Revert "merge: version into staging"

Dockerfile

@@ -22,7 +22,4 @@ COPY core ./core
 COPY app.py .
 COPY config.py .
 
-# run database migrations
-RUN alembic upgrade head  
-
 CMD ["flask", "run", "--host=0.0.0.0", "--port=5000"]

apis/__init__.py

@@ -16,6 +16,7 @@
 from .dataset_metadata.dataset_description import api as description
 from .dataset_metadata.dataset_funder import api as funder
 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_rights import api as rights
@@ -62,6 +63,7 @@
     "description",
     "funder",
     "dataset_other",
+    "readme",
     "record_keys",
     "related_item",
     "api",

apis/dataset.py

@@ -1,6 +1,6 @@
 import typing
 
-from flask import jsonify, request
+from flask import Response, jsonify, request
 from flask_restx import Namespace, Resource, fields
 
 import model
@@ -32,8 +32,6 @@
         "created_at": fields.String(required=True),
         "dataset_versions": fields.Nested(dataset_versions_model, required=True),
         "latest_version": fields.String(required=True),
-        "title": fields.String(required=True),
-        "description": fields.String(required=True),
     },
 )
 
@@ -43,20 +41,20 @@ class DatasetList(Resource):
     @api.response(201, "Success")
     @api.response(400, "Validation Error")
     @api.marshal_with(dataset)
-    @api.doc("view datasets")
     def get(self, study_id):
         study = model.Study.query.get(study_id)
         datasets = model.Dataset.query.filter_by(study=study)
         return [d.to_dict() for d in datasets]
 
     @api.response(201, "Success")
     @api.response(400, "Validation Error")
-    @api.doc("add datasets")
+    @api.doc("update dataset")
     @api.expect(dataset)
     def post(self, study_id):
         study = model.Study.query.get(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
         dataset_ = model.Dataset.from_data(study)
         model.db.session.add(dataset_)
@@ -79,7 +77,6 @@ def post(self, study_id):
 @api.route("/study/<study_id>/dataset/<dataset_id>")
 @api.response(201, "Success")
 @api.response(400, "Validation Error")
-@api.doc("view dataset")
 class DatasetResource(Resource):
     @api.response(201, "Success")
     @api.response(400, "Validation Error")
@@ -89,7 +86,6 @@ def get(self, study_id: int, dataset_id: int):  # pylint: disable= unused-argume
 
     @api.response(201, "Success")
     @api.response(400, "Validation Error")
-    @api.doc("update dataset")
     def put(self, study_id: int, dataset_id: int):
         study = model.Study.query.get(study_id)
 
@@ -106,20 +102,26 @@ def put(self, study_id: int, dataset_id: int):
 
     @api.response(200, "Success")
     @api.response(400, "Validation Error")
-    @api.doc("delete dataset")
     def delete(self, study_id: int, dataset_id: int):
         study = model.Study.query.get(study_id)
         if not is_granted("delete_dataset", study):
             return "Access denied, you can not modify", 403
-
         data_obj = model.Dataset.query.get(dataset_id)
         for version in data_obj.dataset_versions:
             model.db.session.delete(version)
-
         model.db.session.delete(data_obj)
         model.db.session.commit()
         return 204
 
+    # def delete(self, study_id: int, dataset_id: int, version_id: int):
+    #     data_obj = Dataset.query.get(dataset_id)
+    #     for version in data_obj.dataset_versions:
+    #         db.session.delete(version)
+    #         db.session.commit()
+    #     db.session.delete(data_obj)
+    #     db.session.commit()
+    #     return Response(status=204)
+
 
 @api.route("/study/<study_id>/dataset/<dataset_id>/version/<version_id>")
 class VersionResource(Resource):
@@ -129,15 +131,9 @@ class VersionResource(Resource):
     def get(
         self, study_id: int, dataset_id: int, version_id: int
     ):  # pylint: disable= unused-argument
-        study = model.Study.query.get(study_id)
-        if not is_granted("version", study):
-            return "Access denied, you can not modify", 403
         dataset_version = model.Version.query.get(version_id)
         return dataset_version.to_dict()
 
