Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/bioblend/_tests/TestGalaxyObjects.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 # pylint: disable=C0103,E1101 |
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2 import json |
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3 import os |
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4 import shutil |
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5 import socket |
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6 import sys |
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7 import tarfile |
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8 import tempfile |
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9 import uuid |
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10 from ssl import SSLError |
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11 from urllib.error import URLError |
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12 from urllib.request import urlopen |
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13 |
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14 import bioblend |
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15 import bioblend.galaxy.objects.galaxy_instance as galaxy_instance |
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16 import bioblend.galaxy.objects.wrappers as wrappers |
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17 from bioblend.galaxy import dataset_collections |
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18 from . import test_util |
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19 from .test_util import unittest |
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20 |
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21 bioblend.set_stream_logger('test', level='INFO') |
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22 socket.setdefaulttimeout(10.0) |
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23 SAMPLE_FN = test_util.get_abspath(os.path.join('data', 'paste_columns.ga')) |
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24 SAMPLE_WF_COLL_FN = test_util.get_abspath(os.path.join('data', 'paste_columns_collections.ga')) |
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25 SAMPLE_WF_PARAMETER_INPUT_FN = test_util.get_abspath(os.path.join('data', 'workflow_with_parameter_input.ga')) |
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26 FOO_DATA = 'foo\nbar\n' |
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27 FOO_DATA_2 = 'foo2\nbar2\n' |
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28 SAMPLE_WF_DICT = { |
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29 'deleted': False, |
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30 'id': '9005c5112febe774', |
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31 'inputs': { |
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32 '571': {'label': 'Input Dataset', 'value': ''}, |
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33 '572': {'label': 'Input Dataset', 'value': ''}, |
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34 }, |
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35 'model_class': 'StoredWorkflow', |
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36 'name': 'paste_columns', |
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37 'owner': 'user_foo', |
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38 'published': False, |
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39 'steps': { |
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40 '571': { |
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41 'id': 571, |
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42 'input_steps': {}, |
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43 'tool_id': None, |
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44 'tool_inputs': {'name': 'Input Dataset'}, |
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45 'tool_version': None, |
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46 'type': 'data_input', |
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47 }, |
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48 '572': { |
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49 'id': 572, |
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50 'input_steps': {}, |
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51 'tool_id': None, |
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52 'tool_inputs': {'name': 'Input Dataset'}, |
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53 'tool_version': None, |
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54 'type': 'data_input', |
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55 }, |
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56 '573': { |
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57 'id': 573, |
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58 'input_steps': { |
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59 'input1': {'source_step': 571, 'step_output': 'output'}, |
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60 'input2': {'source_step': 572, 'step_output': 'output'}, |
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61 }, |
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62 'tool_id': 'Paste1', |
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63 'tool_inputs': { |
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64 'delimiter': '"T"', |
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65 'input1': 'null', |
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66 'input2': 'null', |
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67 }, |
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68 'tool_version': '1.0.0', |
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69 'type': 'tool', |
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70 } |
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71 }, |
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72 'tags': [], |
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73 'url': '/api/workflows/9005c5112febe774', |
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74 } |
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75 |
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76 |
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77 def is_reachable(url): |
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78 res = None |
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79 try: |
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80 res = urlopen(url, timeout=5) |
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81 except (SSLError, URLError, socket.timeout): |
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82 return False |
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83 if res is not None: |
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84 res.close() |
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85 return True |
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86 |
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87 |
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88 def upload_from_fs(lib, bnames, **kwargs): |
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89 tempdir = tempfile.mkdtemp(prefix='bioblend_test_') |
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90 try: |
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91 fnames = [os.path.join(tempdir, _) for _ in bnames] |
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92 for fn in fnames: |
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93 with open(fn, 'w') as f: |
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94 f.write(FOO_DATA) |
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95 dss = lib.upload_from_galaxy_fs(fnames, **kwargs) |
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96 finally: |
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97 shutil.rmtree(tempdir) |
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98 return dss, fnames |
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99 |
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100 |
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101 class MockWrapper(wrappers.Wrapper): |
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102 BASE_ATTRS = frozenset(['a', 'b']) |
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103 |
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104 def __init__(self, *args, **kwargs): |
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105 super().__init__(*args, **kwargs) |
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106 |
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107 @property |
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108 def gi_module(self): |
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109 return super().gi_module() |
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110 |
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111 |
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112 class TestWrapper(unittest.TestCase): |
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113 |
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114 def setUp(self): |
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115 self.d = {'a': 1, 'b': [2, 3], 'c': {'x': 4}} |
