add zone assay shortcut collection creation (#1869)

CHANGELOG.rst

@@ -8,6 +8,12 @@ Changelog for the SODAR project. Loosely follows the
 Unreleased
 ==========
 
+Added
+-----
+
+- **Landingzones**
+    - Create assay plugin shortcut collections for zones (#1869)
+
 Changed
 -------
 

docs_manual/source/sodar_release_notes.rst

@@ -13,6 +13,7 @@ v0.14.2 (WIP)
 
 Release for minor updates, maintenance and bug fixes.
 
+- Add assay plugin shortcut collection creation in landing zones
 - Fix iRODS data request issues
 - Fix LDAP TLS settings
 - Minor updates and bug fixes

landingzones/tests/test_views_taskflow.py

@@ -67,6 +67,8 @@
 ZONE_BASE_COLLS = [MISC_FILES_COLL, RESULTS_COLL, TRACK_HUBS_COLL]
 ZONE_PLUGIN_COLLS = ['0815-N1-DNA1', '0815-T1-DNA1']
 ZONE_ALL_COLLS = ZONE_BASE_COLLS + ZONE_PLUGIN_COLLS
+RAW_DATA_COLL = 'RawData'
+MAX_QUANT_COLL = 'MaxQuantResults'
 
 
 class LandingZoneTaskflowMixin:
@@ -239,8 +241,7 @@ def test_create_zone_colls(self):
             'configuration': '',
         }
         with self.login(self.user):
-            response = self.client.post(self.url, values)
-            self.assertRedirects(response, self.redirect_url)
+            self.client.post(self.url, values)
 
         self.assert_zone_count(1)
         zone = LandingZone.objects.first()
@@ -287,8 +288,7 @@ def test_create_zone_colls_plugin(self):
             'configuration': '',
         }
         with self.login(self.user):
-            response = self.client.post(self.url, values)
-            self.assertRedirects(response, self.redirect_url)
+            self.client.post(self.url, values)
 
         self.assert_zone_count(1)
         zone = LandingZone.objects.first()
@@ -304,6 +304,38 @@ def test_create_zone_colls_plugin(self):
             self.assert_irods_access(
                 self.user.username, os.path.join(zone_path, c), IRODS_ACCESS_OWN
             )
+        # These should not be created for this plugin
+        for c in [MAX_QUANT_COLL, RAW_DATA_COLL]:
+            self.assert_irods_coll(zone, c, False)
+
+    def test_create_zone_colls_plugin_shortcuts(self):
+        """Test landingzones creation with shortcut collections in plugin"""
+        self.assertEqual(LandingZone.objects.count(), 0)
+        # Set pep_ms plugin
+        self.assay.measurement_type = {'name': 'protein expression profiling'}
+        self.assay.technology_type = {'name': 'mass spectrometry'}
+        self.assay.save()
+        # NOTE: update_cache() not implemented in this plugin
+
+        values = {
+            'assay': str(self.assay.sodar_uuid),
+            'title_suffix': ZONE_SUFFIX,
+            'description': ZONE_DESC,
+            'create_colls': True,
+            'restrict_colls': False,
+            'configuration': '',
+        }
+        with self.login(self.user):
+            self.client.post(self.url, values)
+
+        self.assert_zone_count(1)
+        zone = LandingZone.objects.first()
+        self.assert_zone_status(zone, ZONE_STATUS_ACTIVE)
+        zone_colls = ZONE_BASE_COLLS + [RAW_DATA_COLL, MAX_QUANT_COLL]
+        for c in zone_colls:
+            self.assert_irods_coll(zone, c, True)
+        for c in ZONE_PLUGIN_COLLS:
+            self.assert_irods_coll(zone, c, False)
 
     # TODO: Test without sodarcache (see issue #1157)
 
@@ -332,8 +364,7 @@ def test_create_zone_colls_plugin_restrict(self):
             'configuration': '',
         }
         with self.login(self.user):
-            response = self.client.post(self.url, values)
-            self.assertRedirects(response, self.redirect_url)
+            self.client.post(self.url, values)
 
         self.assert_zone_count(1)
         zone = LandingZone.objects.first()

landingzones/views.py

@@ -187,6 +187,7 @@ def submit_create(
         colls = []
         if create_colls:
             logger.debug('Creating default landing zone collections..')
+            assay_path = irods_backend.get_path(zone.assay)
             colls = [RESULTS_COLL, MISC_FILES_COLL, TRACK_HUBS_COLL]
             plugin = zone.assay.get_plugin()
             # First try the cache
@@ -199,14 +200,24 @@ def submit_create(
                     project=zone.project,
                 )
                 if cache_obj and cache_obj.data:
-                    assay_path = irods_backend.get_path(zone.assay)
                     colls += [
                         p.replace(assay_path + '/', '')
                         for p in cache_obj.data['paths'].keys()
                     ]
                     logger.debug('Retrieved collections from cache')
-            elif plugin:
-                pass  # TODO: Build tables, get rows directly from plugin?
+            # TODO: If no cache, build tables and get rows directly from plugin?
+            # Add shortcut paths
+            if plugin:
+                shortcuts = plugin.get_shortcuts(zone.assay) or []
+                for s in shortcuts:
+                    path = s.get('path')
+                    if path:
+                        path = path.replace(assay_path + '/', '')
+                    if path and path not in colls:
+                        colls.append(path)
+                        logger.debug(
+                            'Added shorctut collection "{}"'.format(s.get('id'))
+                        )
 
         logger.debug('Collections to be created: {}'.format(', '.join(colls)))
         flow_name = 'landing_zone_create'