From 922a7bd668234156171b565894eeaeac9fec5584 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Thu, 22 Feb 2024 15:56:53 -0500 Subject: [PATCH 01/56] chore: removed docker comments --- Dockerfile | 3 --- 1 file changed, 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index a89cada99..13a9a43be 100644 --- a/Dockerfile +++ b/Dockerfile @@ -28,15 +28,12 @@ RUN apt-get update && apt-get install -y --no-install-recommends \ wget \ && rm -rf /var/lib/apt/lists/* -# RUN apt-get update && apt-get install -y python3-pip - RUN apt-get -y update \ \ && apt-get install --no-install-recommends -y \ xvfb \ && mkdir /tmp/.X11-unix \ && chmod 1777 /tmp/.X11-unix \ - \ && rm -rf /var/lib/apt/lists/* COPY scripts/xvfb-startup.sh /xvfb-startup.sh From 5a35207775bdc10992e0878e930e45ef0de60333 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Thu, 22 Feb 2024 16:00:19 -0500 Subject: [PATCH 02/56] removed comment from pyproject --- pyproject.toml | 1 - 1 file changed, 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 5fd65049e..d3cc355af 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,7 +9,6 @@ packages = [{include = "biosimulator_processes"}] [tool.poetry.dependencies] python = ">=3.10" zarr = "*" -# kisao = ">=2.33" termcolor = "*" jupyterlab = "*" bigraph-schema = "*" From df530e0130cf2f186030f1fa2b0499f6512bbbe0 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Thu, 22 Feb 2024 18:43:40 -0500 Subject: [PATCH 03/56] added biomodels yaml examples in spec library --- specs/biomodels-complete.yaml | 271 ++++++++++++++++++++++++++++++++++ specs/biomodels-modelId.yaml | 222 ++++++++++++++++++++++++++++ 2 files changed, 493 insertions(+) create mode 100644 specs/biomodels-complete.yaml create mode 100644 specs/biomodels-modelId.yaml diff --git a/specs/biomodels-complete.yaml b/specs/biomodels-complete.yaml new file mode 100644 index 000000000..64f5ca9d9 --- /dev/null +++ b/specs/biomodels-complete.yaml @@ -0,0 +1,271 @@ +openapi: 3.0.3 +info: + description: | +

BioModels is a repository of mathematical models of biological and biomedical systems. It hosts a vast selection of existing literature-based physiologically and pharmaceutically relevant mechanistic models in standard formats. Our mission is to provide the systems modelling community with reproducible, high-quality, freely-accessible models published in the scientific literature. More information about BioModels can be found in the FAQ.

+

Notes about this API

+

Content negotiation

+

Both XML and JSON MIME types are supported. Clients have two ways of specifying the content type: +

    +
  • an explicit format request parameter (e.g. format=xml)
    • +
  • the Accept request header (e.g. Accept: application/xml).
    • +
+ If both are specified, the format parameter has priority.

+

BioModels content

+

Model information is retrieved based on the a submission identifier, such as MODEL1707110000, or a BioModels identifier, like BIOMD0000000123. BioModels content is versioned and model revision numbers are assigned incrementally starting from 1. If a particular model revision is public, it can be accessed by appending a dot ('.') and its number to the model identifier (e.g. BIOMD0000000123.1).

+

Path2Models

Models from the Path2Models project are now clustered based on their genus. Each Path2Models entry now consists of a representative model and a COMBINE archive of all other models whose organisms belong to that genus. As a result of this shuffle, some models are no longer directly accessible and such requests are redirected to the corresponding representative model. There are dedicated end points for checking which models are now only retrievable indirectly and also to find the representative model(s) for a given set of model identifiers.

