{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Validating against log file example\n",
"\n",
"All communication between PLR and the outside world (the hardware) happens through the io layer. This is a layer below backends, and is responsible for sending and receiving messages to and from the hardware. Schematically,\n",
"\n",
"```\n",
"Frontends <-> backends <-> io <-> hardware\n",
"```\n",
"\n",
"PLR supports capturing all communication in the io layer, both write and read commands. This can later be played back to validate that a protocol has not changed. The key here is that if we send the same commands to the hardware, the hardware will do the same thing. \"Reading\" data (from the capture file) is useful because some protocols are dynamic and depend on responses from the hardware.\n",
"\n",
"In this notebook, we will run a simple protocol on a robot while capturing all data passing through the io layer. We will then replay the capture file while executing the protocol again to demonstrate how validation works. Finally, we slightly modify the protocol and show that the validation fails."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Defining a simple protocol"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"import pylabrobot\n",
"from pylabrobot.liquid_handling import LiquidHandler\n",
"from pylabrobot.liquid_handling.backends import STAR\n",
"from pylabrobot.resources.hamilton import STARDeck\n",
"\n",
"backend = STAR()\n",
"lh = LiquidHandler(backend=backend, deck=STARDeck())"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"from pylabrobot.resources import TIP_CAR_480_A00, HT\n",
"tip_car = TIP_CAR_480_A00(name=\"tip_car\")\n",
"tip_car[0] = tr = HT(name=\"ht\")\n",
"lh.deck.assign_child_resource(tip_car, rails=1)"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"async def simple_protocol(tips):\n",
" await lh.setup()\n",
" await lh.pick_up_tips(tips)\n",
" await lh.return_tips()\n",
" await lh.stop()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Capturing data during protocol execution"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Do a real run first, without validating against a capture file. This will generate the capture file you can later compare against.\n",
"\n",
"While it might seem cumbersome, this actually ensures you have a real working protocol before doing validation. The benefit of using capture files is whenever you change your protocol and have seen it run, you can just grab the capture file and use it for validation. No need to manually write tests."
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Validation file written to validation.json\n"
]
}
],
"source": [
"validation_file = \"./validation.json\"\n",
"pylabrobot.start_capture(validation_file)\n",
"await simple_protocol(tr[\"A1:H1\"])\n",
"pylabrobot.stop_capture()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"The validation file is just json:"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"{\n",
" \"version\": \"0.1.6\",\n",
" \"commands\": [\n",
" {\n",
" \"module\": \"usb\",\n",
" \"device_id\": \"[0x8af:0x8000][][]\",\n",
" \"action\": \"write\",\n",
" \"data\": \"C0RTid0001\"\n",
" },\n",
" {\n",
" \"module\": \"usb\",\n",
" \"device_id\": \"[0x8af:0x8000][][]\",\n",
" \"action\": \"read\",\n",
" \"data\": \"C0RTid0001er00/00rt0 0 0 0 0 0 0 0\"\n",
" },\n"
]
}
],
"source": [
"!head -n15 validation.json"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Replaying the capture file for validation"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"On validation, before calling setup, run `pylabrobot.validate` to enable the validation. Pass a capture file that contains the commands we should check against.\n",
"\n",
"Call `pylabrobot.end_validation` at the end to make sure there are no remaining commands in the capture file. This marks the end of the validation."
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Validation successful!\n"
]
}
],
"source": [
"pylabrobot.validate(validation_file)\n",
"await simple_protocol(tr[\"A1:H1\"])\n",
"pylabrobot.end_validation()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Failing validation"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"When validation is not successful, we use the Needleman-Wunsch algorithm to find the difference between the expected and the actual output."
