Merge pull request #1481 from ScilifelabDataCentre/dev

New release

CHANGELOG.rst

@@ -1,6 +1,15 @@
 Changelog
 ==========
 
+.. _2.5.2:
+
+2.5.2 - 2023-10-25
+~~~~~~~~~~~~~~~~~~~~~
+
+- Users can revoke project access given to unaccepted invites (e.g. after a mistake).
+- Email layout changed. When project is released, important information is now highlighted, and the Project Title is displayed along with the DDS project ID.
+- New endpoint `ProjectStatus.patch`: Unit Admins / Personnel can extend the project deadline.
+
 .. _2.5.1:
 
 2.5.1 - 2023-09-27

SPRINTLOG.md

@@ -303,6 +303,19 @@ _Nothing merged in CLI during this sprint_
 
 # 2023-09-18 - 2023-09-29
 
-- Column `sto4_start_time` is automatically set when the create-unit command is run ([#1668])(https://scilifelab.atlassian.net/jira/software/projects/DDS/boards/13?selectedIssue=DDS-1668)
+- Column `sto4_start_time` is automatically set when the create-unit command is run ([#1469](https://github.com/ScilifelabDataCentre/dds_web/pull/1469))
 - Replace expired invites when there's a new invitation attempt ([#1466](https://github.com/ScilifelabDataCentre/dds_web/pull/1466))
 - New version: 2.5.1 ([#1471](https://github.com/ScilifelabDataCentre/dds_web/pull/1471))
+- Revoke project access for unaccepted invites ([#1468](https://github.com/ScilifelabDataCentre/dds_web/pull/1468))
+
+# 2023-10-02 - 2023-10-13
+
+- Project title displayed along with the internal project ID email sent when a project is released ([#1475](https://github.com/ScilifelabDataCentre/dds_web/pull/1475))
+- Use full DDS name in MOTD email subject ([#1477](https://github.com/ScilifelabDataCentre/dds_web/pull/1477))
+- Add flag --verify-checksum to the comand in email template ([#1478])(https://github.com/ScilifelabDataCentre/dds_web/pull/1478)
+- Improved email layout; Highlighted information and commands when project is released ([#1479])(https://github.com/ScilifelabDataCentre/dds_web/pull/1479)
+
+# 2023-10-16 - 2023-10-27
+
+- Added new API endpoint ProjectStatus.patch to extend the deadline ([#1480])(https://github.com/ScilifelabDataCentre/dds_web/pull/1480)
+- New version: 2.5.2 ([#1482](https://github.com/ScilifelabDataCentre/dds_web/pull/1482))

dds_web/api/project.py

@@ -188,6 +188,135 @@ def post(self):
 