+ version: v1.0 + title: BioModels + termsOfService: https://www.ebi.ac.uk/data-protection/privacy-notice/embl-ebi-public-website + contact: + email: biomodels-developers@lists.sourceforge.net + license: + name: AGPL v3 + url: https://www.gnu.org/licenses/agpl-3.0.en.html +servers: + - url: https://www.ebi.ac.uk/biomodels/ + description: The production API server + - url: https://wwwdev.ebi.ac.uk/biomodels/ + description: The development API server + - url: http://localhost:8080/biomodels/ + description: The local development API server +tags: + - name: Model-related operations + description: Retrieve information about a particular submission. + - name: Search models + description: Find models of interest + - name: Parameters Search + description: Find model parameters of interest + - name: Path2Models operations + description: Find Path2Models models of interest + - name: PDGSMM operations + description: Find Patient-derived genome-scale metabolic models (PDGSMM) of interest +paths: + /{modelId}: + get: + tags: + - Model-related operations + summary: Fetch information about a given model at a particular revision. + operationId: getModelInfo + parameters: + - in: path + name: modelId + description: The identifier of a public model in BioModels. + required: true + schema: + type: string + - in: query + name: format + description: The response format + schema: + type: string + enum: + - json + - xml + - html + required: false + responses: + '200': + description: Successful operation + content: + application/json: + schema: + $ref: '#/components/schemas/Model' + 404: + description: Invalid model id + 415: + description: Unsupported media type. Please see the content negotiation section. + /model/files/{modelId}: + get: + tags: + - Model-related operations + summary: Extract metadata information of model files of a particular model + operationId: getModelFiles + parameters: + - in: path + name: modelId + required: true + schema: + type: string + description: The identifier of the model for which to retrieve the files. + - in: query + name: format + schema: + type: string + required: false + description: The format that the response should return + responses: + '200': + description: Successful operation + content: + application/json: + schema: + $ref: '#/components/schemas/ModelFiles' + 404: + description: Invalid model id supplied + 415: + description: Unsupported media type. Please see the content negotiation section. + /model/download/{modelId}: + get: + tags: + - Model-related operations + summary: Download a particular file associated with a given model or all its files as a COMBINE archive. + operationId: downloadModelFile + parameters: + - in: path + name: modelId + required: true + description: The model identifier that the file in question is associated with + schema: + type: string + - in: query + name: filename + schema: + type: string + description: The name of the file that needs to be downloaded. If not provided, all model files are returned as a COMBINE archive. If the file name is set, then the file contents will be served. + required: false + #produces: + # - application/octet-stream + responses: + 200: + description: Successful operation + 400: + description: File Not Found + 404: + description: Invalid Model ID Supplied + /model/identifiers: + get: + tags: + - Model-related operations + summary: Fetch all model identifiers + operationId: getAllModelIdentifiers + description: Fetch all publicly available model identifiers + parameters: + - in: query + name: format + schema: + type: string + enum: + - json + - xml + - html + required: false + description: The format that the response should return + responses: + '200': + description: Successful operation + content: + application/json: + schema: + $ref: '#/components/schemas/ModelIdentifiers' + 404: + description: Invalid operation + 415: + description: Unsupported media type + /search: + get: + tags: + - Search models + summary: Download search results + operationId: searchModels + description: Search models of interest via keywords. + parameters: + - in: query + name: query + required: true + schema: + type: string + description: Search query. Please note that the colon character in ontology terms must be escaped. + - in: query + name: offset + schema: + type: integer + required: false + description: The number of items to skip before starting to collect the result set + - in: query + name: numResults + schema: + type: integer + required: false + description: The number of items to return + - in: query + name: sort + schema: + type: string + enum: + - relevance-desc + - first_author-asc + - first_author-desc + - id-asc + - id-desc + - name-asc + - name-desc + - publication_year-asc + - publication_year-desc + required: false + description: Sort criteria + - in: query + name: format + schema: + type: string + required: false + description: The format that the response should return + responses: + '200': + description: Successful operation + content: + application/json: + schema: + $ref: '#/components/schemas/SearchResults' + 404: + description: Not Found + /search/download: + get: + tags: + - Search models + summary: Download a single or multiple models + operationId: downloadModels + description: Download the main file of a given single model or multiple models via their model identifiers. + parameters: + - in: query + name: models + required: true + schema: + type: string + description: The list of model identifiers which you want to download their main file. Using the comma to separate if you are requesting more than one model. + # produces: + # - application/zip + responses: + 200: + description: Successful operation + 404: + description: Not Found +components: + schemas: + Model: + type: object + properties: + name: + type: string + description: The name of the model. + ModelFiles: + type: object + properties: + name: + type: string + description: The file of the model. + ModelIdentifiers: + type: object + properties: + name: + type: string + description: The file of the model. + SearchResults: + type: object + properties: + name: + type: string + description: The file of the model. +externalDocs: + description: Find out more about BioModels + url: https://www.ebi.ac.uk/biomodels + diff --git a/specs/biomodels-modelId.yaml b/specs/biomodels-modelId.yaml new file mode 100644 index 000000000..129938ee8 --- /dev/null +++ b/specs/biomodels-modelId.yaml @@ -0,0 +1,222 @@ +# openapi: 3.0.3 +# info: +# title: BioModels +# version: v1.0 +# description: BioModels is a repository of mathematical models of biological and biomedical systems. +# termsOfService: https://www.ebi.ac.uk/data-protection/privacy-notice/embl-ebi-public-website +# contact: +# email: biomodels-developers@lists.sourceforge.net +# license: +# name: AGPL v3 +# url: https://www.gnu.org/licenses/agpl-3.0.en.html +# servers: +# - url: https://www.ebi.ac.uk/biomodels/ +# description: The production API server +# - url: https://wwwdev.ebi.ac.uk/biomodels/ +# description: The development API server +# - url: http://localhost:8080/biomodels/ +# description: The local development API server +# tags: +# - name: Model-related operations +# description: Retrieve information about a particular submission. +# # Paths summary +# paths: +# /{modelId}: +# get: +# tags: [Model-related operations] +# operationId: getModelById +# summary: Fetch information about a given model at a particular revision. +# parameters: +# - in: path +# name: modelId +# required: true +# schema: +# type: string +# description: The identifier of a public model in BioModels. +# - in: query +# name: format +# required: false +# schema: +# type: string +# enum: [json, xml, html] +# description: The response format. +# responses: +# '200': +# description: Successful operation +# content: +# application/json: +# schema: +# $ref: '#/components/schemas/Model' +# '404': +# description: Invalid model id +# '415': +# description: Unsupported media type. Please see the content negotiation section. +# # Additional paths would be defined here following the same structure +# components: +# schemas: +# Model: +# type: object +# properties: +# name: +# type: string +# description: The name of the model. +# # Additional properties would be defined here +# + +openapi: 3.0.3 +info: + title: BioModels + version: v1.0 + description: BioModels is a repository of mathematical models of biological and biomedical systems. + termsOfService: https://www.ebi.ac.uk/data-protection/privacy-notice/embl-ebi-public-website + contact: + email: biomodels-developers@lists.sourceforge.net + license: + name: AGPL v3 + url: https://www.gnu.org/licenses/agpl-3.0.en.html +servers: + - url: https://www.ebi.ac.uk/biomodels/ + description: The production API server + - url: https://wwwdev.ebi.ac.uk/biomodels/ + description: The development API server + - url: http://localhost:8080/biomodels/ + description: The local development API server +tags: + - name: Model-related operations + description: Retrieve information about a particular submission. +# Paths summary +paths: + /{modelId}: + get: + tags: [Model-related operations] + operationId: getModelById + summary: Fetch information about a given model at a particular revision. + parameters: + - in: path + name: modelId + required: true + schema: + type: string + description: The identifier of a public model in BioModels. + - in: query + name: format + required: false + schema: + type: string + enum: [json, xml, html] + description: The response format. + responses: + '200': + description: Successful operation + content: + application/json: + schema: + $ref: '#/components/schemas/Model' + '404': + description: Invalid model id + '415': + description: Unsupported media type. Please see the content negotiation section. +components: + schemas: + Model: + type: object + properties: + name: + type: string + description: The name of the model. + description: + type: string + description: A detailed description of the model including its purpose and how it was tested. + format: + type: object + properties: + name: + type: string + description: The format name of the model. + version: + type: string + description: The version of the format. + publication: + type: object + properties: + journal: + type: string + title: + type: string + affiliation: + type: string + synopsis: + type: string + year: + type: string + month: + type: string + volume: + type: string + pages: + type: string + link: + type: string + authors: + type: array + items: + type: object + properties: + name: + type: string + files: + type: object + properties: + main: + type: array + items: + $ref: '#/components/schemas/File' + additional: + type: array + items: + $ref: '#/components/schemas/File' + history: + type: object + properties: + revisions: + type: array + items: + $ref: '#/components/schemas/Revision' + firstPublished: + type: integer + format: int64 + description: Timestamp of the first publication. + submissionId: + type: string + description: Unique identifier for the submission. + publicationId: + type: string + description: Unique identifier for the publication associated with the model. + File: + type: object + properties: + name: + type: string + description: The file name. + fileSize: + type: string + description: The size of the file in bytes. + description: + type: string + description: A description of the file. + Revision: + type: object + properties: + version: + type: integer + description: The version number of the revision. + submitted: + type: integer + format: int64 + description: The timestamp when the revision was submitted. + submitter: + type: string + description: The name of the submitter. + comment: + type: string + description: A comment regarding the revision. From 89453815ebd5ff446d7bf1f4dcdb97f57c93aed1 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Thu, 22 Feb 2024 20:05:35 -0500 Subject: [PATCH 04/56] updated spec --- specs/biomodels-modelId.yaml | 41 +++++++++++++++++++++++++++++++++--- 1 file changed, 38 insertions(+), 3 deletions(-) diff --git a/specs/biomodels-modelId.yaml b/specs/biomodels-modelId.yaml index 129938ee8..25c287eb3 100644 --- a/specs/biomodels-modelId.yaml +++ b/specs/biomodels-modelId.yaml @@ -75,11 +75,11 @@ info: name: AGPL v3 url: https://www.gnu.org/licenses/agpl-3.0.en.html servers: - - url: https://www.ebi.ac.uk/biomodels/ + - url: https://www.ebi.ac.uk/biomodels description: The production API server - - url: https://wwwdev.ebi.ac.uk/biomodels/ + - url: https://wwwdev.ebi.ac.uk/biomodels description: The development API server - - url: http://localhost:8080/biomodels/ + - url: http://localhost:8080/biomodels description: The local development API server tags: - name: Model-related operations @@ -116,6 +116,30 @@ paths: description: Invalid model id '415': description: Unsupported media type. Please see the content negotiation section. + /model/identifiers: + get: + tags: [Model-related operations] + operationId: getIdentifiers + summary: Fetch all publicly available model identifiers + parameters: + - in: query + name: format + required: true + schema: + type: string + enum: [json, xml, html] + description: The response format. + responses: + '200': + description: Successful operation + content: + application/json: + schema: + $ref: '#/components/schemas/ModelIdentifiers' + '404': + description: Invalid operation + '415': + description: Unsupported media type. Please see the content negotiation section. components: schemas: Model: @@ -220,3 +244,14 @@ components: comment: type: string description: A comment regarding the revision. + ModelIdentifiers: + type: object + properties: + hits: + type: integer + description: Number of downloads + models: + type: array + items: + type: string + description: Each model in the database. From 25965be587b4f8566b9011f7597ae4f2f0c8d026 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Fri, 23 Feb 2024 07:41:47 -0500 Subject: [PATCH 05/56] updated composer-api library and spec --- composer-api/README.md | 0 composer-api/composer_api/__init__.py | 0 composer-api/composer_api/main.py | 45 +++++++++++++++++++ composer-api/pyproject.toml | 32 +++++++++++++ .../specs}/biomodels-complete.yaml | 0 .../specs}/biomodels-modelId.yaml | 0 6 files changed, 77 insertions(+) create mode 100644 composer-api/README.md create mode 100644 composer-api/composer_api/__init__.py create mode 100644 composer-api/composer_api/main.py create mode 100644 composer-api/pyproject.toml rename {specs => composer-api/specs}/biomodels-complete.yaml (100%) rename {specs => composer-api/specs}/biomodels-modelId.yaml (100%) diff --git a/composer-api/README.md b/composer-api/README.md new file mode 100644 index 000000000..e69de29bb diff --git a/composer-api/composer_api/__init__.py b/composer-api/composer_api/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/composer-api/composer_api/main.py b/composer-api/composer_api/main.py new file mode 100644 index 000000000..26187b48d --- /dev/null +++ b/composer-api/composer_api/main.py @@ -0,0 +1,45 @@ +from fastapi import FastAPI, HTTPException +from pydantic import BaseModel +from typing import List, Dict, Optional +from your_module import CopasiProcess, Composite # Adjust import path as needed + +app = FastAPI() + +# Define Pydantic models for request and response bodies +class ProcessConfig(BaseModel): + model_file: str + +class SimulationInput(BaseModel): + time: float + floating_species: Dict[str, float] + model_parameters: Dict[str, float] + reactions: Dict[str, float] + +class SimulationResult(BaseModel): + time: float + floating_species: Dict[str, float] + +# Initialize global or shared state if necessary +processes = {} + +@app.post("/initialize/", response_model=str) +def initialize_process(config: ProcessConfig): + process_id = "unique_process_id" # Generate a unique ID for the process + processes[process_id] = CopasiProcess(config=config.dict()) + return process_id + +@app.post("/run/{process_id}", response_model=SimulationResult) +def run_simulation(process_id: str, sim_input: SimulationInput): + if process_id not in processes: + raise HTTPException(status_code=404, detail="Process not found") + result = processes[process_id].update(sim_input.dict(), sim_input.time) + return result + +@app.get("/results/{process_id}", response_model=SimulationResult) +def get_results(process_id: str): + # This is a placeholder; actual implementation will depend on how results are stored and managed + if process_id not in processes: + raise HTTPException(status_code=404, detail="Process not found") + # Placeholder for result retrieval + results = {} # Implement logic to retrieve results for the given process_id + return results diff --git a/composer-api/pyproject.toml b/composer-api/pyproject.toml new file mode 100644 index 000000000..91d38f9af --- /dev/null +++ b/composer-api/pyproject.toml @@ -0,0 +1,32 @@ +[tool.poetry] +name = "composer-api" +version = "0.0.1" +description = "" +authors = ["Alex Patrie "] +readme = "README.md" +packages = [{ include = "composer_api" }] + +[tool.poetry.dependencies] +python = "^3.11" +fastapi = "^0.109.0" +pyyaml = "^6.0.1" +pydantic = "^2.5.3" +h5py = "^3.10.0" +pydantic-settings = "^2.1.0" +httpx = "^0.26.0" +tensorstore = "^0.1.52" +aiofiles = "^23.2.1" +aiobotocore = "^2.11.0" +uvicorn = {extras = ["standard"], version = "^0.27.0"} + +[tool.poetry.group.dev.dependencies] +pytest = "^7.4.4" +pytest-asyncio = "^0.23.3" +flake8 = "^7.0.0" +black = "^23.12.1" +coverage = "^7.4.0" +mypy = "^1.8.0" + +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" diff --git a/specs/biomodels-complete.yaml b/composer-api/specs/biomodels-complete.yaml similarity index 100% rename from specs/biomodels-complete.yaml rename to composer-api/specs/biomodels-complete.yaml diff --git a/specs/biomodels-modelId.yaml b/composer-api/specs/biomodels-modelId.yaml similarity index 100% rename from specs/biomodels-modelId.yaml rename to composer-api/specs/biomodels-modelId.yaml From 088c07e53c50495a34d432a08a535269f06cf9ce Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Fri, 23 Feb 2024 07:44:06 -0500 Subject: [PATCH 06/56] updated composer spec --- composer-api/specs/composer.yaml | 104 +++++++++++++++++++++++++++++++ 1 file changed, 104 insertions(+) create mode 100644 composer-api/specs/composer.yaml diff --git a/composer-api/specs/composer.yaml b/composer-api/specs/composer.yaml new file mode 100644 index 000000000..9ac02eaff --- /dev/null +++ b/composer-api/specs/composer.yaml @@ -0,0 +1,104 @@ +openapi: 3.0.3 +info: + title: process-bigraph + description: An API for running biosimulation processes. + version: "1.0.0" +servers: + - url: http://localhost:8000 + description: Local server +paths: + /initialize: + post: + summary: Initialize the simulation with a model file. + requestBody: + required: true + content: + application/json: + schema: + type: object + properties: + model_file: + type: string + description: Path to the model file. + responses: + '200': + description: Simulation initialized successfully. + content: + application/json: + schema: + type: object + properties: + message: + type: string + example: Simulation initialized with model_file. + /run: + post: + summary: Run the simulation for a given interval. + requestBody: + required: true + content: + application/json: + schema: + type: object + properties: + interval: + type: integer + description: Interval for which the simulation is run. + responses: + '200': + description: Simulation run successfully. + content: + application/json: + schema: + type: object + properties: + time: + type: float + example: 10 + floating_species: + type: object + additionalProperties: + type: float + example: {"species1": 0.5, "species2": 1.5} + /update: + post: + summary: Update the simulation state. + requestBody: + required: true + content: + application/json: + schema: + type: object + properties: + state: + type: object + description: New state to update the simulation with. + responses: + '200': + description: Simulation state updated successfully. + /results: + get: + summary: Fetch the simulation results. + responses: + '200': + description: Results fetched successfully. + content: + application/json: + schema: + type: object + properties: + results: + type: object + additionalProperties: true + example: {"floating_species": {"species1": 0.5, "species2": 1.5}, "time": 10} +components: + schemas: + SimulationState: + type: object + properties: + time: + type: float + floating_species: + type: object + additionalProperties: + type: float From b4a7709b130cda1745c77c8cb56bc5f037ad5021 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Fri, 23 Feb 2024 07:46:01 -0500 Subject: [PATCH 07/56] updated composer spec for operation ids --- composer-api/specs/composer.yaml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/composer-api/specs/composer.yaml b/composer-api/specs/composer.yaml index 9ac02eaff..e84cbcce1 100644 --- a/composer-api/specs/composer.yaml +++ b/composer-api/specs/composer.yaml @@ -1,15 +1,16 @@ openapi: 3.0.3 info: title: process-bigraph - description: An API for running biosimulation processes. + description: An API for running biosimulation processes using Copasi/Basico. version: "1.0.0" servers: - - url: http://localhost:8000 + - url: https://localhost:8000 description: Local server paths: /initialize: post: summary: Initialize the simulation with a model file. + operationId: initializeSimulation requestBody: required: true content: @@ -34,6 +35,7 @@ paths: /run: post: summary: Run the simulation for a given interval. + operationId: runSimulation requestBody: required: true content: @@ -63,6 +65,7 @@ paths: /update: post: summary: Update the simulation state. + operationId: updateSimulation requestBody: required: true content: @@ -79,6 +82,7 @@ paths: /results: get: summary: Fetch the simulation results. + operationId: fetchResults responses: '200': description: Results fetched successfully. From 2d81a015116e6dd18e9a5a5c685e7ff5da980018 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Fri, 23 Feb 2024 12:53:09 -0500 Subject: [PATCH 08/56] updated scripts and poetry env in container --- Dockerfile | 16 +- composer-api/composer_api/main.py | 4 +- composer-api/poetry.lock | 2547 +++++++++++++++++++++++++++++ composer-api/pyproject.toml | 1 + scripts/build-container.sh | 6 +- 5 files changed, 2570 insertions(+), 4 deletions(-) create mode 100644 composer-api/poetry.lock mode change 100644 => 100755 scripts/build-container.sh diff --git a/Dockerfile b/Dockerfile index 13a9a43be..cd4c514a6 100644 --- a/Dockerfile +++ b/Dockerfile @@ -6,6 +6,8 @@ WORKDIR /app COPY . /app +RUN rm -r /app/composer-api + RUN apt-get update && apt-get install -y --no-install-recommends \ python3 \ python3-pip \ @@ -44,14 +46,24 @@ ENV XVFB_RES="1920x1080x24" \ RUN pip install --upgrade pip \ && pip install poetry +RUN poetry config virtualenvs.in-project true + # Add Poetry to PATH ENV PATH="/root/.local/bin:${PATH}" -# RUN poetry config virtualenvs.create false - RUN poetry run pip install --upgrade pip \ && poetry run pip install python-libnuml --use-pep517 \ && poetry install +# activate poetry virtualenv +ENV PATH="/app/.venv/bin:$PATH" +ENV CONFIG_ENV_FILE="/app/config/config.env" +ENV SECRET_ENV_FILE="/app/secret/secret.env" +ENV STORAGE_GCS_CREDENTIALS_FILE="/app/secret/gcs_credentials.json" +ENV STORAGE_LOCAL_CACHE_DIR="/app/scratch" + +# activate the poetry virtualenv each new non-interative shell +RUN echo "source /app/.venv/bin/activate" >> /etc/bash.bashrc + ENTRYPOINT ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"] diff --git a/composer-api/composer_api/main.py b/composer-api/composer_api/main.py index 26187b48d..db25cf9a0 100644 --- a/composer-api/composer_api/main.py +++ b/composer-api/composer_api/main.py @@ -1,7 +1,9 @@ from fastapi import FastAPI, HTTPException from pydantic import BaseModel from typing import List, Dict, Optional -from your_module import CopasiProcess, Composite # Adjust import path as needed +from biosimulator_processes.copasi_process import CopasiProcess +from process_bigraph import Composite + app = FastAPI() diff --git a/composer-api/poetry.lock b/composer-api/poetry.lock new file mode 100644 index 000000000..e4b9972bc --- /dev/null +++ b/composer-api/poetry.lock @@ -0,0 +1,2547 @@ +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. + +[[package]] +name = "aiobotocore" +version = "2.11.2" +description = "Async client for aws services using botocore and aiohttp" +optional = false +python-versions = ">=3.8" +files = [ + {file = "aiobotocore-2.11.2-py3-none-any.whl", hash = "sha256:487fede588040bfa3a43df945275c28c1c73ca75bf705295adb9fbadd2e89be7"}, + {file = "aiobotocore-2.11.2.tar.gz", hash = "sha256:6dd7352248e3523019c5a54a395d2b1c31080697fc80a9ad2672de4eec8c7abd"}, +] + +[package.dependencies] +aiohttp = 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"97443a7d691c3cd7dff4d7124ffe54718b2f4d7a11f80223be7bd807af3d4cde" diff --git a/composer-api/pyproject.toml b/composer-api/pyproject.toml index 91d38f9af..8a0b01ac4 100644 --- a/composer-api/pyproject.toml +++ b/composer-api/pyproject.toml @@ -18,6 +18,7 @@ tensorstore = "^0.1.52" aiofiles = "^23.2.1" aiobotocore = "^2.11.0" uvicorn = {extras = ["standard"], version = "^0.27.0"} +process-bigraph = "*" [tool.poetry.group.dev.dependencies] pytest = "^7.4.4" diff --git a/scripts/build-container.sh b/scripts/build-container.sh old mode 100644 new mode 100755 index 95550d051..f904475a2 --- a/scripts/build-container.sh +++ b/scripts/build-container.sh @@ -2,7 +2,7 @@ version="$1" -set -e +run="$2" if [ "${version}" == "" ]; then echo "Please enter the version you would like to build as a runtime arg. Exiting." @@ -14,3 +14,7 @@ docker buildx create --name biosimbuilder --use docker buildx inspect --bootstrap docker buildx build --platform linux/amd64 \ -t ghcr.io/biosimulators/biosimulator-processes:"${version}" . + +if [ "${run}" == "-r" ]; then + ./run-container.sh "${version}" +fi From a7e9005fd4b7695e1878cbc6e9dbf5df0386eea9 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Fri, 23 Feb 2024 17:14:54 -0500 Subject: [PATCH 09/56] updated container script --- biosimulator_processes/container.py | 48 ++++++++++++++++++++ biosimulator_processes/copasi_process.py | 47 +++++++++++++++++++- biosimulator_processes/simulators.json | 56 ++++++++++++++++++++++++ scripts/release-container.sh | 2 +- 4 files changed, 150 insertions(+), 3 deletions(-) create mode 100644 biosimulator_processes/container.py create mode 100644 biosimulator_processes/simulators.json diff --git a/biosimulator_processes/container.py b/biosimulator_processes/container.py new file mode 100644 index 000000000..26d445ab1 --- /dev/null +++ b/biosimulator_processes/container.py @@ -0,0 +1,48 @@ +import json +import subprocess + + +def load_config(): + # Load simulator configuration + with open('simulators.json', 'r') as file: + return json.load(file) + +def add_installations_to_dockerfiile(dockerfile_contents: str): + # Add installations for each simulator and its dependencies + for simulator in config['simulators']: + # Example: Assuming dependencies can be installed via apt-get for simplicity + deps = ' '.join(simulator['deps']) + dockerfile_contents += f" {deps} \\\n" + + # Finish the Dockerfile + dockerfile_contents += """ + # Add any additional setup here + """ + return dockerfile_contents + + +def write_dockerfile(dockerfile_contents: str): + # Save the Dockerfile + with open('Dockerfile', 'w') as file: + file.write(dockerfile_contents) + + +def exec_container(name: str): + # Build the Docker image + subprocess.run(["docker", "build", "-t", "simulator_env", "."]) + # Run the Docker container + subprocess.run(["docker", "run", "-d", "--name", "simulator_instance", f"{name}"]) + + +def run(name: str): + config = load_config() + + base_contents = """ + FROM ubuntu:latest + RUN apt-get update && apt-get install -y \\ + """ + dockerfile_contents = add_installations_to_dockerfiile(base_contents) + write_dockerfile(dockerfile_contents) + exec_container(name) + + diff --git a/biosimulator_processes/copasi_process.py b/biosimulator_processes/copasi_process.py index b7ca60a43..67c79f48e 100644 --- a/biosimulator_processes/copasi_process.py +++ b/biosimulator_processes/copasi_process.py @@ -1,5 +1,40 @@ """ -Biosimulator process for Copasi/Basico +Biosimulator process for Copasi/Basico. + +Now lets create a new model, passing along the name that we want to give it. +Additional supported parameters for the model consist of: + + quantity_unit: which sets the unit to use for species concentrations (defaults to mol) + + volume_unit: the unit to use for three dimensional compartments (defaults to litre (l)) + + time_unit: the unit to use for time (defaults to second (s)) + + area_unit: the unit to use for two dimensional compartments + + length_unit: the unit to use for one dimensional compartments + + add_reaction('R1', 'A -> B'); + + Since we had a new model, this created the Species A and B as well as a compartment compartment, in which those + chemicals reside. The species have an initial concentration of 1. + To verify we can call get_species, which return + + get_species().initial_concentration + name + A 1.0 + B 1.0 + Name: initial_concentration, dtype: float64 + to change the initial concentration, we use set_species, and specify which property we want to change: + + set_species('B', initial_concentration=0) + set_species('A', initial_concentration=10) + get_species().initial_concentration + name + A 10.0 + B 0.0 + Name: initial_concentration, dtype: float64 + to see the kinetic paramters of our recation we can use get_reaction_parameters, and we see that the parameter has been created by default with a value of 0.1 """ @@ -17,7 +52,15 @@ class CopasiProcess(Process): - config_schema = {'model_file': 'string'} + config_schema = { + 'model_file': 'string', + 'name': 'string', + 'reactions': 'list[string]', + 'species_types': { + 'name': 'string', + 'initial_concentration': 'int' + } + } def __init__(self, config=None, core=None): super().