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Merge pull request #317 from jbernal0019/master
Add support for 'groupByInstance' special parameter for plugins of type 'ts'
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -3,6 +3,7 @@ | |
| import json | ||
| import time | ||
| import io | ||
| import os | ||
| from unittest import mock, skip | ||
|
|
||
| from django.test import TestCase, TransactionTestCase, tag | ||
|
|
@@ -304,6 +305,117 @@ def test_integration_plugin_instance_create_success(self): | |
| # delete files from swift storage | ||
| self.swift_manager.delete_obj(self.user_space_path + 'test.txt') | ||
|
|
||
| @tag('integration') | ||
| def test_integration_ts_plugin_instance_create_success(self): | ||
| # create an FS plugin instance | ||
| user = User.objects.get(username=self.username) | ||
| plugin = Plugin.objects.get(meta__name="pacspull") | ||
| (fs_plg_inst, tf) = PluginInstance.objects.get_or_create( | ||
| plugin=plugin, owner=user, compute_resource=plugin.compute_resources.all()[0]) | ||
|
|
||
| # upload FS plugin instace output file to Swift storage | ||
| path = os.path.join(fs_plg_inst.get_output_path(), 'test.txt') | ||
| with io.StringIO("test file") as test_file: | ||
| self.swift_manager.upload_obj(path, test_file.read(), | ||
| content_type='text/plain') | ||
| (fs_plg_inst_file, tf) = PluginInstanceFile.objects.get_or_create(plugin_inst=fs_plg_inst) | ||
| fs_plg_inst_file.fname.name = path | ||
| fs_plg_inst_file.save() | ||
| fs_plg_inst.status = 'finishedSuccessfully' | ||
| fs_plg_inst.save() | ||
|
|
||
| # add a TS plugin to the system | ||
| plugin_parameters = [{'name': 'plugininstances', 'type': 'string', | ||
| 'action': 'store', 'optional': True, | ||
| 'flag': '--plugininstances', 'short_flag': '--plugininstances', | ||
| 'help': 'test plugin parameter', 'ui_exposed': True}, | ||
|
|
||
| {'name': 'filter', 'type': 'string', | ||
| 'action': 'store', 'optional': True, | ||
| 'flag': '--filter', | ||
| 'short_flag': '-f', | ||
| 'help': 'test plugin parameter', 'ui_exposed': True} | ||
| ] | ||
| self.plg_data = {'description': 'A toplological copy ts plugin', | ||
| 'version': '0.1', | ||
| 'dock_image': 'fnndsc/pl-topologicalcopy', | ||
| 'execshell': 'python3', | ||
| 'selfpath': '/usr/local/bin', | ||
| 'selfexec': 'topologicalcopy'} | ||
|
|
||
| self.plg_meta_data = {'name': 'topologicalcopy', | ||
| 'title': 'TS copy plugin', | ||
| 'license': 'MIT', | ||
| 'type': 'ts', | ||
| 'icon': 'http://github.com/plugin', | ||
| 'category': 'Utility', | ||
| 'stars': 0, | ||
| 'authors': 'FNNDSC ([email protected])'} | ||
|
|
||
| self.plugin_repr = self.plg_data.copy() | ||
| self.plugin_repr.update(self.plg_meta_data) | ||
| self.plugin_repr['parameters'] = plugin_parameters | ||
|
|
||
| (compute_resource, tf) = ComputeResource.objects.get_or_create( | ||
| name="host", compute_url=COMPUTE_RESOURCE_URL) | ||
|
|
||
| data = self.plg_meta_data.copy() | ||
| (pl_meta, tf) = PluginMeta.objects.get_or_create(**data) | ||
| data = self.plg_data.copy() | ||
| (plugin, tf) = Plugin.objects.get_or_create(meta=pl_meta, **data) | ||
| plugin.compute_resources.set([compute_resource]) | ||
| plugin.save() | ||
|
|
||
| # add plugin's parameters | ||
| parameters = plugin_parameters | ||
| PluginParameter.objects.get_or_create( | ||
| plugin=plugin, | ||
| name=parameters[0]['name'], | ||
| type=parameters[0]['type'], | ||
| flag=parameters[0]['flag']) | ||
|
|
||
| # make POST API request to create a ts plugin instance | ||
| create_read_url = reverse("plugininstance-list", kwargs={"pk": plugin.id}) | ||
| post = json.dumps( | ||
| {"template": {"data": [{"name": "previous_id", "value": fs_plg_inst.id}, | ||
| {"name": "plugininstances", "value": str(fs_plg_inst.id)}, | ||
| {"name": "filter", "value": ".txt$"}]}}) | ||
| self.client.login(username=self.username, password=self.password) | ||
| response = self.client.post(create_read_url, data=post, | ||
| content_type=self.content_type) | ||
| self.assertEqual(response.status_code, status.HTTP_201_CREATED) | ||
|
|
||
| # instance must be 'started' before checking its status | ||
| pl_inst = PluginInstance.objects.get(pk=response.data['id']) | ||
| for _ in range(10): | ||
| time.sleep(3) | ||
| pl_inst.refresh_from_db() | ||
| if pl_inst.status == 'started': break | ||
| self.assertEqual(pl_inst.status, 'started') # instance must be started | ||
|
|
||
| # In the following we keep checking the status until the job ends with | ||
| # 'finishedSuccessfully'. The code runs in a lazy loop poll with a | ||
