Major Changes

This document details highlighted updates and breaking changes in SODAR Core releases. It is recommended to review these notes whenever upgrading from an older SODAR Core version. For a complete list of changes in current and previous releases, see the full changelog.

v0.13.4 (2024-02-16)

Release Highlights

Add login message customization
Add missing LDAP settings in siteinfo
Improve project invite accept link reuse handling
Fix remote sync crash with target sites using SODAR Core <0.13.3
Fix LDAP settings on example site
General bug fixes and minor updates

Breaking Changes

System Prerequisites

The minimum Django version has been bumped to v3.2.24. Optional LDAP requirements in requirements/ldap.txt have also been upgraded.

v0.13.3 (2023-12-06)

Release Highlights

Add common project badge template
Add InvalidFormMixin helper mixin
Add user login/logout logging signals
Add createdevusers management command
Add LDAP TLS and user filter settings for example site
Prevent updating global app settings for remote projects
Fix hidden JSON project setting reset on non-superuser project update
Fix custom app setting validation calls in forms
Fix multiple remote sync app settings updating issues
Fix request object not provided to perform_project_modify() on create
General bug fixes and minor updates

Breaking Changes

System Prerequisites

The minimum Django version has been bumped to v3.2.23.

App Plugin UI Highlighting Changes

To fix issues in highlighting active project and site plugin views in the UI, app plugin detection has been updated. This may have adverse effects on your site if certain guidelines are not followed. To ensure the app highlighting in the UI works as expected, it is recommended to review the following:

The name attribute of each primary plugin in an app is expected to be named identically to the app, e.g. yourapp.
In case of multiple plugins within an app, additional plugins should be named starting with the app name, e.g. yourapp_site for an additional site app plugin for a project app.
In case of multiple plugins within an app, the urls attribute should only contain the views used within that plugin.

For more information on multi-plugin app development, see Multi-Plugin Apps.

v0.13.2 (2023-09-21)

Release Highlights

Add REST API project context queryset field override
Add sodar-btn-submit-once class for forms with usage
Fix project list view rendering issues with finder role
General bug fixes and minor updates

v0.13.1 (2023-08-30)

Release Highlights

Improve member invite views
Improve syncmodifyapi management command
Revise tour help
General bug fixes and minor updates

Breaking Changes

System Prerequisites

The django-plugins and drf-keyed-list dependencies have been upgraded from development installs to PyPI packages. In your site’s requirements/base.txt file, you should remove the existing dependencies for the aforementioned packages, as they will be automatically installed with the django-sodar-core package.

Template Tag get_role_display_name() Updated

The signature of the get_role_display_name() template tag in projectroles_common_tags has been updated. The first argument is now expected as a Role object instead of a RoleAssignment.

v0.13.0 (2023-06-01)

Release Highlights

Extend role inheritance to all roles
Add project finder role
Add periodic remote project sync using Celery
Add custom method support for app settings defaults, options and validation
Add project type restriction to app settings
Add site-wide scope to app settings
Add dismissed alerts view to appalerts
Add sodarcache item deletion via API
Add omitting of apps in search
Add custom template include path
Disallow public guest access for categories
Replace ProjectUserTag model with app settings
Change filesfolders app display name from “Small Files” to “Files”
General bug fixes and minor updates

Breaking Changes

New Context Processor Required

Certain sidebar related functionality has been moved into the new sidebar_processor context processor. You need to add this to your site in base.py under TEMPLATES:

TEMPLATES = [
    {
        'OPTIONS': {
            'context_processors': {
                # ...
                'projectroles.context_processors.sidebar_processor',
            }
        }
    }

New Mandatory Django Settings

The mandatory PROJECTROLES_TEMPLATE_INCLUDE_PATH Django setting has been added in this release. Please add this in your base.py config, preferably with the following syntax:

PROJECTROLES_TEMPLATE_INCLUDE_PATH = env.path(
    'PROJECTROLES_TEMPLATE_INCLUDE_PATH',
    os.path.join(APPS_DIR, 'templates', 'include'),
)

Role Inheritance Extended to All Roles

Inheriting roles from parent categories has been extended from the owner role to all roles. Access to inherited projects will be given automatically when updating your site to SODAR Core v0.13.

Inherited roles override “local” roles assigned to a specific project based on the role rank. Local roles can still be assigned to projects, but only promoting inherited users to a higher role is allowed.

The following steps are recommended:

Review your site’s existing project hierarchy and roles before upgrading to avoid unwanted inheritance.
Update the rules and permission tests in your site to ensure proper access for users to all views.

If your site uses the project modify API to e.g. update user access on external services, you need to update your modify API calls according to the new inheritance policy. The syncmodifyapi management command should be used to update existing roles, which means implemented perform_project_sync() methods should also be updated.

Project Finder Role Added

The project finder role has been added. For more information on this role, see Projectroles Basics. It is recommended to update permission tests and rules as applicable to ensure users with this role have proper access to your apps. The RoleMixin.init_roles() helper should be used in tests to initialize built-in roles correctly, unless inherited from a SODAR Core base test class.

REST API Backwards Compatibility

Due to changes in role inheritance, the REST API is no longer considered backwards compatible with older versions. Version 0.13.0 or higher must now be used. Note that target sites using a SODAR Core v0.12 source site or earlier have to be updated for remote project sync to work.

Projectroles Models API Updated

There have been multiple changes in the projectroles models API due to the role inheritance and ranking updates. Please consult Projectroles Django API Documentation to review specific changes and update any effected code.

RoleAssignmentManager along with the get_assignment() method have been removed. Instead, please use Project.get_role() or direct RoleAssignment model queries.
Project.get_all_roles() has been removed. Project.get_roles() should be used in its place.
Project.get_delegates() returns a list instead of a QuerySet. The method signature has also been changed.
For RoleAssignment.project, the related_name field has been renamed from roles into local_roles.
Project.get_children() returns projects sorted by full_title with the argument flat=True.

