Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/bioblend/galaxy/histories/__init__.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 """ |
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2 Contains possible interactions with the Galaxy Histories |
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3 """ |
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4 import logging |
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5 import re |
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6 import sys |
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7 import time |
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8 import webbrowser |
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9 from urllib.parse import urljoin |
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10 |
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11 import bioblend |
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12 from bioblend import ConnectionError |
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13 from bioblend.galaxy.client import Client |
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14 from bioblend.util import attach_file |
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15 |
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16 log = logging.getLogger(__name__) |
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17 |
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18 |
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19 class HistoryClient(Client): |
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20 |
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21 def __init__(self, galaxy_instance): |
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22 self.module = 'histories' |
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23 super().__init__(galaxy_instance) |
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24 |
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25 def create_history(self, name=None): |
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26 """ |
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27 Create a new history, optionally setting the ``name``. |
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28 |
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29 :type name: str |
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30 :param name: Optional name for new history |
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31 |
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32 :rtype: dict |
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33 :return: Dictionary containing information about newly created history |
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34 """ |
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35 payload = {} |
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36 if name is not None: |
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37 payload['name'] = name |
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38 return self._post(payload) |
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39 |
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40 def import_history(self, file_path=None, url=None): |
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41 """ |
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42 Import a history from an archive on disk or a URL. |
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43 |
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44 :type file_path: str |
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45 :param file_path: Path to exported history archive on disk. |
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46 :type url: str |
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47 :param url: URL for an exported history archive |
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48 """ |
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49 if file_path: |
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50 archive_file = attach_file(file_path) |
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51 payload = dict(archive_source='', archive_file=archive_file, archive_type="file") |
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52 else: |
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53 payload = dict(archive_source=url, archive_type='url') |
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54 |
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55 return self._post(payload=payload, files_attached=file_path is not None) |
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56 |
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57 def _get_histories(self, history_id=None, name=None, deleted=False, filter_user_published=None, get_all_published=False, slug=None): |
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58 """ |
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59 Hidden method to be used by both get_histories() and get_published_histories() |
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60 """ |
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61 if history_id is not None and name is not None: |
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62 raise ValueError('Provide only one argument between name or history_id, but not both') |
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63 assert not (filter_user_published is not None and get_all_published) |
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64 |
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65 params = {} |
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66 if deleted: |
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67 params.setdefault('q', []).append('deleted') |
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68 params.setdefault('qv', []).append(deleted) |
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69 if filter_user_published is not None: |
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70 params.setdefault('q', []).append('published') |
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71 params.setdefault('qv', []).append(filter_user_published) |
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72 if slug is not None: |
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73 params.setdefault('q', []).append('slug') |
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74 params.setdefault('qv', []).append(slug) |
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75 |
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76 url = '/'.join((self._make_url(), 'published')) if get_all_published else None |
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77 histories = self._get(url=url, params=params) |
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78 |
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79 if history_id is not None: |
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80 history = next((_ for _ in histories if _['id'] == history_id), None) |
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81 histories = [history] if history is not None else [] |
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82 elif name is not None: |
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83 histories = [_ for _ in histories if _['name'] == name] |
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84 return histories |
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85 |
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86 def get_histories(self, history_id=None, name=None, deleted=False, published=None, slug=None): |
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87 """ |
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88 Get all histories or filter the specific one(s) by ``name`` or other |
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89 arguments. |
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90 |
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91 :type history_id: str |
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92 :param history_id: Encoded history ID to filter on |
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93 |
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94 .. deprecated:: 0.15.0 |
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95 To get details of a history for which you know the ID, use the much |
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96 more efficient :meth:`show_history` instead. |
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97 |
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98 :type name: str |
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99 :param name: Name of history to filter on |
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100 |
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101 :type deleted: bool |
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102 :param deleted: whether to filter for the deleted histories (``True``) |
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103 or for the non-deleted ones (``False``) |
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104 |
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105 :type published: bool or None |
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106 :param published: whether to filter for the published histories |
