feat: added get biomodel helper

Dockerfile

@@ -0,0 +1,19 @@
+FROM ghcr.io/biosimulators/bio-check-worker:latest
+
+SHELL ["/usr/bin/env", "bash", "-c"]
+
+ENV JUPYTER_TOKEN='' \
+    JUPYTER_ENABLE_LAB=yes \
+    GRANT_SUDO=yes
+
+EXPOSE 8888
+
+WORKDIR /app
+
+COPY dockerfile-assets/requirements.image.txt /tmp/requirements.image.txt
+
+RUN source ~/.bashrc  \
+    && mkdir -p /opt/notebooks \
+    && poetry run pip install -r /tmp/requirements.image.txt
+
+CMD ["bash", "-c", "source ~/.bashrc && poetry run jupyter lab --ip='*' --port=8888 --allow-root --no-browser"]

bio_compose/api.py

@@ -1,8 +1,11 @@
 import os
 import time
+import warnings
 from typing import *
 from functools import wraps
 
+import requests
+
 from bio_compose.processing_tools import get_job_signature
 from bio_compose.runner import SimulationRunner, SimulationResult
 from bio_compose.verifier import Verifier, VerificationResult
@@ -201,3 +204,39 @@ def visualize_rmse(job_id: str, save_dest: str = None, fig_dimensions: tuple[int
     return API_VERIFIER.visualize_rmse(job_id=job_id, save_dest=save_dest, fig_dimensions=fig_dimensions, color_mapping=color_mapping)
 
 
+def get_biomodel(model_id: str, dest_dir: Optional[str] = None) -> str:
+    """
+    Visualize the root-mean-squared error between simulator verification outputs as a heatmap.
+
+    :param model_id: (`Union[str, List[str`]) A single biomodel id passed as a string, or a list of biomodel ids as strings.
+    :param dest_dir: (`str`) destination directory at which to save downloaded file. If `None` is passed, downloads to cwd. Defaults to `None`.
+
+    :return: Filepath of the    downloaded biomodel file
+    :rtype: `str`
+    """
+    url = "https://www.ebi.ac.uk/biomodels/search/download"
+    params = {"models": model_id}
+
+    try:
+        response = requests.get(url, params=params, stream=True)
+
+        # download the file if success, otherwise notify.
+        if response.status_code == 200:
+            file_name = f"{model_id}.omex"
+            dest = dest_dir or os.getcwd()
+            fp = os.path.join(dest, file_name)
+            with open(fp, "wb") as file:
+                for chunk in response.iter_content(chunk_size=8192):
+                    file.write(chunk)
+            warnings.warn(f"File downloaded successfully and saved as {fp}")
+            return fp
+        elif response.status_code == 400:
+            warnings.warn("Error 400: File Not Found")
+        elif response.status_code == 404:
+            warnings.warn("Error 404: Invalid Model ID Supplied")
+        else:
+            warnings.warn(f"Unexpected error: {response.status_code} - {response.text}")
+    except requests.RequestException as e:
+        return f"An error occurred: {e}"
+
+

dockerfile-assets/requirements.image.txt

@@ -0,0 +1,5 @@
+requests-toolbelt
+seaborn
+toml
+process-bigraph
+jupyterlab

pyproject.toml

@@ -1,38 +1,44 @@
 # This project configuration should relate only to the high level notebook api (as primary deps).
 [tool.poetry]
 name = "bio-compose"
-version = "0.7.2"
+version = "0.7.3"
 description = "Create, execute, and introspect reproducible composite simulations of dynamic biological systems."
 authors = ["Alex Patrie <[email protected]>"]
 readme = "README.md"
 packages = [{include = "bio_compose"}, {include = "tests"}]
 include = ["pyproject.toml"]
 
+
 [tool.poetry.scripts]
 verify = "bio_compose.__main__:verification_cli"
 run-simulation = "bio_compose.__main__:simulation_run_cli"
 
+
 [tool.poetry.dependencies]
-python = ">=3.10"
+python = "^3.10"
 requests-toolbelt = "^1.0.0"
 seaborn = "^0.13.2"
-antimony = "^2.15.0"
+antimony = "*"
 toml = "^0.10.2"
 process-bigraph = "^0.0.21"
+requests = "^2.32.3"
+
 
-[tool.poetry.group.dev.dependencies]
-pytest = "^8.3.2"
-sphinx = "^8.0.2"
-sphinx-autodoc-typehints = "^2.2.3"
+[tool.poetry.group.docs.dependencies]
+sphinx = "^8.1.3"
+sphinx-autodoc-typehints = "^2.5.0"
+
+
+[tool.poetry.group.image.dependencies]
+jupyterlab = "^4.3.0"
 
-[project.optional-dependencies]
-documentation = ["sphinx-autodoc-typehints"]
 
 [tool.pytest.ini_options]
 testpaths = ["tests"]
 addopts = "--ignore=setup.py"
 python_files = "main.py"
 
+
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"

tests/main.py

@@ -1,4 +1,7 @@
+import os
+
 from bio_compose import get_compatible_verification_simulators
+from bio_compose.api import get_biomodel
 from bio_compose.verifier import Verifier
 from bio_compose.runner import SimulationRunner
 from bio_compose.composer import Composer
@@ -49,5 +52,14 @@ def test_verify_omex():
 
 
 def test_run_composition():
-    pass 
+    pass
+
+
+def test_get_biomodel():
+    biomd_id = 'BIOMD0000000044'
+    dest = '/Users/alexanderpatrie/Desktop/repos/bio-compose/tests/outputs'
+    fp = get_biomodel(biomd_id, dest)
+    # print(f'Biomodel {biomd_id} exists at {fp}: {os.path.exists(fp)}')
+    print(fp)
+