✨ feat: added email verifications

alembic/versions_backup/6173282aef08_remove_invite_info.py

@@ -0,0 +1,24 @@
+"""remove_invite_info
+
+Revision ID: 6173282aef08
+Revises: f150341d2741
+Create Date: 2023-12-19 00:32:08.157538
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision: str = "6173282aef08"
+down_revision: Union[str, None] = "f150341d2741"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    op.drop_column("invite", "info")
+    with op.batch_alter_table("notification") as batch_op:
+        batch_op.alter_column("target", nullable=True)

alembic/versions/72ac2b020c7c_delete_dataset_readme_table.py → alembic/versions_backup/72ac2b020c7c_delete_dataset_readme_table.py

@@ -8,7 +8,6 @@
 from typing import Sequence, Union
 
 import alembic
-import sqlalchemy as sa
 
 
 # revision identifiers, used by Alembic.

alembic/versions_backup/95d6e53e2578_edit_invite_table_pk.py

@@ -0,0 +1,38 @@
+"""edit invite table PK
+
+Revision ID: 95d6e53e2578
+Revises: db1b62d02def
+Create Date: 2023-11-28 14:58:43.869472
+
+"""
+from typing import Sequence, Union
+
+import sqlalchemy as sa
+from alembic import op
+
+
+# revision identifiers, used by Alembic.
+revision: str = "95d6e53e2578"
+down_revision: Union[str, None] = "db1b62d02def"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade():
+    connection = op.get_bind()
+    inspector = sa.inspect(connection)
+
+    # Check if the table exists before dropping it
+    # if not inspector.has_table("invite"):
+    #     if 'id' not in inspector.get_columns("invite"):
+    op.add_column("invite", sa.Column("id", sa.CHAR(36), nullable=True))
+    op.execute(
+        "UPDATE invite SET id = uuid_in(overlay(overlay(md5(random()::text || ':' "
+        "|| random()::text) placing '4' from 13) placing to_hex(floor(random()*(11-8+1) + 8)::int)"
+        "::text from 17)::cstring);"
+    )
+    op.execute("ALTER TABLE invite DROP CONSTRAINT invited_study_contributor_pkey")
+
+    op.create_primary_key("id", "invite", ["id"])
+    with op.batch_alter_table("invite") as batch_op:
+        batch_op.alter_column("study_id", nullable=True)

alembic/versions_backup/b20e07d8924f_delete_token_fron_user_table.py

@@ -0,0 +1,27 @@
+"""delete_token_fron_user_table
+
+Revision ID: b20e07d8924f
+Revises: f189827ee101
+Create Date: 2023-12-13 13:31:38.810816
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision: str = "b20e07d8924f"
+down_revision: Union[str, None] = "f189827ee101"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    op.drop_column("user", "token")
+    op.drop_column("user", "token_generated")
+
+
+def downgrade() -> None:
+    pass

alembic/versions_backup/db1b62d02def_edit_invite_table.py

@@ -0,0 +1,25 @@
+"""edit invite table
+
+Revision ID: db1b62d02def
+Revises: 72ac2b020c7c
+Create Date: 2023-11-28 13:56:41.821141
+
+"""
+from typing import Sequence, Union
+
+import sqlalchemy as sa
+from alembic import op
+
+
+revision: str = "db1b62d02def"
+down_revision: Union[str, None] = "72ac2b020c7c"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    op.rename_table("invited_study_contributor", "invite")
+    op.add_column("invite", sa.Column("info", sa.String(), nullable=True))
+    op.create_unique_constraint(
+        "study_per_user", "invite", ["study_id", "email_address"]
+    )

alembic/versions_backup/eee9610b2cdc_role_nullable_and_fk_user_id.py

@@ -0,0 +1,56 @@
+"""role_nullable_and_fk_user_id
+
+Revision ID: eee9610b2cdc
+Revises: 95d6e53e2578
+Create Date: 2023-12-01 00:09:44.745776
+
+"""
+from typing import Sequence, Union
+
+import sqlalchemy as sa
+import datetime
+import uuid
+from alembic import op
+
+
+# revision identifiers, used by Alembic.
+revision: str = "eee9610b2cdc"
+down_revision: Union[str, None] = "95d6e53e2578"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+created_at = int(datetime.datetime.now(datetime.timezone.utc).timestamp())
+
+id = str(uuid.uuid4())
+hashed = str(uuid.uuid4())
+
+
+def upgrade() -> None:
+    op.add_column("invite", sa.Column("user_id", sa.CHAR(36)))
+    op.execute(
+        f'INSERT INTO "user" ("id", "email_address", "username", "hash", "created_at", "email_verified") VALUES '
+        f"('{id}', '[email protected]', 'eee9610b2cdc', '{hashed}', '{created_at}', False)"
+    )
+
+    user_obj = f"SELECT * FROM user WHERE id = '{id}'"
+    if len(user_obj) < 1:
+        return "error", 403
+    op.execute(f"UPDATE invite SET user_id ='{id}'")
+
+    with op.batch_alter_table("invite") as batch_op:
+        batch_op.alter_column("permission", nullable=True)
+        batch_op.alter_column("user_id", nullable=False)
+    op.create_foreign_key(
+        "fk_user_id",
+        "invite",
+        "user",
+        ["user_id"],
+        ["id"],
+    )
+
+    with op.batch_alter_table("notification") as batch_op:
+        batch_op.alter_column("title", nullable=False)
+        batch_op.alter_column("message", nullable=False)
+        batch_op.alter_column("type", nullable=False)
+        batch_op.alter_column("target", nullable=False)
+        batch_op.alter_column("read", nullable=False)