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"expected: C0TPid0009xp01179 01179 01179 01179 01179 01179 01179 01179yp1458 1368 1278 1188 1098 1008 0918 0828tm1 1 1 1 1 1 1 1tt01tp2266tz2166th2450td0\n",
"actual: C0TPid0009xp01269 01269 01269 01269 01269 01269 01269 01269yp1458 1368 1278 1188 1098 1008 0918 0828tm1 1 1 1 1 1 1 1tt01tp2266tz2166th2450td0\n",
" ^^ ^^ ^^ ^^ ^^ ^^ ^^ ^^ \n"
]
},
{
"ename": "ValidationError",
"evalue": "Data mismatch: difference was written to stdout.",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mValidationError\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[7], line 2\u001b[0m\n\u001b[1;32m 1\u001b[0m pylabrobot\u001b[38;5;241m.\u001b[39mvalidate(validation_file)\n\u001b[0;32m----> 2\u001b[0m \u001b[38;5;28;01mawait\u001b[39;00m simple_protocol(tr[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mA2:H2\u001b[39m\u001b[38;5;124m\"\u001b[39m])\n\u001b[1;32m 3\u001b[0m pylabrobot\u001b[38;5;241m.\u001b[39mend_validation()\n",
"Cell \u001b[0;32mIn[3], line 3\u001b[0m, in \u001b[0;36msimple_protocol\u001b[0;34m(tips)\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[38;5;28;01masync\u001b[39;00m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21msimple_protocol\u001b[39m(tips):\n\u001b[1;32m 2\u001b[0m \u001b[38;5;28;01mawait\u001b[39;00m lh\u001b[38;5;241m.\u001b[39msetup()\n\u001b[0;32m----> 3\u001b[0m \u001b[38;5;28;01mawait\u001b[39;00m lh\u001b[38;5;241m.\u001b[39mpick_up_tips(tips)\n\u001b[1;32m 4\u001b[0m \u001b[38;5;28;01mawait\u001b[39;00m lh\u001b[38;5;241m.\u001b[39mreturn_tips()\n\u001b[1;32m 5\u001b[0m \u001b[38;5;28;01mawait\u001b[39;00m lh\u001b[38;5;241m.\u001b[39mstop()\n",
"File \u001b[0;32m~/retro/pylabrobot/pylabrobot/machines/machine.py:35\u001b[0m, in \u001b[0;36mneed_setup_finished.<locals>.wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m 33\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msetup_finished:\n\u001b[1;32m 34\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mRuntimeError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mThe setup has not finished. See `setup`.\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m---> 35\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m func(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n",
"File \u001b[0;32m~/retro/pylabrobot/pylabrobot/liquid_handling/liquid_handler.py:467\u001b[0m, in \u001b[0;36mLiquidHandler.pick_up_tips\u001b[0;34m(self, tip_spots, use_channels, offsets, **backend_kwargs)\u001b[0m\n\u001b[1;32m 464\u001b[0m (\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mhead[channel]\u001b[38;5;241m.\u001b[39mcommit \u001b[38;5;28;01mif\u001b[39;00m success \u001b[38;5;28;01melse\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mhead[channel]\u001b[38;5;241m.\u001b[39mrollback)()\n\u001b[1;32m 466\u001b[0m \u001b[38;5;66;03m# trigger callback\u001b[39;00m\n\u001b[0;32m--> 467\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_trigger_callback\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 468\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mpick_up_tips\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 469\u001b[0m \u001b[43m \u001b[49m\u001b[43mliquid_handler\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 470\u001b[0m \u001b[43m \u001b[49m\u001b[43moperations\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mpickups\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 471\u001b[0m \u001b[43m \u001b[49m\u001b[43muse_channels\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43muse_channels\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 472\u001b[0m \u001b[43m \u001b[49m\u001b[43merror\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43merror\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 473\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mbackend_kwargs\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 474\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m~/retro/pylabrobot/pylabrobot/liquid_handling/liquid_handler.py:2204\u001b[0m, in \u001b[0;36mLiquidHandler._trigger_callback\u001b[0;34m(self, method_name, error, *args, **kwargs)\u001b[0m\n\u001b[1;32m 2202\u001b[0m callback(\u001b[38;5;28mself\u001b[39m, \u001b[38;5;241m*\u001b[39margs, error\u001b[38;5;241m=\u001b[39merror, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m 2203\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m error \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[0;32m-> 2204\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m error\n",
