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Release from staging to master 2024-03-04 #1549

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Mar 4, 2024
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944efef
Added data_access module as a mandatory field. Fixes #1535
ESapenaVentura Nov 8, 2023
f467ce6
Added data_access module. Fixes #1535
ESapenaVentura Nov 8, 2023
922e89a
Adds DUO codes to indicate data access type
idazucchi Feb 15, 2024
0c21a7c
removes data access as project module
idazucchi Feb 15, 2024
1f274ac
fix typo
idazucchi Feb 15, 2024
db354a9
removes new line
idazucchi Feb 21, 2024
813d74a
renames to data use restriction
idazucchi Feb 23, 2024
773a3fa
makes ontology id required
idazucchi Feb 23, 2024
4682dbe
makes ontology id and label required
idazucchi Feb 27, 2024
4a4c803
enforces the correct pairs of ontology labels and ids
idazucchi Feb 27, 2024
70b5b1d
Merge branch 'esv-managedAccess-Issue1535' of https://github.com/Huma…
idazucchi Feb 27, 2024
1587e07
fixes linting errors
idazucchi Feb 27, 2024
a946c53
treats NCU as a modifier for GRU and moved module to project
idazucchi Feb 28, 2024
5e01ac7
updates log and version for project module
idazucchi Feb 28, 2024
5607b71
updates field names
idazucchi Feb 28, 2024
9ec18e2
data use restriction formatted as enum field with three letter labels
idazucchi Mar 1, 2024
3b5e5bb
Update src/schema_linter.py
idazucchi Mar 1, 2024
1fc0ae4
Apply suggestions from code review
idazucchi Mar 1, 2024
8bd93a3
Merge branch 'staging' of https://github.com/HumanCellAtlas/metadata-…
idazucchi Mar 4, 2024
33e7fb8
Ran release_prepare.py script.
idazucchi Mar 4, 2024
91adce8
Merge pull request #1537 from HumanCellAtlas/esv-managedAccess-Issue1535
idazucchi Mar 4, 2024
3acbd86
Merge branch 'master' of https://github.com/HumanCellAtlas/metadata-s…
idazucchi Mar 4, 2024
fdeda4e
Release from staging to master 2024-03-04.
idazucchi Mar 4, 2024
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5 changes: 4 additions & 1 deletion changelog.md
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
1 change: 1 addition & 0 deletions docs/jsonBrowser/required_fields.md
Original file line number Diff line number Diff line change
Expand Up @@ -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
--- | --- | --- | --- | --- | --- | ---
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1 change: 1 addition & 0 deletions docs/jsonBrowser/type.md
Original file line number Diff line number Diff line change
Expand Up @@ -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._
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7 changes: 7 additions & 0 deletions json_schema/property_migrations.json
Original file line number Diff line number Diff line change
@@ -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",
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15 changes: 14 additions & 1 deletion json_schema/type/project/project.json
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,8 @@
"describedBy",
"schema_type",
"project_core",
"funders"
"funders",
"data_use_restriction"
],
"title": "Project",
"name": "project",
Expand Down Expand Up @@ -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"
}
}
}
4 changes: 2 additions & 2 deletions json_schema/versions.json
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
{
"last_update_date": "2024-02-05T16:10:39Z",
"last_update_date": "2024-03-04T14:00:53Z",
"version_numbers": {
"core": {
"biomaterial": {
Expand Down Expand Up @@ -110,7 +110,7 @@
"process": "9.2.0"
},
"project": {
"project": "17.1.1"
"project": "18.0.0"
},
"protocol": {
"analysis": {
Expand Down
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