Base Classes for Tests Updated

Base classes such as TestProjectPermissionBase and TestUIBase have been updated. The default test category and project are now set up with separate users for all roles to help test extended role inheritance. This may cause some of your existing tests to fail. In that case, please update your tests to match the updated roles.

For manually populating Role objects in tests, it is strongly recommended for you to use the RoleMixin.init_roles() helper. This ensures roles and their ranks are correctly initialized.

Additionally, TestPermissionMixin._send_request() has been renamed into send_request().

ProjectUserTag Model Removed

The ProjectUserTag model has been removed. To our knowledge, it was only used for project starring in SODAR Core. This functionality has been reimplemented using app settings.

Advanced Search Uses POST Requests

Advanced search has been updated to use POST requests. This should not require any changes in the plugin search implementation. However, if you have set up view tests for advanced search in your apps, they may have to be updated.

Base Template Content Element Changed

The behaviour of the sodar-app-content element in the projectroles base template has changed. The element can now be assigned the sodar-app-content-project class if a project context is present. If you are referring to this element in custom Javascript, it is recommended to refer to the element with the ID #sodar-app-content instead of the class name.

System Prerequisites

Third party Python package dependencies have been upgraded. See the requirements directory for up-to-date package versions and upgrade your project.

Note that the upgrade to django-crispy-forms>=2.0 requires the separate installation of crispy-bootstrap4==2022.1. You also need to add crispy_bootstrap4 under THIRD_PARTY_APPS in your base configuration.

PROJECTROLES_HIDE_APP_LINKS Deprecated

The PROJECTROLES_HIDE_APP_LINKS Django setting has been depreacted. Instead, you should use PROJECTROLES_HIDE_PROJECT_APPS which now handles the same functionality. Support for the PROJECTROLES_HIDE_APP_LINKS setting will be removed in v1.0.

Deprecated App Settings API Methods Removed

The app settings API methods deprecated in v0.12 have been removed in this release. If you are still using deprecated methods, please refer to the list found in the v0.12.0 major changes notes below and update your API calls.

v0.12.0 (2023-02-03)

Release Highlights

Add project archiving
Add role ranking
Add timeline admin view for all events
Add timeline search
Add app settings retrieve/set REST API views
Add current user info Ajax API view
Add superuser info to REST API views
Rename app settings API methods
Fix path URL support

Breaking Changes

System Prerequisites

The minimum Django version has been bumped to v3.2.17.

App Settings API Methods Renamed

Several methods in AppSettingAPI have been renamed. The old named functions are deprecated and will be removed in SODAR Core v0.13. Please rename your method calls. The complete list of changed method names is as follows:

get_default_setting() -> get_default()
get_app_setting() -> get()
get_all_settings() -> get_all()
get_all_defaults() -> get_defaults()
set_app_setting() -> set()
delete_setting() -> delete()
validate_setting() -> validate()
get_setting_def() -> get_definition()
get_setting_defs() -> get_definitions()

Hiding Project App Links Affects Superusers

Hiding project app links from the project sidebar and project dropdown with PROJECTROLES_HIDE_APP_LINKS now also affects superusers. Note that the apps themselves can still be accessed if relevant URL are known or links provided to them elsewhere on the site.

Incorrectly Protected Mixin Methods Renamed

This release renames a large number of mixin methods in SODAR Core which had incorrectly set as protected by the _method_name() syntax. This affects many commonly used helpers in unit tests. If your tests fail with errors regarding undefined methods, rename your calls from _method() into method(). See the complete list of renamed methods for more details.

Timeline get_current_status() Method Removed

The deprecated ProjectEvent.get_current_status() method in the Timeline app has been removed. Please use get_status() instead.

Project Archiving Added

This release of SODAR Core adds the functionality to archive projects to make their data read-only for all users. You should update your project apps to support this behaviour.

For more information, see Project App Development.

v0.11.1 (2023-01-09)

Release Highlights

Add support for models from other apps in project access URL kwargs
Allow enabling project breadcrumb scrolling
Fix timeline app issues
Fix repository and environment issues
General bug fixes and minor updates

Breaking Changes

System Prerequisites

The following minimum versions have been bumped:

django>=3.2.16
setuptools>=65.6.3, <65.7
wheel>=0.38.4, <0.39

Hiding Project App Links Affects Superusers

Hiding project app links from the project sidebar and project dropdown with PROJECTROLES_HIDE_APP_LINKS now also affects superusers. Note that the apps themselves can still be accessed if relevant URL are known or links provided to them elsewhere on the site.

Incorrectly Protected Mixin Methods Renamed

This release renames a large number of mixin methods in SODAR Core which had incorrectly set as protected by the _method_name() syntax. This affects many commonly used helpers in unit tests. If your tests fail with errors regarding undefined methods, rename your calls from _method() into method(). See the complete list of renamed methods for more details.

Timeline get_current_status() Method Removed

The deprecated ProjectEvent.get_current_status() method in the Timeline app has been removed. Please use get_status() instead.

v0.11.0 (2022-09-23)

Release Highlights

Remove taskflowbackend app
Add project modifying API to replace built-in taskflowbackend
Enable including custom content in the login view
Upgrade general dependencies

Breaking Changes

Taskflowbackend Removed

This release of SODAR Core removes the taskflowbackend app. To our knowledge it has not been used in any other projects than SODAR itself. However, it is possible for the app to have been inadvertently enabled on your Django site, resulting in unexpected server errors once removed.

In case this happens, you need to first edit config/settings/base.py to remove taskflowbackend.apps.TaskflowbackendConfig from LOCAL_APPS. Also make sure taskflow is not included in the ENABLED_BACKEND_PLUGINS setting.

Next, run the Django shell and enter the following:

from djangoplugins.models import Plugin
Plugin.objects.get(name='taskflow').delete()

After this the server should run without issues.

Project.submit_status Removed

The submit_status field has been removed from the Project model, along with related helper method arguments and constants. This field was primarily used by SODAR Taskflow, but its removal may raise some issues in e.g. unit tests. If you encounter errors, refactor your code to remove references to the field.