__init__(config, core) diff --git a/biosimulator_processes/simulators.json b/biosimulator_processes/simulators.json new file mode 100644 index 000000000..fa8d7b878 --- /dev/null +++ b/biosimulator_processes/simulators.json @@ -0,0 +1,56 @@ +[[package]] +name = "tellurium" +version = "2.2.10" +description = "Tellurium: An biological modeling environment for Python" +optional = false +python-versions = "*" +files = [ + {file = "tellurium-2.2.10-py3-none-any.whl", hash = "sha256:078dbe5beeef49cc8caa9f626cb9c8e568752ecfaff3370acd32be123d6e24ae"}, +] + +[package.dependencies] +antimony = ">=2.12.0" +appdirs = ">=1.4.3" +ipykernel = ">=4.6.1" +ipython = "*" +jinja2 = ">=3.0.0" +jupyter-client = ">=5.1.0" +jupyter-core = ">=4.3.0" +libroadrunner = ">=2.1" +matplotlib = ">=2.0.2" +numpy = ">=1.23" +pandas = ">=0.20.2" +phrasedml = {version = ">=1.0.9", markers = "platform_machine != \"arm64\""} +plotly = ">=2.0.12" +pytest = "*" +python-libcombine = ">=0.2.2" +python-libnuml = ">=1.0.0" +python-libsbml = ">=5.18.0" +python-libsedml = ">=2.0.17" +requests = "*" +rrplugins = {version = ">=2.1", markers = "platform_system == \"Windows\""} +scipy = ">=1.5.1" + +[[package]] +name = "copasi-basico" +version = "0.58" +description = "Simplified COPASI interface for python" +optional = false +python-versions = "*" +files = [ + {file = "copasi_basico-0.58-py3-none-any.whl", hash = "sha256:d85f4ab39e9ba8dc2ff19e31466883a22ac32a6dbdec9ac595a793507897fa9e"}, + {file = "copasi_basico-0.58.tar.gz", hash = "sha256:f8766aac7afde62cb75fb6701cb868fc0e341c43a0099408dbf073845a146c1c"}, +] + +[package.dependencies] +matplotlib = "*" +numpy = "*" +pandas = "*" +python-copasi = "*" +PyYAML = "*" +scipy = "*" + +[package.extras] +docs = ["sphinx", "sphinx-rtd-theme", "sphinxcontrib", "sphinxcontrib-bibtex", "sphinxcontrib-mermaid", "sphinxcontrib-plantuml", "sphinxcontrib-programoutput"] +petab = ["copasi-petab-importer", "petab", "petab-select"] +tqdm = ["tqdm"] diff --git a/scripts/release-container.sh b/scripts/release-container.sh index 209380223..85411101d 100644 --- a/scripts/release-container.sh +++ b/scripts/release-container.sh @@ -3,7 +3,7 @@ version="$1" -# PLEASE UPDATE THE LATEST VERSION HERE BEFORE RUNNING. CURRENT: 0.0.2 +# PLEASE UPDATE THE LATEST VERSION HERE BEFORE RUNNING. CURRENT: 0.0.3 current="0.0.2" set -e From 8c5b54a508745b018a22f335a53b173fb3e7f2ee Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Fri, 23 Feb 2024 17:52:02 -0500 Subject: [PATCH 10/56] updated container script for updated simulators spec --- biosimulator_processes/Dockerfile | 30 ++++++ biosimulator_processes/container.py | 57 ++++++++--- biosimulator_processes/simulators.json | 132 ++++++++++++++----------- 3 files changed, 147 insertions(+), 72 deletions(-) create mode 100644 biosimulator_processes/Dockerfile diff --git a/biosimulator_processes/Dockerfile b/biosimulator_processes/Dockerfile new file mode 100644 index 000000000..88ce949fe --- /dev/null +++ b/biosimulator_processes/Dockerfile @@ -0,0 +1,30 @@ + + RUN apt-get update && apt-get install -y --no-install-recommends python3 python3-pip build-essential libncurses5 cmake make libx11-dev libc6-dev libx11-6 libc6 gcc swig pkg-config curl tar libgl1-mesa-glx libice6 libpython3.10 wget && rm -rf /var/lib/apt/lists/* + RUN pip install antimony>=2.12.0 \ +RUN pip install appdirs>=1.4.3 \ +RUN pip install ipykernel>=4.6.1 \ +RUN pip install ipython* \ +RUN pip install jinja2>=3.0.0 \ +RUN pip install jupyter-client>=5.1.0 \ +RUN pip install jupyter-core>=4.3.0 \ +RUN pip install libroadrunner>=2.1 \ +RUN pip install matplotlib>=2.0.2 \ +RUN pip install numpy>=1.23 \ +RUN pip install pandas>=0.20.2 \ +RUN pip install phrasedml{'version': '>=1.0.9', 'markers': 'platform_machine != "arm64"'} \ +RUN pip install plotly>=2.0.12 \ +RUN pip install pytest* \ +RUN pip install python-libcombine>=0.2.2 \ +RUN pip install python-libnuml>=1.0.0 \ +RUN pip install python-libsbml>=5.18.0 \ +RUN pip install python-libsedml>=2.0.17 \ +RUN pip install requests* \ +RUN pip install rrplugins{'version': '>=2.1', 'markers': 'platform_system == "Windows"'} \ +RUN pip install scipy>=1.5.1 \ +RUN pip install matplotlib* \ +RUN pip install numpy* \ +RUN pip install pandas* \ +RUN pip install python-copasi* \ +RUN pip install PyYAML* \ +RUN pip install scipy* \ + # Add any additional setup here diff --git a/biosimulator_processes/container.py b/biosimulator_processes/container.py index 26d445ab1..439bfbba0 100644 --- a/biosimulator_processes/container.py +++ b/biosimulator_processes/container.py @@ -7,17 +7,19 @@ def load_config(): with open('simulators.json', 'r') as file: return json.load(file) -def add_installations_to_dockerfiile(dockerfile_contents: str): - # Add installations for each simulator and its dependencies + +def add_installations_to_dockerfile(dockerfile_contents: str, config: dict): + # Iterate over each simulator and add installations for its dependencies for simulator in config['simulators']: - # Example: Assuming dependencies can be installed via apt-get for simplicity - deps = ' '.join(simulator['deps']) - dockerfile_contents += f" {deps} \\\n" + deps = simulator.get('deps', {}) + # Convert dependencies dict to a list of installation commands + for dep, version in deps.items(): + # For simplicity, assuming all dependencies can be installed via pip + # This line might need adjustment based on actual package management needs + dockerfile_contents += f"RUN pip install {dep}{version} \\\n" - # Finish the Dockerfile - dockerfile_contents += """ - # Add any additional setup here - """ + # Finish the Dockerfile with any additional setup + dockerfile_contents += " # Add any additional setup here\n" return dockerfile_contents @@ -28,21 +30,44 @@ def write_dockerfile(dockerfile_contents: str): def exec_container(name: str): - # Build the Docker image - subprocess.run(["docker", "build", "-t", "simulator_env", "."]) - # Run the Docker container - subprocess.run(["docker", "run", "-d", "--name", "simulator_instance", f"{name}"]) + build_command = f"docker buildx create --name biosimbuilder --use && docker buildx build --platform linux/amd64 -t {name}_env ." + subprocess.run(build_command.split()) + run_command = f"docker run --platform linux/amd64 -it -p 8888:8888 {name}_env" + subprocess.run(run_command.split()) def run(name: str): config = load_config() base_contents = """ - FROM ubuntu:latest - RUN apt-get update && apt-get install -y \\ + RUN apt-get update && apt-get install -y --no-install-recommends \ + python3 \ + python3-pip \ + build-essential \ + libncurses5 \ + cmake \ + make \ + libx11-dev \ + libc6-dev \ + libx11-6 \ + libc6 \ + gcc \ + swig \ + pkg-config \ + curl \ + tar \ + libgl1-mesa-glx \ + libice6 \ + libpython3.10 \ + wget \ + && rm -rf /var/lib/apt/lists/* """ - dockerfile_contents = add_installations_to_dockerfiile(base_contents) + dockerfile_contents = add_installations_to_dockerfile(base_contents, config) write_dockerfile(dockerfile_contents) exec_container(name) +if __name__ == '__main__': + run("composite") + + diff --git a/biosimulator_processes/simulators.json b/biosimulator_processes/simulators.json index fa8d7b878..13f2bbe20 100644 --- a/biosimulator_processes/simulators.json +++ b/biosimulator_processes/simulators.json @@ -1,56 +1,76 @@ -[[package]] -name = "tellurium" -version = "2.2.10" -description = "Tellurium: An biological modeling environment for Python" -optional = false -python-versions = "*" -files = [ - {file = "tellurium-2.2.10-py3-none-any.whl", hash = "sha256:078dbe5beeef49cc8caa9f626cb9c8e568752ecfaff3370acd32be123d6e24ae"}, -] - -[package.dependencies] -antimony = ">=2.12.0" -appdirs = ">=1.4.3" -ipykernel = ">=4.6.1" -ipython = "*" -jinja2 = ">=3.0.0" -jupyter-client = ">=5.1.0" -jupyter-core = ">=4.3.0" -libroadrunner = ">=2.1" -matplotlib = ">=2.0.2" -numpy = ">=1.23" -pandas = ">=0.20.2" -phrasedml = {version = ">=1.0.9", markers = "platform_machine != \"arm64\""} -plotly = ">=2.0.12" -pytest = "*" -python-libcombine = ">=0.2.2" -python-libnuml = ">=1.0.0" -python-libsbml = ">=5.18.0" -python-libsedml = ">=2.0.17" -requests = "*" -rrplugins = {version = ">=2.1", markers = "platform_system == \"Windows\""} -scipy = ">=1.5.1" - -[[package]] -name = "copasi-basico" -version = "0.58" -description = "Simplified COPASI interface for python" -optional = false -python-versions = "*" -files = [ - {file = "copasi_basico-0.58-py3-none-any.whl", hash = "sha256:d85f4ab39e9ba8dc2ff19e31466883a22ac32a6dbdec9ac595a793507897fa9e"}, - {file = "copasi_basico-0.58.tar.gz", hash = "sha256:f8766aac7afde62cb75fb6701cb868fc0e341c43a0099408dbf073845a146c1c"}, -] - -[package.dependencies] -matplotlib = "*" -numpy = "*" -pandas = "*" -python-copasi = "*" -PyYAML = "*" -scipy = "*" - -[package.extras] -docs = ["sphinx", "sphinx-rtd-theme", "sphinxcontrib", "sphinxcontrib-bibtex", "sphinxcontrib-mermaid", "sphinxcontrib-plantuml", "sphinxcontrib-programoutput"] -petab = ["copasi-petab-importer", "petab", "petab-select"] -tqdm = ["tqdm"] +{ + "simulators": [ + { + "name": "tellurium", + "version": "2.2.10", + "description": "Tellurium: An biological modeling environment for Python", + "optional": false, + "python-versions": "*", + "files": [ + { + "file": "tellurium-2.2.10-py3-none-any.whl", + "hash": "sha256:078dbe5beeef49cc8caa9f626cb9c8e568752ecfaff3370acd32be123d6e24ae" + } + ], + "deps": { + "antimony": ">=2.12.0", + "appdirs": ">=1.4.3", + "ipykernel": ">=4.6.1", + "ipython": "*", + "jinja2": ">=3.0.0", + "jupyter-client": ">=5.1.0", + "jupyter-core": ">=4.3.0", + "libroadrunner": ">=2.1", + "matplotlib": ">=2.0.2", + "numpy": ">=1.23", + "pandas": ">=0.20.2", + "phrasedml": { + "version": ">=1.0.9", + "markers": "platform_machine != \"arm64\"" + }, + "plotly": ">=2.0.12", + "pytest": "*", + "python-libcombine": ">=0.2.2", + "python-libnuml": ">=1.0.0", + "python-libsbml": ">=5.18.0", + "python-libsedml": ">=2.0.17", + "requests": "*", + "rrplugins": { + "version": ">=2.1", + "markers": "platform_system == \"Windows\"" + }, + "scipy": ">=1.5.1" + } + }, + { + "name": "copasi-basico", + "version": "0.58", + "description": "Simplified COPASI interface for python", + "optional": false, + "python-versions": "*", + "files": [ + { + "file": "copasi_basico-0.58-py3-none-any.whl", + "hash": "sha256:d85f4ab39e9ba8dc2ff19e31466883a22ac32a6dbdec9ac595a793507897fa9e" + }, + { + "file": "copasi_basico-0.58.tar.gz", + "hash": "sha256:f8766aac7afde62cb75fb6701cb868fc0e341c43a0099408dbf073845a146c1c" + } + ], + "deps": { + "matplotlib": "*", + "numpy": "*", + "pandas": "*", + "python-copasi": "*", + "PyYAML": "*", + "scipy": "*" + }, + "extras": { + "docs": ["sphinx", "sphinx-rtd-theme", "sphinxcontrib", "sphinxcontrib-bibtex", "sphinxcontrib-mermaid", "sphinxcontrib-plantuml", "sphinxcontrib-programoutput"], + "petab": ["copasi-petab-importer", "petab", "petab-select"], + "tqdm": ["tqdm"] + } + } + ] +} From b3d0daf6e4adb8572e63528a98bd03a1a50d45bb Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Fri, 23 Feb 2024 17:53:34 -0500 Subject: [PATCH 11/56] added write config func --- biosimulator_processes/container.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/biosimulator_processes/container.py b/biosimulator_processes/container.py index 439bfbba0..583251555 100644 --- a/biosimulator_processes/container.py +++ b/biosimulator_processes/container.py @@ -2,6 +2,12 @@ import subprocess +def write_config(): + config = {} + with open('simulators.json', 'w') as fp: + json.dump(config, fp, indent=4) + + def load_config(): # Load simulator configuration with open('simulators.json', 'r') as file: From 9e27ea9910517e539268af45a7a41d316ee4cc20 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Fri, 23 Feb 2024 18:01:32 -0500 Subject: [PATCH 12/56] updated dockerfile maker --- Dockerfile | 97 +++++++++-------------------- biosimulator_processes/Dockerfile | 78 ++++++++++++++--------- biosimulator_processes/container.py | 55 ++++++++-------- 3 files changed, 104 insertions(+), 126 deletions(-) diff --git a/Dockerfile b/Dockerfile index cd4c514a6..88ce949fe 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,69 +1,30 @@ -FROM ubuntu:latest - -ENV DEBIAN_FRONTEND=noninteractive - -WORKDIR /app - -COPY . /app - -RUN rm -r /app/composer-api - -RUN apt-get update && apt-get install -y --no-install-recommends \ - python3 \ - python3-pip \ - build-essential \ - libncurses5 \ - cmake \ - make \ - libx11-dev \ - libc6-dev \ - libx11-6 \ - libc6 \ - gcc \ - swig \ - pkg-config \ - curl \ - tar \ - libgl1-mesa-glx \ - libice6 \ - libpython3.10 \ - wget \ - && rm -rf /var/lib/apt/lists/* - -RUN apt-get -y update \ - \ - && apt-get install --no-install-recommends -y \ - xvfb \ - && mkdir /tmp/.X11-unix \ - && chmod 1777 /tmp/.X11-unix \ - && rm -rf /var/lib/apt/lists/* - -COPY scripts/xvfb-startup.sh /xvfb-startup.sh - -ENV XVFB_RES="1920x1080x24" \ - XVFB_ARGS="" - -RUN pip install --upgrade pip \ - && pip install poetry - -RUN poetry config virtualenvs.in-project true - -# Add Poetry to PATH -ENV PATH="/root/.local/bin:${PATH}" - -RUN poetry run pip install --upgrade pip \ - && poetry run pip install python-libnuml --use-pep517 \ - && poetry install - -# activate poetry virtualenv -ENV PATH="/app/.venv/bin:$PATH" -ENV CONFIG_ENV_FILE="/app/config/config.env" -ENV SECRET_ENV_FILE="/app/secret/secret.env" -ENV STORAGE_GCS_CREDENTIALS_FILE="/app/secret/gcs_credentials.json" -ENV STORAGE_LOCAL_CACHE_DIR="/app/scratch" - -# activate the poetry virtualenv each new non-interative shell -RUN echo "source /app/.venv/bin/activate" >> /etc/bash.bashrc - -ENTRYPOINT ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"] + RUN apt-get update && apt-get install -y --no-install-recommends python3 python3-pip build-essential libncurses5 cmake make libx11-dev libc6-dev libx11-6 libc6 gcc swig pkg-config curl tar libgl1-mesa-glx libice6 libpython3.10 wget && rm -rf /var/lib/apt/lists/* + RUN pip install antimony>=2.12.0 \ +RUN pip install appdirs>=1.4.3 \ +RUN pip install ipykernel>=4.6.1 \ +RUN pip install ipython* \ +RUN pip install jinja2>=3.0.0 \ +RUN pip install jupyter-client>=5.1.0 \ +RUN pip install jupyter-core>=4.3.0 \ +RUN pip install libroadrunner>=2.1 \ +RUN pip install matplotlib>=2.0.2 \ +RUN pip install numpy>=1.23 \ +RUN pip install pandas>=0.20.2 \ +RUN pip install phrasedml{'version': '>=1.0.9', 'markers': 'platform_machine != "arm64"'} \ +RUN pip install plotly>=2.0.12 \ +RUN pip install pytest* \ +RUN pip install python-libcombine>=0.2.2 \ +RUN pip install python-libnuml>=1.0.0 \ +RUN pip install python-libsbml>=5.18.0 \ +RUN pip install python-libsedml>=2.0.17 \ +RUN pip install requests* \ +RUN pip install rrplugins{'version': '>=2.1', 'markers': 'platform_system == "Windows"'} \ +RUN pip install scipy>=1.5.1 \ +RUN pip install matplotlib* \ +RUN pip install numpy* \ +RUN pip install pandas* \ +RUN pip install python-copasi* \ +RUN pip install PyYAML* \ +RUN pip install scipy* \ + # Add any additional setup here diff --git a/biosimulator_processes/Dockerfile b/biosimulator_processes/Dockerfile index 88ce949fe..00b249b6a 100644 --- a/biosimulator_processes/Dockerfile +++ b/biosimulator_processes/Dockerfile @@ -1,30 +1,48 @@ - - RUN apt-get update && apt-get install -y --no-install-recommends python3 python3-pip build-essential libncurses5 cmake make libx11-dev libc6-dev libx11-6 libc6 gcc swig pkg-config curl tar libgl1-mesa-glx libice6 libpython3.10 wget && rm -rf /var/lib/apt/lists/* - RUN pip install antimony>=2.12.0 \ -RUN pip install appdirs>=1.4.3 \ -RUN pip install ipykernel>=4.6.1 \ -RUN pip install ipython* \ -RUN pip install jinja2>=3.0.0 \ -RUN pip install jupyter-client>=5.1.0 \ -RUN pip install jupyter-core>=4.3.0 \ -RUN pip install libroadrunner>=2.1 \ -RUN pip install matplotlib>=2.0.2 \ -RUN pip install numpy>=1.23 \ -RUN pip install pandas>=0.20.2 \ -RUN pip install phrasedml{'version': '>=1.0.9', 'markers': 'platform_machine != "arm64"'} \ -RUN pip install plotly>=2.0.12 \ -RUN pip install pytest* \ -RUN pip install python-libcombine>=0.2.2 \ -RUN pip install python-libnuml>=1.0.0 \ -RUN pip install python-libsbml>=5.18.0 \ -RUN pip install python-libsedml>=2.0.17 \ -RUN pip install requests* \ -RUN pip install rrplugins{'version': '>=2.1', 'markers': 'platform_system == "Windows"'} \ -RUN pip install scipy>=1.5.1 \ -RUN pip install matplotlib* \ -RUN pip install numpy* \ -RUN pip install pandas* \ -RUN pip install python-copasi* \ -RUN pip install PyYAML* \ -RUN pip install scipy* \ - # Add any additional setup here +RUN apt-get update && apt-get install -y --no-install-recommends \ + python3 \ + python3-pip \ + build-essential \ + libncurses5 \ + cmake \ + make \ + libx11-dev \ + libc6-dev \ + libx11-6 \ + libc6 \ + gcc \ + swig \ + pkg-config \ + curl \ + tar \ + libgl1-mesa-glx \ + libice6 \ + libpython3.10 \ + wget \ + && rm -rf /var/lib/apt/lists/* + RUN pip install antimony>=2.12.0 +RUN pip install appdirs>=1.4.3 +RUN pip install ipykernel>=4.6.1 +RUN pip install ipython* +RUN pip install jinja2>=3.0.0 +RUN pip install jupyter-client>=5.1.0 +RUN pip install jupyter-core>=4.3.0 +RUN pip install libroadrunner>=2.1 +RUN pip install matplotlib>=2.0.2 +RUN pip install numpy>=1.23 +RUN pip install pandas>=0.20.2 +RUN pip install phrasedml{'version': '>=1.0.9', 'markers': 'platform_machine != "arm64"'} +RUN pip install plotly>=2.0.12 +RUN pip install pytest* +RUN pip install python-libcombine>=0.2.2 +RUN pip install python-libnuml>=1.0.0 +RUN pip install python-libsbml>=5.18.0 +RUN pip install python-libsedml>=2.0.17 +RUN pip install requests* +RUN pip install rrplugins{'version': '>=2.1', 'markers': 'platform_system == "Windows"'} +RUN pip install scipy>=1.5.1 +RUN pip install matplotlib* +RUN pip install numpy* +RUN pip install pandas* +RUN pip install python-copasi* +RUN pip install PyYAML* +RUN pip install scipy* diff --git a/biosimulator_processes/container.py b/biosimulator_processes/container.py index 583251555..62fe49dff 100644 --- a/biosimulator_processes/container.py +++ b/biosimulator_processes/container.py @@ -4,13 +4,13 @@ def write_config(): config = {} - with open('simulators.json', 'w') as fp: + with open('biosimulator_processes/simulators.json', 'w') as fp: json.dump(config, fp, indent=4) def load_config(): # Load simulator configuration - with open('simulators.json', 'r') as file: + with open('biosimulator_processes/simulators.json', 'r') as file: return json.load(file) @@ -22,21 +22,21 @@ def add_installations_to_dockerfile(dockerfile_contents: str, config: dict): for dep, version in deps.items(): # For simplicity, assuming all dependencies can be installed via pip # This line might need adjustment based on actual package management needs - dockerfile_contents += f"RUN pip install {dep}{version} \\\n" + dockerfile_contents += f"RUN pip install {dep}{version}\\n" # Finish the Dockerfile with any additional setup - dockerfile_contents += " # Add any additional setup here\n" + # dockerfile_contents += " # Add any additional setup here\n" return dockerfile_contents def write_dockerfile(dockerfile_contents: str): # Save the Dockerfile - with open('Dockerfile', 'w') as file: + with open('biosimulator_processes/Dockerfile', 'w') as file: file.write(dockerfile_contents) def exec_container(name: str): - build_command = f"docker buildx create --name biosimbuilder --use && docker buildx build --platform linux/amd64 -t {name}_env ." + build_command = f"docker build --platform linux/amd64 {name}_env ." subprocess.run(build_command.split()) run_command = f"docker run --platform linux/amd64 -it -p 8888:8888 {name}_env" subprocess.run(run_command.split()) @@ -45,32 +45,31 @@ def exec_container(name: str): def run(name: str): config = load_config() - base_contents = """ - RUN apt-get update && apt-get install -y --no-install-recommends \ - python3 \ - python3-pip \ - build-essential \ - libncurses5 \ - cmake \ - make \ - libx11-dev \ - libc6-dev \ - libx11-6 \ - libc6 \ - gcc \ - swig \ - pkg-config \ - curl \ - tar \ - libgl1-mesa-glx \ - libice6 \ - libpython3.10 \ - wget \ + base_contents = """RUN apt-get update && apt-get install -y --no-install-recommends \\ + python3 \\ + python3-pip \\ + build-essential \\ + libncurses5 \\ + cmake \\ + make \\ + libx11-dev \\ + libc6-dev \\ + libx11-6 \\ + libc6 \\ + gcc \\ + swig \\ + pkg-config \\ + curl \\ + tar \\ + libgl1-mesa-glx \\ + libice6 \\ + libpython3.10 \\ + wget \\ && rm -rf /var/lib/apt/lists/* """ dockerfile_contents = add_installations_to_dockerfile(base_contents, config) write_dockerfile(dockerfile_contents) - exec_container(name) + # exec_container(name) if __name__ == '__main__': From 54870aff3ab036b81ed099d87e5af750e4da27ec Mon Sep 17 00:00:00 2001 From: "A.P" <105522603+AlexPatrie@users.noreply.github.com> Date: Sat, 24 Feb 2024 11:47:53 -0500 Subject: [PATCH 13/56] updated docker config --- biosimulator_processes/container.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/biosimulator_processes/container.py b/biosimulator_processes/container.py index 62fe49dff..063ac948c 100644 --- a/biosimulator_processes/container.py +++ b/biosimulator_processes/container.py @@ -45,7 +45,9 @@ def exec_container(name: str): def run(name: str): config = load_config() - base_contents = """RUN apt-get update && apt-get install -y --no-install-recommends \\ + base_contents = """ + FROM ubuntu:latest \\ + RUN apt-get update && apt-get install -y --no-install-recommends \\ python3 \\ python3-pip \\ build-essential \\ From 387e3211214ca6db0c24bb24f2631469fde6ac81 Mon Sep 17 00:00:00 2001 From: "A.P" <105522603+AlexPatrie@users.noreply.github.com> Date: Sat, 24 Feb 2024 12:02:55 -0500 Subject: [PATCH 14/56] fix: removed new line delim --- biosimulator_processes/container.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/biosimulator_processes/container.py b/biosimulator_processes/container.py index 063ac948c..4f22f10ed 100644 --- a/biosimulator_processes/container.py +++ b/biosimulator_processes/container.py @@ -22,7 +22,7 @@ def add_installations_to_dockerfile(dockerfile_contents: str, config: dict): for dep, version in deps.items(): # For simplicity, assuming all dependencies can be installed via pip # This line might need adjustment based on actual package management needs - dockerfile_contents += f"RUN pip install {dep}{version}\\n" + dockerfile_contents += f"RUN pip install {dep}{version}\n" # Finish the Dockerfile with any additional setup # dockerfile_contents += " # Add any additional setup here\n" From 532fa0f5eede0122ffcf5afa86449859212a2928 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Sun, 25 Feb 2024 08:04:28 -0500 Subject: [PATCH 15/56] updated dockerfile maker --- biosimulator_processes/Dockerfile | 43 ++++++++++++------------- biosimulator_processes/container.py | 49 ++++++++++++++--------------- 2 files changed, 46 insertions(+), 46 deletions(-) diff --git a/biosimulator_processes/Dockerfile b/biosimulator_processes/Dockerfile index 00b249b6a..faef67af6 100644 --- a/biosimulator_processes/Dockerfile +++ b/biosimulator_processes/Dockerfile @@ -1,25 +1,26 @@ + +FROM ubuntu:latest \ RUN apt-get update && apt-get install -y --no-install-recommends \ - python3 \ - python3-pip \ - build-essential \ - libncurses5 \ - cmake \ - make \ - libx11-dev \ - libc6-dev \ - libx11-6 \ - libc6 \ - gcc \ - swig \ - pkg-config \ - curl \ - tar \ - libgl1-mesa-glx \ - libice6 \ - libpython3.10 \ - wget \ - && rm -rf /var/lib/apt/lists/* - RUN pip install antimony>=2.12.0 + python3 \ + python3-pip \ + build-essential \ + libncurses5 \ + cmake \ + make \ + libx11-dev \ + libc6-dev \ + libx11-6 \ + libc6 \ + gcc \ + swig \ + pkg-config \ + curl \ + tar \ + libgl1-mesa-glx \ + libice6 \ + libpython3.10 \ + wget \ + && rm -rf /var/lib/apt/lists/*RUN pip install antimony>=2.12.0 RUN pip install appdirs>=1.4.3 RUN pip install ipykernel>=4.6.1 RUN pip install ipython* diff --git a/biosimulator_processes/container.py b/biosimulator_processes/container.py index 4f22f10ed..4f30769b1 100644 --- a/biosimulator_processes/container.py +++ b/biosimulator_processes/container.py @@ -36,7 +36,7 @@ def write_dockerfile(dockerfile_contents: str): def exec_container(name: str): - build_command = f"docker build --platform linux/amd64 {name}_env ." + build_command = f"docker buildx build --platform linux/amd64 {name}_env ." subprocess.run(build_command.split()) run_command = f"docker run --platform linux/amd64 -it -p 8888:8888 {name}_env" subprocess.run(run_command.split()) @@ -45,30 +45,29 @@ def exec_container(name: str): def run(name: str): config = load_config() - base_contents = """ - FROM ubuntu:latest \\ - RUN apt-get update && apt-get install -y --no-install-recommends \\ - python3 \\ - python3-pip \\ - build-essential \\ - libncurses5 \\ - cmake \\ - make \\ - libx11-dev \\ - libc6-dev \\ - libx11-6 \\ - libc6 \\ - gcc \\ - swig \\ - pkg-config \\ - curl \\ - tar \\ - libgl1-mesa-glx \\ - libice6 \\ - libpython3.10 \\ - wget \\ - && rm -rf /var/lib/apt/lists/* - """ + base_contents = f""" +FROM ubuntu:latest \\ +RUN apt-get update && apt-get install -y --no-install-recommends \\ + python3 \\ + python3-pip \\ + build-essential \\ + libncurses5 \\ + cmake \\ + make \\ + libx11-dev \\ + libc6-dev \\ + libx11-6 \\ + libc6 \\ + gcc \\ + swig \\ + pkg-config \\ + curl \\ + tar \\ + libgl1-mesa-glx \\ + libice6 \\ + libpython3.10 \\ + wget \\ + && rm -rf /var/lib/apt/lists/*""" dockerfile_contents = add_installations_to_dockerfile(base_contents, config) write_dockerfile(dockerfile_contents) # exec_container(name) From 84978edc8faaf134a57c35027ee8a814c6e8d04b Mon Sep 17 00:00:00 2001 From: "A.P" <105522603+AlexPatrie@users.noreply.github.com> Date: Sun, 25 Feb 2024 09:23:28 -0500 Subject: [PATCH 16/56] chore: added docstring and Docker import --- biosimulator_processes/container.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/biosimulator_processes/container.py b/biosimulator_processes/container.py index 4f30769b1..62c6a314d 100644 --- a/biosimulator_processes/container.py +++ b/biosimulator_processes/container.py @@ -1,5 +1,10 @@ import json -import subprocess +import subprocess +import docker + +'''unix:///var/run/docker.sock + +instantiate DockerClient''' def write_config(): From d7d525275827de58afda562625234ef034bc3d67 Mon Sep 17 00:00:00 2001 From: "A.P" <105522603+AlexPatrie@users.noreply.github.com> Date: Sun, 25 Feb 2024 09:27:45 -0500 Subject: [PATCH 17/56] chore: added docker dep to pyproject file --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index d3cc355af..e65287531 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,6 +20,7 @@ tellurium = "*" smoldyn = "*" bigraph-viz = "^0.0.31" python-libsbml = "^5.20.2" +docker = ">=7.0" [tool.poetry.group.dev.dependencies] pytest = "*" From fc5bc10f5332906c119ed61c3748d04305c0e80d Mon Sep 17 00:00:00 2001 From: "A.P" <105522603+AlexPatrie@users.noreply.github.com> Date: Sun, 25 Feb 2024 10:27:53 -0500 Subject: [PATCH 18/56] created client for Docker in container.py --- biosimulator_processes/container.