From 25baba611a9419ae6ce8013333332412bb1c1255 Mon Sep 17 00:00:00 2001
From: rclarke0 <rhyann.clarke@opentrons.com>
Date: Thu, 2 May 2024 17:42:24 -0400
Subject: [PATCH] module counts

---
 .../opentrons/protocol_api/module_contexts.py |  17 +-
 hardware-testing/Normalization_with_PCR.py    | 314 ++++++++++++++++++
 hardware-testing/test.csv                     |   2 +
 3 files changed, 331 insertions(+), 2 deletions(-)
 create mode 100644 hardware-testing/Normalization_with_PCR.py
 create mode 100644 hardware-testing/test.csv

diff --git a/api/src/opentrons/protocol_api/module_contexts.py b/api/src/opentrons/protocol_api/module_contexts.py
index 8605069ccc7..577668dd102 100644
--- a/api/src/opentrons/protocol_api/module_contexts.py
+++ b/api/src/opentrons/protocol_api/module_contexts.py
@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 import logging
-from typing import List, Optional, Union, cast
+from typing import List, Optional, Union, cast, Dict
 
 from opentrons_shared_data.labware.dev_types import LabwareDefinition
 from opentrons_shared_data.module.dev_types import ModuleModel, ModuleType
@@ -62,6 +62,7 @@ def __init__(
         self._protocol_core = protocol_core
         self._core_map = core_map
         self._api_version = api_version
+        self._open_close_count: Dict[str, float] = {}
 
     @property  # type: ignore[misc]
     @requires_version(2, 0)
@@ -109,7 +110,13 @@ def load_labware_object(self, labware: Labware) -> Labware:
         ), "Labware is not configured with this module as its parent"
 
         return self._core.geometry.add_labware(labware)
-
+    
+    def _open_close_counter(self):
+        serial = self._core.get_serial_number()
+        if serial not in self._open_close_count:
+            self._open_close_count[serial] = 0.0
+        self._open_close_count[serial] += 1
+        
     def load_labware(
         self,
         name: str,
@@ -521,12 +528,14 @@ def serial_number(self) -> str:
     @requires_version(2, 0)
     def open_lid(self) -> str:
         """Open the lid."""
+        self._open_close_counter()
         return self._core.open_lid().value
 
     @publish(command=cmds.thermocycler_close)
     @requires_version(2, 0)
     def close_lid(self) -> str:
         """Close the lid."""
+        self._open_close_counter()
         return self._core.close_lid().value
 
     @publish(command=cmds.thermocycler_set_block_temp)
@@ -914,6 +923,8 @@ def open_labware_latch(self) -> None:
             if they are parked adjacent to the left or right of the Heater-Shaker.
         """
         self._core.open_labware_latch()
+        self._open_close_counter()
+
 
     @requires_version(2, 13)
     @publish(command=cmds.heater_shaker_close_labware_latch)
@@ -924,6 +935,8 @@ def close_labware_latch(self) -> None:
         even if the latch was manually closed before starting the protocol.
         """
         self._core.close_labware_latch()
+        self._open_close_counter()
+
 