REST API Backwards Compatibility

Due to some required changes to the REST API, it is no longer considered backwards compatible with older versions. Version 0.11.0 or higher must now be used. Note that target sites using a SODAR Core v0.11 source site also have to be updated for remote project sync to work.

Changes:

Remove owner argument requirement from ProjectUpdateAPIView.
Do not provide submit_status in ProjectListAPIView and ProjectRetrieveAPIView.

System Prerequisites

Changes in system requirements:

PostgreSQL v11 is now the minimum recommended version of the database.
The minimum Django version has been bumped to v3.2.15.
General Python dependencies have been upgraded, see requirements/*.txt

User Autocomplete Fields Updated

The django-autocomplete-light dependency has been upgraded to v3.9, which comes with potential incompatibilities. If you include widgets using DAL in your site’s views, you should upgrade them as follows:

Remove DAL related JS and CSS includes from your template (not including any possible custom event listeners)
Add {{ form.media }} to your template if not present.

For an example, see the roleassignment_form.html template.

Login Template Updated

The default login template login.html has been updated for including extended content via include/_login_extend.html. If you have overridden the login template with your own, ensure to update it accordingly to enable this new functionality.

v0.10.13 (2022-07-15)

Release Highlights

Add support for Taskflow testing from a different host or Docker network
Update contributing and development documentation
Repository updates
Bug fixes

Breaking Changes

System Prerequisites

The minimum Django version has been bumped to v3.2.14.

v0.10.12 (2022-04-19)

Release Highlights

Add support for specifying plugin name for Timeline events
Minor updates and optimization

Breaking Changes

System Prerequisites

The minimum Django version has been bumped to v3.2.13.

v0.10.11 (2022-03-22)

Release Highlights

Add sidebar icon resizing
Change project create form to require manual setting of project type
Fix project visibility in project list for inherited owners
General bug fixes and minor updates

Breaking Changes

Search Result Context Data in Tests

In context data for ProjectSearchResultsView, the app_search_data dictionary has been renamed into app_results. This does not affect implementing the search functionality from your apps, but if you test that functionality by asserting search view output, you have to rename this dict in your test cases.

v0.10.10 (2022-03-03)

Release Highlights

Fix layout issues
Fix search issues
General bug fixes and minor updates

Breaking Changes

N/A

v0.10.9 (2022-02-16)

Release Highlights

Add anonymous access support for Ajax API views
Update project list for client side loading
Update timeline app status change retrieval and rendering
Optimize project list queries
General bug fixes and minor updates

Breaking Changes

N/A

v0.10.8 (2022-02-02)

Release Highlights

Drop Python 3.7 support, add Python 3.10 support
Display missing site settings in siteinfo app
Fix project creation owner assignment for non-owner category members
Improve layout in siteinfo and timeline apps
Upgrade third party Python package dependencies
Optimize queries in timeline app

Breaking Changes

System Prerequisites

SODAR Core no longer supports Python 3.7. Python 3.8 is currently both the minimum and default version to run SODAR Core and its dependencies.

Third party Python package dependencies have been upgraded. See the requirements directory for up-to-date package versions and upgrade your project accordingly.

Deprecated Selenium Methods

The minimum Selenium version has been upgraded to v4.0.x. Some test methods have been deprecated in this version and will be removed in a future releases. UI test helpers from this version onwards will use the non-deprecated versions. You should the dependency in your projects, run tests, check the output and update any deprecated method calls if used.

Timeline App API Updated

If you are using TimelineAPI.get_event_description() in your own apps, please note that the method signature has changed. This may affect the use of positional arguments.

v0.10.7 (2021-12-14)

Release Highlights

Search bug fixes
REST API project type restriction fixes
General bug fixes and minor updates
Upgraded dependencies

Breaking Changes

System Prerequisites

The following minimum versions have been bumped:

django>=3.2.10, <3.3
python-ldap==3.4.0

API View Invalid Project Type Response

If project_type is set in a REST API view and that view is called with an disallowed value, the view will return HTTP 403 instead of 400. The cause for this response is included in the detail field.

v0.10.6 (2021-11-19)

Release Highlights

Add additional emails for users
Add project type restriction for API views
Add profiling middleware
Improve management command output
Improve user representation in email
Optimize project list queries
Timeline app bug fixes
Search results layout fixes
General bug fixes and minor updates
Upgraded dependencies

Breaking Changes

System Prerequisites

The minimum Django version has been bumped to v3.2.9.

Search Results DataTables Upgrade

DataTables includes on the search results page have been upgraded to version bs4/dt-1.11.3/b-2.0.1. You are advised to review the search results layout for your own apps to ensure everything looks correct.

Project.has_public_children() Removed

The Project model has_public_children() helper has been removed. In its place, you should use the Project.has_public_children field.

v0.10.5 (2021-09-20)

Release Highlights

Display project badge in app alerts
Custom email header and footer
Fix remote sync of non-projectroles app settings
Multiple app settings remote sync bug fixes
General bug fixes and minor updates
Upgraded dependencies

Breaking Changes

System Prerequisites

The minimum Django version has been bumped to v3.2.7.

Template Tag Removed

The get_plugin_name_by_id() template tag has been removed from projectroles_common_tags. There should be no reason to query app plugins by database ID. Please use e.g. the utilities found in projectroles.plugins instead.

v0.10.4 (2021-08-19)

Release Highlights

Appalerts list view UI improvements
Siteinfo app and UI improvements
Fix API and UI views to return 404 status code if object is not found
General bug fixes and minor updates
Upgraded dependencies

Breaking Changes

System Prerequisites

The minimum Django version has been bumped to v3.2.6.

Base UI and API View 404 Responses

Base UI and API views have been fixed to correctly return HTTP 404 to authorized users for resources that are not found. This may affect some test cases which still operate under the assumption of the views returning 403 instead.

v0.10.3 (2021-07-01)

Release Highlights

General bug fixes and minor updates
Upgraded dependencies

Breaking Changes

System Prerequisites

The minimum Django version has been bumped to v3.2.5.

