initial commit

.gitignore

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+ .DS_Store
+ app/.DS_Store	

Dockerfile

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+FROM tiangolo/uvicorn-gunicorn-fastapi:python3.9-slim
+
+# need to force reinstall because of dependeincies
+RUN pip install --no-cache-dir --upgrade pip && \
+    pip install --no-cache-dir fastapi uvicorn && \
+    pip install --no-cache-dir  --force-reinstall opentrons
+
+COPY ./app /app
+
+

README.md

@@ -1,11 +1,56 @@
----
-title: Simulator
-emoji: 📚
-colorFrom: purple
-colorTo: red
-sdk: docker
-pinned: false
-license: mit
----
-
-Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
+# api-for-simulator
+
+api server for opentrons-simulator
+
+## how to run locally
+
+```shell
+pip install -r requirements.txt
+
+cd app
+uvicorn main:app --reload
+```
+
+### docs
+
+```shell
+uvicorn main:app
+```
+
+Then go to http://localhost:8000/docs to check the api doc.
+
+`/protocol/id` does not work since it is a dummy function right now.
+
+## How to run the server with Dockerfile
+
+```shell
+git clone https://github.com/koji/api-for-simulator.git
+cd api-for-simulator
+docker build -t simulator-api:1.0.0 .
+```
+
+After building the image
+
+```shell
+docker run -d --name simulator-api-container -p 80:80 simulator-api:1.0.0
+```
+
+Check the container
+
+```shell
+docker ps -q -f "name=simulator-api-container" | xargs docker logs -f
+```
+
+Test the api server with curl or postman/httpie
+
+```shell
+curl localhost:80
+```
+
+## Tool
+
+- postman: https://www.postman.com/
+- httpie: https://httpie.io/
+
+- orbstack https://orbstack.dev/  
+  A GUI app for Docker which is better than Docker Desktop

app/main.py

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+from fastapi import FastAPI
+from pydantic import BaseModel
+from opentrons.simulate import simulate, format_runlog, get_protocol_api
+import os
+import io
+import subprocess
+
+app = FastAPI()
+
+
+@app.get("/")
+async def root():
+    return {"message": "this is a test api server"}
+
+
+@app.get("/protocols")
+def read_protocols():
+    protocols = get_file_names()
+    if len(protocols) == 0:
+        return "no stored protocol"
+    sorted_protocols = sorted(protocols)
+    return {"protocols": sorted_protocols}
+
+
+def get_file_names():
+    folder_path = 'storage'
+    # Check if the storage folder exists
+    if not os.path.exists(folder_path):
+        # Create the storage folder
+        os.makedirs(folder_path)
+        return []
+
+    file_names = []
+    for root, dirs, files in os.walk(folder_path):
+        for file in files:
+            file_names.append(file)
+
+    return file_names
+
+
+# @app.get("/protocols/{protocol_id}")
+# def read_protocol(protocol_id: int, q: str = None):
+#     # ToDo search folder and display a protocol file if there is a target protocol
+#     if q:
+#         return {"protocol_id": protocol_id, "q": q}
+#     return {"protocol_id": protocol_id}
+
+
+class Protocol(BaseModel):
+    name: str
+    content: str
+
+
+@app.post("/protocol")
+def upload_protocol(protocol: Protocol):
+    file_path = 'storage/' + protocol.name
+    save_result = save_text_as_file(protocol.content, file_path)
+
+    if type(save_result) == str:
+        # response = run_protocol_on_simulator(protocol.content)
+        response = call_opentrons_simulate(file_path)
+        print('response', response)
+        if response["status"] == "success":
+            return {"protocol_name": protocol.name, "run_log": response['run_log']}
+        else:
+            return {"error_message": response['error_message']}
+    else:
+        return {"error_message": "something wrong while saving a protocol"}
+
+
+def call_opentrons_simulate(protocol_path: str):
+    command = f"opentrons_simulate {protocol_path}"
+
+    result = subprocess.run(command, shell=True,
+                            capture_output=True, text=True)
+
+    if result.returncode == 0:
+        # print("Command executed successfully! Output:")
+        # print(result.stdout)
+        return {"status": "success", "run_log": result.stdout}
+    else:
+        print("Command failed. Error message:")
+        # print(result.stderr)
+        return {"status": "error", "error_message": result.stderr}
+
+
+def save_text_as_file(text, file_path):
+    base = os.path.splitext(file_path)[0]
+    ext = os.path.splitext(file_path)[1]
+    counter = 1
+
+    while os.path.exists(file_path):
+        file_path = base + "_" + str(counter) + ext
+        counter += 1
+
+    try:
+        with open(file_path, 'w') as file:
+            file.write(text)
+        print("Text saved successfully as", file_path)
+        return file_path
+    except Exception as e:
+        print("An error occurred while saving the file:", str(e))
+        return False

requirements.txt

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+fastapi
+opentrons
+uvicorn