update userprofile and api docs (#1922)

docs_manual/source/api_projectroles.rst

@@ -1,14 +1,21 @@
 .. _api_projectroles:
 
-Project Management API
-^^^^^^^^^^^^^^^^^^^^^^
+Project Management APIs
+^^^^^^^^^^^^^^^^^^^^^^^
 
-The REST API for project access and management operations is described in this
-document.
+The REST APIs for project access and management operations is described in this
+document. These APIs are provided by the SODAR Core package. Thus, detailed
+documentation can be found in the
+`SODAR Core documentation <https://sodar-core.readthedocs.io/en/latest>`_.
 
 
+Projectroles API
+================
+
+This API handles the management of projects, project members and app settings.
+
 Versioning
-==========
+----------
 
 Media Type
     ``application/vnd.bihealth.sodar-core.projectroles+json``
@@ -17,12 +24,37 @@ Current Version
 Accepted Versions
     ``1.0``
 Header Example
-    ``Accept: application/vnd.bihealth.sodar-core.projectroles+json; version=x.y``
+    ``Accept: application/vnd.bihealth.sodar-core.projectroles+json; version=1.0``
+
+API Views
+---------
+
+The projectoles API is provided by the SODAR Core package. Documentation for the
+API views can be found in the
+`Projectroles REST API documentation <https://sodar-core.readthedocs.io/en/latest/app_projectroles_api_rest.html>`_.
+
+
+Timeline API
+============
+
+This API can be used to query events in the
+:ref:`timeline <ui_project_timeline>` audit trail logs.
 
+Versioning
+----------
+
+Media Type
+    ``application/vnd.bihealth.sodar-core.timeline+json``
+Current Version
+    ``1.0``
+Accepted Versions
+    ``1.0``
+Header Example
+    ``Accept: application/vnd.bihealth.sodar-core.timeline+json; version=1.0``
 
 API Views
-=========
+---------
 
-The project management API is provided by the SODAR Core package. The
-documentation for the REST API views can be found in the
-`SODAR Core documentation <https://sodar-core.readthedocs.io/en/latest/app_projectroles_api_rest.html#api-views>`_.
+The timeline API is provided by the SODAR Core package. Documentation for the
+API views can be found in the
+`Timeline REST API documentation <https://sodar-core.readthedocs.io/en/latest/app_timeline_api_rest.html>`_.

docs_manual/source/index.rst

@@ -116,7 +116,7 @@ Table of Contents
     :name: api_docs
 
     api_documentation
-    Project Management API <api_projectroles>
+    Project Management APIs <api_projectroles>
     Sample Sheets API <api_samplesheets>
     Landing Zones API <api_landingzones>
     iRODS Info API <api_irodsinfo>

docs_manual/source/ui_user_profile.rst

@@ -3,38 +3,76 @@
 User Profile
 ^^^^^^^^^^^^
 
-The user profile screen displays information regarding your account.
+The user profile screen displays information regarding your account. The user
+profile displays your information and provides functionality for managing your
+user details.
 
 .. figure:: _static/sodar_ui/user_profile.png
     :align: center
-    :scale: 65%
+    :scale: 60%
 
     User profile view
 
+
+User Settings
+=============
+
 Through the user profile, you can modify global user-specific settings for your
 account by clicking the :guilabel:`Update Settings` button. The following user
 settings are available:
 
-Sample Sheet Table Height
+Sample sheet table height
     Choose the maximum height of study and assay tables in the sample sheets app
     from a set of options. In browsing mode, table height will fit the table
     content if the height of content is lower than the setting. In edit mode,
     the chosen table height will be maintained regardless of content.
-Display Template Output Directory Field
+Display template output directory field
     Display or hide the "output directory" field in sample sheet template
     creation form. This can be enabled if there is need to control the output
     directory in sample sheet ISA-Tab exports. Defaults to false.
-Display Project UUID Copying Link
+Receive email for admin alerts
+    Receive email notifications for admin alerts where the admin has enabled
+    email alering. If unchecked, you can still see the alerts in the SODAR GUI.
+Display project UUID copying link
     Enabling this will add an icon next to the project title on each project
     view. Clicking it will copy the project identifier (UUID) into the
     clipboard.
-Additional Email
-    Additional email addresses for the user can be input here. If email sending
-    is enabled on the server, notification emails will be sent to these
-    addresses in addition to the default user email. Separate multiple addresses
-    with the semicolon character (``;``).
+Receive email for project updates
+    Receive email notifications for category or project creation, updating,
+    moving and archiving.
+Receive email for project membership updates
+    Receive email notifications for category or project membership updates and
+    member invitation activity.
+
+
+.. figure:: _static/sodar_ui/user_profile_settings.png
+    :align: center
+    :scale: 60%
+
+    User settings view
+
+
+Additional Emails
+=================
+
+You can configure additional emails for your user account in case you want to
+receive automated emails to addresses other than your account's primary
+address. The user profile view displays additional emails and provides controls
+for managing these addresses.
+
+A new email address can be added with by clicking on the :guilabel:`Add Email`
+button. After creation, a verification email will be sent to the specified
+address. Opening a link contained in the email will verify the email. Only
+verified email addresses will receive automated emails from SODAR.
+
+For each email address displayed in the list, there are controls to re-send the
+verification email in case of an unverified email and deleting the address.
+
+
+Update User Details
+===================
 
 If local users are enabled on the site and you have a local SODAR account, the
 profile also includes the :guilabel:`Update User` button. This opens a form in
 which you can update your details and password. This form is **not** available
-for users authenticating with an existing user account via LDAP or SAML.
+for users authenticating with an existing user account via LDAP or OIDC.

requirements/base.txt

@@ -77,7 +77,7 @@ django-autocomplete-light==3.11.0
 
 # SODAR Core
 # django-sodar-core==1.0.1
--e git+https://github.com/bihealth/sodar-core.git@631b0063de6f723b0cd11ea1457e36d67ccffae0#egg=django-sodar-core
+-e git+https://github.com/bihealth/sodar-core.git@dac0069d08bb7d2d6e68a30b607eaa86e5cc4425#egg=django-sodar-core
 
 # Celery
 celery==5.3.6