Update to BcoValidator.load_schema

biocompute/services.py

@@ -50,12 +50,16 @@ def load_schema(schema_uri):
         Returns:
         - dict: The loaded JSON schema.
         """
-
-        if schema_uri == \
-          "https://w3id.org/ieee/ieee-2791-schema/2791object.json":
-            return jsonref.load_uri(
-                f"file://{BASE_DIR}/config/IEEE/2791object.json"
-            )
+        schema_mapping = {
+            "https://w3id.org/ieee/ieee-2791-schema/2791object.json": f"{BASE_DIR}/config/schemas/2791object.json",
+            "https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.1.0/dataset_extension.json": f"{BASE_DIR}/config/schemas/dataset_extension.json",
+            "https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.1.0/fhir_extension.json": f"{BASE_DIR}/config/schemas/fhir_extension.json",
+            "https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.1.0/galaxy_extension.json": f"{BASE_DIR}/config/schemas/galaxy_extension.json",
+            "https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.1.0/license_extension.json": f"{BASE_DIR}/config/schemas/license_extension.json",
+            "https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.1.0/scm_extension.json": f"{BASE_DIR}/config/schemas/scm_extension.json"
+        }
+        if schema_uri in schema_mapping:
+            return jsonref.load_uri(f"file://{schema_mapping[schema_uri]}")
         try:
             return jsonref.load_uri(schema_uri)
         except (JSONDecodeError, TypeError, RequestsConnectionError) as e:

config/schemas/dataset_extension.json

@@ -0,0 +1,78 @@
+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "$id": "http://www.w3id.org/biocompute/extension_domain/1.1.0/dataset/dataset_extension.json",
+  "title": "dataset_extension",
+  "type": "object",
+  "description": "The external references extension to list additional licenses and dataset catagories for a dataset BCO (dsBCO).",
+  "required": ["dataset_extension", "extension_schema"],
+  "additionalProperties": false,
+  "properties": {
+    "dataset_extension": {
+      "type": "object",
+      "additionalProperties": false,
+      "required": ["dataset_categories"],
+      "properties": {
+        "additional_license": {
+          "type": "object",
+          "description": "The additional license property contains the details about the licenses applied to the dataset and the script or tool/software used to process the given dataset.",
+          "additionalProperties": false,
+          "properties": {
+            "data_license": {
+              "title": "data_license",
+              "type": "string",
+              "description": "The license applied to the data or the dataset by the author",
+              "examples": ["https://creativecommons.org/licenses/by/4.0/"]
+            },
+            "script_license": {
+              "title": "script_license",
+              "type": "string",
+              "description": "The license applied to the computational script or the tool/software developed to process (parse, QC, align) the input dataset for a final output dataset.",
+              "examples": ["https://www.gnu.org/licenses/gpl-3.0.en.html"]
+            }
+          }
+        },
+        "dataset_categories": {
+          "title": "dataset_categories",
+          "type": "array",
+          "description": "Dataset categories describe and provide more information about the dataset which can be used to classify, group, sort and filter datasets.",
+          "items": {
+            "required": ["category_value", "category_name"],
+            "additionalProperties": false,
+            "properties": {
+              "category_value": {
+                "type": "string",
+                "title": "category_value",
+                "description": "An explanation about the purpose of this instance.",
+                "examples": ["Homo sapiens"]
+              },
+              "category_name": {
+                "type": "string",
+                "title": "category_name",
+                "description": "An explanation about the purpose of this instance.",
+                "enum": [
+                  "species",
+                  "molecule",
+                  "tag",
+                  "tags",
+                  "priority",
+                  "file_type",
+                  "status",
+                  "scope"
+                ]
+              }
+            }
+          }
+        }
+      }
+    },
+    "extension_schema": {
+      "title": "extension_schema",
+      "type": "string",
+      "format": "uri",
+      "description": "The schema applied to the extension object",
+      "examples": [
+        "http://www.w3id.org/biocompute/extension_domain/example.json"
+      ]
+    }
+  }
+}

config/schemas/fhir_extension.json

@@ -0,0 +1,57 @@
+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "$id": "https://w3id.org/biocompute/extension_domain/1.1.0/fhir/fhir_extension.json",
+  "title": "fhir_extension",
+  "type": "object",
+  "description": "The external references extension to FHIR resource",
+  "required": ["fhir_extension", "extension_schema"],
+  "additionalProperties": false,
+  "properties": {
+    "extension_schema": {
+      "title": "extension_schema",
+      "type": "string",
+      "format": "uri",
+      "description": "The schema applied to the extension object",
+      "examples": [
+        "http://www.w3id.org/biocompute/extension_domain/example.json"
+      ]
+    },
+    "fhir_extension": {
+      "title": "",
+      "type": "array",
+      "decription": "",
+      "items": {
+        "required": ["fhir_endpoint", "fhir_version", "fhir_resources"],
+        "properties": {
+          "fhir_endpoint": {
+            "type": "string",
+            "description": "Base URI of FHIR server where the resources are stored",
+            "examples": ["http://fhirtest.uhn.ca/baseDstu3"],
+            "format": "uri"
+          },
+          "fhir_version": {
+            "type": "string",
+            "description": "FHIR version of the server endpoint"
+          },
+          "fhir_resources": {
+            "type": "array",
+            "items": {
+              "type": "object",
+              "required": ["fhir_resource", "fhir_id"],
+              "properties": {
+                "fhir_resource": {
+                  "type": "string",
+                  "description": "Type of FHIR resource used"
+                },
+                "fhir_id": {
+                  "type": "string",
+                  "description": "Server-specific identifier string"
+                }
+              }
+            }
+          }
+        }
+      }
+    }
+  }
+}

