Merge pull request #1457 from ScilifelabDataCentre/dev

New release

CHANGELOG.rst

@@ -1,9 +1,24 @@
 Changelog
 ==========
 
-.. _2.3.1:
+.. _2.5.0:
 
-2.3.1 - 2023-07-05
+version 2.5.0 - 2023-08-30
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+- Dependencies: 
+    - `cryptography` from `39.0.1` to `41.0.3`
+    - `certifi` from `2022.12.07` to `2023.07.22`
+- _New_ project buckets will be created at a new storage location if Unit information has been updated with storage keys and information.
+- Bug fixed: Listing projects via web interface works again
+- Endpoint `ProjectBusy` is no longer usable; `dds-cli` versions prior to `2.2.0` will no longer work
+- New endpoint `UnitUserEmails`: Super Admins can get primary emails for Unit Admins- and Personnel. This is for emailing purposes.
+- Message about project being busy has been changed to a more accurate and understandable statement
+- Documentation: Typo fixed in Technical Overview
+
+.. _2.4.0:
+
+2.4.0 - 2023-07-05
 ~~~~~~~~~~~~~~~~~~~
 
 - Dependencies:

SPRINTLOG.md

@@ -267,7 +267,26 @@ _Nothing merged in CLI during this sprint_
 - Change from personal name to unit name if / where it's displayed in emails ([#1439](https://github.com/ScilifelabDataCentre/dds_web/pull/1439))
 - Refactoring: `lost_files_s3_db` flask command changed to group with subcommands ([#1438](https://github.com/ScilifelabDataCentre/dds_web/pull/1438))
 
-# 2023-06-26 - 2023-07-14
+# 2023-06-26 - 2023-08-04 (Summer)
 
 - Change display project info depending on the user role ([#1440](https://github.com/ScilifelabDataCentre/dds_web/pull/1440))
 - New version: 2.4.0 ([#1443](https://github.com/ScilifelabDataCentre/dds_web/pull/1443))
+- Bug fix: Web UI project listing fix ([#1445](https://github.com/ScilifelabDataCentre/dds_web/pull/1445))
+- Documentation: Technical Overview, section Creating a Unit in the DDS ([#1449](https://github.com/ScilifelabDataCentre/dds_web/pull/1449))
+
+# 2023-08-07 - 2023-08-18
+
+- Empty endpoint: `ProjectBusy` ([#1446](https://github.com/ScilifelabDataCentre/dds_web/pull/1446))
+
+# 2023-08-04 - 2023-08-18
+
+- Rename storage-related columns in `Unit` table ([#1447](https://github.com/ScilifelabDataCentre/dds_web/pull/1447))
+- Dependency: Bump `cryptography` to 41.0.3 due to security vulnerability alerts(s) ([#1451](https://github.com/ScilifelabDataCentre/dds_web/pull/1451))
+- Allow for change of storage location ([#1448](https://github.com/ScilifelabDataCentre/dds_web/pull/1448))
+- Endpoint: `UnitUserEmails`; Return primary emails for Unit Personnel- and Admins ([#1454](https://github.com/ScilifelabDataCentre/dds_web/pull/1454))
+- Change message about project being busy with upload etc ([#1450](https://github.com/ScilifelabDataCentre/dds_web/pull/1450))
+
+# 2023-08-21 - 2023-09-01
+
+- Dependency: Bump `certifi` to 2023.07.22 due to security vulnerability alert(s) ([#1452](https://github.com/ScilifelabDataCentre/dds_web/pull/1452))
+- New version: 2.5.0 ([#1458](https://github.com/ScilifelabDataCentre/dds_web/pull/1458))

dds_web/__init__.py

@@ -277,11 +277,13 @@ def load_user(user_id):
             quarterly_usage,
             collect_stats,
             monitor_usage,
+            update_unit,
         )
 
         # Add flask commands - general
         app.cli.add_command(fill_db_wrapper)
         app.cli.add_command(create_new_unit)
+        app.cli.add_command(update_unit)
         app.cli.add_command(update_uploaded_file_with_log)
         app.cli.add_command(lost_files_s3_db)
 

dds_web/api/__init__.py

@@ -91,6 +91,7 @@ def output_json(data, code, headers=None):
 )
 api.add_resource(superadmin_only.AnyProjectsBusy, "/proj/busy/any", endpoint="projects_busy_any")
 api.add_resource(superadmin_only.Statistics, "/stats", endpoint="stats")
+api.add_resource(superadmin_only.UnitUserEmails, "/user/emails", endpoint="user_emails")
 
 # Invoicing ############################################################################ Invoicing #
 api.add_resource(user.ShowUsage, "/usage", endpoint="usage")

dds_web/api/api_s3_connector.py

@@ -17,6 +17,7 @@
 )
 
 from dds_web.database import models
+import dds_web.utils
 
 
 ####################################################################################################
@@ -51,14 +52,19 @@ def __exit__(self, exc_type, exc_value, tb):
         return True
 
     def get_s3_info(self):
-        """Get information required to connect to cloud."""
+        """Get information required to connect to cloud storage."""
+        # Check if to use sto4
+        use_sto4 = dds_web.utils.use_sto4(
+            unit_object=self.project.responsible_unit, project_object=self.project
+        )
+
         endpoint, name, accesskey, secretkey = (
             models.Unit.query.filter_by(id=self.project.responsible_unit.id)
             .with_entities(
-                models.Unit.safespring_endpoint,
-                models.Unit.safespring_name,
-                models.Unit.safespring_access,
-                models.Unit.safespring_secret,
+                models.Unit.sto4_endpoint if use_sto4 else models.Unit.sto2_endpoint,
+                models.Unit.sto4_name if use_sto4 else models.Unit.sto2_name,