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116 self.assertRaises(TypeError, wrappers.Wrapper, self.d) |
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117 self.w = MockWrapper(self.d) |
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118 |
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119 def test_initialize(self): |
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120 for k in MockWrapper.BASE_ATTRS: |
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121 self.assertEqual(getattr(self.w, k), self.d[k]) |
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122 self.w.a = 222 |
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123 self.w.b[0] = 222 |
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124 self.assertEqual(self.w.a, 222) |
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125 self.assertEqual(self.w.b[0], 222) |
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126 self.assertEqual(self.d['a'], 1) |
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127 self.assertEqual(self.d['b'][0], 2) |
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128 self.assertRaises(AttributeError, getattr, self.w, 'foo') |
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129 self.assertRaises(AttributeError, setattr, self.w, 'foo', 0) |
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130 |
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131 def test_taint(self): |
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132 self.assertFalse(self.w.is_modified) |
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133 self.w.a = 111 # pylint: disable=W0201 |
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134 self.assertTrue(self.w.is_modified) |
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135 |
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136 def test_serialize(self): |
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137 w = MockWrapper.from_json(self.w.to_json()) |
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138 self.assertEqual(w.wrapped, self.w.wrapped) |
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139 |
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140 def test_clone(self): |
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141 w = self.w.clone() |
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142 self.assertEqual(w.wrapped, self.w.wrapped) |
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143 w.b[0] = 111 |
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144 self.assertEqual(self.w.b[0], 2) |
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145 |
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146 def test_kwargs(self): |
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147 parent = MockWrapper({'a': 10}) |
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148 w = MockWrapper(self.d, parent=parent) |
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149 self.assertIs(w.parent, parent) |
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150 self.assertRaises(AttributeError, setattr, w, 'parent', 0) |
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151 |
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152 |
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153 class TestWorkflow(unittest.TestCase): |
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154 |
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155 def setUp(self): |
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156 self.wf = wrappers.Workflow(SAMPLE_WF_DICT) |
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157 |
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158 def test_initialize(self): |
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159 self.assertEqual(self.wf.id, '9005c5112febe774') |
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160 self.assertEqual(self.wf.name, 'paste_columns') |
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161 self.assertEqual(self.wf.deleted, False) |
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162 self.assertEqual(self.wf.owner, 'user_foo') |
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163 self.assertEqual(self.wf.published, False) |
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164 self.assertEqual(self.wf.tags, []) |
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165 self.assertEqual( |
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166 self.wf.input_labels_to_ids, {'Input Dataset': {'571', '572'}}) |
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167 self.assertEqual(self.wf.tool_labels_to_ids, {'Paste1': {'573'}}) |
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168 self.assertEqual(self.wf.data_input_ids, {'571', '572'}) |
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169 self.assertEqual(self.wf.source_ids, {'571', '572'}) |
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170 self.assertEqual(self.wf.sink_ids, {'573'}) |
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171 |
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172 def test_dag(self): |
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173 inv_dag = {} |
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174 for h, tails in self.wf.dag.items(): |
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175 for t in tails: |
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176 inv_dag.setdefault(str(t), set()).add(h) |
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177 self.assertEqual(self.wf.inv_dag, inv_dag) |
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178 heads = set(self.wf.dag) |
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179 self.assertEqual(heads, set.union(*self.wf.inv_dag.values())) |
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180 tails = set(self.wf.inv_dag) |
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181 self.assertEqual(tails, set.union(*self.wf.dag.values())) |
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182 ids = self.wf.sorted_step_ids() |
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183 self.assertEqual(set(ids), heads | tails) |
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184 for h, tails in self.wf.dag.items(): |
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185 for t in tails: |
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186 self.assertLess(ids.index(h), ids.index(t)) |
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187 |
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188 def test_steps(self): |
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189 steps = SAMPLE_WF_DICT['steps'] |
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190 for sid, s in self.wf.steps.items(): |
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191 self.assertIsInstance(s, wrappers.Step) |
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192 self.assertEqual(s.id, sid) |
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193 self.assertIn(sid, steps) |
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194 self.assertIs(s.parent, self.wf) |
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195 self.assertEqual(self.wf.data_input_ids, {'571', '572'}) |
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196 self.assertEqual(self.wf.tool_ids, {'573'}) |
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197 |
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198 def test_taint(self): |
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199 self.assertFalse(self.wf.is_modified) |
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200 self.wf.steps['571'].tool_id = 'foo' |
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201 self.assertTrue(self.wf.is_modified) |
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202 |
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203 def test_input_map(self): |
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204 class DummyLD: |
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205 SRC = 'ld' |
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206 |
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207 def __init__(self, id_): |
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208 self.id = id_ |
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209 |
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210 label = 'Input Dataset' |
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211 self.assertEqual(self.wf.input_labels, {label}) |
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212 input_map = self.wf.convert_input_map( |
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213 {label: [DummyLD('a'), DummyLD('b')]}) |
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214 # {'571': {'id': 'a', 'src': 'ld'}, '572': {'id': 'b', 'src': 'ld'}} |
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215 # OR |
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216 # {'571': {'id': 'b', 'src': 'ld'}, '572': {'id': 'a', 'src': 'ld'}} |
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217 self.assertEqual(set(input_map), {'571', '572'}) |
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218 for d in input_map.values(): |
