Fixes from testing platecrane in BIO

Dockerfile

@@ -12,7 +12,6 @@ RUN apt update && apt install -y libusb-1.0-0-dev && rm -rf /var/lib/apt/lists/*
 
 RUN mkdir -p hudson_platecrane_module
 
-COPY ./platecrane_driver hudson_platecrane_module/platecrane_driver
 COPY ./src hudson_platecrane_module/src
 COPY ./README.md hudson_platecrane_module/README.md
 COPY ./pyproject.toml hudson_platecrane_module/pyproject.toml
@@ -21,5 +20,7 @@ COPY ./tests hudson_platecrane_module/tests
 RUN --mount=type=cache,target=/root/.cache \
     pip install -e ./hudson_platecrane_module
 
-CMD ["python", "hudson_platecrane_module/src/sciclops_rest_node.py"]
+RUN usermod -aG dialout app
+
+CMD ["python", "-,", "sciclops_rest_node"]
 #########################################

Makefile

@@ -7,8 +7,6 @@ PROJECT_VERSION := $(shell grep -oP '(?<=version = ")[^"]+' $(PYPROJECT_TOML) |
 .PHONY += init paths checks test clean
 init: # Do the initial configuration of the project
 	@test -e .env || cp example.env .env
-	@sed -i 's/^USER_ID=.*/USER_ID=$(shell id -u)/' .env
-	@sed -i 's/^GROUP_ID=.*/GROUP_ID=$(shell id -g)/' .env
 	@sed -i 's/^PROJECT_VERSION=.*/PROJECT_VERSION=$(PROJECT_VERSION)/' .env
 	@sed -i 's/^PROJECT_PATH=.*/PROJECT_PATH=$(shell pwd | sed 's/\//\\\//g')/' .env
 

compose.yaml

@@ -10,11 +10,11 @@ services:
         - ${IMAGE}:latest
         - ${IMAGE}:${PROJECT_VERSION}
         - ${IMAGE}:dev
-    command: python hudson_platecrane_module/src/sciclops_rest_node.py --port 2000
+    command: python -m platecrane_rest_node --port 2000 --device ${DEVICE}
     privileged: true
     env_file: .env
     volumes:
-      - ${DEVICE}:/dev/ttyUSB0
+      - /dev:/dev
       - ./src:/home/app/hudson_platecrane_module/src
       - ./tests:/home/app/hudson_platecrane_module/tests
     ports:

example.env

@@ -1,6 +1,4 @@
 # Note: all paths are relative to the docker compose file
-USER_ID=
-GROUP_ID=
 DEVICE=/dev/ttyUSB2
 PROJECT_PATH=
 PROJECT_VERSION=1.2.0

pyproject.toml

@@ -33,12 +33,6 @@ homepage = "https://github.com/AD-SDL/hudson_platecrane_module"
 requires = ["setuptools", "wheel"]
 build-backend = "setuptools.build_meta"
 
-
-[tool.setuptools.packages.find]
-where = ["."]
-include = ["src*", "platecrane_driver*"]
-exclude = ["*tests*"]
-
 #####################
 # Development Tools #
 #####################

platecrane_driver/platecrane_driver.py → src/platecrane_driver/platecrane_driver.py

@@ -2,7 +2,9 @@
 import json
 import re
 
-from serial_port import SerialPort
+from pathlib import Path
+
+from platecrane_driver.serial_port import SerialPort
 
 
 class PlateCrane:
@@ -46,12 +48,12 @@ def __init__(self, host_path="/dev/ttyUSB2", baud_rate=9600):
 
         self.plate_resources = json.load(
             open(
-                "/home/rpl/wei_ws/src/platecrane_module/platecrane_driver/platecrane_driver/plate_resources.json"
+                Path(__file__).parent / "plate_resources.json"
             )
         )
         self.stack_resources = json.load(
             open(
-                "/home/rpl/wei_ws/src/platecrane_module/platecrane_driver/platecrane_driver/stack_resources.json"
+                Path(__file__).parent / "stack_resources.json"
             )
         )
 

