feat: refactored architecture to use a simple websocket connection manager

Dockerfile

@@ -36,11 +36,10 @@ RUN echo "Server" > /app/README.md \
     && chmod +x /app/entrypoint.sh
 #
 RUN conda update -n base -c conda-forge conda \
-    && conda env create -f /app/environment.yml -y \
-    && conda run -n server poetry self update \
-    && echo "conda activate server" >> /.bashrc \
-    && conda run -n server pip install --upgrade pip
-    # && conda run -n server pip install --no-cache-dir git+https://github.com/vivarium-collective/process-bigraph.git@main
+    && conda env create -f /app/env.yml -y \
+    && conda update -n compose-server numpy -y \
+    && pip install -e .
+
 
 ENTRYPOINT ["/bin/bash"]
 

README.md

@@ -2,3 +2,22 @@
 ![Worker Deployment](https://github.com/biosimulators/compose-server/actions/workflows/deploy-worker.yml/badge.svg)
 
 # BioCompose Server
+
+## *FOR DEVS*:
+
+### _Generate gRPC service stubs:_
+```bash
+python shared/parse_proto.py
+```
+
+### _Generate OpenAPI spec yml:_
+```bash
+python client/openapi_spec.py
+```
+
+### _Apply overlay changes_:
+```bash
+cd kustomize \
+  && kubectl kustomize overlays/compose | kubectl apply -f - \
+  && cd ..
+```

app/DataService.js

@@ -0,0 +1,55 @@
+class VivariumService {
+    constructor(root= 'http://127.0.0.1:3001') {
+        this.root = root;
+        this.testId = 'test';
+    }
+
+    formatUrl(root, duration, id) {
+        return `${root}/run-vivarium?duration=${duration}&vivarium_id=${id}`;
+    }
+
+    async fetchStream(url) {
+        const response = await fetch(url);
+        const reader = response.body.getReader();
+        const decoder = new TextDecoder();
+
+        let jsonData = "";
+        let isFirstChunk = true;
+
+        while (true) {
+            const {done, value} = await reader.read();
+            if (done) {
+                console.log("Stream finished.");
+                break;
+            }
+
+            jsonData += decoder.decode(value);
+
+            try {
+                if (isFirstChunk) {
+                    jsonData = jsonData.replace('{"updates": [', "[");  // ✅ Handle initial chunk
+                    isFirstChunk = false;
+                }
+
+                if (jsonData.endsWith("]}")) {
+                    const parsedData = JSON.parse(jsonData);
+                    console.log("Final JSON:", parsedData);
+                    break;
+                } else {
+                    console.log("Streaming JSON chunk received:", jsonData);
+                }
+            } catch (e) {
+                console.log("Waiting for more JSON data...");
+            }
+        }
+    }
+
+    submitRequest(duration, id) {
+        const url = this.formatUrl(this.root, duration, id);
+        return this.fetchStream(url);
+    }
+
+    sendTestRequest(duration) {
+        return this.submitRequest(duration, this.testId);
+    }
+}

assets/deployment/compose.envoy.yml

@@ -0,0 +1,12 @@
+version: "3"
+services:
+  envoy:
+    image: envoyproxy/envoy:v1.21.0
+    ports:
+      - "9901:9901"
+    volumes:
+      - ./envoy.yaml:/etc/envoy/envoy.yaml
+  grpc_server:
+    image: my_grpc_service
+    ports:
+      - "50051:50051"

assets/deployment/envoy.yml

@@ -0,0 +1,60 @@
+static_resources:
+  listeners:
+    - name: grpc_listener
+      address:
+        socket_address:
+          address: 0.0.0.0
+          port_value: 9901
+      filter_chains:
+        - filters:
+            - name: envoy.filters.network.http_connection_manager
+              typed_config:
+                "@type": type.googleapis.com/envoy.extensions.filters.network.http_connection_manager.v3.HttpConnectionManager
+                codec_type: AUTO
+                stat_prefix: grpc_proxy
+                route_config:
+                  name: local_route
+                  virtual_hosts:
+                    - name: grpc_services
+                      domains: ["*"]
+                      routes:
+                        - match: { prefix: "/" }
+                          route:
+                            cluster: grpc_service
+                            timeout: 0s
+                http_filters:
+                  - name: envoy.filters.http.grpc_json_transcoder
+                    typed_config:
+                      "@type": type.googleapis.com/envoy.extensions.filters.http.grpc_json_transcoder.v3.GrpcJsonTranscoder
+                      proto_descriptor: "/path/to/proto.pb"
+                      services:
+                        - my.grpc.Service
+                      print_options:
+                        add_whitespace: true
+                        always_print_primitive_fields: true
+                        always_print_enums_as_ints: false
+                  - name: envoy.filters.http.router
+
+
+
+  clusters:
+    - name: grpc_service
+      type: STRICT_DNS
+      connect_timeout: 5s
+      lb_policy: ROUND_ROBIN
+      http2_protocol_options: { }
+      load_assignment:
+        cluster_name: grpc_service
+        endpoints:
+          - lb_endpoints:
+              - endpoint:
+                  address:
+                    socket_address:
+                      address: grpc_server1
+                      port_value: 50051
+              - endpoint:
+                  address:
+                    socket_address:
+                      address: grpc_server2
+                      port_value: 50052
+

