prepare v0.14.0 release (#1638)

CHANGELOG.rst

@@ -5,14 +5,15 @@ Changelog for the SODAR project. Loosely follows the
 `Keep a Changelog <http://keepachangelog.com/en/1.0.0/>`_ guidelines.
 
 
-Unreleased
-==========
+v0.14.0 (2023-09-27)
+====================
 
 Added
 -----
 
 - **General**
     - Release cleanup issue template (#1797)
+    - LDAP settings for TLS and user filter (#1803)
 - **Irodsbackend**
     - ``get_trash_path()`` helper (#1658)
     - iRODS trash statistics for siteinfo (#1658)

config/settings/base.py

@@ -608,7 +608,7 @@ def set_logging(level=None):
 
 
 # General API settings
-SODAR_API_DEFAULT_VERSION = '0.13.4'
+SODAR_API_DEFAULT_VERSION = '0.14.0'
 SODAR_API_ALLOWED_VERSIONS = [
     '0.7.0',
     '0.7.1',
@@ -627,6 +627,7 @@ def set_logging(level=None):
     '0.13.2',
     '0.13.3',
     '0.13.4',
+    '0.14.0',
 ]
 SODAR_API_MEDIA_TYPE = 'application/vnd.bihealth.sodar+json'
 SODAR_API_DEFAULT_HOST = env.url(

docs_manual/source/api_documentation.rst

@@ -45,7 +45,7 @@ expected version.
 
 .. code-block:: console
 
-    Accept: application/vnd.bihealth.sodar+json; version=0.13.3
+    Accept: application/vnd.bihealth.sodar+json; version=0.14.0
 
 Specific sections of the SODAR API may require their own accept header. See the
 exact header requirement in the respective documentation on each section of the

docs_manual/source/api_examples.rst

@@ -41,9 +41,9 @@ the SODAR API:
     # Token authorization header (required)
     auth_header = {'Authorization': 'token {}'.format(api_token)}
     # Use core_headers for project management API endpoints
-    core_headers = {**auth_header, 'Accept': 'application/vnd.bihealth.sodar-core+json; version=0.13.0'}
+    core_headers = {**auth_header, 'Accept': 'application/vnd.bihealth.sodar-core+json; version=0.13.2'}
     # Use sodar_headers for sample sheet and landing zone API endpoints
-    sodar_headers = {**auth_header, 'Accept': 'application/vnd.bihealth.sodar+json; version=0.13.4'}
+    sodar_headers = {**auth_header, 'Accept': 'application/vnd.bihealth.sodar+json; version=0.14.0'}
 
 .. note::
 

docs_manual/source/api_irodsinfo.rst

@@ -1,9 +1,9 @@
 .. _api_irodsinfo:
 
 Irods Info API
-^^^^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^
 
-The REST API for irods info operations is described in this document.
+The REST API for the iRODS Info app is described in this document.
 
 
 API Views
@@ -22,4 +22,4 @@ SODAR version:
 
 .. code-block:: console
 
-    Accept: application/vnd.bihealth.sodar+json; version=0.13.4
+    Accept: application/vnd.bihealth.sodar+json; version=0.14.0

docs_manual/source/api_landingzones.rst

@@ -32,4 +32,4 @@ SODAR version:
 
 .. code-block:: console
 
-    Accept: application/vnd.bihealth.sodar+json; version=0.13.4
+    Accept: application/vnd.bihealth.sodar+json; version=0.14.0

docs_manual/source/api_projectroles.rst

@@ -23,4 +23,4 @@ in the current SODAR version:
 
 .. code-block:: console
 
-    Accept: application/vnd.bihealth.sodar-core+json; version=0.13.0
+    Accept: application/vnd.bihealth.sodar-core+json; version=0.13.2

docs_manual/source/api_samplesheets.rst

@@ -68,4 +68,4 @@ SODAR version:
 
