fix: constants

irodsadmin/management/commands/irodsorphans.py

@@ -12,6 +12,7 @@
 from projectroles.plugins import get_backend_api
 
 # Landingzones dependency
+from landingzones.constants import ZONE_STATUS_MOVED, ZONE_STATUS_DELETED
 from landingzones.models import LandingZone
 
 # Samplesheets dependency
@@ -84,7 +85,7 @@ def get_zone_collections(irods_backend):
     return [
         irods_backend.get_path(lz)
         for lz in LandingZone.objects.filter(
-            ~(Q(status='MOVED') & Q(status='DELETED'))
+            ~(Q(status=ZONE_STATUS_MOVED) & Q(status=ZONE_STATUS_DELETED))
         )
     ]
 

landingzones/constants.py

@@ -0,0 +1,91 @@
+"""Constants for the landingzones app"""
+
+# Status types for landing zones
+ZONE_STATUS_OK = 'OK'
+ZONE_STATUS_CREATING = 'CREATING'
+ZONE_STATUS_NOT_CREATED = 'NOT CREATED'
+ZONE_STATUS_ACTIVE = 'ACTIVE'
+ZONE_STATUS_PREPARING = 'PREPARING'
+ZONE_STATUS_VALIDATING = 'VALIDATING'
+ZONE_STATUS_MOVING = 'MOVING'
+ZONE_STATUS_MOVED = 'MOVED'
+ZONE_STATUS_FAILED = 'FAILED'
+ZONE_STATUS_DELETING = 'DELETING'
+ZONE_STATUS_DELETED = 'DELETED'
+
+ZONE_STATUS_TYPES = [
+    ZONE_STATUS_CREATING,
+    ZONE_STATUS_NOT_CREATED,
+    ZONE_STATUS_ACTIVE,
+    ZONE_STATUS_PREPARING,
+    ZONE_STATUS_VALIDATING,
+    ZONE_STATUS_MOVING,
+    ZONE_STATUS_MOVED,
+    ZONE_STATUS_FAILED,
+    ZONE_STATUS_DELETING,
+    ZONE_STATUS_DELETED,
+]
+
+DEFAULT_STATUS_INFO = {
+    ZONE_STATUS_CREATING: 'Creating landing zone in iRODS',
+    ZONE_STATUS_NOT_CREATED: 'Creating landing zone in iRODS failed (unknown problem)',
+    ZONE_STATUS_ACTIVE: 'Available with write access for user',
+    ZONE_STATUS_PREPARING: 'Preparing transaction for validation and moving',
+    ZONE_STATUS_VALIDATING: 'Validation in progress, write access disabled',
+    ZONE_STATUS_MOVING: 'Validation OK, moving files into sample data repository',
+    ZONE_STATUS_MOVED: 'Files moved successfully, landing zone removed',
+    ZONE_STATUS_FAILED: 'Validation/moving failed (unknown problem)',
+    ZONE_STATUS_DELETING: 'Deleting landing zone',
+    ZONE_STATUS_DELETED: 'Landing zone deleted',
+}
+STATUS_INFO_DELETE_NO_COLL = (
+    'No iRODS collection for zone found, marked as deleted'
+)
+
+STATUS_STYLES = {
+    ZONE_STATUS_CREATING: 'bg-warning',
+    ZONE_STATUS_NOT_CREATED: 'bg-danger',
+    ZONE_STATUS_ACTIVE: 'bg-info',
+    ZONE_STATUS_PREPARING: 'bg-warning',
+    ZONE_STATUS_VALIDATING: 'bg-warning',
+    ZONE_STATUS_MOVING: 'bg-warning',
+    ZONE_STATUS_MOVED: 'bg-success',
+    ZONE_STATUS_FAILED: 'bg-danger',
+    ZONE_STATUS_DELETING: 'bg-warning',
+    ZONE_STATUS_DELETED: 'bg-secondary',
+}
+
+# Status types for which zone validation, moving and deletion are allowed
+STATUS_ALLOW_UPDATE = [ZONE_STATUS_ACTIVE, ZONE_STATUS_FAILED]
+
+# Status types for zones for which activities have finished
+STATUS_FINISHED = [
+    ZONE_STATUS_MOVED,
+    ZONE_STATUS_NOT_CREATED,
+    ZONE_STATUS_DELETED,
+]
+
+# Status types which lock the project in Taskflow
+STATUS_LOCKING = [
+    ZONE_STATUS_PREPARING,
+    ZONE_STATUS_VALIDATING,
+    ZONE_STATUS_MOVING,
+]
+
+# Status types for busy landing zones
+STATUS_BUSY = [
+    ZONE_STATUS_CREATING,
+    ZONE_STATUS_PREPARING,
+    ZONE_STATUS_VALIDATING,
+    ZONE_STATUS_MOVING,
+    ZONE_STATUS_DELETING,
+]
+
+# Status types during which file lists and stats should be displayed
+STATUS_DISPLAY_FILES = [
+    ZONE_STATUS_ACTIVE,
+    ZONE_STATUS_PREPARING,
+    ZONE_STATUS_VALIDATING,
+    ZONE_STATUS_MOVING,
+    ZONE_STATUS_FAILED,
+]