The following third party Python package requirements have been upgraded:

sphinx-rtd-theme>=0.5.2, <0.6 (base)
black==21.6b0 (test)

v0.10.2 (2021-06-03)

Release Highlights

Project list bug fixes
General bug fixes and minor updates
Upgraded dependencies
Minor changes

Breaking Changes

System Prerequisites

The minimum Django version has been bumped to v3.2.4.

Third party Python package requirements have been upgraded. See the requirements directory for up-to-date package versions.

v0.10.1 (2021-05-06)

Release Highlights

Add JQuery status updating for app alerts
Make project available in PyPI
Critical bug fixes for remote sync
Bug fixes and minor updates

Breaking Changes

System Prerequisites

The minimum versions of dependencies have been bumped as follows:

Django: v3.2.1
Django-debug-toolbar: v3.2.1

Base Template Updated

If you are overriding the base_site.html with your own template and intend to use the appalerts app, please add the following snippet into the javascript block in {SITE}/templates/base.html:

{% block javascript %}
  {# ... #}
  <!-- App alerts Javascript -->
  {% include 'projectroles/_appalerts_include.html' %}
{% endblock javascript %}

Remote Sync Bug in v0.9

A bug in remote project sync was recently discovered in SODAR Core v0.9.x and v0.10.0. The bug has been fixed in this release, but the complete fix requires for both the SOURCE and TARGET sites to be upgraded to v0.10. If you need to use a site based on SODAR Core v0.9 as a remote sync target, please upgrade your site to this hotfix branch. Note that it is recommended to upgrade all your sites to v0.10 as soon as possible.

v0.10.0 (2021-04-28)

Release Highlights

Project upgraded to Django v3.2
Minimum Python version requirement upgraded to 3.7
Site icons access via Iconify
Material Design Icons used as default icon set
Appalerts app for app-generated user alerts
Site-wide timeline events
Timeline events without user
Allow public guest access to projects for authenticated and anonymous users
Display Django settings in Site Info app

Breaking Changes

System Prerequisites

Python version requirements have been upgraded as follows:

The minimum Python version is 3.7
The recommended Python version is 3.8
CI tests are run on Python 3.7, 3.8 and 3.9
Support for Python 3.6 has been dropped.

It is recommended to always use the most recent minor version of a Python release.

Third party Python package requirements have been upgraded. See the requirements directory for up-to-date package versions.

Ubuntu 20.04 Focal is now the recommended OS version for development.

Django v3.2 Upgrade

This release updates SODAR Core from Django v1.11 to v3.2. This is a breaking change which causes many updates and also requires updating several dependencies.

To upgrade, please update the Django requirement along with your site’s other Python requirements to match ones in requirements/*.txt. See Django deprecation documentation for details about what has been deprecated in Django and which changes are mandatory.

Common known issues:

Minimum version of PostgreSQL has been raised to v9.5.
ForeignKey fields in models must explicitly declare an on_delete argument.
is_authenticated() and is_anonymous() in the user model no longer work: use is_authenticated and is_anonymous instead.
Replace imports from django.core.urlresolvers with django.urls.
Replace django.contrib.postgres.fields.JSONField with django.db.models.JSONField.
Add DEFAULT_AUTO_FIELD = 'django.db.models.AutoField' in config/settings/base.py to get rid of database migration warnings.
Replace {% load staticfiles %} with {% load static %}.

In the future, the goal is to keep SODAR Core at the latest stable major version of Django, except for potential cases in which a critical third party package has not yet been updated to support a new release.

New Context Processors Required

The following new context processors are required if you intend to include any site apps to your projects, or make use of site-wide app alerts, respectively. To make use of these features, please add the following processors in base.py under TEMPLATES:

TEMPLATES = [
    {
        'OPTIONS': {
            'context_processors': {
                # ...
                'projectroles.context_processors.site_app_processor',
                'projectroles.context_processors.app_alerts_processor',
            }
        }
    }

REST API Updates

The following changes have been made to REST API views:

public_guest_access parameter added to project API views.

Site Icons Updated

Instead of directly including Font Awesome, site icons are now accessed as SVG using Iconify. The default icon set has been changed from Font Awesome to Material Design Icons. It is however possible to use other icon sets supported by Iconify for your own SODAR Core apps.

To make your icons work with SODAR Core v0.10+, you will need to take the following steps.

First, make sure django-iconify is installed. Add dj_iconify.apps.DjIconifyConfig to your Django site settings under THIRD_PARTY_APPS and dj_iconify.urls to your site URLs in config/urls.py. See SODAR Core or SODAR Django Site settings for an example.

You will also need to set ICONIFY_JSON_ROOT in the base Django settings.

ICONIFY_JSON_ROOT = os.path.join(STATIC_ROOT, 'iconify')

If you are overriding the base_site.html template, add the following lines to your base template:

<script type="text/javascript" src="{% url 'config.js' %}"></script>
<script type="text/javascript" src="{% static 'projectroles/js/iconify.min.js' %}"></script>

Next, you must download the Iconify JSON collection files required for hosting the icons on your Django server. It is recommended to use the geticons management command for this. By default, this downloads the required collections.json file along with the mdi.json file for the MDI icon collection.

$ ./manage.py geticons

If you wish to also use other collections than MDI, add them as a list using the -c argument. The following example downloads the additional carbon and clarity icon sets.

$ ./manage.py geticons -c carbon clarity

Make sure you run collectstatic after retrieving the collections for development.

Before committing your code, it is recommended to update your .gitignore file with the following lines:

*/static/iconify/*.json
*/static/iconify/json/*.json

To make the icons in your apps work with this change, you must change the icon syntax in your Django templates. Use iconify as the base class of the icon element. Enter the collection and icon name into the data-icon attribute.

Example:

<i class="iconify" data-icon="mdi:home"></i>

Also make sure to modify the icon attribute of your app plugins to include the full collection:name syntax for Iconify icons.

You may have to specify icon sizing manually in certain elements. In that case, use the data-height and/or data-width attributes. For spinning icons, add the spin class provided in projectroles.css.

Once you have updated all your icons, you can remove the Font Awesome CSS include from your base template if you are not directly importing it from base_site.html.

