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

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:18:57 -0400
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1 """
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2 """
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3 import os
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4
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5 from bioblend.galaxy.tools.inputs import (
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6 conditional,
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7 dataset,
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8 inputs,
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9 repeat,
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10 )
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11 from . import GalaxyTestBase, test_util
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12
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13
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14 class TestGalaxyTools(GalaxyTestBase.GalaxyTestBase):
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15
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16 def test_get_tools(self):
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17 # Test requires target Galaxy is configured with at least one tool.
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18 tools = self.gi.tools.get_tools()
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19 self.assertGreater(len(tools), 0)
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20 self.assertTrue(all(map(self._assert_is_tool_rep, tools)))
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21
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22 def test_get_tool_panel(self):
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23 # Test requires target Galaxy is configured with at least one tool
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24 # section.
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25 tool_panel = self.gi.tools.get_tool_panel()
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26 sections = [s for s in tool_panel if "elems" in s]
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27 self.assertGreater(len(sections), 0)
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28 self.assertTrue(all(map(self._assert_is_tool_rep, sections[0]["elems"])))
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29
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30 def _assert_is_tool_rep(self, data):
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31 self.assertTrue(data["model_class"].endswith("Tool"))
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32 # Special tools like SetMetadataTool may have different model_class
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33 # than Tool - but they all seem to end in tool.
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34
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35 for key in ["name", "id", "version"]:
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36 self.assertIn(key, data)
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37 return True
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38
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39 def test_paste_content(self):
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40 history = self.gi.histories.create_history(name="test_paste_data history")
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41 paste_text = 'line 1\nline 2\rline 3\r\nline 4'
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42 tool_output = self.gi.tools.paste_content(paste_text, history["id"])
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43 self.assertEqual(len(tool_output["outputs"]), 1)
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44 # All lines in the resulting dataset should end with "\n"
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45 expected_contents = ("\n".join(paste_text.splitlines()) + "\n").encode()
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46 self._wait_and_verify_dataset(tool_output['outputs'][0]['id'], expected_contents)
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47 # Same with space_to_tab=True
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48 tool_output = self.gi.tools.paste_content(paste_text, history["id"], space_to_tab=True)
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49 self.assertEqual(len(tool_output["outputs"]), 1)
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50 expected_contents = ("\n".join("\t".join(_.split()) for _ in paste_text.splitlines()) + "\n").encode()
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51 self._wait_and_verify_dataset(tool_output['outputs'][0]['id'], expected_contents)
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52
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53 def test_upload_file(self):
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54 history = self.gi.histories.create_history(name="test_upload_file history")
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55
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56 fn = test_util.get_abspath("test_util.py")
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57 file_name = "test1"
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58 tool_output = self.gi.tools.upload_file(
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59 fn,
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60 # First param could be a regular path also of course...
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61 history_id=history["id"],
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62 file_name=file_name,
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63 dbkey="?",
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64 file_type="txt",
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65 )
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66 self._wait_for_and_verify_upload(tool_output, file_name, fn, expected_dbkey="?")
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67
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68 def test_upload_file_dbkey(self):
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69 history = self.gi.histories.create_history(name="test_upload_file history")
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70 fn = test_util.get_abspath("test_util.py")
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71 file_name = "test1"
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72 dbkey = "hg19"
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73 tool_output = self.gi.tools.upload_file(
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74 fn,
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75 history_id=history["id"],
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76 file_name=file_name,
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77 dbkey=dbkey,
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78 file_type="txt",
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79 )
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80 self._wait_for_and_verify_upload(tool_output, file_name, fn, expected_dbkey=dbkey)
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81
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82 @test_util.skip_unless_tool("random_lines1")
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83 def test_run_random_lines(self):
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84 # Run second test case from randomlines.xml
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85 history_id = self.gi.histories.create_history(name="test_run_random_lines history")["id"]
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86 with open(test_util.get_abspath(os.path.join("data", "1.bed"))) as f:
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87 contents = f.read()
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88 dataset_id = self._test_dataset(history_id, contents=contents)
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89 tool_inputs = inputs().set(
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90 "num_lines", "1"
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91 ).set(
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92 "input", dataset(dataset_id)
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93 ).set(
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94 "seed_source", conditional().set(
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95 "seed_source_selector", "set_seed"
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96 ).set(
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97 "seed", "asdf"
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98 )
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99 )
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100 tool_output = self.gi.tools.run_tool(
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101 history_id=history_id,
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102 tool_id="random_lines1",
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103 tool_inputs=tool_inputs
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104 )
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105 self.assertEqual(len(tool_output["outputs"]), 1)
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106 # TODO: Wait for results and verify has 1 line and is
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107 # chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 +
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108
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109 @test_util.skip_unless_tool("cat1")
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110 def test_run_cat1(self):
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111 history_id = self.gi.histories.create_history(name="test_run_cat1 history")["id"]
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112 dataset1_id = self._test_dataset(history_id, contents="1 2 3")
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113 dataset2_id = self._test_dataset(history_id, contents="4 5 6")
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114 dataset3_id = self._test_dataset(history_id, contents="7 8 9")
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115 tool_inputs = inputs().set(
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116 "input1", dataset(dataset1_id)
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117 ).set(
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118 "queries", repeat().instance(
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119 inputs().set("input2", dataset(dataset2_id))
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120 ).instance(
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121 inputs().set("input2", dataset(dataset3_id))
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122 )
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123 )
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124 tool_output = self.gi.tools.run_tool(
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125 history_id=history_id,
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126 tool_id="cat1",
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127 tool_inputs=tool_inputs
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128 )
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129 self.assertEqual(len(tool_output["outputs"]), 1)
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130 # TODO: Wait for results and verify it has 3 lines - 1 2 3, 4 5 6,
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131 # and 7 8 9.
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132
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133 def test_tool_dependency_install(self):
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134 installed_dependencies = self.gi.tools.install_dependencies('CONVERTER_fasta_to_bowtie_color_index')
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135 self.assertTrue(any(True for d in installed_dependencies if d.get('name') == 'bowtie' and d.get('dependency_type') == 'conda'), "installed_dependencies is %s" % installed_dependencies)
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136
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137 def _wait_for_and_verify_upload(self, tool_output, file_name, fn, expected_dbkey="?"):
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138 self.assertEqual(len(tool_output["outputs"]), 1)
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139 output = tool_output['outputs'][0]
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140 self.assertEqual(output['name'], file_name)
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141 expected_contents = open(fn, "rb").read()
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142 self._wait_and_verify_dataset(output["id"], expected_contents)
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143 self.assertEqual(output["genome_build"], expected_dbkey)