     @requires_version(2, 13)
     @publish(command=cmds.heater_shaker_deactivate_shaker)
diff --git a/hardware-testing/Normalization_with_PCR.py b/hardware-testing/Normalization_with_PCR.py
new file mode 100644
index 00000000000..ab07e5ca3ae
--- /dev/null
+++ b/hardware-testing/Normalization_with_PCR.py
@@ -0,0 +1,314 @@
+def get_values(*names):
+            import json
+            _all_values = json.loads("""{"csv_samp":"Destination Well,Water Transfer Volume (ul),DNA Transfer Volume (ul),Mastermix Volume (ul),Mastermix Source Tube\\nA1,3,7,40,A1\\nB1,3,7,40,A1","temp_mod_on":true,"rxn_vol":50,"p50_mount":"right","protocol_filename":"Normalization_with_PCR"}""")
+            return [_all_values[n] for n in names]
+
+
+# flake8: noqa
+
+from opentrons import protocol_api
+from opentrons import types
+import random
+import math
+
+metadata = {
+    'ctx.Name': 'PCR Protocol',
+    'author': 'Rami Farawi <ndiehl@opentrons.com',
+}
+requirements = {
+    'robotType': 'OT-3',
+    'apiLevel': '2.15'
+}
+
+
+def run(ctx: protocol_api.ProtocolContext):
+
+
+    temp_mod_on = False
+    p50_mount = "right"
+    real_mode = True
+    rxn_vol = 50
+
+    [csv_samp, temp_mod_on, rxn_vol, p50_mount] = get_values(  # noqa: F821
+        "csv_samp", "temp_mod_on", "rxn_vol", "p50_mount")
+
+    csv_samp = """
+Destination Well,Water Transfer Volume (ul),DNA Transfer Volume (ul),Mastermix Volume (ul),Mastermix Source Tube
+A1,3,7,40,A1
+B1,x,10,40,A1
+C1,10,x,40,A1
+D1,3,7,40,A1
+E1,2,8,40,A2
+F1,1,9,40,A2
+G1,5,5,40,A2
+H1,3,7,40,A3
+"""
+# A2,3,7,40,A3
+# B2,3,7,40,A3
+# C2,3,7,40,A3
+# D2,3,7,40,A3
+# E2,3,7,40,A3
+# F2,3,7,40,A3
+# G2,3,7,40,A3
+# H2,3,7,40,A3
+# A3,3,7,40,A3
+# B3,3,7,40,A3
+# C3,3,7,45,A3
+# D3,3,7,45,A3
+# E3,3,5,45,A3
+# F3,3,5,45,A3
+# G3,3,5,45,A6
+# H3,3,4,45,A5
+# A4,0,0,0,A1
+# B4,0,0,0,A1
+# C4,0,0,0,A1
+# D4,0,0,0,A1
+# E4,0,0,0,A1
+# F4,0,0,0,A1
+# G4,0,0,0,A1
+# H4,0,0,0,A1
+# A5,0,0,0,A1
+# B5,0,0,0,A1
+# C5,0,0,0,A1
+# D5,0,0,0,A1
+# E5,0,0,0,A1
+# F5,0,0,0,A1
+# G5,0,0,0,A1
+# H5,0,0,0,A1
+# A6,0,0,0,A1
+# B6,0,0,0,A1
+# C6,0,0,0,A1
+# D6,0,0,0,A1
+# E6,0,0,0,A1
+# F6,0,0,0,A1
+# G6,0,0,0,A1
+# H6,0,0,0,A1
+# A7,0,0,0,A1
+# B7,0,0,0,A1
+# C7,0,0,0,A1
+# D7,0,0,0,A1
+# E7,0,0,0,A1
+# F7,0,0,0,A1
+# G7,0,0,0,A1
+# H7,0,0,0,A1
+# A8,0,0,0,A1
+# B8,0,0,0,A1
+# C8,0,0,0,A1
+# D8,0,0,0,A1
+# E8,0,0,0,A1
+# F8,0,0,0,A1
+# G8,0,0,0,A1
+# H8,0,0,0,A1
+# A9,0,0,0,A1
+# B9,0,0,0,A1
+# C9,0,0,0,A1
+# D9,0,0,0,A1
+# E9,0,0,0,A1
+# F9,0,0,0,A1
+# G9,0,0,0,A1
+# H9,0,0,0,A1
+# A10,0,0,0,A1
+# B10,0,0,0,A1
+# C10,0,0,0,A1
+# D10,0,0,0,A1
+# E10,0,0,0,A1
+# F10,0,0,0,A1
+# G10,0,0,0,A1
+# H10,0,0,0,A1
+# A11,0,0,0,A1
+# B11,0,0,0,A1
+# C11,0,0,0,A1
+# D11,0,0,0,A1
+# E11,0,0,0,A1
+# F11,0,0,0,A1
+# G11,0,0,0,A1
+# H11,0,0,0,A1
+# A12,0,0,0,A1
+# B12,0,0,0,A1
+# C12,0,0,0,A1
+# D12,0,0,0,A1
+# E12,0,0,0,A1
+# F12,0,0,0,A1
+# G12,0,0,0,A1
+# H12,0,0,0,A1
+# """
+
+
+
+
+    # DECK SETUP AND LABWARE
+
+    tc_mod = ctx.load_module('thermocyclerModuleV2')
+    tc_mod.open_lid()
+    if real_mode:
+        tc_mod.set_lid_temperature(105)
+
+    temp_mod = ctx.load_module('temperature module gen2', '1')
+    reagent_rack = temp_mod.load_labware(
+        'opentrons_24_aluminumblock_nest_1.5ml_snapcap')  # check if 2mL
+
+    dest_plate = tc_mod.load_labware('opentrons_96_wellplate_200ul_pcr_full_skirt')  # do I change this to tough plate if they run pcr?
+
+    source_plate = ctx.load_labware('opentrons_96_wellplate_200ul_pcr_full_skirt', 3) # do I change this to their plate?
+
+    tiprack_50 = [ctx.load_labware('opentrons_flex_96_tiprack_50ul',  slot) for slot in [8, 9]]
+
+    # LOAD PIPETTES
+    p50 = ctx.load_instrument(
+        "flex_1channel_50", p50_mount, tip_racks=tiprack_50)
+
+    # mmx_liq = ctx.define_liquid(name="Mastermix", description='Mastermix', display_color='#008000')
+    # water_liq = ctx.define_liquid(name="Water", description='Water', display_color='#A52A2A')
+    # dna_liq = ctx.define_liquid(name="DNA", description='DNA', display_color='#A52A2A')
+
+    # mapping
+    csv_lines = [[val.strip() for val in line.split(',')]
+                 for line in csv_samp.splitlines()
+                 if line.split(',')[0].strip()][1:]
+
+    if temp_mod_on:
+        temp_mod.set_temperature(4)
+
+    water = reagent_rack['B1']
+    # water.load_liquid(liquid=water_liq, volume=1500)
+    #
