updated for dynamic env

Dockerfile

@@ -1,4 +1,5 @@
 FROM condaforge/miniforge3:latest
+# FROM continuumio/miniconda3:main
 
 LABEL org.opencontainers.image.title="bio-compose-server-base" \
     org.opencontainers.image.description="Base Docker image for BioCompose REST API management, job processing, and datastorage with MongoDB, ensuring scalable and robust performance." \
@@ -15,53 +16,74 @@ COPY assets/docker/config/.pys_usercfg.ini /Pysces/.pys_usercfg.ini
 COPY assets/docker/config/.pys_usercfg.ini /root/Pysces/.pys_usercfg.ini
 COPY tests/test_fixtures /test_fixtures
 
-WORKDIR /app
+WORKDIR /bio-compose-server
 
 # copy container libs
-COPY ./gateway /app/gateway
-COPY ./shared /app/shared
-COPY ./worker /app/worker
+COPY ./gateway /bio-compose-server/gateway
+COPY ./shared /bio-compose-server/shared
+COPY ./worker /bio-compose-server/worker
 
 # copy env configs
-COPY ./environment.yml /app/environment.yml
-COPY ./pyproject.toml /app/pyproject.toml
+COPY ./environment.yml /bio-compose-server/environment.yml
+COPY ./pyproject.toml /bio-compose-server/pyproject.toml
+RUN echo "Server" > /bio-compose-server/README.md
 
-
-# install deps
 RUN mkdir config \
-    && apt-get update  \
-    && apt install -y \
-    meson \
-    g++ \
-    gfortran \
-    libblas-dev \
-    liblapack-dev \
-    libgfortran5 \
-    libhdf5-dev \
-    libhdf5-serial-dev \
-    libatlas-base-dev \
-    cmake \
-    make \
-    git \
-    build-essential \
-    python3-dev \
-    swig \
-    libc6-dev \
-    libx11-dev \
-    libc6 \
-    libgl1-mesa-dev \
-    pkg-config \
-    curl \
-    tar \
-    libgl1-mesa-glx \
-    libice6 \
-    libsm6 \
-    gnupg \
-    nano \
-    libstdc++6 \
-    && conda update -n base -c conda-forge conda \
-    && conda env create -f environment.yml -y
+    && apt-get update \
+    && apt-get install -y \
+        meson \
+        g++ \
+        gfortran \
+        libblas-dev \
+        liblapack-dev \
+        libgfortran5 \
+        libhdf5-dev \
+        libhdf5-serial-dev \
+        libatlas-base-dev \
+        cmake \
+        make \
+        git \
+        build-essential \
+        python3-dev \
+        swig \
+        libc6-dev \
+        libx11-dev \
+        libc6 \
+        libgl1-mesa-dev \
+        pkg-config \
+        curl \
+        tar \
+        libgl1-mesa-glx \
+        libice6 \
+        libsm6 \
+        gnupg \
+        libstdc++6
+
+RUN conda update -n base -c conda-forge conda \
+    && conda env create -f /bio-compose-server/environment.yml -y \
+    && echo "conda activate server" >> /.bashrc
+
+RUN conda run -n server poetry config virtualenvs.create false \
+    && conda run -n server poetry lock \
+    && conda run -n server poetry install \
+    && conda run -n server poetry run pip install biosimulator-processes[cobra,copasi,smoldyn] \
+    && conda install -n server pymem3dg -y
+
+
+# && conda run -n server poetry config virtualenvs.create false \
+# && conda run -n server poetry lock \
+# && conda run -n server poetry install \
+# && poetry run pip install
+
+# && conda create -n server python=3.10 -y \
+# && conda run -n server pip install --upgrade pip
+# && conda run -n server pip install -e .
 
+# && conda config --env --add channels conda-forge \
+# && conda config --set channel_priority strict \
+# && conda install readdy \
+# && conda env create -f environment.yml -y
+# && conda install -c conda-forge pymem3dg -y \
 # && echo 'export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:\$LD_LIBRARY_PATH' >> ~/.bashrc
 
