feat: update dataset metadata endpoints

apis/__init__.py

@@ -10,23 +10,15 @@
 from .dataset_metadata.dataset_access import api as access
 from .dataset_metadata.dataset_alternate_identifier import api as alternate_identifier
 from .dataset_metadata.dataset_consent import api as consent
+from .dataset_metadata.dataset_contributor import api as dataset_contributor
 from .dataset_metadata.dataset_date import api as date
 from .dataset_metadata.dataset_de_ident_level import api as de_ident_level
 from .dataset_metadata.dataset_description import api as description
 from .dataset_metadata.dataset_funder import api as funder
-from .dataset_metadata.dataset_managing_organization import api as managing_organization
 from .dataset_metadata.dataset_other import api as dataset_other
 from .dataset_metadata.dataset_readme import api as readme
 from .dataset_metadata.dataset_record_keys import api as record_keys
 from .dataset_metadata.dataset_related_item import api as related_item
-from .dataset_metadata.dataset_related_item_contributor import (
-    api as related_item_contributor,
-)
-from .dataset_metadata.dataset_related_item_identifier import (
-    api as related_item_identifier,
-)
-from .dataset_metadata.dataset_related_item_other import api as related_item_other
-from .dataset_metadata.dataset_related_item_title import api as related_item_title
 from .dataset_metadata.dataset_rights import api as rights
 from .dataset_metadata.dataset_subject import api as subject
 from .dataset_metadata.dataset_title import api as title
@@ -69,16 +61,11 @@
     "de_ident_level",
     "description",
     "funder",
-    "managing_organization",
     "dataset_other",
     "readme",
     "record_keys",
     "related_item",
-    "related_item_contributor",
-    "related_item_identifier",
     "api",
-    "related_item_other",
-    "related_item_title",
     "rights",
     "subject",
     "title",
@@ -101,6 +88,7 @@
     "user",
     "identification",
     "study_description",
+    "dataset_contributor",
 ]
 
 

apis/authentication.py

@@ -297,6 +297,7 @@ def is_granted(permission: str, study=None):
             "add_dataset",
             "update_dataset",
             "delete_dataset",
+            "version",
             "publish_version",
             "participant",
             "study_metadata",
@@ -314,6 +315,7 @@ def is_granted(permission: str, study=None):
             "add_dataset",
             "update_dataset",
             "delete_dataset",
+            "version",
             "publish_version",
             "participant",
             "study_metadata",
@@ -329,6 +331,7 @@ def is_granted(permission: str, study=None):
             "delete_dataset",
             "participant",
             "study_metadata",
+            "version",
             "dataset_metadata",
         ],
         "viewer": ["viewer", "view"],

apis/contributor.py

@@ -8,6 +8,7 @@
 
 from .authentication import is_granted
 
+
 api = Namespace("Contributor", description="Contributors", path="/")
 
 
@@ -44,15 +45,28 @@ def post(self, study_id: int):
         if not is_granted("invite_contributor", study_obj):
             return "Access denied, you can not modify", 403
         data: Union[dict, Any] = request.json
+
         email_address = data["email_address"]
         user = model.User.query.filter_by(email_address=email_address).first()
         permission = data["role"]
+        # encoded_jwt_code = jwt.encode(
+        #     {
+        #         "user": user.id,
+        #         "exp": datetime.datetime.now(timezone.utc)
+        #         + datetime.timedelta(minutes=180),  # noqa: W503
+        #         "jti": str(uuid.uuid4()),
+        #     },  # noqa: W503
+        #     config.FAIRHUB_SECRET,
+        #     algorithm="HS256",
+        # )
         contributor_ = None
+
         try:
             if user:
                 contributor_ = study_obj.add_user_to_study(user, permission)
             else:
                 contributor_ = study_obj.invite_user_to_study(email_address, permission)
+
         except model.StudyException as ex:
             return ex.args[0], 409
         model.db.session.commit()

apis/dataset.py

@@ -55,9 +55,20 @@ def post(self, study_id):
         if not is_granted("add_dataset", study):
             return "Access denied, you can not modify", 403
         # todo if study.participant id== different study Throw error
-        # data: typing.Union[typing.Any, dict] = request.json
+        data: typing.Union[typing.Any, dict] = request.json
         dataset_ = model.Dataset.from_data(study)
         model.db.session.add(dataset_)
+
+        title_element = model.DatasetTitle.query.filter_by(
+            dataset_id=dataset_.id
+        ).first()
+        title_element.title = data["title"]
+
+        description_element = model.DatasetDescription.query.filter_by(
+            dataset_id=dataset_.id
+        ).first()
+        description_element.description = data["description"]
+
         model.db.session.commit()
         return dataset_.to_dict()
 
