Mercurial > repos > guerler > springsuite

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

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:32:28 -0400
parents d30785e31577
children
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1 """ General support infrastructure not tied to any particular test.
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2 """
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3 import os
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4 import random
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5 import string
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6 import unittest
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7
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8 import bioblend
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9
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10 NO_CLOUDMAN_MESSAGE = "CloudMan required and no CloudMan AMI configured."
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11 NO_GALAXY_MESSAGE = "Externally configured Galaxy required, but not found. Set BIOBLEND_GALAXY_URL and BIOBLEND_GALAXY_API_KEY to run this test."
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12 OLD_GALAXY_RELEASE = "Testing on Galaxy %s, but need %s to run this test."
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13 MISSING_TOOL_MESSAGE = "Externally configured Galaxy instance requires tool %s to run test."
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14
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15
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16 def skip_unless_cloudman():
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17 """ Decorate tests with this to skip the test if CloudMan is not
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18 configured.
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19 """
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20 if 'BIOBLEND_AMI_ID' not in os.environ:
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21 return unittest.skip(NO_CLOUDMAN_MESSAGE)
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22 else:
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23 return lambda f: f
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24
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25
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26 def skip_unless_galaxy(min_release=None):
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27 """ Decorate tests with this to skip the test if Galaxy is not
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28 configured.
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29 """
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30 if min_release is not None:
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31 galaxy_release = os.environ.get('GALAXY_VERSION', None)
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32 if galaxy_release is not None and galaxy_release != 'dev':
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33 if not galaxy_release.startswith('release_'):
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34 raise ValueError("The value of GALAXY_VERSION environment variable should start with 'release_'")
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35 if not min_release.startswith('release_'):
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36 raise Exception("min_release should start with 'release_'")
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37 if galaxy_release[8:] < min_release[8:]:
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38 return unittest.skip(OLD_GALAXY_RELEASE % (galaxy_release, min_release))
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39
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40 if 'BIOBLEND_GALAXY_URL' not in os.environ:
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41 return unittest.skip(NO_GALAXY_MESSAGE)
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42
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43 if 'BIOBLEND_GALAXY_API_KEY' not in os.environ and 'BIOBLEND_GALAXY_MASTER_API_KEY' in os.environ:
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44 galaxy_url = os.environ['BIOBLEND_GALAXY_URL']
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45 galaxy_master_api_key = os.environ['BIOBLEND_GALAXY_MASTER_API_KEY']
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46 gi = bioblend.galaxy.GalaxyInstance(galaxy_url, galaxy_master_api_key)
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47
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48 if 'BIOBLEND_GALAXY_USER_EMAIL' in os.environ:
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49 galaxy_user_email = os.environ['BIOBLEND_GALAXY_USER_EMAIL']
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50 else:
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51 galaxy_user_email = ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(5)) + "@localhost.localdomain"
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52
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53 galaxy_user_id = None
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54 for user in gi.users.get_users():
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55 if user["email"] == galaxy_user_email:
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56 galaxy_user_id = user["id"]
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57 break
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58
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59 if galaxy_user_id is None:
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60 try:
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61 config = gi.config.get_config()
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62 except Exception:
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63 # If older Galaxy for instance just assume use_remote_user is False.
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64 config = {}
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65
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66 if config.get("use_remote_user", False):
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67 new_user = gi.users.create_remote_user(galaxy_user_email)
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68 else:
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69 galaxy_user = galaxy_user_email.split("@", 1)[0]
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70 galaxy_password = ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(20))
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71
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72 # Create a new user and get a new API key for her
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73 new_user = gi.users.create_local_user(galaxy_user, galaxy_user_email, galaxy_password)
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74 galaxy_user_id = new_user["id"]
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75
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76 api_key = gi.users.create_user_apikey(galaxy_user_id)
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77 os.environ["BIOBLEND_GALAXY_API_KEY"] = api_key
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78
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79 if 'BIOBLEND_GALAXY_API_KEY' not in os.environ:
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80 return unittest.skip(NO_GALAXY_MESSAGE)
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81
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82 return lambda f: f
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83
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84
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85 def skip_unless_tool(tool_id):
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86 """ Decorate a Galaxy test method as requiring a specific tool,
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87 skip the test case if the tool is unavailable.
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88 """
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89
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90 def method_wrapper(method):
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91
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92 def wrapped_method(has_gi, *args, **kwargs):
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93 tools = has_gi.gi.tools.get_tools()
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94 # In panels by default, so flatten out sections...
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95 tool_ids = [_['id'] for _ in tools]
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96 if tool_id not in tool_ids:
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97 raise unittest.SkipTest(MISSING_TOOL_MESSAGE % tool_id)
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98
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99 return method(has_gi, *args, **kwargs)
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100
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101 # Must preserve method name so nose can detect and report tests by
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102 # name.
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103 wrapped_method.__name__ = method.__name__
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104 return wrapped_method
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105
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106 return method_wrapper
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107
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108
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109 def get_abspath(path):
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110 return os.path.abspath(os.path.join(os.path.dirname(__file__), path))