         return {"message": return_message}
 
+    @auth.login_required(role=["Unit Admin", "Unit Personnel"])
+    @logging_bind_request
+    @json_required
+    @handle_validation_errors
+    @handle_db_error
+    def patch(self):
+        """Partially update a the project status"""
+        # Get project ID, project and verify access
+        project_id = dds_web.utils.get_required_item(obj=flask.request.args, req="project")
+        project = dds_web.utils.collect_project(project_id=project_id)
+        dds_web.utils.verify_project_access(project=project)
+
+        # Get json input from request
+        json_input = flask.request.get_json(silent=True)  # Already checked by json_required
+
+        # the status has changed at least two times,
+        # next time the project expires it wont change again -> error
+        if project.times_expired >= 2:
+            raise DDSArgumentError(
+                "Project availability limit: The maximum number of changes in data availability has been reached."
+            )
+
+        # Operation must be confirmed by the user - False by default
+        confirmed_operation = json_input.get("confirmed", False)
+        if not isinstance(confirmed_operation, bool):
+            raise DDSArgumentError(message="`confirmed` is a boolean value: True or False.")
+        if not confirmed_operation:
+            warning_message = "Operation must be confirmed before proceding."
+            # When not confirmed, return information about the project
+            project_info = ProjectInfo().get()
+            project_status = self.get()
+            json_returned = {
+                **project_info,
+                "project_status": project_status,
+                "warning": warning_message,
+                "default_unit_days": project.responsible_unit.days_in_available,
+            }
+            return json_returned
+
+        # Cannot change project status if project is busy
+        if project.busy:
+            raise ProjectBusyError(
+                message=(
+                    f"The deadline for the project '{project_id}' is already in the process of being changed. "
+                    "Please try again later. \n\nIf you know that the project is not busy, contact support."
+                )
+            )
+
+        self.set_busy(project=project, busy=True)
+
+        # Extend deadline
+        try:
+            new_deadline_in = json_input.get(
+                "new_deadline_in", None
+            )  # if not provided --> is None -> deadline is not updated
+
+            # some variable definition
+            send_email = False
+            default_unit_days = project.responsible_unit.days_in_available
+
+            # Update the deadline functionality
+            if new_deadline_in:
+                # deadline can only be extended from Available
+                if not project.current_status == "Available":
+                    raise DDSArgumentError(
+                        "You can only extend the deadline for a project that has the status 'Available'."
+                    )
+
+                if type(new_deadline_in) is not int:
+                    raise DDSArgumentError(
+                        message="The deadline attribute passed should be of type Int (i.e a number)."
+                    )
+
+                # New deadline shouldnt surpass the default unit days
+                if new_deadline_in > default_unit_days:
+                    raise DDSArgumentError(
+                        message=f"You requested the deadline to be extended {new_deadline_in} days. The number of days has to be lower than the default deadline extension number of {default_unit_days} days"
+                    )
+
+                # the new deadline + days left shouldnt surpass 90 days
+                curr_date = dds_web.utils.current_time()
+                current_deadline = (project.current_deadline - curr_date).days
+                if new_deadline_in + current_deadline > 90:
+                    raise DDSArgumentError(
+                        message=f"You requested the deadline to be extended with {new_deadline_in} days (from {current_deadline}), giving a new total deadline of {new_deadline_in + current_deadline} days. The new deadline needs to be less than (or equal to) 90 days."
+                    )
+                try:
+                    # add a fake expire status to mimick a re-release in order to have an udpated deadline
+                    curr_date = (
+                        dds_web.utils.current_time()
+                    )  # call current_time before each call so it is stored with different timestamps
+                    new_status_row = self.expire_project(
+                        project=project,
+                        current_time=curr_date,
+                        deadline_in=1,  # some dummy deadline bc it will re-release now again
+                    )
+                    project.project_statuses.append(new_status_row)
+
+                    curr_date = (
+                        dds_web.utils.current_time()
+                    )  # call current_time before each call so it is stored with different timestamps
+                    new_status_row = self.release_project(
+                        project=project,
+                        current_time=curr_date,
+                        deadline_in=new_deadline_in + current_deadline,
+                    )
+                    project.project_statuses.append(new_status_row)
+
+                    project.busy = False  # return to not busy
+                    db.session.commit()
+
+                except (sqlalchemy.exc.OperationalError, sqlalchemy.exc.SQLAlchemyError) as err:
+                    flask.current_app.logger.exception("Failed to extend deadline")
+                    db.session.rollback()
+                    raise
+
+                return_message = (
+                    f"The project '{project.public_id}' has been given a new deadline. "
+                    f"An e-mail notification has{' not ' if not send_email else ' '}been sent."
+                )
+            else:
+                # leave it for future new functionality of updating the status
+                return_message = "Nothing to update."
+        except:
+            self.set_busy(project=project, busy=False)
+            raise
+
+        return {"message": return_message}
+
     @staticmethod
     @dbsession
     def set_busy(project: models.Project, busy: bool) -> None:

dds_web/api/superadmin_only.py

@@ -164,7 +164,7 @@ def post(self):
 
