metabolomics

This repository, in collaboration with mtbls-service, provides functionalities to interact with MetaboLights, Metabolomics Workbench and Metabobank study data.

• MetaboLights service: Provides user login functionality, detailed study and assays information retrieval, and downloading study-related result files via its API.
• Metabolomics Workbench service: Allows viewing of study details and its assays retrieved via its API.
• Metabobank service: Integrates with its API for retrieving and downloading study-related files.

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MetaboLights Service

General Features

• Retrieval of Study Metadata:
  Retrieve metadata for studies, including the study title and description.

• Assay Data Extraction:
  Access detailed assay information, including:

  • Assay Number
  • Measurement
  • Technology
  • Platform
  • File Name
  • Reported Metabolite Names
  • A list of Raw Data File Names used in the assay

• Result Files Access (Authenticated):
  Upon successful authentication via the login form, you gain access to additional study result files (displayed in the Result Files section) that can be downloaded through provided links.

Endpoints

• Main Page:
  /metabolomics
  The main page where you can access the study selection and authentication form.

• MetaboLights Study Details:
  /metabolights_get_study_details_info/<study_id>
  A page that displays detailed study data for a given MetaboLights study, including metadata, assay data, and (if authenticated) result files.

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Metabolomics Workbench Service

General Features

• Study Metadata Retrieval:
  Retrieve key metadata for studies, including:

  • Study Title
  • Species
  • Institute
  • Analysis Type
  • Number of Samples

• Assay Data Extraction:
  Access detailed assay information for each study, including:

  • Assay Number
  • Analysis Id
  • Analysis Summary
  • Reported Metabolite Name
  • Refmet Name

Endpoints

• Metabolomics Workbench Study Details:
  /metabolomics_workbench_get_study_details_info/<study_id>
  A page that displays detailed study data for a given Metabolomics Workbench study, including study metadata and assay data.

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Metabobank Service

General Features

• File Listings:
  Access detailed study file information, including:
  • Results Files: A list of result files, which can be downloaded via provided links.
  • Raw Files: A list of raw data files used in the study.

Endpoints

• Metabobank Study Details:
  /metabobank_get_study_details_info/<study_id>
  A page that displays detailed study data for a given Metabobank study, including the lists of results files and raw files.

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Running the Project

Install dependencies:

pip install -r requirements.txt

Using the Flask CLI:

• Standard Run:

export FLASK_APP=api.py && flask run

This starts the application without explicitly enabling development features.

• Development Mode:

export FLASK_APP=api.py && export FLASK_ENV=development && flask run

By setting FLASK_ENV=development, Flask:

• Enables debug mode (auto-reloading on code changes)
• Provides detailed error messages
• Automatically re-imports modules when changes are detected

The service will be available at: http://127.0.0.1:5000/metabolomics

Running in Docker:

docker build -t metabolomics-app .
docker run -p 5000:5000 metabolomics-app

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Unit Tests (made by ChatGPT o3-mini)

cd ./tests && python3 -m unittest test_app.py