landingzones/management/commands/busyzones.py

@@ -5,7 +5,8 @@
 # Projectroles dependency
 from projectroles.management.logging import ManagementCommandLogger
 
-from landingzones.models import LandingZone, STATUS_BUSY
+from landingzones.constants import STATUS_BUSY
+from landingzones.models import LandingZone
 
 
 logger = ManagementCommandLogger(__name__)

landingzones/management/commands/inactivezones.py

@@ -10,6 +10,7 @@
 from projectroles.management.logging import ManagementCommandLogger
 from projectroles.plugins import get_backend_api
 
+from landingzones.constants import ZONE_STATUS_MOVED, ZONE_STATUS_DELETED
 from landingzones.models import LandingZone
 
 
@@ -20,7 +21,7 @@ def get_inactive_zones(weeks=2):
     """Return landing zones last modified over n weeks ago"""
     return LandingZone.objects.filter(
         date_modified__lte=localtime() - timedelta(weeks=weeks)
-    ).exclude(status__in=('DELETED', 'MOVED'))
+    ).exclude(status__in=(ZONE_STATUS_MOVED, ZONE_STATUS_DELETED))
 
 
 def get_output(zones, irods_backend, irods):

landingzones/models.py

@@ -9,81 +9,12 @@
 # Samplesheets dependency
 from samplesheets.models import Assay
 
+import landingzones.constants as lc
+
 # Access Django user model
 AUTH_USER_MODEL = getattr(settings, 'AUTH_USER_MODEL', 'auth.User')
 
