Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/bioblend/_tests/test_util.py @ 0:4f3585e2f14b draft default tip
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author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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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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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
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109 def get_abspath(path): |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
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110 return os.path.abspath(os.path.join(os.path.dirname(__file__), path)) |