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219 self.assertEqual(set(d), {'id', 'src'}) |
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220 self.assertEqual(d['src'], 'ld') |
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221 self.assertIn(d['id'], 'ab') |
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222 |
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223 |
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224 @test_util.skip_unless_galaxy() |
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225 class GalaxyObjectsTestBase(unittest.TestCase): |
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226 |
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227 def setUp(self): |
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228 galaxy_key = os.environ['BIOBLEND_GALAXY_API_KEY'] |
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229 galaxy_url = os.environ['BIOBLEND_GALAXY_URL'] |
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230 self.gi = galaxy_instance.GalaxyInstance(galaxy_url, galaxy_key) |
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231 |
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232 |
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233 class TestGalaxyInstance(GalaxyObjectsTestBase): |
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234 |
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235 def test_library(self): |
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236 name = 'test_%s' % uuid.uuid4().hex |
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237 description, synopsis = 'D', 'S' |
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238 lib = self.gi.libraries.create( |
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239 name, description=description, synopsis=synopsis) |
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240 self.assertEqual(lib.name, name) |
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241 self.assertEqual(lib.description, description) |
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242 self.assertEqual(lib.synopsis, synopsis) |
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243 self.assertEqual(len(lib.content_infos), 1) # root folder |
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244 self.assertEqual(len(lib.folder_ids), 1) |
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245 self.assertEqual(len(lib.dataset_ids), 0) |
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246 self.assertIn(lib.id, [_.id for _ in self.gi.libraries.list()]) |
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247 lib.delete() |
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248 self.assertFalse(lib.is_mapped) |
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249 |
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250 def test_workflow_from_str(self): |
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251 with open(SAMPLE_FN) as f: |
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252 wf = self.gi.workflows.import_new(f.read()) |
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253 self._check_and_del_workflow(wf) |
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254 |
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255 def test_workflow_collections_from_str(self): |
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256 with open(SAMPLE_WF_COLL_FN) as f: |
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257 wf = self.gi.workflows.import_new(f.read()) |
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258 self._check_and_del_workflow(wf) |
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259 |
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260 @test_util.skip_unless_galaxy('release_19.01') |
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261 def test_workflow_parameter_input(self): |
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262 with open(SAMPLE_WF_PARAMETER_INPUT_FN) as f: |
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263 self.gi.workflows.import_new(f.read()) |
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264 |
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265 def test_workflow_from_dict(self): |
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266 with open(SAMPLE_FN) as f: |
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267 wf = self.gi.workflows.import_new(json.load(f)) |
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268 self._check_and_del_workflow(wf) |
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269 |
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270 def test_workflow_publish_from_dict(self): |
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271 with open(SAMPLE_FN) as f: |
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272 wf = self.gi.workflows.import_new(json.load(f), publish=True) |
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273 self._check_and_del_workflow(wf, check_is_public=True) |
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274 |
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275 def test_workflow_missing_tools(self): |
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276 with open(SAMPLE_FN) as f: |
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277 wf_dump = json.load(f) |
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278 wf_info = self.gi.gi.workflows.import_workflow_dict(wf_dump) |
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279 wf_dict = self.gi.gi.workflows.show_workflow(wf_info['id']) |
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280 for id_, step in wf_dict['steps'].items(): |
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281 if step['type'] == 'tool': |
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282 for k in 'tool_inputs', 'tool_version': |
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283 wf_dict['steps'][id_][k] = None |
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284 wf = wrappers.Workflow(wf_dict, gi=self.gi) |
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285 self.assertFalse(wf.is_runnable) |
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286 self.assertRaises(RuntimeError, wf.run) |
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287 wf.delete() |
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288 |
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289 def test_workflow_export(self): |
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290 with open(SAMPLE_FN) as f: |
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291 wf1 = self.gi.workflows.import_new(f.read()) |
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292 wf2 = self.gi.workflows.import_new(wf1.export()) |
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293 self.assertNotEqual(wf1.id, wf2.id) |
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294 for wf in wf1, wf2: |
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295 self._check_and_del_workflow(wf) |
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296 |
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297 def _check_and_del_workflow(self, wf, check_is_public=False): |
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298 # Galaxy appends additional text to imported workflow names |
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299 self.assertTrue(wf.name.startswith('paste_columns')) |
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300 self.assertEqual(type(wf.owner), str) |
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301 self.assertEqual(len(wf.steps), 3) |
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302 for step_id, step in wf.steps.items(): |
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303 self.assertIsInstance(step, wrappers.Step) |
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304 self.assertEqual(step_id, step.id) |
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305 self.assertIsInstance(step.tool_inputs, dict) |
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306 if step.type == 'tool': |
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307 self.assertIsNotNone(step.tool_id) |
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308 self.assertIsNotNone(step.tool_version) |
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309 self.assertIsInstance(step.input_steps, dict) |
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310 elif step.type in ('data_collection_input', 'data_input'): |
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311 self.assertIsNone(step.tool_id) |
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312 self.assertIsNone(step.tool_version) |
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313 self.assertEqual(step.input_steps, {}) |
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314 wf_ids = {_.id for _ in self.gi.workflows.list()} |
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315 self.assertIn(wf.id, wf_ids) |
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316 if check_is_public: |
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317 self.assertTrue(wf.published) |
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318 wf.delete() |
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319 |
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320 # not very accurate: |
