feat(api,robot-server): Add Dockerfile and docker-compose file (#7836)

* docker file.

* docker-compose

* Controller will build simulating gpio object so no reason for the check.

* Update docker-compose.yml

Co-authored-by: Sam! Bonfante <[email protected]>

* Update docker-compose.yml

Co-authored-by: Sam! Bonfante <[email protected]>

* override config dir

* only copy files needed for the build.

* need manifest

* added readme.

* formatter

Co-authored-by: Sam! Bonfante <[email protected]>

closes #7674

.dockerignore

@@ -0,0 +1,38 @@
+./api-server
+./app
+./labware-library
+./node_modules
+./protocol-designer
+./discovery-client
+./coverage
+./components
+./app-shell
+./update-server
+./step-generation
+
+.pytest_cache
+.flake8
+.idea
+.pypy_cache
+dist
+build
+yarn.lock
+Pipfile.lock
+
+__pycache__
+*.pyc
+*.pyo
+*.pyd
+.Python
+env
+pip-log.txt
+pip-delete-this-directory.txt
+.tox
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+*.log
+.git

.opentrons_config/config.json

@@ -0,0 +1,18 @@
+{
+  "labware_database_file": "/config/opentrons.db",
+  "labware_calibration_offsets_dir_v2": "/config/labware/v2/offsets",
+  "labware_user_definitions_dir_v2": "/config/labware/v2/custom_definitions",
+  "feature_flags_file": "/config/feature_flags.json",
+  "robot_settings_file": "/config/robot_settings.json",
+  "deck_calibration_file": "/config/deck_calibration.json",
+  "log_dir": "/config/logs",
+  "api_log_file": "/config/logs/api.log",
+  "serial_log_file": "/config/logs/serial.log",
+  "wifi_keys_dir": "/config/user_storage/opentrons_data/network_keys",
+  "hardware_controller_lockfile": "/config/hardware.lock",
+  "pipette_config_overrides_dir": "/config/pipettes",
+  "tip_length_calibration_dir": "/config/tip_lengths",
+  "robot_calibration_dir": "/config/robot",
+  "pipette_calibration_dir": "/config/robot/pipettes",
+  "custom_tiprack_dir": "/config/tip_lengths/custom_tiprack_definitions"
+}

.opentrons_config/feature_flags.json

@@ -0,0 +1,17 @@
+{
+  "shortFixedTrash": null,
+  "calibrateToBottom": null,
+  "deckCalibrationDots": null,
+  "useProtocolApi2": null,
+  "disableHomeOnBoot": null,
+  "useOldAspirationFunctions": null,
+  "enableDoorSafetySwitch": null,
+  "enableTipLengthCalibration": null,
+  "enableHttpProtocolSessions": null,
+  "enableFastProtocolUpload": null,
+  "enableProtocolEngine": null,
+  "disableLogAggregation": null,
+  "enableApi1BackCompat": null,
+  "useV1HttpApi": null,
+  "_version": 9
+}

