Merge pull request #984 from parklab/scottx611x/galaxy_deletion

Scottx611x/galaxy deletion
refinery-platform · Mar 24, 2016 · d9d6d81 · d9d6d81
2 parents 8cc8586 + 010c6b7
commit d9d6d81
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Showing 3 changed files with 39 additions and 19 deletions.
diff --git a/refinery/config/config.json.erb b/refinery/config/config.json.erb
@@ -101,6 +101,11 @@
   "REFINERY_EXTERNAL_AUTH": false,
   "REFINERY_EXTERNAL_AUTH_MESSAGE": "",
   "REFINERY_FILE_SOURCE_MAP": {},
+  "REFINERY_GALAXY_ANALYSIS_CLEANUP": {
+    "ALWAYS": "always",
+    "ON_SUCCESS": "on_success",
+    "NEVER": "never"
+  },
   "REFINERY_GOOGLE_ANALYTICS_ID": "",
   "REFINERY_INNER_NAVBAR_HEIGHT": 20,
   "REFINERY_MAIN_LOGO": "",

diff --git a/refinery/config/settings/base.py b/refinery/config/settings/base.py
@@ -418,6 +418,11 @@ def get_setting(name, settings=local_settings):
 # Display REFINERY_BANNER to anonymous users only
 REFINERY_BANNER_ANONYMOUS_ONLY = get_setting("REFINERY_BANNER_ANONYMOUS_ONLY")
 
+# Setting to allow users to select if they want to keep workflows,
+# histories, and libraries in Galaxy or not.
+# Deletion options are ALWAYS, ON_SUCCESS, and NEVER
+REFINERY_GALAXY_ANALYSIS_CLEANUP = get_setting(
+    "REFINERY_GALAXY_ANALYSIS_CLEANUP")["ON_SUCCESS"]
 # Subject and message body of the welcome email sent to new users
 REFINERY_WELCOME_EMAIL_SUBJECT = get_setting("REFINERY_WELCOME_EMAIL_SUBJECT")
 REFINERY_WELCOME_EMAIL_MESSAGE = get_setting("REFINERY_WELCOME_EMAIL_MESSAGE")

diff --git a/refinery/core/models.py b/refinery/core/models.py
@@ -1061,28 +1061,38 @@ def galaxy_progress(self):
         return history['percent_complete']
 
     def galaxy_cleanup(self):
-        """Delete library, workflow and history from Galaxy if they exist"""
-        connection = self.galaxy_connection()
-        error_msg = "Error deleting Galaxy %s for analysis '%s': %s"
+        """Determine when/if Galaxy libraries, workflows and histories are
+        to be deleted based on the value of
+        global setting: REFINERY_GALAXY_ANALYSIS_CLEANUP"""
 
-        if self.library_id:
-            try:
-                connection.libraries.delete_library(self.library_id)
-            except galaxy.client.ConnectionError as e:
-                logger.error(error_msg, 'library', self.name, e.message)
+        cleanup = settings.REFINERY_GALAXY_ANALYSIS_CLEANUP
 
-        if self.workflow_galaxy_id:
-            try:
-                connection.workflows.delete_workflow(self.workflow_galaxy_id)
-            except galaxy.client.ConnectionError as e:
-                logger.error(error_msg, 'workflow', self.name, e.message)
+        if cleanup == 'always' or cleanup == 'on_success' and \
+                      self.get_status() == self.SUCCESS_STATUS:
 
-        if self.history_id:
-            try:
-                connection.histories.delete_history(
-                    self.history_id, purge=True)
-            except galaxy.client.ConnectionError as e:
-                logger.error(error_msg, 'history', self.name, e.message)
+            connection = self.galaxy_connection()
+            error_msg = "Error deleting Galaxy %s for analysis '%s': %s"
+
+            # Delete Galaxy libraries, workflows and histories
+            if self.library_id:
+                try:
+                    connection.libraries.delete_library(self.library_id)
+                except galaxy.client.ConnectionError as e:
+                    logger.error(error_msg, 'library', self.name, e.message)
+
+            if self.workflow_galaxy_id:
+                try:
+                    connection.workflows.delete_workflow(
+                        self.workflow_galaxy_id)
+                except galaxy.client.ConnectionError as e:
+                    logger.error(error_msg, 'workflow', self.name, e.message)
+
+            if self.history_id:
+                try:
+                    connection.histories.delete_history(self.history_id,
+                                                        purge=True)
+                except galaxy.client.ConnectionError as e:
+                    logger.error(error_msg, 'history', self.name, e.message)
 
     def cancel(self):
         """Mark analysis as cancelled"""