"File \u001b[0;32m~/retro/pylabrobot/pylabrobot/liquid_handling/liquid_handler.py:451\u001b[0m, in \u001b[0;36mLiquidHandler.pick_up_tips\u001b[0;34m(self, tip_spots, use_channels, offsets, **backend_kwargs)\u001b[0m\n\u001b[1;32m 449\u001b[0m error: Optional[\u001b[38;5;167;01mException\u001b[39;00m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m 450\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 451\u001b[0m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mbackend\u001b[38;5;241m.\u001b[39mpick_up_tips(ops\u001b[38;5;241m=\u001b[39mpickups, use_channels\u001b[38;5;241m=\u001b[39muse_channels, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mbackend_kwargs)\n\u001b[1;32m 452\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mException\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m 453\u001b[0m error \u001b[38;5;241m=\u001b[39m e\n",
"File \u001b[0;32m~/retro/pylabrobot/pylabrobot/liquid_handling/backends/hamilton/STAR.py:1484\u001b[0m, in \u001b[0;36mSTAR.pick_up_tips\u001b[0;34m(self, ops, use_channels, begin_tip_pick_up_process, end_tip_pick_up_process, minimum_traverse_height_at_beginning_of_a_command, pickup_method)\u001b[0m\n\u001b[1;32m 1481\u001b[0m pickup_method \u001b[38;5;241m=\u001b[39m pickup_method \u001b[38;5;129;01mor\u001b[39;00m tip\u001b[38;5;241m.\u001b[39mpickup_method\n\u001b[1;32m 1483\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m-> 1484\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mpick_up_tip(\n\u001b[1;32m 1485\u001b[0m x_positions\u001b[38;5;241m=\u001b[39mx_positions,\n\u001b[1;32m 1486\u001b[0m y_positions\u001b[38;5;241m=\u001b[39my_positions,\n\u001b[1;32m 1487\u001b[0m tip_pattern\u001b[38;5;241m=\u001b[39mchannels_involved,\n\u001b[1;32m 1488\u001b[0m tip_type_idx\u001b[38;5;241m=\u001b[39mttti,\n\u001b[1;32m 1489\u001b[0m begin_tip_pick_up_process\u001b[38;5;241m=\u001b[39mbegin_tip_pick_up_process,\n\u001b[1;32m 1490\u001b[0m end_tip_pick_up_process\u001b[38;5;241m=\u001b[39mend_tip_pick_up_process,\n\u001b[1;32m 1491\u001b[0m minimum_traverse_height_at_beginning_of_a_command\u001b[38;5;241m=\u001b[39mminimum_traverse_height_at_beginning_of_a_command,\n\u001b[1;32m 1492\u001b[0m pickup_method\u001b[38;5;241m=\u001b[39mpickup_method,\n\u001b[1;32m 1493\u001b[0m )\n\u001b[1;32m 1494\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m STARFirmwareError \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m 1495\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m plr_e \u001b[38;5;241m:=\u001b[39m convert_star_firmware_error_to_plr_error(e):\n",
"File \u001b[0;32m~/retro/pylabrobot/pylabrobot/liquid_handling/backends/hamilton/STAR.py:98\u001b[0m, in \u001b[0;36mneed_iswap_parked.<locals>.wrapper\u001b[0;34m(self, *args, **kwargs)\u001b[0m\n\u001b[1;32m 93\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39miswap_installed \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39miswap_parked:\n\u001b[1;32m 94\u001b[0m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mpark_iswap(\n\u001b[1;32m 95\u001b[0m minimum_traverse_height_at_beginning_of_a_command\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mint\u001b[39m(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_iswap_traversal_height \u001b[38;5;241m*\u001b[39m \u001b[38;5;241m10\u001b[39m)\n\u001b[1;32m 96\u001b[0m )\n\u001b[0;32m---> 98\u001b[0m result \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m method(\u001b[38;5;28mself\u001b[39m, \u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m 100\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m result\n",
