Merge branch 'dev' into 'master'

merge v0.6.1 release

See merge request CUBI_Engineering/CUBI_Data_Mgmt/sodar_core!64

.travis.yml

@@ -5,6 +5,9 @@ language: python
 python:
   - "3.6"
 
+env:
+  - CHROME_DRIVER_VERSION="74.0.3729.6"
+
 before_install:
   - sudo apt-get update -qq
   - sudo apt-get install -qq build-essential zlib1g-dev libtiff5-dev libjpeg8-dev libfreetype6-dev
@@ -17,7 +20,6 @@ addons:
     packages:
       - python3.6
       - python3.6-dev
-      - chromium-chromedriver
   postgresql: "9.6"
   chrome: stable
 
@@ -29,7 +31,10 @@ before_script:
   - psql -c "CREATE USER sodar_core WITH PASSWORD 'sodar_core';" -U postgres
   - psql -c "GRANT ALL PRIVILEGES ON DATABASE sodar_core to sodar_core;" -U postgres
   - psql -c "ALTER USER sodar_core CREATEDB;" -U postgres
-  - ln -s /usr/lib/chromium-browser/chromedriver ~/bin/chromedriver
+  - wget -N http://chromedriver.storage.googleapis.com/$CHROME_DRIVER_VERSION/chromedriver_linux64.zip -P ~/
+  - unzip ~/chromedriver_linux64.zip -d ~/
+  - sudo mv -f ~/chromedriver /usr/bin/chromedriver
+  - sudo chmod ugo+rx /usr/bin/chromedriver
 
 script:
   - python manage.py collectstatic --noinput

CHANGELOG.rst

@@ -7,6 +7,51 @@ Changelog for the **SODAR Core** Django app package. Loosely follows the
 Note that the issue IDs here refer to ones in the private CUBI GitLab.
 
 
+v0.6.1 (2019-06-05)
+===================
+
+Added
+-----
+
+- **Filesfolders**
+    - Example project list columns (#265)
+    - Setting ``FILESFOLDERS_SHOW_LIST_COLUMNS`` to manage example project list columns (#265)
+- **Projectroles**
+    - Optional project list columns for project apps (#265)
+- **Sodarcache**
+    - ``delete_cache()`` API function (#257)
+
+Changed
+-------
+
+- **Projectroles**
+    - Refactor ``RemoteProject.get_project()`` (#262)
+    - Use ``get_info_link()`` in remote site list (#264)
+    - Define ``SYSTEM_USER_GROUP`` in ``SODAR_CONSTANTS`` (#251)
+    - Make pagedown textarea element resizeable and increase minimum height (#273)
+- **Sodarcache**
+    - Handle and log raised exceptions in ``synccache`` management command (#272)
+- **Userprofile**
+    - Disable user settings link if no settings are available (#260)
+
+Fixed
+-----
+
+- **General**
+    - Chrome and Chromedriver version mismatch in Travis-CI config (#254)
+- **Projectroles**
+    - Remove redundant ``get_project_list()`` call from ``project_detail.html``
+
+Removed
+-------
+
+- **Projectroles**
+    - Unused project statistics in the home view (#269)
+    - App settings deprecation protection (#245)
+- **Sodarcache**
+    - Unused ``TaskflowCacheUpdateAPIView`` (#205)
+
+
 v0.6.0 (2019-05-10)
 ===================
 
@@ -20,7 +65,7 @@ Added
     - ``user_settings`` field in project plugins (#16)
     - Optional ``label`` key for settings
     - Optional "wait for element" args in UI test helpers to ease Javascript testing (#230)
-    - ``get_info_link()``template tag (#239)
+    - ``get_info_link()`` template tag (#239)
     - ``get_setting_defs()`` API function for retrieving project and user setting definitions (#225)
     - ``get_all_defaults()`` API function for retrieving all default setting values (#225)
     - Human readable labels for app settings (#9)
@@ -39,7 +84,7 @@ Changed
 - **General**
     - Upgrade to ChromeDriver v74 (#221)
 - **Bgjobs**
-    - Ordering of background job for homgenization with downstream Varfish
+    - Job order to match downstream Varfish
 - **Filesfolders**
     - Update app settings (#246)
 - **Projectroles**

README.rst

@@ -1,8 +1,8 @@
 SODAR Core
 ^^^^^^^^^^
 
-.. image:: https://travis-ci.com/bihealth/sodar_core.svg?branch=master
-    :target: https://travis-ci.com/bihealth/sodar_core
+.. image:: https://travis-ci.org/bihealth/sodar_core.svg?branch=master
+    :target: https://travis-ci.org/bihealth/sodar_core
 
