Scottx611x/workflow launching and monitoring (#1949)

* Add galaxy_workflow_task_group_id field to AnalysisStatus

* Add field `galaxy_import_state` to AnalysisStatus

* Update docstring

* Organize analysis_manager.tasks

* Add some constants to Tool model

* Add methods to Tool model

* Update docstring

* Add test coverage

* Add decorators to designate methods for specific Tool types

* Update tests

* Fix Test

* Add test coverage for `_get_nesting_string`

* Organizing these methods in a prior commit made for a difficult to read diff, and isn't crucial

* Remove redundant decorator

* Remove redundant tests

* Remove unutilized function

* Designate `_launch_workflow` to only work for workflow-based tools

* Add test for update_galaxy_data

* Add test coverage for `_invoke_tool_based_galaxy_workflow`

* Rename method and adhere to style guide

* Fix naming

* Consolidate migrations

* Just use a placeholder method for now

* DRY

* Add appropriate error msg and fail task

* Fix typo

* Update docdtring

* Fix test

* Add test coverage for `_check_galaxy_history_state`

* Polymorphic approach for Tools since Tools were becoming too heavily saturated with Workflow-based Tool specific methods

* Add test coverage for `_run_tool_based_galaxy_file_import`

* Consolidate migrations

* Add `galaxy_connection` property and more class methods to WorkflowTool

* Add `set_galaxy_workflow_task_group_id` to AnalysisStatus

* Utilize `set_galaxy_workflow_task_group_id()`

* Update test mock arg order, add test coverage for `_run_tool_based_galaxy_workflow`

* Add test coverage

* Fix test

* Add api test to check that polymorphism behaves appropriately

* DRY

* Fix Tests

* Fix ordering of arguments

* Method renaming and Docstring updates

* Rename method to: `import_library_dataset_to_history`

* We already have access to the analysis through Tool here

* Add abstract `launch()` to Tool and test it

* Refactor `_get_nesting_string` into another step: `_flatten_file_relationships_nesting`

* Pull out parameters common to both Tools and ToolDefinitions and use splat syntax

* Set this value upon a Tool's creation

* DRY and style fix

* Add test coverage for `_flatten_file_relationships_nesting()`

* Update `_get_file_relationships_galaxy` to access value at new location

refinery/analysis_manager/migrations/0003_auto_20170726_1601.py

@@ -0,0 +1,27 @@
+# -*- coding: utf-8 -*-
+from __future__ import unicode_literals
+
+from django.db import models, migrations
+import django_extensions.db.fields
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('analysis_manager', '0002_analysisstatus_galaxy_import_progress'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='analysisstatus',
+            name='galaxy_import_state',
+            field=models.CharField(blank=True, max_length=10, choices=[(b'SUCCESS', b'OK'), (b'FAILURE', b'Error'), (b'PROGRESS', b'Running'), (b'PENDING', b'Unknown')]),
+            preserve_default=True,
+        ),
+        migrations.AddField(
+            model_name='analysisstatus',
+            name='galaxy_workflow_task_group_id',
+            field=django_extensions.db.fields.UUIDField(max_length=36, null=True, editable=False, blank=True),
+            preserve_default=True,
+        ),
+    ]

refinery/analysis_manager/models.py

@@ -26,6 +26,12 @@ class AnalysisStatus(models.Model):
                                               auto=False)
     galaxy_import_task_group_id = UUIDField(blank=True, null=True, auto=False)
     galaxy_export_task_group_id = UUIDField(blank=True, null=True, auto=False)
+    galaxy_workflow_task_group_id = UUIDField(blank=True,
+                                              null=True,
+                                              auto=False)
+    #: state of Galaxy file imports
+    galaxy_import_state = CharField(max_length=10, blank=True,
+                                    choices=GALAXY_HISTORY_STATES)
     #: state of Galaxy history
     galaxy_history_state = CharField(max_length=10, blank=True,
                                      choices=GALAXY_HISTORY_STATES)
@@ -42,22 +48,37 @@ def __unicode__(self):
         return self.analysis.name
 
     def set_galaxy_history_state(self, state):
+        """
+        Set the `galaxy_history_state` of an analysis
+        :param state: a valid GALAXY_HISTORY_STATE
+        """
         if state in dict(self.GALAXY_HISTORY_STATES).keys():
             self.galaxy_history_state = state
             self.save()
         else:
             raise ValueError("Invalid Galaxy history state given")
 
+    def set_galaxy_import_state(self, state):
+        """
+        Set the `galaxy_import_state` of an analysis
+        :param state: a valid GALAXY_HISTORY_STATE
+        """
+        if state in dict(self.GALAXY_HISTORY_STATES).keys():
+            self.galaxy_import_state = state
+            self.save()
+        else:
+            raise ValueError("Invalid Galaxy history state given")
+
     def refinery_import_state(self):
         return get_task_group_state(self.refinery_import_task_group_id)
 
     def galaxy_file_import_state(self):
         return get_task_group_state(self.galaxy_import_task_group_id)
 
     def tool_based_galaxy_file_import_state(self):
-        if self.galaxy_history_state and self.galaxy_import_progress != 0:
+        if self.galaxy_import_state and self.galaxy_import_progress != 0:
             galaxy_file_import_state = [{
-                'state': self.galaxy_history_state,
+                'state': self.galaxy_import_state,
                 'percent_done': self.galaxy_import_progress
             }]
         else:
@@ -77,6 +98,14 @@ def galaxy_analysis_state(self):
     def galaxy_export_state(self):
         return get_task_group_state(self.galaxy_export_task_group_id)
 
+    def set_galaxy_import_task_group_id(self, galaxy_import_task_group_id):
+        self.galaxy_import_task_group_id = galaxy_import_task_group_id
+        self.save()
+
+    def set_galaxy_workflow_task_group_id(self, galaxy_workflow_task_group_id):
+        self.galaxy_workflow_task_group_id = galaxy_workflow_task_group_id
+        self.save()
+
 
 def get_task_group_state(task_group_id):
     """return a list containing states of all tasks given a task set ID"""