"File \u001b[0;32m~/retro/pylabrobot/pylabrobot/liquid_handling/backends/hamilton/STAR.py:4062\u001b[0m, in \u001b[0;36mSTAR.pick_up_tip\u001b[0;34m(self, x_positions, y_positions, tip_pattern, tip_type_idx, begin_tip_pick_up_process, end_tip_pick_up_process, minimum_traverse_height_at_beginning_of_a_command, pickup_method)\u001b[0m\n\u001b[1;32m 4055\u001b[0m \u001b[38;5;28;01massert\u001b[39;00m (\n\u001b[1;32m 4056\u001b[0m \u001b[38;5;241m0\u001b[39m \u001b[38;5;241m<\u001b[39m\u001b[38;5;241m=\u001b[39m end_tip_pick_up_process \u001b[38;5;241m<\u001b[39m\u001b[38;5;241m=\u001b[39m \u001b[38;5;241m3600\u001b[39m\n\u001b[1;32m 4057\u001b[0m ), \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mend_tip_pick_up_process must be between 0 and 3600\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[1;32m 4058\u001b[0m \u001b[38;5;28;01massert\u001b[39;00m (\n\u001b[1;32m 4059\u001b[0m \u001b[38;5;241m0\u001b[39m \u001b[38;5;241m<\u001b[39m\u001b[38;5;241m=\u001b[39m minimum_traverse_height_at_beginning_of_a_command \u001b[38;5;241m<\u001b[39m\u001b[38;5;241m=\u001b[39m \u001b[38;5;241m3600\u001b[39m\n\u001b[1;32m 4060\u001b[0m ), \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mminimum_traverse_height_at_beginning_of_a_command must be between 0 and 3600\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m-> 4062\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msend_command(\n\u001b[1;32m 4063\u001b[0m module\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mC0\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m 4064\u001b[0m command\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mTP\u001b[39m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m 4065\u001b[0m tip_pattern\u001b[38;5;241m=\u001b[39mtip_pattern,\n\u001b[1;32m 4066\u001b[0m read_timeout\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m60\u001b[39m,\n\u001b[1;32m 4067\u001b[0m xp\u001b[38;5;241m=\u001b[39m[\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mx\u001b[38;5;132;01m:\u001b[39;00m\u001b[38;5;124m05\u001b[39m\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;28;01mfor\u001b[39;00m x \u001b[38;5;129;01min\u001b[39;00m x_positions],\n\u001b[1;32m 4068\u001b[0m yp\u001b[38;5;241m=\u001b[39m[\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00my\u001b[38;5;132;01m:\u001b[39;00m\u001b[38;5;124m04\u001b[39m\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;28;01mfor\u001b[39;00m y \u001b[38;5;129;01min\u001b[39;00m y_positions],\n\u001b[1;32m 4069\u001b[0m tm\u001b[38;5;241m=\u001b[39mtip_pattern,\n\u001b[1;32m 4070\u001b[0m tt\u001b[38;5;241m=\u001b[39m\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mtip_type_idx\u001b[38;5;132;01m:\u001b[39;00m\u001b[38;5;124m02\u001b[39m\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m 4071\u001b[0m tp\u001b[38;5;241m=\u001b[39m\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mbegin_tip_pick_up_process\u001b[38;5;132;01m:\u001b[39;00m\u001b[38;5;124m04\u001b[39m\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m 4072\u001b[0m tz\u001b[38;5;241m=\u001b[39m\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mend_tip_pick_up_process\u001b[38;5;132;01m:\u001b[39;00m\u001b[38;5;124m04\u001b[39m\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m 4073\u001b[0m th\u001b[38;5;241m=\u001b[39m\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mminimum_traverse_height_at_beginning_of_a_command\u001b[38;5;132;01m:\u001b[39;00m\u001b[38;5;124m04\u001b[39m\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m,\n\u001b[1;32m 4074\u001b[0m td\u001b[38;5;241m=\u001b[39mpickup_method\u001b[38;5;241m.\u001b[39mvalue,\n\u001b[1;32m 4075\u001b[0m )\n",
"File \u001b[0;32m~/retro/pylabrobot/pylabrobot/liquid_handling/backends/hamilton/base.py:247\u001b[0m, in \u001b[0;36mHamiltonLiquidHandler.send_command\u001b[0;34m(self, module, command, auto_id, tip_pattern, write_timeout, read_timeout, wait, fmt, **kwargs)\u001b[0m\n\u001b[1;32m 222\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"Send a firmware command to the Hamilton machine.\u001b[39;00m\n\u001b[1;32m 223\u001b[0m \n\u001b[1;32m 224\u001b[0m \u001b[38;5;124;03mArgs:\u001b[39;00m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 237\u001b[0m \u001b[38;5;124;03m A dictionary containing the parsed response, or None if no response was read within `timeout`.