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321 # * we can't publish a wf from the API |
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322 # * we can't directly get another user's wf |
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323 def test_workflow_from_shared(self): |
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324 all_prevs = { |
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325 _.id: _ for _ in self.gi.workflows.get_previews(published=True) |
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326 } |
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327 pub_only_ids = set(all_prevs).difference( |
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328 _.id for _ in self.gi.workflows.get_previews()) |
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329 if pub_only_ids: |
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330 wf_id = pub_only_ids.pop() |
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331 imported = self.gi.workflows.import_shared(wf_id) |
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332 self.assertIsInstance(imported, wrappers.Workflow) |
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333 imported.delete() |
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334 else: |
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335 self.skipTest('no published workflows, manually publish a workflow to run this test') |
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336 |
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337 def test_get_libraries(self): |
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338 self._test_multi_get('library') |
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339 |
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340 def test_get_histories(self): |
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341 self._test_multi_get('history') |
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342 |
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343 def test_get_workflows(self): |
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344 self._test_multi_get('workflow') |
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345 |
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346 def _normalized_functions(self, obj_type): |
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347 if obj_type == 'library': |
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348 create = self.gi.libraries.create |
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349 get_objs = self.gi.libraries.list |
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350 get_prevs = self.gi.libraries.get_previews |
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351 del_kwargs = {} |
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352 elif obj_type == 'history': |
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353 create = self.gi.histories.create |
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354 get_objs = self.gi.histories.list |
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355 get_prevs = self.gi.histories.get_previews |
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356 del_kwargs = {'purge': True} |
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357 elif obj_type == 'workflow': |
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358 def create(name): |
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359 with open(SAMPLE_FN) as f: |
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360 d = json.load(f) |
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361 d['name'] = name |
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362 return self.gi.workflows.import_new(d) |
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363 |
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364 get_objs = self.gi.workflows.list |
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365 get_prevs = self.gi.workflows.get_previews |
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366 del_kwargs = {} |
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367 return create, get_objs, get_prevs, del_kwargs |
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368 |
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369 def _test_multi_get(self, obj_type): |
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370 create, get_objs, get_prevs, del_kwargs = self._normalized_functions( |
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371 obj_type) |
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372 |
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373 def ids(seq): |
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374 return {_.id for _ in seq} |
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375 |
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376 names = ['test_%s' % uuid.uuid4().hex for _ in range(2)] |
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377 objs = [] |
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378 try: |
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379 objs = [create(_) for _ in names] |
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380 self.assertLessEqual(ids(objs), ids(get_objs())) |
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381 if obj_type != 'workflow': |
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382 filtered = get_objs(name=names[0]) |
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383 self.assertEqual(len(filtered), 1) |
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384 self.assertEqual(filtered[0].id, objs[0].id) |
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385 del_id = objs[-1].id |
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386 objs.pop().delete(**del_kwargs) |
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387 self.assertIn(del_id, ids(get_prevs(deleted=True))) |
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388 else: |
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389 # Galaxy appends info strings to imported workflow names |
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390 prev = get_prevs()[0] |
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391 filtered = get_objs(name=prev.name) |
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392 self.assertEqual(len(filtered), 1) |
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393 self.assertEqual(filtered[0].id, prev.id) |
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394 finally: |
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395 for o in objs: |
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396 o.delete(**del_kwargs) |
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397 |
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398 def test_delete_libraries_by_name(self): |
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399 self._test_delete_by_name('library') |
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400 |
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401 def test_delete_histories_by_name(self): |
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402 self._test_delete_by_name('history') |
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403 |
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404 def test_delete_workflows_by_name(self): |
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405 self._test_delete_by_name('workflow') |
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406 |
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407 def _test_delete_by_name(self, obj_type): |
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408 create, _, get_prevs, del_kwargs = self._normalized_functions( |
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409 obj_type) |
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410 name = 'test_%s' % uuid.uuid4().hex |
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411 objs = [create(name) for _ in range(2)] # noqa: F812 |
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412 final_name = objs[0].name |
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413 prevs = [_ for _ in get_prevs(name=final_name) if not _.deleted] |
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414 self.assertEqual(len(prevs), len(objs)) |
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415 del_kwargs['name'] = final_name |
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416 objs[0].gi_module.delete(**del_kwargs) |
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417 prevs = [_ for _ in get_prevs(name=final_name) if not _.deleted] |
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418 self.assertEqual(len(prevs), 0) |
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419 |
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420 |
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421 class TestLibrary(GalaxyObjectsTestBase): |
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422 # just something that can be expected to be always up |
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423 DS_URL = 'https://tools.ietf.org/rfc/rfc1866.txt' |
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424 |
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425 def setUp(self): |