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107 (``True``) or for the non-published ones (``False``). If not set, no |
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108 filtering is applied. Note the filtering is only applied to the user's |
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109 own histories; to access all histories published by any user, use the |
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110 ``get_published_histories`` method. |
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111 |
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112 :type slug: str |
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113 :param slug: History slug to filter on |
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114 |
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115 :rtype: list |
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116 :return: List of history dicts. |
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117 """ |
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118 return self._get_histories(history_id=history_id, name=name, deleted=deleted, filter_user_published=published, get_all_published=False, slug=slug) |
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119 |
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120 def get_published_histories(self, name=None, deleted=False, slug=None): |
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121 """ |
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122 Get all published histories (by any user) or filter the specific one(s) |
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123 by ``name`` or other arguments. |
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124 |
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125 :type name: str |
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126 :param name: Name of history to filter on |
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127 |
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128 :type deleted: bool |
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129 :param deleted: whether to filter for the deleted histories (``True``) |
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130 or for the non-deleted ones (``False``) |
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131 |
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132 :type slug: str |
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133 :param slug: History slug to filter on |
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134 |
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135 :rtype: list |
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136 :return: List of history dicts. |
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137 """ |
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138 return self._get_histories(name=name, deleted=deleted, filter_user_published=None, get_all_published=True, slug=slug) |
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139 |
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140 def show_history(self, history_id, contents=False, deleted=None, visible=None, details=None, types=None): |
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141 """ |
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142 Get details of a given history. By default, just get the history meta |
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143 information. |
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144 |
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145 :type history_id: str |
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146 :param history_id: Encoded history ID to filter on |
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147 |
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148 :type contents: bool |
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149 :param contents: When ``True``, instead of the history details, return |
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150 a list with info for all datasets in the given history. |
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151 Note that inside each dataset info dict, the id which should be used |
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152 for further requests about this history dataset is given by the value |
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153 of the `id` (not `dataset_id`) key. |
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154 |
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155 :type deleted: bool or None |
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156 :param deleted: When ``contents=True``, whether to filter for the |
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157 deleted datasets (``True``) or for the non-deleted ones (``False``). |
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158 If not set, no filtering is applied. |
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159 |
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160 :type visible: bool or None |
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161 :param visible: When ``contents=True``, whether to filter for the |
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162 visible datasets (``True``) or for the hidden ones (``False``). If not |
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163 set, no filtering is applied. |
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164 |
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165 :type details: str |
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166 :param details: When ``contents=True``, include dataset details. Set to |
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167 'all' for the most information. |
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168 |
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169 :type types: list |
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170 :param types: When ``contents=True``, filter for history content types. |
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171 If set to ``['dataset']``, return only datasets. If set to |
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172 ``['dataset_collection']``, return only dataset collections. If not |
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173 set, no filtering is applied. |
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174 |
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175 :rtype: dict or list of dicts |
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176 :return: details of the given history or list of dataset info |
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177 """ |
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178 params = {} |
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179 if contents: |
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180 if details: |
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181 params['details'] = details |
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182 if deleted is not None: |
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183 params['deleted'] = deleted |
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184 if visible is not None: |
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185 params['visible'] = visible |
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186 if types is not None: |
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187 params['types'] = types |
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188 return self._get(id=history_id, contents=contents, params=params) |
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189 |
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190 def delete_dataset(self, history_id, dataset_id, purge=False): |
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191 """ |
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192 Mark corresponding dataset as deleted. |
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193 |
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194 :type history_id: str |
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195 :param history_id: Encoded history ID |
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196 |
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197 :type dataset_id: str |
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198 :param dataset_id: Encoded dataset ID |
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199 |
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200 :type purge: bool |
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201 :param purge: if ``True``, also purge (permanently delete) the dataset |
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202 |
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203 :rtype: None |
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204 :return: None |
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205 |
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206 .. note:: |
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207 For the purge option to work, the Galaxy instance must have the |
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208 ``allow_user_dataset_purge`` option set to ``true`` in the |
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209 ``config/galaxy.yml`` configuration file. |
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210 """ |
