Mercurial > repos > guerler > springsuite

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