Merge pull request #1525 from ScilifelabDataCentre/dev

New release
ScilifelabDataCentre · Apr 9, 2024 · 781cacf · 781cacf
2 parents ef0761e + 2856b68
commit 781cacf
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,6 +1,18 @@
 Changelog
 ==========
 
+.. _2.6.4:
+
+2.6.4 - 2023-04-10
+~~~~~~~~~~~~~~~~~~~~~~~
+
+- New features:
+    - Fix the files endpoint acording to openAPI standar .
+    - Added email contact to troubleshouting page
+- Dependencies: 
+    - `jwcrypto` from `1.5.1` to `1.5.6`
+- Update base image for the docker containers from `python:3.10-alpine` to `python:3.11-alpine`
+
 .. _2.6.3:
 
 2.6.3 - 2023-02-27

diff --git a/Dockerfiles/backend.Dockerfile b/Dockerfiles/backend.Dockerfile
@@ -3,7 +3,7 @@
 #############################
 
 # Set official image -- parent image
-FROM python:3.10-alpine as base
+FROM python:3.11-alpine as base
 
 ARG USERNAME=dds-user
 ARG USER_UID=1001

diff --git a/Dockerfiles/cli.Dockerfile b/Dockerfiles/cli.Dockerfile
@@ -1,5 +1,5 @@
 # Set official image
-FROM python:3.10-alpine as base
+FROM python:3.11-alpine as base
 
 # Update and upgrade
 RUN apk update && apk upgrade

diff --git a/SPRINTLOG.md b/SPRINTLOG.md
@@ -344,6 +344,8 @@ _Nothing merged in CLI during this sprint_
 - Minor update jinja2 package to address cve ([#1503](https://github.com/ScilifelabDataCentre/dds_web/pull/1503))
 - Minor update jwcrypto package to address cve ([#1504](https://github.com/ScilifelabDataCentre/dds_web/pull/1504))
 
+# 2023-01-15 - 2024-01-25
+
 # 2024-01-15 - 2024-01-26
 
 - Document Superadmin endpoints ([#1507](https://github.com/ScilifelabDataCentre/dds_web/pull/1507))
@@ -367,3 +369,16 @@ _Nothing merged in CLI during this sprint_
 
 - Add link in footer for new User Agreement and Privacy Policy ([#1516](https://github.com/ScilifelabDataCentre/dds_web/pull/1516))
 - New extra release, outside maintenance window, version 2.6.3 ([#1518](https://github.com/ScilifelabDataCentre/dds_web/pull/1518))
+
+# 2024-03-11 - 2024-03-22
+
+- Fix the files endpoints according to the openAPI standards, providing new endpoint version that co-exists with the current one ([#1505](https://github.com/ScilifelabDataCentre/dds_web/pull/1505))
+- Added email to troubleshouting webpage, with obfuscation ([#1520](https://github.com/ScilifelabDataCentre/dds_web/pull/1520))
+
+# 2024-03-25 - 2024-04-5
+
+- Update base image and packages to address cve in docker containers ([#1523](https://github.com/ScilifelabDataCentre/dds_web/pull/1523))
+
+# 2024-04-8 - 2024-04-19
+
+- New version: 2.6.4 ([#1526](https://github.com/ScilifelabDataCentre/dds_web/pull/1526))
diff --git a/dds_web/__init__.py b/dds_web/__init__.py
@@ -194,6 +194,10 @@ def prepare():
             # Verify cli version compatible
             if "api/v1" in flask.request.path:
                 verify_cli_version(version_cli=flask.request.headers.get("X-Cli-Version"))
+            elif "api/v3" in flask.request.path:  # experimental v3 version
+                # If version api is not provided, it gets the data from the __version__ file
+                # When v3 is finallized, this should be removed and the __version__ file should be updated
+                pass
 
             # Get message of the day
             flask.g.motd = get_active_motds()
@@ -309,28 +313,44 @@ def dds_version_filter(_):
             import dds_web.security.auth
 
             # Register blueprints
-            from dds_web.api import api_blueprint
+            from dds_web.api import api_blueprint, api_blueprint_v3
             from dds_web.web.root import pages
             from dds_web.web.user import auth_blueprint
             from flask_swagger_ui import get_swaggerui_blueprint
 
-            # url for the documentation
-            SWAGGER_URL = "/documentation"
-            # path where the swagger file is localted in the repository
-            API_URL = "/static/swagger.yaml"
+            # base url for the api documentation
+            SWAGGER_URL_1 = "/api/documentation/v1"
+            SWAGGER_URL_3 = "/api/documentation/v3"
 
