Merge branch 'dev' into davrods-link-and-irods-batch-accept

CHANGELOG.rst

@@ -22,7 +22,7 @@ Added
     - Enable ``stem_cell_core_bulk`` ISA-Tab template (#1697)
     - Enable ``stem_cell_core_sc`` ISA-Tab template (#1697)
     - Enable ``tumor_normal_dna`` ISA-Tab template (#1697)
-    - General iRODS access ticket management for assay collections (#804)
+    - General iRODS access ticket management for assay collections (#804, #1717)
 - **Taskflowbackend**
     - ``BatchCalculateChecksumTask`` iRODS task (#1634)
     - Automated generation of missing checksums in ``zone_move`` flow (#1634)

docs_manual/source/api_irodsinfo.rst

@@ -0,0 +1,25 @@
+.. _api_irodsinfo:
+
+Irods Info API
+^^^^^^^^^^^^^^^^^
+
+The REST API for irods info operations is described in this document.
+
+
+API Views
+=========
+
+.. currentmodule:: irodsinfo.views_api
+
+.. autoclass:: IrodsConfigRetrieveAPIView
+
+
+Versioning
+==========
+
+For accept header versioning, the following header is expected in the current
+SODAR version:
+
+.. code-block:: console
+
+    Accept: application/vnd.bihealth.sodar+json; version=0.13.4

docs_manual/source/api_samplesheets.rst

@@ -15,6 +15,18 @@ API Views
 
 .. autoclass:: IrodsCollsCreateAPIView
 
+.. autoclass:: IrodsDataRequestListAPIView
+
+.. autoclass:: IrodsRequestCreateAPIView
+
+.. autoclass:: IrodsRequestUpdateAPIView
+
+.. autoclass:: IrodsRequestDeleteAPIView
+
+.. autoclass:: IrodsRequestAcceptAPIView
+
+.. autoclass:: IrodsRequestRejectAPIView
+
 .. autoclass:: SheetImportAPIView
 
 .. autoclass:: SheetISAExportAPIView

docs_manual/source/data_transfer_irods.rst

@@ -27,12 +27,6 @@ access the data from elsewhere on the network, you need to install the
 `official installation instructions <https://irods.org/download/>`_ for more
 information.
 
-.. note::
-
-    On Ubuntu 20.04, installing iCommands is not officially supported at the
-    time of writing. For workarounds,
-    `see this discussion <https://github.com/irods/irods/issues/4883>`_.
-
 To configure your iCommands connection, open the
 :ref:`ui_irods_info` application. In the app, click the
 :guilabel:`Download Configuration` button to download a configuration file

docs_manual/source/index.rst

@@ -117,6 +117,7 @@ Table of Contents
     Project Management API <api_projectroles>
     Sample Sheets API <api_samplesheets>
     Landing Zones API <api_landingzones>
+    iRODS Info API <api_irodsinfo>
     api_examples
 
 .. toctree::

irodsinfo/tests/test_permissions_api.py

@@ -0,0 +1,27 @@
+"""Tests for API view permissions in the irodsinfo app"""
+
+from django.urls import reverse
+
+# Projectroles dependency
+from projectroles.tests.test_permissions import TestPermissionBase
+
+
+class TestIrodsConfigRetrieveAPIView(TestPermissionBase):
+    """Tests for irodsinfo API"""
+
+    def setUp(self):
+        # Create users
+        self.superuser = self.make_user('superuser')
+        self.superuser.is_superuser = True
+        self.superuser.save()
+        self.regular_user = self.make_user('regular_user')
+        # No user
+        self.anonymous = None
+
+    def test_irods_config(self):
+        """Test permissions for IrodsConfigRetrieveAPIView"""
+        url = reverse('irodsinfo:api_env')
+        good_users = [self.superuser, self.regular_user]
+        bad_users = [self.anonymous]
+        self.assert_response(url, good_users, 200)
+        self.assert_response(url, bad_users, 401)

