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annotate planemo/lib/python3.7/site-packages/bioblend/_tests/TestGalaxyWorkflows.py @ 0:d30785e31577 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:18:57 -0400
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1 import json
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2 import os
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3 import shutil
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4 import tempfile
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5 import time
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6
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7 from . import GalaxyTestBase, test_util
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8
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9
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10 class TestGalaxyWorkflows(GalaxyTestBase.GalaxyTestBase):
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11
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12 @test_util.skip_unless_tool("cat1")
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13 @test_util.skip_unless_tool("cat")
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14 def test_workflow_scheduling(self):
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15 path = test_util.get_abspath(os.path.join('data', 'test_workflow_pause.ga'))
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16 workflow = self.gi.workflows.import_workflow_from_local_path(path)
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17 workflow_id = workflow["id"]
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18 history_id = self.gi.histories.create_history(name="TestWorkflowState")["id"]
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19 dataset1_id = self._test_dataset(history_id)
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20
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21 invocations = self.gi.workflows.get_invocations(workflow_id)
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22 self.assertEqual(len(invocations), 0)
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23
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24 invocation = self.gi.workflows.invoke_workflow(
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25 workflow["id"],
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26 inputs={"0": {"src": "hda", "id": dataset1_id}},
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27 )
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28 invocation_id = invocation["id"]
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29 invocations = self.gi.workflows.get_invocations(workflow_id)
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30 self.assertEqual(len(invocations), 1)
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31 self.assertEqual(invocations[0]["id"], invocation_id)
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32
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33 def invocation_steps_by_order_index():
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34 invocation = self.gi.workflows.show_invocation(workflow_id, invocation_id)
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35 return dict((s["order_index"], s) for s in invocation["steps"])
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36
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37 for _ in range(20):
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38 if 2 in invocation_steps_by_order_index():
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39 break
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40 time.sleep(.5)
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41
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42 invocation = self.gi.workflows.show_invocation(workflow_id, invocation_id)
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43 self.assertEqual(invocation['state'], "ready")
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44
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45 steps = invocation_steps_by_order_index()
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46 pause_step = steps[2]
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47 self.assertIsNone(
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48 self.gi.workflows.show_invocation_step(workflow_id, invocation_id, pause_step["id"])["action"])
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49 self.gi.workflows.run_invocation_step_action(workflow_id, invocation_id, pause_step["id"], action=True)
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50 self.assertTrue(self.gi.workflows.show_invocation_step(workflow_id, invocation_id, pause_step["id"])["action"])
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51 for _ in range(20):
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52 invocation = self.gi.workflows.show_invocation(workflow_id, invocation_id)
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53 if invocation["state"] == "scheduled":
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54 break
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55
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56 time.sleep(.5)
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57
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58 invocation = self.gi.workflows.show_invocation(workflow_id, invocation_id)
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59 self.assertEqual(invocation["state"], "scheduled")
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60
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61 @test_util.skip_unless_tool("cat1")
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62 @test_util.skip_unless_tool("cat")
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63 def test_cancelling_workflow_scheduling(self):
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64 path = test_util.get_abspath(os.path.join('data', 'test_workflow_pause.ga'))
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65 workflow = self.gi.workflows.import_workflow_from_local_path(path)
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66 workflow_id = workflow["id"]
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67 history_id = self.gi.histories.create_history(name="TestWorkflowState")["id"]
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68 dataset1_id = self._test_dataset(history_id)
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69
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70 invocations = self.gi.workflows.get_invocations(workflow_id)
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71 self.assertEqual(len(invocations), 0)
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72
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73 invocation = self.gi.workflows.invoke_workflow(