+                models.Unit.sto4_access if use_sto4 else models.Unit.sto2_access,
+                models.Unit.sto4_secret if use_sto4 else models.Unit.sto2_secret,
             )
             .one_or_none()
         )

dds_web/api/project.py

@@ -39,6 +39,7 @@
     ProjectBusyError,
     S3ConnectionError,
     NoSuchUserError,
+    VersionMismatchError,
 )
 from dds_web.api.user import AddUser
 from dds_web.api.schemas import project_schemas, user_schemas
@@ -94,7 +95,7 @@ def post(self):
         if project.busy:
             raise ProjectBusyError(
                 message=(
-                    f"The project '{project_id}' is currently busy with upload/download/deletion. "
+                    f"The status for the project '{project_id}' is already in the process of being changed. "
                     "Please try again later. \n\nIf you know the project is not busy, contact support."
                 )
             )
@@ -144,8 +145,11 @@ def post(self):
 
             try:
                 project.project_statuses.append(new_status_row)
-                project.busy = False
+                project.busy = False  # TODO: Use set_busy instead?
                 db.session.commit()
+                flask.current_app.logger.info(
+                    f"Busy status set. Project: '{project.public_id}', Busy: False"
+                )
             except (sqlalchemy.exc.OperationalError, sqlalchemy.exc.SQLAlchemyError) as err:
                 flask.current_app.logger.exception(err)
                 db.session.rollback()
@@ -489,7 +493,7 @@ def format_project_dict(self, current_user):
         user_projects = models.Project.query.filter(sqlalchemy.and_(*all_filters)).all()
 
         researcher = False
-        if auth.current_user().role not in ["Super Admin", "Unit Admin", "Unit Personnel"]:
+        if current_user.role not in ["Super Admin", "Unit Admin", "Unit Personnel"]:
             researcher = True
 
         # Get info for all projects
@@ -922,45 +926,20 @@ def give_project_access(project_list, current_user, user):
 
 
 class ProjectBusy(flask_restful.Resource):
-    @auth.login_required(role=["Unit Admin", "Unit Personnel", "Project Owner", "Researcher"])
+    @auth.login_required
     @logging_bind_request
-    @dbsession
-    @json_required
     def put(self):
-        """Set project to busy / not busy."""
-        # 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)
+        """OLD ENDPOINT.
+        Previously set project status to busy.
 
-        # Get busy or not busy
-        request_json = flask.request.get_json(silent=True)
-        set_to_busy = request_json.get("busy")  # Already checked by json_required
-        if set_to_busy is None:
-            raise DDSArgumentError(message="Missing information about setting busy or not busy.")
-
-        if set_to_busy:
-            # Check if project is busy
-            if project.busy:
-                return {"ok": False, "message": "The project is already busy, cannot proceed."}
-
-            # Set project as busy
-            project.busy = True
-        else:
-            # Check if project is not busy
-            if not project.busy:
-                return {
-                    "ok": False,
-                    "message": "The project is already not busy, cannot proceed.",
-                }
-
-            # Set project to not busy
-            project.busy = False
-
-        return {
-            "ok": True,
-            "message": f"Project {project_id} was set to {'busy' if set_to_busy else 'not busy'}.",
-        }
+        TODO: Can remove from 2024. Will otherwise cause breaking changes for old CLI versions.
+        """
+        raise VersionMismatchError(
+            message=(
+                "Your CLI version is trying to use functionality which is no longer in use. "
+                "Upgrade your version to the latest one and run your command again."
+            )
+        )
 
 
 class ProjectInfo(flask_restful.Resource):

dds_web/api/superadmin_only.py

@@ -47,7 +47,7 @@ def get(self):
                 "Public ID": u.public_id,
                 "External Display Name": u.external_display_name,
                 "Contact Email": u.contact_email,
-                "Safespring Endpoint": u.safespring_endpoint,
+                "Safespring Endpoint": u.sto2_endpoint,
                 "Days In Available": u.days_in_available,
                 "Days In Expired": u.days_in_expired,
                 "Size": u.size,
@@ -345,3 +345,23 @@ def get(self):
                 if stat_rows
             ]
         }
+
+
+class UnitUserEmails(flask_restful.Resource):
+    """Get emails for Unit Admins and Unit Personnel."""
+
+    @auth.login_required(role=["Super Admin"])
+    @logging_bind_request
+    @handle_db_error
+    def get(self):
+        """Collect the user emails and return a list."""
+        # Get all emails connected to a Unit Admin or Personnel account
+        user_emails = [user.primary_email for user in models.UnitUser.query.all()]
+
+        # Return empty if no emails
+        if not user_emails:
+            flask.current_app.logger.info("There are no primary emails to return.")
+            return {"empty": True}
+
+        # Return emails
+        return {"emails": user_emails}