 .. image:: https://api.codacy.com/project/badge/Grade/404e8515825548b1aa5a44dbe3d45ece
     :target: https://www.codacy.com/app/bihealth/sodar_core

config/settings/base.py

@@ -501,7 +501,7 @@ def set_logging(debug):
 )
 FILESFOLDERS_SERVE_AS_ATTACHMENT = False
 FILESFOLDERS_LINK_BAD_REQUEST_MSG = 'Invalid request'
-
+FILESFOLDERS_SHOW_LIST_COLUMNS = True  # Custom project list column example
 
 # Adminalerts app settings
 ADMINALERTS_PAGINATION = 15

docs/source/breaking_changes.rst

@@ -13,6 +13,17 @@ version. For a complete list of changes in the current release, see the
 be missing. Please click "display source" if you want to read this in GitLab.
 
 
+v0.6.1 (2019-06-05)
+===================
+
+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)
 ===================
 

docs/source/conf.py

@@ -29,7 +29,7 @@
 # The short X.Y version
 version = '0.6'
 # The full version, including alpha/beta/rc tags
-release = '0.6.0'
+release = '0.6.1'
 
 
 # -- General configuration ---------------------------------------------------

docs/source/dev_project_app.rst

@@ -209,6 +209,8 @@ Implementing the following is **optional**:
   are needed. See the plugin point definition for an example.
 - ``search_types``: Implement if searching the data of the app is enabled
 - ``search_template``: Implement if searching the data of the app is enabled
+- ``project_list_columns``: Optional custom columns do be shown in the project
+  list. See the plugin point definition for an example.
 - ``get_taskflow_sync_data()``: Applicable only if working with
   ``sodar_taskflow`` and iRODS
 - ``get_object_link()``: If Django models are associated with the app. Used e.g.
@@ -217,6 +219,9 @@ Implementing the following is **optional**:
   search is enabled
 - ``get_statistics()``: Return statistics for the siteinfo app. See details in
   :ref:`the siteinfo documentation <app_siteinfo>`.
+- ``get_project_list_value()``: A function which **must** be implemented if
+  ``project_list_columns`` are defined, to retrieve a column cell value for a
+  specific project.
 
 Once you have implemented the ``rules.py`` and ``plugins.py`` files and added
 the app and its URL patterns to the Django site configuration, you can create
@@ -630,7 +635,7 @@ the result:
        }
 
 Search Template
-----------------
+---------------
 
 Projectroles will provide your template context the ``search_results`` object,
 which corresponds to the result dict of the aforementioned function. There are

docs/source/index.rst

@@ -26,6 +26,8 @@ which wants to make use of the following features:
 - Advanced project activity logging
 - Small file uploading and browsing
 - Managing server-side background jobs
+- Caching and aggregation of data from external services
+- Tracking site information and statistics
 
 Basics of Django site setup and instructions for third party packages used are
 considered out of scope for this documentation. Please refer instead to official

filesfolders/plugins.py

@@ -1,3 +1,4 @@
+from django.conf import settings
 from django.urls import reverse
 
 # Projectroles dependency
@@ -11,6 +12,13 @@
 # SODAR Constants
 APP_SETTING_SCOPE_PROJECT = SODAR_CONSTANTS['APP_SETTING_SCOPE_PROJECT']
 
+# Local constants
+SHOW_LIST_COLUMNS = (
+    settings.FILESFOLDERS_SHOW_LIST_COLUMNS
+    if hasattr(settings, 'FILESFOLDERS_SHOW_LIST_COLUMNS')
+    else False
+)
+
 
 class ProjectAppPlugin(ProjectAppPluginPoint):
     """Plugin for registering app with Projectroles"""
@@ -71,6 +79,23 @@ class ProjectAppPlugin(ProjectAppPluginPoint):
     #: Position in plugin ordering
     plugin_ordering = 30
 
+    project_list_columns = {
+        'files': {
+            'title': 'Files',
+            'width': 75,
+            'description': 'Small files stored for the project',
+            'active': SHOW_LIST_COLUMNS,
+            'align': 'right',
+        },
+        'links': {
+            'title': 'Links',
+            'width': 75,
+            'description': 'Hyperlinks defined in the small files app',
+            'active': SHOW_LIST_COLUMNS,
+            'align': 'right',
+        },
+    }
+
     def get_taskflow_sync_data(self):
         """
         Return data for syncing taskflow operations
@@ -174,3 +199,28 @@ def get_statistics(self):
                 'value': HyperLink.objects.all().count(),
             },
         }
+
+    def get_project_list_value(self, column_id, project):
+        """
+        Return a value for the optional additional project list column specific
+        to a project.
+
+        :param column_id: ID of the column (string)
+        :param project: Project object
+        :return: String (may contain HTML) or None
+        """
+        if column_id == 'files':
+            count = File.objects.filter(project=project).count()
+
+        elif column_id == 'links':
+            count = HyperLink.objects.filter(project=project).count()
+
+        if count > 0:
+            return '<a href="{}">{}'.format(
+                reverse(
+                    'filesfolders:list', kwargs={'project': project.sodar_uuid}
+                ),
+                count,
+            )
+
+        return count

