fix: merge version into staging

.flake8

@@ -1,3 +1,3 @@
 [flake8]
 max-line-length = 120
-ignore= W293
+ignore= W293,W503

.markdownlint.json

@@ -4,6 +4,7 @@
   "MD024": {
     "siblings_only": true
   },
+  "MD033": false,
   "MD036": false,
   "MD046": false
 }

alembic/env.py

@@ -12,7 +12,7 @@
 
 config = context.config
 section = config.config_ini_section
-print(section, environ.get("FAIRHUB_DATABASE_URL"))
+
 config.set_section_option(
     section, "FAIRHUB_DATABASE_URL", str(environ.get("FAIRHUB_DATABASE_URL"))
 )

apis/__init__.py

@@ -21,6 +21,7 @@
 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
+from .file import api as file_api
 from .participant import api as participants_api
 from .study import api as study_api
 from .study_metadata.study_arm import api as arm
@@ -96,7 +97,9 @@
 
 
 @api.route("/echo", endpoint="echo")
-class HelloWorld(Resource):
+class HelloEverynyan(Resource):
+    """Test if the server is active"""
+
     @api.response(200, "Success")
     @api.response(400, "Validation Error")
     def get(self):
@@ -106,6 +109,7 @@ def get(self):
 
 
 api.add_namespace(study_api)
+api.add_namespace(file_api)
 api.add_namespace(dataset_api)
 api.add_namespace(participants_api)
 api.add_namespace(contributors_api)

apis/authentication.py

@@ -1,9 +1,10 @@
+"""This module is used to authenticate users to the system and
+handle few authentication errors. Also, it sets token for logged user
+along with expiration date"""
 import datetime
 import importlib
 import os
 import re
-
-# import config
 import uuid
 from datetime import timezone
 from typing import Any, Union
@@ -37,11 +38,16 @@
 
 
 class UnauthenticatedException(Exception):
+    """Exception raised when a user is not authenticated."""
+
+    # TODO: Implement this exception
     pass
 
 
 @api.route("/auth/signup")
 class SignUpUser(Resource):
+    """SignUpUser class is used to sign up new users to the system"""
+
     @api.response(200, "Success")
     @api.response(400, "Validation Error")
     # @api.marshal_with(signup_model)
@@ -50,7 +56,14 @@ def post(self):
         """signs up the new users and saves data in DB"""
         data: Union[Any, dict] = request.json
         if os.environ.get("FLASK_ENV") != "testing":
-            if data["email_address"] not in ["[email protected]"]:
+            bypassed_emails = [
+                "[email protected]",
+                "[email protected]",
+                "[email protected]",
+                "[email protected]",
+            ]
+
+            if data["email_address"] not in bypassed_emails:
                 invite = model.StudyInvitedContributor.query.filter_by(
                     email_address=data["email_address"]
                 ).one_or_none()
@@ -144,6 +157,8 @@ def validate_password(instance):
 
 @api.route("/auth/login")
 class Login(Resource):
+    """Login class is used to login users to the system"""
+
     @api.response(200, "Success")
     @api.response(400, "Validation Error")
     # @api.marshal_with(login_model)
@@ -156,9 +171,8 @@ def post(self):
         email_address = data["email_address"]
 
         def validate_is_valid_email(instance):
-            print("within is_valid_email")
             email_address = instance
-            print(email_address)
+
             try:
                 validate_email(email_address)
                 return True
@@ -352,16 +366,10 @@ def is_granted(permission: str, study=None):
     return permission in role[contributor.permission]
 
 
-#
-# def is_study_metadata(study_id: int):
-#     study_obj = model.Study.query.get(study_id)
-#     if not is_granted("study_metadata", study_obj):
-#         return "Access denied, you can not delete study", 403
-#
-
-
 @api.route("/auth/logout")
 class Logout(Resource):
+    """Logout class is used to log out users from the system"""
+
     @api.response(200, "Success")
     @api.response(400, "Validation Error")
     def post(self):
@@ -379,14 +387,15 @@ def post(self):
         return resp
 
