From 85bb7fdb5779e2ff7d1a803c4b0651ad5d061812 Mon Sep 17 00:00:00 2001 From: Vilem Ded Date: Fri, 3 Sep 2021 12:00:18 +0200 Subject: [PATCH] bump version of JSON schemas to 0.0.3 --- core/fixtures/json_schemas/elu-core.json | 2 +- core/fixtures/json_schemas/elu-dataset.json | 114 +++++++++--------- .../json_schemas/elu-institution.json | 4 +- core/fixtures/json_schemas/elu-project.json | 4 +- core/fixtures/json_schemas/elu-study.json | 4 +- .../fixtures/json_schemas/elu-submission.json | 8 +- elixir_daisy/settings.py | 2 +- 7 files changed, 67 insertions(+), 71 deletions(-) diff --git a/core/fixtures/json_schemas/elu-core.json b/core/fixtures/json_schemas/elu-core.json index cd901e93..783c0e35 100644 --- a/core/fixtures/json_schemas/elu-core.json +++ b/core/fixtures/json_schemas/elu-core.json @@ -1,5 +1,5 @@ { - "$id": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.2/schemas/elu-core.json", + "$id": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.3/schemas/elu-core.json", "title": "ELIXIR Luxembourg Core json schema", "description": "Schema containing core attributes for any json serialisable ELIXIR Luxembourg record.", "$schema": "http://json-schema.org/draft-04/schema#", diff --git a/core/fixtures/json_schemas/elu-dataset.json b/core/fixtures/json_schemas/elu-dataset.json index 3a8464e8..9884bd44 100644 --- a/core/fixtures/json_schemas/elu-dataset.json +++ b/core/fixtures/json_schemas/elu-dataset.json @@ -1,12 +1,12 @@ { - "$id": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.2/schemas/elu-dataset.json", + "$id": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.3/schemas/elu-dataset.json", "title": "ELIXIR Luxembourg Datasets Schema", "description": "A JSON Schema for describing biomedical research Datasets.", "$schema": "http://json-schema.org/draft-04/schema#", "type": "object", "allOf": [ { - "$ref": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.2/schemas/elu-core.json" + "$ref": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.3/schemas/elu-core.json" } ], "properties": { @@ -217,64 +217,60 @@ "Other_Phenotype_data", "Other" ] - }, - "data_type_notes": { - "type": "string" - }, - "access_category": { - "type": "string", - "enum": [ - "open-access", - "controlled-access", - "registered-access" - ] - }, - "subjects_category": { - "type": "array", - "items": { - "type": "string", - "enum": [ - "cases", - "controls", - "cases_and_controls" - ] - } - }, - "de_identification": { - "type": "string", - "enum": [ - "anonymized", - "pseudonymized" - ] - }, - "consent_status": { - "type": "string", - "enum": [ - "heterogeneous", - "homogeneous" - ] - }, - "consent_status_description": { - "type": "string" - }, - "has_special_subjects": { - "type": "boolean" - }, - "special_subjects_description": { - "type": "string" - }, - "embargo_date": { - "type": "string", - "pattern": "^[0-9]{4}-[0-9]{2}-[0-9]{2}$" - }, - "storage_end_date": { - "type": "string", - "pattern": "^[0-9]{4}-[0-9]{2}-[0-9]{2}$" - }, - "storage_duration_criteria": { - "type": "string", - "pattern": "^[0-9]{4}-[0-9]{2}-[0-9]{2}$" } + }, + "data_type_notes": { + "type": "string" + }, + "access_category": { + "type": "string", + "enum": [ + "open_access", + "controlled_access", + "registered_access" + ] + }, + "subjects_category": { + "type": "string", + "enum": [ + "cases", + "controls", + "cases_and_controls" + ] + }, + "de_identification": { + "type": "string", + "enum": [ + "anonymization", + "pseudonymization" + ] + }, + "consent_status": { + "type": "string", + "enum": [ + "heterogeneous", + "homogeneous" + ] + }, + "consent_status_description": { + "type": "string" + }, + "has_special_subjects": { + "type": "boolean" + }, + "special_subjects_description": { + "type": "string" + }, + "embargo_date": { + "type": ["string","null"], + "pattern": "^[0-9]{4}-[0-9]{2}-[0-9]{2}$" + }, + "storage_end_date": { + "type": "string", + "pattern": "^[0-9]{4}-[0-9]{2}-[0-9]{2}$" + }, + "storage_duration_criteria": { + "type": ["string", "null"] } } } diff --git a/core/fixtures/json_schemas/elu-institution.json b/core/fixtures/json_schemas/elu-institution.json index 53e1fa81..5a48afa5 100644 --- a/core/fixtures/json_schemas/elu-institution.json +++ b/core/fixtures/json_schemas/elu-institution.json @@ -1,5 +1,5 @@ { - "$id": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.2/schemas/elu-institution.json", + "$id": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.3/schemas/elu-institution.json", "title": "ELIXIR Luxembourg Partner Schema", "description": "A JSON Schema for describing partners institutes.", "$schema": "http://json-schema.org/draft-04/schema#", @@ -12,7 +12,7 @@ "type": "object", "allOf": [ { - "$ref": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.2/schemas/elu-core.json" + "$ref": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.3/schemas/elu-core.json" } ], "properties": { diff --git a/core/fixtures/json_schemas/elu-project.json b/core/fixtures/json_schemas/elu-project.json index fbcd531c..317d498a 100644 --- a/core/fixtures/json_schemas/elu-project.json +++ b/core/fixtures/json_schemas/elu-project.json @@ -1,5 +1,5 @@ { - "$id": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.2/schemas/elu-project.json", + "$id": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.3/schemas/elu-project.json", "title": "ELIXIR Luxembourg Projects Schema", "description": "A JSON Schema for describing biomedical research Projects.", "$schema": "http://json-schema.org/draft-04/schema#", @@ -12,7 +12,7 @@ "type": "object", "allOf": [ { - "$ref": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.2/schemas/elu-study.json" + "$ref": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.3/schemas/elu-study.json" } ], "properties": { diff --git a/core/fixtures/json_schemas/elu-study.json b/core/fixtures/json_schemas/elu-study.json index 7ad05e2c..c6a972a0 100644 --- a/core/fixtures/json_schemas/elu-study.json +++ b/core/fixtures/json_schemas/elu-study.json @@ -1,5 +1,5 @@ { - "$id": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.2/schemas/elu-study.json", + "$id": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.3/schemas/elu-study.json", "title": "Study-Project Schema", "description": "A JSON Schema for describing Studies-Projects within the ELIXIR Data Submission System.", "$schema": "http://json-schema.org/draft-04/schema#", @@ -14,7 +14,7 @@ "type": "object", "allOf": [ { - "$ref": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.2/schemas/elu-core.json" + "$ref": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.3/schemas/elu-core.json" } ], "properties": { diff --git a/core/fixtures/json_schemas/elu-submission.json b/core/fixtures/json_schemas/elu-submission.json index 634d6382..33cb4e57 100644 --- a/core/fixtures/json_schemas/elu-submission.json +++ b/core/fixtures/json_schemas/elu-submission.json @@ -1,5 +1,5 @@ { - "$id": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.2/schemas/elu-submission.json", + "$id": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.3/schemas/elu-submission.json", "title": "Submission Schema", "description": "A JSON Schema for describing submissions in the ELIXIR Data Submission System a.k.a. DISH.", "$schema": "http://json-schema.org/draft-04/schema#", @@ -14,7 +14,7 @@ "type": "object", "allOf": [ { - "$ref": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.2/schemas/elu-core.json" + "$ref": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.3/schemas/elu-core.json" } ], "properties": { @@ -24,7 +24,7 @@ "type": "object", "allOf": [ { - "$ref": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.2/schemas/elu-study.json" + "$ref": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.3/schemas/elu-study.json" } ] }, @@ -34,7 +34,7 @@ "type": "object", "allOf": [ { - "$ref": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.2/schemas/elu-dataset.json" + "$ref": "https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.3/schemas/elu-dataset.json" } ] } diff --git a/elixir_daisy/settings.py b/elixir_daisy/settings.py index 9d6172bb..caf3fd34 100644 --- a/elixir_daisy/settings.py +++ b/elixir_daisy/settings.py @@ -317,7 +317,7 @@ EXPLORER_DEFAULT_CONNECTION = 'default' # JSON schemas used for validation on import -IMPORT_JSON_SCHEMAS_URI = 'https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.2/schemas/' +IMPORT_JSON_SCHEMAS_URI = 'https://raw.githubusercontent.com/elixir-luxembourg/json-schemas/v0.0.3/schemas/' IMPORT_JSON_SCHEMAS_DIR = os.path.join(BASE_DIR, 'core', 'fixtures', 'json_schemas') # REMS (http://rems2docs.rahtiapp.fi/) Integration