         # Create email content
         # put motd_obj.message etc in there etc
-        subject: str = "DDS Important Information"
+        subject: str = "Important Information: Data Delivery System"
         body: str = flask.render_template(f"mail/motd.txt", motd=motd_obj.message)
         html = flask.render_template(f"mail/motd.html", motd=motd_obj.message)
 

dds_web/api/user.py

@@ -423,6 +423,7 @@ def compose_and_send_email_to_user(userobj, mail_type, link=None, project=None):
 
         unit_email = None
         project_id = None
+        project_title = None
         deadline = None
 
         # Don't display unit admins or personnels name
@@ -440,6 +441,7 @@ def compose_and_send_email_to_user(userobj, mail_type, link=None, project=None):
         elif mail_type == "project_release":
             subject = f"Project made available by {displayed_sender} in the SciLifeLab Data Delivery System"
             project_id = project.public_id
+            project_title = project.title
             deadline = project.current_deadline.astimezone(datetime.timezone.utc).strftime(
                 "%Y-%m-%d %H:%M:%S %Z"
             )
@@ -470,6 +472,7 @@ def compose_and_send_email_to_user(userobj, mail_type, link=None, project=None):
             displayed_sender=displayed_sender,
             unit_email=unit_email,
             project_id=project_id,
+            project_title=project_title,
             deadline=deadline,
         )
         msg.html = flask.render_template(
@@ -478,6 +481,7 @@ def compose_and_send_email_to_user(userobj, mail_type, link=None, project=None):
             displayed_sender=displayed_sender,
             unit_email=unit_email,
             project_id=project_id,
+            project_title=project_title,
             deadline=deadline,
         )
 
@@ -864,7 +868,7 @@ def delete_invite(email):
 
 
 class RemoveUserAssociation(flask_restful.Resource):
-    @auth.login_required(role=["Unit Admin", "Unit Personnel", "Project Owner", "Researcher"])
+    @auth.login_required(role=["Unit Admin", "Unit Personnel", "Project Owner"])
     @logging_bind_request
     @json_required
     @handle_validation_errors
@@ -876,34 +880,81 @@ def post(self):
         if not (user_email := json_input.get("email")):
             raise ddserr.DDSArgumentError(message="User email missing.")
 
-        # Check if email is registered to a user
+        # Check if the user exists or has a pending invite
         try:
             existing_user = user_schemas.UserSchema().load({"email": user_email})
+            unanswered_invite = user_schemas.UnansweredInvite().load({"email": user_email})
         except sqlalchemy.exc.OperationalError as err:
             raise ddserr.DatabaseError(message=str(err), alt_message="Unexpected database error.")
 
-        if not existing_user:
+        # If the user doesn't exist and doesn't have a pending invite
+        if not existing_user and not unanswered_invite:
             raise ddserr.NoSuchUserError(
-                f"The user with email '{user_email}' does not have access to the specified project."
-                " Cannot remove non-existent project access."
+                f"The user / invite with email '{user_email}' does not have access to the specified project. "
+                "Cannot remove non-existent project access."
             )
 
