Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/galaxy/api.py @ 3:758bc20232e8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -0400
parents 26e78fe6e8c4
children
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0
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1 """A high-level interface to local Galaxy instances using bioblend."""
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2 from six import StringIO
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3
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4 from planemo.bioblend import ensure_module
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5 from planemo.bioblend import galaxy
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6
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7 DEFAULT_MASTER_API_KEY = "test_key"
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8
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9
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10 def gi(port=None, url=None, key=None):
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11 """Return a bioblend ``GalaxyInstance`` for Galaxy on this port."""
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12 ensure_module()
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13 if key is None:
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14 key = DEFAULT_MASTER_API_KEY
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15 if port is None:
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16 url = url
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17 else:
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18 url = "http://localhost:%d" % int(port)
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19
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20 return galaxy.GalaxyInstance(
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21 url=url,
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22 key=key
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23 )
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24
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25
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26 def user_api_key(admin_gi):
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27 """Use an admin authenticated account to generate a user API key."""
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28 ensure_module()
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29 # TODO: thread-safe
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30 users = admin_gi.users
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31 all_users = users.get_users()
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32
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33 user_id = None
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34 for user in all_users:
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35 if user["email"] == "planemo@galaxyproject.org":
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36 user_id = user["id"]
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37
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38 if user_id is None:
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39 # TODO: Allow override with --user_api_key.
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40 galaxy_config = admin_gi.config.get_config()
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41 use_remote_user = bool(galaxy_config["use_remote_user"])
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42 if not use_remote_user:
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43 user_response = users.create_local_user(
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44 "planemo",
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45 "planemo@galaxyproject.org",
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46 "planemo",
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47 )
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48 user_id = user_response["id"]
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49 else:
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50 user_response = users.create_remote_user(
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51 "planemo@galaxyproject.org",
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52 )
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53 user_id = user_response["id"]
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54 return users.create_user_apikey(user_id)
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55
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56
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57 def summarize_history(ctx, gi, history_id):
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58 """Summarize a history with print() based on similar code in Galaxy for populators.
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59 """
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60 if not ctx.verbose:
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61 return
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62
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63 if history_id is None:
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64 raise ValueError("summarize_history passed empty history_id")
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65 try:
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66 history_contents = gi.histories.show_history(history_id, contents=True)
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67 except Exception:
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68 print("Failed to fetch history contents in summarize_history.")
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69 return
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70
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71 for history_content in history_contents:
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72 history_content_id = history_content.get('id', None)
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73 print("| %d - %s (HID - NAME) " % (int(history_content['hid']), history_content['name']))
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74 if history_content['history_content_type'] == 'dataset_collection':
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75 history_contents_json = gi.histories.show_dataset_collection(history_id, history_content["id"])
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76 print("| Dataset Collection: %s" % history_contents_json)
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77 continue
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78 try:
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79 dataset_info = gi.histories.show_dataset(history_id, history_content_id)
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80 print("| Dataset State:")
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81 print(_format_for_summary(dataset_info.get("state"), "Dataset state is unknown."))
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82 print("| Dataset Blurb:")
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83 print(_format_for_summary(dataset_info.get("misc_blurb", ""), "Dataset blurb was empty."))
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84 print("| Dataset Info:")
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85 print(_format_for_summary(dataset_info.get("misc_info", ""), "Dataset info is empty."))
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86 print("| Peek:")
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87 print(_format_for_summary(dataset_info.get("peek", ""), "Peek unavilable."))
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88 except Exception:
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89 print("| *PLANEMO ERROR FETCHING DATASET DETAILS*")
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90 try:
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91 provenance_info = _dataset_provenance(gi, history_id, history_content_id)
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92 print("| Dataset Job Standard Output:")
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93 print(_format_for_summary(provenance_info.get("stdout", ""), "Standard output was empty."))
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94 print("| Dataset Job Standard Error:")
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95 print(_format_for_summary(provenance_info.get("stderr", ""), "Standard error was empty."))
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96 except Exception:
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97 print("| *PLANEMO ERROR FETCHING JOB DETAILS*")
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98 print("|")
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99
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100
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101 def _format_for_summary(blob, empty_message, prefix="| "):
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102 contents = "\n".join(["%s%s" % (prefix, line.strip()) for line in StringIO(blob).readlines() if line.rstrip("\n\r")])
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103 return contents or "%s*%s*" % (prefix, empty_message)
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104
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105
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106 def _dataset_provenance(gi, history_id, id):
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107 provenance = gi.histories.show_dataset_provenance(history_id, id)
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108 return provenance
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109
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110
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111 __all__ = (
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112 "DEFAULT_MASTER_API_KEY",
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113 "gi",
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114 "user_api_key",
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115 )