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211 url = '/'.join((self._make_url(history_id, contents=True), dataset_id)) |
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212 payload = {} |
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213 if purge is True: |
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214 payload['purge'] = purge |
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215 self._delete(payload=payload, url=url) |
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216 |
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217 def delete_dataset_collection(self, history_id, dataset_collection_id): |
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218 """ |
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219 Mark corresponding dataset collection as deleted. |
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220 |
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221 :type history_id: str |
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222 :param history_id: Encoded history ID |
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223 |
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224 :type dataset_collection_id: str |
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225 :param dataset_collection_id: Encoded dataset collection ID |
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226 |
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227 :rtype: None |
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228 :return: None |
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229 """ |
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230 url = '/'.join((self._make_url(history_id, contents=True), 'dataset_collections', dataset_collection_id)) |
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231 self._delete(url=url) |
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232 |
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233 def show_dataset(self, history_id, dataset_id): |
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234 """ |
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235 Get details about a given history dataset. |
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236 |
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237 :type history_id: str |
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238 :param history_id: Encoded history ID |
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239 |
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240 :type dataset_id: str |
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241 :param dataset_id: Encoded dataset ID |
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242 |
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243 :rtype: dict |
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244 :return: Information about the dataset |
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245 """ |
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246 url = '/'.join((self._make_url(history_id, contents=True), dataset_id)) |
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247 return self._get(url=url) |
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248 |
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249 def show_dataset_collection(self, history_id, dataset_collection_id): |
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250 """ |
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251 Get details about a given history dataset collection. |
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252 |
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253 :type history_id: str |
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254 :param history_id: Encoded history ID |
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255 |
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256 :type dataset_collection_id: str |
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257 :param dataset_collection_id: Encoded dataset collection ID |
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258 |
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259 :rtype: dict |
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260 :return: Information about the dataset collection |
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261 """ |
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262 url = '/'.join((self._make_url(history_id, contents=True), 'dataset_collections', dataset_collection_id)) |
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263 return self._get(url=url) |
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264 |
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265 def show_matching_datasets(self, history_id, name_filter=None): |
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266 """ |
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267 Get dataset details for matching datasets within a history. |
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268 |
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269 :type history_id: str |
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270 :param history_id: Encoded history ID |
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271 |
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272 :type name_filter: str |
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273 :param name_filter: Only datasets whose name matches the |
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274 ``name_filter`` regular expression will be |
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275 returned; use plain strings for exact matches and |
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276 None to match all datasets in the history |
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277 |
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278 :rtype: list |
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279 :return: List of dictionaries |
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280 """ |
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281 if isinstance(name_filter, str): |
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282 name_filter = re.compile(name_filter + '$') |
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283 return [self.show_dataset(history_id, h['id']) |
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284 for h in self.show_history(history_id, contents=True) |
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285 if name_filter is None or name_filter.match(h['name'])] |
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286 |
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287 def show_dataset_provenance(self, history_id, dataset_id, follow=False): |
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288 """ |
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289 Get details related to how dataset was created (``id``, ``job_id``, |
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290 ``tool_id``, ``stdout``, ``stderr``, ``parameters``, ``inputs``, |
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291 etc...). |
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292 |
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293 :type history_id: str |
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294 :param history_id: Encoded history ID |
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295 |
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296 :type dataset_id: str |
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297 :param dataset_id: Encoded dataset ID |
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298 |
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299 :type follow: bool |
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300 :param follow: If ``True``, recursively fetch dataset provenance |
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301 information for all inputs and their inputs, etc. |
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302 |
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303 :rtype: dict |
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304 :return: Dataset provenance information |
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305 For example:: |
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306 |
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307 {'id': '6fbd9b2274c62ebe', |
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308 'job_id': '5471ba76f274f929', |
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309 'parameters': {'chromInfo': '"/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm9.len"', |
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310 'dbkey': '"mm9"', |
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311 'experiment_name': '"H3K4me3_TAC_MACS2"', |
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312 'input_chipseq_file1': {'id': '6f0a311a444290f2', |
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313 'uuid': 'null'}, |
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314 'input_control_file1': {'id': 'c21816a91f5dc24e', |
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315 'uuid': '16f8ee5e-228f-41e2-921e-a07866edce06'}, |