-    @api.response(201, "Success")
-    @api.response(400, "Validation Error")
-    @api.doc("update dataset version")
     def put(
         self, study_id: int, dataset_id: int, version_id: int
     ):  # pylint: disable= unused-argument
@@ -149,86 +145,26 @@ def put(
         model.db.session.commit()
         return jsonify(data_version_obj.to_dict()), 201
 
-    @api.response(201, "Success")
-    @api.response(400, "Validation Error")
-    @api.doc("delete dataset version")
     def delete(
         self, study_id: int, dataset_id: int, version_id: int
     ):  # pylint: disable= unused-argument
         study = model.Study.query.get(study_id)
         if not is_granted("delete_dataset", study):
             return "Access denied, you can not modify", 403
-        version_obj = model.Version.query.get(version_id)
-        model.db.session.delete(version_obj)
-        model.db.session.commit()
-        return 204
-
-
-@api.route("/study/<study_id>/dataset/<dataset_id>/version/<version_id>/changelog")
-class VersionDatasetChangelog(Resource):
-    @api.response(201, "Success")
-    @api.response(400, "Validation Error")
-    @api.doc("version changelog")
-    def get(self, study_id: str, dataset_id: str, version_id: str):
-        study = model.Study.query.get(study_id)
-        if not is_granted("version", study):
-            return "Access denied, you can not modify", 403
-        version = model.Version.query.filter_by(
-            id=version_id, dataset_id=dataset_id
-        ).one_or_none()
-        return {"changelog": version.changelog}
-
-    @api.response(201, "Success")
-    @api.response(400, "Validation Error")
-    @api.doc("version changelog update")
-    def put(
-        self, study_id: str, dataset_id: str, version_id: str
-    ):  # pylint: disable= unused-argument
-        study = model.Study.query.get(study_id)
-        if not is_granted("version", study):
-            return "Access denied, you can not modify", 403
-        data: typing.Union[typing.Any, dict] = request.json
-        version_ = model.Version.query.get(version_id)
-        version_.changelog = data["changelog"]
-        model.db.session.commit()
-        return 201
-
-
-@api.route("/study/<study_id>/dataset/<dataset_id>/version/<version_id>/readme")
-class VersionDatasetReadme(Resource):
-    @api.response(201, "Success")
-    @api.response(400, "Validation Error")
-    @api.doc("version readme")
-    def get(self, study_id: str, dataset_id: str, version_id: str):
-        study = model.Study.query.get(study_id)
-        if not is_granted("version", study):
-            return "Access denied, you can not modify", 403
-        version = model.Version.query.filter_by(
-            id=version_id, dataset_id=dataset_id
-        ).one_or_none()
-        return version.version_readme.to_dict(), 200
-
-    @api.response(201, "Success")
-    @api.response(400, "Validation Error")
-    @api.doc("version readme update")
-    def put(
-        self, study_id: str, dataset_id: str, version_id: str
-    ):  # pylint: disable= unused-argument
-        study = model.Study.query.get(study_id)
-        if not is_granted("version", study):
-            return "Access denied, you can not modify", 403
-        data = request.json
-        version_ = model.Version.query.get(version_id)
-        version_.version_readme.update(data)
+        data_obj = model.Dataset.query.get(dataset_id)
+        for version in data_obj.dataset_versions:
+            model.db.session.delete(version)
+            model.db.session.commit()
+        model.db.session.delete(data_obj)
         model.db.session.commit()
-        return 201
+        return Response(status=204)
 
 
 @api.route("/study/<study_id>/dataset/<dataset_id>/version")
 class VersionList(Resource):
     @api.response(201, "Success")
     @api.response(400, "Validation Error")
-    @api.doc("view versions")
+    @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):
@@ -266,37 +202,21 @@ def post(self, study_id: int, dataset_id: int):
 #             return "Access denied, you can not modify", 403
 #         data_obj = model.Version.query.get(version_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()
 