assets/docker/Dockerfile-base

@@ -0,0 +1,87 @@
+# FROM condaforge/miniforge3:24.9.2-0
+FROM condaforge/miniforge3:latest
+
+LABEL org.opencontainers.image.title="bio-compose-server-worker" \
+    org.opencontainers.image.description="Base Docker image for BioCompose REST API management, job processing, and datastorage with MongoDB, ensuring scalable and robust performance." \
+    org.opencontainers.image.url="https://compose.biosimulators.org/" \
+    org.opencontainers.image.source="https://github.com/biosimulators/bio-compose-server" \
+    org.opencontainers.image.authors="Alexander Patrie <[email protected]>, BioSimulators Team <[email protected]>" \
+    org.opencontainers.image.vendor="BioSimulators Team"
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+ARG INSTALL_WORKER
+
+# RUN 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 \
+#         && apt-get clean
+
+# copy assets
+COPY assets/docker/config/.biosimulations.json /.google/.bio-compose.json
+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
+
+# copy env configs
+COPY ./environment.yml /app/environment.yml
+COPY ./pyproject.toml /app/pyproject.toml
+COPY ./gateway /app/gateway
+COPY ./shared /app/shared
+COPY ./worker /app/worker
+COPY ./common /app/common
+
+RUN echo "Server" > /app/README.md \
+    && mkdir /app/config
+
+# create base env
+RUN conda install cmake ninja pybind11 scikit-build-core -y
+RUN conda run pip install -e . \
+    && conda env export --from-history > /app/env-export.yml
+
+# && conda install --file=/app/environment.yml \
+# RUN mamba install conda-forge::readdy -y
+# RUN mamba create -n server python=3.11 cmake ninja pybind11 scikit-build-core -y
+# RUN mamba run -n server pip install -e . \
+#     && mamba env export -n server --from-history > /app/env-export.yml
+
+# handle worker(simulators)
+# RUN if [ "$INSTALL_WORKER" == "1" ]; then \
+#     mamba install conda-forge::pymem3dg -y conda-forge::readdy \
+# fi
+
+#     && conda install -n bsp conda-forge::readdy -y
+
+
+# build alone with:
+# docker build -f ./assets/docker/Dockerfile-base -t BASE .
+
+

client/.VERSION

@@ -0,0 +1 @@
+0.0.1

client/Dockerfile-client

@@ -0,0 +1,41 @@
+FROM condaforge/miniforge3:24.9.2-0
+
+LABEL org.opencontainers.image.title="bio-compose-server-gateway" \
+    org.opencontainers.image.description="Base Docker image for BioCompose REST API management, job processing, and datastorage with MongoDB, ensuring scalable and robust performance." \
+    org.opencontainers.image.url="https://compose.biosimulators.org/" \
+    org.opencontainers.image.source="https://github.com/biosimulators/bio-compose-server" \
+    org.opencontainers.image.authors="Alexander Patrie <[email protected]>, BioSimulators Team <[email protected]>" \
+    org.opencontainers.image.vendor="BioSimulators Team"
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+# copy assets
+COPY assets/docker/config/.biosimulations.json /.google/.bio-compose.json
+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
+
+# copy env configs
+COPY ./environment.yml /app/environment.yml
+COPY ./pyproject.toml /app/pyproject.toml
+COPY ./gateway /app/gateway
+COPY ./shared /app/shared
+COPY ./worker /app/worker
+COPY ./common /app/common
+
+RUN echo "Server" > /app/README.md \
+    && mkdir /app/config
+#
+RUN conda update -n base -c conda-forge conda \
+    && conda env create -f /app/environment.yml -y \
+    && conda run -n compose-server pip install -e . \
+    && conda run -n compose-server python /app/gateway/openapi_spec.py
+
+# CMD ["conda", "run", "-n", "compose-server", "uvicorn", "gateway.main:app", "--host", "0.0.0.0", "--port", "3001", "--reload"]
+
+# EXPOSE 3001
+
+CMD ["conda", "run", "-n", "compose-server", "uvicorn", "gateway.main:app", "--host", "0.0.0.0", "--port", "3001", "--reload"]
+