From de518f1683f1327986e5b315ad0aa6cbb6872c6a Mon Sep 17 00:00:00 2001 From: idazucchi <45209056+idazucchi@users.noreply.github.com> Date: Mon, 4 Mar 2024 15:46:00 +0100 Subject: [PATCH] Release from staging to master 2024-03-04 (#1549) * Added data_access module as a mandatory field. Fixes #1535 * Added data_access module. Fixes #1535 * Adds DUO codes to indicate data access type * removes data access as project module * fix typo * removes new line Co-authored-by: ESapenaVentura <38617863+ESapenaVentura@users.noreply.github.com> * renames to data use restriction * makes ontology id required * makes ontology id and label required * enforces the correct pairs of ontology labels and ids * fixes linting errors * treats NCU as a modifier for GRU and moved module to project * updates log and version for project module * updates field names * data use restriction formatted as enum field with three letter labels * Update src/schema_linter.py Co-authored-by: ESapenaVentura <38617863+ESapenaVentura@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: ESapenaVentura <38617863+ESapenaVentura@users.noreply.github.com> * Ran release_prepare.py script. * Release from staging to master 2024-03-04. --------- Co-authored-by: ESapenaVentura Co-authored-by: ESapenaVentura <38617863+ESapenaVentura@users.noreply.github.com> --- changelog.md | 5 ++++- docs/jsonBrowser/required_fields.md | 1 + docs/jsonBrowser/type.md | 1 + json_schema/property_migrations.json | 7 +++++++ json_schema/type/project/project.json | 15 ++++++++++++++- json_schema/versions.json | 4 ++-- 6 files changed, 29 insertions(+), 4 deletions(-) diff --git a/changelog.md b/changelog.md index 28b2299d..fa9396d6 100644 --- a/changelog.md +++ b/changelog.md @@ -6,9 +6,12 @@ Starting after v5.0.0 release, updates will be declared for schemas independentl and (starting with v4.0.0) this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html). Unreleased changes may be indicated under the `Unreleased` heading. ## [Unreleased](https://github.com/HumanCellAtlas/metadata-schema/tree/staging) - ## [Released](https://github.com/HumanCellAtlas/metadata-schema/) +### [type/project/project.json - v18.0.0] - 2024-03-04 +### Added +Added data_use_restriction field + ### [type/protocol/analysis/analysis_protocol.json - v10.2.0] - 2024-02-05 ### Added Added gene_annotation_version field in analysis_protocol Fixes#1543 diff --git a/docs/jsonBrowser/required_fields.md b/docs/jsonBrowser/required_fields.md index 8889b160..9a69dd26 100644 --- a/docs/jsonBrowser/required_fields.md +++ b/docs/jsonBrowser/required_fields.md @@ -147,6 +147,7 @@ Property name | Description | Type | Object reference? | User friendly name | Al schema_type | The type of the metadata schema entity. | string | | | project | project_core | Core project-level information. | object | [See core project_core](core.md#project-core) | Project core | | funders | Funding source(s) supporting the project. | array | [See module funder](module.md#funder) | Funding source(s) | | +data_use_restriction | Data use restrictions that apply to the project. | string | | Data use restriction | NRES, GRU, GRU-NCU | GRU ### Specimen from organism Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example --- | --- | --- | --- | --- | --- | --- diff --git a/docs/jsonBrowser/type.md b/docs/jsonBrowser/type.md index c6b8b98d..61e78cf6 100644 --- a/docs/jsonBrowser/type.md +++ b/docs/jsonBrowser/type.md @@ -327,6 +327,7 @@ insdc_study_accessions | An International Nucleotide Sequence Database Collabora biostudies_accessions | A BioStudies study accession. | array | no | | BioStudies accession | | S-EXMP1; S-HCAS33 funders | Funding source(s) supporting the project. | array | yes | [See module funder](module.md#funder) | Funding source(s) | | estimated_cell_count | An estimated number of cells in this project | integer | no | | Estimated cell count | | 10000; 2100000 +data_use_restriction | Data use restrictions that apply to the project. | string | yes | | Data use restriction | NRES, GRU, GRU-NCU | GRU ## Specimen from organism _Information about the specimen that was collected from the donor organism._ diff --git a/json_schema/property_migrations.json b/json_schema/property_migrations.json index 9e94837b..fbdfbdd2 100644 --- a/json_schema/property_migrations.json +++ b/json_schema/property_migrations.json @@ -1,5 +1,12 @@ { "migrations": [ + { + "source_schema": "project", + "property": "data_use_restriction", + "effective_from": "18.0.0", + "reason": "Data access is now recorded as a mandatory field", + "type": "new required property" + }, { "source_schema": "cell_line", "property": "timecourse", diff --git a/json_schema/type/project/project.json b/json_schema/type/project/project.json index 4213b4aa..895d99c7 100644 --- a/json_schema/type/project/project.json +++ b/json_schema/type/project/project.json @@ -6,7 +6,8 @@ "describedBy", "schema_type", "project_core", - "funders" + "funders", + "data_use_restriction" ], "title": "Project", "name": "project", @@ -164,6 +165,18 @@ "type": "integer", "example": "10000; 2100000", "user_friendly": "Estimated cell count" + }, + "data_use_restriction": { + "description": "Data use restrictions that apply to the project.", + "type": "string", + "enum": [ + "NRES", + "GRU", + "GRU-NCU" + ], + "user_friendly": "Data use restriction", + "guidelines": "Must be one of: NRES, GRU, GRU-NCU. The use restriction codes are based on the DUO ontology where NRES corresponds to DUO:0000004, GRU corresponds to DUO:0000042, GRU-NCU corresponds to a combination of DUO:0000042 and DUO:0000046", + "example": "GRU" } } } diff --git a/json_schema/versions.json b/json_schema/versions.json index 8f47b78e..9cc9a4d8 100644 --- a/json_schema/versions.json +++ b/json_schema/versions.json @@ -1,5 +1,5 @@ { - "last_update_date": "2024-02-05T16:10:39Z", + "last_update_date": "2024-03-04T14:00:53Z", "version_numbers": { "core": { "biomaterial": { @@ -110,7 +110,7 @@ "process": "9.2.0" }, "project": { - "project": "17.1.1" + "project": "18.0.0" }, "protocol": { "analysis": {