.opentrons_config/pipettes/P20SV202020070101.json

@@ -0,0 +1 @@
+{ "model": "p20_single_v2.0" }

.opentrons_config/pipettes/P3HMV202020041605.json

@@ -0,0 +1 @@
+{ "model": "p20_multi_v2.0" }

CONTRIBUTING.md

@@ -1,4 +1,3 @@
-
 # Contributing Guide
 
 Thanks for your interest in contributing to the Opentrons platform! This Contributing Guide is intended to ensure best practices for both internal Opentrons contributors as well as any external contributors. We want to make sure you’re set up to contribute effectively, no matter if you’re helping us out with bug reports, code, documentation, feature suggestions, or anything else. This guide covers:
@@ -150,6 +149,7 @@ Your computer will need the following tools installed to be able to develop with
   ```
 
   **MacOS Big Sur Note:** due to this [known issue](https://github.com/pyenv/pyenv/issues/1737) we recommend using:
+
   ```shell
   pyenv install 3.7.10
   ```

DOCKER.md

@@ -0,0 +1,28 @@
+Docker Guide  
+=======================  
+Included in this repo are the tools to run a containerized Opentrons robot stack in docker.
+
+This includes the `robot-server` connected to the hardware emulation application. The emulation application includes the Smoothie and magnetic, temperature, and thermocycler modules.
+
+## Requirements
+
+- A clone of this repo.
+- An installation [docker](https://docs.docker.com/get-docker/)
+- An installation of [docker-compose](https://docs.docker.com/compose/install/)
+
+## How to use
+
+Start a terminal and change directory to the root of this repo.
+
+1. Build
+   Enter `docker-compose build --force-rm` at the terminal.
+
+2. Run
+   Enter `docker-compose up` at the terminal. _The build and run stages can be combined `docker-compose up --build`._
+
+3. Start the Opentrons application. The docker container will appear as `dev`. Connect and run just as you would on a robot.
+
+## Known Issues
+
+- Pipettes cannot be changed at run time.
+- Pipettes are fixed as `p20_multi_v2.0` on the left mount and `p20_single_v2.0` on the right.

Dockerfile

@@ -0,0 +1,29 @@
+FROM ubuntu as base
+RUN apt-get update && apt-get install -y python3 pip
+
+FROM base as builder
+COPY scripts scripts
+COPY LICENSE LICENSE
+
+COPY shared-data shared-data
+
+COPY api/MANIFEST.in api/MANIFEST.in
+COPY api/setup.py api/setup.py
+COPY api/pypi-readme.rst api/pypi-readme.rst
+COPY api/src/opentrons api/src/opentrons
+
+COPY notify-server/setup.py notify-server/setup.py
+COPY notify-server/README.rst notify-server/README.rst
+COPY notify-server/notify_server notify-server/notify_server
+
+COPY robot-server/setup.py robot-server/setup.py
+COPY robot-server/robot_server robot-server/robot_server
+
+RUN cd shared-data/python && python3 setup.py bdist_wheel -d /dist/
+RUN cd api && python3 setup.py bdist_wheel -d /dist/
+RUN cd notify-server && python3 setup.py bdist_wheel -d /dist/
+RUN cd robot-server && python3 setup.py bdist_wheel -d /dist/
+
+FROM base
+COPY --from=builder /dist /dist
+RUN pip install /dist/*

api/MANIFEST.in

@@ -1,5 +1,4 @@
 include src/opentrons/package.json
 graft src/opentrons/config
 graft src/opentrons/resources
-include src/opentrons/server/openapi.json
 exclude pyproject.toml

api/src/opentrons/hardware_control/controller.py

@@ -269,17 +269,16 @@ def disengage_axes(self, axes: List[str]):
         self._smoothie_driver.disengage_axis(''.join(axes))
 
     def set_lights(self, button: Optional[bool], rails: Optional[bool]):
-        if opentrons.config.IS_ROBOT:
-            if button is not None:
-                self.gpio_chardev.set_button_light(blue=button)
-            if rails is not None:
-                self.gpio_chardev.set_rail_lights(rails)
+        if button is not None:
+            self.gpio_chardev.set_button_light(blue=button)
+        if rails is not None:
+            self.gpio_chardev.set_rail_lights(rails)
 
     def get_lights(self) -> Dict[str, bool]:
-        if not opentrons.config.IS_ROBOT:
-            return {}
-        return {'button': self.gpio_chardev.get_button_light()[2],
-                'rails': self.gpio_chardev.get_rail_lights()}
+        return {
+            'button': self.gpio_chardev.get_button_light()[2],
+            'rails': self.gpio_chardev.get_rail_lights()
+        }
 
     def pause(self):
         self._smoothie_driver.pause()

api/src/opentrons/hardware_control/emulation/app.py

@@ -28,7 +28,7 @@ async def run_server(host: str, port: int, handler: ConnectionHandler) -> None:
 
 async def run() -> None:
     """Run the module emulators."""
-    host = "127.0.0.1"
+    host = "0.0.0.0"
 
     await asyncio.gather(
         run_server(host=host,

docker-compose.yml

@@ -0,0 +1,27 @@
+version: '3'
+services:
+  emulator:
+    build: .
+    command: python3 -m opentrons.hardware_control.emulation.app
+    ports:
+      - '9996:9996'
+      - '9997:9997'
+      - '9998:9998'
+      - '9999:9999'
+  robot-server:
+    build: .
+    command: uvicorn "robot_server:app" --host 0.0.0.0 --port 31950 --ws wsproto --reload
+    ports:
+      - '31950:31950'
+    environment:
+      - OT_API_CONFIG_DIR=/config
+      - OT_SMOOTHIE_EMULATOR_URI=socket://emulator:9996
+      - OT_THERMOCYCLER_EMULATOR_URI=socket://emulator:9997
+      - OT_TEMPERATURE_EMULATOR_URI=socket://emulator:9998
+      - OT_MAGNETIC_EMULATOR_URI=socket://emulator:9999
+    links:
+      - 'emulator'
+    depends_on:
+      - 'emulator'
+    volumes:
+      - .opentrons_config:/config:rw

robot-server/setup.py

@@ -52,7 +52,11 @@ def get_version():
 INSTALL_REQUIRES = [
     'fastapi==0.54.1',
     'python-multipart==0.0.5',
+    'uvicorn==0.11.3',
+    'python-dotenv',
     'opentrons',
+    'wsproto==0.15.0',
+    'typing-extensions>=3.7.4.3',
 ]