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/biosimulator_processes/container.py b/biosimulator_processes/container.py index 62c6a314d..a19d6513e 100644 --- a/biosimulator_processes/container.py +++ b/biosimulator_processes/container.py @@ -7,6 +7,10 @@ instantiate DockerClient''' +CLIENT = docker.DockerClient( + base_url='unix:///var/run/docker.sock' +) + def write_config(): config = {} with open('biosimulator_processes/simulators.json', 'w') as fp: From ad8c1445e1a791c90b787e5d37027284e15892a1 Mon Sep 17 00:00:00 2001 From: "A.P" <105522603+AlexPatrie@users.noreply.github.com> Date: Sun, 25 Feb 2024 10:56:48 -0500 Subject: [PATCH 19/56] Update container.py --- biosimulator_processes/container.py | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/biosimulator_processes/container.py b/biosimulator_processes/container.py index a19d6513e..82b5aeeaf 100644 --- a/biosimulator_processes/container.py +++ b/biosimulator_processes/container.py @@ -51,6 +51,16 @@ def exec_container(name: str): subprocess.run(run_command.split()) +def build_image(name: str): + return CLIENT.images.build( + path='.', + tag=name) + + +def exec_container(img_name: str): + img = build_image(name) + + def run(name: str): config = load_config() From 7089648ef00a5fabf5394c9bdbac578443349419 Mon Sep 17 00:00:00 2001 From: "A.P" <105522603+AlexPatrie@users.noreply.github.com> Date: Sun, 25 Feb 2024 11:06:35 -0500 Subject: [PATCH 20/56] Update container.py for running --- biosimulator_processes/container.py | 1 + 1 file changed, 1 insertion(+) diff --git a/biosimulator_processes/container.py b/biosimulator_processes/container.py index 82b5aeeaf..b4ec094c4 100644 --- a/biosimulator_processes/container.py +++ b/biosimulator_processes/container.py @@ -59,6 +59,7 @@ def build_image(name: str): def exec_container(img_name: str): img = build_image(name) + CLIENT.containers.run(img.id) def run(name: str): From 058fab5ae3c45eacf8ce88870b5dc86c8d89e564 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Sun, 25 Feb 2024 11:58:48 -0500 Subject: [PATCH 21/56] updated dockerfile base --- Dockerfile | 30 -- Dockerfile-base | 72 ++++ biosimulator_processes/Dockerfile | 49 --- biosimulator_processes/container.py | 2 +- poetry.lock | 627 ++++++++++++++-------------- 5 files changed, 398 insertions(+), 382 deletions(-) delete mode 100644 Dockerfile create mode 100644 Dockerfile-base delete mode 100644 biosimulator_processes/Dockerfile diff --git a/Dockerfile b/Dockerfile deleted file mode 100644 index 88ce949fe..000000000 --- a/Dockerfile +++ /dev/null @@ -1,30 +0,0 @@ - - RUN apt-get update && apt-get install -y --no-install-recommends python3 python3-pip build-essential libncurses5 cmake make libx11-dev libc6-dev libx11-6 libc6 gcc swig pkg-config curl tar libgl1-mesa-glx libice6 libpython3.10 wget && rm -rf /var/lib/apt/lists/* - RUN pip install antimony>=2.12.0 \ -RUN pip install appdirs>=1.4.3 \ -RUN pip install ipykernel>=4.6.1 \ -RUN pip install ipython* \ -RUN pip install jinja2>=3.0.0 \ -RUN pip install jupyter-client>=5.1.0 \ -RUN pip install jupyter-core>=4.3.0 \ -RUN pip install libroadrunner>=2.1 \ -RUN pip install matplotlib>=2.0.2 \ -RUN pip install numpy>=1.23 \ -RUN pip install pandas>=0.20.2 \ -RUN pip install phrasedml{'version': '>=1.0.9', 'markers': 'platform_machine != "arm64"'} \ -RUN pip install plotly>=2.0.12 \ -RUN pip install pytest* \ -RUN pip install python-libcombine>=0.2.2 \ -RUN pip install python-libnuml>=1.0.0 \ -RUN pip install python-libsbml>=5.18.0 \ -RUN pip install python-libsedml>=2.0.17 \ -RUN pip install requests* \ -RUN pip install rrplugins{'version': '>=2.1', 'markers': 'platform_system == "Windows"'} \ -RUN pip install scipy>=1.5.1 \ -RUN pip install matplotlib* \ -RUN pip install numpy* \ -RUN pip install pandas* \ -RUN pip install python-copasi* \ -RUN pip install PyYAML* \ -RUN pip install scipy* \ - # Add any additional setup here diff --git a/Dockerfile-base b/Dockerfile-base new file mode 100644 index 000000000..ba6cf7725 --- /dev/null +++ b/Dockerfile-base @@ -0,0 +1,72 @@ +FROM ubuntu:latest + +ENV DEBIAN_FRONTEND=noninteractive + +WORKDIR /app + +# COPY . /app + +# COPY ./scripts /app + +# RUN rm -r /app/composer-api + +RUN apt-get update && apt-get install -y --no-install-recommends \ + python3 \ + python3-pip \ + build-essential \ + libncurses5 \ + cmake \ + make \ + libx11-dev \ + libc6-dev \ + libx11-6 \ + libc6 \ + gcc \ + swig \ + pkg-config \ + curl \ + tar \ + libgl1-mesa-glx \ + libice6 \ + libpython3.10 \ + wget \ + && rm -rf /var/lib/apt/lists/* + +RUN apt-get -y update \ + \ + && apt-get install --no-install-recommends -y \ + xvfb \ + && mkdir /tmp/.X11-unix \ + && chmod 1777 /tmp/.X11-unix \ + && rm -rf /var/lib/apt/lists/* + +COPY scripts/xvfb-startup.sh /xvfb-startup.sh + +# RUN rm -r ./scripts + +ENV XVFB_RES="1920x1080x24" \ + XVFB_ARGS="" + +RUN pip install --upgrade pip \ + && pip install poetry + +RUN poetry config virtualenvs.in-project true + +# Add Poetry to PATH +ENV PATH="/root/.local/bin:${PATH}" + +RUN poetry run pip install --upgrade pip \ + && poetry run pip install python-libnuml --use-pep517 \ + && poetry install + +# activate poetry virtualenv +ENV PATH="/app/.venv/bin:$PATH" +ENV CONFIG_ENV_FILE="/app/config/config.env" +ENV SECRET_ENV_FILE="/app/secret/secret.env" +ENV STORAGE_GCS_CREDENTIALS_FILE="/app/secret/gcs_credentials.json" +ENV STORAGE_LOCAL_CACHE_DIR="/app/scratch" + +# activate the poetry virtualenv each new non-interative shell +RUN echo "source /app/.venv/bin/activate" >> /etc/bash.bashrc + +# ENTRYPOINT ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"] diff --git a/biosimulator_processes/Dockerfile b/biosimulator_processes/Dockerfile deleted file mode 100644 index faef67af6..000000000 --- a/biosimulator_processes/Dockerfile +++ /dev/null @@ -1,49 +0,0 @@ - -FROM ubuntu:latest \ -RUN apt-get update && apt-get install -y --no-install-recommends \ - python3 \ - python3-pip \ - build-essential \ - libncurses5 \ - cmake \ - make \ - libx11-dev \ - libc6-dev \ - libx11-6 \ - libc6 \ - gcc \ - swig \ - pkg-config \ - curl \ - tar \ - libgl1-mesa-glx \ - libice6 \ - libpython3.10 \ - wget \ - && rm -rf /var/lib/apt/lists/*RUN pip install antimony>=2.12.0 -RUN pip install appdirs>=1.4.3 -RUN pip install ipykernel>=4.6.1 -RUN pip install ipython* -RUN pip install jinja2>=3.0.0 -RUN pip install jupyter-client>=5.1.0 -RUN pip install jupyter-core>=4.3.0 -RUN pip install libroadrunner>=2.1 -RUN pip install matplotlib>=2.0.2 -RUN pip install numpy>=1.23 -RUN pip install pandas>=0.20.2 -RUN pip install phrasedml{'version': '>=1.0.9', 'markers': 'platform_machine != "arm64"'} -RUN pip install plotly>=2.0.12 -RUN pip install pytest* -RUN pip install python-libcombine>=0.2.2 -RUN pip install python-libnuml>=1.0.0 -RUN pip install python-libsbml>=5.18.0 -RUN pip install python-libsedml>=2.0.17 -RUN pip install requests* -RUN pip install rrplugins{'version': '>=2.1', 'markers': 'platform_system == "Windows"'} -RUN pip install scipy>=1.5.1 -RUN pip install matplotlib* -RUN pip install numpy* -RUN pip install pandas* -RUN pip install python-copasi* -RUN pip install PyYAML* -RUN pip install scipy* diff --git a/biosimulator_processes/container.py b/biosimulator_processes/container.py index b4ec094c4..1e8c5bc1e 100644 --- a/biosimulator_processes/container.py +++ b/biosimulator_processes/container.py @@ -57,7 +57,7 @@ def build_image(name: str): tag=name) -def exec_container(img_name: str): +def execute_container(img_name: str): img = build_image(name) CLIENT.containers.run(img.id) diff --git a/poetry.lock b/poetry.lock index 075b07576..3c070c62a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -611,43 +611,43 @@ tqdm = ["tqdm"] [[package]] name = "cryptography" -version = "42.0.3" +version = "42.0.5" description = "cryptography is a package which provides 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[package.dependencies] @@ -4515,4 +4538,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = ">=3.10" -content-hash = "780c0143114975709aa119547fd82225963301641c4c735249e973021b03bec5" +content-hash = "1a85b23e06cff73e3302a865efd11a5a13905e02917f8744124891040a06baef" From 14482f571808a890c557fbf1e4ab3d71ac8961fd Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Sun, 25 Feb 2024 12:07:46 -0500 Subject: [PATCH 22/56] updated container script for install --- biosimulator_processes/container.py | 77 +++++++++++++++++++++++++++-- 1 file changed, 74 insertions(+), 3 deletions(-) diff --git a/biosimulator_processes/container.py b/biosimulator_processes/container.py index 1e8c5bc1e..4c1e42e2a 100644 --- a/biosimulator_processes/container.py +++ b/biosimulator_processes/container.py @@ -23,7 +23,78 @@ def load_config(): return json.load(file) +def add_installations(base_path: str, config: dict): + """ + Args: + + """ + with open(base_path, 'r') as fp: + dockerfile_contents = fp.read() + # Iterate over each simulator and add installations for its dependencies + for simulator in config['simulators']: + deps = simulator.get('deps', {}) + # Convert dependencies dict to a list of installation commands + for dep, version in deps.items(): + # For simplicity, assuming all dependencies can be installed via pip + # This line might need adjustment based on actual package management needs + dockerfile_contents += f"RUN pip install {dep}{version}\n" + + # common entrypoint used by all processes + dockerfile_contents += 'ENTRYPOINT ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"]' + return dockerfile_contents + def add_installations_to_dockerfile(dockerfile_contents: str, config: dict): + """ + Args: + dockerfile_contents:`str`: starting content for your dockerfile. + config:`dict`: simulator configuration containing simulator version and dependencies. Derived + possibly from poetry.lock. For example: + + { + "simulators": [ + { + "name": "tellurium", + "version": "2.2.10", + "description": "Tellurium: An biological modeling environment for Python", + "optional": false, + "python-versions": "*", + "files": [ + { + "file": "tellurium-2.2.10-py3-none-any.whl", + "hash": "sha256:078dbe5beeef49cc8caa9f626cb9c8e568752ecfaff3370acd32be123d6e24ae" + } + ], + "deps": { + "antimony": ">=2.12.0", + "appdirs": ">=1.4.3", + "ipykernel": ">=4.6.1", + "ipython": "*", + "jinja2": ">=3.0.0", + "jupyter-client": ">=5.1.0", + "jupyter-core": ">=4.3.0", + "libroadrunner": ">=2.1", + "matplotlib": ">=2.0.2", + "numpy": ">=1.23", + "pandas": ">=0.20.2", + "phrasedml": { + "version": ">=1.0.9", + "markers": "platform_machine != \"arm64\"" + }, + "plotly": ">=2.0.12", + "pytest": "*", + "python-libcombine": ">=0.2.2", + "python-libnuml": ">=1.0.0", + "python-libsbml": ">=5.18.0", + "python-libsedml": ">=2.0.17", + "requests": "*", + "rrplugins": { + "version": ">=2.1", + "markers": "platform_system == \"Windows\"" + }, + "scipy": ">=1.5.1" + } + }, + """ # Iterate over each simulator and add installations for its dependencies for simulator in config['simulators']: deps = simulator.get('deps', {}) @@ -33,8 +104,8 @@ def add_installations_to_dockerfile(dockerfile_contents: str, config: dict): # This line might need adjustment based on actual package management needs dockerfile_contents += f"RUN pip install {dep}{version}\n" - # Finish the Dockerfile with any additional setup - # dockerfile_contents += " # Add any additional setup here\n" + # common entrypoint used by all processes + dockerfile_contents += 'ENTRYPOINT ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"]' return dockerfile_contents @@ -90,7 +161,7 @@ def run(name: str): && rm -rf /var/lib/apt/lists/*""" dockerfile_contents = add_installations_to_dockerfile(base_contents, config) write_dockerfile(dockerfile_contents) - # exec_container(name) + # execute_container(name) if __name__ == '__main__': From 021d770b5cec56bd5964bf707ebf371ed009d92b Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Sun, 25 Feb 2024 15:25:06 -0500 Subject: [PATCH 23/56] updated container logic --- biosimulator_processes/container.py | 55 +++++++++++++++++++++++++++-- 1 file changed, 53 insertions(+), 2 deletions(-) diff --git a/biosimulator_processes/container.py b/biosimulator_processes/container.py index 4c1e42e2a..7d47166ee 100644 --- a/biosimulator_processes/container.py +++ b/biosimulator_processes/container.py @@ -23,11 +23,57 @@ def load_config(): return json.load(file) -def add_installations(base_path: str, config: dict): +def find_package_info(package: str): + # TODO: Finish this + package = {} + with open('poetry.lock', 'r') as f: + pass + + +def add_simulator_installations(base_path: str, config: dict): """ Args: + base_path:`str`: path to the base dockerfile on which to append installations. + config:`dict`: a dictionary specifying simulator versions and their dependencies. The schema for + this dictionary should be (for example): + { + "simulators": [ + { + "name": "tellurium", + "version": "2.2.10", + "deps": { + "antimony": ">=2.12.0", + "appdirs": ">=1.4.3", + "ipykernel": ">=4.6.1", + "ipython": "*", + "jinja2": ">=3.0.0", + "jupyter-client": ">=5.1.0", + "jupyter-core": ">=4.3.0", + "libroadrunner": ">=2.1", + "matplotlib": ">=2.0.2", + "numpy": ">=1.23", + "pandas": ">=0.20.2", + "phrasedml": { + "version": ">=1.0.9", + "markers": "platform_machine != \"arm64\"" + }, + "plotly": ">=2.0.12", + "pytest": "*", + "python-libcombine": ">=0.2.2", + "python-libnuml": ">=1.0.0", + "python-libsbml": ">=5.18.0", + "python-libsedml": ">=2.0.17", + "requests": "*", + "rrplugins": { + "version": ">=2.1", + "markers": "platform_system == \"Windows\"" + }, + "scipy": ">=1.5.1" + } + }, """ + # TODO: automate mapping simulators to poetry.lock: ie: simulators arg that searches the lock file with open(base_path, 'r') as fp: dockerfile_contents = fp.read() # Iterate over each simulator and add installations for its dependencies @@ -159,7 +205,12 @@ def run(name: str): libpython3.10 \\ wget \\ && rm -rf /var/lib/apt/lists/*""" - dockerfile_contents = add_installations_to_dockerfile(base_contents, config) + # dockerfile_contents = add_installations_to_dockerfile(base_contents, config) + + dockerfile_contents = add_simulator_installations( + base_path='Dockerfile-base', + config=config + ) write_dockerfile(dockerfile_contents) # execute_container(name) From 47bbc13623d24ea7bafe9631ab2007c6f9f0c483 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Sun, 25 Feb 2024 15:29:24 -0500 Subject: [PATCH 24/56] updated script to install with poetry within the container for version control --- biosimulator_processes/container.py | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/biosimulator_processes/container.py b/biosimulator_processes/container.py index 7d47166ee..175b7310b 100644 --- a/biosimulator_processes/container.py +++ b/biosimulator_processes/container.py @@ -76,19 +76,17 @@ def add_simulator_installations(base_path: str, config: dict): # TODO: automate mapping simulators to poetry.lock: ie: simulators arg that searches the lock file with open(base_path, 'r') as fp: dockerfile_contents = fp.read() - # Iterate over each simulator and add installations for its dependencies for simulator in config['simulators']: deps = simulator.get('deps', {}) - # Convert dependencies dict to a list of installation commands for dep, version in deps.items(): - # For simplicity, assuming all dependencies can be installed via pip - # This line might need adjustment based on actual package management needs - dockerfile_contents += f"RUN pip install {dep}{version}\n" + # dockerfile_contents += f"RUN pip install {dep}{version}\n" + dockerfile_contents += f"RUN poetry add {dep}{version}\n" # common entrypoint used by all processes dockerfile_contents += 'ENTRYPOINT ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"]' return dockerfile_contents + def add_installations_to_dockerfile(dockerfile_contents: str, config: dict): """ Args: From d1898b9657b938b2ebd3c1edcaafc7fbf3795a62 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Sun, 25 Feb 2024 15:30:24 -0500 Subject: [PATCH 25/56] minor reformat of base dockerfile --- Dockerfile-base | 1 - 1 file changed, 1 deletion(-) diff --git a/Dockerfile-base b/Dockerfile-base index ba6cf7725..9143bad22 100644 --- a/Dockerfile-base +++ b/Dockerfile-base @@ -33,7 +33,6 @@ RUN apt-get update && apt-get install -y --no-install-recommends \ && rm -rf /var/lib/apt/lists/* RUN apt-get -y update \ - \ && apt-get install --no-install-recommends -y \ xvfb \ && mkdir /tmp/.X11-unix \ From e6e1311b8cbc9833455afd6dd80f53f78a32a3fc Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Sun, 25 Feb 2024 15:35:37 -0500 Subject: [PATCH 26/56] updated script for docker build --- biosimulator_processes/container.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/biosimulator_processes/container.py b/biosimulator_processes/container.py index 175b7310b..c03e268f8 100644 --- a/biosimulator_processes/container.py +++ b/biosimulator_processes/container.py @@ -1,5 +1,6 @@ import json -import subprocess +import subprocess +import tempfile import docker '''unix:///var/run/docker.sock @@ -166,14 +167,15 @@ def exec_container(name: str): subprocess.run(run_command.split()) -def build_image(name: str): +def build_image(name: str, p: str = '.'): return CLIENT.images.build( - path='.', + path=p, tag=name) def execute_container(img_name: str): - img = build_image(name) + container_dir = tempfile.mkdtemp() + img = build_image(img_name) CLIENT.containers.run(img.id) From df93a48f0d9b60d3c7cfbe12e24c2e510aea4f23 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Sun, 25 Feb 2024 15:39:38 -0500 Subject: [PATCH 27/56] updated script to tempfile for container --- biosimulator_processes/container.py | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/biosimulator_processes/container.py b/biosimulator_processes/container.py index c03e268f8..e813d7ec0 100644 --- a/biosimulator_processes/container.py +++ b/biosimulator_processes/container.py @@ -1,4 +1,5 @@ import json +import os import subprocess import tempfile import docker @@ -154,9 +155,9 @@ def add_installations_to_dockerfile(dockerfile_contents: str, config: dict): return dockerfile_contents -def write_dockerfile(dockerfile_contents: str): +def write_dockerfile(dockerfile_contents: str, path: str = 'biosimulator_processes/Dockerfile'): # Save the Dockerfile - with open('biosimulator_processes/Dockerfile', 'w') as file: + with open(path, 'w') as file: file.write(dockerfile_contents) @@ -211,8 +212,10 @@ def run(name: str): base_path='Dockerfile-base', config=config ) - write_dockerfile(dockerfile_contents) - # execute_container(name) + + container_dir = tempfile.mkdtemp() + write_dockerfile(dockerfile_contents, path=os.path.join(container_dir, 'Dockerfile')) + execute_container(name) if __name__ == '__main__': From c4efdd94fc186f35da360e3c3f7547c1cfe5c53a Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Sun, 25 Feb 2024 15:41:19 -0500 Subject: [PATCH 28/56] feat: implemented dockerfile gen path --- Dockerfile | 99 +++++++++++++++++++++++++++++ biosimulator_processes/container.py | 2 +- 2 files changed, 100 insertions(+), 1 deletion(-) create mode 100644 Dockerfile diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 000000000..e5fbc17bd --- /dev/null +++ b/Dockerfile @@ -0,0 +1,99 @@ +FROM ubuntu:latest + +ENV DEBIAN_FRONTEND=noninteractive + +WORKDIR /app + +# COPY . /app + +# COPY ./scripts /app + +# RUN rm -r /app/composer-api + +RUN apt-get update && apt-get install -y --no-install-recommends \ + python3 \ + python3-pip \ + build-essential \ + libncurses5 \ + cmake \ + make \ + libx11-dev \ + libc6-dev \ + libx11-6 \ + libc6 \ + gcc \ + swig \ + pkg-config \ + curl \ + tar \ + libgl1-mesa-glx \ + libice6 \ + libpython3.10 \ + wget \ + && rm -rf /var/lib/apt/lists/* + +RUN apt-get -y update \ + && apt-get install --no-install-recommends -y \ + xvfb \ + && mkdir /tmp/.X11-unix \ + && chmod 1777 /tmp/.X11-unix \ + && rm -rf /var/lib/apt/lists/* + +COPY scripts/xvfb-startup.sh /xvfb-startup.sh + +# RUN rm -r ./scripts + +ENV XVFB_RES="1920x1080x24" \ + XVFB_ARGS="" + +RUN pip install --upgrade pip \ + && pip install poetry + +RUN poetry config virtualenvs.in-project true + +# Add Poetry to PATH +ENV PATH="/root/.local/bin:${PATH}" + +RUN poetry run pip install --upgrade pip \ + && poetry run pip install python-libnuml --use-pep517 \ + && poetry install + +# activate poetry virtualenv +ENV PATH="/app/.venv/bin:$PATH" +ENV CONFIG_ENV_FILE="/app/config/config.env" +ENV SECRET_ENV_FILE="/app/secret/secret.env" +ENV STORAGE_GCS_CREDENTIALS_FILE="/app/secret/gcs_credentials.json" +ENV STORAGE_LOCAL_CACHE_DIR="/app/scratch" + +# activate the poetry virtualenv each new non-interative shell +RUN echo "source /app/.venv/bin/activate" >> /etc/bash.bashrc + +# ENTRYPOINT ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"] +RUN poetry add antimony>=2.12.0 +RUN poetry add appdirs>=1.4.3 +RUN poetry add ipykernel>=4.6.1 +RUN poetry add ipython* +RUN poetry add jinja2>=3.0.0 +RUN poetry add jupyter-client>=5.1.0 +RUN poetry add jupyter-core>=4.3.0 +RUN poetry add libroadrunner>=2.1 +RUN poetry add matplotlib>=2.0.2 +RUN poetry add numpy>=1.23 +RUN poetry add pandas>=0.20.2 +RUN poetry add phrasedml{'version': '>=1.0.9', 'markers': 'platform_machine != "arm64"'} +RUN poetry add plotly>=2.0.12 +RUN poetry add pytest* +RUN poetry add python-libcombine>=0.2.2 +RUN poetry add python-libnuml>=1.0.0 +RUN poetry add python-libsbml>=5.18.0 +RUN poetry add python-libsedml>=2.0.17 +RUN poetry add requests* +RUN poetry add rrplugins{'version': '>=2.1', 'markers': 'platform_system == "Windows"'} +RUN poetry add scipy>=1.5.1 +RUN poetry add matplotlib* +RUN poetry add numpy* +RUN poetry add pandas* +RUN poetry add python-copasi* +RUN poetry add PyYAML* +RUN poetry add scipy* +ENTRYPOINT ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"] \ No newline at end of file diff --git a/biosimulator_processes/container.py b/biosimulator_processes/container.py index e813d7ec0..6d8fcc630 100644 --- a/biosimulator_processes/container.py +++ b/biosimulator_processes/container.py @@ -214,7 +214,7 @@ def run(name: str): ) container_dir = tempfile.mkdtemp() - write_dockerfile(dockerfile_contents, path=os.path.join(container_dir, 'Dockerfile')) + write_dockerfile(dockerfile_contents, path='Dockerfile') execute_container(name) From 79f287d628d3ddecdfef40afec7f00c3abd92af7 Mon Sep 17 00:00:00 2001 From: "A.P" <105522603+AlexPatrie@users.noreply.github.com> Date: Sun, 25 Feb 2024 16:26:34 -0500 Subject: [PATCH 29/56] added to does for container.py --- biosimulator_processes/container.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/biosimulator_processes/container.py b/biosimulator_processes/container.py index 6d8fcc630..9808876b9 100644 --- a/biosimulator_processes/container.py +++ b/biosimulator_processes/container.py @@ -32,10 +32,10 @@ def find_package_info(package: str): pass -def add_simulator_installations(base_path: str, config: dict): +def add_simulator_installations(config: dict): """ Args: - base_path:`str`: path to the base dockerfile on which to append installations. + # base_path:`str`: path to the base dockerfile on which to append installations. config:`dict`: a dictionary specifying simulator versions and their dependencies. The schema for this dictionary should be (for example): @@ -75,6 +75,8 @@ def add_simulator_installations(base_path: str, config: dict): } }, """ + + base_path = 'Dockerfile-base' # TODO: automate mapping simulators to poetry.lock: ie: simulators arg that searches the lock file with open(base_path, 'r') as fp: dockerfile_contents = fp.read() From f595d8c88076f36a9d60a2134d257cd997fd3559 Mon Sep 17 00:00:00 2001 From: "A.P" <105522603+AlexPatrie@users.noreply.github.com> Date: Sun, 25 Feb 2024 16:27:59 -0500 Subject: [PATCH 30/56] Update container.py --- biosimulator_processes/container.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/biosimulator_processes/container.py b/biosimulator_processes/container.py index 9808876b9..40303147e 100644 --- a/biosimulator_processes/container.py +++ b/biosimulator_processes/container.py @@ -9,6 +9,8 @@ instantiate DockerClient''' +# TODO: Move Dockerfile-base to this dir + CLIENT = docker.DockerClient( base_url='unix:///var/run/docker.sock' ) From 9d1dabc6b0d9a22f0146bec9c7dcf8e10a13a684 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Mon, 26 Feb 2024 10:57:23 -0500 Subject: [PATCH 31/56] updated readme and refactored for container package --- Dockerfile | 99 -------- README.md | 6 + .../container-assets/Dockerfile-base | 2 +- .../container-assets/poetry.lock | 0 .../container-assets/pyproject.toml | 0 biosimulator_processes/container.py | 228 ------------------ biosimulator_processes/container/__init__.py | 0 biosimulator_processes/container/container.py | 109 +++++++++ biosimulator_processes/container/exec.py | 0 biosimulator_processes/container/io.py | 75 ++++++ 10 files changed, 191 insertions(+), 328 deletions(-) delete mode 100644 Dockerfile rename Dockerfile-base => biosimulator_processes/container-assets/Dockerfile-base (96%) rename poetry.lock => biosimulator_processes/container-assets/poetry.lock (100%) rename pyproject.toml => biosimulator_processes/container-assets/pyproject.toml (100%) delete mode 100644 biosimulator_processes/container.py create mode 100644 biosimulator_processes/container/__init__.py create mode 100644 biosimulator_processes/container/container.py create mode 100644 biosimulator_processes/container/exec.py create mode 100644 biosimulator_processes/container/io.py diff --git a/Dockerfile b/Dockerfile deleted file mode 100644 index e5fbc17bd..000000000 --- a/Dockerfile +++ /dev/null @@ -1,99 +0,0 @@ -FROM ubuntu:latest - -ENV DEBIAN_FRONTEND=noninteractive - -WORKDIR /app - -# COPY . /app - -# COPY ./scripts /app - -# RUN rm -r /app/composer-api - -RUN apt-get update && apt-get install -y --no-install-recommends \ - python3 \ - python3-pip \ - build-essential \ - libncurses5 \ - cmake \ - make \ - libx11-dev \ - libc6-dev \ - libx11-6 \ - libc6 \ - gcc \ - swig \ - pkg-config \ - curl \ - tar \ - libgl1-mesa-glx \ - libice6 \ - libpython3.10 \ - wget \ - && rm -rf /var/lib/apt/lists/* - -RUN apt-get -y update \ - && apt-get install --no-install-recommends -y \ - xvfb \ - && mkdir /tmp/.X11-unix \ - && chmod 1777 /tmp/.X11-unix \ - && rm -rf /var/lib/apt/lists/* - -COPY scripts/xvfb-startup.sh /xvfb-startup.sh - -# RUN rm -r ./scripts - -ENV XVFB_RES="1920x1080x24" \ - XVFB_ARGS="" - -RUN pip install --upgrade pip \ - && pip install poetry - -RUN poetry config virtualenvs.in-project true - -# Add Poetry to PATH -ENV PATH="/root/.local/bin:${PATH}" - -RUN poetry run pip install --upgrade pip \ - && poetry run pip install python-libnuml --use-pep517 \ - && poetry install - -# activate poetry virtualenv -ENV PATH="/app/.venv/bin:$PATH" -ENV CONFIG_ENV_FILE="/app/config/config.env" -ENV SECRET_ENV_FILE="/app/secret/secret.env" -ENV STORAGE_GCS_CREDENTIALS_FILE="/app/secret/gcs_credentials.json" -ENV STORAGE_LOCAL_CACHE_DIR="/app/scratch" - -# activate the poetry virtualenv each new non-interative shell -RUN echo "source /app/.venv/bin/activate" >> /etc/bash.bashrc - -# ENTRYPOINT ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"] -RUN poetry add antimony>=2.12.0 -RUN poetry add appdirs>=1.4.3 -RUN poetry add ipykernel>=4.6.1 -RUN poetry add ipython* -RUN poetry add jinja2>=3.0.0 -RUN poetry add jupyter-client>=5.1.0 -RUN poetry add jupyter-core>=4.3.0 -RUN poetry add libroadrunner>=2.1 -RUN poetry add matplotlib>=2.0.2 -RUN poetry add numpy>=1.23 -RUN poetry add pandas>=0.20.2 -RUN poetry add phrasedml{'version': '>=1.0.9', 'markers': 'platform_machine != "arm64"'} -RUN poetry add plotly>=2.0.12 -RUN poetry add pytest* -RUN poetry add python-libcombine>=0.2.2 -RUN poetry add python-libnuml>=1.0.0 -RUN poetry add python-libsbml>=5.18.0 -RUN poetry add python-libsedml>=2.0.17 -RUN poetry add requests* -RUN poetry add rrplugins{'version': '>=2.1', 'markers': 'platform_system == "Windows"'} -RUN poetry add scipy>=1.5.1 -RUN poetry add matplotlib* -RUN poetry add numpy* -RUN poetry add pandas* -RUN poetry add python-copasi* -RUN poetry add PyYAML* -RUN poetry add scipy* -ENTRYPOINT ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"] \ No newline at end of file diff --git a/README.md b/README.md index fd8dbd31b..daac37398 100644 --- a/README.md +++ b/README.md @@ -176,3 +176,9 @@ A simplified view of the above script: >> workflow.run(10) >> results = workflow.gather_results() >> print(f'RESULTS: {pf(results)}') + + +### A NOTE FOR DEVELOPERS: +This tooling implements version control for dynamically-created composite containers through +`poetry`. The version control for content on the Python Package Index is performed by +`setup.py`. diff --git a/Dockerfile-base b/biosimulator_processes/container-assets/Dockerfile-base similarity index 96% rename from Dockerfile-base rename to biosimulator_processes/container-assets/Dockerfile-base index 9143bad22..7545d05bb 100644 --- a/Dockerfile-base +++ b/biosimulator_processes/container-assets/Dockerfile-base @@ -39,7 +39,7 @@ RUN apt-get -y update \ && chmod 1777 /tmp/.X11-unix \ && rm -rf /var/lib/apt/lists/* -COPY scripts/xvfb-startup.sh /xvfb-startup.sh +COPY ../../scripts/xvfb-startup.sh /xvfb-startup.sh # RUN rm -r ./scripts diff --git a/poetry.lock b/biosimulator_processes/container-assets/poetry.lock similarity index 100% rename from poetry.lock rename to biosimulator_processes/container-assets/poetry.lock diff --git a/pyproject.toml b/biosimulator_processes/container-assets/pyproject.toml similarity index 100% rename from pyproject.toml rename to biosimulator_processes/container-assets/pyproject.toml diff --git a/biosimulator_processes/container.py b/biosimulator_processes/container.py deleted file mode 100644 index 40303147e..000000000 --- a/biosimulator_processes/container.py +++ /dev/null @@ -1,228 +0,0 @@ -import json -import os -import subprocess -import tempfile -import docker - -'''unix:///var/run/docker.sock - -instantiate DockerClient''' - - -# TODO: Move Dockerfile-base to this dir - -CLIENT = docker.DockerClient( - base_url='unix:///var/run/docker.sock' -) - -def write_config(): - config = {} - with open('biosimulator_processes/simulators.json', 'w') as fp: - json.dump(config, fp, indent=4) - - -def load_config(): - # Load simulator configuration - with open('biosimulator_processes/simulators.json', 'r') as file: - return json.load(file) - - -def find_package_info(package: str): - # TODO: Finish this - package = {} - with open('poetry.lock', 'r') as f: - pass - - -def add_simulator_installations(config: dict): - """ - Args: - # base_path:`str`: path to the base dockerfile on which to append installations. - config:`dict`: a dictionary specifying simulator versions and their dependencies. The schema for - this dictionary should be (for example): - - { - "simulators": [ - { - "name": "tellurium", - "version": "2.2.10", - "deps": { - "antimony": ">=2.12.0", - "appdirs": ">=1.4.3", - "ipykernel": ">=4.6.1", - "ipython": "*", - "jinja2": ">=3.0.0", - "jupyter-client": ">=5.1.0", - "jupyter-core": ">=4.3.0", - "libroadrunner": ">=2.1", - "matplotlib": ">=2.0.2", - "numpy": ">=1.23", - "pandas": ">=0.20.2", - "phrasedml": { - "version": ">=1.0.9", - "markers": "platform_machine != \"arm64\"" - }, - "plotly": ">=2.0.12", - "pytest": "*", - "python-libcombine": ">=0.2.2", - "python-libnuml": ">=1.0.0", - "python-libsbml": ">=5.18.0", - "python-libsedml": ">=2.0.17", - "requests": "*", - "rrplugins": { - "version": ">=2.1", - "markers": "platform_system == \"Windows\"" - }, - "scipy": ">=1.5.1" - } - }, - """ - - base_path = 'Dockerfile-base' - # TODO: automate mapping simulators to poetry.lock: ie: simulators arg that searches the lock file - with open(base_path, 'r') as fp: - dockerfile_contents = fp.read() - for simulator in config['simulators']: - deps = simulator.get('deps', {}) - for dep, version in deps.items(): - # dockerfile_contents += f"RUN pip install {dep}{version}\n" - dockerfile_contents += f"RUN poetry add {dep}{version}\n" - - # common entrypoint used by all processes - dockerfile_contents += 'ENTRYPOINT ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"]' - return dockerfile_contents - - -def add_installations_to_dockerfile(dockerfile_contents: str, config: dict): - """ - Args: - dockerfile_contents:`str`: starting content for your dockerfile. - config:`dict`: simulator configuration containing simulator version and dependencies. Derived - possibly from poetry.lock. For example: - - { - "simulators": [ - { - "name": "tellurium", - "version": "2.2.10", - "description": "Tellurium: An biological modeling environment for Python", - "optional": false, - "python-versions": "*", - "files": [ - { - "file": "tellurium-2.2.10-py3-none-any.whl", - "hash": "sha256:078dbe5beeef49cc8caa9f626cb9c8e568752ecfaff3370acd32be123d6e24ae" - } - ], - "deps": { - "antimony": ">=2.12.0", - "appdirs": ">=1.4.3", - "ipykernel": ">=4.6.1", - "ipython": "*", - "jinja2": ">=3.0.0", - "jupyter-client": ">=5.1.0", - "jupyter-core": ">=4.3.0", - "libroadrunner": ">=2.1", - "matplotlib": ">=2.0.2", - "numpy": ">=1.23", - "pandas": ">=0.20.2", - "phrasedml": { - "version": ">=1.0.9", - "markers": "platform_machine != \"arm64\"" - }, - "plotly": ">=2.0.12", - "pytest": "*", - "python-libcombine": ">=0.2.2", - "python-libnuml": ">=1.0.0", - "python-libsbml": ">=5.18.0", - "python-libsedml": ">=2.0.17", - "requests": "*", - "rrplugins": { - "version": ">=2.1", - "markers": "platform_system == \"Windows\"" - }, - "scipy": ">=1.5.1" - } - }, - """ - # Iterate over each simulator and add installations for its dependencies - for simulator in config['simulators']: - deps = simulator.get('deps', {}) - # Convert dependencies dict to a list of installation commands - for dep, version in deps.items(): - # For simplicity, assuming all dependencies can be installed via pip - # This line might need adjustment based on actual package management needs - dockerfile_contents += f"RUN pip install {dep}{version}\n" - - # common entrypoint used by all processes - dockerfile_contents += 'ENTRYPOINT ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"]' - return dockerfile_contents - - -def write_dockerfile(dockerfile_contents: str, path: str = 'biosimulator_processes/Dockerfile'): - # Save the Dockerfile - with open(path, 'w') as file: - file.write(dockerfile_contents) - - -def exec_container(name: str): - build_command = f"docker buildx build --platform linux/amd64 {name}_env ." - subprocess.run(build_command.split()) - run_command = f"docker run --platform linux/amd64 -it -p 8888:8888 {name}_env" - subprocess.run(run_command.split()) - - -def build_image(name: str, p: str = '.'): - return CLIENT.images.build( - path=p, - tag=name) - - -def execute_container(img_name: str): - container_dir = tempfile.mkdtemp() - img = build_image(img_name) - CLIENT.containers.run(img.id) - - -def run(name: str): - config = load_config() - - base_contents = f""" -FROM ubuntu:latest \\ -RUN apt-get update && apt-get install -y --no-install-recommends \\ - python3 \\ - python3-pip \\ - build-essential \\ - libncurses5 \\ - cmake \\ - make \\ - libx11-dev \\ - libc6-dev \\ - libx11-6 \\ - libc6 \\ - gcc \\ - swig \\ - pkg-config \\ - curl \\ - tar \\ - libgl1-mesa-glx \\ - libice6 \\ - libpython3.10 \\ - wget \\ - && rm -rf /var/lib/apt/lists/*""" - # dockerfile_contents = add_installations_to_dockerfile(base_contents, config) - - dockerfile_contents = add_simulator_installations( - base_path='Dockerfile-base', - config=config - ) - - container_dir = tempfile.mkdtemp() - write_dockerfile(dockerfile_contents, path='Dockerfile') - execute_container(name) - - -if __name__ == '__main__': - run("composite") - - diff --git a/biosimulator_processes/container/__init__.py b/biosimulator_processes/container/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/biosimulator_processes/container/container.py b/biosimulator_processes/container/container.py new file mode 100644 index 000000000..d1efe5d72 --- /dev/null +++ b/biosimulator_processes/container/container.py @@ -0,0 +1,109 @@ +import json +import os +import subprocess +import tempfile +import docker + + +CLIENT = docker.DockerClient( + base_url='unix:///var/run/docker.sock' +) + + +def add_simulator_installations(config: dict): + """ + Args: + # base_path:`str`: path to the base dockerfile on which to append installations. + config:`dict`: a dictionary specifying simulator versions and their dependencies. The schema for + this dictionary should be (for example): + + { + "simulators": [ + { + "name": "tellurium", + "version": "2.2.10", + "deps": { + "antimony": ">=2.12.0", + "appdirs": ">=1.4.3", + "ipykernel": ">=4.6.1", + "ipython": "*", + "jinja2": ">=3.0.0", + "jupyter-client": ">=5.1.0", + "jupyter-core": ">=4.3.0", + "libroadrunner": ">=2.1", + "matplotlib": ">=2.0.2", + "numpy": ">=1.23", + "pandas": ">=0.20.2", + "phrasedml": { + "version": ">=1.0.9", + "markers": "platform_machine != \"arm64\"" + }, + "plotly": ">=2.0.12", + "pytest": "*", + "python-libcombine": ">=0.2.2", + "python-libnuml": ">=1.0.0", + "python-libsbml": ">=5.18.0", + "python-libsedml": ">=2.0.17", + "requests": "*", + "rrplugins": { + "version": ">=2.1", + "markers": "platform_system == \"Windows\"" + }, + "scipy": ">=1.5.1" + } + }, + """ + + base_path = 'Dockerfile-base' + # TODO: automate mapping simulators to poetry.lock: ie: simulators arg that searches the lock file + with open(base_path, 'r') as fp: + dockerfile_contents = fp.read() + for simulator in config['simulators']: + deps = simulator.get('deps', {}) + for dep, version in deps.items(): + # dockerfile_contents += f"RUN pip install {dep}{version}\n" + dockerfile_contents += f"RUN poetry add {dep}{version}\n" + + # common entrypoint used by all processes + dockerfile_contents += 'ENTRYPOINT ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"]' + return dockerfile_contents + + + + +def exec_container(name: str): + build_command = f"docker buildx build --platform linux/amd64 {name}_env ." + subprocess.run(build_command.split()) + run_command = f"docker run --platform linux/amd64 -it -p 8888:8888 {name}_env" + subprocess.run(run_command.split()) + + +def build_image(name: str, p: str = '.'): + return CLIENT.images.build( + path=p, + tag=name) + + +def execute_container(img_name: str): + container_dir = tempfile.mkdtemp() + img = build_image(img_name) + CLIENT.containers.run(img.id) + + +def run(name: str): + config = load_config() + + dockerfile_contents = add_simulator_installations( + base_path='Dockerfile-base', + config=config + ) + + container_dir = tempfile.mkdtemp() + write_dockerfile(dockerfile_contents, path='Dockerfile') + execute_container(name) + + +if __name__ == '__main__': + run("composite") + + diff --git a/biosimulator_processes/container/exec.py b/biosimulator_processes/container/exec.py new file mode 100644 index 000000000..e69de29bb diff --git a/biosimulator_processes/container/io.py b/biosimulator_processes/container/io.py new file mode 100644 index 000000000..129cc6248 --- /dev/null +++ b/biosimulator_processes/container/io.py @@ -0,0 +1,75 @@ +import json +import toml + + +def write_config(): + config = {} + with open('biosimulator_processes/simulators.json', 'w') as fp: + json.dump(config, fp, indent=4) + + +def load_config(): + # Load simulator configuration + with open('biosimulator_processes/simulators.json', 'r') as file: + return json.load(file) + + +def find_package_info(package: str): + # TODO: Finish this + package = {} + with open('poetry.lock', 'r') as f: + pass + + +def write_dockerfile(dockerfile_contents: str, path: str = 'biosimulator_processes/Dockerfile'): + # Save the Dockerfile + with open(path, 'w') as file: + file.write(dockerfile_contents) + + +def parse_simulator_deps(deps): + """Parse dependencies, handling conditional dependencies.""" + parsed_deps = {} + for dep in deps: + if isinstance(dep, str): + # Simple dependency + if " " in dep: + name, version = dep.split(" ", 1) + else: + name, version = dep, "*" + parsed_deps[name] = version + elif isinstance(dep, dict): + # Conditional dependency + for name, info in dep.items(): + if "version" in info: + parsed_deps[name] = { + "version": info["version"], + "markers": info.get("markers", "") + } + return parsed_deps + + +def get_simulator(sim: str): + # Load the poetry.lock file + with open('poetry.lock') as file: + lock_data = toml.load(file) + + simulators = [] + + # Iterate through the packages in the poetry.lock file + for package in lock_data.get('package', []): + if package['name'] == sim: + # Found the simulator, now get its dependencies + deps = parse_simulator_deps(package.get('dependencies', [])) + simulators.append({ + "name": package['name'], + "version": package['version'], + "deps": deps + }) + break + + return {"simulators": simulators} + +# Example usage +simulator_info = get_simulator("tellurium") +print(simulator_info) From 93299cfe74a7863d7b1ef21dcd32aa211a86353a Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Mon, 26 Feb 2024 11:21:55 -0500 Subject: [PATCH 32/56] updated library for exec and io files --- biosimulator_processes/container/exec.py | 30 ++++++++++ biosimulator_processes/container/io.py | 47 --------------- biosimulator_processes/simulators.json | 76 ------------------------ setup.py | 3 +- 4 files changed, 32 insertions(+), 124 deletions(-) delete mode 100644 biosimulator_processes/simulators.json diff --git a/biosimulator_processes/container/exec.py b/biosimulator_processes/container/exec.py index e69de29bb..7d0341e04 100644 --- a/biosimulator_processes/container/exec.py +++ b/biosimulator_processes/container/exec.py @@ -0,0 +1,30 @@ +import toml +from typing import * + + +def get_simulators(*sims: str): + """Get specified simulator installation information including required dependencies + and format as a dictionary. This dictionary is used as configuration for the dynamic + creation of containers. + + Args: + sims:`args, str`: names of the simulators to be included within the + container. + + """ + with open('biosimulator_processes/container-assets/poetry.lock') as file: + lock_data = toml.load(file) + + simulators = [] + for sim in sims: + for package in lock_data.get('package', []): + if package['name'] == sim: + simulators.append({ + "name": package['name'], + "version": package['version'], + "deps": package.get('dependencies', {}), + "extras": package.get('extras', {}) + }) + break + + return {"simulators": simulators} diff --git a/biosimulator_processes/container/io.py b/biosimulator_processes/container/io.py index 129cc6248..24cecffca 100644 --- a/biosimulator_processes/container/io.py +++ b/biosimulator_processes/container/io.py @@ -26,50 +26,3 @@ def write_dockerfile(dockerfile_contents: str, path: str = 'biosimulator_process with open(path, 'w') as file: file.write(dockerfile_contents) - -def parse_simulator_deps(deps): - """Parse dependencies, handling conditional dependencies.""" - parsed_deps = {} - for dep in deps: - if isinstance(dep, str): - # Simple dependency - if " " in dep: - name, version = dep.split(" ", 1) - else: - name, version = dep, "*" - parsed_deps[name] = version - elif isinstance(dep, dict): - # Conditional dependency - for name, info in dep.items(): - if "version" in info: - parsed_deps[name] = { - "version": info["version"], - "markers": info.get("markers", "") - } - return parsed_deps - - -def get_simulator(sim: str): - # Load the poetry.lock file - with open('poetry.lock') as file: - lock_data = toml.load(file) - - simulators = [] - - # Iterate through the packages in the poetry.lock file - for package in lock_data.get('package', []): - if package['name'] == sim: - # Found the simulator, now get its dependencies - deps = parse_simulator_deps(package.get('dependencies', [])) - simulators.append({ - "name": package['name'], - "version": package['version'], - "deps": deps - }) - break - - return {"simulators": simulators} - -# Example usage -simulator_info = get_simulator("tellurium") -print(simulator_info) diff --git a/biosimulator_processes/simulators.json b/biosimulator_processes/simulators.json deleted file mode 100644 index 13f2bbe20..000000000 --- a/biosimulator_processes/simulators.json +++ /dev/null @@ -1,76 +0,0 @@ -{ - "simulators": [ - { - "name": "tellurium", - "version": "2.2.10", - "description": "Tellurium: An biological modeling environment for Python", - "optional": false, - "python-versions": "*", - "files": [ - { - "file": "tellurium-2.2.10-py3-none-any.whl", - "hash": "sha256:078dbe5beeef49cc8caa9f626cb9c8e568752ecfaff3370acd32be123d6e24ae" - } - ], - "deps": { - "antimony": ">=2.12.0", - "appdirs": ">=1.4.3", - "ipykernel": ">=4.6.1", - "ipython": "*", - "jinja2": ">=3.0.0", - "jupyter-client": ">=5.1.0", - "jupyter-core": ">=4.3.0", - "libroadrunner": ">=2.1", - "matplotlib": ">=2.0.2", - "numpy": ">=1.23", - "pandas": ">=0.20.2", - "phrasedml": { - "version": ">=1.0.9", - "markers": "platform_machine != \"arm64\"" - }, - "plotly": ">=2.0.12", - "pytest": "*", - "python-libcombine": ">=0.2.2", - "python-libnuml": ">=1.0.0", - "python-libsbml": ">=5.18.0", - "python-libsedml": ">=2.0.17", - "requests": "*", - "rrplugins": { - "version": ">=2.1", - "markers": "platform_system == \"Windows\"" - }, - "scipy": ">=1.5.1" - } - }, - { - "name": "copasi-basico", - "version": "0.58", - "description": "Simplified COPASI interface for python", - "optional": false, - "python-versions": "*", - "files": [ - { - "file": "copasi_basico-0.58-py3-none-any.whl", - "hash": "sha256:d85f4ab39e9ba8dc2ff19e31466883a22ac32a6dbdec9ac595a793507897fa9e" - }, - { - "file": "copasi_basico-0.58.tar.gz", - "hash": "sha256:f8766aac7afde62cb75fb6701cb868fc0e341c43a0099408dbf073845a146c1c" - } - ], - "deps": { - "matplotlib": "*", - "numpy": "*", - "pandas": "*", - "python-copasi": "*", - "PyYAML": "*", - "scipy": "*" - }, - "extras": { - "docs": ["sphinx", "sphinx-rtd-theme", "sphinxcontrib", "sphinxcontrib-bibtex", "sphinxcontrib-mermaid", "sphinxcontrib-plantuml", "sphinxcontrib-programoutput"], - "petab": ["copasi-petab-importer", "petab", "petab-select"], - "tqdm": ["tqdm"] - } - } - ] -} diff --git a/setup.py b/setup.py index 04b85ccae..f67a7906d 100644 --- a/setup.py +++ b/setup.py @@ -48,7 +48,8 @@ "pytest>=6.2.5", "tellurium", "copasi-basico", - "cobra" + "cobra", + "docker" ], extras_require={ "smoldyn": ["smoldyn", "simulariumio"], From b7c2ffd446a2d6c5e49bdeb70a4c487bc2614ec3 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Mon, 26 Feb 2024 11:44:00 -0500 Subject: [PATCH 33/56] updated exec and container files chore --- .../container-assets/Dockerfile-base | 2 +- biosimulator_processes/container/container.py | 84 --------------- biosimulator_processes/container/exec.py | 100 +++++++++++++++++- biosimulator_processes/container/io.py | 26 ++--- 4 files changed, 109 insertions(+), 103 deletions(-) diff --git a/biosimulator_processes/container-assets/Dockerfile-base b/biosimulator_processes/container-assets/Dockerfile-base index 7545d05bb..8c0607cab 100644 --- a/biosimulator_processes/container-assets/Dockerfile-base +++ b/biosimulator_processes/container-assets/Dockerfile-base @@ -4,7 +4,7 @@ ENV DEBIAN_FRONTEND=noninteractive WORKDIR /app -# COPY . /app +COPY ./biosimulator_processes /app # COPY ./scripts /app diff --git a/biosimulator_processes/container/container.py b/biosimulator_processes/container/container.py index d1efe5d72..d304b327b 100644 --- a/biosimulator_processes/container/container.py +++ b/biosimulator_processes/container/container.py @@ -5,68 +5,10 @@ import docker -CLIENT = docker.DockerClient( - base_url='unix:///var/run/docker.sock' -) -def add_simulator_installations(config: dict): - """ - Args: - # base_path:`str`: path to the base dockerfile on which to append installations. - config:`dict`: a dictionary specifying simulator versions and their dependencies. The schema for - this dictionary should be (for example): - { - "simulators": [ - { - "name": "tellurium", - "version": "2.2.10", - "deps": { - "antimony": ">=2.12.0", - "appdirs": ">=1.4.3", - "ipykernel": ">=4.6.1", - "ipython": "*", - "jinja2": ">=3.0.0", - "jupyter-client": ">=5.1.0", - "jupyter-core": ">=4.3.0", - "libroadrunner": ">=2.1", - "matplotlib": ">=2.0.2", - "numpy": ">=1.23", - "pandas": ">=0.20.2", - "phrasedml": { - "version": ">=1.0.9", - "markers": "platform_machine != \"arm64\"" - }, - "plotly": ">=2.0.12", - "pytest": "*", - "python-libcombine": ">=0.2.2", - "python-libnuml": ">=1.0.0", - "python-libsbml": ">=5.18.0", - "python-libsedml": ">=2.0.17", - "requests": "*", - "rrplugins": { - "version": ">=2.1", - "markers": "platform_system == \"Windows\"" - }, - "scipy": ">=1.5.1" - } - }, - """ - - base_path = 'Dockerfile-base' - # TODO: automate mapping simulators to poetry.lock: ie: simulators arg that searches the lock file - with open(base_path, 'r') as fp: - dockerfile_contents = fp.read() - for simulator in config['simulators']: - deps = simulator.get('deps', {}) - for dep, version in deps.items(): - # dockerfile_contents += f"RUN pip install {dep}{version}\n" - dockerfile_contents += f"RUN poetry add {dep}{version}\n" - # common entrypoint used by all processes - dockerfile_contents += 'ENTRYPOINT ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"]' - return dockerfile_contents @@ -78,32 +20,6 @@ def exec_container(name: str): subprocess.run(run_command.split()) -def build_image(name: str, p: str = '.'): - return CLIENT.images.build( - path=p, - tag=name) - -def execute_container(img_name: str): - container_dir = tempfile.mkdtemp() - img = build_image(img_name) - CLIENT.containers.run(img.id) - - -def run(name: str): - config = load_config() - - dockerfile_contents = add_simulator_installations( - base_path='Dockerfile-base', - config=config - ) - - container_dir = tempfile.mkdtemp() - write_dockerfile(dockerfile_contents, path='Dockerfile') - execute_container(name) - - -if __name__ == '__main__': - run("composite") diff --git a/biosimulator_processes/container/exec.py b/biosimulator_processes/container/exec.py index 7d0341e04..aa68dea9a 100644 --- a/biosimulator_processes/container/exec.py +++ b/biosimulator_processes/container/exec.py @@ -1,14 +1,19 @@ import toml +import os from typing import * +from docker import DockerClient -def get_simulators(*sims: str): +CLIENT = DockerClient(base_url='unix:///var/run/docker.sock') + + +def get_simulators(simulators: List[str]): """Get specified simulator installation information including required dependencies and format as a dictionary. This dictionary is used as configuration for the dynamic creation of containers. Args: - sims:`args, str`: names of the simulators to be included within the + simulators:`List[str]`: names of the simulators to be included within the container. """ @@ -16,7 +21,7 @@ def get_simulators(*sims: str): lock_data = toml.load(file) simulators = [] - for sim in sims: + for sim in simulators: for package in lock_data.get('package', []): if package['name'] == sim: simulators.append({ @@ -28,3 +33,92 @@ def get_simulators(*sims: str): break return {"simulators": simulators} + + +def generate_dockerfile_contents(config: dict) -> str: + """Generate contents to be written out to a Dockerfile derived from the base Dockerfile. + + Args: + config:`dict`: a dictionary specifying simulator versions and their dependencies. The schema for + this dictionary should be (for example): + + { + "simulators": [ + { + "name": "tellurium", + "version": "2.2.10", + "deps": { + "antimony": ">=2.12.0", + "appdirs": ">=1.4.3", + "ipykernel": ">=4.6.1", + "ipython": "*", + "jinja2": ">=3.0.0", + "jupyter-client": ">=5.1.0", + "jupyter-core": ">=4.3.0", + "libroadrunner": ">=2.1", + "matplotlib": ">=2.0.2", + "numpy": ">=1.23", + "pandas": ">=0.20.2", + "phrasedml": { + "version": ">=1.0.9", + "markers": "platform_machine != \"arm64\"" + }, + "plotly": ">=2.0.12", + "pytest": "*", + "python-libcombine": ">=0.2.2", + "python-libnuml": ">=1.0.0", + "python-libsbml": ">=5.18.0", + "python-libsedml": ">=2.0.17", + "requests": "*", + "rrplugins": { + "version": ">=2.1", + "markers": "platform_system == \"Windows\"" + }, + "scipy": ">=1.5.1" + } + }, + """ + + base_path = 'biosimulator_processes/container-assets/Dockerfile-base' + # TODO: automate mapping simulators to poetry.lock: ie: simulators arg that searches the lock file + with open(base_path, 'r') as fp: + dockerfile_contents = fp.read() + for simulator in config['simulators']: + # copy the appropriate process files + name = simulator['name'] + if name == 'copasi-basico': + name = 'copasi' + dockerfile_contents += f"COPY ./biosimulator_processes/{simulator['name']}_process.py" + + deps = simulator.get('deps', {}) + for dep, version in deps.items(): + # dockerfile_contents += f"RUN pip install {dep}{version}\n" + dockerfile_contents += f"RUN poetry add {dep}{version}\n" + + # common entrypoint used by all processes + dockerfile_contents += 'ENTRYPOINT ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"]' + return dockerfile_contents + + +def build_image(name: str, p: str = '.'): + return CLIENT.images.build( + path=p, + tag=name) + + +def execute_container(img_name: str): + img = build_image(img_name) + CLIENT.containers.run(img.id) + + +def run(simulators: List[str]): + config = get_simulators(simulators) + dockerfile_contents = generate_dockerfile_contents(config) + write_dockerfile(dockerfile_contents, path='Dockerfile') + execute_container(name) + + +if __name__ == '__main__': + run("composite") + + diff --git a/biosimulator_processes/container/io.py b/biosimulator_processes/container/io.py index 24cecffca..aa2f50d45 100644 --- a/biosimulator_processes/container/io.py +++ b/biosimulator_processes/container/io.py @@ -1,5 +1,15 @@ import json -import toml + + +def write_dockerfile(dockerfile_contents: str, out_path: str): + """ + Args: + dockerfile_contents:`str`: content to write to Dockerfile + out_path:`str`: path to save the Dockerfile + + """ + with open(out_path, 'w') as file: + file.write(dockerfile_contents) def write_config(): @@ -12,17 +22,3 @@ def load_config(): # Load simulator configuration with open('biosimulator_processes/simulators.json', 'r') as file: return json.load(file) - - -def find_package_info(package: str): - # TODO: Finish this - package = {} - with open('poetry.lock', 'r') as f: - pass - - -def write_dockerfile(dockerfile_contents: str, path: str = 'biosimulator_processes/Dockerfile'): - # Save the Dockerfile - with open(path, 'w') as file: - file.write(dockerfile_contents) - From ce3491a686710365124ddfde0cd7921be074422f Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Mon, 26 Feb 2024 11:49:49 -0500 Subject: [PATCH 34/56] feat: implemented run container pipeline for dynamic container --- biosimulator_processes/container/container.py | 25 ------------------- biosimulator_processes/container/exec.py | 20 ++++++++++++--- 2 files changed, 16 insertions(+), 29 deletions(-) delete mode 100644 biosimulator_processes/container/container.py diff --git a/biosimulator_processes/container/container.py b/biosimulator_processes/container/container.py deleted file mode 100644 index d304b327b..000000000 --- a/biosimulator_processes/container/container.py +++ /dev/null @@ -1,25 +0,0 @@ -import json -import os -import subprocess -import tempfile -import docker - - - - - - - - - - -def exec_container(name: str): - build_command = f"docker buildx build --platform linux/amd64 {name}_env ." - subprocess.run(build_command.split()) - run_command = f"docker run --platform linux/amd64 -it -p 8888:8888 {name}_env" - subprocess.run(run_command.split()) - - - - - diff --git a/biosimulator_processes/container/exec.py b/biosimulator_processes/container/exec.py index aa68dea9a..afa0c1b9c 100644 --- a/biosimulator_processes/container/exec.py +++ b/biosimulator_processes/container/exec.py @@ -1,7 +1,10 @@ import toml import os +import subprocess +from tempfile import mkdtemp from typing import * from docker import DockerClient +from biosimulator_processes.container.io import write_dockerfile CLIENT = DockerClient(base_url='unix:///var/run/docker.sock') @@ -106,7 +109,7 @@ def build_image(name: str, p: str = '.'): tag=name) -def execute_container(img_name: str): +def execute_container(img_name: str = 'composition'): img = build_image(img_name) CLIENT.containers.run(img.id) @@ -114,11 +117,20 @@ def execute_container(img_name: str): def run(simulators: List[str]): config = get_simulators(simulators) dockerfile_contents = generate_dockerfile_contents(config) - write_dockerfile(dockerfile_contents, path='Dockerfile') - execute_container(name) + dockerfile_dir = mkdtemp() + write_dockerfile(dockerfile_contents, out_path=os.path.join(dockerfile_dir, 'Dockerfile')) + return execute_container() + + +def exec_container(name: str): + build_command = f"docker buildx build --platform linux/amd64 {name}_env ." + subprocess.run(build_command.split()) + run_command = f"docker run --platform linux/amd64 -it -p 8888:8888 {name}_env" + subprocess.run(run_command.split()) if __name__ == '__main__': - run("composite") + simulators = ["tellurium", "copasi-basico"] + run(simulators) From c49b73cb558691e6c8207ca884d354bc21c77542 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Mon, 26 Feb 2024 12:59:50 -0500 Subject: [PATCH 35/56] updated exec container script for feature --- .../{container-assets => }/Dockerfile-base | 2 +- biosimulator_processes/container/__init__.py | 0 biosimulator_processes/copasi_process.py | 2 + .../{container => }/exec.py | 41 ++++++++----------- biosimulator_processes/{container => }/io.py | 0 .../{container-assets => }/poetry.lock | 0 .../{container-assets => }/pyproject.toml | 0 7 files changed, 19 insertions(+), 26 deletions(-) rename biosimulator_processes/{container-assets => }/Dockerfile-base (96%) delete mode 100644 biosimulator_processes/container/__init__.py rename biosimulator_processes/{container => }/exec.py (82%) rename biosimulator_processes/{container => }/io.py (100%) rename biosimulator_processes/{container-assets => }/poetry.lock (100%) rename biosimulator_processes/{container-assets => }/pyproject.toml (100%) diff --git a/biosimulator_processes/container-assets/Dockerfile-base b/biosimulator_processes/Dockerfile-base similarity index 96% rename from biosimulator_processes/container-assets/Dockerfile-base rename to biosimulator_processes/Dockerfile-base index 8c0607cab..98ccca3ac 100644 --- a/biosimulator_processes/container-assets/Dockerfile-base +++ b/biosimulator_processes/Dockerfile-base @@ -39,7 +39,7 @@ RUN apt-get -y update \ && chmod 1777 /tmp/.X11-unix \ && rm -rf /var/lib/apt/lists/* -COPY ../../scripts/xvfb-startup.sh /xvfb-startup.sh +COPY ../scripts/xvfb-startup.sh /xvfb-startup.sh # RUN rm -r ./scripts diff --git a/biosimulator_processes/container/__init__.py b/biosimulator_processes/container/__init__.py deleted file mode 100644 index e69de29bb..000000000 diff --git a/biosimulator_processes/copasi_process.py b/biosimulator_processes/copasi_process.py index 67c79f48e..1c931a8ce 100644 --- a/biosimulator_processes/copasi_process.py +++ b/biosimulator_processes/copasi_process.py @@ -60,6 +60,8 @@ class CopasiProcess(Process): 'name': 'string', 'initial_concentration': 'int' } + # model_changes: dict paramName: new value + # solver } def __init__(self, config=None, core=None): diff --git a/biosimulator_processes/container/exec.py b/biosimulator_processes/exec.py similarity index 82% rename from biosimulator_processes/container/exec.py rename to biosimulator_processes/exec.py index afa0c1b9c..320f2db28 100644 --- a/biosimulator_processes/container/exec.py +++ b/biosimulator_processes/exec.py @@ -1,30 +1,23 @@ import toml -import os import subprocess -from tempfile import mkdtemp from typing import * from docker import DockerClient -from biosimulator_processes.container.io import write_dockerfile +from biosimulator_processes.io import write_dockerfile CLIENT = DockerClient(base_url='unix:///var/run/docker.sock') -def get_simulators(simulators: List[str]): +def get_simulators(sims: List[str]): """Get specified simulator installation information including required dependencies and format as a dictionary. This dictionary is used as configuration for the dynamic creation of containers. - - Args: - simulators:`List[str]`: names of the simulators to be included within the - container. - """ - with open('biosimulator_processes/container-assets/poetry.lock') as file: + with open('biosimulator_processes/poetry.lock') as file: lock_data = toml.load(file) simulators = [] - for sim in simulators: + for sim in sims: for package in lock_data.get('package', []): if package['name'] == sim: simulators.append({ @@ -82,22 +75,23 @@ def generate_dockerfile_contents(config: dict) -> str: }, """ - base_path = 'biosimulator_processes/container-assets/Dockerfile-base' + base_path = 'biosimulator_processes/Dockerfile-base' # TODO: automate mapping simulators to poetry.lock: ie: simulators arg that searches the lock file with open(base_path, 'r') as fp: dockerfile_contents = fp.read() for simulator in config['simulators']: # copy the appropriate process files name = simulator['name'] - if name == 'copasi-basico': - name = 'copasi' - dockerfile_contents += f"COPY ./biosimulator_processes/{simulator['name']}_process.py" - deps = simulator.get('deps', {}) for dep, version in deps.items(): - # dockerfile_contents += f"RUN pip install {dep}{version}\n" - dockerfile_contents += f"RUN poetry add {dep}{version}\n" - + if not version == "*": + complete_version = f'{dep}{version}' + else: + complete_version = f'{dep}' + dockerfile_contents += f"RUN poetry add {complete_version}\n" + if name == 'copasi-basico': + name = 'copasi' + dockerfile_contents += f"COPY ./biosimulator_processes/{simulator['name']}_process.py /app/{simulator['name']}_process.py\n" # common entrypoint used by all processes dockerfile_contents += 'ENTRYPOINT ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"]' return dockerfile_contents @@ -117,8 +111,8 @@ def execute_container(img_name: str = 'composition'): def run(simulators: List[str]): config = get_simulators(simulators) dockerfile_contents = generate_dockerfile_contents(config) - dockerfile_dir = mkdtemp() - write_dockerfile(dockerfile_contents, out_path=os.path.join(dockerfile_dir, 'Dockerfile')) + dockerfile_path = 'Dockerfile' + write_dockerfile(dockerfile_contents, out_path=dockerfile_path) return execute_container() @@ -129,8 +123,5 @@ def exec_container(name: str): subprocess.run(run_command.split()) -if __name__ == '__main__': - simulators = ["tellurium", "copasi-basico"] - run(simulators) - +run(['tellurium', 'copasi-basico']) diff --git a/biosimulator_processes/container/io.py b/biosimulator_processes/io.py similarity index 100% rename from biosimulator_processes/container/io.py rename to biosimulator_processes/io.py diff --git a/biosimulator_processes/container-assets/poetry.lock b/biosimulator_processes/poetry.lock similarity index 100% rename from biosimulator_processes/container-assets/poetry.lock rename to biosimulator_processes/poetry.lock diff --git a/biosimulator_processes/container-assets/pyproject.toml b/biosimulator_processes/pyproject.toml similarity index 100% rename from biosimulator_processes/container-assets/pyproject.toml rename to biosimulator_processes/pyproject.toml From 584b369f07b0c21c3082abfd870b8b6a1f98715e Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Mon, 26 Feb 2024 13:21:25 -0500 Subject: [PATCH 36/56] refactored libs and files --- .../Dockerfile-base => Dockerfile | 10 +- .../container-assets/Dockerfile-base | 72 + .../{ => container-assets}/poetry.lock | 0 .../{ => container-assets}/pyproject.toml | 0 biosimulator_processes/containers/__init__.py | 0 .../{ => containers}/exec.py | 11 +- biosimulator_processes/{ => containers}/io.py | 0 poetry.lock | 4541 +++++++++++++++++ pyproject.toml | 33 + 9 files changed, 4656 insertions(+), 11 deletions(-) rename biosimulator_processes/Dockerfile-base => Dockerfile (83%) create mode 100644 biosimulator_processes/container-assets/Dockerfile-base rename biosimulator_processes/{ => container-assets}/poetry.lock (100%) rename biosimulator_processes/{ => container-assets}/pyproject.toml (100%) create mode 100644 biosimulator_processes/containers/__init__.py rename biosimulator_processes/{ => containers}/exec.py (91%) rename biosimulator_processes/{ => containers}/io.py (100%) create mode 100644 poetry.lock create mode 100644 pyproject.toml diff --git a/biosimulator_processes/Dockerfile-base b/Dockerfile similarity index 83% rename from biosimulator_processes/Dockerfile-base rename to Dockerfile index 98ccca3ac..98f93b5a2 100644 --- a/biosimulator_processes/Dockerfile-base +++ b/Dockerfile @@ -39,9 +39,7 @@ RUN apt-get -y update \ && chmod 1777 /tmp/.X11-unix \ && rm -rf /var/lib/apt/lists/* -COPY ../scripts/xvfb-startup.sh /xvfb-startup.sh - -# RUN rm -r ./scripts +COPY ./scripts/xvfb-startup.sh /xvfb-startup.sh ENV XVFB_RES="1920x1080x24" \ XVFB_ARGS="" @@ -55,8 +53,8 @@ RUN poetry config virtualenvs.in-project true ENV PATH="/root/.local/bin:${PATH}" RUN poetry run pip install --upgrade pip \ - && poetry run pip install python-libnuml --use-pep517 \ - && poetry install + && poetry run pip install python-libnuml --use-pep517 \ + && poetry install # activate poetry virtualenv ENV PATH="/app/.venv/bin:$PATH" @@ -68,4 +66,4 @@ ENV STORAGE_LOCAL_CACHE_DIR="/app/scratch" # activate the poetry virtualenv each new non-interative shell RUN echo "source /app/.venv/bin/activate" >> /etc/bash.bashrc -# ENTRYPOINT ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"] +ENTRYPOINT ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"] diff --git a/biosimulator_processes/container-assets/Dockerfile-base b/biosimulator_processes/container-assets/Dockerfile-base new file mode 100644 index 000000000..ace3074a6 --- /dev/null +++ b/biosimulator_processes/container-assets/Dockerfile-base @@ -0,0 +1,72 @@ +FROM ubuntu:latest + +ENV DEBIAN_FRONTEND=noninteractive + +WORKDIR /app + +COPY ./biosimulator_processes /app + +# COPY ./scripts /app + +# RUN rm -r /app/composer-api + +RUN apt-get update && apt-get install -y --no-install-recommends \ + python3 \ + python3-pip \ + build-essential \ + libncurses5 \ + cmake \ + make \ + libx11-dev \ + libc6-dev \ + libx11-6 \ + libc6 \ + gcc \ + swig \ + pkg-config \ + curl \ + tar \ + libgl1-mesa-glx \ + libice6 \ + libpython3.10 \ + wget \ + && rm -rf /var/lib/apt/lists/* + +RUN apt-get -y update \ + && apt-get install --no-install-recommends -y \ + xvfb \ + && mkdir /tmp/.X11-unix \ + && chmod 1777 /tmp/.X11-unix \ + && rm -rf /var/lib/apt/lists/* + +COPY ./scripts/xvfb-startup.sh /xvfb-startup.sh + +# RUN rm -r ./scripts + +ENV XVFB_RES="1920x1080x24" \ + XVFB_ARGS="" + +# RUN pip install --upgrade pip \ +# && pip install poetry + +# RUN poetry config virtualenvs.in-project true + +# Add Poetry to PATH +# ENV PATH="/root/.local/bin:${PATH}" + +# RUN poetry run pip install --upgrade pip \ +# && poetry run pip install python-libnuml --use-pep517 \ +# && poetry install + +# activate poetry virtualenv +# ENV PATH="/app/.venv/bin:$PATH" +# ENV CONFIG_ENV_FILE="/app/config/config.env" +# ENV SECRET_ENV_FILE="/app/secret/secret.env" +# ENV STORAGE_GCS_CREDENTIALS_FILE="/app/secret/gcs_credentials.json" +# ENV STORAGE_LOCAL_CACHE_DIR="/app/scratch" +# +# # activate the poetry virtualenv each new non-interative shell +# RUN echo "source /app/.venv/bin/activate" >> /etc/bash.bashrc + +RUN pip install --upgrade pip && pip install jupyterlab +# ENTRYPOINT ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"] diff --git a/biosimulator_processes/poetry.lock b/biosimulator_processes/container-assets/poetry.lock similarity index 100% rename from biosimulator_processes/poetry.lock rename to biosimulator_processes/container-assets/poetry.lock diff --git a/biosimulator_processes/pyproject.toml b/biosimulator_processes/container-assets/pyproject.toml similarity index 100% rename from biosimulator_processes/pyproject.toml rename to biosimulator_processes/container-assets/pyproject.toml diff --git a/biosimulator_processes/containers/__init__.py b/biosimulator_processes/containers/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/biosimulator_processes/exec.py b/biosimulator_processes/containers/exec.py similarity index 91% rename from biosimulator_processes/exec.py rename to biosimulator_processes/containers/exec.py index 320f2db28..eb5fb951b 100644 --- a/biosimulator_processes/exec.py +++ b/biosimulator_processes/containers/exec.py @@ -2,7 +2,7 @@ import subprocess from typing import * from docker import DockerClient -from biosimulator_processes.io import write_dockerfile +from biosimulator_processes.containers.io import write_dockerfile CLIENT = DockerClient(base_url='unix:///var/run/docker.sock') @@ -88,12 +88,13 @@ def generate_dockerfile_contents(config: dict) -> str: complete_version = f'{dep}{version}' else: complete_version = f'{dep}' - dockerfile_contents += f"RUN poetry add {complete_version}\n" + # dockerfile_contents += f"RUN poetry add {complete_version}\n" + dockerfile_contents += f"RUN pip install {complete_version}\n" if name == 'copasi-basico': name = 'copasi' dockerfile_contents += f"COPY ./biosimulator_processes/{simulator['name']}_process.py /app/{simulator['name']}_process.py\n" # common entrypoint used by all processes - dockerfile_contents += 'ENTRYPOINT ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"]' + dockerfile_contents += 'ENTRYPOINT ["jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"]' return dockerfile_contents @@ -113,7 +114,7 @@ def run(simulators: List[str]): dockerfile_contents = generate_dockerfile_contents(config) dockerfile_path = 'Dockerfile' write_dockerfile(dockerfile_contents, out_path=dockerfile_path) - return execute_container() + # return execute_container() def exec_container(name: str): @@ -124,4 +125,4 @@ def exec_container(name: str): -run(['tellurium', 'copasi-basico']) +# run(['tellurium', 'copasi-basico']) diff --git a/biosimulator_processes/io.py b/biosimulator_processes/containers/io.py similarity index 100% rename from biosimulator_processes/io.py rename to biosimulator_processes/containers/io.py diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 000000000..3c070c62a --- /dev/null +++ b/poetry.lock @@ -0,0 +1,4541 @@ +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. + +[[package]] +name = "annotated-types" +version = "0.6.0" +description = "Reusable constraint types to use with typing.Annotated" +optional = false +python-versions = ">=3.8" +files = [ + {file = "annotated_types-0.6.0-py3-none-any.whl", hash = "sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43"}, + 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@@ -0,0 +1,33 @@ +[tool.poetry] +name = "biosimulator-processes" +version = "0.0.16" +description = "Core implementations of process-bigraph.composite.Process aligning with BioSimulators simulator tools." +authors = ["Alex Patrie "] +readme = "README.md" +packages = [{include = "biosimulator_processes"}] + +[tool.poetry.dependencies] +python = ">=3.10" +zarr = "*" +termcolor = "*" +jupyterlab = "*" +bigraph-schema = "*" +process-bigraph = "*" +numpy = "*" # "^1.26.4" +copasi-basico = "*" +cobra = "*" +tellurium = "*" +smoldyn = "*" +bigraph-viz = "^0.0.31" +python-libsbml = "^5.20.2" +docker = ">=7.0" + +[tool.poetry.group.dev.dependencies] +pytest = "*" +mypy = ">=1.8.0" +flake8 = "*" +twine = "*" + +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" From 3c2e0accf031ce442144c4268cb7a54ff17f5866 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Mon, 26 Feb 2024 13:26:59 -0500 Subject: [PATCH 37/56] updated dockerfile to include pyproject and lock --- Dockerfile | 4 ++++ scripts/build-container.sh | 2 +- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 98f93b5a2..57eaa8b63 100644 --- a/Dockerfile +++ b/Dockerfile @@ -6,6 +6,10 @@ WORKDIR /app COPY ./biosimulator_processes /app +COPY ./pyproject.toml /app + +COPY ./poetry.lock /app + # COPY ./scripts /app # RUN rm -r /app/composer-api diff --git a/scripts/build-container.sh b/scripts/build-container.sh index f904475a2..68ef3a0d4 100755 --- a/scripts/build-container.sh +++ b/scripts/build-container.sh @@ -16,5 +16,5 @@ docker buildx build --platform linux/amd64 \ -t ghcr.io/biosimulators/biosimulator-processes:"${version}" . if [ "${run}" == "-r" ]; then - ./run-container.sh "${version}" + ./scripts/run-container.sh "${version}" fi From 9cf767c673b026f16b5912128fd862600e3d57ca Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Mon, 26 Feb 2024 14:21:21 -0500 Subject: [PATCH 38/56] added notebooks library and adjusted dockerfile for specific copy --- Dockerfile | 24 ++++++++++----------- notebooks/cobra_process.ipynb | 35 +++++++++++++++++++++++++++++++ notebooks/copasi_process.ipynb | 35 +++++++++++++++++++++++++++++++ notebooks/smoldyn_process.ipynb | 35 +++++++++++++++++++++++++++++++ notebooks/tellurium_process.ipynb | 35 +++++++++++++++++++++++++++++++ 5 files changed, 151 insertions(+), 13 deletions(-) create mode 100644 notebooks/cobra_process.ipynb create mode 100644 notebooks/copasi_process.ipynb create mode 100644 notebooks/smoldyn_process.ipynb create mode 100644 notebooks/tellurium_process.ipynb diff --git a/Dockerfile b/Dockerfile index 57eaa8b63..a0c0ea634 100644 --- a/Dockerfile +++ b/Dockerfile @@ -4,15 +4,13 @@ ENV DEBIAN_FRONTEND=noninteractive WORKDIR /app -COPY ./biosimulator_processes /app +COPY ./biosimulator_processes /app/biosimulator_processes COPY ./pyproject.toml /app COPY ./poetry.lock /app -# COPY ./scripts /app - -# RUN rm -r /app/composer-api +COPY ./notebooks /app/notebooks RUN apt-get update && apt-get install -y --no-install-recommends \ python3 \ @@ -34,11 +32,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \ libice6 \ libpython3.10 \ wget \ - && rm -rf /var/lib/apt/lists/* - -RUN apt-get -y update \ - && apt-get install --no-install-recommends -y \ - xvfb \ + xvfb \ && mkdir /tmp/.X11-unix \ && chmod 1777 /tmp/.X11-unix \ && rm -rf /var/lib/apt/lists/* @@ -53,11 +47,8 @@ RUN pip install --upgrade pip \ RUN poetry config virtualenvs.in-project true -# Add Poetry to PATH -ENV PATH="/root/.local/bin:${PATH}" - RUN poetry run pip install --upgrade pip \ - && poetry run pip install python-libnuml --use-pep517 \ + && poetry add python-libnuml --use-pep517 \ && poetry install # activate poetry virtualenv @@ -70,4 +61,11 @@ ENV STORAGE_LOCAL_CACHE_DIR="/app/scratch" # activate the poetry virtualenv each new non-interative shell RUN echo "source /app/.venv/bin/activate" >> /etc/bash.bashrc +# RUN rm /app/poetry.lock + +# RUN rm /app/pyproject.toml + +# TODO: ADD VOLUME MOUNT +# VOLUME + ENTRYPOINT ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"] diff --git a/notebooks/cobra_process.ipynb b/notebooks/cobra_process.ipynb new file mode 100644 index 000000000..29cd7437e --- /dev/null +++ b/notebooks/cobra_process.ipynb @@ -0,0 +1,35 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "id": "initial_id", + "metadata": { + "collapsed": true + }, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 2 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython2", + "version": "2.7.6" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/notebooks/copasi_process.ipynb b/notebooks/copasi_process.ipynb new file mode 100644 index 000000000..29cd7437e --- /dev/null +++ b/notebooks/copasi_process.ipynb @@ -0,0 +1,35 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "id": "initial_id", + "metadata": { + "collapsed": true + }, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 2 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython2", + "version": "2.7.6" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/notebooks/smoldyn_process.ipynb b/notebooks/smoldyn_process.ipynb new file mode 100644 index 000000000..29cd7437e --- /dev/null +++ b/notebooks/smoldyn_process.ipynb @@ -0,0 +1,35 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "id": "initial_id", + "metadata": { + "collapsed": true + }, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 2 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython2", + "version": "2.7.6" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/notebooks/tellurium_process.ipynb b/notebooks/tellurium_process.ipynb new file mode 100644 index 000000000..29cd7437e --- /dev/null +++ b/notebooks/tellurium_process.ipynb @@ -0,0 +1,35 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "id": "initial_id", + "metadata": { + "collapsed": true + }, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 2 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython2", + "version": "2.7.6" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} From 0fe130085a2b1b321a9bba9ecce4aa73b7c9363f Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Mon, 26 Feb 2024 14:27:35 -0500 Subject: [PATCH 39/56] updated dockerfile to remove manual libnuml and added to lock file --- Dockerfile | 4 ---- poetry.lock | 2 +- pyproject.toml | 1 + 3 files changed, 2 insertions(+), 5 deletions(-) diff --git a/Dockerfile b/Dockerfile index a0c0ea634..bfde8ca34 100644 --- a/Dockerfile +++ b/Dockerfile @@ -61,10 +61,6 @@ ENV STORAGE_LOCAL_CACHE_DIR="/app/scratch" # activate the poetry virtualenv each new non-interative shell RUN echo "source /app/.venv/bin/activate" >> /etc/bash.bashrc -# RUN rm /app/poetry.lock - -# RUN rm /app/pyproject.toml - # TODO: ADD VOLUME MOUNT # VOLUME diff --git a/poetry.lock b/poetry.lock index 3c070c62a..b4ac102cd 100644 --- a/poetry.lock +++ b/poetry.lock @@ -4538,4 +4538,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = ">=3.10" -content-hash = "1a85b23e06cff73e3302a865efd11a5a13905e02917f8744124891040a06baef" +content-hash = "cd6d7425448035b909d563817fc0ff783d815426d50be25d0fb0efc100433b1a" diff --git a/pyproject.toml b/pyproject.toml index e65287531..40a7ba09a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,6 +21,7 @@ smoldyn = "*" bigraph-viz = "^0.0.31" python-libsbml = "^5.20.2" docker = ">=7.0" +python-libnuml = "^1.1.6" [tool.poetry.group.dev.dependencies] pytest = "*" From b719f78e94008addf487a3f2f082935af314c906 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Mon, 26 Feb 2024 14:28:35 -0500 Subject: [PATCH 40/56] chore: added comment option for numl --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 40a7ba09a..9defe90ed 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,7 +21,7 @@ smoldyn = "*" bigraph-viz = "^0.0.31" python-libsbml = "^5.20.2" docker = ">=7.0" -python-libnuml = "^1.1.6" +python-libnuml = "^1.1.6" # ">=1.0.0" [tool.poetry.group.dev.dependencies] pytest = "*" From 5f55d5c830ea5f71186759966476a35c13db336f Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Mon, 26 Feb 2024 14:34:05 -0500 Subject: [PATCH 41/56] added path insert for notebook repo access and added basic copasi use in notebook --- notebooks/cobra_process.ipynb | 6 +- notebooks/copasi_process.ipynb | 118 +++++++++++++++++++++++++++++- notebooks/smoldyn_process.ipynb | 6 +- notebooks/tellurium_process.ipynb | 6 +- 4 files changed, 132 insertions(+), 4 deletions(-) diff --git a/notebooks/cobra_process.ipynb b/notebooks/cobra_process.ipynb index 29cd7437e..22f085322 100644 --- a/notebooks/cobra_process.ipynb +++ b/notebooks/cobra_process.ipynb @@ -8,7 +8,11 @@ "collapsed": true }, "outputs": [], - "source": [] + "source": [ + "import sys \n", + "\n", + "sys.path.insert(0, '..')" + ] } ], "metadata": { diff --git a/notebooks/copasi_process.ipynb b/notebooks/copasi_process.ipynb index 29cd7437e..9c5a5e741 100644 --- a/notebooks/copasi_process.ipynb +++ b/notebooks/copasi_process.ipynb @@ -8,7 +8,123 @@ "collapsed": true }, "outputs": [], - "source": [] + "source": [ + "import sys \n", + "\n", + "sys.path.insert(0, '..')" + ] + }, + { + "cell_type": "code", + "outputs": [], + "source": [ + "from process_bigraph import Composite, pf \n", + "from biosimulator_processes.copasi_process import CopasiProcess" + ], + "metadata": { + "collapsed": false + }, + "id": "c6c10dc5988e52d4" + }, + { + "cell_type": "code", + "outputs": [], + "source": [ + "# 1. Define the sim state schema:\n", + "initial_sim_state = {\n", + " 'copasi': {\n", + " '_type': 'process',\n", + " 'address': 'local:copasi',\n", + " 'config': {\n", + " 'model_file': 'biosimulator_processes/model_files/Caravagna2010.xml'\n", + " },\n", + " 'inputs': {\n", + " 'floating_species': ['floating_species_store'],\n", + " 'model_parameters': ['model_parameters_store'],\n", + " 'time': ['time_store'],\n", + " 'reactions': ['reactions_store']\n", + " },\n", + " 'outputs': {\n", + " 'floating_species': ['floating_species_store'],\n", + " 'time': ['time_store'],\n", + " }\n", + " },\n", + " # TODO: Add emitter schema\n", + " 'emitter': {\n", + " '_type': 'step',\n", + " 'address': 'local:ram-emitter',\n", + " 'config': {\n", + " 'emit': {\n", + " 'floating_species': 'tree[float]',\n", + " 'time': 'float',\n", + " },\n", + " },\n", + " 'inputs': {\n", + " 'floating_species': ['floating_species_store'],\n", + " 'time': ['time_store'],\n", + " }\n", + " }\n", + "}\n", + "\n", + "\n", + "\n", + "\n", + "\n" + ], + "metadata": { + "collapsed": false + }, + "id": "77636dbde3fa6b74" + }, + { + "cell_type": "code", + "outputs": [], + "source": [ + "# 2. Make the composite:\n", + "workflow = Composite({\n", + " 'state': initial_sim_state\n", + "})" + ], + "metadata": { + "collapsed": false + }, + "id": "4c2ef631b005be61" + }, + { + "cell_type": "code", + "outputs": [], + "source": [ + "# 3. Run the composite workflow:\n", + "workflow.run(10)" + ], + "metadata": { + "collapsed": false + }, + "id": "98676149a4ce822f" + }, + { + "cell_type": "code", + "outputs": [], + "source": [ + "# 4. Gather and pretty print results\n", + "results = workflow.gather_results()\n", + "print(f'RESULTS: {pf(results)}')" + ], + "metadata": { + "collapsed": false + }, + "id": "c15cee593ef000a7" + }, + { + "cell_type": "code", + "outputs": [], + "source": [ + "# 5. Plot/Analyze the results" + ], + "metadata": { + "collapsed": false + }, + "id": "297504800772775e" } ], "metadata": { diff --git a/notebooks/smoldyn_process.ipynb b/notebooks/smoldyn_process.ipynb index 29cd7437e..22f085322 100644 --- a/notebooks/smoldyn_process.ipynb +++ b/notebooks/smoldyn_process.ipynb @@ -8,7 +8,11 @@ "collapsed": true }, "outputs": [], - "source": [] + "source": [ + "import sys \n", + "\n", + "sys.path.insert(0, '..')" + ] } ], "metadata": { diff --git a/notebooks/tellurium_process.ipynb b/notebooks/tellurium_process.ipynb index 29cd7437e..22f085322 100644 --- a/notebooks/tellurium_process.ipynb +++ b/notebooks/tellurium_process.ipynb @@ -8,7 +8,11 @@ "collapsed": true }, "outputs": [], - "source": [] + "source": [ + "import sys \n", + "\n", + "sys.path.insert(0, '..')" + ] } ], "metadata": { From e82c8934d66e29fbe91914be398215f9150a2e84 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Mon, 26 Feb 2024 14:48:13 -0500 Subject: [PATCH 42/56] added jupyteruser and cmd in dockerfile with volume example --- Dockerfile | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/Dockerfile b/Dockerfile index bfde8ca34..548e8a5fe 100644 --- a/Dockerfile +++ b/Dockerfile @@ -12,6 +12,8 @@ COPY ./poetry.lock /app COPY ./notebooks /app/notebooks +COPY ./data /app/data + RUN apt-get update && apt-get install -y --no-install-recommends \ python3 \ python3-pip \ @@ -48,7 +50,6 @@ RUN pip install --upgrade pip \ RUN poetry config virtualenvs.in-project true RUN poetry run pip install --upgrade pip \ - && poetry add python-libnuml --use-pep517 \ && poetry install # activate poetry virtualenv @@ -61,7 +62,16 @@ ENV STORAGE_LOCAL_CACHE_DIR="/app/scratch" # activate the poetry virtualenv each new non-interative shell RUN echo "source /app/.venv/bin/activate" >> /etc/bash.bashrc -# TODO: ADD VOLUME MOUNT -# VOLUME +# add volume mount for co-simulation data +VOLUME /app/data + +# Using VOLUME allows different sim tools to share inputs and outputs +# For example: docker volume create sim-data +# docker run -v sim-data:/app/data --name simulator1 simulator1-image +# docker run -v sim-data:/app/data --name simulator2 simulator2-image + +RUN useradd -m -s /bin/bash jupyteruser +RUN chown -R jupyteruser:jupyteruser /app +USER jupyteruser -ENTRYPOINT ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"] +CMD ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"] From 27db13438cf1300de38d2866987f500b25604c51 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Mon, 26 Feb 2024 14:57:48 -0500 Subject: [PATCH 43/56] refactored dockerfile for optimizing build --- Dockerfile | 182 ++++++++++++++++++++++++++++++++++------------------- 1 file changed, 118 insertions(+), 64 deletions(-) diff --git a/Dockerfile b/Dockerfile index 548e8a5fe..223d6eb55 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,77 +1,131 @@ -FROM ubuntu:latest - -ENV DEBIAN_FRONTEND=noninteractive +# Use a more specific tag than latest for reproducibility +# FROM ubuntu:20.04 +# +# ENV DEBIAN_FRONTEND=noninteractive +# +# WORKDIR /app +# +# COPY ./biosimulator_processes /app/biosimulator_processes +# +# COPY ./pyproject.toml /app +# +# COPY ./poetry.lock /app +# +# COPY ./notebooks /app/notebooks +# +# COPY ./data /app/data +# +# RUN apt-get update && apt-get install -y --no-install-recommends \ +# python3 \ +# python3-pip \ +# build-essential \ +# libncurses5 \ +# cmake \ +# make \ +# libx11-dev \ +# libc6-dev \ +# libx11-6 \ +# libc6 \ +# gcc \ +# swig \ +# pkg-config \ +# curl \ +# tar \ +# libgl1-mesa-glx \ +# libice6 \ +# libpython3.10 \ +# wget \ +# xvfb \ +# && mkdir /tmp/.X11-unix \ +# && chmod 1777 /tmp/.X11-unix \ +# && rm -rf /var/lib/apt/lists/* +# +# COPY ./scripts/xvfb-startup.sh /xvfb-startup.sh +# +# ENV XVFB_RES="1920x1080x24" \ +# XVFB_ARGS="" +# +# RUN pip install --upgrade pip \ +# && pip install poetry +# +# RUN poetry config virtualenvs.in-project true +# +# RUN poetry run pip install --upgrade pip \ +# && poetry install +# +# # activate poetry virtualenv +# ENV PATH="/app/.venv/bin:$PATH" +# ENV CONFIG_ENV_FILE="/app/config/config.env" +# ENV SECRET_ENV_FILE="/app/secret/secret.env" +# ENV STORAGE_GCS_CREDENTIALS_FILE="/app/secret/gcs_credentials.json" +# ENV STORAGE_LOCAL_CACHE_DIR="/app/scratch" +# +# # activate the poetry virtualenv each new non-interative shell +# RUN echo "source /app/.venv/bin/activate" >> /etc/bash.bashrc +# +# # add volume mount for co-simulation data +# VOLUME /app/data +# +# # Using VOLUME allows different sim tools to share inputs and outputs +# # For example: docker volume create sim-data +# # docker run -v sim-data:/app/data --name simulator1 simulator1-image +# # docker run -v sim-data:/app/data --name simulator2 simulator2-image +# +# RUN useradd -m -s /bin/bash jupyteruser +# RUN chown -R jupyteruser:jupyteruser /app +# USER jupyteruser +# +# CMD ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"] + +# Use a more specific tag instead of latest for reproducibility +FROM ubuntu:20.04 + +ENV DEBIAN_FRONTEND=noninteractive \ + XVFB_RES="1920x1080x24" \ + XVFB_ARGS="" \ + PATH="/app/.venv/bin:$PATH" \ + CONFIG_ENV_FILE="/app/config/config.env" \ + SECRET_ENV_FILE="/app/secret/secret.env" \ + STORAGE_GCS_CREDENTIALS_FILE="/app/secret/gcs_credentials.json" \ + STORAGE_LOCAL_CACHE_DIR="/app/scratch" WORKDIR /app -COPY ./biosimulator_processes /app/biosimulator_processes - -COPY ./pyproject.toml /app - -COPY ./poetry.lock /app - -COPY ./notebooks /app/notebooks - -COPY ./data /app/data +COPY ./biosimulator_processes ./pyproject.toml ./poetry.lock ./notebooks ./data /app/ +COPY ./scripts/xvfb-startup.sh /xvfb-startup.sh RUN apt-get update && apt-get install -y --no-install-recommends \ - python3 \ - python3-pip \ - build-essential \ - libncurses5 \ - cmake \ - make \ - libx11-dev \ - libc6-dev \ - libx11-6 \ - libc6 \ - gcc \ + python3.10 \ + python3-pip \ + build-essential \ + libncurses5 \ + cmake \ + make \ + libx11-dev \ + libc6-dev \ + libx11-6 \ + libc6 \ + gcc \ swig \ - pkg-config \ - curl \ - tar \ - libgl1-mesa-glx \ - libice6 \ - libpython3.10 \ - wget \ + pkg-config \ + curl \ + tar \ + libgl1-mesa-glx \ + libice6 \ + libpython3.10 \ + wget \ xvfb \ - && mkdir /tmp/.X11-unix \ - && chmod 1777 /tmp/.X11-unix \ - && rm -rf /var/lib/apt/lists/* - -COPY ./scripts/xvfb-startup.sh /xvfb-startup.sh + && mkdir /tmp/.X11-unix \ + && chmod 1777 /tmp/.X11-unix \ + && rm -rf /var/lib/apt/lists/* \ + && pip install --upgrade pip && pip install poetry \ + && poetry config virtualenvs.in-project true \ + && poetry install -ENV XVFB_RES="1920x1080x24" \ - XVFB_ARGS="" +RUN useradd -m -s /bin/bash jupyteruser && chown -R jupyteruser:jupyteruser /app -RUN pip install --upgrade pip \ - && pip install poetry - -RUN poetry config virtualenvs.in-project true - -RUN poetry run pip install --upgrade pip \ - && poetry install - -# activate poetry virtualenv -ENV PATH="/app/.venv/bin:$PATH" -ENV CONFIG_ENV_FILE="/app/config/config.env" -ENV SECRET_ENV_FILE="/app/secret/secret.env" -ENV STORAGE_GCS_CREDENTIALS_FILE="/app/secret/gcs_credentials.json" -ENV STORAGE_LOCAL_CACHE_DIR="/app/scratch" - -# activate the poetry virtualenv each new non-interative shell -RUN echo "source /app/.venv/bin/activate" >> /etc/bash.bashrc +USER jupyteruser -# add volume mount for co-simulation data VOLUME /app/data -# Using VOLUME allows different sim tools to share inputs and outputs -# For example: docker volume create sim-data -# docker run -v sim-data:/app/data --name simulator1 simulator1-image -# docker run -v sim-data:/app/data --name simulator2 simulator2-image - -RUN useradd -m -s /bin/bash jupyteruser -RUN chown -R jupyteruser:jupyteruser /app -USER jupyteruser - CMD ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"] From f8fe25134444131f3e0b8b4a0e1d914423506737 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Mon, 26 Feb 2024 15:18:07 -0500 Subject: [PATCH 44/56] updated dockerfile for chmod and copasi process --- Dockerfile | 6 ++++-- biosimulator_processes/copasi_process.py | 16 +++++++++++++++- 2 files changed, 19 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index 223d6eb55..652a5ebe4 100644 --- a/Dockerfile +++ b/Dockerfile @@ -77,8 +77,8 @@ # # CMD ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"] -# Use a more specific tag instead of latest for reproducibility -FROM ubuntu:20.04 +# TODO: Use a more specific tag instead of latest for reproducibility +FROM ubuntu:latest ENV DEBIAN_FRONTEND=noninteractive \ XVFB_RES="1920x1080x24" \ @@ -126,6 +126,8 @@ RUN useradd -m -s /bin/bash jupyteruser && chown -R jupyteruser:jupyteruser /app USER jupyteruser +RUN chmod +x /app/notebooks + VOLUME /app/data CMD ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"] diff --git a/biosimulator_processes/copasi_process.py b/biosimulator_processes/copasi_process.py index 1c931a8ce..cb00b6bb5 100644 --- a/biosimulator_processes/copasi_process.py +++ b/biosimulator_processes/copasi_process.py @@ -46,11 +46,25 @@ set_species, run_time_course, get_compartments, - model_info + model_info, + biomodels ) from process_bigraph import Process, Composite, pf +def find_models(term: str): + return biomodels.search_for_model(term) + + +def fetch_model(term: str, index: int = 0): + """Searrch for models matching the term and return an instantiated model from BioModels. + + TODO: Implement a dynamic search of this + """ + + + + class CopasiProcess(Process): config_schema = { 'model_file': 'string', From a3b0797617ccb245b81029549ccec73ff8e55ce4 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Mon, 26 Feb 2024 15:27:44 -0500 Subject: [PATCH 45/56] fix: removed chmod notebooks temporarily --- Dockerfile | 2 +- biosimulator_processes/copasi_process.py | 7 +++++-- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index 652a5ebe4..debcb3f99 100644 --- a/Dockerfile +++ b/Dockerfile @@ -126,7 +126,7 @@ RUN useradd -m -s /bin/bash jupyteruser && chown -R jupyteruser:jupyteruser /app USER jupyteruser -RUN chmod +x /app/notebooks +# RUN chmod +x /app/notebooks VOLUME /app/data diff --git a/biosimulator_processes/copasi_process.py b/biosimulator_processes/copasi_process.py index cb00b6bb5..60081efb2 100644 --- a/biosimulator_processes/copasi_process.py +++ b/biosimulator_processes/copasi_process.py @@ -47,6 +47,7 @@ run_time_course, get_compartments, model_info, + load_model_from_string, biomodels ) from process_bigraph import Process, Composite, pf @@ -61,8 +62,10 @@ def fetch_model(term: str, index: int = 0): TODO: Implement a dynamic search of this """ - - + models = find_models(term) + model = models[index] + sbml = biomodels.get_content_for_model(model['id']) + return load_model_from_string(sbml) class CopasiProcess(Process): From f676f8addb44c7a184ad6d51616cb0d3058de796 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Mon, 26 Feb 2024 15:37:15 -0500 Subject: [PATCH 46/56] cleaned up dockerfile and added specific dir copy --- Dockerfile | 86 +--- biosimulator_processes/copasi_process.py | 14 +- biosimulator_processes/processes/__init__.py | 0 .../processes/cobra_process.py | 157 +++++++ .../processes/copasi_process.py | 220 ++++++++++ .../processes/smoldyn_process.py | 383 ++++++++++++++++++ .../processes/tellurium_process.py | 223 ++++++++++ 7 files changed, 1000 insertions(+), 83 deletions(-) create mode 100644 biosimulator_processes/processes/__init__.py create mode 100644 biosimulator_processes/processes/cobra_process.py create mode 100644 biosimulator_processes/processes/copasi_process.py create mode 100644 biosimulator_processes/processes/smoldyn_process.py create mode 100644 biosimulator_processes/processes/tellurium_process.py diff --git a/Dockerfile b/Dockerfile index debcb3f99..eb03252c5 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,82 +1,3 @@ -# Use a more specific tag than latest for reproducibility -# FROM ubuntu:20.04 -# -# ENV DEBIAN_FRONTEND=noninteractive -# -# WORKDIR /app -# -# COPY ./biosimulator_processes /app/biosimulator_processes -# -# COPY ./pyproject.toml /app -# -# COPY ./poetry.lock /app -# -# COPY ./notebooks /app/notebooks -# -# COPY ./data /app/data -# -# RUN apt-get update && apt-get install -y --no-install-recommends \ -# python3 \ -# python3-pip \ -# build-essential \ -# libncurses5 \ -# cmake \ -# make \ -# libx11-dev \ -# libc6-dev \ -# libx11-6 \ -# libc6 \ -# gcc \ -# swig \ -# pkg-config \ -# curl \ -# tar \ -# libgl1-mesa-glx \ -# libice6 \ -# libpython3.10 \ -# wget \ -# xvfb \ -# && mkdir /tmp/.X11-unix \ -# && chmod 1777 /tmp/.X11-unix \ -# && rm -rf /var/lib/apt/lists/* -# -# COPY ./scripts/xvfb-startup.sh /xvfb-startup.sh -# -# ENV XVFB_RES="1920x1080x24" \ -# XVFB_ARGS="" -# -# RUN pip install --upgrade pip \ -# && pip install poetry -# -# RUN poetry config virtualenvs.in-project true -# -# RUN poetry run pip install --upgrade pip \ -# && poetry install -# -# # activate poetry virtualenv -# ENV PATH="/app/.venv/bin:$PATH" -# ENV CONFIG_ENV_FILE="/app/config/config.env" -# ENV SECRET_ENV_FILE="/app/secret/secret.env" -# ENV STORAGE_GCS_CREDENTIALS_FILE="/app/secret/gcs_credentials.json" -# ENV STORAGE_LOCAL_CACHE_DIR="/app/scratch" -# -# # activate the poetry virtualenv each new non-interative shell -# RUN echo "source /app/.venv/bin/activate" >> /etc/bash.bashrc -# -# # add volume mount for co-simulation data -# VOLUME /app/data -# -# # Using VOLUME allows different sim tools to share inputs and outputs -# # For example: docker volume create sim-data -# # docker run -v sim-data:/app/data --name simulator1 simulator1-image -# # docker run -v sim-data:/app/data --name simulator2 simulator2-image -# -# RUN useradd -m -s /bin/bash jupyteruser -# RUN chown -R jupyteruser:jupyteruser /app -# USER jupyteruser -# -# CMD ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"] - # TODO: Use a more specific tag instead of latest for reproducibility FROM ubuntu:latest @@ -91,7 +12,12 @@ ENV DEBIAN_FRONTEND=noninteractive \ WORKDIR /app -COPY ./biosimulator_processes ./pyproject.toml ./poetry.lock ./notebooks ./data /app/ +# copy and make dirs +COPY ./biosimulator_processes/processes /app/biosimulator_processes +COPY ./notebooks /app/notebooks + +# copy files +COPY ./pyproject.toml ./poetry.lock ./data /app/ COPY ./scripts/xvfb-startup.sh /xvfb-startup.sh RUN apt-get update && apt-get install -y --no-install-recommends \ diff --git a/biosimulator_processes/copasi_process.py b/biosimulator_processes/copasi_process.py index 60081efb2..83b6d10c5 100644 --- a/biosimulator_processes/copasi_process.py +++ b/biosimulator_processes/copasi_process.py @@ -46,6 +46,7 @@ set_species, run_time_course, get_compartments, + new_model, model_info, load_model_from_string, biomodels @@ -76,7 +77,8 @@ class CopasiProcess(Process): 'species_types': { 'name': 'string', 'initial_concentration': 'int' - } + }, + 'model_search_term': 'string' # model_changes: dict paramName: new value # solver } @@ -84,8 +86,14 @@ class CopasiProcess(Process): def __init__(self, config=None, core=None): super().