-            # register blueprint for the documentation
-            swagger_ui_blueprint = get_swaggerui_blueprint(
-                SWAGGER_URL,
-                API_URL,
+            # path where the swagger file(s) are localted in the repository
+            API_URL_V1 = "/static/swagger.yaml"
+            API_URL_V3 = "/static/swaggerv3.yaml"
+
+            # register blueprint(s) for the documentation
+            swagger_ui_blueprint_v1 = get_swaggerui_blueprint(
+                SWAGGER_URL_1,
+                API_URL_V1,
+                config={
+                    "app_name": "DDS API Documentation",
+                    "defaultModelsExpandDepth": -1,
+                    "layout": "BaseLayout",
+                },
+            )
+            swagger_ui_blueprint_v3 = get_swaggerui_blueprint(
+                SWAGGER_URL_3,
+                API_URL_V3,
                 config={
                     "app_name": "DDS API Documentation",
                     "defaultModelsExpandDepth": -1,
                     "layout": "BaseLayout",
                 },
             )
-            app.register_blueprint(swagger_ui_blueprint, url_prefix=SWAGGER_URL)
+
+            # two documentation and api versions, v3 will contain the new endpoints fixed
+            app.register_blueprint(swagger_ui_blueprint_v1, url_prefix=SWAGGER_URL_1, name="v1")
+            app.register_blueprint(swagger_ui_blueprint_v3, url_prefix=SWAGGER_URL_3, name="v3")
             app.register_blueprint(api_blueprint, url_prefix="/api/v1")
+            app.register_blueprint(api_blueprint_v3, url_prefix="/api/v3")
             app.register_blueprint(pages, url_prefix="")
             app.register_blueprint(auth_blueprint, url_prefix="")
 

diff --git a/dds_web/api/__init__.py b/dds_web/api/__init__.py
@@ -22,8 +22,12 @@
 api_blueprint = flask.Blueprint("api_blueprint", __name__)
 api = flask_restful.Api(api_blueprint)
 
+api_blueprint_v3 = flask.Blueprint("api_blueprint_v3", __name__)
+api_v3 = flask_restful.Api(api_blueprint_v3)
+
 