| # max number of attempts at 10 second intervals. | ||
| plg_inst_manager = PluginInstanceManager(pl_inst) | ||
| maxLoopTries = 10 | ||
| currentLoop = 1 | ||
| b_checkAgain = True | ||
| time.sleep(10) | ||
| while b_checkAgain: | ||
| str_responseStatus = plg_inst_manager.check_plugin_instance_app_exec_status() | ||
| if str_responseStatus == 'finishedSuccessfully': | ||
| b_checkAgain = False | ||
| elif currentLoop < maxLoopTries: | ||
| time.sleep(10) | ||
| if currentLoop == maxLoopTries: | ||
| b_checkAgain = False | ||
| currentLoop += 1 | ||
| self.assertEqual(pl_inst.status, 'finishedSuccessfully') | ||
| self.assertEqual(pl_inst.files.count(), 3) | ||
|
|
||
| # delete files from swift storage | ||
| self.swift_manager.delete_obj(path) | ||
|
|
||
| def test_plugin_instance_create_failure_unauthenticated(self): | ||
| response = self.client.post(self.create_read_url, data=self.post, | ||
| content_type=self.content_type) | ||
|
|
@@ -603,6 +715,74 @@ def test_plugin_instance_descendant_list_failure_unauthenticated(self): | |
| self.assertEqual(response.status_code, status.HTTP_401_UNAUTHORIZED) | ||
|
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||
|
|
||
| class PluginInstanceSplitListViewTests(ViewTests): | ||
| """ | ||
| Test the plugininstancesplit-list view. | ||
| """ | ||
|
|
||
| def setUp(self): | ||
| super(PluginInstanceSplitListViewTests, self).setUp() | ||
|
|
||
| user = User.objects.get(username=self.username) | ||
|
|
||
| # create an 'fs' plugin instance | ||
| plugin = Plugin.objects.get(meta__name="pacspull") | ||
| (self.fs_inst, tf) = PluginInstance.objects.get_or_create( | ||
| plugin=plugin, owner=user, compute_resource=plugin.compute_resources.all()[0]) | ||
|
|
||
| # create a 'ts' plugin | ||
| (pl_meta, tf) = PluginMeta.objects.get_or_create(name='pl-topologicalcopy', type='ts') | ||
| (plugin_ts, tf) = Plugin.objects.get_or_create(meta=pl_meta, version='0.1') | ||
| plugin_ts.compute_resources.set([self.compute_resource]) | ||
| plugin_ts.save() | ||
|
|
||
| self.create_read_url = reverse("plugininstancesplit-list", kwargs={"pk": self.fs_inst.id}) | ||
|
|
||
| def test_plugin_instance_split_create_failure_access_denied(self): | ||
| post = json.dumps({"template": {"data": [{"name": "filter", "value": ""}]}}) | ||
| self.client.login(username=self.other_username, password=self.other_password) | ||
| response = self.client.post(self.create_read_url, data=post, | ||
| content_type=self.content_type) | ||
| self.assertEqual(response.status_code, status.HTTP_403_FORBIDDEN) | ||
|
|
||
| def test_plugin_instance_split_create_success(self): | ||
| post = json.dumps({"template": {"data": [{"name": "filter", "value": ""}]}}) | ||
|
|
||
| # add parameters to the plugin before the POST request | ||
| plugin = Plugin.objects.get(meta__name="pl-topologicalcopy") | ||
| PluginParameter.objects.get_or_create(plugin=plugin, name='filter', type='string') | ||
| PluginParameter.objects.get_or_create(plugin=plugin, name='plugininstances', | ||
| type='string') | ||
|
|
||
| self.client.login(username=self.username, password=self.password) | ||
|
|
||
| # make API requests | ||
| response = self.client.post(self.create_read_url, data=post, | ||
| content_type=self.content_type) | ||
| self.assertEqual(response.status_code, status.HTTP_201_CREATED) | ||
|
|
||
| self.fs_inst.status = 'finishedSuccessfully' | ||
| self.fs_inst.save() | ||
| with mock.patch.object(views.run_plugin_instance, 'delay', | ||
| return_value=None) as delay_mock: | ||
|
|
||
| response = self.client.post(self.create_read_url, data=post, | ||
| content_type=self.content_type) | ||
| self.assertEqual(response.status_code, status.HTTP_201_CREATED) | ||
| # check that the run_plugin_instance task was called with appropriate args | ||
| delay_mock.assert_called_once() | ||
|
|
||
| def test_plugin_instance_split_list_success(self): | ||
| self.client.login(username=self.username, password=self.password) | ||
| response = self.client.get(self.create_read_url) | ||
| # response should contain all the instances in the tree | ||
| self.assertContains(response, "filter") | ||
|
|
||
| def test_plugin_instance_split_list_failure_unauthenticated(self): | ||
| response = self.client.get(self.create_read_url) | ||
| self.assertEqual(response.status_code, status.HTTP_401_UNAUTHORIZED) | ||
|
|
||
|
|
||
| class PluginInstanceParameterListViewTests(ViewTests): | ||
| """ | ||
| Test the plugininstance-parameter-list view. | ||
|
|
||
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