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74 workflow["id"],
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75 inputs={"0": {"src": "hda", "id": dataset1_id}},
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76 )
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77 invocation_id = invocation["id"]
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78 invocations = self.gi.workflows.get_invocations(workflow_id)
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79 self.assertEqual(len(invocations), 1)
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80 self.assertEqual(invocations[0]["id"], invocation_id)
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81
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82 invocation = self.gi.workflows.show_invocation(workflow_id, invocation_id)
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83 self.assertIn(invocation['state'], ['new', 'ready'])
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84
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85 self.gi.workflows.cancel_invocation(workflow_id, invocation_id)
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86 invocation = self.gi.workflows.show_invocation(workflow_id, invocation_id)
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87 self.assertEqual(invocation['state'], 'cancelled')
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88
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89 def test_import_export_workflow_from_local_path(self):
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90 with self.assertRaises(Exception):
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91 self.gi.workflows.import_workflow_from_local_path(None)
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92 path = test_util.get_abspath(os.path.join('data', 'paste_columns.ga'))
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93 imported_wf = self.gi.workflows.import_workflow_from_local_path(path)
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94 self.assertIsInstance(imported_wf, dict)
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95 self.assertEqual(imported_wf['name'], 'paste_columns')
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96 self.assertTrue(imported_wf['url'].startswith('/api/workflows/'))
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97 self.assertFalse(imported_wf['deleted'])
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98 self.assertFalse(imported_wf['published'])
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99 with self.assertRaises(Exception):
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100 self.gi.workflows.export_workflow_to_local_path(None, None, None)
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101 export_dir = tempfile.mkdtemp(prefix='bioblend_test_')
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102 try:
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103 self.gi.workflows.export_workflow_to_local_path(imported_wf['id'], export_dir)
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104 dir_contents = os.listdir(export_dir)
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105 self.assertEqual(len(dir_contents), 1)
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106 export_path = os.path.join(export_dir, dir_contents[0])
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107 with open(export_path, 'r') as f:
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108 exported_wf_dict = json.load(f)
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109 finally:
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110 shutil.rmtree(export_dir)
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111 self.assertIsInstance(exported_wf_dict, dict)
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112
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113 def test_import_publish_workflow_from_local_path(self):
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114 path = test_util.get_abspath(os.path.join('data', 'paste_columns.ga'))
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115 imported_wf = self.gi.workflows.import_workflow_from_local_path(path, publish=True)
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116 self.assertIsInstance(imported_wf, dict)
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117 self.assertFalse(imported_wf['deleted'])
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118 self.assertTrue(imported_wf['published'])
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119
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120 def test_import_export_workflow_dict(self):
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121 path = test_util.get_abspath(os.path.join('data', 'paste_columns.ga'))
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122 with open(path, 'r') as f:
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123 wf_dict = json.load(f)
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124 imported_wf = self.gi.workflows.import_workflow_dict(wf_dict)
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125 self.assertIsInstance(imported_wf, dict)
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126 self.assertEqual(imported_wf['name'], 'paste_columns')
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127 self.assertTrue(imported_wf['url'].startswith('/api/workflows/'))
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128 self.assertFalse(imported_wf['deleted'])
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129 self.assertFalse(imported_wf['published'])
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130 exported_wf_dict = self.gi.workflows.export_workflow_dict(imported_wf['id'])
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131 self.assertIsInstance(exported_wf_dict, dict)
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132
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133 def test_import_publish_workflow_dict(self):
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134 path = test_util.get_abspath(os.path.join('data', 'paste_columns.ga'))
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135 with open(path, 'r') as f:
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136 wf_dict = json.load(f)
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137 imported_wf = self.gi.workflows.import_workflow_dict(wf_dict, publish=True)
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138 self.assertIsInstance(imported_wf, dict)
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139 self.assertFalse(imported_wf['deleted'])
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140 self.assertTrue(imported_wf['published'])
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141
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142 def test_get_workflows(self):