In certain client side Javascript implementations in which icons are loaded or replaced dynamically, you may have to refer to these URLs as a direct img element:

<img src="/icons/mdi/home.svg" />

For modifiers such as color and size when using img tags, see here.

Deprecated Features Removed

The following previously deprecated features have been removed in this release:

Project.get_full_title() has been removed. Use Project.full_title instead.
Old style search with a single search_term argument has been removed. Make sure your search implementation expects and uses a search_terms list instead.

Timeline API Changes

The signatures for get_object_url() and get_object_link() helpers have changed. They now expect the object itself as first argument, followed by an optional Project object. The same also applies for get_history_dropdown() in projectroles common template tags.

Public Guest Access Support

This version adds public guest access support for projects. By setting PROJECTROLES_ALLOW_ANONYMOUS true, this can be extended to anonymous users. For your views to properly support anonymous access, please use the override of LoginRequiredMixin provided in projectroles.views instead of the original mixin supplied in Django.

GitHub Repository Updates

The GitHub repository for the project has been renamed from sodar_core to sodar-core. Otherwise the URL remains the same: https://github.com/bihealth/sodar-core/

GitHub should redirect from the old name indefinitely. However, just to be sure it is recommend to update your site’s dependencies.

Additionally, the former master branch has been renamed to main.

v0.9.1 (2021-03-05)

Release Highlights

Add inline head include from environment variables in base template
Duplicate object UUIDs in REST API view nested lists

Breaking Changes

Base Template Updated

The base site template in projectroles/base_site.html has been updated. If you have copied the template to your own site’s base template to extend it, please make sure to copy the latest changes to maintain full compatibility. See diff between templates or search for lines containing inline_head_include.

Duplicate UUIDs in Nested REST API Lists

Nested object lists in SODAR Core REST API views are grouped into dictionaries using each object’s sodar_uuid. From this version onwards, the UUID fields are duplicated within each object as well. While this isn’t a breaking change in itself, if you use SODARNestedListSerializer it may cause some of your test cases to fail unless altered.

v0.9.0 (2021-02-03)

Release Highlights

Last major update based on Django v1.11
Enable modifying local app settings in project update form on target sites
Add projectroles app settings
Add remote sync for global projectroles app settings
Add IP address based access restriction for projects
Add SSO support via SAML
Add support for local user invites and local user account creation
Add batch invites and role updates via management command
Add REST API views for project invite management
Add advanced search with multiple terms
Add REST API view for current user info retrieval

Breaking Changes

Development Helper Scripts

Development helper scripts (.sh) have been replaced by a Makefile. Get an overview of the available commands via make usage.

System Prerequisites

Third party Python package requirements have been upgraded. See the requirements directory for up-to-date package versions.

The following third party JS/CSS requirements have been updated:

JQuery v3.5.1
Bootstrap v4.5.3

Note

This is the last major update of SODAR Core based on and supporting Django v1.11, which is now out of long term support. From v0.10 onwards, SODAR Core based sites must be implemented on Django v3.x+.

ProjectAppPlugin Search Updates

The expected signature for ProjectAppPluginPoint.search() has changed. Instead of the search_term string argument, search_terms is expected. This argument is a list of strings expected to be combined with OR operators.

See the filesfolders app for an example of the new implementation.

In SODAR Core v0.9, the old deprecated implementation still works, but searching for multiple terms in the “Advanced Search” view will only return results for the first search term given. This deprecation protection will be removed in the next major version. Please update the search() methods in your project app plugins if you have implemented them.

Project Full Title Field

The full title of a project, including the entire category path, can now be accessed via the Project.full_title. This enables you to use the field directly in your Django queries and ordering. The value of the field is auto-populated on Project.save() and in a database migration accompanied in this release.

As a result, the Project.get_full_title() has been deprecated and will be removed in the next major SODAR Core release. Please refactor your usage of that helper into referring to Project.full_title directly.

v0.8.4 (2020-11-12)

Release Highlights

This release updates documentation for JOSS submission.

Breaking Changes

N/A

v0.8.3 (2020-09-28)

Release Highlights

Fix issues in remote project synchronization
Fix crashes in siteinfo app from exceptions raised by plugins

Breaking Changes

Remote Project Sync and Local Categories

When working on a TARGET site, creating local projects under categories synchronized from a SOURCE site is no longer allowed. This is done to avoid synchronization clashes. If you want to enable local projects on your site in addition to remote ones, you will need to create a local root category for them.

API Changes

ProjectCreateAPIView now returns status 403 if called on a target site with disabled local projects, instead of 400 as before.

v0.8.2 (2020-07-22)

Release Highlights

Enable site-wide background jobs
Critical bug fixes for project member management
Minor fixes and updates

Breaking Changes

N/A

v0.8.1 (2020-04-24)

Release Highlights

Fix checking for remote project status in projectroles REST API views
Miscellaneous bug fixes

Breaking Changes

SODARAPIObjectInProjectPermissions Removed

The deprecated SODARAPIObjectInProjectPermissions base class has been removed from projectroles.views_api. Please base your REST API views to one of the remaining base classes instead.

v0.8.0 (2020-04-08)

Release Highlights

Add API views for the projectroles and filesfolders apps
Add new base view classes and mixins for API/Ajax views
Import the tokens API token management app from VarFish
Allow assigning roles other than owner for categories
Allow category delegates and owners to create sub-categories and projects
Allow moving categories and projects under different categories
Inherit owner permissions from parent categories
Allow displaying project apps in categories with category_enable
Reorganization of views in apps

Breaking Changes

Owner Permissions Inherited from Categories

Starting in this version of SODAR Core, category owner permissions are automatically inherited by projects below those categories, as well as possible subcategories. If this does not fit your use case, it is recommend to reorganize your project structure and/or give category access to admin users who have access to all projects anyway.

Projectroles Views Reorganized

Views, base views related mixins for the projectroles app have been reorganized in this version. Please review your projectroles imports.

