Mercurial > repos > bcclaywell > argo_navis

annotate venv/lib/python2.7/site-packages/planemo/shed/interface.py @ 0:d67268158946 draft

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planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
author bcclaywell
date Mon, 12 Oct 2015 17:43:33 -0400
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1 """ Interface over bioblend and direct access to ToolShed
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2 API via requests.
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3 """
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4 import json
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5 from planemo.io import untar_to
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6 from planemo.bioblend import (
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7 toolshed,
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8 ensure_module,
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9 )
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10
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11 REPOSITORY_DOWNLOAD_TEMPLATE = (
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12 "%srepository/download?repository_id=%s"
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13 "&changeset_revision=default&file_type=gz"
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14 )
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15
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16
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17 def tool_shed_instance(url, key, email, password):
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18 ensure_module(toolshed)
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19 tsi = toolshed.ToolShedInstance(
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20 url=url,
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21 key=key,
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22 email=email,
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23 password=password
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24 )
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25 return tsi
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26
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27
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28 def find_repository(tsi, owner, name):
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29 """ Find repository information for given owner and repository
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30 name.
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31 """
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32 repos = tsi.repositories.get_repositories()
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33
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34 def matches(r):
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35 return r["owner"] == owner and r["name"] == name
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36
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37 matching_repos = list(filter(matches, repos))
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38 if not matching_repos:
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39 return None
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40 else:
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41 return matching_repos[0]
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42
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43
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44 def latest_installable_revision(tsi, repository_id):
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45 info = tsi.repositories.show_repository(repository_id)
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46 owner = info["owner"]
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47 name = info["name"]
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48 revisions = tsi.repositories.get_ordered_installable_revisions(
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49 name, owner
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50 )
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51 if len(revisions) == 0:
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52 msg = "Failed to find installable revisions for [{0}, {1}].".format(
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53 owner,
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54 name,
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55 )
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56 raise Exception(msg)
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57 else:
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58 return revisions[-1]
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59
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60
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61 def username(tsi):
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62 """ Fetch current username from shed given API key/auth.
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63 """
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64 user = _user(tsi)
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65 return user["username"]
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66
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67
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68 def api_exception_to_message(e):
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69 """ Convert API exception to human digestable error message - parsing
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70 out the shed generate message if possible.
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71 """
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72 message = str(e)
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73 if hasattr(e, "read"):
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74 message = e.read()
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75 try:
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76 # Galaxy passes nice JSON messages as their errors, which bioblend
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77 # blindly returns. Attempt to parse those.
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78 upstream_error = json.loads(message)
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79 message = upstream_error['err_msg']
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80 except Exception:
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81 pass
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82 return message
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83
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84
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85 def find_category_ids(tsi, categories):
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86 """ Translate human readable category names into their associated IDs.
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87 """
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88 category_list = tsi.repositories.get_categories()
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89
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90 category_ids = []
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91 for cat in categories:
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92 matching_cats = [x for x in category_list if x['name'] == cat]
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93 if not matching_cats:
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94 message = "Failed to find category %s" % cat
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95 raise Exception(message)
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96 category_ids.append(matching_cats[0]['id'])
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97 return category_ids
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98
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99
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100 def download_tar(tsi, repo_id, destination, to_directory):
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101 base_url = tsi.base_url
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102 if not base_url.endswith("/"):
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103 base_url += "/"
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104 download_url = REPOSITORY_DOWNLOAD_TEMPLATE % (base_url, repo_id)
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105 if to_directory:
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106 untar_args = "-xzf - -C %s --strip-components 1" % destination
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107 else:
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108 untar_args = None
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109 untar_to(download_url, destination, untar_args)
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110
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111
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112 def _user(tsi):
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113 """ Fetch user information from the ToolShed API for given
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114 key.
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115 """
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116 # TODO: this should be done with an actual bioblend method,
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117 # see https://github.com/galaxyproject/bioblend/issues/130.
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118 response = tsi.make_get_request(tsi.url + "/users")
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119 return response.json()[0]