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316 'major_command': '{"gsize": "2716965481.0", "bdg": "False", "__current_case__": 0, "advanced_options": {"advanced_options_selector": "off", "__current_case__": 1}, "input_chipseq_file1": 104715, "xls_to_interval": "False", "major_command_selector": "callpeak", "input_control_file1": 104721, "pq_options": {"pq_options_selector": "qvalue", "qvalue": "0.05", "__current_case__": 1}, "bw": "300", "nomodel_type": {"nomodel_type_selector": "create_model", "__current_case__": 1}}'}, |
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317 'stderr': '', |
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318 'stdout': '', |
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319 'tool_id': 'toolshed.g2.bx.psu.edu/repos/ziru-zhou/macs2/modencode_peakcalling_macs2/2.0.10.2', |
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320 'uuid': '5c0c43f5-8d93-44bd-939d-305e82f213c6'} |
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321 """ |
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322 url = '/'.join((self._make_url(history_id, contents=True), dataset_id, 'provenance')) |
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323 return self._get(url=url) |
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324 |
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325 def update_history(self, history_id, **kwds): |
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326 """ |
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327 Update history metadata information. Some of the attributes that can be |
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328 modified are documented below. |
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329 |
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330 :type history_id: str |
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331 :param history_id: Encoded history ID |
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332 |
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333 :type name: str |
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334 :param name: Replace history name with the given string |
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335 |
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336 :type annotation: str |
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337 :param annotation: Replace history annotation with given string |
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338 |
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339 :type deleted: bool |
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340 :param deleted: Mark or unmark history as deleted |
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341 |
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342 :type purged: bool |
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343 :param purged: If ``True``, mark history as purged (permanently deleted). |
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344 |
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345 :type published: bool |
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346 :param published: Mark or unmark history as published |
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347 |
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348 :type importable: bool |
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349 :param importable: Mark or unmark history as importable |
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350 |
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351 :type tags: list |
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352 :param tags: Replace history tags with the given list |
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353 |
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354 :rtype: dict |
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355 :return: details of the updated history |
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356 |
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357 .. versionchanged:: 0.8.0 |
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358 Changed the return value from the status code (type int) to a dict. |
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359 """ |
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360 return self._put(payload=kwds, id=history_id) |
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361 |
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362 def update_dataset(self, history_id, dataset_id, **kwds): |
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363 """ |
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364 Update history dataset metadata. Some of the attributes that can be |
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365 modified are documented below. |
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366 |
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367 :type history_id: str |
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368 :param history_id: Encoded history ID |
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369 |
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370 :type dataset_id: str |
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371 :param dataset_id: ID of the dataset |
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372 |
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373 :type name: str |
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374 :param name: Replace history dataset name with the given string |
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375 |
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376 :type datatype: str |
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377 :param datatype: Replace the datatype of the history dataset with the |
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378 given string. The string must be a valid Galaxy datatype, both the |
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379 current and the target datatypes must allow datatype changes, and the |
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380 dataset must not be in use as input or output of a running job |
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381 (including uploads), otherwise an error will be raised. |
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382 |
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383 :type genome_build: str |
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384 :param genome_build: Replace history dataset genome build (dbkey) |
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385 |
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386 :type annotation: str |
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387 :param annotation: Replace history dataset annotation with given string |
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388 |
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389 :type deleted: bool |
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390 :param deleted: Mark or unmark history dataset as deleted |
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391 |
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392 :type visible: bool |
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393 :param visible: Mark or unmark history dataset as visible |
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394 |
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395 :rtype: dict |
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396 :return: details of the updated dataset |
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397 |
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398 .. versionchanged:: 0.8.0 |
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399 Changed the return value from the status code (type int) to a dict. |
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400 """ |
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401 url = '/'.join((self._make_url(history_id, contents=True), dataset_id)) |
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402 return self._put(payload=kwds, url=url) |
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403 |
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404 def update_dataset_collection(self, history_id, dataset_collection_id, **kwds): |
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405 """ |
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406 Update history dataset collection metadata. Some of the attributes that |
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407 can be modified are documented below. |
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408 |
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409 :type history_id: str |
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410 :param history_id: Encoded history ID |
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411 |
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412 :type dataset_collection_id: str |
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413 :param dataset_collection_id: Encoded dataset_collection ID |
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414 |
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415 :type name: str |
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416 :param name: Replace history dataset collection name with the given |
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417 string |
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418 |