 .. code-block:: console
 
-    Accept: application/vnd.bihealth.sodar+json; version=0.13.4
+    Accept: application/vnd.bihealth.sodar+json; version=0.14.0

docs_manual/source/app_samplesheets_irods_delete.rst

@@ -54,19 +54,22 @@ requests in the project as a project owner or delegate, open the
 
     iRODS delete request list
 
-The list provides a button for copying the iRODS path into the clipboard, status
-information for the requests, WebDAV link as well as dropdowns allowing you to
-either update or delete your requests. On the top of the page you can see a
-*Request Operations* dropdown with *Create Request* link for manual creation of
-delete requests.
+The list displays the label and status for existing requests. Buttons for
+copying the iRODS path into clipboard and opening the data object or collection
+in WebDAV are provided for each request. The request dropdown contains
+operations for updating, deleting, accepting and/or rejecting requests depending
+on your role in the project. The :guilabel:`Request Operations` dropdown on the
+top of the view contains options for manually creating a new requests as well
+as accepting and rejecting requests multiple requests at once.
 
 
 Manual Request Creation
 =======================
 
-Clicking the :guilabel:`Create Request` button takes you to a simple form where
-you can create a delete request by manually entering an iRODS path and an
-optional description.
+Selecting the :guilabel:`Create Request` option in the
+:guilabel:`Request Operations` dropdown takes you to a form in which you can
+create a delete request by manually entering an iRODS path. An optional
+description can also be provided.
 
 .. figure:: _static/app_samplesheets/irods_del_form.png
     :align: center
@@ -112,6 +115,7 @@ the request list. Once you have selected the requests, click the
 :guilabel:`Request Operations` dropdown and select either
 :guilabel:`Accept Selected` or :guilabel:`Reject Selected`.
 
-.. warning::
+.. note::
 
-    The requests for entire collections must be accepted or rejected individually.
+    Batch accepting or rejeting requests for entire collections is disabled.
+    They must be accepted or rejected individually from the request dropdown.

docs_manual/source/conf.py

@@ -26,7 +26,7 @@
 author = 'BIH Core Unit Bioinformatics'
 
 # The full version, including alpha/beta/rc tags
-release = '0.14.0-WIP'
+release = '0.14.0'
 
 
 # -- General configuration ---------------------------------------------------

docs_manual/source/sodar_release_notes.rst

@@ -8,8 +8,8 @@ list of changes in current and previous releases, see the
 :ref:`full changelog<sodar_changelog>`.
 
 
-v0.14.0 (WIP)
-=============
+v0.14.0 (2023-09-27)
+====================
 
 Major feature update.
 

docs_manual/source/ui_project_members.rst

@@ -61,10 +61,10 @@ inherited roles is not allowed. Inherited roles are marked in the member list
 with a downwards arrow along with a link to the category from which the role is
 inherited.
 
-Each project must have exactly one "local" (or non-inherited) owner. The amount
-of allowed delegates is set by the server administrators. The number of
-inherited owners and delegates are not limited. For contributors and guests, the
-amount per project or category is not limited.
+Each project must have exactly one "local" (non-inherited) owner. The amount of
+allowed delegates is set by the server administrators. The number of inherited
+owners and delegates are not limited. For contributors and guests, the amount
+per project or category is not limited.
 
 .. figure:: _static/sodar_ui/project_members_inherit.png
     :align: center

irodsadmin/tests/test_commands.py

@@ -222,8 +222,7 @@ def test_get_orphans_none(self):
         )
         output = out.getvalue()
         sys.stdout = sys.__stdout__
-
-        self.assertEqual('', output)
+        self.assertEqual(output, '')
 
     def test_get_orphans_assay(self):
         """Test get_orphans() with orphan assay"""
@@ -249,7 +248,7 @@ def test_get_orphans_assay(self):
             + orphan_path
             + ';0;0 bytes\n'
         )
-        self.assertEqual(expected, output)
+        self.assertEqual(output, expected)
 
     def test_get_orphans_study(self):
         """Test get_orphans() with orphan study"""
@@ -275,7 +274,7 @@ def test_get_orphans_study(self):
             + orphan_path
             + ';0;0 bytes\n'
         )
-        self.assertEqual(expected, output)
+        self.assertEqual(output, expected)
 
