Added data_access module for managed access data. Fixes #1535

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 
 --- | --- | --- | --- | --- | --- | --- 

docs/jsonBrowser/type.md

@@ -326,6 +326,7 @@ 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._

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",

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 DUO:0000042;DUO:0000046",
+            "example": "GRU"
         }
     }
 }

json_schema/update_log.csv

@@ -1 +1,2 @@
 Schema,Change type,Change message,Version,Date
+type/project/project,major,"Added data_use_restriction field",,

json_schema/versions.json

@@ -137,4 +137,4 @@
             }
         }
     }
-}
+}

src/schema_linter.py

@@ -16,7 +16,7 @@
 
 required_schema_fields = ['$schema', 'description', 'additionalProperties', 'title', 'name', 'type', 'properties']
 
-allowed_schema_fields = ['$schema', 'description', 'additionalProperties', 'required', 'title', 'name', 'type', 'properties', 'definitions', 'dependencies']
+allowed_schema_fields = ['$schema', 'description', 'additionalProperties', 'required', 'title', 'name', 'type', 'properties', 'definitions', 'dependencies','allOf']
 
 # Properties