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419 :type deleted: bool |
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420 :param deleted: Mark or unmark history dataset collection as deleted |
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421 |
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422 :type visible: bool |
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423 :param visible: Mark or unmark history dataset collection as visible |
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424 |
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425 :rtype: dict |
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426 :return: the updated dataset collection attributes |
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427 |
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428 .. versionchanged:: 0.8.0 |
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429 Changed the return value from the status code (type int) to a dict. |
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430 """ |
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431 url = '/'.join((self._make_url(history_id, contents=True), 'dataset_collections', dataset_collection_id)) |
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432 return self._put(payload=kwds, url=url) |
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433 |
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434 def create_history_tag(self, history_id, tag): |
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435 """ |
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436 Create history tag |
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437 |
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438 :type history_id: str |
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439 :param history_id: Encoded history ID |
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440 |
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441 :type tag: str |
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442 :param tag: Add tag to history |
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443 |
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444 :rtype: dict |
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445 :return: A dictionary with information regarding the tag. |
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446 For example:: |
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447 |
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448 {'id': 'f792763bee8d277a', |
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449 'model_class': 'HistoryTagAssociation', |
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450 'user_tname': 'NGS_PE_RUN', |
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451 'user_value': None} |
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452 """ |
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453 # empty payload since we are adding the new tag using the url |
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454 payload = {} |
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455 url = '/'.join((self._make_url(history_id), 'tags', tag)) |
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456 return self._post(payload, url=url) |
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457 |
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458 def upload_dataset_from_library(self, history_id, lib_dataset_id): |
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459 """ |
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460 Upload a dataset into the history from a library. Requires the |
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461 library dataset ID, which can be obtained from the library |
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462 contents. |
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463 |
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464 :type history_id: str |
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465 :param history_id: Encoded history ID |
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466 |
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467 :type lib_dataset_id: str |
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468 :param lib_dataset_id: Encoded library dataset ID |
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469 |
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470 :rtype: dict |
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471 :return: Information about the newly created HDA |
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472 """ |
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473 payload = { |
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474 'content': lib_dataset_id, |
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475 'source': 'library', |
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476 'from_ld_id': lib_dataset_id, # compatibility with old API |
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477 } |
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478 return self._post(payload, id=history_id, contents=True) |
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479 |
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480 def create_dataset_collection(self, history_id, collection_description): |
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481 """ |
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482 Create a new dataset collection |
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483 |
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484 :type history_id: str |
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485 :param history_id: Encoded history ID |
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486 |
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487 :type collection_description: bioblend.galaxy.dataset_collections.CollectionDescription |
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488 :param collection_description: a description of the dataset collection |
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489 For example:: |
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490 |
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491 {'collection_type': 'list', |
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492 'element_identifiers': [{'id': 'f792763bee8d277a', |
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493 'name': 'element 1', |
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494 'src': 'hda'}, |
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495 {'id': 'f792763bee8d277a', |
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496 'name': 'element 2', |
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497 'src': 'hda'}], |
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498 'name': 'My collection list'} |
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499 |
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500 :rtype: dict |
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501 :return: Information about the new HDCA |
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502 """ |
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503 try: |
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504 collection_description = collection_description.to_dict() |
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505 except AttributeError: |
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506 pass |
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507 payload = dict( |
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508 name=collection_description["name"], |
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509 type="dataset_collection", |
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510 collection_type=collection_description["collection_type"], |
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511 element_identifiers=collection_description["element_identifiers"], |
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512 ) |
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513 return self._post(payload, id=history_id, contents=True) |
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514 |
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515 def delete_history(self, history_id, purge=False): |
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516 """ |
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517 Delete a history. |
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518 |
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519 :type history_id: str |
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520 :param history_id: Encoded history ID |
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521 |
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522 :type purge: bool |
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523 :param purge: if ``True``, also purge (permanently delete) the history |
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524 |
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525 :rtype: dict |
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526 :return: An error object if an error occurred or a dictionary |
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527 containing: ``id`` (the encoded id of the history), ``deleted`` (if the |