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426 super().setUp() |
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427 self.lib = self.gi.libraries.create('test_%s' % uuid.uuid4().hex) |
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428 |
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429 def tearDown(self): |
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430 self.lib.delete() |
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431 |
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432 def test_root_folder(self): |
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433 r = self.lib.root_folder |
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434 self.assertIsNone(r.parent) |
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435 |
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436 def test_folder(self): |
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437 name, desc = 'test_%s' % uuid.uuid4().hex, 'D' |
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438 folder = self.lib.create_folder(name, description=desc) |
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439 self.assertEqual(folder.name, name) |
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440 self.assertEqual(folder.description, desc) |
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441 self.assertIs(folder.container, self.lib) |
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442 self.assertEqual(folder.parent.id, self.lib.root_folder.id) |
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443 self.assertEqual(len(self.lib.content_infos), 2) |
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444 self.assertEqual(len(self.lib.folder_ids), 2) |
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445 self.assertIn(folder.id, self.lib.folder_ids) |
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446 retrieved = self.lib.get_folder(folder.id) |
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447 self.assertEqual(folder.id, retrieved.id) |
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448 |
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449 def _check_datasets(self, dss): |
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450 self.assertEqual(len(dss), len(self.lib.dataset_ids)) |
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451 self.assertEqual({_.id for _ in dss}, set(self.lib.dataset_ids)) |
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452 for ds in dss: |
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453 self.assertIs(ds.container, self.lib) |
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454 |
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455 def test_dataset(self): |
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456 folder = self.lib.create_folder('test_%s' % uuid.uuid4().hex) |
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457 ds = self.lib.upload_data(FOO_DATA, folder=folder) |
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458 self.assertEqual(len(self.lib.content_infos), 3) |
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459 self.assertEqual(len(self.lib.folder_ids), 2) |
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460 self._check_datasets([ds]) |
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461 |
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462 def test_dataset_from_url(self): |
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463 if is_reachable(self.DS_URL): |
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464 ds = self.lib.upload_from_url(self.DS_URL) |
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465 self._check_datasets([ds]) |
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466 else: |
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467 self.skipTest('%s not reachable' % self.DS_URL) |
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468 |
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469 def test_dataset_from_local(self): |
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470 with tempfile.NamedTemporaryFile(mode='w', prefix='bioblend_test_') as f: |
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471 f.write(FOO_DATA) |
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472 f.flush() |
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473 ds = self.lib.upload_from_local(f.name) |
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474 self._check_datasets([ds]) |
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475 |
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476 def test_datasets_from_fs(self): |
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477 bnames = ['f%d.txt' % i for i in range(2)] |
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478 dss, fnames = upload_from_fs(self.lib, bnames) |
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479 self._check_datasets(dss) |
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480 dss, fnames = upload_from_fs( |
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481 self.lib, bnames, link_data_only='link_to_files') |
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482 for ds, fn in zip(dss, fnames): |
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483 self.assertEqual(ds.file_name, fn) |
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484 |
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485 def test_copy_from_dataset(self): |
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486 hist = self.gi.histories.create('test_%s' % uuid.uuid4().hex) |
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487 try: |
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488 hda = hist.paste_content(FOO_DATA) |
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489 ds = self.lib.copy_from_dataset(hda) |
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490 finally: |
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491 hist.delete(purge=True) |
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492 self._check_datasets([ds]) |
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493 |
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494 def test_get_dataset(self): |
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495 ds = self.lib.upload_data(FOO_DATA) |
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496 retrieved = self.lib.get_dataset(ds.id) |
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497 self.assertEqual(ds.id, retrieved.id) |
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498 |
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499 def test_get_datasets(self): |
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500 bnames = ['f%d.txt' % _ for _ in range(2)] |
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501 dss, _ = upload_from_fs(self.lib, bnames) |
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502 retrieved = self.lib.get_datasets() |
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503 self.assertEqual(len(dss), len(retrieved)) |
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504 self.assertEqual({_.id for _ in dss}, {_.id for _ in retrieved}) |
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505 name = '/%s' % bnames[0] |
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506 selected = self.lib.get_datasets(name=name) |
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507 self.assertEqual(len(selected), 1) |
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508 self.assertEqual(selected[0].name, bnames[0]) |
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509 |
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510 |
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511 class TestLDContents(GalaxyObjectsTestBase): |
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512 |
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513 def setUp(self): |
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514 super().setUp() |
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515 self.lib = self.gi.libraries.create('test_%s' % uuid.uuid4().hex) |
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516 self.ds = self.lib.upload_data(FOO_DATA) |
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517 self.ds.wait() |
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518 |
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519 def tearDown(self): |
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520 self.lib.delete() |
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521 |
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522 def test_dataset_get_stream(self): |
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523 for idx, c in enumerate(self.ds.get_stream(chunk_size=1)): |
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524 self.assertEqual(FOO_DATA[idx].encode(), c) |
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525 |
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526 def test_dataset_peek(self): |
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527 fetched_data = self.ds.peek(chunk_size=4) |
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528 self.assertEqual(FOO_DATA[0:4].encode(), fetched_data) |
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529 |