 # expose for gateway

README.md

@@ -1,55 +1 @@
-![Deploy API](https://github.com/biosimulators/bio-check/actions/workflows/deploy-gateway.yml/badge.svg)
-![Deploy Worker](https://github.com/biosimulators/bio-check/actions/workflows/deploy-worker.yml/badge.svg)
-
-# BioCompose Server: A Biological Simulation Verification Service
-### __This service utilizes separate containers for REST API management, job processing, and datastorage with MongoDB, ensuring scalable and robust performance.__
-
-## **The REST API can be accessed via Swagger UI here: [https://compose.biosimulations.org/docs](https://compose.biosimulations.org/docs)
-
-## **For Developers:**
-
-### This application ("BioCompose") uses a microservices architecture which presents the following libraries:
-
-- `gateway`: This library handles all requests including saving uploaded files, pending job creation, fetching results, and contains the user-facing endpoints.
-- `shared`: A library of common objects/pointers used by both `gateway` and `worker`.
-- `worker`: This library handles all job processing tasks for verification services such as job status adjustment, job retrieval, and more.
-
-### The simulators used by this application consist of multiple python language bindings of C/C++ libraries. Given this fact, is it helpful to be aware of the dependency network required by each simulator. See the following documentation for simulators used in this application:
-
-- [AMICI](https://amici.readthedocs.io/en/latest/python_installation.html)
-- [COPASI(basico)](https://basico.readthedocs.io/en/latest/quickstart/get-started.html#installation)
-- [PySCes](https://pyscesdocs.readthedocs.io/en/latest/userguide_doc.html#installing-and-configuring)
-- [Tellurium](https://tellurium.readthedocs.io/en/latest/installation.html)
-- [Simulator-specific implementations of the Biosimulators-Utils interface](https://docs.biosimulations.org/users/biosimulators-packages)
-- [Smoldyn](https://www.smoldyn.org/SmoldynManual.pdf)
-- *(Coming soon:)* [ReaDDy](https://readdy.github.io/installation.html)
-
-
-### Dependency management scopes are handled as follows:
-
-#### _*Locally/Dev*_:
-- Anaconda via `environment.yml` - the closest to local development at root level which mimics what actually happens in the containers (conda deps tend to break more frequently than poetry.)
-
-_*Remotely in microservice containers*_:
-- Remote microservice container management is handled by `conda` via `environment.yml` files for the respective containers.
-
-### The installation process is outlined as follows:
-
-1. `git clone https://github.com/biosimulators/bio-compose-server.git`
-2. `cd bio-compose-server/shared`
-3. `mv .env_template .env`
-4. Enter the following fields into the `.env` file: 
-
-        MONGO_URI=<uri of your mongo instance. In this case we use the standard mongodb image with the app name bio-check>
-        GOOGLE_APPLICATION_CREDENTIALS=<path to your gcloud credentials .json file. Contact us for access>
-        BUCKET_NAME=bio-check-requests-1  # name of the bucket used in this app
-5. `cd ..`
-6. Pull and run the latest version of Mongo from the Docker Hub. (`docker run -d -it mongo:latest` or similar.)
-7. `sudo chmod +x ./assets/dev/scripts/install.sh`
-8. `./install.sh`
-
-
-## Notes:
-- This application currently uses MongoDB as the database store in which jobs are read/written. Database access is given to both the `api` and `worker` libraries. Such database access is 
-executed/implemented with the use of a `Supervisor` singleton.
-
+#BioCompose Server

docker-compose.yaml

@@ -8,6 +8,7 @@ services:
       - appnetwork
 
   gateway:
+    platform: linux/amd64
     build:
       context: .
       dockerfile: Dockerfile
@@ -17,19 +18,20 @@ services:
       - "3001:3001"
     networks:
       - appnetwork
-    command: poetry run uvicorn gateway.main:app --host 0.0.0.0 --port 3001 --reload
+    command: conda run -n server uvicorn gateway.main:app --host 0.0.0.0 --port 3001 --reload
     depends_on:
       - mongodb
 
   compose-worker:
+    platform: linux/amd64
     build:
       context: .
       dockerfile: Dockerfile
     image: ghcr.io/biosimulators/bio-compose-server-worker:0.0.1
     container_name: worker
     networks:
       - appnetwork
-    command: poetry run python worker/main.py
+    command: conda run -n server python worker/main.py
     depends_on:
       - mongodb
 

