Merge pull request #20 from biosimulators/major-bigraph-refactor

major refactor for process-bigraph content

.dockerignore

@@ -42,4 +42,6 @@ __pycache__/
 api/__pycache__
 worker/__pycache__
 test.ipynb
-worker/.composition
+worker/.composition
+worker/.worker_STABLE
+*.egg-info

.github/workflows/ci.yml

@@ -21,10 +21,9 @@ jobs:
       - name: Install deps and run tests
         run: |
           pip install --upgrade pip
-          pip install poetry 
-          poetry env use 3.10
-          poetry install --only=github
-          poetry run pytest
+          pip install -r assets/pipeline/config/requirements.github.ci.txt 
+          cd worker
+          python -B test_worker.py 
 
   build-base-image:
     runs-on: ubuntu-latest
@@ -58,15 +57,15 @@ jobs:
       - name: Extract API container version
         id: extract_api_version
         run: |
-          API_VERSION=$(python3 .github/parse_container_version.py api)
+          API_VERSION=$(python -B .github/parse_container_version.py api)
           echo "API_VERSION=$API_VERSION" >> $GITHUB_ENV
           echo "API Version: $API_VERSION"
 
       # Step 6: Extract worker container version
       - name: Extract worker container version
         id: extract_worker_version
         run: |
-          WORKER_VERSION=$(python3 .github/parse_container_version.py worker)
+          WORKER_VERSION=$(python -B .github/parse_container_version.py worker)
           echo "WORKER_VERSION=$WORKER_VERSION" >> $GITHUB_ENV
           echo "WORKER Version: $WORKER_VERSION"
 

.github/workflows/deploy-microservices.yml

@@ -1,7 +1,5 @@
 name: Deploy Microservices
 
-# on:
-#   workflow_dispatch:
 on:
   workflow_run:
     workflows: ["Deploy Base Image"]
@@ -20,15 +18,15 @@ jobs:
       - name: Extract API container version
         id: extract_api_version
         run: |
-          API_VERSION=$(python3 .github/parse_container_version.py api)
+          API_VERSION=$(python -B .github/parse_container_version.py api)
           echo "API_VERSION=$API_VERSION" >> $GITHUB_ENV
           echo "API Version: $API_VERSION"
 
       # Step 6: Extract worker container version
       - name: Extract worker container version
         id: extract_worker_version
         run: |
-          WORKER_VERSION=$(python3 .github/parse_container_version.py worker)
+          WORKER_VERSION=$(python -B .github/parse_container_version.py worker)
           echo "WORKER_VERSION=$WORKER_VERSION" >> $GITHUB_ENV
           echo "WORKER Version: $WORKER_VERSION"
 
@@ -59,7 +57,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -r assets/pipeline/config/requirements.github.txt
+          pip install -r assets/pipeline/config/requirements.github.cd.txt
 
       - name: Install Docker Compose
         run: |
@@ -76,7 +74,7 @@ jobs:
       - name: Deploy API microservice container to GHCR
         run: |
           rm api/spec/openapi_3_1_0_generated.yaml
-          python3 api/openapi_spec.py
+          python -B api/openapi_spec.py
           sudo rm -r api/__pycache__
           ./assets/docker/scripts/push_image.sh api ${{ env.API_VERSION }}
         env:
@@ -88,7 +86,7 @@ jobs:
 
       - name: Deploy worker microservice container to GHCR
         run: |
-          sudo rm -r compose_api/__pycache__
+          sudo rm -r worker/__pycache__
           ./assets/docker/scripts/push_image.sh worker ${{ env.WORKER_VERSION }}
         # STABLE CONTENT:
         # run: |

.gitignore

@@ -24,3 +24,5 @@ test.ipynb
 poetry.lock
 *_parsetab.py
 condaenv.n_dn60fa.requirements.txt
+worker/.worker_STABLE
+build

Dockerfile-base

@@ -14,13 +14,17 @@ SHELL ["/usr/bin/env", "bash", "-c"]
 ENV DEBIAN_FRONTEND=noninteractive \
     MONGO_URI="mongodb://mongodb/?retryWrites=true&w=majority&appName=bio-check" \
     POETRY_VIRTUALENVS_CREATE=false \
-    POETRY_NO_INTERACTION=1
+    POETRY_NO_INTERACTION=1 \
+    TEST_SBML_FP="test-fixtures/sbml-core/Elowitz-Nature-2000-Repressilator/BIOMD0000000012_url.xml" \
+    TEST_PSC_FP="/Pysces/psc/BIOMD0000000012_url.xml.psc" \
+    TEST_OMEX_FP="test-fixtures/sbml-core/Elowitz-Nature-2000-Repressilator.omex"
 
 # copy docker
 COPY assets/docker/config/.biosimulations.json /.google/.bio-check.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 assets/docker/shared.py assets/test_fixtures /app/
+COPY assets/docker/shared.py /app/shared.py
+COPY assets/test-fixtures /app/test-fixtures
 COPY assets/docker/config/environment.base.yml /app/environment.base.yml
 
