From d9cc6506c301242d5e9b5397ba6f63716729db09 Mon Sep 17 00:00:00 2001 From: "spaceBearAmadeus (Alex)" Date: Fri, 13 Dec 2024 10:38:08 -0500 Subject: [PATCH] feat: added get biomodel helper --- Dockerfile | 19 + bio_compose/api.py | 39 + dockerfile-assets/requirements.image.txt | 5 + poetry.lock | 2557 ++++++++++++++++++---- pyproject.toml | 24 +- tests/main.py | 14 +- tests/outputs/BIOMD0000000044.omex | Bin 0 -> 4557 bytes 7 files changed, 2250 insertions(+), 408 deletions(-) create mode 100644 Dockerfile create mode 100644 dockerfile-assets/requirements.image.txt create mode 100644 tests/outputs/BIOMD0000000044.omex diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..22158f7 --- /dev/null +++ b/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"] diff --git a/bio_compose/api.py b/bio_compose/api.py index f7c3b01..0e2d2df 100644 --- a/bio_compose/api.py +++ b/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}" + + diff --git 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+content-hash = "27b68892e6a31f671970881f68bb9e0c93b254773e84e428fda21664c31347e9" diff --git a/pyproject.toml b/pyproject.toml index 719c5e6..4b875e9 100644 --- a/pyproject.toml +++ b/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 "] 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" diff --git a/tests/main.py b/tests/main.py index 590eff1..c2b0df7 100644 --- a/tests/main.py +++ b/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) + diff --git a/tests/outputs/BIOMD0000000044.omex b/tests/outputs/BIOMD0000000044.omex new file mode 100644 index 0000000000000000000000000000000000000000..3e3b781399afa77487dcad915ea7e06ece015c4b GIT binary patch literal 4557 zcmZvg^-~m#w}*jU8Y!ul5)kQFLPFQ2ySuxE1(sHpZkA>NK|(+pmRw3&gjJA5mu^KQ zMY`j@-Z11NC2QZ@GgX3(7ou^m81ok^x+WLrZq&pat2TpWn;Az=aR4r84l+)np;rPG?sM z)isgInnwuh^E8}?Q`DMcb4bv+1)iVY-DOxIleD<#PoWoK&8DjG%#*+My0jkvv2Ijn6F9ffU-8SZBQNMP)9v&YKH3Z=<0Xsl7^G$tRzl0WAv z%tl4A?E9>Vc*HzclA$VQ$0z#aktb-@Ig;3|kz(DskTjpEcJqS}jdrd$FQep-!vJjv zJy@64QZZu4os%%?k;sZ2oO4soE(_uBH!*e*pL-yW*)2@2^<>CAFDYWDmq#PhHn!J< z#~qb%Lu5*;GU7X8sWWdTUss@8(Y5cq3UXSi!{haY9=1|GTz=JE3lVl>g!rf#O5<21%ZZyqZ5O3BoPYEMk0`f;~f=ZaM&arW!A zaE}SjTR3aClqFhl4Z5;QCLv&@1?z3&{COJUI_};FmW^JeW)3Ot4j_J`fl1?GLsn+i z0w+#?Jf@UM=ZlbH2id`V3tfshy&b*4K;biNm?^r*p?Gyd&lIIxFimn44sGmr{!Lp-Ia7~(xwE*76TkMDS`bsn-N5AE63PkLJQXOJK3VsZCf}T&jPoH` zn7_~KCnn9U&V=hIr7Cw@_nQ5y@VDAnT`osE`4|VJ?g9hdt#utJU!%ITxlcfp#-MP(WK0sQSjXX2xsddT zWD$S80tFLb2|pxp+XO>!SeB=rr&)QE}}nJ;d6y~&^0T*$_qS=U5xKe z^Wngo{>?|3%EdBf86@__+rewh|CSAEHqybOcbMA7iRLNddBR>Ln13a{F-|V9&7^| zB>B0;nT@3ByVAOxp@TkwzOi~S0-(h@>|@H+4=g${ocX4Tp7MQpP=1iFIQJFlq>Z~s zud&W2;V`PPWG=sW?R;R7PydhdkZUxED{m)mL7iBv+Tc6c4}SS_F%wVUg$$x{73Ny6 zJbDIx^SE|iP==VfpFh*b@epSi=JkC-)G zRAH^j7A+t+>seLA_^#>K05rja+xgP#!!bov)h}_}ij7oAT@(43Au*3R`v%2ASKHN? 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