alembic/versions_backup/f150341d2741_modify_email_verification.py

@@ -0,0 +1,35 @@
+"""modify_email_verification
+
+Revision ID: f150341d2741
+Revises: b20e07d8924f
+Create Date: 2023-12-13 20:43:24.637259
+
+"""
+from typing import Sequence, Union
+
+import sqlalchemy as sa
+import datetime
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision: str = "f150341d2741"
+down_revision: Union[str, None] = "b20e07d8924f"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+created_at = int(datetime.datetime.now(datetime.timezone.utc).timestamp())
+
+
+def upgrade() -> None:
+    op.alter_column("email_verification", "token", type_=sa.String)
+    op.alter_column("email_verification", "user_id", type_=sa.CHAR(36))
+
+    op.drop_column("email_verification", "created_at")
+
+    op.add_column(
+        "email_verification", sa.Column("created_at", sa.BIGINT(), nullable=True)
+    )
+
+    op.execute(f"UPDATE \"email_verification\" SET created_at ='{created_at}'")
+
+    op.alter_column("email_verification", "created_at", nullable=False)

alembic/versions_backup/f189827ee101_user_table_email_verfication.py

@@ -0,0 +1,36 @@
+"""user_table_email_verfication
+
+Revision ID: f189827ee101
+Revises: fed13d793eff
+Create Date: 2023-12-11 14:54:31.303523
+
+"""
+from typing import Sequence, Union
+import sqlalchemy as sa
+import datetime
+import random
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision: str = "f189827ee101"
+down_revision: Union[str, None] = "fed13d793eff"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+token_generated = int(datetime.datetime.now(datetime.timezone.utc).timestamp())
+token = random.randint(10 ** (7 - 1), (10**7) - 1)
+
+
+def upgrade():
+    op.add_column("user", sa.Column("token_generated", sa.BIGINT, nullable=True))
+    op.add_column("user", sa.Column("token", sa.String, nullable=True))
+    op.execute(f"UPDATE \"user\" SET token_generated ='{token_generated}'")
+    op.execute(f"UPDATE \"user\" SET token ='{token}'")
+    op.execute("UPDATE invite SET info ='info'")
+    op.execute(f'UPDATE "user" SET email_verified = FALSE')
+
+    with op.batch_alter_table("user") as batch_op:
+        batch_op.alter_column("token", nullable=False)
+        batch_op.alter_column("token_generated", nullable=False)
+        batch_op.alter_column("email_verified", nullable=False)
+    with op.batch_alter_table("invite") as batch_op:
+        batch_op.alter_column("info", nullable=False)

alembic/versions_backup/fed13d793eff_email_verified_type.py

@@ -0,0 +1,27 @@
+"""email_verified_type
+
+Revision ID: fed13d793eff
+Revises: eee9610b2cdc
+Create Date: 2023-12-05 16:03:51.166254
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision: str = "fed13d793eff"
+down_revision: Union[str, None] = "eee9610b2cdc"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    with op.batch_alter_table("user") as batch_op:
+        batch_op.alter_column(
+            "email_verified",
+            type_=sa.Boolean(),
+            postgresql_using="email_verified::boolean",
+        )

apis/__init__.py

@@ -1,6 +1,5 @@
 """Initialize the api system for the backend"""
 from flask_restx import Api, Resource
-
 from apis.dataset_metadata_namespace import api as dataset_metadata_namespace
 from apis.study_metadata_namespace import api as study_metadata_namespace
 
@@ -22,6 +21,7 @@
 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 .invite_users import api as invite_general_users
 from .participant import api as participants_api
 from .study import api as study_api
 from .study_metadata.study_arm import api as arm
@@ -88,12 +88,14 @@
     "identification",
     "study_description",
     "dataset_contributor",
+    "invite_general_users",
 ]
 
 
 api.add_namespace(dataset_metadata_namespace)
 api.add_namespace(study_metadata_namespace)
 api.add_namespace(authentication)
+api.add_namespace(invite_general_users)
 
 
 @api.route("/echo", endpoint="echo")
@@ -104,7 +106,6 @@ class HelloEverynyan(Resource):
     @api.response(400, "Validation Error")
     def get(self):
         """Returns a simple 'Server Active' message"""
-
         return "Server active!"