__init__(config, core) - # Load the single cell model into Basico - self.copasi_model_object = load_model(self.config['model_file']) + try: + if self.config.get('model_file'): + # Load the single cell model into Basico + self.copasi_model_object = load_model(self.config['model_file']) + else: + self.copasi_model_object = new_model(name=self.config['name']) + except: + raise KeyError('You must enter either a model file or model name') # Get the species (floating only) TODO: add boundary species self.floating_species_list = get_species(model=self.copasi_model_object).index.tolist() diff --git a/biosimulator_processes/processes/__init__.py b/biosimulator_processes/processes/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/biosimulator_processes/processes/cobra_process.py b/biosimulator_processes/processes/cobra_process.py new file mode 100644 index 000000000..5feb7859f --- /dev/null +++ b/biosimulator_processes/processes/cobra_process.py @@ -0,0 +1,157 @@ +""" +COBRA FBA Process +""" + + +import cobra.io +from cobra.io import read_sbml_model +from process_bigraph import Process, core, Composite, pf, pp + + +def check_sbml(state, schema, core): + # Do something to check that the value is a valid SBML file + valid = cobra.io.sbml.validate_sbml_model(state) # TODO -- this requires XML + # valid = cobra.io.load_json_model(value) + if valid: + return True + else: + return False + + +bounds_type = { + 'lower_bound': {'_type': 'float', '_default': -1000.0}, + 'upper_bound': {'_type': 'float', '_default': 1000.0}, +} +bounds_tree_type = { + '_type': 'tree[bounds]', # TODO -- make this a dict, to make it only one level deep +} +sbml_type = { + '_inherit': 'string', + '_check': check_sbml, + '_apply': 'set', +} + +# register new types +core.register('bounds', bounds_type) +core.register('sbml', sbml_type) + + +class CobraProcess(Process): + + config_schema = { + 'model_file': 'sbml', + } + + def __init__(self, config=None, core=None): + super().__init__(config, core) + self.model = read_sbml_model(self.config['model_file']) + self.reactions = self.model.reactions + self.metabolites = self.model.metabolites + self.objective = self.model.objective.to_json()['expression']['args'][0]['args'][1]['name'] # TODO -- fix this in cobra + self.boundary = self.model.boundary + + def initial_state(self): + solution = self.model.optimize() + optimized_fluxes = solution.fluxes + + state = { + 'inputs': { + 'reaction_bounds': {} + }, + 'outputs': { + 'fluxes': {} + } + } + for reaction in self.model.reactions: + state['inputs']['reaction_bounds'][reaction.id] = { + 'lower_bound': reaction.lower_bound, + 'upper_bound': reaction.upper_bound + } + state['outputs']['fluxes'][reaction.id] = optimized_fluxes[reaction.id] + return state + + def inputs(self): + return { + 'model': 'sbml', + 'reaction_bounds': { + reaction.id: 'bounds' for reaction in self.reactions + }, + 'objective_reaction': { + '_type': 'string', + '_default': self.objective + }, + } + + def outputs(self): + return { + 'fluxes': { + reaction.id: 'float' for reaction in self.reactions + }, + 'objective_value': 'float', + 'reaction_dual_values': { + reaction.id: 'float' for reaction in self.reactions + }, + 'metabolite_dual_values': { + metabolite.id: 'float' for metabolite in self.metabolites + }, + 'status': 'string', + } + + + def update(self, inputs, interval): + # set reaction bounds + reaction_bounds = inputs['reaction_bounds'] + for reaction_id, bounds in reaction_bounds.items(): + self.model.reactions.get_by_id(reaction_id).bounds = (bounds['lower_bound'], bounds['upper_bound']) + + # set objective + # TODO -- look into optlang for specifying objective and constraints + self.model.objective = self.model.reactions.get_by_id(inputs['objective_reaction']) + + # run solver + solution = self.model.optimize() + + return { + 'fluxes': solution.fluxes.to_dict(), + 'objective_value': solution.objective_value, + 'reaction_dual_values': solution.reduced_costs.to_dict(), + 'metabolite_dual_values': solution.shadow_prices.to_dict(), + 'status': solution.status, + } + + +def test_process(): + instance = { + 'fba': { + '_type': 'process', + 'address': 'local:cobra', # TODO 'biosimulators:cobra[1.0]', + 'config': { + 'model_file': 'biosimulator_processes/model_files/e_coli_core.xml' + }, + 'inputs': { + 'model': ['model_store'], + 'reaction_bounds': ['reaction_bounds_store'], + 'objective_reaction': ['objective_reaction_store'], + }, + 'outputs': { + 'fluxes': ['fluxes_store'], + 'objective_value': ['objective_value_store'], + 'reaction_dual_values': ['reaction_dual_values_store'], + 'metabolite_dual_values': ['metabolite_dual_values_store'], + 'status': ['status_store'], + } + }, + # insert emitter schema + } + + # make the composite + workflow = Composite({ + 'state': instance + }) + + # run + workflow.run(1) + + # gather results + results = workflow.gather_results() + print(f'RESULTS: {pf(results)}') diff --git a/biosimulator_processes/processes/copasi_process.py b/biosimulator_processes/processes/copasi_process.py new file mode 100644 index 000000000..83b6d10c5 --- /dev/null +++ b/biosimulator_processes/processes/copasi_process.py @@ -0,0 +1,220 @@ +""" +Biosimulator process for Copasi/Basico. + +Now lets create a new model, passing along the name that we want to give it. +Additional supported parameters for the model consist of: + + quantity_unit: which sets the unit to use for species concentrations (defaults to mol) + + volume_unit: the unit to use for three dimensional compartments (defaults to litre (l)) + + time_unit: the unit to use for time (defaults to second (s)) + + area_unit: the unit to use for two dimensional compartments + + length_unit: the unit to use for one dimensional compartments + + add_reaction('R1', 'A -> B'); + + Since we had a new model, this created the Species A and B as well as a compartment compartment, in which those + chemicals reside. The species have an initial concentration of 1. + To verify we can call get_species, which return + + get_species().initial_concentration + name + A 1.0 + B 1.0 + Name: initial_concentration, dtype: float64 + to change the initial concentration, we use set_species, and specify which property we want to change: + + set_species('B', initial_concentration=0) + set_species('A', initial_concentration=10) + get_species().initial_concentration + name + A 10.0 + B 0.0 + Name: initial_concentration, dtype: float64 + to see the kinetic paramters of our recation we can use get_reaction_parameters, and we see that the parameter has been created by default with a value of 0.1 +""" + + +from basico import ( + load_model, + get_species, + get_parameters, + get_reactions, + set_species, + run_time_course, + get_compartments, + new_model, + model_info, + load_model_from_string, + biomodels + ) +from process_bigraph import Process, Composite, pf + + +def find_models(term: str): + return biomodels.search_for_model(term) + + +def fetch_model(term: str, index: int = 0): + """Searrch for models matching the term and return an instantiated model from BioModels. + + TODO: Implement a dynamic search of this + """ + models = find_models(term) + model = models[index] + sbml = biomodels.get_content_for_model(model['id']) + return load_model_from_string(sbml) + + +class CopasiProcess(Process): + config_schema = { + 'model_file': 'string', + 'name': 'string', + 'reactions': 'list[string]', + 'species_types': { + 'name': 'string', + 'initial_concentration': 'int' + }, + 'model_search_term': 'string' + # model_changes: dict paramName: new value + # solver + } + + def __init__(self, config=None, core=None): + super().__init__(config, core) + + try: + if self.config.get('model_file'): + # Load the single cell model into Basico + self.copasi_model_object = load_model(self.config['model_file']) + else: + self.copasi_model_object = new_model(name=self.config['name']) + except: + raise KeyError('You must enter either a model file or model name') + + # Get the species (floating only) TODO: add boundary species + self.floating_species_list = get_species(model=self.copasi_model_object).index.tolist() + self.floating_species_initial = get_species(model=self.copasi_model_object)['concentration'].tolist() + + # Get the list of parameters and their values + self.model_parameters_list = get_parameters(model=self.copasi_model_object).index.tolist() + self.model_parameter_values = get_parameters(model=self.copasi_model_object)['initial_value'].tolist() + + # Get a list of reactions + self.reaction_list = get_reactions(model=self.copasi_model_object).index.tolist() + + # Get a list of compartments + self.compartments_list = get_compartments(model=self.copasi_model_object).index.tolist() + + def initial_state(self): + floating_species_dict = dict(zip(self.floating_species_list, self.floating_species_initial)) + model_parameters_dict = dict(zip(self.model_parameters_list, self.model_parameter_values)) + return { + 'time': 0.0, + 'floating_species': floating_species_dict, + 'model_parameters': model_parameters_dict + } + + def inputs(self): + floating_species_type = { + species_id: { + '_type': 'float', + '_apply': 'set', + } for species_id in self.floating_species_list + } + return { + 'time': 'float', + 'floating_species': floating_species_type, + 'model_parameters': { + param_id: 'float' for param_id in self.model_parameters_list}, + 'reactions': { + reaction_id: 'float' for reaction_id in self.reaction_list}, + } + + def outputs(self): + floating_species_type = { + species_id: { + '_type': 'float', + '_apply': 'set', + } for species_id in self.floating_species_list + } + return { + 'time': 'float', + 'floating_species': floating_species_type + } + + def update(self, inputs, interval): + + # set copasi values according to what is passed in states + for cat_id, value in inputs['floating_species'].items(): + set_species(name=cat_id, initial_concentration=value, model=self.copasi_model_object) + + # run model for "interval" length; we only want the state at the end + timecourse = run_time_course( + start_time=inputs['time'], + duration=interval, + intervals=1, + update_model=True, + model=self.copasi_model_object) + + # extract end values of concentrations from the model and set them in results + results = {'time': interval} + results['floating_species'] = { + mol_id: float(get_species(name=mol_id, exact=True, model=self.copasi_model_object).concentration[0]) + for mol_id in self.floating_species_list} + + return results + + +def test_process(): + # 1. Define the sim state schema: + initial_sim_state = { + 'copasi': { + '_type': 'process', + 'address': 'local:copasi', + 'config': { + 'model_file': 'biosimulator_processes/model_files/Caravagna2010.xml' + }, + 'inputs': { + 'floating_species': ['floating_species_store'], + 'model_parameters': ['model_parameters_store'], + 'time': ['time_store'], + 'reactions': ['reactions_store'] + }, + 'outputs': { + 'floating_species': ['floating_species_store'], + 'time': ['time_store'], + } + }, + # TODO: Add emitter schema + 'emitter': { + '_type': 'step', + 'address': 'local:ram-emitter', + 'config': { + 'emit': { + 'floating_species': 'tree[float]', + 'time': 'float', + }, + }, + 'inputs': { + 'floating_species': ['floating_species_store'], + 'time': ['time_store'], + } + + } + } + + # 2. Make the composite: + workflow = Composite({ + 'state': initial_sim_state + }) + + # 3. Run the composite workflow: + workflow.run(10) + + # 4. Gather and pretty print results + results = workflow.gather_results() + print(f'RESULTS: {pf(results)}') diff --git a/biosimulator_processes/processes/smoldyn_process.py b/biosimulator_processes/processes/smoldyn_process.py new file mode 100644 index 000000000..a4395a330 --- /dev/null +++ b/biosimulator_processes/processes/smoldyn_process.py @@ -0,0 +1,383 @@ +"""The output data returned by that which is required by simularium (executiontime, listmols), + when written and read into the same file for a given global time is as follows: + + [identity, state, x, y, z, serial number], where: + + identity = species identity for molecule + state = state of the given molecule + x, y, z = values for the relative coordinates + serial_number = monotonically decreasing timestamp for the given species_id + + At each global timestep (`executiontime`), a new 'cast of characters' are introduced that may resemble the + cast of characters at the first timestep, but are in fact different and thus all the molecules provided + from the `listmols` command will in fact all be unique. + + + I propose the following consideration at each `update` step: + + The `smoldyn.Simulation().connect()` method can be used to (for example) tell the + simulation about external environmental parameters that change over the course of + the simulation. For example: + + a = None + avals = [] + + def new_difc(t, args): + global a, avals + x, y = args + avals.append((t, a.difc['soln'])) + return x * math.sin(t) + y + + def update_difc(val): + global a + a.difc = val + + def test_connect(): + global a, avals + sim = smoldyn.Simulation(low=(....... + a = sim.addSpecies('a', color=black, difc=0.1) + + # specify either function as target: + sim.connect(new_dif, update_difc, step=10, args=[1,1]) + + # ...or species as target: + sim.connect(func = new_dif, target = 'a.difc', step=10, args=[0, 1]) + + sim.run(.... + + +""" +from typing import * +from uuid import uuid4 +from process_bigraph import Process, Composite, pf, pp +try: + import smoldyn as sm + from smoldyn._smoldyn import MolecState +except: + raise ImportError( + '\nPLEASE NOTE: Smoldyn is not correctly installed on your system which prevents you from ' + 'using the SmoldynProcess. Please refer to the README for further information ' + 'on installing Smoldyn.' + ) + + +class SmoldynProcess(Process): + """Smoldyn-based implementation of bi-graph process' `Process` API. Please note the following: + + For the purpose of this `Process` implementation, + at each `update`, we need the function to do the following for each molecule/species in the simulation: + + - Get the molecule count with Smoldyn lang: (`molcount {molecule_name}`) shape: [time, ...speciesN], + so in the case of a two species simulation: [timestamp, specACounts, specBCounts] + - Get the molecule positions and relative corresponding time steps, + indexed by the molecule name with Smoldyn lang: (`listmols`)[molecule_name] + - ?Get the molecule state? + - Kill the molecule with smoldyn lang: (`killmol {molecule_name}`) + - Add the molecule back to the solution(cytoplasm), effectively resetting it at boundary coordinates with Python API: (`simulation.addMolecules() + + PLEASE NOTE: + + The current implementation of this class assumes 3 key conditions: + 1. that a smoldyn model file is present and working + 2. output commands from the aforementioned model file that are left un-commented (disabled) will yield a + smoldyn model output file whose data could potentially reflect something other than what is returned by + this Process' `schema()`. + # TODO: Expand the config_schema to allow model_filepath to be None. + + + Config Attributes: + model_filepath:`str`: filepath to the smoldyn model you want to reference in this Process + animate:`bool`: Displays graphical simulation output from smoldyn if set to `True`. Defaults to `False`. + """ + + # TODO: Add the ability to pass model parameters and not just a model file. + config_schema = { + 'model_filepath': 'string', + 'animate': 'bool', + } + + def __init__(self, config: Dict[str, Any] = None, core=None): + """A new instance of `SmoldynProcess` based on the `config` that is passed. The schema for the config to be passed in + this object's constructor is as follows: + + config_schema = { + 'model_filepath': 'string', <-- analogous to python `str` + 'animate': 'bool' <-- of type `bigraph_schema.base_types.bool` + + # TODO: It would be nice to have classes associated with this. + """ + super().__init__(config, core) + + # specify the model fp for clarity + self.model_filepath = self.config.get('model_filepath') + + # enforce model filepath passing + if not self.model_filepath: + raise ValueError( + ''' + The Process configuration requires a Smoldyn model filepath to be passed. + Please specify a 'model_filepath' in your instance configuration. + ''' + ) + + # initialize the simulator from a Smoldyn model.txt file. + self.simulation: sm.Simulation = sm.Simulation.fromFile(self.model_filepath) + + # get a list of the simulation species + species_count = self.simulation.count()['species'] + self.species_names: List[str] = [] + for index in range(species_count): + species_name = self.simulation.getSpeciesName(index) + if 'empty' not in species_name.lower(): + self.species_names.append(species_name) + # sort for logistical mapping to species names (i.e: ['a', 'b', c'] == ['0', '1', '2'] + self.species_names.sort() + + # make species counts of molecules dataset for output + self.simulation.addOutputData('species_counts') + # write molcounts to counts dataset at every timestep (shape=(n_timesteps, 1+n_species <-- one for time)): [timestep, countSpec1, countSpec2, ...] + self.simulation.addCommand(cmd='molcount species_counts', cmd_type='E') + + # make molecules dataset (molecule information) for output + self.simulation.addOutputData('molecules') + # write coords to dataset at every timestep (shape=(n_output_molecules, 7)): seven being [timestep, smol_id(species), mol_state, x, y, z, mol_serial_num] + self.simulation.addCommand(cmd='listmols2 molecules', cmd_type='E') + + # initialize the molecule ids based on the species names. We need this value to properly emit the schema, which expects a single value from this to be a str(int) + # the format for molecule_ids is expected to be: 'speciesId_moleculeNumber' + self.molecule_ids: List[str] = [str(uuid4()) for n in list(range(len(self.species_names)))] + + # get the simulation boundaries, which in the case of Smoldyn denote the physical boundaries + # TODO: add a verification method to ensure that the boundaries do not change on the next step... + self.boundaries: Dict[str, List[float]] = dict(zip(['low', 'high'], self.simulation.getBoundaries())) + + # set graphics (defaults to False) + if self.config['animate']: + self.simulation.addGraphics('opengl_better') + + # create a re-usable counts and molecules type to be used by both inputs and outputs + self.counts_type = { + species_name: 'int' + for species_name in self.species_names + } + + # self.molecules_type = { + # mol_id: { + # 'coordinates': 'list[float]', + # 'species_id': 'string', + # 'state': 'string' + # } for mol_id in self.molecule_ids + # } + + def set_uniform( + self, + species_name: str, + count: int, + kill_mol: bool = True + ) -> None: + """Add a distribution of molecules to the solution in + the simulation memory given a higher and lower bound x,y coordinate. Smoldyn assumes + a global boundary versus individual species boundaries. Kills the molecule before dist if true. + + TODO: If pymunk expands the species compartment, account for + expanding `highpos` and `lowpos`. This method should be used within the body/logic of + the `update` class method. + + Args: + species_name:`str`: name of the given molecule. + count:`int`: number of molecules of the given `species_name` to add. + kill_mol:`bool`: kills the molecule based on the `name` argument, which effectively + removes the molecule from simulation memory. + """ + # kill the mol, effectively resetting it + if kill_mol: + self.simulation.runCommand(f'killmol {species_name}') + + # TODO: eventually allow for an expanding boundary ie in the configuration parameters (pymunk?), which is defies the methodology of smoldyn + + # redistribute the molecule according to the bounds + self.simulation.addSolutionMolecules( + species=species_name, + number=count, + highpos=self.boundaries['high'], + lowpos=self.boundaries['low'] + ) + + def initial_state(self) -> Dict[str, Union[int, Dict]]: + """Set the initial parameter state of the simulation. This method should return an implementation of + that which is returned by `self.schema()`. + + + NOTE: Due to the nature of this model, + Smoldyn assigns a random uniform distribution of integers as the initial coordinate (x, y, z) + values for the simulation. As such, the `set_uniform` method will uniformly distribute + the molecules according to a `highpos`[x,y] and `lowpos`[x,y] where high and low pos are + the higher and lower bounds of the molecule spatial distribution. + + NOTE: This method should provide an implementation of the structure denoted in `self.schema`. + """ + # get the initial species counts + initial_species_counts = { + spec_name: self.simulation.getMoleculeCount(spec_name, MolecState.all) + for spec_name in self.species_names + } + + print(f'INITAL: {initial_species_counts}') + + return { + 'species_counts': initial_species_counts, + 'molecules': { + mol_id: { + 'coordinates': [0.0, 0.0, 0.0], + 'species_id': self.species_names[i], + 'state': 0 + } + for i, mol_id in enumerate(self.molecule_ids) + } + } + + def inputs(self): + # TODO: include velocity and state to this schema (add to constructor as well) + counts_type = { + species_name: 'int' + for species_name in self.species_names + } + + return { + 'species_counts': counts_type, + 'molecules': 'tree[string]' # self.molecules_type + } + + def outputs(self): + counts_type = { + species_name: 'int' + for species_name in self.species_names + } + + return { + 'species_counts': counts_type, + 'molecules': 'tree[string]' # self.molecules_type + } + + def update(self, inputs: Dict, interval: int) -> Dict: + """Callback method to be evoked at each Process interval. We want to get the + last of each dataset type as that is the relevant data in regard to the Process timescale scope. + + Args: + inputs:`Dict`: current state of the Smoldyn simulation, expressed as a `Dict` whose + schema matches that which is returned by the `self.schema()` API method. + interval:`int`: Analogous to Smoldyn's `time_stop`, this is the + timestep interval at which to provide the update as the output of this method. + NOTE: This update is iteratively called with the `Process` API. + + Returns: + `Dict`: New state according to the update at interval + + + TODO: We must account for the mol_ids that are generated in the output based on the interval run, + i.e: Shorter intervals will yield both less output molecules and less unique molecule ids. + """ + # reset the molecules, distribute the mols according to self.boundarieså + for name in self.species_names: + self.set_uniform( + species_name=name, + count=inputs['species_counts'][name], + ) + + # run the simulation for a given interval + self.simulation.run( + stop=interval, + dt=self.simulation.dt + ) + + # get the counts data, clear the buffer + counts_data = self.simulation.getOutputData('species_counts') + + # get the final counts for the update + final_count = counts_data[-1] + # remove the timestep from the list + final_count.pop(0) + + # get the data based on the commands added in the constructor, clear the buffer + molecules_data = self.simulation.getOutputData('molecules') + + # create an empty simulation state mirroring that which is specified in the schema + simulation_state = { + 'species_counts': {}, + 'molecules': {} + } + + # get and populate the species counts + for index, name in enumerate(self.species_names): + input_counts = inputs['species_counts'][name] + print(f'INPUT COUNTS: {input_counts}') + simulation_state['species_counts'][name] = int(final_count[index]) - input_counts + + # clear the list of known molecule ids and update the list of known molecule ids (convert to an intstring) + self.molecule_ids.clear() + for molecule in molecules_data: + self.molecule_ids.append(str(uuid4())) + + # get and populate the output molecules + mols = [] + for index, mol_id in enumerate(self.molecule_ids): + single_molecule_data = molecules_data[index] + single_molecule_species_index = int(single_molecule_data[1]) - 1 + mols.append(single_molecule_species_index) + simulation_state['molecules'][mol_id] = { + 'coordinates': single_molecule_data[3:6], + 'species_id': self.species_names[single_molecule_species_index], + 'state': str(int(single_molecule_data[2])) + } + + # TODO -- post processing to get effective rates + + return simulation_state + + +def test_process(): + """Test the smoldyn process using the crowding model.""" + + # this is the instance for the composite process to run + print("RUNNING") + instance = { + 'smoldyn': { + '_type': 'process', + 'address': 'local:smoldyn', + 'config': { + 'model_filepath': 'biosimulator_processes/model_files/minE_model.txt', + 'animate': False}, + 'inputs': { + 'species_counts': ['species_counts_store'], + 'molecules': ['molecules_store']}, + 'outputs': { + 'species_counts': ['species_counts_store'], + 'molecules': ['molecules_store']} + }, + 'emitter': { + '_type': 'step', + 'address': 'local:ram-emitter', + 'config': { + 'emit': { + 'species_counts': 'tree[string]', + 'molecules': 'tree[string]'} + }, + 'inputs': { + 'species_counts': ['species_counts_store'], + 'molecules': ['molecules_store']} + } + } + + total_time = 2 + + # make the composite + workflow = Composite({ + 'state': instance + }) + + # run + workflow.run(total_time) + + # gather results + results = workflow.gather_results() + pp(f'RESULTS: {pf(results)}') diff --git a/biosimulator_processes/processes/tellurium_process.py b/biosimulator_processes/processes/tellurium_process.py new file mode 100644 index 000000000..513f5c4be --- /dev/null +++ b/biosimulator_processes/processes/tellurium_process.py @@ -0,0 +1,223 @@ +""" +Tellurium Process +""" + + +import numpy as np +import tellurium as te +from process_bigraph import Process, Composite, pf, Step + + +class TelluriumStep(Step): + + config_schema = { + 'sbml_model_path': 'string', + 'antimony_string': 'string', + } + + def __init__(self, config=None, core=None): + super().__init__(config, core) + + # initialize a tellurium(roadrunner) simulation object. Load the model in using either sbml(default) or antimony + if self.config.get('antimony_string') and not self.config.get('sbml_model_path'): + self.simulator = te.loada(self.config['antimony_string']) + elif self.config.get('sbml_model_path') and not self.config.get('antimony_string'): + self.simulator: te.roadrunner.extended_roadrunner.ExtendedRoadRunner = te.loadSBMLModel(self.config['sbml_model_path']) + else: + raise Exception('the config requires either an "antimony_string" or an "sbml_model_path"') + + self.input_ports = [ + 'floating_species', + 'boundary_species', + 'model_parameters' + ] + + self.output_ports = [ + 'floating_species', + ] + + # Get the species (floating and boundary) + self.floating_species_list = self.simulator.getFloatingSpeciesIds() + self.boundary_species_list = self.simulator.getBoundarySpeciesIds() + self.floating_species_initial = self.simulator.getFloatingSpeciesConcentrations() + self.boundary_species_initial = self.simulator.getBoundarySpeciesConcentrations() + + # Get the list of parameters and their values + self.model_parameters_list = self.simulator.getGlobalParameterIds() + self.model_parameter_values = self.simulator.getGlobalParameterValues() + + # Get a list of reactions + self.reaction_list = self.simulator.getReactionIds() + + # TODO -- is initial state even working for steps? + def initial_state(self, config=None): + return { + 'inputs': { + 'time': 0, + }, + } + + def inputs(self): + return { + 'time': 'float', + 'run_time': 'float', + } + + def outputs(self): + return { + 'results': { + '_type': 'numpy_array', + '_apply': 'set' + } # This is a roadrunner._roadrunner.NamedArray + } + + def update(self, inputs): + results = self.simulator.simulate( + inputs['time'], + inputs['run_time'], + 10 + ) # TODO -- adjust the number of saves teps + return { + 'results': results} + + +class TelluriumProcess(Process): + config_schema = { + 'sbml_model_path': 'string', + 'antimony_string': 'string', + 'record_history': 'bool', # TODO -- do we have this type? + } + + def __init__(self, config=None): + super().