docs(guides): add general information for processing sensitive data by svedziok · Pull Request #30 · elixir-cloud-aai/elixir-cloud-aai.github.io

svedziok · 2025-06-24T11:48:55Z

add section for working with sensitive data in the ELIXIR-on-Cloud framework

Summary by Sourcery

Add a new ELIXIR-on-Cloud documentation guide on processing sensitive human data, covering legal frameworks, secure environment definitions, and use cases, and expose it in the site navigation.

Build:

Update mkdocs.yml navigation to include the new guides index and Sensitive Data page

Documentation:

Add docs/guides/index.md as the main entry point for ELIXIR-on-Cloud documentation
Add docs/guides/guide-info/sensitive_data.md with guidance on legal requirements, environments (TEE, SPE, TRE), similarities, differences, and use cases for sensitive data processing

sourcery-ai · 2025-06-24T11:49:00Z

Reviewer's Guide

This PR adds a new section on processing sensitive data to the ELIXIR-on-Cloud documentation by updating the site navigation, creating a guides index page, and introducing a detailed guide covering legal frameworks, secure environments, and use cases.

Class diagram for secure environments in sensitive data processing

classDiagram
    class Environment {
      +Isolation
      +Security
      +Integrity
      +Confidentiality
      +Controlled Access and Authentication
      +Collaboration and Analysis
    }
    class TEE {
      +Secures startup, code, and data during execution
      +Used in secure mobile/cloud environments
    }
    class SPE {
      +Ensures secure data processing and computation
      +Applied in secure analytics/cryptographic computation
    }
    class TRE {
      +Comprehensive secure research environment
      +Emphasizes privacy, governance, compliance
    }
    Environment <|-- TEE
    Environment <|-- SPE
    Environment <|-- TRE

Flow diagram for sensitive data processing use cases

flowchart TD
    A[Researcher needs to process sensitive data]
    B{Where is the data stored?}
    C[Central data]
    D[Federated data]
    E{Where is the data processed?}
    F[Local processing]
    G[Cloud processing]
    H[Data repository]
    I[Cloud platform]
    J[Federated database]
    K[Federated processing]

    A --> B
    B --> C
    B --> D
    C --> E
    D --> E
    E --> F
    E --> G
    C --> E
    D --> E
    C --> F --> H
    C --> G --> I
    D --> F --> J
    D --> G --> K

File-Level Changes

Change	Details	Files
Updated documentation navigation	Added guides index entry under Guides Inserted 'Sensitive Data' sub-section under Information Updated mkdocs.yml nav structure	`mkdocs.yml`
Introduced Guides landing page	Created ELIXIR-on-Cloud overview content Described project goals and GA4GH Cloud Work Stream compliance Outlined documentation scope and best practices	`docs/guides/index.md`
Added processing sensitive data documentation	Outlined GDPR and EHDS legal frameworks Defined and compared TEE, SPE, and TRE environments Detailed use cases with a storage vs. processing matrix	`docs/guides/guide-info/sensitive_data.md`

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sourcery-ai

Hey @svedziok - I've reviewed your changes and they look great!

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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Copilot

Pull Request Overview

This PR introduces a new documentation guide for handling sensitive human data within the ELIXIR-on-Cloud framework and exposes it in the site navigation.

Update mkdocs.yml to add a Guides index and link to the Sensitive Data page
Create docs/guides/index.md as the main entry point for ELIXIR-on-Cloud documentation
Add docs/guides/guide-info/sensitive_data.md covering legal frameworks, secure environments, and use cases

Reviewed Changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated no comments.

File	Description
mkdocs.yml	Inserted new nav entries for the guides index and Sensitive Data page
docs/guides/index.md	Added top-level documentation landing page
docs/guides/guide-info/sensitive_data.md	Added detailed guide on processing sensitive human data

Comments suppressed due to low confidence (1)

mkdocs.yml:85

[nitpick] The navigation entry for the guides index uses only the file path. Consider adding a user-friendly title (e.g., Guides Overview: guides/index.md) so the link displays clearly in the site menu.

      - "guides/index.md"

uniqueg

Thanks, @svedziok - looks good.