 
-@api.route("/auth/current-users")
-class CurrentUsers(Resource):
-    """function is used to see all logged users in
-    the system. For now, it is used for testing purposes"""
+# @api.route("/auth/current-users")
+# class CurrentUsers(Resource):
+#     """function is used to see all logged users in
+#     the system. For now, it is used for testing purposes"""
 
-    @api.response(200, "Success")
-    @api.response(400, "Validation Error")
-    def get(self):
-        if not g.user:
-            return None
-        return g.user.to_dict()
+#     @api.response(200, "Success")
+#     @api.response(400, "Validation Error")
+#     def get(self):
+#         """returns all logged users in the system"""
+#         if not g.user:
+#             return None
+#         return g.user.to_dict()

apis/dataset_metadata/dataset_access.py

@@ -1,5 +1,8 @@
+"""API for dataset access metadata"""
+
 from flask import request
 from flask_restx import Resource, fields
+from jsonschema import ValidationError, validate
 
 import model
 from apis.authentication import is_granted
@@ -19,11 +22,14 @@
 
 @api.route("/study/<study_id>/dataset/<dataset_id>/metadata/access")
 class DatasetAccessResource(Resource):
+    """Dataset Access 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):  # pylint: disable= unused-argument
+        """Get dataset access"""
         dataset_ = model.Dataset.query.get(dataset_id)
         dataset_access_ = dataset_.dataset_access
         return dataset_access_.to_dict()
@@ -32,10 +38,34 @@ def get(self, study_id: int, dataset_id: int):  # pylint: disable= unused-argume
     @api.response(200, "Success")
     @api.response(400, "Validation Error")
     def put(self, study_id: int, dataset_id: int):  # pylint: disable= unused-argument
+        """Update dataset access"""
         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
 
+        schema = {
+            "type": "object",
+            "additionalProperties": False,
+            "properties": {
+                "description": {"type": "string", "minLength": 1},
+                "type": {"type": "string", "minLength": 1},
+                "url": {"type": "string"},
+                "url_last_checked": {"type": ["integer", "null"]},
+            },
+            "required": [
+                "description",
+                "type",
+                "url",
+                "url_last_checked",
+            ],
+        }
+
+        try:
+            validate(instance=request.json, schema=schema)
+        except ValidationError as err:
+            return err.message, 400
+
         dataset_ = model.Dataset.query.get(dataset_id)
         dataset_.dataset_access.update(request.json)
         model.db.session.commit()

apis/dataset_metadata/dataset_alternate_identifier.py

@@ -1,7 +1,9 @@
+"""API endpoints for dataset alternate identifier"""
 from typing import Any, Union
 
 from flask import request
 from flask_restx import Resource, fields
+from jsonschema import ValidationError, validate
 
