Data Ingestion Pipeline Design

---
name: data-ingestion-pipeline-design
description: Use when when building a platform that must accept raw MS data files (e.g., .raw, .mzML, .mzXML) from instrument runs or external sources as the first stage of an automated omics workflow.
license: CC-BY-4.0
metadata:
  edam_operation: http://edamontology.org/operation_3443
  edam_topics:
  - http://edamontology.org/topic_0121
  - http://edamontology.org/topic_3520
  tools:
  - Python
  - JavaScript
  - HTML
  - Raw File Uploader
  - Django
  - MSConnect
  techniques:
  - mass-spectrometry
derived_from:
- doi: 10.1021/acs.jproteome.4c00854
  title: MSConnect
evidence_spans:
- The platform is built with Python, Django, JavaScript, and HTML
claims: []
provenance:
  collection: https://w3id.org/holobiomicslab/asb-skill/collection/metabolomics/v2
  assembled_by: scripts/collect_metabolomics_collection.py
  sources:
  - build: coll_msconnect_cq
    doi: 10.1021/acs.jproteome.4c00854
    title: MSConnect
  dedup_kept_from: coll_msconnect_cq
schema_version: 0.2.0
attribution:
  generator: AgenticScienceBuilder
  original_doi: 10.1021/acs.jproteome.4c00854
  all_source_dois:
  - 10.1021/acs.jproteome.4c00854
  zenodo_doi: 10.5281/zenodo.20794027
  curators: []
  promoter: Louis-Félix Nothias
  sponsor: CNRS & Université Côte d'Azur
---

# data-ingestion-pipeline-design

## Summary

Design and implement an automated data ingestion pipeline that accepts raw mass spectrometry files, validates their format and integrity, persists them in a managed repository, and tracks ingestion outcomes. This skill is essential for establishing the entry point of high-throughput MS-based omics workflows where data collection must flow seamlessly into downstream processing and management layers.

## When to use

When building a platform that must accept raw MS data files (e.g., .raw, .mzML, .mzXML) from instrument runs or external sources as the first stage of an automated omics workflow. Use this skill when you need to enforce data quality constraints (file format, size, integrity), route validated files to persistent storage, and maintain audit trails of ingestion success/failure for compliance and troubleshooting.

## When NOT to use

- Files have already been validated and stored in the repository — skip to data management layer
- Input is a processed feature table or quantitative result rather than raw instrumental output
- The workflow does not require persistent storage or audit trails (e.g., one-off exploratory analysis)

## Inputs

- Raw mass spectrometry files (.raw, .mzML, .mzXML formats)
- File upload HTTP requests with multipart form data
- File format specification and validation schema

## Outputs

- Persisted raw MS files in designated repository
- File metadata records (filename, upload timestamp, file hash, status)
- Ingestion status logs (success/failure/pending entries)
- Audit trail of upload events with timestamps and outcome codes

## How to apply

Design a modular HTTP/HTML form-based uploader using Python and Django that accepts raw MS files and immediately validates them against expected formats (.raw, .mzML, .mzXML) and size/integrity constraints. Implement file persistence logic that stores validated files in a designated repository accessible to downstream data management and processing layers. Integrate upload status tracking (success/failure/pending) with comprehensive logging to report ingestion outcomes and enable operators to identify failed uploads. Configure the storage backend to maintain file metadata alongside the raw data so that the data management layer can reference and retrieve files programmatically. Test the complete pipeline end-to-end using representative MS raw files from your instrumentation to verify that files are correctly stored, metadata is accurately recorded, and status tracking is reliable.

## Related tools

- **Raw File Uploader** (Third-party uploader component that integrates with MSConnect to provide file upload UI and initial validation; receives raw MS files and metadata annotations from users) — https://github.com/RTKlab-BYU/Raw_File_Uploader
- **Django** (Web framework used to build the HTTP/HTML form interface and implement file validation and status tracking logic)
- **Python** (Core language for implementing file validation logic, persistence handlers, and metadata recording)
- **MSConnect** (Parent platform that integrates the Raw File Uploader as the data collection entry point, connecting ingestion to data management, processing, and visualization layers) — https://github.com/RTKlab-BYU/MSConnect

## Evaluation signals

- All uploaded raw MS files (.raw, .mzML, .mzXML) are correctly stored in the designated repository with no file corruption or truncation
- File metadata (filename, upload timestamp, file hash) is accurately recorded and retrievable by downstream data management modules
- Ingestion status logs record all upload events with appropriate success/failure/pending codes and human-readable error messages for failed uploads
- Files rejected for format or integrity violations are logged with specific failure reasons and do not enter the repository
- End-to-end test confirms that persisted files and their metadata are accessible to the data processing layer without additional retrieval or validation steps

## Limitations

- Raw File Uploader is implemented in C# with .NET 4.5.1 for Windows platform only; cross-platform support requires alternative tooling or containerization
- Pipeline design does not include automatic format conversion; if vendor-specific formats (e.g., Thermo .raw) require normalization to mzML/mzXML, that must be handled as a separate post-ingestion step
- File size and storage constraints are not specified in the workflow; operators must configure repository capacity and upload quotas independently
- The article and README do not specify supported authentication/authorization mechanisms, so multi-user or role-based access control design is left to implementation

## Evidence

- [other] raw MS file formats (.raw, .mzML, .mzXML) and size/integrity constraints: "Implement file validation logic to verify raw MS file formats (e.g., .raw, .mzML, .mzXML) and enforce size/integrity constraints."
- [other] file storage backend persistence and data management layer integration: "Configure file storage backend to persist uploaded raw files in a designated repository accessible to the MSConnect data management layer."
- [other] upload status tracking and logging for ingestion outcomes: "Integrate upload status tracking (success/failure/pending) and logging to report ingestion outcomes."
- [readme] Python, Django, and form-based interface design: "The platform is built with Python, Django, JavaScript, and HTML"
- [readme] Raw File Uploader as third-party integration component: "MSConnect works with [Raw file uploader](https://github.com/RTKlab-BYU/Raw_File_Uploader)"
- [readme] streamlined entry point for data collection in automated workflows: "streamlines the entire process from data collection, data management, data processing and to data visualization by integrating and supporting various third-party tools"