The revised structure is as follows:

UI views and related mixins remain in projectroles.views
Ajax API view classes were moved into projectroles.views_ajax
REST API view classes moved into projectroles.views_api
Taskflow API view classes moved into projectroles.views_taskflow

The same applies to classes and mxins in view tests. See projectroles.tests.test_views* to update imports in your tests.

Renamed Projectroles View Classes

In addition to reorganizing classes into different views, certain view classes intended to be usable by other apps have been renamed. They are listed below.

UserAutocompleteAPIView -> UserAutocompleteAjaxView
UserAutocompleteRedirectAPIView -> UserAutocompleteRedirectAjaxView

API View Class Changes

SODARAPIBaseView and APIPermissionMixin have been removed. Please use appropriate classes and mixins found in projectroles.views_api and projectroles.views_ajax instead.

Base Test Class and Mixin Changes

Base test classes and helper mixins in projectroles have been changed as detailed below.

SODARAPIViewMixin has been moved into projectroles.test_views_api and renamed into SODARAPIViewTestMixin.
KnoxAuthMixin has been combined into SODARAPIViewTestMixin.
get_accept_header() returns the header as dict instead of a string.
assert_render200_ok() and assert_redirect() have been removed from TestPermissionBase. Please use assert_response() instead.

In addition to the aforementioned changes, certain minor setup details such as default user rights and may have changed. If you experience unexpected failures in your tests, please review the SODAR Core base test classes and helper methods, refactoring your tests where required.

User Group Updating

The set_user_group() helper has been moved from projectroles.utils into the SODARUser model. It is called automatically on SODARUser.save(), so manual calling of the method is not required for most cases.

System Prerequisites

The following third party JS/CSS requirements have been updated:

JQuery v3.4.1
Bootstrap v4.4.1
Popper.js v1.16.0

The minimum supported versions have been upgraded for a number of Python packages in this release. It is highly recommended to also upgrade these for your SODAR Core based site. See the requirements directory for up-to date dependencies.

The minimum version requirement for Django has been bumped to 1.11.29.

Default Templates Modified

The default template base_site.html has been modified in this version. If you override it with your own altered version, please review the difference and update your templates as appropriate.

SODAR Taskflow v0.4.0 Required

If using SODAR Taskflow, this release requires release v0.4.0 or higher due to required support for the role_update_irods_batch flow.

Known Issues

Category roles beyond owner are not synchronized to target sites in remote project sync. This was omitted to maintain compatibility in existing APIs in this release. The feature is intended to be implemented in SODAR Core v0.9.
Project/user app settings cannot be set or updated in the project REST API. A separate API for this will be developed. Currently the only way to modify app settings is via the GUI.

v0.7.2 (2020-01-31)

Release Highlights

Enforce API versions in remote project sync
Separate base API views for SODAR Core API and external SODAR site APIs
Redesign user autocomplete field
Set issuing user email to reply-to header for role and invite emails
Display hidden project app settings to superusers in project update form
Allow providing custom keyword arguments for backend plugin get_api() through get_backend_api()
Enable sorting custom project list columns in plugin definition
Bug fixes for project list columns

Breaking Changes

User Autocomplete Field Redesigned

User autocomplete field for forms with its related widget(s) have been redesigned with breaking API changes. Please review the Project App Development documentation and modify your implementation accordingly.

Remote Project Sync API Version Enforcing

The remote project sync view initiated from a TARGET site now sends the version number, making the SOURCE site enforce allowed API versions in its request. Hence, when a major breaking change is made on the source site and version requirements updated, requests from the target site will no longer work without upgrading to the latest SODAR Core version.

Exceptions Raised by get_backend_api()

The get_backend_api() method for retrieving backend plugin API objects no longer suppresses potential exceptions raised by API object initialization. If it is possible for your API object to raise an exception on initialization, you will need to handle it when calling this method.

System Prerequisites

The minimum version requirement for Django has been bumped to 1.11.27.

KnoxAuthMixin in Tests

Default API configuration for methods in KnoxAuthMixin are now set to internal SODAR Core API values. If you use the mixin in the tests of your site, please update the arguments in your method calls accordingly. You can also now supply the media_type argument for relevant functions. The get_accept_header() method has been moved to a separate SODARAPIViewMixin helper mixin.

v0.7.1 (2019-12-18)

Release Highlights

Project list layout and extra column handling improved
Allow customizing widgets in app settings
Enable managing global JS/CSS includes in Django settings
Initial support for deploying site in kiosk mode
Critical bug fixes for category and project owner management

Breaking Changes

Default Templates Modified

The default templates base_site.html and login.html have been modified in this version. If you override them with your own altered versions, please review the difference and update your templates as appropriate.

User Added to get_project_list_value()

The signature of the get_project_list_value() method implemented by project app plugins to return data for extra project list columns has changed. The user argument which provides the current user has been added. If using this feature, please make sure to update your implementation(s) of the method.

See Projectroles Django API Documentation to review the API changes.

v0.7.0 (2019-10-09)

Release Highlights

Sync peer project information for remote target sites
Enable revoking access to remote projects
Allow defining app settings in site apps
“User in project” scope added into app settings
Support JSON in app settings
Project owner management moved to project member views

Breaking Changes

System Prerequisites

The minimum supported versions have been upgraded for a number of Python packages in this release. It is highly recommended to also upgrade these for your SODAR Core based site. See the requirements directory for up-to date dependencies.

Backend Javascript Include

The code in base.html which was including javascript from backend apps to all templates in projectsroles was removed. Instead, Javascript and CSS associated to a backend plugin should now be included in app templates as needed. This is done using the newly introduced get_backend_include() template tag in projectroles_common_tags.

Deprecated get_setting() Tag Removed

The deprecated get_setting() template tag has been removed from projectroles_common_tags. Please use get_django_setting() in your templates instead.

ProjectSettingMixin Removed

In projectroles.tests.test_views, the deprecated ProjectSettingMixin was removed. If you need to populate app settings in your tests, use the AppSettingAPI instead.