 @api.representation("application/json")
+@api_v3.representation("application/json")
 def output_json(data, code, headers=None):
     resp = flask.make_response(flask.json.dumps(data), code)
     resp.headers.extend(headers or {})
@@ -33,66 +37,74 @@ def output_json(data, code, headers=None):
 ####################################################################################################
 # RESOURCES ############################################################################ RESOURCES #
 ####################################################################################################
-
-# Login/access ###################################################################### Login/access #
-api.add_resource(user.EncryptedToken, "/user/encrypted_token", endpoint="encrypted_token")
-api.add_resource(user.SecondFactor, "/user/second_factor", endpoint="second_factor")
-
-# S3 ########################################################################################## S3 #
-api.add_resource(s3.S3Info, "/s3/proj", endpoint="proj_s3_info")
-
-# Files #################################################################################### Files #
-api.add_resource(files.NewFile, "/file/new", endpoint="new_file")
-api.add_resource(files.MatchFiles, "/file/match", endpoint="match_files")
-api.add_resource(files.ListFiles, "/files/list", endpoint="list_files")
-api.add_resource(files.RemoveFile, "/file/rm", endpoint="remove_file")
-api.add_resource(files.RemoveDir, "/file/rmdir", endpoint="remove_dir")
-api.add_resource(files.FileInfo, "/file/info", endpoint="file_info")
-api.add_resource(files.FileInfoAll, "/file/all/info", endpoint="all_file_info")
-api.add_resource(files.UpdateFile, "/file/update", endpoint="update_file")
-api.add_resource(files.AddFailedFiles, "/file/failed/add", endpoint="add_failed_files")
-
-# Projects ############################################################################## Projects #
-api.add_resource(project.UserProjects, "/proj/list", endpoint="list_projects")
-api.add_resource(project.RemoveContents, "/proj/rm", endpoint="remove_contents")
-api.add_resource(project.GetPublic, "/proj/public", endpoint="public_key")
-api.add_resource(project.GetPrivate, "/proj/private", endpoint="private_key")
-api.add_resource(project.CreateProject, "/proj/create", endpoint="create_project")
-api.add_resource(project.ProjectUsers, "/proj/users", endpoint="list_project_users")
-api.add_resource(project.ProjectStatus, "/proj/status", endpoint="project_status")
-api.add_resource(project.ProjectAccess, "/proj/access", endpoint="project_access")
-api.add_resource(project.ProjectBusy, "/proj/busy", endpoint="project_busy")
-api.add_resource(project.ProjectInfo, "/proj/info", endpoint="project_info")
-
-# User management ################################################################ User management #
-api.add_resource(user.RetrieveUserInfo, "/user/info", endpoint="user_info")
-api.add_resource(user.AddUser, "/user/add", endpoint="add_user")
-api.add_resource(user.DeleteUser, "/user/delete", endpoint="delete_user")
-api.add_resource(user.DeleteUserSelf, "/user/delete_self", endpoint="delete_user_self")
-api.add_resource(user.RemoveUserAssociation, "/user/access/revoke", endpoint="revoke_from_project")
-api.add_resource(user.UserActivation, "/user/activation", endpoint="user_activation")
-api.add_resource(
-    user.RequestHOTPActivation, "/user/hotp/activate", endpoint="request_hotp_activation"
-)
-api.add_resource(
-    user.RequestTOTPActivation, "/user/totp/activate", endpoint="request_totp_activation"
-)
-api.add_resource(user.Users, "/users", endpoint="users")
-api.add_resource(user.InvitedUsers, "/user/invites", endpoint="list_invites")
-
-# Super Admins ###################################################################### Super Admins #
-
-api.add_resource(superadmin_only.MaintenanceMode, "/maintenance", endpoint="maintenance")
-api.add_resource(superadmin_only.AllUnits, "/unit/info/all", endpoint="all_units")
-api.add_resource(superadmin_only.MOTD, "/motd", endpoint="motd")
-api.add_resource(superadmin_only.SendMOTD, "/motd/send", endpoint="send_motd")
-api.add_resource(superadmin_only.FindUser, "/user/find", endpoint="find_user")
-api.add_resource(
-    superadmin_only.ResetTwoFactor, "/user/totp/deactivate", endpoint="reset_user_hotp"
-)
-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")
+def add_resources(api):
+    # Login/access ###################################################################### Login/access #
+    api.add_resource(user.EncryptedToken, "/user/encrypted_token", endpoint="encrypted_token")
+    api.add_resource(user.SecondFactor, "/user/second_factor", endpoint="second_factor")
+
+    # S3 ########################################################################################## S3 #
+    api.add_resource(s3.S3Info, "/s3/proj", endpoint="proj_s3_info")
+
+    # Files #################################################################################### Files #
+    api.add_resource(files.NewFile, "/file/new", endpoint="new_file")
+    api.add_resource(files.MatchFiles, "/file/match", endpoint="match_files")
+    api.add_resource(files.ListFiles, "/files/list", endpoint="list_files")
+    api.add_resource(files.RemoveFile, "/file/rm", endpoint="remove_file")
+    api.add_resource(files.RemoveDir, "/file/rmdir", endpoint="remove_dir")
+    api.add_resource(files.FileInfo, "/file/info", endpoint="file_info")
+    api.add_resource(files.FileInfoAll, "/file/all/info", endpoint="all_file_info")
+    api.add_resource(files.UpdateFile, "/file/update", endpoint="update_file")
+    api.add_resource(files.AddFailedFiles, "/file/failed/add", endpoint="add_failed_files")
+
+    # Projects ############################################################################## Projects #
+    api.add_resource(project.UserProjects, "/proj/list", endpoint="list_projects")
+    api.add_resource(project.RemoveContents, "/proj/rm", endpoint="remove_contents")
+    api.add_resource(project.GetPublic, "/proj/public", endpoint="public_key")
+    api.add_resource(project.GetPrivate, "/proj/private", endpoint="private_key")
+    api.add_resource(project.CreateProject, "/proj/create", endpoint="create_project")
+    api.add_resource(project.ProjectUsers, "/proj/users", endpoint="list_project_users")
+    api.add_resource(project.ProjectStatus, "/proj/status", endpoint="project_status")
+    api.add_resource(project.ProjectAccess, "/proj/access", endpoint="project_access")
+    api.add_resource(project.ProjectBusy, "/proj/busy", endpoint="project_busy")
+    api.add_resource(project.ProjectInfo, "/proj/info", endpoint="project_info")
+
+    # User management ################################################################ User management #
+    api.add_resource(user.RetrieveUserInfo, "/user/info", endpoint="user_info")
+    api.add_resource(user.AddUser, "/user/add", endpoint="add_user")
+    api.add_resource(user.DeleteUser, "/user/delete", endpoint="delete_user")
+    api.add_resource(user.DeleteUserSelf, "/user/delete_self", endpoint="delete_user_self")
+    api.add_resource(
+        user.RemoveUserAssociation, "/user/access/revoke", endpoint="revoke_from_project"
+    )
+    api.add_resource(user.UserActivation, "/user/activation", endpoint="user_activation")
+    api.add_resource(
+        user.RequestHOTPActivation, "/user/hotp/activate", endpoint="request_hotp_activation"
+    )
+    api.add_resource(
+        user.RequestTOTPActivation, "/user/totp/activate", endpoint="request_totp_activation"
+    )
+    api.add_resource(user.Users, "/users", endpoint="users")
+    api.add_resource(user.InvitedUsers, "/user/invites", endpoint="list_invites")
+
+    # Super Admins ###################################################################### Super Admins #
+
+    api.add_resource(superadmin_only.MaintenanceMode, "/maintenance", endpoint="maintenance")
+    api.add_resource(superadmin_only.AllUnits, "/unit/info/all", endpoint="all_units")
+    api.add_resource(superadmin_only.MOTD, "/motd", endpoint="motd")
+    api.add_resource(superadmin_only.SendMOTD, "/motd/send", endpoint="send_motd")
+    api.add_resource(superadmin_only.FindUser, "/user/find", endpoint="find_user")
+    api.add_resource(
+        superadmin_only.ResetTwoFactor, "/user/totp/deactivate", endpoint="reset_user_hotp"
+    )
+    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")
+
+
+add_resources(api)
+add_resources(api_v3)