src/platecrane_driver/test.py

@@ -0,0 +1,152 @@
+
+
+
+
+
+if __name__ == "__main__":
+    import platecrane_driver
+    """
+    Runs given function.
+    """
+    s = platecrane_driver.PlateCrane("/dev/ttyUSB2")
+    # s.initialize()
+    # s.home()
+    stack4 = "Stack4"
+    stack5 = "Stack5"
+    solo6 = "Solo.Position6"
+    solo4 = "Solo.Position4"
+    solo3 = "Solo.Position3"
+    target_loc = "HidexNest2"
+    lidnest3 = "LidNest3"
+    sealer = "SealerNest"
+    # s.move_location("Safe")
+
+    # s.move_location("Stack4")
+    #s.move_single_axis("Z", "Safe", delay_time=1)  # move all the way up in z height
+
+    # print(s.get_location_list())
+
+    # s.transfer("Stack4","Solo.Position1",source_type="stack",target_type="stack",height_offset=800)  # test from stack to solo pos 1
+    #s.transfer("Stack4","Solo.Position1",source_type="stack",target_type="stack")   # Stack 4 to SOLO 1
+
+    # s.transfer("Solo.Position1","Stack5",source_type="stack",target_type="stack")   # SOLO 1 --> Stack 5
+
+    # s.transfer("Stack5","Solo.Position1",source_type="stack",target_type="stack")   # Stack 4 to SOLO 1
+
+    ###
+    #s.transfer("Solo.Position1","Stack3",source_type="stack",target_type="stack")   
+
+    # s.transfer("Stack2","PeelerNest",source_type="stack",target_type="stack")   
+
+    # s.transfer("PeelerNest","Stack2",source_type="stack",target_type="stack")   
+
+    #s.transfer("Stack2","LidNest1",source_type="stack",target_type="stack")   
+    # s.transfer("Stack1","LidNest1",source_type="stack",target_type="stack") 
+    # s.transfer("LidNest1","Solo.Position1",source_type="stack",target_type="stack")  
+    # s.transfer("Solo.Position1","PeelerNest", source_type="stack", target_type="stack") 
+    # s.transfer("PeelerNest","Stack1",source_type="stack",target_type="stack")   
+
+    #s.transfer("Solo.Position1","Hidex.Nest",source_type="stack",target_type="module") 
+
+
+
+    # s.transfer("LidNest2","LidNest3",source_type="stack",target_type="stack")  
+
+    # s.transfer("LidNest3". "Solo.Position2", source_type="stack", target_type="stack")
+    # s.transfer("PeelerNest","Stack2",source_type="stack",target_type="stack")   
+
+    # s.transfer("PeelerNest","Stack2",source_type="stack",target_type="stack")   
+
+
+
+    ###
+    # s.transfer("Solo.Position1","Hidex.Nest",source_type="stack",target_type="module", height_offset=700)   # SOLO 1 to Hidex 
+
+    # s.transfer("Hidex.Nest","Solo.Position1",source_type="module",target_type="module")   # Stack 4 to SOLO 1
+
+
+
+
+    ### Hidex Recalibration
+
+    #print(s.get_position())
+
+    #s.set_location("Safe", 195399, 2646, 0, 0)
+
+
+    s.transfer("Hidex.Nest","Sealer.Nest",source_type="module",target_type="stack", height_offset = 650)
+
+
+    print(s.get_location_list())
+
+
+# old sealer nest 28:SealerNest, 210256, -1050, 491, 5730
+
+
+
+# ----------------------------------------------------------------------------------------------------------------------------------------
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+    # s.pick_stack_plate("Stack1")  
+    # a = s.get_position()
+    # s.set_location("LidNest3",R=231449,Z=-31500,P=484,Y=-306)
+
+    # s.set_location("Hidex.Nest",R=a[0],Z=a[1],P=a[2],Y=a[3])
+    # s.place_module_plate("Hidex.Nest")
+    # s.move_single_axis("Z","Hidex.Nest")
+    # s.transfer("Hidex.Nest","Solo.Position1",source_type="module",target_type="stack",height_offset=800)
+    # s.transfer("Stack1", "PeelerNest",source_type="stack",target_type="stack")
+
+    # s.place_module_plate()
+    # s.get_location_list()
+
+    # s.move_joints_neutral()
+    # s.move_single_axis("R", "Safe", delay_time=1)
+    # s.set_location("Safe",R=195399,Z=0,P=0,Y=0)
+    # s.set_location("LidNest2",R=131719,Z=-31001,P=-5890,Y=-315)
+    # s.transfer(source="LidNest1",target="LidNest2",source_type="stack",target_type="stack", plate_type="96_well")
+
+    # s.transfer(source="LidNest2",target="LidNest3",source_type="stack",target_type="stack", plate_type="96_well")
+    # s.transfer("Stack1","Stack1")
+    # s.free_joints()
+    # s.lock_joints()
+
+    # s.set_location("LidNest3",R=99817,Z=-31001,P=-5890,Y=-315)
+
+    # s.get_location_joint_values("HidexNest2")
+    # s.set_location("HidexNest2", R=210015,Z=-30400,P=490,Y=2323)
+
+    # s.transfer(stack5, solo4, source_type = "stack", target_type = "module", plate_type = "96_deep_well")
+    # s.transfer(solo4, stack5, source_type = "module", target_type = "stack", plate_type = "96_deep_well")
+
+    # s.remove_lid(source = "LidNest1", target="LidNest2", plate_type="96_well")
+    # s.transfer("Stack4", solo3, source_type = "stack", target_type = "stack", plate_type = "tip_box_lid_off")
+    # s.remove_lid(source = solo6, target="LidNest3", plate_type="tip_box_lid_on")
+    # s.replace_lid(source = "LidNest3", target = solo6, plate_type = "tip_box_lid_on")
+    # s.replace_lid(source = "LidNest2", target = solo4, plate_type = "96_well")
+    # s.transfer(solo4, stack5, source_type = "module", target_type = "stack", plate_type = "96_well")
+    # s.transfer(solo6, "Stack2", source_type = "module", target_type = "stack", plate_type = "tip_box_lid_on")
+
+
+#    Crash error outputs 21(R axis),14(z axis), 02 Wrong location name. 1400 (Z axis hits the plate), 00 success 
+# TODO: Need a response handler function. Unkown error messages T1, ATS, TU these are about connection issues (multiple access?)
+# TODO: Slow the arm before hitting the plate in pick_stack_plate
+# TODO: Create a plate detect function within pick stack plate function
+# TODO: Maybe write another pick stack funtion to remove the plate detect movement
+