 # cd /app
@@ -35,9 +39,16 @@ RUN mkdir -p /Pysces \
     && echo "conda activate server" >> ~/.bashrc \
     && source ~/.bashrc \
     && conda env export --no-builds -f config/environment.base.lock.yml \
-    && rm -f environment.base.yml
+    && rm -f environment.base.yml \
+    && conda clean --all -y
 
 
+# to run with a local network:
+# net=app-net
+# docker network create "$net"
+# docker run -d --rm --name "$lib" --net "$net" --platform linux/amd64 "$PKG_ROOT"-"$lib":latest
+# docker run -it --name "$lib" --net "$net" --platform linux/amd64 "$PKG_ROOT"-"$lib"
+
 # # create conda env from yml and ensure env activation
 # RUN conda env create -f config/environment.base.yml -y \
 #     && rm -f config/environment.base.yml \

README.md

@@ -7,7 +7,7 @@
 
 ## **For Developers:**
 
-### This application (`bio_check`) uses a microservices architecture which presents the following libraries:
+### This application ("BioCompose") uses a microservices architecture which presents the following libraries:
 
 - `api`: This library handles all requests including saving uploaded files, pending job creation, fetching results, and contains the user-facing endpoints.
 - `storage`: This library handles MongoDB configs as well as bucket-like storages for uploaded files.
@@ -28,8 +28,7 @@ the dependency network required by each simulator. See the following documentati
 ### Dependency management scopes are handled as follows:
 
 #### _*Locally/Dev*_:
-- Python poetry via `pyproject.toml` - the most stable/reproducible method, yet the farthest from what is actually happening in the service containers as they use conda.
-- Anaconda via `environment.yml` - the closest to local development at root level which micics what actually happens in the containers (conda deps tend to break more frequently than poetry.)
+- 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.
@@ -46,12 +45,17 @@ _*Remotely in microservice containers*_:
         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. Run one of the following commands based on your preference:
+7. Create a conda env from the environment file at the root of this repo:
 
-        conda env create -n bio-compose-server-dev -f environment.yml
-
-        # OR
-        poetry env use 3.10 && poetry install
+        conda env create -f environment.yml -y && conda activate bio-composer-server-dev
+8. Install pysces with conda and amici with pip:
+
+        conda install -c conda-forge -c pysces pysces
+        conda run pip3 install biosimulators-amici  # installs both biosimulators and amici
+9. If using Smoldyn, there is a arm-based mac installation script in `assets/dev/` called `install-smoldyn-mac-silicon.sh`. So run the following:
+
+        sudo chmod +x ./assets/dev/scripts/install-smoldyn-mac-silicon.sh  # or whichever method you are using to install
+        ./assets/dev/scripts/install-smoldyn-mac-silicon.sh  # conda is configured to install Smoldyn into its environment
 
 
 ## Notes:

api/Dockerfile-api

@@ -4,20 +4,21 @@
 # FROM ghcr.io/biosimulators/bio-compose-server-base:latest
 
 # TODO: change this back to latest once stable
-FROM ghcr.io/biosimulators/bio-compose-server-base:0.0.5-test
+FROM ghcr.io/biosimulators/bio-compose-server-base:0.0.5
 
 SHELL ["/usr/bin/env", "bash", "-c"]
 
-COPY ./ .
+COPY . .
 
 EXPOSE 3001
 
 RUN source ~/.bashrc \
-    && conda env update -n server -f config/environment.api.yml \
-    && conda run pip install -e . --root-user-action=ignore \
+    && conda env update -n server -f environment.api.yml \
     && conda env export --no-builds > config/environment.api.lock.yml \
+    && rm -f service/spec/openapi_3_1_0_generated.yaml \
+    && conda run python3 openapi_spec.py \
     && conda clean --all --json -y \
-    && rm -f config/environment.api.yml
+    && rm -f environment.api.yml
 
 # RUN source ~/.bashrc \
 #     && poetry install --without=composition,dev,worker --no-cache

api/data_model.py

@@ -1,11 +1,10 @@
 # -- api models -- #
-from enum import Enum
 from typing import List, Optional, Any, Dict, Union
 
 from pydantic import Field
 from fastapi.responses import FileResponse
 
-from api.shared_api import BaseModel, Job, JobStatus
+from shared_api import BaseModel, Job, JobStatus
 
 
 # PENDING JOBS:

api/log_config.py

@@ -10,14 +10,11 @@ def start_logging(fname: str):
     )
 
 
-def setup_logging():
+def setup_logging(logger: logging.Logger):
     # Create a root logger
     root_logger = logging.getLogger()
     root_logger.setLevel(logging.INFO)
 
-    # Create a uvicorn access logger
-    uvicorn_logger = logging.getLogger("uvicorn.access")
-
     # Create a console handler
     console_handler = logging.StreamHandler(stream=sys.stdout)
     console_handler.setLevel(logging.INFO)
@@ -32,4 +29,4 @@ def setup_logging():
 
     # Add the console handler to the root logger and uvicorn logger
     root_logger.addHandler(console_handler)
-    uvicorn_logger.addHandler(console_handler)
+    logger.addHandler(console_handler)