[Feature] Immunopeptidomic Measurement and Data Registration

[Steffengreiner]

Feature ID

FEAT-IMMUNOPEPTIDOMICS-MEASUREMENT

Requirement IDs

MEASUREMENT-R-01, MEASUREMENT-R-02, MEASUREMENT-R-03, MEASUREMENT-R-04, DATA-R-01, DATA-R-02, DATA-R-03

Description

The Data Manager shall support the full lifecycle of immunopeptidomics measurements — from metadata registration and editing, through deletion with data-integrity guards, to raw data upload, visualisation, and download. The capability is delivered through domain-specific Excel templates for registration and editing, a dedicated measurement tab with domain-specific columns and filtering, a dedicated raw data tab, and integration with the data scanner (SFTP upload) and data download server (wget/cURL download) systems. Immunopeptidomics measurements are assigned a unique IP- prefixed measurement code and stored in a dedicated OpenBIS object type, keeping them distinct from NGS and proteomics datasets.

Scope / Boundaries

In scope:

• Immunopeptidomics measurement registration via domain-specific Excel template
• Immunopeptidomics measurement editing via pre-filled Excel template
• Immunopeptidomics measurement deletion with attached-dataset guard
• Immunopeptidomics measurement view (dedicated tab, domain columns, filtering)
• Immunopeptidomics raw dataset view (dedicated tab, dataset info, filtering)
• Raw data upload integration with the data scanner (SFTP, IP- prefix recognition)
• Raw data download integration with the data download server (standard protocols)
• OpenBIS object type extension for immunopeptidomics measurements

Out of scope:

• Raw data processing or analysis pipelines
• Real-time instrument integration
• Deletion of attached raw datasets (a prerequisite for measurement deletion, but not part of this Feature)
• Changes to NGS or proteomics measurement workflows

Stories

• [Story] FEAT-IP-MEAS-01 Register Immunopeptidomics Measurements via Excel Template #1428 Register Immunopeptidomics Measurements via Excel Template
• [Story] FEAT-IP-MEAS-02 Edit Immunopeptidomics Measurements via Pre-filled Excel Template #1429 Edit Immunopeptidomics Measurements via Pre-filled Excel Template
• [Story] FEAT-IP-MEAS-03 Delete Immunopeptidomics Measurements #1430 Delete Immunopeptidomics Measurements
• [Story] FEAT-IP-MEAS-04 View Immunopeptidomics Measurements in Measurement View #1431 View Immunopeptidomics Measurements in Measurement View
• [Story] FEAT-IP-MEAS-05 View and Access Immunopeptidomics Raw Datasets #1432 View and Access Immunopeptidomics Raw Datasets

Tasks

Story #1428

• [Task] Registration of Immunopeptidomics Measurements #1413 Registration of Immunopeptidomics Measurements
• [Task] Integration Test — Register Immunopeptidomics Measurements #1437 Integration Test — Register Immunopeptidomics Measurements

Story #1429

• [Task] Editing of Immunopeptidomics Measurements #1414 Editing of Immunopeptidomics Measurements
• [Task] Integration Test — Edit Immunopeptidomics Measurements #1438 Integration Test — Edit Immunopeptidomics Measurements

Story #1430

• [Task] Deletion of Immunopeptidomics Measurements #1415 Deletion of Immunopeptidomics Measurements
• [Task] Integration Test — Delete Immunopeptidomics Measurements #1439 Integration Test — Delete Immunopeptidomics Measurements

Story #1431

• [Task] Show the Immunopeptidomics Measurements in the Measurement View #1417 Show the Immunopeptidomics Measurements in the Measurement View
• [Task] Integration Test — View Immunopeptidomics Measurements #1440 Integration Test — View Immunopeptidomics Measurements

Story #1432

• [Task] Show Immunopeptidomic datasets within the raw data view #1416 Show Immunopeptidomic datasets within the raw data view
• [Task] Integration Test — View and Access Immunopeptidomics Raw Datasets #1441 Integration Test — View and Access Immunopeptidomics Raw Datasets

Note: Per project governance, each Story owns its own integration-test Task. The previous monolithic IT Task (#1434) has been superseded by the per-Story IT Tasks above.

Notes & Context

• The existing NGS/proteomics parallel-class pattern is replicated for immunopeptidomics (Path A). A future unified mass-spectrometry read model may be introduced via SQL views without schema migration.
• OpenBIS requires a new object type Q_IMMUNOPEPTIDOMICS_MEASUREMENT.
• The data-scanner and data-download-server repositories host the upload/download backend implementations; the Data Manager provides the measurement metadata and user-facing views.