AppSettingAPI get_setting_defs() Signature Changed

The get_settings_defs() function in the app settings API now accepts either a project app plugin or simply the name of the plugin as string. Due to this change, the signature of the API function including argument order has changed. Please see the API documentation for more details and update your function calls accordingly.

v0.6.2 (2019-06-21)

Release Highlights

Allow hiding app settings from UI forms
Add template tag for retrieving app settings

Breaking Changes

System Prerequisites

The minimum version requirement for Django has been bumped to 1.11.21.

Template Tag for Django Settings Access Renamed

The get_setting() template tag in projectroles_common_tags has been renamed into get_django_setting(). In this version the old tag still works, but this deprecation protection will be removed in the next release. Please update any references to this tag in your templates.

v0.6.1 (2019-06-05)

Release Highlights

Add custom project list columns definable in ProjectAppPlugin
Add example project list column implementation in the filesfolders app

Breaking Changes

App Settings Deprecation Protection Removed

The deprecation protection set up in the previous release has been removed. Project app plugins are now expected to declare app_settings in the format introduced in v0.6.0.

v0.6.0 (2019-05-10)

Release Highlights

Add user specific settings
Refactor project settings into project/user specific app settings
Add siteinfo app

Breaking Changes

App Settings (Formerly Project Settings)

The former Project Settings module has been completely overhauled in this version and requries changes to your app plugins.

The projectroles.project_settings module has been renamed into projectroles.app_settings. Please update your dependencies accordingly.

Settings must now be defined in app_settings. The format is identical to the previous project_settings dictionary, except that a scope field is expected for each settings. Currently valid values are “PROJECT” and “USER”. It is recommended to use the related constants from SODAR_CONSTANTS instead of hard coded strings.

Example of settings:

#: Project and user settings
app_settings = {
    'project_bool_setting': {
        'scope': 'PROJECT',
        'type': 'BOOLEAN',
        'default': False,
        'description': 'Example project setting',
    },
    'user_str_setting': {
        'scope': 'USER',
        'type': 'STRING',
        'label': 'String example',
        'default': '',
        'description': 'Example user setting',
    },
}

Warning

Deprecation protection is place in this version for retrieving settings from project_settings if it has not been changed into app_settings in your project apps. This protection will be removed in the next SODAR Core release.

v0.5.1 (2019-04-16)

Release Highlights

Sodarcache refactoring and improvements for API, models, management and app config
New default error templates

Breaking Changes

Site App Templates

Templates for site apps should extend projectroles/base.html. In earlier versions the documentation erroneously stated projectroles/project_base.html as the base template to use. Extending that document does work in this version as long as you override the given template blocks. However, it is not recommended and may break in the future.

Sodarcache App Changes

The following potentially breaking changes have been made to the sodarcache app.

App configuration naming has been changed to sodarcache.apps.SodarcacheConfig. Please update config/settings/base.py accordingly.

The field user has been made optional in models and the API.

An optional user argument has been added to ProjectAppPlugin.update_cache(). Correspondingly, the similar argument in ProjectCacheAPI.set_cache_item() has been made optional. Please update your plugin implementations and function calls accordingly.

The updatecache management command has been renamed to synccache.

Helper get_app_names() Fixed

The projectroles.utils.get_app_names() function will now return nested app names properly instead of omitting everything beyond the topmost module.

Default Admin Setting Deprecation Removed

The PROJECTROLES_ADMIN_OWNER setting no longer works. Use PROJECTROLES_DEFAULT_ADMIN instead.

v0.5.0 (2019-04-03)

Release Highlights

New sodarcache app for caching and aggregating data from external services
Local user mode for site UI and remote sync
Improved display and logging of remote project sync
Upgrade to Bootstrap 4.3.1

Breaking Changes

Default Admin Setting Renamed

The setting PROJECTROLES_ADMIN_OWNER has been renamed into PROJECTROLES_DEFAULT_ADMIN to better reflect its uses. Please rename this settings variable on your site configuration to prevent issues.

Note

In this release, the old settings value is still accepted in remote project management to avoid sudden crashes. This deprecation will be removed in the next release.

Bootstrap 4.3.1 Upgrade

The Bootstrap and Popper dependencies have been updated to the latest versions. Please test your site to make sure this does not result in compatibility issues. The known issue of HTML content not showing in popovers has already been fixed in projectroles.js.

Default Templates Modified

The default templates base_site.html and login.html have been modified in this version. If you override them with your own altered versions, please review the difference and update your templates as appropriate.

v0.4.5 (2019-03-06)

Release Highlights

Add user autocomplete in forms
Allow multiple delegates per project

Breaking Changes

System Prerequisites

The minimum version requirement for Django has been bumped to 1.11.20.

Project.get_delegate() Helper Renamed

As the limit for delegates per project is now arbitrary, the Project.get_delegate() helper function has been replaced by Project.get_delegates(). The new function returns a QuerySet.

Bootstrap 4 Crispy Forms Overrides Removed

Deprecated site-wide Bootstrap 4 theme overrides for django-crispy-forms were removed from the example site and are no longer supported. These workarounds were located in {SITE_NAME}/templates/bootstrap4/. Unless specifically required forms on your site, it is recommended to remove the files from your project.

Note

If you choose to keep the files or similar workarounds in your site, you are responsible of maintaining them and ensuring SODAR compatibility. Such site-wide template overrides are outside of the scope for SODAR Core components. Leaving the existing files in without maintenance may cause undesirable effects in the future.

Database File Upload Widget

Within SODAR Core apps, the only known issue caused by removal of the aforementioned Bootstrap 4 form overrides in the file upload widget of the django-db-file-upload package. If you are using the file upload package in your own SODAR apps and have removed the site-wide Crispy overrides, you can fix this particular widget by adding the following snippet into your form template. Make sure to replace {FIELD_NAME} with the name of your form field.

{% block css %}
  {{ block.super }}
  {# Workaround for django-db-file-storage Bootstrap4 issue (#164) #}
  <style type="text/css">
    div#div_id_{FIELD_NAME} div p.invalid-feedback {
    display: block;
  }
  </style>
{% endblock css %}

Alternatively, you can create a common override in your project-wide CSS file.

v0.4.4 (2019-02-19)

Release Highlights

N/A (maintenance/bugfix release)

Breaking Changes

Textarea Height in Forms

Due to this feature breaking the layout of certain third party components, textarea height in forms is no longer adjusted automatically. An exception to this are Pagedown-specific markdown fields.