-        user_in_project = False
-        for user_association in project.researchusers:
-            if user_association.user_id == existing_user.username:
-                user_in_project = True
-                db.session.delete(user_association)
-                project_user_key = models.ProjectUserKeys.query.filter_by(
-                    project_id=project.id, user_id=existing_user.username
-                ).first()
-                if project_user_key:
-                    db.session.delete(project_user_key)
-
-        if not user_in_project:
-            raise ddserr.NoSuchUserError(
-                f"The user with email '{user_email}' does not have access to the specified project."
-                " Cannot remove non-existent project access."
-            )
+        if unanswered_invite:
+            # If there is a unit_id value, it means the invite was associated to a unit
+            # i.e The invite is for a Unit Personel which shouldn't be removed from individual projects
+            if unanswered_invite.unit_id:
+                raise ddserr.UserDeletionError(
+                    "Cannot remove a Unit Admin / Unit Personnel from individual projects."
+                )
+
+            invite_id = unanswered_invite.id
+
+            # Check if the unanswered invite is associated with the project
+            project_invite_key = models.ProjectInviteKeys.query.filter_by(
+                invite_id=invite_id, project_id=project.id
+            ).one_or_none()
+
+            if project_invite_key:
+                msg = (
+                    f"Invited user is no longer associated with the project '{project.public_id}'."
+                )
+                # Remove the association if it exists
+                db.session.delete(project_invite_key)
+
+                # Check if the invite is associated with only one project, if it is -> delete the invite
+                project_invite_key = models.ProjectInviteKeys.query.filter_by(
+                    invite_id=invite_id
+                ).one_or_none()
+
+                if not project_invite_key:
+                    db.session.delete(unanswered_invite)
+            else:
+                # The unanswered invite is not associated with the project
+                raise ddserr.NoSuchUserError(
+                    f"The invite with email '{user_email}' does not have access to the specified project. "
+                    "Cannot remove non-existent project access."
+                )
+
+        else:
+            if auth.current_user().username == existing_user.username:
+                raise ddserr.AccessDeniedError(message="You cannot revoke your own access.")
+
+            # Search the user in the project, when found delete from the database all references to them
+            user_in_project = False
+            for (
+                user_association
+            ) in project.researchusers:  # TODO Possible optimization -> comprehesion list
+                if user_association.user_id == existing_user.username:
+                    user_in_project = True
+                    db.session.delete(user_association)
+                    project_user_key = models.ProjectUserKeys.query.filter_by(
+                        project_id=project.id, user_id=existing_user.username
+                    ).first()
+                    if project_user_key:
+                        db.session.delete(project_user_key)
+                    break
+
+            if not user_in_project:
+                raise ddserr.NoSuchUserError(
+                    f"The user with email '{user_email}' does not have access to the specified project. "
+                    "Cannot remove non-existent project access."
+                )
+            msg = f"User with email {user_email} no longer associated with {project.public_id}."
 
         try:
             db.session.commit()
@@ -924,13 +975,7 @@ def post(self):
                 ),
             ) from err
 
-        flask.current_app.logger.debug(
-            f"User {existing_user.username} no longer associated with project {project.public_id}."
-        )
-
-        return {
-            "message": f"User with email {user_email} no longer associated with {project.public_id}."
-        }
+        return {"message": msg}
 
 
 class EncryptedToken(flask_restful.Resource):

dds_web/database/models.py

@@ -195,7 +195,7 @@ class Unit(db.Model):
     sto2_access = db.Column(db.String(255), unique=False, nullable=True)  # unique=True later
     sto2_secret = db.Column(db.String(255), unique=False, nullable=True)  # unique=True later
 
-    # New safespring storage
+    # New safespring storage - NOTE: MAKE SURE IPS ARE WHITELISTED ON UPPMAX AND OTHER SERVERS
     sto4_start_time = db.Column(db.DateTime(), nullable=True)
     sto4_endpoint = db.Column(db.String(255), unique=False, nullable=True)  # unique=True later
     sto4_name = db.Column(db.String(255), unique=False, nullable=True)  # unique=True later

dds_web/templates/mail/mail_base.html

@@ -1,6 +1,23 @@
 <!doctype html>
 <html>
-
+  <script>
+    function copyTextProjectRelease(copyOption) {
+      // Get the text field
+      let copyText;
+      if (copyOption == 1){
+        copyText = document.getElementById("ProjectListing").innerHTML;
+      }
+      else if (copyOption == 2){
+        copyText = document.getElementById("ProjectDownload").innerHTML;
+      }
+       // Copy the text inside the text field
+      navigator.clipboard.writeText(copyText);
+
+      // Alert the copied text
+      alert("Copied the text: " + copyText);
+    }  
+  </script>
+
 <head>
   <meta name="viewport" content="width=device-width">
   <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
@@ -122,6 +139,10 @@
         border-color: #a00202 !important;
       }
     }
+  code { 
+    background-color: pink;
+    color: black;
+}    
   </style>
 </head>