src/platecrane_rest_node.py

@@ -2,8 +2,9 @@
 """The server for the Hudson Platecrane/Sciclops that takes incoming WEI flow requests from the experiment application"""
 
 import json
-from argparse import ArgumentParser
+from argparse import ArgumentParser, Namespace
 from contextlib import asynccontextmanager
+import traceback
 from pathlib import Path
 
 from fastapi import FastAPI
@@ -22,6 +23,17 @@
 
 global platecrane, state
 
+def parse_args() -> Namespace:
+    parser = ArgumentParser()
+    parser.add_argument(
+        "--host",
+        type=str,
+        default="0.0.0.0",
+        help="Hostname that the REST API will be accessible on",
+    )
+    parser.add_argument("--port", type=int, default=2002)
+    parser.add_argument("--device", type=str, default="/dev/ttyUSB0")
+    return parser.parse_args()
 
 @asynccontextmanager
 async def lifespan(app: FastAPI):
@@ -36,10 +48,13 @@ async def lifespan(app: FastAPI):
     None"""
     global platecrane, state
 
+    args = parse_args()
+
     try:
-        platecrane = PlateCrane()
+        platecrane = PlateCrane(host_path=args.device)
 
     except Exception as error_msg:
+        traceback.print_exc()
         state = "PLATECRANE CONNECTION ERROR"
         print("------- PlateCrane Error message: " + str(error_msg) + (" -------"))
 
@@ -67,8 +82,8 @@ async def about():
     """Returns a description of the actions and resources the module supports"""
     global state
     about = ModuleAbout(
-        name="Sciclops Robotic Arm",
-        description="Sciclops is a robotic arm module that grabs a plate from a specific tower location.",
+        name="Hudson Platecrane",
+        description="Platecrane is a robotic arm module that can pick up and move plates between locations.",
         interface="wei_rest_node",
         version=extract_version(Path(__file__).parent.parent / "pyproject.toml"),
         actions=[
@@ -274,15 +289,8 @@ def do_action(action_handle: str, action_vars):
 if __name__ == "__main__":
     import uvicorn
 
-    parser = ArgumentParser()
-    parser.add_argument(
-        "--host",
-        type=str,
-        default="0.0.0.0",
-        help="Hostname that the REST API will be accessible on",
-    )
-    parser.add_argument("--port", type=int, default=2002)
-    args = parser.parse_args()
+    args = parse_args()
+
     uvicorn.run(
         "platecrane_rest_node:app",
         host=args.host,