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annotate planemo/lib/python3.7/site-packages/bioblend/_tests/TestGalaxyInvocations.py @ 1:56ad4e20f292 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:32:28 -0400
parents d30785e31577
children
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1 import os
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2 import time
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3
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4 from . import GalaxyTestBase, test_util
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7 class TestGalaxyInvocations(GalaxyTestBase.GalaxyTestBase):
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8 @test_util.skip_unless_galaxy('release_19.09')
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9 def test_invocation(self):
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10 path = test_util.get_abspath(os.path.join('data', 'paste_columns.ga'))
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11 workflow = self.gi.workflows.import_workflow_from_local_path(path)
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12 history_id = self.gi.histories.create_history(name="TestWorkflowState")["id"]
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13 dataset1_id = self._test_dataset(history_id)
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14 dataset = {'src': 'hda', 'id': dataset1_id}
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15
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16 invocation = self.gi.workflows.invoke_workflow(
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17 workflow['id'],
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18 inputs={'Input 1': dataset, 'Input 2': dataset},
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19 history_id=history_id,
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20 inputs_by='name',
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21 )
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22
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23 invocation_id = invocation["id"]
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24 invocations = self.gi.invocations.get_invocations()
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25 self.assertEqual(len(invocations), 1)
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26 self.assertEqual(invocations[0]["id"], invocation_id)
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27 self.gi.invocations.cancel_invocation(invocation_id)
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28 invocation = self.gi.invocations.show_invocation(invocation_id)
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29 self.assertEqual(invocation['state'], 'cancelled')
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30
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31 summary = self.gi.invocations.get_invocation_summary(invocation_id)
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32 report = self.gi.invocations.get_invocation_report(invocation_id)
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33
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34 assert summary['states'] == {}
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35 assert report['workflows'] == {workflow['id']: {'name': 'paste_columns'}}
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36
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37 @test_util.skip_unless_galaxy('release_19.09')
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38 @test_util.skip_unless_tool("cat1")
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39 @test_util.skip_unless_tool("cat")
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40 def test_workflow_scheduling(self):
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41 path = test_util.get_abspath(os.path.join('data', 'test_workflow_pause.ga'))
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42 workflow = self.gi.workflows.import_workflow_from_local_path(path)
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43 history_id = self.gi.histories.create_history(name="TestWorkflowState")["id"]
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44 dataset1_id = self._test_dataset(history_id)
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45
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46 invocation = self.gi.workflows.invoke_workflow(
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47 workflow["id"],
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48 inputs={"0": {"src": "hda", "id": dataset1_id}},
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49 )
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50 invocation_id = invocation["id"]
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51
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52 def invocation_steps_by_order_index():
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53 invocation = self.gi.invocations.show_invocation(invocation_id)
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54 return dict((s["order_index"], s) for s in invocation["steps"])
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55
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56 for _ in range(20):
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57 if 2 in invocation_steps_by_order_index():
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58 break
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59 time.sleep(.5)
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60
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61 steps = invocation_steps_by_order_index()
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62 pause_step = steps[2]
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63 self.assertIsNone(
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64 self.gi.invocations.show_invocation_step(invocation_id, pause_step["id"])["action"])
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65 self.gi.invocations.run_invocation_step_action(invocation_id, pause_step["id"], action=True)
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66 self.assertTrue(self.gi.invocations.show_invocation_step(invocation_id, pause_step["id"])["action"])
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67 for _ in range(20):
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68 invocation = self.gi.invocations.show_invocation(invocation_id)
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69 if invocation["state"] == "scheduled":
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70 break
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71
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72 time.sleep(.5)
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73
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74 invocation = self.gi.invocations.show_invocation(invocation_id)
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75 self.assertEqual(invocation["state"], "scheduled")