     def test_get_output_zone(self):
         """Test get_orphans() with orphan landing zone"""
@@ -306,7 +305,7 @@ def test_get_output_zone(self):
             + orphan_path
             + ';0;0 bytes\n'
         )
-        self.assertEqual(expected, output)
+        self.assertEqual(output, expected)
 
     def test_get_output_project(self):
         """Test get_orphans() with orphan project"""
@@ -332,7 +331,7 @@ def test_get_output_project(self):
         expected = (
             collection[3:] + ';' + DELETED + ';' + orphan_path + ';0;0 bytes\n'
         )
-        self.assertEqual(expected, output)
+        self.assertEqual(output, expected)
 
     def test_get_output_assay_subs(self):
         """Test get_orphans() with orphan assay subcollections"""
@@ -360,7 +359,7 @@ def test_get_output_assay_subs(self):
             + orphan_path
             + ';0;0 bytes\n'
         )
-        self.assertEqual(expected, output)
+        self.assertEqual(output, expected)
 
     def test_get_output_deleted_project(self):
         """Test get_output() with a deleted project"""
@@ -387,7 +386,7 @@ def test_get_output_deleted_project(self):
         expected = (
             project_uuid + ';' + DELETED + ';' + orphan_path + ';0;0 bytes\n'
         )
-        self.assertEqual(expected, output)
+        self.assertEqual(output, expected)
 
     def test_command_no_orphans(self):
         """Test command with no orphans"""
@@ -396,7 +395,7 @@ def test_command_no_orphans(self):
         call_command('irodsorphans', stdout=out)
         output = out.getvalue()
         sys.stdout = sys.__stdout__
-        self.assertEqual('', output)
+        self.assertEqual(output, '')
 
     def test_command_orphan_assay(self):
         """Test command with orphan assay"""
@@ -410,7 +409,7 @@ def test_command_orphan_assay(self):
             self.project.full_title,
             orphan_path,
         )
-        self.assertEqual(expected, output)
+        self.assertEqual(output, expected)
 
     def test_command_orphan_study(self):
         """Test command with orphan study"""
@@ -424,7 +423,7 @@ def test_command_orphan_study(self):
             self.project.full_title,
             orphan_path,
         )
-        self.assertEqual(expected, output)
+        self.assertEqual(output, expected)
 
     def test_command_orphan_zone(self):
         """Test command with orphan landing zone"""
@@ -442,7 +441,7 @@ def test_command_orphan_zone(self):
             self.project.full_title,
             orphan_path,
         )
-        self.assertEqual(expected, output)
+        self.assertEqual(output, expected)
 
     def test_command_orphan_project(self):
         """Test command with orphan project"""
@@ -459,7 +458,7 @@ def test_command_orphan_project(self):
         expected = '{};{};{};0;0 bytes\n'.format(
             project_uuid, DELETED, orphan_path
         )
-        self.assertEqual(expected, output)
+        self.assertEqual(output, expected)
 
     def test_command_orphan_assay_sub(self):
         """Test command with orphan assay subcollection"""
@@ -474,7 +473,7 @@ def test_command_orphan_assay_sub(self):
             self.project.full_title,
             orphan_path,
         )
-        self.assertEqual(expected, output)
+        self.assertEqual(output, expected)
 
     def test_command_multiple(self):
         """Test command with multiple orphans"""
@@ -501,7 +500,7 @@ def test_command_multiple(self):
             self.project.full_title,
             orphan_path,
         )
-        self.assertEqual(expected, output)
+        self.assertEqual(output, expected)
 
     def test_command_ordering(self):
         """Test ordering of orphans in command output"""
@@ -510,25 +509,22 @@ def test_command_ordering(self):
         )
         self.irods.collections.create(orphan_path)
 