To adjust the height of a textarea field in your forms, the easiest way is to modify the widget of the related field in the __init__() function of your form as follows:

self.fields['field_name'].widget.attrs['rows'] = 4

v0.4.3 (2019-01-31)

Release Highlights

Add display name configuration for projects and categories
Hide immutable fields in projectroles forms

Breaking Changes

SODAR Constants

PROJECT_TYPE_CHOICES has been removed from SODAR_CONSTANTS, as it can vary depending on implemented DISPLAY_NAMES. If needed, the currently applicable form structure can be imported from projectroles.forms.

v0.4.2 (2019-01-25)

Release Highlights

N/A (maintenance/bugfix release)

Breaking Changes

System Prerequisites

The following minimum version requirements have been upgraded in this release:

Django 1.11.18+
Bootstrap 4.2.1
JQuery 3.3.1
Numerous required Python packages (see requirements/*.txt)

Please go through your site requirements and update dependencies accordingly. For project stability, it is still recommended to use exact version numbers for Python requirements in your SODAR Core based site.

If you are overriding the projectroles/base_site.html in your site, make sure to update Javascript and CSS includes accordingly.

Note

Even though the recommended Python version from Django 1.11.17+ is 3.7, we only support Python 3.6 for this release. The reason is that some dependencies still exhibit problems with the most recent Python release at the time of writing.

ProjectAccessMixin

The _get_project() function in ProjectAccessMixin has been renamed into get_project(). Arguments for the function are now optional and may be removed in a subsequent release: self.request and self.kwargs of the view class will be used if the arguments are not present.

Base API View

The base SODAR API view has been renamed from BaseAPIView into SODARAPIBaseView.

Taskflow Backend API

The cleanup() function in TaskflowAPI now correctly raises a CleanupException if SODAR Taskflow encounters an error upon calling its cleanup operation. This change should not affect normally running your site, as the function in question should only be called during Taskflow testing.

v0.4.1 (2019-01-11)

Release Highlights

Configuration updates for API and Projectroles
Travis-CI setup

Breaking Changes

System Prerequisites

Changes in system requirements:

Ubuntu 16.04 Xenial is the target OS version.
Python 3.6 or newer required: 3.5 and older releases no longer supported.
PostgreSQL 9.6 is the recommended minimum version for the database.

Site Messages in Login Template

If your site overrides the default login template in projectroles/login.html, make sure your overridden version contains an include for projectroles/_messages.html. Following the SODAR Core template conventions, it should be placed as the first element under the container-fluid div in the content block. Otherwise, site app messages not requiring user authorization will not be visible on the login page. Example:

{% block content %}
  <div class="container-fluid">
    {# Django messages / site app messages #}
    {% include 'projectroles/_messages.html' %}
    {# ... #}
  </div>
{% endblock content %}

v0.4.0 (2018-12-19)

Release Highlights

Add filesfolders app from SODAR v0.4.0
Add bgjobs app from Varfish-Web
Secure SODAR Taskflow API views
Separate test server configuration for SODAR Taskflow
Extra data variable rendering for timeline
Additional site settings

Breaking Changes

List Button Classes in Templates

Custom small button and dropdown classes for including buttons within tables and lists have been modified. The naming has also been unified. The following classes should now be used:

Button group: sodar-list-btn-group (formerly sodar-edit-button-group)
Button: sodar-list-btn
Dropdown: sodar-list-dropdown (formerly sodar-edit-dropdown)

See projectroles templates for examples.

Warning

The standard bootstrap class btn-sm should not be used with these custom classes!

SODAR Taskflow v0.3.1 Required

If using SODAR Taskflow, this release requires release v0.3.1 or higher due to mandatory support of the TASKFLOW_SODAR_SECRET setting.

Taskflow Secret String

If you are using the taskflow backend app, you must set the value of TASKFLOW_SODAR_SECRET in your Django settings. Note that this must match the similarly named setting in your SODAR Taskflow instance!

v0.3.0 (2018-10-26)

Release Highlights

Add remote project metadata and member synchronization between multiple SODAR sites
Add adminalerts app
Add taskflowbackend app

Breaking Changes

Remote Site Setup

For specifying the role of your site in remote project metadata synchronization, you will need to add two new settings to your Django site configuration:

The PROJECTROLES_SITE_MODE setting sets the role of your site in remote project sync and it is mandatory. Accepted values are SOURCE and TARGET. For deployment, it is recommended to fetch this setting from environment variables.

If your site is set in TARGET mode, the boolean setting PROJECTROLES_TARGET_CREATE must also be included to control whether creation of local projects is allowed. If your site is in SOURCE mode, this setting can be included but will have no effect.

Furthermore, if your site is in TARGET mode you must include the PROJECTROLES_ADMIN_OWNER setting, which must point to an existing local superuser account on your site.

Example for a SOURCE site:

# Projectroles app settings
PROJECTROLES_SITE_MODE = env.str('PROJECTROLES_SITE_MODE', 'SOURCE')

Example for a TARGET site:

# Projectroles app settings
PROJECTROLES_SITE_MODE = env.str('PROJECTROLES_SITE_MODE', 'TARGET')
PROJECTROLES_TARGET_CREATE = env.bool('PROJECTROLES_TARGET_CREATE', True)
PROJECTROLES_ADMIN_OWNER = env.str('PROJECTROLES_ADMIN_OWNER', 'admin')

General API Settings

Add the following lines to your configuration to enable the general API settings:

SODAR_API_DEFAULT_VERSION = '0.1'
SODAR_API_MEDIA_TYPE = 'application/vnd.bihealth.sodar+json'

DataTables Includes

Includes for the DataTables Javascript library are no longer included in templates by default. If you want to use DataTables, include the required CSS and Javascript in relevant templates. See the projectroles/search.html template for an example.