irodsinfo/tests/test_views_api.py

@@ -0,0 +1,37 @@
+"""Tests for API views in the irodsinfo app"""
+
+from django.test import override_settings
+from django.urls import reverse
+from rest_framework import status
+
+from test_plus.test import TestCase
+
+from irodsinfo.tests.test_views import PLUGINS_DISABLE_IRODS
+
+
+class TestIrodsConfigRetrieveAPIView(TestCase):
+    """Tests for IrodsConfigRetrieveAPIView"""
+
+    def setUp(self):
+        # Create users
+        self.superuser = self.make_user('superuser')
+        self.superuser.is_superuser = True
+        self.superuser.save()
+        self.regular_user = self.make_user('regular_user')
+
+    def test_get_irods_config(self):
+        """Test GET request to retrieve iRODS config"""
+        url = reverse('irodsinfo:api_env')
+        with self.login(self.regular_user):
+            response = self.client.get(url)
+        self.assertEqual(response.status_code, status.HTTP_200_OK)
+        self.assertIn('irods_environment', response.data)
+
+    @override_settings(ENABLED_BACKEND_PLUGINS=PLUGINS_DISABLE_IRODS)
+    def test_get_irods_config_with_disabled_backend(self):
+        """Test GET request to retrieve iRODS config with disabled backend"""
+        url = reverse('irodsinfo:api_env')
+        with self.login(self.regular_user):
+            response = self.client.get(url)
+        self.assertEqual(response.status_code, status.HTTP_404_NOT_FOUND)
+        self.assertIn('iRODS backend not enabled', response.data['detail'])

irodsinfo/urls.py

@@ -1,10 +1,13 @@
+"""URL patterns for the irodsinfo app"""
+
 from django.urls import path
 
-from . import views
+from irodsinfo import views, views_api
 
 app_name = 'irodsinfo'
 
-urlpatterns = [
+# UI views
+urls_ui = [
     path(
         route='info',
         view=views.IrodsInfoView.as_view(),
@@ -16,3 +19,14 @@
         name='config',
     ),
 ]
+
+# REST API views
+urls_api = [
+    path(
+        route='api/environment',
+        view=views_api.IrodsEnvRetrieveAPIView.as_view(),
+        name='api_env',
+    ),
+]
+
+urlpatterns = urls_ui + urls_api

irodsinfo/views.py

@@ -22,6 +22,45 @@
 logger = logging.getLogger(__name__)
 
 
+class IrodsConfigMixin:
+    """Mixin for iRODS configuration views"""
+
+    @staticmethod
+    def get_irods_client_env(user, irods_backend):
+        """
+        Create iRODS configuration file for the current user.
+        """
+        user_name = user.username
+        # Just in case Django mangles the user name case, as it might
+        if user_name.find('@') != -1:
+            user_name = (
+                user_name.split('@')[0] + '@' + user_name.split('@')[1].upper()
+            )
+        home_path = '/{}/home/{}'.format(settings.IRODS_ZONE, user_name)
+        cert_file_name = settings.IRODS_HOST + '.crt'
+
+        # Set up irods_environment.json
+        irods_env = dict(settings.IRODS_ENV_DEFAULT)
+        irods_env.update(
+            {
+                'irods_authentication_scheme': 'PAM',
+                'irods_cwd': home_path,
+                'irods_home': home_path,
+                'irods_host': settings.IRODS_HOST_FQDN,
+                'irods_port': settings.IRODS_PORT,
+                'irods_user_name': user_name,
+                'irods_zone_name': settings.IRODS_ZONE,
+            }
+        )
+        if settings.IRODS_CERT_PATH:
+            irods_env['irods_ssl_certificate_file'] = cert_file_name
+        # Get optional client environment overrides
+        irods_env.update(dict(settings.IRODS_ENV_CLIENT))
+        irods_env = irods_backend.format_env(irods_env)
+        logger.debug('iRODS environment: {}'.format(irods_env))
+        return irods_env
+
+
 class IrodsInfoView(LoggedInPermissionMixin, HTTPRefererMixin, TemplateView):
     """iRODS Information View"""
 