\u001b[39;00m\n\u001b[1;32m 238\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 240\u001b[0m cmd, id_ \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_assemble_command(\n\u001b[1;32m 241\u001b[0m module\u001b[38;5;241m=\u001b[39mmodule,\n\u001b[1;32m 242\u001b[0m command\u001b[38;5;241m=\u001b[39mcommand,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 245\u001b[0m \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs,\n\u001b[1;32m 246\u001b[0m )\n\u001b[0;32m--> 247\u001b[0m resp \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mawait\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_write_and_read_command(\n\u001b[1;32m 248\u001b[0m id_\u001b[38;5;241m=\u001b[39mid_,\n\u001b[1;32m 249\u001b[0m cmd\u001b[38;5;241m=\u001b[39mcmd,\n\u001b[1;32m 250\u001b[0m write_timeout\u001b[38;5;241m=\u001b[39mwrite_timeout,\n\u001b[1;32m 251\u001b[0m read_timeout\u001b[38;5;241m=\u001b[39mread_timeout,\n\u001b[1;32m 252\u001b[0m wait\u001b[38;5;241m=\u001b[39mwait,\n\u001b[1;32m 253\u001b[0m )\n\u001b[1;32m 254\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m resp \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m \u001b[38;5;129;01mand\u001b[39;00m fmt \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 255\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_parse_response(resp, fmt)\n",
"File \u001b[0;32m~/retro/pylabrobot/pylabrobot/liquid_handling/backends/hamilton/base.py:267\u001b[0m, in \u001b[0;36mHamiltonLiquidHandler._write_and_read_command\u001b[0;34m(self, id_, cmd, write_timeout, read_timeout, wait)\u001b[0m\n\u001b[1;32m 258\u001b[0m \u001b[38;5;28;01masync\u001b[39;00m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_write_and_read_command\u001b[39m(\n\u001b[1;32m 259\u001b[0m \u001b[38;5;28mself\u001b[39m,\n\u001b[1;32m 260\u001b[0m id_: Optional[\u001b[38;5;28mint\u001b[39m],\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 264\u001b[0m wait: \u001b[38;5;28mbool\u001b[39m \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mTrue\u001b[39;00m,\n\u001b[1;32m 265\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m Optional[\u001b[38;5;28mstr\u001b[39m]:\n\u001b[1;32m 266\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"Write a command to the Hamilton machine and read the response.\"\"\"\u001b[39;00m\n\u001b[0;32m--> 267\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mio\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mwrite\u001b[49m\u001b[43m(\u001b[49m\u001b[43mcmd\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mencode\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtimeout\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mwrite_timeout\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 269\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m wait:\n\u001b[1;32m 270\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m\n",
"File \u001b[0;32m~/retro/pylabrobot/pylabrobot/io/usb.py:325\u001b[0m, in \u001b[0;36mUSBValidator.write\u001b[0;34m(self, data, timeout)\u001b[0m\n\u001b[1;32m 323\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m next_command\u001b[38;5;241m.\u001b[39mdata \u001b[38;5;241m==\u001b[39m data\u001b[38;5;241m.\u001b[39mdecode(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124municode_escape\u001b[39m\u001b[38;5;124m\"\u001b[39m):\n\u001b[1;32m 324\u001b[0m align_sequences(expected\u001b[38;5;241m=\u001b[39mnext_command\u001b[38;5;241m.\u001b[39mdata, actual\u001b[38;5;241m=\u001b[39mdata\u001b[38;5;241m.\u001b[39mdecode(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124municode_escape\u001b[39m\u001b[38;5;124m\"\u001b[39m))\n\u001b[0;32m--> 325\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m ValidationError(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mData mismatch: difference was written to stdout.\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n",
"\u001b[0;31mValidationError\u001b[0m: Data mismatch: difference was written to stdout."
]
}
],
"source": [
"pylabrobot.validate(validation_file)\n",
"await simple_protocol(tr[\"A2:H2\"])\n",
"pylabrobot.end_validation()"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "env",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.19"
}
},
"nbformat": 4,
"nbformat_minor": 2
}