-        project1 = self.make_project('A_Project', PROJECT_TYPE_PROJECT, None)
-        self.make_assignment(project1, self.user, self.role_owner)
+        project2 = self.make_project('TestProject2', PROJECT_TYPE_PROJECT, None)
+        self.make_assignment(project2, self.user, self.role_owner)
         orphan_path2 = '{}/sample_data/study_{}'.format(
-            self.irods_backend.get_path(project1), str(uuid.uuid4())
+            self.irods_backend.get_path(project2), str(uuid.uuid4())
         )
         self.irods.collections.create(orphan_path2)
 
-        # Run the orphans management command
         output = self.catch_stdout()
-        # As the title of self.project is 'Test Project', it should be ordered
-        # after project1 with title 'A_Project'
         expected = '{};{};{};0;0 bytes\n'.format(
-            str(project1.sodar_uuid),
-            project1.full_title,
-            orphan_path2,
-        )
-        expected += '{};{};{};0;0 bytes\n'.format(
             str(self.project.sodar_uuid),
             self.project.full_title,
             orphan_path,
         )
-        self.assertEqual(expected, output)
+        expected += '{};{};{};0;0 bytes\n'.format(
+            str(project2.sodar_uuid),
+            project2.full_title,
+            orphan_path2,
+        )
+        self.assertEqual(output, expected)

irodsbackend/tests/test_views.py

@@ -46,8 +46,6 @@ class IrodsbackendViewTestBase(TaskflowViewTestBase):
     def setUp(self):
         super().setUp()
         self.req_factory = RequestFactory()
-        # self.irods_backend = get_backend_api('omics_irods')
-        # self.irods = self.irods_backend.get_session_obj()
         # Init project with owner in taskflow
         self.project, self.owner_as = self.make_project_taskflow(
             'TestProject', PROJECT_TYPE_PROJECT, self.category, self.user

irodsinfo/views_api.py

@@ -40,7 +40,6 @@ def get(self, request, *args, **kwargs):
                 )
             env = self.get_irods_client_env(request.user, irods_backend)
             return Response({'irods_environment': env})
-
         except Exception as ex:
             logger.error('iRODS config retrieval failed: {}'.format(ex))
             return Response(

samplesheets/assayapps/cytof/plugins.py

@@ -45,7 +45,8 @@ class SampleSheetAssayPlugin(SampleSheetAssayPluginPoint):
     #: Toggle displaying of row-based iRODS links in the assay table
     display_row_links = True
 
-    def __get_mc_assay_name(self, row, table):
+    @classmethod
+    def _get_mc_assay_name(cls, row, table):
         """
         Return assay name of last mass cytometry process.
         Also works when there are consecutive processes of the same name.
@@ -66,8 +67,7 @@ def __get_mc_assay_name(self, row, table):
             ):
                 top_header = get_top_header(table, i)
                 span_end = i + top_header['colspan']
-
-            # consider only columns of mass cytometry process
+            # Consider only columns of mass cytometry process
             if i < span_end and header['value'].lower() == 'assay name':
                 name = cell['value']
         return name
@@ -85,7 +85,7 @@ def get_row_path(self, row, table, assay, assay_path):
         :return: String with full iRODS path or None
         """
         # Get the value of Mass cytometry Assay Name column
-        mc_assay_name = self.__get_mc_assay_name(row, table)
+        mc_assay_name = self._get_mc_assay_name(row, table)
         if mc_assay_name:
             return assay_path + '/' + mc_assay_name
 
@@ -100,14 +100,11 @@ def update_row(self, row, table, assay):
         """
         if not settings.IRODS_WEBDAV_ENABLED or not assay:
             return row
-
         assay_path = self.get_assay_path(assay)
         if not assay_path:
             return row
-
         # Get the value of Mass cytometry Assay Name column
-        mc_assay_name = self.__get_mc_assay_name(row, table)
-
+        mc_assay_name = self._get_mc_assay_name(row, table)
         if not mc_assay_name:
             return row
 
@@ -157,7 +154,6 @@ def update_row(self, row, table, assay):
                 row[i]['link'] = (
                     base_url + '/' + mc_assay_name + '/' + row[i]['value']
                 )
-
         return row
 
     def update_cache(self, name=None, project=None, user=None):