@@ -66,7 +105,9 @@ def get_context_data(self, *args, **kwargs):
         return context
 
 
-class IrodsConfigView(LoggedInPermissionMixin, HTTPRefererMixin, View):
+class IrodsConfigView(
+    IrodsConfigMixin, LoggedInPermissionMixin, HTTPRefererMixin, View
+):
     """iRODS Configuration file download view"""
 
     permission_required = 'irodsinfo.get_config'
@@ -77,34 +118,8 @@ def get(self, request, *args, **kwargs):
             messages.error(request, 'iRODS Backend not enabled.')
             return redirect(reverse('irodsinfo:info'))
 
-        user_name = request.user.username
-        # Just in case Django mangles the user name case, as it might
-        if user_name.find('@') != -1:
-            user_name = (
-                user_name.split('@')[0] + '@' + user_name.split('@')[1].upper()
-            )
-        home_path = '/{}/home/{}'.format(settings.IRODS_ZONE, user_name)
-        cert_file_name = settings.IRODS_HOST + '.crt'
-
-        # Set up irods_environment.json
-        irods_env = dict(settings.IRODS_ENV_DEFAULT)
-        irods_env.update(
-            {
-                'irods_authentication_scheme': 'PAM',
-                'irods_cwd': home_path,
-                'irods_home': home_path,
-                'irods_host': settings.IRODS_HOST_FQDN,
-                'irods_port': settings.IRODS_PORT,
-                'irods_user_name': user_name,
-                'irods_zone_name': settings.IRODS_ZONE,
-            }
-        )
-        if settings.IRODS_CERT_PATH:
-            irods_env['irods_ssl_certificate_file'] = cert_file_name
-        # Get optional client environment overrides
-        irods_env.update(dict(settings.IRODS_ENV_CLIENT))
-        irods_env = irods_backend.format_env(irods_env)
-        logger.debug('iRODS environment: {}'.format(irods_env))
+        # Create iRODS environment file
+        irods_env = self.get_irods_client_env(request.user, irods_backend)
         env_json = json.dumps(irods_env, indent=2)
 
         # Create zip archive
@@ -117,6 +132,7 @@ def get(self, request, *args, **kwargs):
         if settings.IRODS_CERT_PATH:
             try:
                 with open(settings.IRODS_CERT_PATH) as cert_file:
+                    cert_file_name = irods_env['irods_ssl_certificate_file']
                     zip_file.writestr(cert_file_name, cert_file.read())
             except FileNotFoundError:
                 logger.warning(

irodsinfo/views_api.py

@@ -0,0 +1,48 @@
+"""REST API views for the irodsinfo app"""
+
+import logging
+
+from rest_framework.permissions import IsAuthenticated
+from rest_framework.response import Response
+from rest_framework.views import APIView
+
+# Projectroles dependency
+from projectroles.plugins import get_backend_api
+
+from irodsinfo.views import IrodsConfigMixin
+
+
+logger = logging.getLogger(__name__)
+
+
+class IrodsEnvRetrieveAPIView(IrodsConfigMixin, APIView):
+    """
+    Retrieve iRODS environment file for the current user.
+
+    **URL:** ``/irods/api/environment``
+
+    **Methods:** ``GET``
+
+    **Returns:**
+
+    - ``irods_environment``: iRODS client environment
+    """
+
+    permission_classes = [IsAuthenticated]
+
+    def get(self, request, *args, **kwargs):
+        """Get iRODS environment file"""
+        try:
+            irods_backend = get_backend_api('omics_irods')
+            if not irods_backend:
+                return Response(
+                    {'detail': 'iRODS backend not enabled'}, status=404
+                )
+            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(
+                {'detail': 'iRODS config retrieval failed'}, status=400
+            )