Perhaps three minor suggestions:

Perhaps better to name the new section "General" rather than "Information", given that all the other guides also contain "information"?
Throughout the organization, we are using semantic commit messages of 50 chars or less as PR titles. The precise guidelines are here: https://elixir-cloud-aai.github.io/guides/guide-contributor/general-guidelines/#commit-messages Together with squash merging commits from a feature branch, this keeps our commit histories clean, consistent and amenable to release automation when we squash merge commits. See example titles here (admittedly, it's a little boring for a docs page): https://github.com/elixir-cloud-aai/elixir-cloud-aai.github.io/pulls?q=is%3Apr+is%3Aclosed
Note that throughout the repo, only named references are used, and that all of the named references are listed in file includes/references.md. This makes it easier to read the raw files and makes the reuse and maintenance of references easier. Btw, there is also includes/abbreviations.md, where one can define abbreviations centrally. Every time an abbreviation listed in the file is used, there will be a tool tip created in the docs that resolves the abbreviation. Very useful!

Copilot

Pull request overview

Copilot reviewed 5 out of 5 changed files in this pull request and generated 5 comments.

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docs/guides/guide-info/sensitive_data.md

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

svedziok · 2026-01-23T08:03:20Z

@copilot open a new pull request to apply changes based on the comments in this thread

Copilot · 2026-01-23T08:03:29Z

@svedziok I've opened a new pull request, #33, to work on those changes. Once the pull request is ready, I'll request review from you.

Copilot

Pull request overview

Copilot reviewed 5 out of 5 changed files in this pull request and generated 7 comments.

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docs/guides/guide-info/sensitive_data.md

docs/guides/index.md

docs/guides/guide-info/sensitive_data.md

svedziok · 2026-01-23T08:14:26Z

@copilot open a new pull request to apply changes based on the comments in this thread

Copilot · 2026-01-23T08:14:35Z

@svedziok I've opened a new pull request, #34, to work on those changes. Once the pull request is ready, I'll request review from you.

svedziok

done

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: svedziok <17719296+svedziok@users.noreply.github.com>

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>

all requested changes are solved

vschnei

looks good

Sven Twardziok added 3 commits June 24, 2025 13:43

add small summary

77aac34

add sensitive data guideline

98551ae

adapt nav

0635ffc

svedziok requested a review from Copilot June 24, 2025 11:48

svedziok self-assigned this Jun 24, 2025

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Update docs/guides/guide-info/sensitive_data.md

e92ee54

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svedziok requested a review from Copilot June 24, 2025 11:52

Copilot AI reviewed Jun 24, 2025

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svedziok requested a review from uniqueg June 24, 2025 11:55

uniqueg previously requested changes Jul 4, 2025

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svedziok changed the title ~~Processing sensitive data~~ docs(guides): add general information for processing sensitive data Jan 12, 2026

Sven Twardziok added 2 commits January 12, 2026 13:14

change section to general

2255d6c

use abbreviations and referneces

0b47090

svedziok requested a review from uniqueg January 12, 2026 12:26

svedziok requested a review from Copilot January 23, 2026 07:12

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svedziok and others added 5 commits January 23, 2026 08:59

Update docs/guides/guide-info/sensitive_data.md

d9da884

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Update docs/guides/guide-info/sensitive_data.md

1714a78

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Update docs/guides/guide-info/sensitive_data.md

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Update docs/guides/guide-info/sensitive_data.md

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Update docs/guides/guide-info/sensitive_data.md

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Copilot AI mentioned this pull request Jan 23, 2026

docs(guides): apply review feedback to sensitive data guide #33

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svedziok requested a review from Copilot January 23, 2026 08:06

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fix: correct markdown reference syntax and grammar #34

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Copilot AI and others added 2 commits January 23, 2026 09:45

fix: correct markdown reference syntax and grammar (#34)

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Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: svedziok <17719296+svedziok@users.noreply.github.com>

docs(guides): apply review feedback to sensitive data guide (#33)

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svedziok requested review from vschnei and removed request for uniqueg January 26, 2026 07:23

svedziok added 2 commits January 26, 2026 10:03

Merge branch 'main' into processing_sensitive_data

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Merge branch 'main' into processing_sensitive_data

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vschnei approved these changes Jan 26, 2026

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svedziok merged commit f0fd5ad into main Jan 26, 2026
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svedziok deleted the processing_sensitive_data branch January 26, 2026 13:14

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Reviewer's Guide

Class diagram for secure environments in sensitive data processing

Flow diagram for sensitive data processing use cases

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