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530 def test_dataset_download(self): |
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531 with tempfile.TemporaryFile() as f: |
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532 self.ds.download(f) |
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533 f.seek(0) |
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534 self.assertEqual(FOO_DATA.encode(), f.read()) |
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535 |
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536 def test_dataset_get_contents(self): |
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537 self.assertEqual(FOO_DATA.encode(), self.ds.get_contents()) |
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538 |
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539 def test_dataset_delete(self): |
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540 self.ds.delete() |
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541 # Cannot test this yet because the 'deleted' attribute is not exported |
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542 # by the API at the moment |
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543 # self.assertTrue(self.ds.deleted) |
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544 |
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545 def test_dataset_update(self): |
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546 new_name = 'test_%s' % uuid.uuid4().hex |
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547 new_misc_info = 'Annotation for %s' % new_name |
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548 new_genome_build = 'hg19' |
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549 updated_ldda = self.ds.update(name=new_name, misc_info=new_misc_info, genome_build=new_genome_build) |
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550 self.assertEqual(self.ds.id, updated_ldda.id) |
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551 self.assertEqual(self.ds.name, new_name) |
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552 self.assertEqual(self.ds.misc_info, new_misc_info) |
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553 self.assertEqual(self.ds.genome_build, new_genome_build) |
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554 |
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555 |
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556 class TestHistory(GalaxyObjectsTestBase): |
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557 |
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558 def setUp(self): |
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559 super().setUp() |
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560 self.hist = self.gi.histories.create('test_%s' % uuid.uuid4().hex) |
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561 |
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562 def tearDown(self): |
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563 self.hist.delete(purge=True) |
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564 |
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565 def test_create_delete(self): |
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566 name = 'test_%s' % uuid.uuid4().hex |
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567 hist = self.gi.histories.create(name) |
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568 self.assertEqual(hist.name, name) |
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569 hist_id = hist.id |
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570 self.assertIn(hist_id, [_.id for _ in self.gi.histories.list()]) |
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571 hist.delete(purge=True) |
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572 self.assertFalse(hist.is_mapped) |
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573 h = self.gi.histories.get(hist_id) |
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574 self.assertTrue(h.deleted) |
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575 |
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576 def _check_dataset(self, hda): |
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577 self.assertIsInstance(hda, wrappers.HistoryDatasetAssociation) |
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578 self.assertIs(hda.container, self.hist) |
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579 self.assertEqual(len(self.hist.dataset_ids), 1) |
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580 self.assertEqual(self.hist.dataset_ids[0], hda.id) |
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581 |
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582 def test_import_dataset(self): |
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583 lib = self.gi.libraries.create('test_%s' % uuid.uuid4().hex) |
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584 lds = lib.upload_data(FOO_DATA) |
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585 self.assertEqual(len(self.hist.dataset_ids), 0) |
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586 hda = self.hist.import_dataset(lds) |
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587 lib.delete() |
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588 self._check_dataset(hda) |
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589 |
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590 def test_upload_file(self): |
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591 with tempfile.NamedTemporaryFile(mode='w', prefix='bioblend_test_') as f: |
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592 f.write(FOO_DATA) |
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593 f.flush() |
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594 hda = self.hist.upload_file(f.name) |
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595 self._check_dataset(hda) |
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596 |
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597 def test_paste_content(self): |
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598 hda = self.hist.paste_content(FOO_DATA) |
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599 self._check_dataset(hda) |
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600 |
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601 def test_get_dataset(self): |
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602 hda = self.hist.paste_content(FOO_DATA) |
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603 retrieved = self.hist.get_dataset(hda.id) |
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604 self.assertEqual(hda.id, retrieved.id) |
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605 |
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606 def test_get_datasets(self): |
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607 bnames = ['f%d.txt' % _ for _ in range(2)] |
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608 lib = self.gi.libraries.create('test_%s' % uuid.uuid4().hex) |
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609 lds = upload_from_fs(lib, bnames)[0] |
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610 hdas = [self.hist.import_dataset(_) for _ in lds] |
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611 lib.delete() |
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612 retrieved = self.hist.get_datasets() |
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613 self.assertEqual(len(hdas), len(retrieved)) |
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614 self.assertEqual({_.id for _ in hdas}, {_.id for _ in retrieved}) |
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615 selected = self.hist.get_datasets(name=bnames[0]) |
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616 self.assertEqual(len(selected), 1) |
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617 self.assertEqual(selected[0].name, bnames[0]) |
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618 |
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619 def test_export_and_download(self): |
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620 jeha_id = self.hist.export(wait=True, maxwait=60) |
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621 self.assertTrue(jeha_id) |
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622 tempdir = tempfile.mkdtemp(prefix='bioblend_test_') |
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623 temp_fn = os.path.join(tempdir, 'export.tar.gz') |
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624 try: |
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625 with open(temp_fn, 'wb') as fo: |
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626 self.hist.download(jeha_id, fo) |
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627 self.assertTrue(tarfile.is_tarfile(temp_fn)) |
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628 finally: |
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629 shutil.rmtree(tempdir) |
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630 |
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631 def test_update(self): |
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632 new_name = 'test_%s' % uuid.uuid4().hex |