 import model
 from apis.authentication import is_granted
@@ -20,11 +22,14 @@
 
 @api.route("/study/<study_id>/dataset/<dataset_id>/metadata/alternative-identifier")
 class DatasetAlternateIdentifierResource(Resource):
+    """Dataset Alternate Identifier Resource"""
+
     @api.doc("identifier")
     @api.response(200, "Success")
     @api.response(400, "Validation Error")
     # @api.marshal_with(dataset_identifier)
     def get(self, study_id: int, dataset_id: int):  # pylint: disable = unused-argument
+        """Get dataset alternate identifier"""
         dataset_ = model.Dataset.query.get(dataset_id)
         dataset_identifier_ = dataset_.dataset_alternate_identifier
         return [d.to_dict() for d in dataset_identifier_]
@@ -33,10 +38,59 @@ def get(self, study_id: int, dataset_id: int):  # pylint: disable = unused-argum
     @api.response(200, "Success")
     @api.response(400, "Validation Error")
     def post(self, study_id: int, dataset_id: int):
+        """Update dataset alternate identifier"""
         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
-        # pylint: disable= unused-argument
+
+        schema = {
+            "type": "array",
+            "items": {
+                "type": "object",
+                "additionalProperties": False,
+                "properties": {
+                    "id": {"type": "string"},
+                    "identifier": {
+                        "type": "string",
+                        "minLength": 1,
+                    },
+                    "type": {
+                        "type": "string",
+                        "enum": [
+                            "ARK",
+                            "arXiv",
+                            "bibcode",
+                            "DOI",
+                            "EAN13",
+                            "EISSN",
+                            "Handle",
+                            "IGSN",
+                            "ISBN",
+                            "ISSN",
+                            "ISTC",
+                            "LISSN",
+                            "LSID",
+                            "PMID",
+                            "PURL",
+                            "UPC",
+                            "URL",
+                            "URN",
+                            "w3id",
+                            "Other",
+                        ],
+                    },
+                },
+                "required": ["identifier", "type"],
+            },
+            "uniqueItems": True,
+        }
+
+        try:
+            validate(request.json, schema)
+        except ValidationError as e:
+            return e.message, 400
+
         data: Union[Any, dict] = request.json
         data_obj = model.Dataset.query.get(dataset_id)
         list_of_elements = []
@@ -63,12 +117,15 @@ def post(self, study_id: int, dataset_id: int):
         "metadata/alternative-identifier/<identifier_id>"
     )
     class DatasetAlternateIdentifierUpdate(Resource):
+        """Dataset Alternate Identifier Update Resource"""
+
         @api.doc("delete identifier")
         @api.response(200, "Success")
         @api.response(400, "Validation Error")
         def delete(
             self, study_id: int, dataset_id: int, identifier_id: int
         ):  # pylint: disable= unused-argument
+            """Delete dataset alternate identifier"""
             dataset_identifier_ = model.DatasetAlternateIdentifier.query.get(
                 identifier_id
             )

apis/dataset_metadata/dataset_consent.py

@@ -1,5 +1,7 @@
+"""API for dataset consent metadata"""
 from flask import request
 from flask_restx import Resource, fields
+from jsonschema import ValidationError, validate
 
 import model
 from apis.authentication import is_granted
@@ -22,11 +24,14 @@
 
 @api.route("/study/<study_id>/dataset/<dataset_id>/metadata/consent")
 class DatasetConsentResource(Resource):
+    """Dataset Consent Resource"""
+
     @api.doc("consent")
     @api.response(200, "Success")
     @api.response(400, "Validation Error")
     # @api.marshal_with(dataset_consent)
     def get(self, study_id: int, dataset_id: int):  # pylint: disable= unused-argument
+        """Get dataset consent"""
         dataset_ = model.Dataset.query.get(dataset_id)
         dataset_consent_ = dataset_.dataset_consent
         return dataset_consent_.to_dict()
@@ -35,9 +40,42 @@ def get(self, study_id: int, dataset_id: int):  # pylint: disable= unused-argume
     @api.response(200, "Success")
     @api.response(400, "Validation Error")
     def put(self, study_id: int, dataset_id: int):
+        """Update dataset consent"""
         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
+
+        schema = {
+            "type": "object",
+            "additionalProperties": False,
+            "properties": {
+                "type": {"type": "string", "minLength": 1},
+                "details": {
+                    "type": "string",
+                },
+                "genetic_only": {"type": "boolean"},
+                "geog_restrict": {"type": "boolean"},
+                "no_methods": {"type": "boolean"},
+                "noncommercial": {"type": "boolean"},
+                "research_type": {"type": "boolean"},
+            },
+            "required": [
+                "type",
+                "details",
+                "genetic_only",
+                "geog_restrict",
+                "no_methods",
+                "noncommercial",
+                "research_type",
+            ],
+        }
+
+        try:
+            validate(instance=request.json, schema=schema)
+        except ValidationError as err:
+            return err.message, 400
+
         data = request.json
         dataset_ = model.Dataset.query.get(dataset_id)
         dataset_.dataset_consent.update(data)