filesfolders/tests/test_ui.py

@@ -450,3 +450,27 @@ def test_search_type_nonexisting(self):
             + urlencode({'s': 'test type:Jaix1au'})
         )
         self.assert_element_count(expected, url, 'sodar-ff-search-item')
+
+
+class TestHomeView(TestUIBase):
+    """Tests for appearance of filesfolders specific data in the home view"""
+
+    def test_project_list(self):
+        """Test custom filesfolders project list column visibility"""
+
+        users = [
+            self.superuser,
+            self.as_owner.user,
+            self.as_delegate.user,
+            self.as_contributor.user,
+            self.as_guest.user,
+            self.user_no_roles,
+        ]
+        url = reverse('home')
+
+        self.assert_element_exists(
+            users, url, 'sodar-pr-project-list-header-filesfolders-files', True
+        )
+        self.assert_element_exists(
+            users, url, 'sodar-pr-project-list-header-filesfolders-links', True
+        )

projectroles/app_settings.py

@@ -13,20 +13,6 @@
 
 
 class AppSettingAPI:
-    @classmethod
-    def _get_settings_dict(cls, app_plugin):
-        """
-        TEMPORARY DEPRECATION PROTECTION HELPER, TO BE REMOVED IN THE NEXT
-        RELEASE
-
-        :param app_plugin: Project app plugin object
-        :return: Dict
-        """
-        if not app_plugin.app_settings and app_plugin.project_settings:
-            return app_plugin.project_settings
-
-        return app_plugin.app_settings
-
     @classmethod
     def _check_project_and_user(cls, project, user):
         """
@@ -68,11 +54,8 @@ def get_default_setting(cls, app_name, setting_name):
         """
         app_plugin = get_app_plugin(app_name)
 
-        # NOTE: Deprecation protection, to be removed in the next release
-        settings_defs = cls._get_settings_dict(app_plugin)
-
-        if setting_name in settings_defs:
-            return settings_defs[setting_name]['default']
+        if setting_name in app_plugin.app_settings:
+            return app_plugin.app_settings[setting_name]['default']
 
         raise KeyError(
             'Setting "{}" not found in app plugin "{}"'.format(
@@ -202,17 +185,15 @@ def set_app_setting(
 
         except AppSetting.DoesNotExist:
             app_plugin = get_app_plugin(app_name)
-            # NOTE: Deprecation protection, to be removed in the next release
-            settings_defs = cls._get_settings_dict(app_plugin)
 
-            if setting_name not in settings_defs:
+            if setting_name not in app_plugin.app_settings:
                 raise KeyError(
                     'Setting "{}" not found in app plugin "{}"'.format(
                         setting_name, app_name
                     )
                 )
 
-            s_type = settings_defs[setting_name]['type']
+            s_type = app_plugin.app_settings[setting_name]['type']
 
             if validate:
                 cls.validate_setting(s_type, value)
@@ -267,22 +248,8 @@ def get_setting_defs(cls, plugin, scope):
         """
         cls._check_scope(scope)
 
-        # NOTE: Deprecation protection, to be removed in the next release
-        if (
-            not plugin.app_settings
-            and plugin.project_settings
-            and scope == APP_SETTING_SCOPE_PROJECT
-        ):
-            ret = plugin.project_settings
-
-        elif plugin.app_settings:
-            ret = {
-                k: v
-                for k, v in plugin.app_settings.items()
-                if 'scope' in v and v['scope'] == scope
-            }
-
-        else:
-            ret = {}
-
-        return ret
+        return {
+            k: v
+            for k, v in plugin.app_settings.items()
+            if 'scope' in v and v['scope'] == scope
+        }

projectroles/constants.py

@@ -40,6 +40,8 @@
         'CATEGORY': {'default': 'category', 'plural': 'categories'},
         'PROJECT': {'default': 'project', 'plural': 'projects'},
     },
+    # System user group
+    'SYSTEM_USER_GROUP': 'system',
 }
 
 

projectroles/models.py

@@ -902,11 +902,10 @@ def __repr__(self):
 
     def get_project(self):
         """Get the related Project object"""
-        try:
-            return Project.objects.get(sodar_uuid=self.project_uuid)
-
-        except Project.DoesNotExist:
-            return None
+        return (
+            self.project
+            or Project.objects.filter(sodar_uuid=self.project_uuid).first()
+        )
 
 
 # Abstract User Model ----------------------------------------------------------