 
-@api.route("/study/<study_id>/dataset/<dataset_id>/version/<version_id>/study-metadata")
-class VersionDatasetMetadataResource(Resource):
-    @api.response(201, "Success")
-    @api.response(400, "Validation Error")
-    @api.doc("version study metadata get")
-    def get(self, study_id: str, dataset_id: str, version_id: str):
-        study = model.Study.query.get(study_id)
-        if not is_granted("version", study):
-            return "Access denied, you can not modify", 403
-        version = model.Version.query.filter_by(
-            id=version_id, dataset_id=dataset_id
-        ).one_or_none()
-        return version.dataset.study.to_dict_study_metadata()
-
-
-@api.route(
-    "/study/<study_id>/dataset/<dataset_id>/version/<version_id>/dataset-metadata"
-)
-class VersionStudyMetadataResource(Resource):
-    @api.response(201, "Success")
-    @api.response(400, "Validation Error")
-    @api.doc("version dataset metadata get")
-    def get(self, study_id: str, dataset_id: str, version_id: str):
-        study = model.Study.query.get(study_id)
-        if not is_granted("version", study):
-            return "Access denied, you can not modify", 403
-        version = model.Version.query.filter_by(
-            id=version_id, dataset_id=dataset_id
-        ).one_or_none()
-        return version.dataset.to_dict_dataset_metadata()
+#
+# @api.route("/study/<study_id>/dataset/<dataset_id>
+# /version/<version_id>/dataset-metadata")
+# class VersionStudyMetadataResource(Resource):
+#     @api.response(201, "Success")
+#     @api.response(400, "Validation Error")
+#     @api.doc("version dataset metadata get")
+#     def get(self, study_id: int, dataset_id: int, version_id):
+#         study = model.Study.query.get(study_id)
+#         if not is_granted("dataset", study):
+#             return "Access denied, you can not modify", 403
+#     version = dataset.dataset_version.get(version_id)
+#         pass

apis/dataset_metadata/dataset_readme.py

@@ -0,0 +1,33 @@
+from flask import request
+from flask_restx import Resource, fields
+
+import model
+from apis.authentication import is_granted
+from apis.dataset_metadata_namespace import api
+
+dataset_readme = api.model(
+    "DatasetReadme",
+    {"id": fields.String(required=True), "content": fields.String(required=True)},
+)
+
+
+@api.route("/study/<study_id>/dataset/<dataset_id>/metadata/readme")
+class DatasetReadmeResource(Resource):
+    @api.doc("readme")
+    @api.response(200, "Success")
+    @api.response(400, "Validation Error")
+    @api.marshal_with(dataset_readme)
+    def get(self, study_id: int, dataset_id: int):  # pylint: disable= unused-argument
+        dataset_ = model.Dataset.query.get(dataset_id)
+        dataset_readme_ = dataset_.dataset_readme
+        return dataset_readme_.to_dict()
+
+    def put(self, study_id: int, dataset_id: int):
+        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
+        data = request.json
+        dataset_ = model.Dataset.query.get(dataset_id)
+        dataset_.dataset_readme.update(data)
+        model.db.session.commit()
+        return dataset_.dataset_readme.to_dict()

apis/dataset_metadata/dataset_related_item.py

@@ -160,6 +160,7 @@ def post(self, study_id: int, dataset_id: int):
                                         "Subtitle",
                                         "TranslatedTitle",
                                         "OtherTitle",
+                                        "MainTitle",
                                     ],
                                 },
                             },

apis/dataset_metadata/dataset_title.py

@@ -63,6 +63,7 @@ def post(self, study_id: int, dataset_id: int):
                             "Subtitle",
                             "TranslatedTitle",
                             "OtherTitle",
+                            "MainTitle",
                         ],
                     },
                 },
@@ -82,12 +83,17 @@ def post(self, study_id: int, dataset_id: int):
         for i in data:
             if "id" in i and i["id"]:
                 dataset_title_ = model.DatasetTitle.query.get(i["id"])
+                # if dataset_title_.type == "MainTitle":
+                #     return (
+                #         "Main Title type can not be modified",
+                #         403,
+                #
                 dataset_title_.update(i)
                 list_of_elements.append(dataset_title_.to_dict())
             elif "id" not in i or not i["id"]:
                 if i["type"] == "MainTitle":
                     return (
-                        "Main Title type can not be given",
+                        "MainTitle type can not be given",
                         403,
                     )
                 dataset_title_ = model.DatasetTitle.from_data(data_obj, i)
@@ -119,7 +125,7 @@ def delete(
             dataset_title_ = model.DatasetTitle.query.get(title_id)
             if dataset_title_.type == "MainTitle":
                 return (
-                    "Main Title type can not be deleted",
+                    "MainTitle type can not be deleted",
                     403,
                 )
             model.db.session.delete(dataset_title_)