Mercurial > repos > shellac > sam_consensus_v3

annotate env/lib/python3.9/site-packages/planemo/shed/interface.py @ 0:4f3585e2f14b draft default tip

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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
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0
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1 """Interface over bioblend and direct access to ToolShed API via requests."""
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2
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3 import json
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4
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5 from galaxy.util import unicodify
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6
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7 from planemo.bioblend import (
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8 ensure_module,
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9 toolshed,
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10 )
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11 from planemo.io import untar_to
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12
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13 REPOSITORY_DOWNLOAD_TEMPLATE = (
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14 "%srepository/download?repository_id=%s"
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15 "&changeset_revision=default&file_type=gz"
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16 )
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17
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18
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19 def tool_shed_instance(url, key, email, password):
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20 ensure_module()
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21 tsi = toolshed.ToolShedInstance(
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22 url=url,
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23 key=key,
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24 email=email,
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25 password=password
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26 )
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27 return tsi
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28
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29
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30 def find_repository(tsi, owner, name):
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31 """ Find repository information for given owner and repository
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32 name.
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33 """
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34 repos = tsi.repositories.get_repositories()
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35
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36 def matches(r):
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37 return r["owner"] == owner and r["name"] == name
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38
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39 matching_repos = list(filter(matches, repos))
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40 if not matching_repos:
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41 return None
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42 else:
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43 return matching_repos[0]
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44
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45
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46 def latest_installable_revision(tsi, repository_id):
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47 info = tsi.repositories.show_repository(repository_id)
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48 owner = info["owner"]
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49 name = info["name"]
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50 revisions = tsi.repositories.get_ordered_installable_revisions(
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51 name, owner
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52 )
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53 if len(revisions) == 0:
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54 msg = "Failed to find installable revisions for [{0}, {1}].".format(
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55 owner,
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56 name,
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57 )
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58 raise Exception(msg)
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59 else:
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60 return revisions[-1]
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61
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62
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63 def username(tsi):
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64 """ Fetch current username from shed given API key/auth.
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65 """
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66 user = _user(tsi)
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67 return user["username"]
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68
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69
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70 def api_exception_to_message(e):
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71 """ Convert API exception to human digestable error message - parsing
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72 out the shed generate message if possible.
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73 """
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74 message = unicodify(e)
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75 if hasattr(e, "read"):
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76 message = e.read()
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77 try:
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78 # Galaxy passes nice JSON messages as their errors, which bioblend
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79 # blindly returns. Attempt to parse those.
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80 upstream_error = json.loads(message)
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81 message = upstream_error['err_msg']
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82 except Exception:
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83 pass
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84 return message
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85
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86
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87 def find_category_ids(tsi, categories):
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88 """ Translate human readable category names into their associated IDs.
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89 """
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90 category_list = tsi.categories.get_categories()
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91
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92 category_ids = []
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93 for cat in categories:
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94 matching_cats = [x for x in category_list if x['name'] == cat]
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95 if not matching_cats:
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96 message = "Failed to find category %s" % cat
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97 raise Exception(message)
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98 category_ids.append(matching_cats[0]['id'])
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99 return category_ids
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100
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101
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102 def download_tar(tsi, repo_id, destination, to_directory):
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103 base_url = tsi.base_url
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104 if not base_url.endswith("/"):
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105 base_url += "/"
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106 download_url = REPOSITORY_DOWNLOAD_TEMPLATE % (base_url, repo_id)
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107 if to_directory:
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108 tar_args = ['-xzf', '-', '--strip-components=1']
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109 untar_to(download_url, tar_args=tar_args, dest_dir=destination)
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110 else:
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111 untar_to(download_url, path=destination)
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112
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113
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114 def _user(tsi):
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115 """ Fetch user information from the ToolShed API for given
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116 key.
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117 """
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118 # TODO: this should be done with an actual bioblend method,
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119 # see https://github.com/galaxyproject/bioblend/issues/130.
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120 response = tsi.make_get_request(tsi.url + "/users")
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121 return response.json()[0]