Merge branch 'release/1.4'

CHANGELOG

@@ -0,0 +1,30 @@
+## Version 1.4
+Documentation:
+- Added user manual in spanish and english.
+- Added how to ethernet connect your robot.
+- Added how to calibrate.
+- Added ssh connection guide.
+
+New features:
+- Voice messages language optional (spanish and english)
+- Added tip count reset option.
+- Added calibration scripts checking for all protocols.
+- Now beads dilution is optional in protocol 2 station A. #b2b5444
+- Only pause for empty trash if samples > 48 in protocol B. #406c79a
+- Added json generation with run info in each protocol. This will be used for api connection with openrobots web.
+- New labware configuration for ecogen deep well, added to station A and B protocols.
+
+Protocol modifications:
+- Now incubation time in protocol B is 7 minutes.
+- Reduced height in beads mix in protocol 2 station A, as it was taking some air sometimes. #53789ad
+- Increased height in beads mix in protocol 1 station B, as it was too close to the bottom.
+- Increased height in aspirates on on the plate above the magdeck, as it was sometimes touching the bottom.
+- Protocol now B starts with magdeck off. #6031d94
+- Fixed issue where m300 would go too deep and not aspire correctly in elution buffer. #40410be
+- Fixed issue where m300 would not aspirate correctly in all wells in supernatant removal, washes an elution when magnet is engaged. Aspiration height is increase to 1.5.
+
+Bug fixes:
+- Fixed tip not dropping tip in p300 (protocol C) #9280ae8
+- Fixed correct pick up and drop tip for correct tip count for negative control (protocol C) #3483d15
+- Fixed correct drop tip for p300 (protocol C) #2e6cca7
+- Fixed tip count issue when only one pipette is used. #80b9567

experiments/20200427-stationA_protocol1_buffer_S3/stationA_protocol1_buffer_S3.ot2.apiv2.py → calibration_check/stationA_protocol1_buffer_S3_calibration.py

@@ -1,14 +1,15 @@
-from opentrons.types import Point
 from opentrons import protocol_api
+from opentrons.types import Point
 from opentrons.drivers.rpi_drivers import gpio
 import time
 import math
-import json
 import os
+import subprocess
+import json
 
 # Metadata
 metadata = {
-    'protocolName': 'S3 Station A Protocol 1 buffer Version 1',
+    'protocolName': 'Calibration check for S3 Station A Protocol 1 buffer Version 1',
     'author': 'Sara <smonzon@isciii.es>, Miguel <mjuliam@isciii.es>',
     'source': 'Custom Protocol Request',
     'apiLevel': '2.3'
@@ -23,6 +24,8 @@
 DESTINATION_LABWARE = 'opentrons plastic 2ml tubes'
 DEST_TUBE = '2ml tubes'
 VOLUME_BUFFER = 300
+LANGUAGE = 'esp'
+RESET_TIPCOUNT = False
 
 # End Parameters to adapt the protocol
 
@@ -67,30 +70,70 @@
     '2ml tubes': 4
 }
 
+LANGUAGE_DICT = {
+    'esp': 'esp',
+    'eng': 'eng'
+}
+
+if LANGUAGE_DICT[LANGUAGE] == 'eng':
+    VOICE_FILES_DICT = {
+        'start': './data/sounds/started_process.mp3',
+        'finish': './data/sounds/finished_process.mp3',
+        'close_door': './data/sounds/close_door.mp3',
+        'replace_tipracks': './data/sounds/replace_tipracks.mp3',
+        'empty_trash': './data/sounds/empty_trash.mp3'
+    }
+elif LANGUAGE_DICT[LANGUAGE] == 'esp':
+    VOICE_FILES_DICT = {
+        'start': './data/sounds/started_process_esp.mp3',
+        'finish': './data/sounds/finished_process_esp.mp3',
+        'close_door': './data/sounds/close_door_esp.mp3',
+        'replace_tipracks': './data/sounds/replace_tipracks_esp.mp3',
+        'empty_trash': './data/sounds/empty_trash_esp.mp3'
+    }
+
 # Function definitions
 def check_door():
     return gpio.read_window_switches()
 