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528 history was marked as deleted), ``purged`` (if the history was |
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529 purged). |
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530 |
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531 .. note:: |
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532 For the purge option to work, the Galaxy instance must have the |
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533 ``allow_user_dataset_purge`` option set to ``true`` in the |
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534 ``config/galaxy.yml`` configuration file. |
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535 """ |
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536 payload = {} |
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537 if purge is True: |
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538 payload['purge'] = purge |
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539 return self._delete(payload=payload, id=history_id) |
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540 |
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541 def undelete_history(self, history_id): |
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542 """ |
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543 Undelete a history |
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544 |
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545 :type history_id: str |
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546 :param history_id: Encoded history ID |
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547 |
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548 :rtype: str |
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549 :return: 'OK' if it was deleted |
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550 """ |
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551 url = self._make_url(history_id, deleted=True) + '/undelete' |
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552 return self._post(payload={}, url=url) |
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553 |
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554 def get_status(self, history_id): |
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555 """ |
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556 Returns the state of this history |
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557 |
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558 :type history_id: str |
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559 :param history_id: Encoded history ID |
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560 |
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561 :rtype: dict |
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562 :return: A dict documenting the current state of the history. Has the following keys: |
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563 'state' = This is the current state of the history, such as ok, error, new etc. |
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564 'state_details' = Contains individual statistics for various dataset states. |
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565 'percent_complete' = The overall number of datasets processed to completion. |
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566 """ |
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567 state = {} |
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568 history = self.show_history(history_id) |
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569 state['state'] = history['state'] |
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570 if history.get('state_details') is not None: |
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571 state['state_details'] = history['state_details'] |
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572 total_complete = sum(history['state_details'].values()) |
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573 if total_complete > 0: |
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574 state['percent_complete'] = 100 * history['state_details']['ok'] / total_complete |
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575 else: |
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576 state['percent_complete'] = 0 |
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577 return state |
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578 |
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579 def get_most_recently_used_history(self): |
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580 """ |
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581 Returns the current user's most recently used history (not deleted). |
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582 |
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583 :rtype: dict |
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584 :return: History representation |
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585 """ |
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586 url = self._make_url() + '/most_recently_used' |
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587 return self._get(url=url) |
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588 |
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589 def export_history(self, history_id, gzip=True, include_hidden=False, |
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590 include_deleted=False, wait=False, maxwait=None): |
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591 """ |
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592 Start a job to create an export archive for the given history. |
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593 |
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594 :type history_id: str |
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595 :param history_id: history ID |
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596 |
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597 :type gzip: bool |
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598 :param gzip: create .tar.gz archive if ``True``, else .tar |
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599 |
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600 :type include_hidden: bool |
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601 :param include_hidden: whether to include hidden datasets |
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602 in the export |
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603 |
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604 :type include_deleted: bool |
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605 :param include_deleted: whether to include deleted datasets |
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606 in the export |
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607 |
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608 :type wait: bool |
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609 :param wait: if ``True``, block until the export is ready; else, return |
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610 immediately |
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611 |
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612 :type maxwait: float |
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613 :param maxwait: Total time (in seconds) to wait for the export to become |
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614 ready. When set, implies that ``wait`` is ``True``. |
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615 |
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616 :rtype: str |
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617 :return: ``jeha_id`` of the export, or empty if ``wait`` is ``False`` |
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618 and the export is not ready. |
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619 """ |
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620 if maxwait is not None: |
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621 assert maxwait >= 0 |
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622 else: |
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623 if wait: |
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624 maxwait = sys.maxsize |
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625 else: |
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626 maxwait = 0 |
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627 params = { |
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628 'gzip': gzip, |
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629 'include_hidden': include_hidden, |
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630 'include_deleted': include_deleted, |
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631 } |
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632 url = '%s/exports' % self._make_url(history_id) |
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633 time_left = maxwait |
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634 while True: |
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635 try: |
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636 r = self._put(payload={}, url=url, params=params) |
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637 except ConnectionError as e: |
