Skip to content

Chapter 11: two points from running a national node #130

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
adrianfako wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Chapter 11: two points from running a national node #130

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
15 changes: 15 additions & 0 deletions docs/arc42/11-risks-and-technical-debt/index.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,9 @@ governance_refs:
- "V.1.3"
- "VI.1.3"
- "VI.1.5"
- "VII.2.1"
- "VII.2.2"
- "VII.2.3"
- "VII.3.1"
- "VII.3.3"
- "VII.4.3"
Expand Down Expand Up @@ -94,6 +97,12 @@ The governance doesn't answer these questions, but the architecture needs an ans
- **Why it matters:** the catalogue and access request management must know the type of every dataset in a request.
- **Tracked in:** [issue #105](https://github.com/GenomicDataInfrastructure/system-architecture/issues/105); related to [issue #85](https://github.com/GenomicDataInfrastructure/system-architecture/issues/85).

#### Whether the filter list of subject-level discovery is public {#discovery-filter-list}

- **What is open:** a subject-level discovery endpoint publishes the list of filters it accepts: ontology terms such as phenotypes and diagnoses. In Beacon v2, this is the `/filtering_terms` endpoint. The list is built from the data the node holds, so a rare term in it tells the [User](/glossary#user) that at least one record has that term. The governance asks for a <Acronym id="DPIA" /> of subject-level discovery that considers the results returned to the User <GovRef id="VII.2.2" />, and for a search engine with built-in safeguards <GovRef id="VII.2.3" />. It doesn't say whether the filter list is metadata, like the catalogue, or a discovery result under these safeguards.
- **Why it matters:** Beacon network clients read the list to learn what a node can be asked. A node that withholds it can't be queried without help. A node that publishes it shows the presence of a term below any count threshold its DPIA sets. The Beacon v2 reference implementation applies the same limit to the list as to the records: a node that returns counts only publishes an empty list, and fails the Beacon v2 verifier.
- **Tracked in:** [issue #128](https://github.com/GenomicDataInfrastructure/system-architecture/issues/128).

#### Who chooses the type of a dataset {#dataset-type-choice}

- **What is open:** for the access decision, the governance describes two scenarios: a decision at national level, for [1+MG compliant datasets](/concepts/dataset-types), or by the Genome EDIC, for 1+MG cohort datasets <GovRef id="II.1" />. Who chooses between them is settled in part: each Genome EDIC Member Country decides on "a national strategy for the responsibility of downstream data disclosure" and nominates, where applicable, the 1+MG Data Holders in the country <GovRef id="VI.1.3" />. It does so before any data are included, because the choice becomes part of the consent for inclusion <GovRef id="VI.1.5" />. The governance doesn't say at which level the choice is made: for the whole country, per [1+MG Data Provider](/glossary#1mg-data-provider), or per dataset. Nor does it say whether "where applicable" lets a country nominate no 1+MG Data Holder and make all its data available as 1+MG cohort data. [ADR-0002](/decisions/0002-disclosure-paths-per-dataset) proposes that the Member Country chooses, on the basis of VI.1.3, and leaves the level open.
Expand Down Expand Up @@ -122,6 +131,12 @@ Work outside this architecture that it depends on.
- **Why it matters:** until then, the system offers only externally governed datasets. [ADR-0002](/decisions/0002-disclosure-paths-per-dataset) proposes to add the other two types in later steps.
- **Tracked in:** [issue #116](https://github.com/GenomicDataInfrastructure/system-architecture/issues/116).

#### The Starter Kit FAIR Data Point uses its own metadata schemas {#starter-kit-fdp-schemas}

- **What is open:** the national catalogue of the <Acronym id="GDI" /> Starter Kit <Cite id="gdi-starter-kit" /> runs the stock FAIR Data Point. It loads the FAIR Data Point's own metadata schemas (version 1.0.0), not the GDI metadata shapes (`gdi-metadata`, version 1.1). The two disagree. The stock schema accepts the media type of a distribution only as text, and rejects the registered media type as a web address, which DCAT-AP 3.0 requires. A node on the defaults can't publish conformant distributions until it loads the GDI shapes itself.
- **Why it matters:** the national catalogues feed the central data catalogue, which must be interoperable with the EU dataset catalogue of the EHDS <GovRef id="VII.2.1" />. If each node fixes this by itself, the nodes run different schema versions.
- **Tracked in:** [issue #129](https://github.com/GenomicDataInfrastructure/system-architecture/issues/129).

## Risks {#risks}

_None recorded yet._ A risk is something that could go wrong and harm the system or its users: for example, a Member Country not ready in time. Each risk gets an entry here, in the format of the [page recipe](/handbook/recipes#risks-and-technical-debt).
Expand Down
Loading