__init__(config) + + # initialize a tellurium(roadrunner) simulation object. Load the model in using either sbml(default) or antimony + if self.config.get('antimony_string') and not self.config.get('sbml_model_path'): + self.simulator = te.loada(self.config['antimony_string']) + elif self.config.get('sbml_model_path') and not self.config.get('antimony_string'): + self.simulator: te.roadrunner.extended_roadrunner.ExtendedRoadRunner = te.loadSBMLModel(self.config['sbml_model_path']) + else: + raise Exception('the config requires either an "antimony_string" or an "sbml_model_path"') + + # TODO -- make this configurable. + self.input_ports = [ + 'floating_species', + 'boundary_species', + 'model_parameters' + 'time', + # 'compartments', + # 'parameters', + # 'stoichiometries', + ] + + self.output_ports = [ + 'floating_species', + 'time', + ] + + # Get the species (floating and boundary) + self.floating_species_list = self.simulator.getFloatingSpeciesIds() + self.boundary_species_list = self.simulator.getBoundarySpeciesIds() + self.floating_species_initial = self.simulator.getFloatingSpeciesConcentrations() + self.boundary_species_initial = self.simulator.getBoundarySpeciesConcentrations() + + # Get the list of parameters and their values + self.model_parameters_list = self.simulator.getGlobalParameterIds() + self.model_parameter_values = self.simulator.getGlobalParameterValues() + + # Get a list of reactions + self.reaction_list = self.simulator.getReactionIds() + + def initial_state(self, config=None): + floating_species_dict = dict(zip(self.floating_species_list, self.floating_species_initial)) + boundary_species_dict = dict(zip(self.boundary_species_list, self.boundary_species_initial)) + model_parameters_dict = dict(zip(self.model_parameters_list, self.model_parameter_values)) + return { + 'time': 0.0, + 'floating_species': floating_species_dict, + 'boundary_species': boundary_species_dict, + 'model_parameters': model_parameters_dict + } + + def inputs(self): + float_set = {'_type': 'float', '_apply': 'set'} + return { + 'time': 'float', + 'run_time': 'float', + 'floating_species': { + species_id: float_set for species_id in self.floating_species_list}, + 'boundary_species': { + species_id: float_set for species_id in self.boundary_species_list}, + 'model_parameters': { + param_id: float_set for param_id in self.model_parameters_list}, + 'reactions': { + reaction_id: float_set for reaction_id in self.reaction_list}, + } + + def outputs(self): + float_set = {'_type': 'float', '_apply': 'set'} + return { + 'floating_species': { + species_id: float_set for species_id in self.floating_species_list}, + 'time': 'float' + } + + def update(self, inputs, interval): + + # set tellurium values according to what is passed in states + for port_id, values in inputs.items(): + if port_id in self.input_ports: # only update from input ports + for cat_id, value in values.items(): + self.simulator.setValue(cat_id, value) + + # run the simulation + new_time = self.simulator.oneStep(inputs['time'], interval) + + # extract the results and convert to update + update = {'time': new_time} + for port_id, values in inputs.items(): + if port_id in self.output_ports: + update[port_id] = {} + for cat_id in values.keys(): + update[port_id][cat_id] = self.simulator.getValue(cat_id) + return update + + +def test_process(): + # 1. define the instance of the Composite(in this case singular) by its schema + instance = { + # 'start_time_store': 0, + # 'run_time_store': 1, + # 'results_store': None, # TODO -- why is this not automatically added into the schema because of tellurium schema? + 'tellurium': { + '_type': 'process', + 'address': 'local:tellurium', # using a local toy process + 'config': { + 'sbml_model_path': 'biosimulator_processes/model_files/BIOMD0000000061_url.xml', + }, + 'inputs': { + 'time': ['start_time_store'], + 'run_time': ['run_time_store'], + 'floating_species': ['floating_species_store'], + 'boundary_species': ['boundary_species_store'], + 'model_parameters': ['model_parameters_store'], + 'reactions': ['reactions_store'], + # 'interval': ['interval_store'], + }, + 'outputs': { + 'results': ['results_store'], + } + } + } + + # 2. make the composite + workflow = Composite({ + 'state': instance + }) + + # 3. run + update = workflow.run(10) + + # 4. gather results + results = workflow.gather_results() + print(f'RESULTS: {pf(results)}') From 2f8134e6107bf41dd7d61b5f5107092b5587ada1 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Mon, 26 Feb 2024 16:12:43 -0500 Subject: [PATCH 47/56] added notebook truster script and spec to dockerfile --- Dockerfile | 10 ++++++---- biosimulator_processes/copasi_process.py | 12 +++++++++++- scripts/trust-notebooks.sh | 4 ++++ 3 files changed, 21 insertions(+), 5 deletions(-) create mode 100644 scripts/trust-notebooks.sh diff --git a/Dockerfile b/Dockerfile index eb03252c5..1687b4321 100644 --- a/Dockerfile +++ b/Dockerfile @@ -17,7 +17,7 @@ COPY ./biosimulator_processes/processes /app/biosimulator_processes COPY ./notebooks /app/notebooks # copy files -COPY ./pyproject.toml ./poetry.lock ./data /app/ +COPY ./pyproject.toml ./poetry.lock ./data ./scripts/trust-notebooks.sh /app/ COPY ./scripts/xvfb-startup.sh /xvfb-startup.sh RUN apt-get update && apt-get install -y --no-install-recommends \ @@ -46,11 +46,13 @@ RUN apt-get update && apt-get install -y --no-install-recommends \ && rm -rf /var/lib/apt/lists/* \ && pip install --upgrade pip && pip install poetry \ && poetry config virtualenvs.in-project true \ - && poetry install + && poetry install \ + && chmod +x /app/trust-notebooks.sh \ + && /app/trust-notebook.sh -RUN useradd -m -s /bin/bash jupyteruser && chown -R jupyteruser:jupyteruser /app +# RUN useradd -m -s /bin/bash jupyteruser && chown -R jupyteruser:jupyteruser /app -USER jupyteruser +# USER jupyteruser # RUN chmod +x /app/notebooks diff --git a/biosimulator_processes/copasi_process.py b/biosimulator_processes/copasi_process.py index 83b6d10c5..ef470c5bf 100644 --- a/biosimulator_processes/copasi_process.py +++ b/biosimulator_processes/copasi_process.py @@ -69,6 +69,10 @@ def fetch_model(term: str, index: int = 0): return load_model_from_string(sbml) +# 1. Add useful config params +# 2. Devise use cases +# 3. Update constructor conditionally +# 4. Devise parameter scan class CopasiProcess(Process): config_schema = { 'model_file': 'string', @@ -78,7 +82,13 @@ class CopasiProcess(Process): 'name': 'string', 'initial_concentration': 'int' }, - 'model_search_term': 'string' + 'model_search_term': 'string', + 'model_changes': { + 'parameter': { + 'new_value': 'float' + } + } + # model_changes: dict paramName: new value # solver } diff --git a/scripts/trust-notebooks.sh b/scripts/trust-notebooks.sh new file mode 100644 index 000000000..0dc85c0f0 --- /dev/null +++ b/scripts/trust-notebooks.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +# Trust all notebooks in a specific directory +find /app/notebooks -name "*.ipynb" -exec jupyter trust {} \; From cd4236c68f9b28824870bf5016b0abe0ca3a3e80 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Mon, 26 Feb 2024 16:16:41 -0500 Subject: [PATCH 48/56] fixed path in script for dockerfile --- Dockerfile | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/Dockerfile b/Dockerfile index 1687b4321..452ce6eea 100644 --- a/Dockerfile +++ b/Dockerfile @@ -47,15 +47,13 @@ RUN apt-get update && apt-get install -y --no-install-recommends \ && pip install --upgrade pip && pip install poetry \ && poetry config virtualenvs.in-project true \ && poetry install \ - && chmod +x /app/trust-notebooks.sh \ - && /app/trust-notebook.sh - -# RUN useradd -m -s /bin/bash jupyteruser && chown -R jupyteruser:jupyteruser /app - -# USER jupyteruser - -# RUN chmod +x /app/notebooks + && chmod +x ./trust-notebooks.sh \ + && ./trust-notebook.sh VOLUME /app/data CMD ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"] + + +# PLEASE NOTE: We do not need to add a USER in the Dockerfile as Singularity will handle + # such logic in conversion on the HPC. From 42e9481ffb8beda498a8b3c1a4e8fdbf063175b0 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Mon, 26 Feb 2024 16:28:05 -0500 Subject: [PATCH 49/56] added buildDockerImage workflow from Biosimulators repo and adjusted trust notebooks remove --- .github/workflows/buildDockerImage.yaml | 168 ++++++++++++++++++++++++ Dockerfile | 3 +- 2 files changed, 170 insertions(+), 1 deletion(-) create mode 100644 .github/workflows/buildDockerImage.yaml diff --git a/.github/workflows/buildDockerImage.yaml b/.github/workflows/buildDockerImage.yaml new file mode 100644 index 000000000..efe57f071 --- /dev/null +++ b/.github/workflows/buildDockerImage.yaml @@ -0,0 +1,168 @@ +name: Build and push Docker image + +on: + push: + paths: + - '.github/workflows/buildDockerImage.yml' + - 'Dockerfile' + - 'Dockerfile-base' + - 'Dockerfile-assets/**' + +jobs: + buildAndPushImage: + name: Build and push Docker image + if: "!contains(github.event.head_commit.message, '[skip ci]') && github.actor != 'allcontributors'" + runs-on: ubuntu-20.04 + + steps: + # Free disk space + # Inspiration + # - https://github.com/easimon/maximize-build-space/blob/master/action.yml + # - https://githubmemory.com/repo/ros-industrial/industrial_ci/issues/648 + # - https://github.community/t/bigger-github-hosted-runners-disk-space/17267/11 + - name: Maximize build space + run: | + sudo apt-get -qq purge build-essential ghc* + sudo apt-get clean + sudo rm -rf /usr/share/dotnet + sudo rm -rf /usr/local/lib/android + sudo rm -rf /opt/ghc + sudo rm -rf /usr/local/share/boost + sudo rm -rf "$AGENT_TOOLSDIRECTORY" + docker system prune -f + + # checkout repository + - name: Checkout repository + uses: actions/checkout@v3 + with: + fetch-depth: 1 + + # Build Docker image + - name: Set up Docker Buildx + uses: docker/setup-buildx-action@v1 + + - name: Cache Docker layers + uses: actions/cache@v2 + with: + path: /tmp/.buildx-cache + key: ${{ runner.os }}-buildx-${{ github.sha }} + restore-keys: | + ${{ runner.os }}-buildx- + + - name: Login to GHCR + uses: docker/login-action@v1 + with: + registry: ghcr.io + username: "${{ secrets.DOCKER_REGISTRY_USERNAME }}" + password: "${{ secrets.DOCKER_REGISTRY_TOKEN }}" + + - id: get-timestamp + name: Get timestamp + run: | + TIMESTAMP=$(date --rfc-3339=seconds | sed 's/ /T/') + echo "timestamp=$TIMESTAMP" >> $GITHUB_OUTPUT + + - name: Copy Dockerfile to Dockerfile-assets + run: | + cp Dockerfile Dockerfile-assets/ + cp Dockerfile-base Dockerfile-assets/ + + - name: Build base image + uses: docker/build-push-action@v2 + with: + context: Dockerfile-assets + file: Dockerfile-base + pull: true + load: true + push: false + tags: | + ghcr.io/biosimulators/biosimulator-processes:sha-${{github.sha}} + labels: | + org.opencontainers.image.revision=${{github.sha}} + org.opencontainers.image.created=${{steps.get-timestamp.outputs.timestamp}}" + cache-from: type=registry,ref=ghcr.io/biosimulators/biosimulators-base:buildcache + cache-to: type=registry,ref=ghcr.io/biosimulators/biosimulators-base:buildcache,mode=max + + - name: Push base Docker image + run: docker image push ghcr.io/biosimulators/biosimulators-base:sha-${{github.sha}} + + - name: Label base Docker image + run: docker image tag ghcr.io/biosimulators/biosimulators-base:sha-${{github.sha}} ghcr.io/biosimulators/biosimulators-base:latest + + - name: Maximize build space + run: | + docker system prune -f + + - name: Build image + uses: docker/build-push-action@v2 + with: + context: Dockerfile-assets + file: Dockerfile + pull: false + load: true + push: false + tags: | + ghcr.io/biosimulators/biosimulators:sha-${{github.sha}} + labels: | + org.opencontainers.image.revision=${{github.sha}} + org.opencontainers.image.created=${{steps.get-timestamp.outputs.timestamp}}" + cache-from: type=registry,ref=ghcr.io/biosimulators/biosimulators:buildcache + cache-to: type=registry,ref=ghcr.io/biosimulators/biosimulators:buildcache,mode=max + + - name: Push Docker image + run: docker image push ghcr.io/biosimulators/biosimulators:sha-${{github.sha}} + + - name: Label Docker image + run: docker image tag ghcr.io/biosimulators/biosimulators:sha-${{github.sha}} ghcr.io/biosimulators/biosimulators:latest + + - name: Maximize build space + run: | + docker system prune -f + + # Test Docker image + - name: Test Docker image + run: | + cwd=$(pwd) + docker run \ + --rm \ + --entrypoint bash \ + --mount type=bind,source=${cwd},target=/app/Biosimulators \ + ghcr.io/biosimulators/biosimulators:latest \ + -c " + pipenv install --dev --system --deploy + /bin/bash /xvfb-startup.sh python -m pytest --forked --verbose Biosimulators/tests/ + " + + # Get version number + - id: get-version-number + name: Get version number + if: startsWith(github.ref, 'refs/tags/') + env: + TAG: ${{ github.ref }} + run: | + version="${TAG/refs\/tags\//}" + echo "version=$version" >> $GITHUB_OUTPUT + + # Create GitHub release + - name: Create GitHub release + if: startsWith(github.ref, 'refs/tags/') + uses: actions/create-release@v1 + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + with: + tag_name: ${{ steps.get-version-number.outputs.version }} + release_name: Release ${{ steps.get-version-number.outputs.version }} + + # Push Docker image + - name: Push Docker image + if: startsWith(github.ref, 'refs/tags/') + env: + VERSION: ${{ steps.get-version-number.outputs.version }} + run: | + docker image tag ghcr.io/biosimulators/biosimulators-base:sha-${{github.sha}} ghcr.io/biosimulators/biosimulators-base:${VERSION} + docker image tag ghcr.io/biosimulators/biosimulators:sha-${{github.sha}} ghcr.io/biosimulators/biosimulators:${VERSION} + + docker push ghcr.io/biosimulators/biosimulators-base:${VERSION} + docker push ghcr.io/biosimulators/biosimulators-base:latest + docker push ghcr.io/biosimulators/biosimulators:${VERSION} + docker push ghcr.io/biosimulators/biosimulators:latest diff --git a/Dockerfile b/Dockerfile index 452ce6eea..82ee716cb 100644 --- a/Dockerfile +++ b/Dockerfile @@ -48,7 +48,8 @@ RUN apt-get update && apt-get install -y --no-install-recommends \ && poetry config virtualenvs.in-project true \ && poetry install \ && chmod +x ./trust-notebooks.sh \ - && ./trust-notebook.sh + && ./trust-notebooks.sh \ + && rm ./trust-notebooks.sh VOLUME /app/data From 390321b04d1a13e806c4cbbe6d4da8fd5cfb540a Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Mon, 26 Feb 2024 16:29:49 -0500 Subject: [PATCH 50/56] removed workflow temp --- .github/workflows/buildDockerImage.yaml | 168 ------------------------ 1 file changed, 168 deletions(-) delete mode 100644 .github/workflows/buildDockerImage.yaml diff --git a/.github/workflows/buildDockerImage.yaml b/.github/workflows/buildDockerImage.yaml deleted file mode 100644 index efe57f071..000000000 --- a/.github/workflows/buildDockerImage.yaml +++ /dev/null @@ -1,168 +0,0 @@ -name: Build and push Docker image - -on: - push: - paths: - - '.github/workflows/buildDockerImage.yml' - - 'Dockerfile' - - 'Dockerfile-base' - - 'Dockerfile-assets/**' - -jobs: - buildAndPushImage: - name: Build and push Docker image - if: "!contains(github.event.head_commit.message, '[skip ci]') && github.actor != 'allcontributors'" - runs-on: ubuntu-20.04 - - steps: - # Free disk space - # Inspiration - # - https://github.com/easimon/maximize-build-space/blob/master/action.yml - # - https://githubmemory.com/repo/ros-industrial/industrial_ci/issues/648 - # - https://github.community/t/bigger-github-hosted-runners-disk-space/17267/11 - - name: Maximize build space - run: | - sudo apt-get -qq purge build-essential ghc* - sudo apt-get clean - sudo rm -rf /usr/share/dotnet - sudo rm -rf /usr/local/lib/android - sudo rm -rf /opt/ghc - sudo rm -rf /usr/local/share/boost - sudo rm -rf "$AGENT_TOOLSDIRECTORY" - docker system prune -f - - # checkout repository - - name: Checkout repository - uses: actions/checkout@v3 - with: - fetch-depth: 1 - - # Build Docker image - - name: Set up Docker Buildx - uses: docker/setup-buildx-action@v1 - - - name: Cache Docker layers - uses: actions/cache@v2 - with: - path: /tmp/.buildx-cache - key: ${{ runner.os }}-buildx-${{ github.sha }} - restore-keys: | - ${{ runner.os }}-buildx- - - - name: Login to GHCR - uses: docker/login-action@v1 - with: - registry: ghcr.io - username: "${{ secrets.DOCKER_REGISTRY_USERNAME }}" - password: "${{ secrets.DOCKER_REGISTRY_TOKEN }}" - - - id: get-timestamp - name: Get timestamp - run: | - TIMESTAMP=$(date --rfc-3339=seconds | sed 's/ /T/') - echo "timestamp=$TIMESTAMP" >> $GITHUB_OUTPUT - - - name: Copy Dockerfile to Dockerfile-assets - run: | - cp Dockerfile Dockerfile-assets/ - cp Dockerfile-base Dockerfile-assets/ - - - name: Build base image - uses: docker/build-push-action@v2 - with: - context: Dockerfile-assets - file: Dockerfile-base - pull: true - load: true - push: false - tags: | - ghcr.io/biosimulators/biosimulator-processes:sha-${{github.sha}} - labels: | - org.opencontainers.image.revision=${{github.sha}} - org.opencontainers.image.created=${{steps.get-timestamp.outputs.timestamp}}" - cache-from: type=registry,ref=ghcr.io/biosimulators/biosimulators-base:buildcache - cache-to: type=registry,ref=ghcr.io/biosimulators/biosimulators-base:buildcache,mode=max - - - name: Push base Docker image - run: docker image push ghcr.io/biosimulators/biosimulators-base:sha-${{github.sha}} - - - name: Label base Docker image - run: docker image tag ghcr.io/biosimulators/biosimulators-base:sha-${{github.sha}} ghcr.io/biosimulators/biosimulators-base:latest - - - name: Maximize build space - run: | - docker system prune -f - - - name: Build image - uses: docker/build-push-action@v2 - with: - context: Dockerfile-assets - file: Dockerfile - pull: false - load: true - push: false - tags: | - ghcr.io/biosimulators/biosimulators:sha-${{github.sha}} - labels: | - org.opencontainers.image.revision=${{github.sha}} - org.opencontainers.image.created=${{steps.get-timestamp.outputs.timestamp}}" - cache-from: type=registry,ref=ghcr.io/biosimulators/biosimulators:buildcache - cache-to: type=registry,ref=ghcr.io/biosimulators/biosimulators:buildcache,mode=max - - - name: Push Docker image - run: docker image push ghcr.io/biosimulators/biosimulators:sha-${{github.sha}} - - - name: Label Docker image - run: docker image tag ghcr.io/biosimulators/biosimulators:sha-${{github.sha}} ghcr.io/biosimulators/biosimulators:latest - - - name: Maximize build space - run: | - docker system prune -f - - # Test Docker image - - name: Test Docker image - run: | - cwd=$(pwd) - docker run \ - --rm \ - --entrypoint bash \ - --mount type=bind,source=${cwd},target=/app/Biosimulators \ - ghcr.io/biosimulators/biosimulators:latest \ - -c " - pipenv install --dev --system --deploy - /bin/bash /xvfb-startup.sh python -m pytest --forked --verbose Biosimulators/tests/ - " - - # Get version number - - id: get-version-number - name: Get version number - if: startsWith(github.ref, 'refs/tags/') - env: - TAG: ${{ github.ref }} - run: | - version="${TAG/refs\/tags\//}" - echo "version=$version" >> $GITHUB_OUTPUT - - # Create GitHub release - - name: Create GitHub release - if: startsWith(github.ref, 'refs/tags/') - uses: actions/create-release@v1 - env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - with: - tag_name: ${{ steps.get-version-number.outputs.version }} - release_name: Release ${{ steps.get-version-number.outputs.version }} - - # Push Docker image - - name: Push Docker image - if: startsWith(github.ref, 'refs/tags/') - env: - VERSION: ${{ steps.get-version-number.outputs.version }} - run: | - docker image tag ghcr.io/biosimulators/biosimulators-base:sha-${{github.sha}} ghcr.io/biosimulators/biosimulators-base:${VERSION} - docker image tag ghcr.io/biosimulators/biosimulators:sha-${{github.sha}} ghcr.io/biosimulators/biosimulators:${VERSION} - - docker push ghcr.io/biosimulators/biosimulators-base:${VERSION} - docker push ghcr.io/biosimulators/biosimulators-base:latest - docker push ghcr.io/biosimulators/biosimulators:${VERSION} - docker push ghcr.io/biosimulators/biosimulators:latest From 65e8fd9adadd3499d26aff39606fdf0a0d9b6937 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Mon, 26 Feb 2024 16:31:00 -0500 Subject: [PATCH 51/56] added workflow to gitignore and locally copied --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index 78ebc3414..2620c89f8 100644 --- a/.gitignore +++ b/.gitignore @@ -20,3 +20,4 @@ submit-biosimulators-container.sh .vagrant ._vagrant .THIS-IS-FOR-CONTAINER-DEV-ONLY +buildDockerImage.yml From 7980f67564e70fa50bfd70c7f148dcd3962a84b6 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Mon, 26 Feb 2024 16:38:09 -0500 Subject: [PATCH 52/56] added comments and vals to copasi process --- biosimulator_processes/__init__.py | 6 ++++++ biosimulator_processes/copasi_process.py | 20 +++++++++----------- 2 files changed, 15 insertions(+), 11 deletions(-) diff --git a/biosimulator_processes/__init__.py b/biosimulator_processes/__init__.py index 91ef57eab..4d376e1d4 100644 --- a/biosimulator_processes/__init__.py +++ b/biosimulator_processes/__init__.py @@ -22,3 +22,9 @@ print(f"{class_name} registered successfully.") except ImportError as e: print(f"{class_name} not available. Error: {e}") + + +from biosimulator_processes.copasi_process import CopasiProcess +from biosimulator_processes.smoldyn_process import SmoldynProcess +from biosimulator_processes.cobra_process import CobraProcess +from biosimulator_processes.tellurium_process import TelluriumProcess diff --git a/biosimulator_processes/copasi_process.py b/biosimulator_processes/copasi_process.py index ef470c5bf..02ce45df7 100644 --- a/biosimulator_processes/copasi_process.py +++ b/biosimulator_processes/copasi_process.py @@ -54,16 +54,12 @@ from process_bigraph import Process, Composite, pf -def find_models(term: str): - return biomodels.search_for_model(term) - - -def fetch_model(term: str, index: int = 0): - """Searrch for models matching the term and return an instantiated model from BioModels. +def fetch_biomodel(term: str, index: int = 0): + """Search for models matching the term and return an instantiated model from BioModels. TODO: Implement a dynamic search of this """ - models = find_models(term) + models = biomodels.search_for_model(term) model = models[index] sbml = biomodels.get_content_for_model(model['id']) return load_model_from_string(sbml) @@ -73,7 +69,10 @@ def fetch_model(term: str, index: int = 0): # 2. Devise use cases # 3. Update constructor conditionally # 4. Devise parameter scan + + class CopasiProcess(Process): + # TODO: Update this in constructor config_schema = { 'model_file': 'string', 'name': 'string', @@ -87,15 +86,14 @@ class CopasiProcess(Process): 'parameter': { 'new_value': 'float' } - } - - # model_changes: dict paramName: new value - # solver + }, + 'solver': 'string' } def __init__(self, config=None, core=None): super().__init__(config, core) + # TODO: Update set/get with optional config params and make logic try: if self.config.get('model_file'): # Load the single cell model into Basico From 554f8cf482ad0572da2d12a21f4e9d029f0c89d7 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Mon, 26 Feb 2024 17:01:58 -0500 Subject: [PATCH 53/56] updated copasi process constructor with optional default values --- biosimulator_processes/copasi_process.py | 21 +++++++++++++++------ 1 file changed, 15 insertions(+), 6 deletions(-) diff --git a/biosimulator_processes/copasi_process.py b/biosimulator_processes/copasi_process.py index 02ce45df7..ab6ff6f76 100644 --- a/biosimulator_processes/copasi_process.py +++ b/biosimulator_processes/copasi_process.py @@ -47,6 +47,7 @@ run_time_course, get_compartments, new_model, + add_reaction, model_info, load_model_from_string, biomodels @@ -74,9 +75,15 @@ def fetch_biomodel(term: str, index: int = 0): class CopasiProcess(Process): # TODO: Update this in constructor config_schema = { - 'model_file': 'string', - 'name': 'string', - 'reactions': 'list[string]', + 'model_file': { + '_type': 'string', + '_default': '' + }, + 'reactions': { + 'name': { + 'scheme': 'string' + }, + }, 'species_types': { 'name': 'string', 'initial_concentration': 'int' @@ -96,10 +103,12 @@ def __init__(self, config=None, core=None): # TODO: Update set/get with optional config params and make logic try: if self.config.get('model_file'): - # Load the single cell model into Basico self.copasi_model_object = load_model(self.config['model_file']) + self.reaction_list = get_reactions(model=self.copasi_model_object).index.tolist() else: - self.copasi_model_object = new_model(name=self.config['name']) + self.copasi_model_object = new_model(name='CopasiProcess Model') + for reaction_name, reaction_spec in self.config['reactions'].items(): + add_reaction(name=reaction_name, scheme=reaction_spec['scheme']) except: raise KeyError('You must enter either a model file or model name') @@ -112,7 +121,7 @@ def __init__(self, config=None, core=None): self.model_parameter_values = get_parameters(model=self.copasi_model_object)['initial_value'].tolist() # Get a list of reactions - self.reaction_list = get_reactions(model=self.copasi_model_object).index.tolist() + # self.reaction_list = get_reactions(model=self.copasi_model_object).index.tolist() # Get a list of compartments self.compartments_list = get_compartments(model=self.copasi_model_object).index.tolist() From e04ce8966c5e8c6840a678bcbe05a467ddf58ca2 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Mon, 26 Feb 2024 17:02:38 -0500 Subject: [PATCH 54/56] chore: added comment for error handling in constructor --- biosimulator_processes/copasi_process.py | 1 + 1 file changed, 1 insertion(+) diff --git a/biosimulator_processes/copasi_process.py b/biosimulator_processes/copasi_process.py index ab6ff6f76..5e5f008b8 100644 --- a/biosimulator_processes/copasi_process.py +++ b/biosimulator_processes/copasi_process.py @@ -110,6 +110,7 @@ def __init__(self, config=None, core=None): for reaction_name, reaction_spec in self.config['reactions'].items(): add_reaction(name=reaction_name, scheme=reaction_spec['scheme']) except: + # TODO: More completely and more gracefully handle these errors raise KeyError('You must enter either a model file or model name') # Get the species (floating only) TODO: add boundary species From 55a648124c44c6ee00c62511cd5570067f13517b Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Mon, 26 Feb 2024 17:04:51 -0500 Subject: [PATCH 55/56] chore: updated release-container script for optional run arg --- scripts/release-container.sh | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/scripts/release-container.sh b/scripts/release-container.sh index 85411101d..89216445f 100644 --- a/scripts/release-container.sh +++ b/scripts/release-container.sh @@ -6,6 +6,8 @@ version="$1" # PLEASE UPDATE THE LATEST VERSION HERE BEFORE RUNNING. CURRENT: 0.0.3 current="0.0.2" +run="$2" + set -e if [ "${version}" == "" ]; then @@ -36,3 +38,7 @@ docker buildx build --platform linux/amd64 \ --push docker tag ghcr.io/biosimulators/biosimulator-processes:"${version}" ghcr.io/biosimulators/biosimulator-processes:latest docker push ghcr.io/biosimulators/biosimulator-processes:latest + +if [ "${run}" == "-r" ]; then + ./scripts/run-container.sh "${version}" +fi From fb6c32ff6eec09ae36fcdf4a6a153afba5401af4 Mon Sep 17 00:00:00 2001 From: alexPatrie Date: Mon, 26 Feb 2024 17:55:21 -0500 Subject: [PATCH 56/56] updated copasi_process --- Dockerfile | 4 ++++ biosimulator_processes/copasi_process.py | 4 ++-- scripts/release-container.sh | 6 ++---- 3 files changed, 8 insertions(+), 6 deletions(-) mode change 100644 => 100755 scripts/release-container.sh diff --git a/Dockerfile b/Dockerfile index 82ee716cb..8e9e57d1d 100644 --- a/Dockerfile +++ b/Dockerfile @@ -58,3 +58,7 @@ CMD ["poetry", "run", "jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-bro # PLEASE NOTE: We do not need to add a USER in the Dockerfile as Singularity will handle # such logic in conversion on the HPC. + +# type imports +# dist +# param scan demo/location diff --git a/biosimulator_processes/copasi_process.py b/biosimulator_processes/copasi_process.py index 5e5f008b8..2dc4435c7 100644 --- a/biosimulator_processes/copasi_process.py +++ b/biosimulator_processes/copasi_process.py @@ -69,8 +69,8 @@ def fetch_biomodel(term: str, index: int = 0): # 1. Add useful config params # 2. Devise use cases # 3. Update constructor conditionally -# 4. Devise parameter scan - +# 4. Devise parameter scan --> create Step() implementation that creates copasi1, 2, 3... + # and provides num iterations and parameter in model_changes class CopasiProcess(Process): # TODO: Update this in constructor diff --git a/scripts/release-container.sh b/scripts/release-container.sh old mode 100644 new mode 100755 index 89216445f..e07d09204 --- a/scripts/release-container.sh +++ b/scripts/release-container.sh @@ -3,13 +3,11 @@ version="$1" -# PLEASE UPDATE THE LATEST VERSION HERE BEFORE RUNNING. CURRENT: 0.0.3 -current="0.0.2" +# PLEASE UPDATE THE LATEST VERSION HERE BEFORE RUNNING. CURRENT: 0.0.4 +current="0.0.3" run="$2" -set -e - if [ "${version}" == "" ]; then echo "You must pass the container version you wish to release as an argument to this script. Exiting." exit 1