 
-# Status types for landing zones
-ZONE_STATUS_OK = 'OK'
-ZONE_STATUS_CREATING = 'CREATING'
-ZONE_STATUS_NOT_CREATED = 'NOT CREATED'
-ZONE_STATUS_ACTIVE = 'ACTIVE'
-ZONE_STATUS_PREPARING = 'PREPARING'
-ZONE_STATUS_VALIDATING = 'VALIDATING'
-ZONE_STATUS_MOVING = 'MOVING'
-ZONE_STATUS_MOVED = 'MOVED'
-ZONE_STATUS_FAILED = 'FAILED'
-ZONE_STATUS_DELETING = 'DELETING'
-ZONE_STATUS_DELETED = 'DELETED'
-
-ZONE_STATUS_TYPES = [
-    ZONE_STATUS_CREATING,
-    ZONE_STATUS_NOT_CREATED,
-    ZONE_STATUS_ACTIVE,
-    ZONE_STATUS_PREPARING,
-    ZONE_STATUS_VALIDATING,
-    ZONE_STATUS_MOVING,
-    ZONE_STATUS_MOVED,
-    ZONE_STATUS_FAILED,
-    ZONE_STATUS_DELETING,
-    ZONE_STATUS_DELETED,
-]
-
-DEFAULT_STATUS_INFO = {
-    ZONE_STATUS_CREATING: 'Creating landing zone in iRODS',
-    ZONE_STATUS_NOT_CREATED: 'Creating landing zone in iRODS failed (unknown problem)',
-    ZONE_STATUS_ACTIVE: 'Available with write access for user',
-    ZONE_STATUS_PREPARING: 'Preparing transaction for validation and moving',
-    ZONE_STATUS_VALIDATING: 'Validation in progress, write access disabled',
-    ZONE_STATUS_MOVING: 'Validation OK, moving files into sample data repository',
-    ZONE_STATUS_MOVED: 'Files moved successfully, landing zone removed',
-    ZONE_STATUS_FAILED: 'Validation/moving failed (unknown problem)',
-    ZONE_STATUS_DELETING: 'Deleting landing zone',
-    ZONE_STATUS_DELETED: 'Landing zone deleted',
-}
-STATUS_INFO_DELETE_NO_COLL = (
-    'No iRODS collection for zone found, marked as deleted'
-)
-
-STATUS_STYLES = {
-    ZONE_STATUS_CREATING: 'bg-warning',
-    ZONE_STATUS_NOT_CREATED: 'bg-danger',
-    ZONE_STATUS_ACTIVE: 'bg-info',
-    ZONE_STATUS_PREPARING: 'bg-warning',
-    ZONE_STATUS_VALIDATING: 'bg-warning',
-    ZONE_STATUS_MOVING: 'bg-warning',
-    ZONE_STATUS_MOVED: 'bg-success',
-    ZONE_STATUS_FAILED: 'bg-danger',
-    ZONE_STATUS_DELETING: 'bg-warning',
-    ZONE_STATUS_DELETED: 'bg-secondary',
-}
-
-# Status types for which zone validation, moving and deletion are allowed
-STATUS_ALLOW_UPDATE = ['ACTIVE', 'FAILED']
-
-# Status types for zones for which activities have finished
-STATUS_FINISHED = ['MOVED', 'NOT CREATED', 'DELETED']
-
-# Status types which lock the project in Taskflow
-STATUS_LOCKING = ['PREPARING', 'VALIDATING', 'MOVING']
-
-# Status types for busy landing zones
-STATUS_BUSY = ['CREATING', 'PREPARING', 'VALIDATING', 'MOVING', 'DELETING']
-
-# Status types during which file lists and stats should be displayed
-STATUS_DISPLAY_FILES = ['ACTIVE', 'PREPARING', 'VALIDATING', 'MOVING', 'FAILED']
-
-
 class LandingZone(models.Model):
     """Class representing an user's iRODS landing zone for an assay"""
 
@@ -121,7 +52,7 @@ class LandingZone(models.Model):
         max_length=64,
         null=False,
         blank=False,
-        default='CREATING',
+        default=lc.ZONE_STATUS_CREATING,
         help_text='Status of landing zone',
     )
 
@@ -130,7 +61,7 @@ class LandingZone(models.Model):
         max_length=1024,
         null=True,
         blank=True,
-        default=DEFAULT_STATUS_INFO['CREATING'],
+        default=lc.DEFAULT_STATUS_INFO[lc.ZONE_STATUS_CREATING],
         help_text='Additional status information',
     )
 
@@ -198,24 +129,24 @@ def get_project(self):
 
     def set_status(self, status, status_info=None):
         """Set zone status"""
-        if status not in ZONE_STATUS_TYPES:
+        if status not in lc.ZONE_STATUS_TYPES:
             raise TypeError('Unknown status "{}"'.format(status))
         self.status = status
         if status_info:
             self.status_info = status_info
         else:
-            self.status_info = DEFAULT_STATUS_INFO[status][:1024]
+            self.status_info = lc.DEFAULT_STATUS_INFO[status][:1024]
         self.save()
 
     def is_locked(self):
         """
         Return True/False depending whether write access to zone is currently
         locked.
         """
-        return self.status in STATUS_LOCKING
+        return self.status in lc.STATUS_LOCKING
 
     def can_display_files(self):
         """
         Return True/False depending whether file info should be displayed.
         """
-        return self.status in STATUS_DISPLAY_FILES
+        return self.status in lc.STATUS_DISPLAY_FILES

landingzones/plugins.py

@@ -17,7 +17,12 @@
 # Samplesheets dependency
 from samplesheets.models import Investigation, Assay
 
-from landingzones.models import LandingZone, STATUS_ALLOW_UPDATE
+from landingzones.constants import (
+    STATUS_ALLOW_UPDATE,
+    ZONE_STATUS_MOVED,
+    ZONE_STATUS_DELETED,
+)
+from landingzones.models import LandingZone
 from landingzones.urls import urlpatterns
 from landingzones.views import ZoneModifyMixin
 