environment.yml

@@ -11,33 +11,36 @@ dependencies:
   - poetry
   # - readdy
   # - pymem3dg
-  - pip:
-      - uvicorn
-      - fastapi
-      - mypy
-      - pytest
-      - pip-autoremove
-      - networkx
-      - rustworkx
-      - qiskit
-      - qiskit-ibm-runtime
-      - qiskit-nature
-      - pylatexenc
-      - numpy
-      - pandas
-      - process-bigraph==0.0.22
-      - copasi-basico
-      - tellurium
-      - python-libsbml
-      - smoldyn
-      - requests-toolbelt
-      - python-dotenv
-      - google-cloud-storage
-      - python-multipart
-      - toml
-      - typing-extensions
-      - pymongo
-      - pydantic
-      - pydantic-settings
-      - chardet
-      - pyyaml
+  # - pip:
+      # - google-cloud-storage
+      # - typing-extensions
+      # - uvicorn
+      # - fastapi
+      # - mypy
+      # - pytest
+      # - pip-autoremove
+      # - networkx
+      # - rustworkx
+      # - qiskit
+      # - qiskit-ibm-runtime
+      # - qiskit-nature
+      # - pylatexenc
+      # - numpy
+      # - pandas
+      # - process-bigraph==0.0.22
+      # - copasi-basico
+      # - tellurium
+      # - python-libsbml
+      # - smoldyn
+      # - requests-toolbelt
+      # - python-dotenv
+      # - google-cloud-storage
+      # - python-multipart
+      # - toml
+      # - typing-extensions
+      # - pymongo
+      # - pydantic
+      # - pydantic-settings
+      # - chardet
+      # - pyyaml
+      # - biosimulator-processes

gateway/main.py

@@ -21,10 +21,15 @@
     DbClientResponse,
     AgentParameters,
     BigraphRegistryAddresses,
-    IncompleteJob
+    IncompleteJob,
+    DB_TYPE,
+    DB_NAME,
+    BUCKET_NAME,
+    JobStatus,
+    DatabaseCollections
 )
-from shared_api import MongoDbConnector, DB_NAME, DB_TYPE, BUCKET_NAME, JobStatus, DatabaseCollections, file_upload_prefix
-from io_api import write_uploaded_file, download_file_from_bucket
+from shared.database import MongoDbConnector
+from shared.io import write_uploaded_file, download_file_from_bucket
 from shared.log_config import setup_logging
 
 
@@ -509,7 +514,7 @@ async def generate_simularium_file(
 ):
     job_id = "files-generate-simularium-file" + str(uuid.uuid4())
     _time = db_connector.timestamp()
-    upload_prefix, bucket_prefix = file_upload_prefix(job_id)
+    # upload_prefix, bucket_prefix = file_upload_prefix(job_id)
     uploaded_file_location = await write_uploaded_file(job_id=job_id, uploaded_file=uploaded_file, bucket_name=BUCKET_NAME, extension='.txt')
 
     # new simularium job in db
@@ -542,21 +547,36 @@ async def generate_simularium_file(
     # raise HTTPException(status_code=404, detail=f"A simularium file cannot be parsed from your input. Please check your input file and refer to the simulariumio documentation for more details.")
 
 
+# @app.get(
+#     "/get-process-bigraph-addresses",
+#     operation_id="get-process-bigraph-addresses",
+#     response_model=BigraphRegistryAddresses,
+#     tags=["Composition"],
+#     summary="Get process bigraph implementation addresses for composition specifications.")
+# async def get_process_bigraph_addresses() -> BigraphRegistryAddresses:
+#     registry = await db_connector.read(collection_name="bigraph_registry", version="latest")
+#     if registry is not None:
+#         addresses = registry.get('registered_addresses')
+#         version = registry.get('version')
+#
+#         return BigraphRegistryAddresses(registered_addresses=addresses, version=version)
+#     else:
+#         raise HTTPException(status_code=500, detail="Addresses not found.")
+
+
 @app.get(
     "/get-process-bigraph-addresses",
     operation_id="get-process-bigraph-addresses",
     response_model=BigraphRegistryAddresses,
     tags=["Composition"],
     summary="Get process bigraph implementation addresses for composition specifications.")
 async def get_process_bigraph_addresses() -> BigraphRegistryAddresses:
-    registry = await db_connector.read(collection_name="bigraph_registry", version="latest")
-    if registry is not None:
-        addresses = registry.get('registered_addresses')
-        version = registry.get('version')
-
-        return BigraphRegistryAddresses(registered_addresses=addresses, version=version)
-    else:
-        raise HTTPException(status_code=500, detail="Addresses not found.")
+    from bsp import app_registrar
+    addresses = list(app_registrar.core.process_registry.registry.keys())
+    version = "latest"
+    return BigraphRegistryAddresses(registered_addresses=addresses, version=version)
+    # else:
+    #     raise HTTPException(status_code=500, detail="Addresses not found.")
 
 
 @app.get(