config/schemas/galaxy_extension.json

@@ -0,0 +1,36 @@
+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "$id": "http://www.w3id.org/biocompute/extension_domain/1.1.0/galaxy/galaxy_extension.json",
+  "title": "galaxy_extension",
+  "type": "object",
+  "description": "The external references **example** extension for a Galaxy BCO.",
+  "required": ["galaxy_extension", "extension_schema"],
+  "additionalProperties": false,
+  "properties": {
+    "extension_schema": {
+      "type": "string",
+      "format": "uri",
+      "description": "The schema applied to the extension object",
+      "examples": [
+        "http://www.w3id.org/biocompute/extension_domain/example.json"
+      ]
+    },
+    "galaxy_extension": {
+      "type": "object",
+      "required": ["galaxy_url", "galaxy_version"],
+      "properties": {
+        "galaxy_url": {
+          "type": "string",
+          "description": "The base url for the galaxy instance used to create the BioCompute Object.",
+          "examples": ["https://galaxy.aws.biochemistry.gwu.edu/"],
+          "format": "uri"
+        },
+        "galaxy_version": {
+          "type": "string",
+          "description": "The specific version of the Galaxy software used to generate the BioCompute Object.",
+          "examples": ["20.01"]
+        }
+      }
+    }
+  }
+}

config/schemas/license_extension.json

@@ -0,0 +1,34 @@
+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "$id": "http://www.w3id.org/biocompute/extension_domain/1.1.0/license/license_extension.json",
+  "type": "object",
+  "description": "The extension to add additional licenses.",
+  "required": ["licence_extension", "extension_schema"],
+  "additionalProperties": false,
+  "properties": {
+    "extension_schema": {
+      "title": "extension_schema",
+      "type": "string",
+      "format": "uri",
+      "description": "The schema applied to the extension object",
+      "examples": [
+        "http://www.w3id.org/biocompute/extension_domain/example.json"
+      ]
+    },
+    "licence_extension": {
+      "required": ["data_license", "scripts_license"],
+      "properties": {
+        "data_license": {
+          "type": "string",
+          "examples": ["https://github.com/example/repo1"],
+          "format": "uri"
+        },
+        "scripts_license": {
+          "type": "string",
+          "examples": ["https://github.com/example/repo1"],
+          "format": "uri"
+        }
+      }
+    }
+  }
+}

config/schemas/scm_extension.json

@@ -0,0 +1,50 @@
+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "$id": "https://w3id.org/biocompute/extension_domain/1.1.0/scm/scm_extension.json",
+  "title": "scm_extension",
+  "type": "object",
+  "description": "The external references extension to a SCM repository",
+  "required": ["scm_extension", "extension_schema"],
+  "additionalProperties": false,
+  "properties": {
+    "extension_schema": {
+      "title": "extension_schema",
+      "type": "string",
+      "format": "uri",
+      "description": "The schema applied to the extension object",
+      "examples": [
+        "http://www.w3id.org/biocompute/extension_domain/example.json"
+      ]
+    },
+    "scm_extension": {
+      "required": ["scm_repository", "scm_type", "scm_commit", "scm_path"],
+      "properties": {
+        "scm_repository": {
+          "type": "string",
+          "examples": ["https://github.com/example/repo1"],
+          "format": "uri"
+        },
+        "scm_type": {
+          "type": "string",
+          "enum": ["git", "svn", "hg", "other"]
+        },
+        "scm_commit": {
+          "type": "string",
+          "examples": ["c9ffea0b60fa3bcf8e138af7c99ca141a6b8fb21"]
+        },
+        "scm_path": {
+          "type": "string",
+          "examples": ["workflow/hive-viral-mutation-detection.cwl"],
+          "format": "string"
+        },
+        "scm_preview": {
+          "type": "string",
+          "examples": [
+            "https://github.com/example/repo1/blob/c9ffea0b60fa3bcf8e138af7c99ca141a6b8fb21/workflow/hive-viral-mutation-detection.cwl"
+          ],
+          "format": "uri"
+        }
+      }
+    }
+  }
+}