@@ -125,7 +130,7 @@ def get_object_link(self, model_str, uuid):
         obj = self.get_object(eval(model_str), uuid)
         if not obj:
             return None
-        if obj.__class__ == LandingZone and obj.status != 'MOVED':
+        if obj.__class__ == LandingZone and obj.status != ZONE_STATUS_MOVED:
             return {
                 'url': reverse(
                     'landingzones:list',
@@ -166,7 +171,9 @@ def get_project_list_value(self, column_id, project, user):
             zones = LandingZone.objects.filter(project=project)
         else:
             zones = LandingZone.objects.filter(project=project, user=user)
-        active_count = zones.exclude(status__in=['MOVED', 'DELETED']).count()
+        active_count = zones.exclude(
+            status__in=[ZONE_STATUS_MOVED, ZONE_STATUS_DELETED]
+        ).count()
 
         if investigation and investigation.irods_status and active_count > 0:
             return (

landingzones/serializers.py

@@ -12,12 +12,12 @@
 # Samplesheets dependency
 from samplesheets.models import Assay
 
-from landingzones.models import (
-    LandingZone,
+from landingzones.constants import (
     ZONE_STATUS_OK,
     ZONE_STATUS_DELETED,
     ZONE_STATUS_NOT_CREATED,
 )
+from landingzones.models import LandingZone
 from landingzones.utils import get_zone_title
 
 

landingzones/tasks_celery.py

@@ -1,4 +1,5 @@
 """Celery tasks for the landingzones app"""
+
 import logging
 
 from django.conf import settings
@@ -10,7 +11,7 @@
 from projectroles.models import Project
 from projectroles.plugins import get_backend_api
 
-from landingzones.models import STATUS_ALLOW_UPDATE, STATUS_LOCKING
+from landingzones.constants import STATUS_ALLOW_UPDATE, STATUS_LOCKING
 from landingzones.views import ZoneMoveMixin
 
 logger = logging.getLogger(__name__)

landingzones/tasks_taskflow.py

@@ -17,7 +17,7 @@
 # Taskflowbackend dependency
 from taskflowbackend.tasks.sodar_tasks import SODARBaseTask
 
-from landingzones.models import (
+from landingzones.constants import (
     STATUS_BUSY,
     ZONE_STATUS_FAILED,
     ZONE_STATUS_NOT_CREATED,

landingzones/templatetags/landingzones_tags.py

@@ -6,7 +6,8 @@
 # Projectroles dependency
 from projectroles.plugins import get_backend_api
 
-from landingzones.models import LandingZone, STATUS_STYLES, STATUS_FINISHED
+from landingzones.constants import STATUS_STYLES, STATUS_FINISHED
+from landingzones.models import LandingZone
 from landingzones.plugins import get_zone_config_plugin
 
 

landingzones/tests/test_commands.py

@@ -23,7 +23,7 @@
     get_inactive_zones,
     get_output,
 )
-from landingzones.models import (
+from landingzones.constants import (
     ZONE_STATUS_MOVED,
     ZONE_STATUS_DELETED,
     ZONE_STATUS_ACTIVE,

landingzones/tests/test_models.py

@@ -15,13 +15,13 @@
 # Samplesheets dependency
 from samplesheets.tests.test_io import SampleSheetIOMixin, SHEET_DIR
 
-from landingzones.models import (
-    LandingZone,
+from landingzones.constants import (
     DEFAULT_STATUS_INFO,
     ZONE_STATUS_CREATING,
     ZONE_STATUS_ACTIVE,
     ZONE_STATUS_MOVING,
 )
+from landingzones.models import LandingZone
 
 
 # SODAR constants
@@ -37,7 +37,7 @@
 ZONE_TITLE = '20180503_1724_test_zone'
 ZONE_DESC = 'description'
 ZONE_MSG = 'user message'
-ZONE_STATUS_INFO_INIT = DEFAULT_STATUS_INFO['CREATING']
+ZONE_STATUS_INFO_INIT = DEFAULT_STATUS_INFO[ZONE_STATUS_CREATING]
 
 
 class LandingZoneMixin:

landingzones/tests/test_permissions.py

@@ -10,7 +10,7 @@
 # Samplesheets dependency
 from samplesheets.tests.test_io import SampleSheetIOMixin, SHEET_DIR
 
-from landingzones.models import ZONE_STATUS_ACTIVE
+from landingzones.constants import ZONE_STATUS_ACTIVE
 from landingzones.tests.test_models import (
     LandingZoneMixin,
     ZONE_TITLE,