Added Dockerfile and endpoints

Dockerfile

@@ -0,0 +1,18 @@
+FROM python:3.9-slim
+WORKDIR /app
+
+COPY . /app
+
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends git \
+    && apt-get install -y --no-install-recommends gcc \
+    && apt-get install -y --no-install-recommends cmake \
+    && apt-get purge -y --auto-remove
+
+
+RUN pip3 install . --no-cache-dir
+
+COPY pyenzyme_server.py /app
+
+ENTRYPOINT ["uvicorn"]
+CMD ["pyenzyme_server.py"]

pyenzyme/enzymeml/tools/enzymemlwriter.py

@@ -555,7 +555,7 @@ def _addReactions(self, model: libsbml.Model, reaction_dict: dict[str, EnzymeRea
             conditionsMapping = {
                 'enzymeml:temperature': {
                     'value': 'temperature',
-                    'unit': 'temperature_unit_id'
+                    'unit': '_temperature_unit_id'
                 },
                 'enzymeml:ph': {
                     'value': 'ph'

pyenzyme_server.py

@@ -1,16 +1,21 @@
 import os
-import shutil
 
-from fastapi import FastAPI
+from fastapi import FastAPI, UploadFile, File
 from starlette.responses import FileResponse
+from starlette.background import BackgroundTasks
 
 from pyenzyme.enzymeml.core.enzymemldocument import EnzymeMLDocument
+from pyenzyme.enzymeml.core.measurement import Measurement
 
 app = FastAPI()
 
 
+def remove_file(path: str) -> None:
+    os.unlink(path)
+
+
 @app.post("/create")
-def create_EnzymeML(enzmldoc: EnzymeMLDocument):
+async def create_EnzymeML(enzmldoc: EnzymeMLDocument, background_tasks: BackgroundTasks):
 
     def _convertUnits(dictionary: dict, key: str):
         """Converts all units to unit_ids and stores them in the model"""
@@ -77,4 +82,67 @@ def _convertUnits(dictionary: dict, key: str):
         return str(e)
 
     finally:
-        shutil.rmt
+        background_tasks.add_task(remove_file, path=file_name)
+
+
+@app.post("/read")
+async def read_enzymeml(background_tasks: BackgroundTasks, omex_archive: UploadFile = File(...)):
+
+    # Write to file
+    file_name = omex_archive.filename
+    content = await omex_archive.read()
+    with open(file_name, "wb") as file_handle:
+        file_handle.write(content)
+
+    # Read EnzymeML document
+    try:
+        enzmldoc = EnzymeMLDocument.fromFile(file_name)
+        return enzmldoc.dict(exclude_none=True)
+    except Exception as e:
+        return str(e)
+    finally:
+        background_tasks.add_task(remove_file, path=file_name)
+
+
+@app.post("/add_measurement")
+async def add_Measurement(
+    background_tasks: BackgroundTasks,
+    measurement: Measurement,
+    omex_archive: UploadFile = File(...)
+):
+
+    # Check if the species_dict keys are correct
+    for key in measurement.species_dict:
+        if key not in ["reactants", "proteins"]:
+            return {"error": f"Key '{key}' is not valid for species dict. Please use either 'reactants' or 'proteins'"}
+
+    # Write to file
+    file_name = omex_archive.filename
+    content = await omex_archive.read()
+    with open(file_name, "wb") as file_handle:
+        file_handle.write(content)
+
+    # Read EnzymeML document
+    enzmldoc = EnzymeMLDocument.fromFile(file_name)
+
+    # Add the measurement
+    enzmldoc.addMeasurement(measurement)
+
+    # Write the new EnzymeML file
+    try:
+        dirpath = "."
+        file_name = f"{enzmldoc.name.replace(' ', '_')}.omex"
+        file_path = os.path.join(
+            dirpath,
+            file_name
+        )
+
+        enzmldoc.toFile(dirpath)
+
+        return FileResponse(file_path, filename=file_name)
+
+    except Exception as e:
+        return str(e)
+
+    finally:
+        background_tasks.add_task(remove_file, path=file_name)

setup.py

@@ -31,7 +31,6 @@
         'numpy',
         'pandas',
         'python-libcombine',
-        'python-copasi',
         'openpyxl',
         'marshmallow',
         'scipy',
@@ -40,7 +39,9 @@
         'pydataverse',
         'pydantic',
         'deprecation',
-        'deepdiff'
+        'deepdiff',
+        'python-multipart',
+        'uvicorn'
     ],
     extras_require={
         'test': [