+    # mmx_pic = reagent_rack.rows()[0]
+    # for mmx_well in mmx_pic:
+    #     mmx_well.load_liquid(liquid=mmx_liq, volume=1500)
+    #
+    # dna_pic = source_plate.wells()
+    # for dna_well in dna_pic:
+    #     dna_well.load_liquid(liquid=dna_liq, volume=50)
+
+    # adding water
+    ctx.comment('\n\n----------ADDING WATER----------\n')
+    p50.pick_up_tip()
+    # p50.aspirate(40, water) # prewet
+    # p50.dispense(40, water)
+    for row in csv_lines:
+        water_vol = row[1]
+        if water_vol.lower() == 'x':
+            continue
+        water_vol = int(row[1])
+        dest_well = row[0]
+        if water_vol == 0:
+            break
+
+
+
+        p50.configure_for_volume(water_vol)
+        p50.aspirate(water_vol, water)
+        p50.dispense(water_vol, dest_plate[dest_well], rate=0.5)
+        p50.configure_for_volume(50)
+
+        # p50.blow_out()
+    p50.drop_tip() if real_mode else p50.return_tip()
+
+    # adding Mastermix
+    ctx.comment('\n\n----------ADDING MASTERMIX----------\n')
+    p50.pick_up_tip()
+    for i, row in enumerate(csv_lines):
+        mmx_vol = row[3]
+        if mmx_vol.lower() == 'x':
+            continue
+
+        if i == 0:
+            mmx_tube = row[4]
+        mmx_tube_check = mmx_tube
+        mmx_tube = row[4]
+        if mmx_tube_check != mmx_tube:
+
+            p50.drop_tip() if real_mode else p50.return_tip()
+            p50.pick_up_tip()
+
+        if not p50.has_tip:
+            p50.pick_up_tip()
+
+        mmx_vol = int(row[3])
+        dest_well = row[0]
+
+        if mmx_vol == 0:
+            break
+        p50.configure_for_volume(mmx_vol)
+        p50.aspirate(mmx_vol, reagent_rack[mmx_tube])
+        p50.dispense(mmx_vol, dest_plate[dest_well].top())
+        ctx.delay(seconds=2)
+        p50.blow_out()
+        p50.touch_tip()
+        p50.configure_for_volume(50)
+
+
+    if p50.has_tip:
+        p50.drop_tip() if real_mode else p50.return_tip()
+
+    # adding DNA
+    ctx.comment('\n\n----------ADDING DNA----------\n')
+    for row in csv_lines:
+
+        dna_vol = row[2]
+        if dna_vol.lower() == 'x':
+            continue
+
+        p50.pick_up_tip()
+
+        dna_vol = int(row[2])
+        dest_and_source_well = row[0]
+
+
+        if dna_vol == 0:
+            break
+        p50.configure_for_volume(dna_vol)
+        p50.aspirate(dna_vol, source_plate[dest_and_source_well])
+        p50.dispense(dna_vol, dest_plate[dest_and_source_well], rate=0.5)
+
+        p50.mix(10, 0.7*rxn_vol if 0.7*rxn_vol < 30 else 30, dest_plate[dest_and_source_well])
+        p50.drop_tip() if real_mode else p50.return_tip() if real_mode else p50.return_tip()
+        p50.configure_for_volume(50)
+
+    ctx.comment('\n\n-----------Running PCR------------\n')
+
+    if real_mode:
+
+        profile1 = [
+
+                    {'temperature': 95, 'hold_time_minutes': 2},
+
+        ]
+
+        profile2 = [
+
+                    {'temperature': 98, 'hold_time_seconds': 10},
+                    {'temperature': 58, 'hold_time_seconds': 10},
+                    {'temperature': 72, 'hold_time_seconds': 30}
+
+        ]
+
+        profile3 = [
+
+                    {'temperature': 72, 'hold_time_minutes': 5}
+
+        ]
+
+        tc_mod.close_lid()
+        tc_mod.execute_profile(steps=profile1, repetitions=1, block_max_volume=50)
+        tc_mod.execute_profile(steps=profile2, repetitions=30, block_max_volume=50)
+        tc_mod.execute_profile(steps=profile3, repetitions=1, block_max_volume=50)
+        tc_mod.set_block_temperature(4)
+
+    tc_mod.open_lid()
+
+    open_close_count = tc_mod._open_close_count
+    print("---------open close count-----------")
+    for k,v in open_close_count.items():
+        print(k, v)
+    #  Specify CSV file name
+    import csv
+    csv_file = 'test.csv'
+    # Write dictionary to CSV
+    with open(csv_file, 'w', newline='') as file:
+        writer = csv.writer(file)
+        # writer.writeheader()
+        writer.writerow(['module', 'count'])
+        for key, value in open_close_count.items():
+            writer.writerow([key, value])
+    
\ No newline at end of file
diff --git a/hardware-testing/test.csv b/hardware-testing/test.csv
new file mode 100644
index 00000000000..d43fd44a35b
--- /dev/null
+++ b/hardware-testing/test.csv
@@ -0,0 +1,2 @@
+module,count
+fake-serial-number-347b222a-0a1d-45f0-8dd8-10dea49a551d,3.0