 def confirm_door_is_closed():
-    #Check if door is opened
-    if check_door() == False:
-        #Set light color to red and pause
-        gpio.set_button_light(1,0,0)
-        robot.pause(f"Please, close the door")
-        time.sleep(3)
-        confirm_door_is_closed()
-    else:
-        #Set light color to green
-        gpio.set_button_light(0,1,1)
+    if not robot.is_simulating():
+        #Check if door is opened
+        if check_door() == False:
+            #Set light color to red and pause
+            gpio.set_button_light(1,0,0)
+            robot.pause()
+            voice_notification('close_door')
+            time.sleep(5)
+            confirm_door_is_closed()
+        else:
+            #Set light color to green
+            gpio.set_button_light(0,1,0)
 
 def finish_run():
+    voice_notification('finish')
     #Set light color to blue
     gpio.set_button_light(0,0,1)
 
+def voice_notification(action):
+    if not robot.is_simulating():
+        fname = VOICE_FILES_DICT[action]
+        if os.path.isfile(fname) is True:
+                subprocess.run(
+                ['mpg123', fname],
+                stdout=subprocess.PIPE,
+                stderr=subprocess.PIPE
+                )
+        else:
+            robot.comment(f"Sound file does not exist. Call the technician")
+
+def reset_tipcount():
+    os.remove('/data/A/tip_log.json', 'w')
 
 def retrieve_tip_info(pip,tipracks,file_path = '/data/A/tip_log.json'):
     global tip_log
     if not tip_log['count'] or pip not in tip_log['count']:
+        tip_log['count'][pip] = 0
         if not robot.is_simulating():
             if os.path.isfile(file_path):
                 with open(file_path) as json_file:
@@ -99,12 +142,8 @@ def retrieve_tip_info(pip,tipracks,file_path = '/data/A/tip_log.json'):
                         tip_log['count'][pip] = data['tips1000']
                     elif 'P300' in str(pip):
                         tip_log['count'][pip] = data['tips300']
-                    else:
-                        tip_log['count'][pip] = 0
-            else:
-                tip_log['count'][pip] = 0
-        else:
-            tip_log['count'][pip] = 0
+                    elif 'P20' in str(pip):
+                        tip_log['count'][pip] = data['tips20']
 
         if "8-Channel" in str(pip):
             tip_log['tips'][pip] =  [tip for rack in tipracks for tip in rack.rows()[0]]
@@ -118,12 +157,15 @@ def retrieve_tip_info(pip,tipracks,file_path = '/data/A/tip_log.json'):
 def save_tip_info(file_path = '/data/A/tip_log.json'):
     data = {}
     if not robot.is_simulating():
-        os.rename(file_path,file_path + ".bak")
+        if os.path.isfile(file_path):
+            os.rename(file_path,file_path + ".bak")
         for pip in tip_log['count']:
             if "P1000" in str(pip):
                 data['tips1000'] = tip_log['count'][pip]
             elif "P300" in str(pip):
                 data['tips300'] = tip_log['count'][pip]
+            elif "P20" in str(pip):
+                data['tips20'] = tip_log['count'][pip]
 
         with open(file_path, 'a+') as outfile:
             json.dump(data, outfile)
@@ -135,21 +177,27 @@ def pick_up(pip,tiprack):
         tip_log = {}
     tip_log = retrieve_tip_info(pip,tiprack)
     if tip_log['count'][pip] == tip_log['max'][pip]:
+        voice_notification('replace_tipracks')
         robot.pause('Replace ' + str(pip.max_volume) + 'µl tipracks before \
 resuming.')
+        confirm_door_is_closed()
         pip.reset_tipracks()
         tip_log['count'][pip] = 0
     pip.pick_up_tip(tip_log['tips'][pip][tip_log['count'][pip]])
     tip_log['count'][pip] += 1
 
 def drop(pip):
     global switch
-    side = 1 if switch else -1
-    drop_loc = robot.loaded_labwares[12].wells()[0].top().move(Point(x=side*20))
-    pip.drop_tip(drop_loc,home_after=False)
-    switch = not switch
+    if "8-Channel" not in str(pip):
+        side = 1 if switch else -1
+        drop_loc = robot.loaded_labwares[12].wells()[0].top().move(Point(x=side*20))
+        pip.drop_tip(drop_loc,home_after=False)
+        switch = not switch
+    else:
+        drop_loc = robot.loaded_labwares[12].wells()[0].top().move(Point(x=20))
+        pip.drop_tip(drop_loc,home_after=False)
 
