaml"
+
+    plate_prep_and_first_inoculation_protocol = protocol_directory / "plate_prep_first_inoculation.py"
+
+    # important variables 
+    loop_num = 0
+    total_loops = 24
+    incubation_time = 86400 # 86400 seconds = 24 hours 
+
+    # initial payload setup
+    payload = {
+        "current_ot2_protocol": plate_prep_and_first_inoculation_protocol,
+        "assay_plate_ot2_replacement_location": "1"
+    }
+
+
+    # RUN THE EXPERIMENT
+
+    # 1.) Human loads the ot-2 deck with the correct labware
+
+    # 2.) Run first OT-2 protocol with the OT-2 running workflow 
+    #        --> Dispense 150uL from substrate columns into each well of 6 substrate plates (OT-2 pos 1,7,8,9,10,11)
+    #        --> Innoculate the first substrate plate (OT-2 position 1)
+
+    exp.start_run(
+        run_ot2_workflow.resolve(),
+        payload=payload,
+        blocking=True,
+        simulate=False,
+    )
+
+    # 3.) Run the 
+
+
+
+if __name__ == "__main__":
+    main()