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633 new_annotation = 'Annotation for %s' % new_name |
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634 new_tags = ['tag1', 'tag2'] |
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635 updated_hist = self.hist.update(name=new_name, annotation=new_annotation, tags=new_tags) |
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636 self.assertEqual(self.hist.id, updated_hist.id) |
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637 self.assertEqual(self.hist.name, new_name) |
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638 self.assertEqual(self.hist.annotation, new_annotation) |
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639 self.assertEqual(self.hist.tags, new_tags) |
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640 updated_hist = self.hist.update(published=True) |
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641 self.assertEqual(self.hist.id, updated_hist.id) |
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642 self.assertTrue(self.hist.published) |
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643 |
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644 def test_create_dataset_collection(self): |
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645 self._create_collection_description() |
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646 hdca = self.hist.create_dataset_collection(self.collection_description) |
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647 self.assertIsInstance(hdca, wrappers.HistoryDatasetCollectionAssociation) |
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648 self.assertEqual(hdca.collection_type, 'list') |
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649 self.assertIs(hdca.container, self.hist) |
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650 self.assertEqual(len(hdca.elements), 2) |
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651 self.assertEqual(self.dataset1.id, hdca.elements[0]['object']['id']) |
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652 self.assertEqual(self.dataset2.id, hdca.elements[1]['object']['id']) |
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653 |
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654 def test_delete_dataset_collection(self): |
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655 self._create_collection_description() |
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656 hdca = self.hist.create_dataset_collection(self.collection_description) |
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657 hdca.delete() |
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658 self.assertTrue(hdca.deleted) |
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659 |
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660 def _create_collection_description(self): |
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661 self.dataset1 = self.hist.paste_content(FOO_DATA) |
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662 self.dataset2 = self.hist.paste_content(FOO_DATA_2) |
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663 self.collection_description = dataset_collections.CollectionDescription( |
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664 name="MyDatasetList", |
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665 elements=[ |
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666 dataset_collections.HistoryDatasetElement(name="sample1", id=self.dataset1.id), |
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667 dataset_collections.HistoryDatasetElement(name="sample2", id=self.dataset2.id), |
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668 ] |
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669 ) |
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670 |
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671 |
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672 class TestHDAContents(GalaxyObjectsTestBase): |
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673 |
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674 def setUp(self): |
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675 super().setUp() |
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676 self.hist = self.gi.histories.create('test_%s' % uuid.uuid4().hex) |
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677 self.ds = self.hist.paste_content(FOO_DATA) |
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678 self.ds.wait() |
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679 |
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680 def tearDown(self): |
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681 self.hist.delete(purge=True) |
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682 |
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683 def test_dataset_get_stream(self): |
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684 for idx, c in enumerate(self.ds.get_stream(chunk_size=1)): |
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685 self.assertEqual(FOO_DATA[idx].encode(), c) |
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686 |
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687 def test_dataset_peek(self): |
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688 fetched_data = self.ds.peek(chunk_size=4) |
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689 self.assertEqual(FOO_DATA[0:4].encode(), fetched_data) |
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690 |
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691 def test_dataset_download(self): |
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692 with tempfile.TemporaryFile() as f: |
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693 self.ds.download(f) |
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694 f.seek(0) |
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695 self.assertEqual(FOO_DATA.encode(), f.read()) |
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696 |
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697 def test_dataset_get_contents(self): |
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698 self.assertEqual(FOO_DATA.encode(), self.ds.get_contents()) |
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699 |
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700 def test_dataset_update(self): |
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701 new_name = 'test_%s' % uuid.uuid4().hex |
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702 new_annotation = 'Annotation for %s' % new_name |
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703 new_genome_build = 'hg19' |
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704 updated_hda = self.ds.update(name=new_name, annotation=new_annotation, genome_build=new_genome_build) |
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705 self.assertEqual(self.ds.id, updated_hda.id) |
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706 self.assertEqual(self.ds.name, new_name) |
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707 self.assertEqual(self.ds.annotation, new_annotation) |
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708 self.assertEqual(self.ds.genome_build, new_genome_build) |
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709 |
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710 def test_dataset_delete(self): |
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711 self.ds.delete() |
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712 self.assertTrue(self.ds.deleted) |
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713 self.assertFalse(self.ds.purged) |
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714 |
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715 def test_dataset_purge(self): |
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716 self.ds.delete(purge=True) |
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717 self.assertTrue(self.ds.deleted) |
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718 self.assertTrue(self.ds.purged) |
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719 |
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720 |
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721 class TestRunWorkflow(GalaxyObjectsTestBase): |
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722 |
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723 def setUp(self): |
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724 super().setUp() |
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725 self.lib = self.gi.libraries.create('test_%s' % uuid.uuid4().hex) |
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726 with open(SAMPLE_FN) as f: |
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727 self.wf = self.gi.workflows.import_new(f.read()) |
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728 self.contents = ['one\ntwo\n', '1\n2\n'] |
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729 self.inputs = [self.lib.upload_data(_) for _ in self.contents] |
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730 |
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731 def tearDown(self): |
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732 self.wf.delete() |