-def transfer_buffer(bf_tube, dests, volume, pip,tiprack):
+def transfer_buffer(bf_tube, dests, pip,tiprack):
     max_trans_per_asp = 3  # 1000/VOLUME_BUFFER = 3
     split_ind = [ind for ind in range(0, len(dests), max_trans_per_asp)]
     dest_sets = [dests[split_ind[i]:split_ind[i+1]]
@@ -167,16 +215,17 @@ def transfer_buffer(bf_tube, dests, volume, pip,tiprack):
 def run(ctx: protocol_api.ProtocolContext):
     global robot
     robot = ctx
-    # confirm door is close
-    if not ctx.is_simulating():
-        confirm_door_is_closed()
+
+    # check if tipcount is being reset
+    if RESET_TIPCOUNT:
+        reset_tipcount()
 
     # define tips
-    tips1000 = [ctx.load_labware('opentrons_96_filtertiprack_1000ul',
+    tips1000 = [robot.load_labware('opentrons_96_filtertiprack_1000ul',
                                      3, '1000µl tiprack')]
 
     # define pipettes
-    p1000 = ctx.load_instrument('p1000_single_gen2', 'left', tip_racks=tips1000)
+    p1000 = robot.load_instrument('p1000_single_gen2', 'left', tip_racks=tips1000)
 
 
     # check buffer labware type
@@ -185,7 +234,7 @@ def run(ctx: protocol_api.ProtocolContext):
 following:\nopentrons plastic 50ml tubes')
 
     # load mastermix labware
-    buffer_rack = ctx.load_labware(
+    buffer_rack = robot.load_labware(
         BUFFER_LW_DICT[BUFFER_LABWARE], '10',
         BUFFER_LABWARE)
 
@@ -196,30 +245,36 @@ def run(ctx: protocol_api.ProtocolContext):
 
     # load elution labware
     dest_racks = [
-            ctx.load_labware(DESTINATION_LW_DICT[DESTINATION_LABWARE], slot,
+            robot.load_labware(DESTINATION_LW_DICT[DESTINATION_LABWARE], slot,
                             'Destination tubes labware ' + str(i+1))
             for i, slot in enumerate(['4', '1', '5', '2'])
     ]
 
     # setup sample sources and destinations
     bf_tubes = buffer_rack.wells()[:4]
     number_racks = math.ceil(NUM_SAMPLES/len(dest_racks[0].wells()))
+    dests = [
+        tube
+        for rack in dest_racks
+        for tube in rack.wells()
+    ]
 
-    # dest_sets is a list of lists. Each list is the destination well for each rack
-    # example: [[tube1,tube2,...tube24](first rack),[tube1,tube2(second rack),...]
-    dest_sets = [
-        [tube
-         for rack in dest_racks
-         for tube in rack.wells()
-        ][:NUM_SAMPLES][i*len(dest_racks[0].wells()):(i+1)*len(dest_racks[0].wells())]
-        for i in range(number_racks)
-        ]
+    # check top-left and bottom-right well of each labware with each pipette which uses them
+    pick_up(p1000, tips1000)
+    for position in [bf_tubes[0], bf_tubes[-1]]:
+        p1000.move_to(position.top())
+        robot.pause(f"Is it at the top of the well?")
+        p1000.aspirate(800, position.bottom(2))
+        p1000.move_to(position.top())
+        robot.pause(f"Did it aspirate correctly?")
+        p1000.dispense(800, position.top(-20))
+        p1000.move_to(position.top())
+        robot.pause(f"Did it dispense all the liquid?")
+    for position in [dests[0], dests[23], dests[24], dests[47], dests[48], dests[71], dests[72], dests[-1]]:
+        p1000.move_to(position.top())
+        robot.pause(f"Is it at the top of the well?")
+    drop(p1000)
 
-    # transfer buffer to tubes
-    for bf_tube,dests in zip(bf_tubes,dest_sets):
-        transfer_buffer(bf_tube, dests,VOLUME_BUFFER, p1000, tips1000)
 
     # track final used tip
     save_tip_info()
-
-    finish_run()