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638 if e.status_code == 202: # export is not ready |
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639 if time_left > 0: |
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640 log.warning("Waiting for the export of history %s to complete. Will wait %i more s", history_id, time_left) |
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641 time.sleep(1) |
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642 time_left -= 1 |
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643 else: |
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644 return '' |
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645 else: |
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646 raise |
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647 else: |
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648 break |
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649 jeha_id = r['download_url'].rsplit('/', 1)[-1] |
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650 return jeha_id |
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651 |
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652 def download_history(self, history_id, jeha_id, outf, |
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653 chunk_size=bioblend.CHUNK_SIZE): |
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654 """ |
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655 Download a history export archive. Use :meth:`export_history` |
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656 to create an export. |
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|
657 |
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658 :type history_id: str |
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659 :param history_id: history ID |
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660 |
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661 :type jeha_id: str |
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662 :param jeha_id: jeha ID (this should be obtained via |
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663 :meth:`export_history`) |
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664 |
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665 :type outf: file |
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666 :param outf: output file object, open for writing in binary mode |
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667 |
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668 :type chunk_size: int |
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669 :param chunk_size: how many bytes at a time should be read into memory |
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670 |
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671 :rtype: None |
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672 :return: None |
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673 """ |
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674 url = '{}/exports/{}'.format( |
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675 self._make_url(module_id=history_id), jeha_id) |
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676 r = self.gi.make_get_request(url, stream=True) |
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677 r.raise_for_status() |
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678 for chunk in r.iter_content(chunk_size): |
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679 outf.write(chunk) |
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680 |
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681 def copy_dataset(self, history_id, dataset_id, source='hda'): |
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682 """ |
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683 Copy a dataset to a history. |
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684 |
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685 :type history_id: str |
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686 :param history_id: history ID to which the dataset should be copied |
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687 |
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688 :type dataset_id: str |
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689 :param dataset_id: dataset ID |
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690 |
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691 :type source: str |
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692 :param source: Source of the dataset to be copied: 'hda' (the default), 'library' or 'library_folder' |
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693 |
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694 :rtype: dict |
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695 :return: Information about the copied dataset |
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696 """ |
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697 return self.copy_content(history_id, dataset_id, source) |
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698 |
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699 def copy_content(self, history_id, content_id, source='hda'): |
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700 """ |
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701 Copy existing content (e.g. a dataset) to a history. |
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702 |
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703 :type history_id: str |
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704 :param history_id: ID of the history to which the content should be copied |
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705 |
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706 :type content_id: str |
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707 :param content_id: ID of the content to copy |
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708 |
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709 :type source: str |
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710 :param source: Source of the content to be copied: 'hda' (for a history |
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711 dataset, the default), 'hdca' (for a dataset collection), 'library' |
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712 (for a library dataset) or 'library_folder' (for all datasets in a |
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713 library folder). |
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714 |
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715 :rtype: dict |
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716 :return: Information about the copied content |
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717 """ |
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718 |
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719 payload = { |
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720 'content': content_id, |
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721 'source': source, |
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722 'type': 'dataset' if source != 'hdca' else 'dataset_collection', |
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723 } |
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724 |
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725 url = self._make_url(history_id, contents=True) |
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726 return self._post(payload=payload, url=url) |
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727 |
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728 def open_history(self, history_id): |
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729 """ |
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730 Open Galaxy in a new tab of the default web browser and switch to the |
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731 specified history. |
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732 |
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733 :type history_id: str |
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734 :param history_id: ID of the history to switch to |
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735 |
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736 :rtype: NoneType |
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737 :return: ``None`` |
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738 |
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739 .. warning:: |
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740 After opening the specified history, all previously opened Galaxy tabs |
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741 in the browser session will have the current history changed to this |
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742 one, even if the interface still shows another history. Refreshing |
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743 any such tab is recommended. |
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744 """ |
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745 |
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746 url = urljoin(self.gi.base_url, f"history/switch_to_history?hist_id={history_id}") |
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747 webbrowser.open_new_tab(url) |