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733 self.lib.delete() |
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734 |
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735 def _test(self, existing_hist=False, params=False): |
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736 hist_name = 'test_%s' % uuid.uuid4().hex |
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737 if existing_hist: |
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738 hist = self.gi.histories.create(hist_name) |
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739 else: |
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740 hist = hist_name |
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741 if params: |
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742 params = {'Paste1': {'delimiter': 'U'}} |
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743 sep = '_' # 'U' maps to '_' in the paste tool |
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744 else: |
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745 params = None |
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746 sep = '\t' # default |
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747 input_map = {'Input 1': self.inputs[0], 'Input 2': self.inputs[1]} |
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748 sys.stderr.write(os.linesep) |
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749 outputs, out_hist = self.wf.run( |
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750 input_map, hist, params=params, wait=True, polling_interval=1) |
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751 self.assertEqual(len(outputs), 1) |
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752 out_ds = outputs[0] |
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753 self.assertIn(out_ds.id, out_hist.dataset_ids) |
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754 res = out_ds.get_contents() |
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755 exp_rows = zip(*(_.splitlines() for _ in self.contents)) |
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756 exp_res = ("\n".join(sep.join(t) for t in exp_rows) + "\n").encode() |
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757 self.assertEqual(res, exp_res) |
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758 if existing_hist: |
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759 self.assertEqual(out_hist.id, hist.id) |
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760 out_hist.delete(purge=True) |
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761 |
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762 def test_existing_history(self): |
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763 self._test(existing_hist=True) |
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764 |
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765 def test_new_history(self): |
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766 self._test(existing_hist=False) |
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767 |
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768 def test_params(self): |
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769 self._test(params=True) |
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770 |
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771 |
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772 class TestRunDatasetCollectionWorkflow(GalaxyObjectsTestBase): |
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773 |
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774 def setUp(self): |
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775 super().setUp() |
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776 with open(SAMPLE_WF_COLL_FN) as f: |
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777 self.wf = self.gi.workflows.import_new(f.read()) |
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778 self.hist = self.gi.histories.create('test_%s' % uuid.uuid4().hex) |
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779 |
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780 def tearDown(self): |
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781 self.wf.delete() |
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782 self.hist.delete(purge=True) |
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783 |
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784 def test_run_workflow_with_dataset_collection(self): |
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785 dataset1 = self.hist.paste_content(FOO_DATA) |
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786 dataset2 = self.hist.paste_content(FOO_DATA_2) |
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787 collection_description = dataset_collections.CollectionDescription( |
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788 name="MyDatasetList", |
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789 elements=[ |
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790 dataset_collections.HistoryDatasetElement(name="sample1", id=dataset1.id), |
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791 dataset_collections.HistoryDatasetElement(name="sample2", id=dataset2.id), |
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792 ] |
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793 ) |
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794 dataset_collection = self.hist.create_dataset_collection(collection_description) |
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795 input_map = {"Input Dataset Collection": dataset_collection, |
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796 "Input 2": dataset1} |
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797 outputs, out_hist = self.wf.run(input_map, self.hist, wait=True) |
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798 self.assertEqual(len(outputs), 1) |
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799 out_hdca = outputs[0] |
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800 self.assertIsInstance(out_hdca, wrappers.HistoryDatasetCollectionAssociation) |
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801 self.assertEqual(out_hdca.collection_type, 'list') |
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802 self.assertEqual(len(out_hdca.elements), 2) |
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803 self.assertEqual(out_hist.id, self.hist.id) |
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804 |
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805 |
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806 class TestJob(GalaxyObjectsTestBase): |
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807 |
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808 def test_get(self): |
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809 job_prevs = self.gi.jobs.get_previews() |
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810 if len(job_prevs) > 0: |
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811 job_prev = job_prevs[0] |
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812 self.assertIsInstance(job_prev, wrappers.JobPreview) |
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813 job = self.gi.jobs.get(job_prev.id) |
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814 self.assertIsInstance(job, wrappers.Job) |
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815 self.assertEqual(job.id, job_prev.id) |
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816 for job in self.gi.jobs.list(): |
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817 self.assertIsInstance(job, wrappers.Job) |
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818 |
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819 |
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820 def suite(): |
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821 loader = unittest.TestLoader() |
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822 s = unittest.TestSuite() |
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823 s.addTests([loader.loadTestsFromTestCase(c) for c in ( |
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824 TestWrapper, |
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825 TestWorkflow, |
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826 TestGalaxyInstance, |
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827 TestLibrary, |
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828 TestLDContents, |
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829 TestHistory, |
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830 TestHDAContents, |
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831 TestRunWorkflow, |
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832 )]) |
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833 return s |
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834 |
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835 |
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836 if __name__ == '__main__': |
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837 tests = suite() |
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838 RUNNER = unittest.TextTestRunner(verbosity=2) |
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839 RUNNER.run(tests) |