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143 path = test_util.get_abspath(os.path.join('data', 'paste_columns.ga'))
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144 wf = self.gi.workflows.import_workflow_from_local_path(path)
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145 all_wfs = self.gi.workflows.get_workflows()
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146 self.assertGreater(len(all_wfs), 0)
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147 wf_data = self.gi.workflows.get_workflows(workflow_id=wf['id'])[0]
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148 self.assertEqual(wf['id'], wf_data['id'])
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149 self.assertEqual(wf['name'], wf_data['name'])
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150 self.assertEqual(wf['url'], wf_data['url'])
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151 wf_data_list = self.gi.workflows.get_workflows(name=wf['name'])
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152 self.assertTrue(any(_['id'] == wf['id'] for _ in wf_data_list))
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153
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154 def test_show_workflow(self):
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155 path = test_util.get_abspath(os.path.join('data', 'paste_columns.ga'))
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156 wf = self.gi.workflows.import_workflow_from_local_path(path)
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157 wf_data = self.gi.workflows.show_workflow(wf['id'])
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158 self.assertEqual(wf_data['id'], wf['id'])
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159 self.assertEqual(wf_data['name'], wf['name'])
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160 self.assertEqual(wf_data['url'], wf['url'])
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161 self.assertEqual(len(wf_data['steps']), 3)
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162 self.assertIsNotNone(wf_data['inputs'])
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163
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164 @test_util.skip_unless_galaxy('release_18.05')
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165 def test_update_workflow_name(self):
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166 path = test_util.get_abspath(os.path.join('data', 'paste_columns.ga'))
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167 wf = self.gi.workflows.import_workflow_from_local_path(path)
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168 new_name = 'new name'
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169 updated_wf = self.gi.workflows.update_workflow(wf['id'], name=new_name)
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170 self.assertEqual(updated_wf['name'], new_name)
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171
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172 @test_util.skip_unless_galaxy('release_19.09') # due to Galaxy bug fixed in https://github.com/galaxyproject/galaxy/pull/9014
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173 def test_show_workflow_versions(self):
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174 path = test_util.get_abspath(os.path.join('data', 'paste_columns.ga'))
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175 wf = self.gi.workflows.import_workflow_from_local_path(path)
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176 wf_data = self.gi.workflows.show_workflow(wf['id'])
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177 self.assertEqual(wf_data['version'], 0)
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178 new_name = 'new name'
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179 self.gi.workflows.update_workflow(wf['id'], name=new_name)
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180 updated_wf = self.gi.workflows.show_workflow(wf['id'])
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181 self.assertEqual(updated_wf['name'], new_name)
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182 self.assertEqual(updated_wf['version'], 1)
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183 updated_wf = self.gi.workflows.show_workflow(wf['id'], version=0)
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184 self.assertEqual(updated_wf['name'], 'paste_columns')
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185 self.assertEqual(updated_wf['version'], 0)
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186 updated_wf = self.gi.workflows.show_workflow(wf['id'], version=1)
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187 self.assertEqual(updated_wf['name'], new_name)
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188 self.assertEqual(updated_wf['version'], 1)
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189
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190 def test_run_workflow(self):
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191 path = test_util.get_abspath(os.path.join('data', 'paste_columns.ga'))
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192 wf = self.gi.workflows.import_workflow_from_local_path(path)
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193 # Try invalid run of workflow
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194 with self.assertRaises(Exception):
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195 self.gi.workflows.run_workflow(wf['id'], None)
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196
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197 def test_invoke_workflow(self):
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198 path = test_util.get_abspath(os.path.join('data', 'paste_columns.ga'))
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199 wf = self.gi.workflows.import_workflow_from_local_path(path)
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200 history_id = self.gi.histories.create_history(name="test_wf_invocation")['id']
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201 dataset1_id = self._test_dataset(history_id)
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202 dataset = {'src': 'hda', 'id': dataset1_id}
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203 invoke_response = self.gi.workflows.invoke_workflow(
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204 wf['id'],
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205 inputs={'Input 1': dataset, 'Input 2': dataset},
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206 history_id=history_id,
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207 inputs_by='name',
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208 )
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209 assert invoke_response['state'] == 'new', invoke_response