@@ -114,7 +125,6 @@ class VersionResource(Resource):
     @api.response(201, "Success")
     @api.response(400, "Validation Error")
     @api.doc("dataset version")
-    @api.marshal_with(dataset_versions_model)
     def get(
         self, study_id: int, dataset_id: int, version_id: int
     ):  # pylint: disable= unused-argument
@@ -148,19 +158,47 @@ def delete(
 
 
 @api.route("/study/<study_id>/dataset/<dataset_id>/version")
-@api.response(201, "Success")
-@api.response(400, "Validation Error")
 class VersionList(Resource):
+    @api.response(201, "Success")
+    @api.response(400, "Validation Error")
+    @api.doc("versions")
+    def get(self, study_id: int, dataset_id: int):
+        study = model.Study.query.get(study_id)
+        if not is_granted("version", study):
+            return "Access denied, you can not modify", 403
+        dataset_obj = model.Dataset.query.get(dataset_id)
+        return [i.to_dict() for i in dataset_obj.dataset_versions.all()], 200
+
+    @api.response(201, "Success")
+    @api.response(400, "Validation Error")
+    @api.doc("version add")
     def post(self, study_id: int, dataset_id: int):
         study = model.Study.query.get(study_id)
-        if not is_granted("publish_version", study):
+        if not is_granted("version", study):
             return "Access denied, you can not modify", 403
+
         data: typing.Union[typing.Any, dict] = request.json
-        data["participants"] = [
-            model.Participant.query.get(i) for i in data["participants"]
-        ]
+        # data["participants"] = [
+        #     model.Participant.query.get(i) for i in data["participants"]
+        # ]
         data_obj = model.Dataset.query.get(dataset_id)
         dataset_versions = model.Version.from_data(data_obj, data)
         model.db.session.add(dataset_versions)
         model.db.session.commit()
-        return jsonify(dataset_versions.to_dict())
+        return dataset_versions.to_dict()
+
+
+@api.route("/study/<study_id>/dataset/<dataset_id>/version/<version_id>/publish")
+class PublishResource(Resource):
+    @api.response(201, "Success")
+    @api.response(400, "Validation Error")
+    @api.doc("version publish")
+    def post(self, study_id: int, dataset_id: int):
+        study = model.Study.query.get(study_id)
+        if not is_granted("publish_version", study):
+            return "Access denied, you can not modify", 403
+        data_obj = model.Dataset.query.get(dataset_id)
+        data: typing.Union[typing.Any, dict] = request.json
+        dataset_versions = model.Version.from_data(data_obj, data)
+        model.db.session.commit()
+        return dataset_versions.to_dict()

apis/dataset_metadata/dataset_access.py

@@ -2,6 +2,7 @@
 from flask_restx import Resource, fields
 
 import model
+from apis.authentication import is_granted
 from apis.dataset_metadata_namespace import api
 
 dataset_access = api.model(
@@ -21,14 +22,21 @@ class DatasetAccessResource(Resource):
     @api.doc("access")
     @api.response(200, "Success")
     @api.response(400, "Validation Error")
-    @api.marshal_with(dataset_access)
-    def get(self, study_id: int, dataset_id: int):
+    # @api.marshal_with(dataset_access)
+    def get(self, study_id: int, dataset_id: int):  # pylint: disable= unused-argument
         dataset_ = model.Dataset.query.get(dataset_id)
         dataset_access_ = dataset_.dataset_access
-        return [d.to_dict() for d in dataset_access_]
+        return dataset_access_.to_dict()
+
+    @api.doc("update access")
+    @api.response(200, "Success")
+    @api.response(400, "Validation Error")
+    def put(self, study_id: int, dataset_id: int):  # pylint: disable= unused-argument
+        study_obj = model.Study.query.get(study_id)
+        if not is_granted("dataset_metadata", study_obj):
+            return "Access denied, you can not make any change in dataset metadata", 403
 
-    def put(self, study_id: int, dataset_id: int):
         dataset_ = model.Dataset.query.get(dataset_id)
-        dataset_access_ = dataset_.dataset_access.update(request.json)
+        dataset_.dataset_access.update(request.json)
         model.db.session.commit()
-        return dataset_access_.to_dict()
+        return dataset_.dataset_access.to_dict()