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annotate planemo/lib/python3.7/site-packages/bioblend/galaxy/objects/client.py @ 1:56ad4e20f292 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:32:28 -0400
parents d30785e31577
children
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1 """
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2 Clients for interacting with specific Galaxy entity types.
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3
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4 Classes in this module should not be instantiated directly, but used
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5 via their handles in :class:`~.galaxy_instance.GalaxyInstance`.
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6 """
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7 import abc
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8 import json
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9 from collections.abc import (
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10 Mapping,
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11 Sequence,
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12 )
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13
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14 import bioblend
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15 from . import wrappers
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16
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17
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18 class ObjClient(object, metaclass=abc.ABCMeta):
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19
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20 @abc.abstractmethod
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21 def __init__(self, obj_gi):
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22 self.obj_gi = obj_gi
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23 self.gi = self.obj_gi.gi
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24 self.log = bioblend.log
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25
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26 @abc.abstractmethod
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27 def get_previews(self, **kwargs):
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28 """
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29 Get a list of object previews.
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30
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31 Previews entity summaries provided by REST collection URIs, e.g.
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32 ``http://host:port/api/libraries``. Being the most lightweight objects
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33 associated to the various entities, these are the ones that should be
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34 used to retrieve their basic info.
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35
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36 :rtype: list
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37 :return: a list of object previews
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38 """
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39 pass
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40
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41 @abc.abstractmethod
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42 def list(self, **kwargs):
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43 """
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44 Get a list of objects.
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45
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46 This method first gets the entity summaries, then gets the complete
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47 description for each entity with an additional GET call, so may be slow.
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48
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49 :rtype: list
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50 :return: a list of objects
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51 """
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52 pass
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53
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54 def _select_ids(self, id_=None, name=None):
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55 """
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56 Return the id list that corresponds to the given id or name info.
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57 """
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58 if id_ is None and name is None:
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59 self._error('neither id nor name provided', err_type=TypeError)
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60 if id_ is not None and name is not None:
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61 self._error('both id and name provided', err_type=TypeError)
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62 if id_ is None:
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63 return [_.id for _ in self.get_previews(name=name)]
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64 else:
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65 return [id_]
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66
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67 def _error(self, msg, err_type=RuntimeError):
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68 self.log.error(msg)
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69 raise err_type(msg)
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70
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71 def _get_dict(self, meth_name, reply):
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72 if reply is None:
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73 self._error('%s: no reply' % meth_name)
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74 elif isinstance(reply, Mapping):
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75 return reply
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76 try:
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77 return reply[0]
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78 except (TypeError, IndexError):
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79 self._error('%s: unexpected reply: %r' % (meth_name, reply))
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80
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81
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82 class ObjDatasetContainerClient(ObjClient):
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83
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84 def _get_container(self, id_, ctype):
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85 show_fname = 'show_%s' % ctype.__name__.lower()
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86 gi_client = getattr(self.gi, ctype.API_MODULE)
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87 show_f = getattr(gi_client, show_fname)
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88 res = show_f(id_)
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89 cdict = self._get_dict(show_fname, res)
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90 cdict['id'] = id_ # overwrite unencoded id
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91 c_infos = show_f(id_, contents=True)
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92 if not isinstance(c_infos, Sequence):
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93 self._error('%s: unexpected reply: %r' % (show_fname, c_infos))
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94 c_infos = [ctype.CONTENT_INFO_TYPE(_) for _ in c_infos]
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95 return ctype(cdict, content_infos=c_infos, gi=self.obj_gi)
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96
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97
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98 class ObjLibraryClient(ObjDatasetContainerClient):
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99 """
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100 Interacts with Galaxy libraries.
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101 """
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102
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103 def __init__(self, obj_gi):
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104 super().__init__(obj_gi)
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105
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106 def create(self, name, description=None, synopsis=None):
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107 """
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108 Create a data library with the properties defined in the arguments.
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109
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110 :rtype: :class:`~.wrappers.Library`
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111 :return: the library just created
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112 """
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113 res = self.gi.libraries.create_library(name, description, synopsis)
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114 lib_info = self._get_dict('create_library', res)
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115 return self.get(lib_info['id'])
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116
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117 def get(self, id_):
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118 """
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119 Retrieve the data library corresponding to the given id.
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120
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121 :rtype: :class:`~.wrappers.Library`
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122 :return: the library corresponding to ``id_``
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123 """
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124 return self._get_container(id_, wrappers.Library)
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125
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126 def get_previews(self, name=None, deleted=False):
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127 dicts = self.gi.libraries.get_libraries(name=name, deleted=deleted)
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128 return [wrappers.LibraryPreview(_, gi=self.obj_gi) for _ in dicts]
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129
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130 def list(self, name=None, deleted=False):
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131 """
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132 Get libraries owned by the user of this Galaxy instance.
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133
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134 :type name: str
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135 :param name: return only libraries with this name
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136 :type deleted: bool
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137 :param deleted: if ``True``, return libraries that have been deleted
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138
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139 :rtype: list of :class:`~.wrappers.Library`
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140 """
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141 dicts = self.gi.libraries.get_libraries(name=name, deleted=deleted)
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142 if not deleted:
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143 # return Library objects only for not-deleted libraries since Galaxy
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144 # does not filter them out and Galaxy release_14.08 and earlier
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145 # crashes when trying to get a deleted library
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146 return [self.get(_['id']) for _ in dicts if not _['deleted']]
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147 else:
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148 return [self.get(_['id']) for _ in dicts]
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149
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150 def delete(self, id_=None, name=None):
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151 """
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152 Delete the library with the given id or name.
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153
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154 Note that the same name can map to multiple libraries.
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155
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156 .. warning::
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157 Deleting a data library is irreversible - all of the data from
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158 the library will be permanently deleted.
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159 """
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160 for id_ in self._select_ids(id_=id_, name=name):
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161 res = self.gi.libraries.delete_library(id_)
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162 if not isinstance(res, Mapping):
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163 self._error('delete_library: unexpected reply: %r' % (res,))
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164
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165
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166 class ObjHistoryClient(ObjDatasetContainerClient):
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167 """
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168 Interacts with Galaxy histories.
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169 """
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170
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171 def __init__(self, obj_gi):
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172 super().__init__(obj_gi)
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173
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174 def create(self, name=None):
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175 """
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176 Create a new Galaxy history, optionally setting its name.
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177
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178 :rtype: :class:`~.wrappers.History`
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179 :return: the history just created
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180 """
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181 res = self.gi.histories.create_history(name=name)
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182 hist_info = self._get_dict('create_history', res)
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183 return self.get(hist_info['id'])
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184
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185 def get(self, id_):
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186 """
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187 Retrieve the history corresponding to the given id.
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188
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189 :rtype: :class:`~.wrappers.History`
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190 :return: the history corresponding to ``id_``
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191 """
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192 return self._get_container(id_, wrappers.History)
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193
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194 def get_previews(self, name=None, deleted=False):
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195 dicts = self.gi.histories.get_histories(name=name, deleted=deleted)
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196 return [wrappers.HistoryPreview(_, gi=self.obj_gi) for _ in dicts]
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197
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198 def list(self, name=None, deleted=False):
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199 """
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200 Get histories owned by the user of this Galaxy instance.
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201
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202 :type name: str
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203 :param name: return only histories with this name
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204 :type deleted: bool
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205 :param deleted: if ``True``, return histories that have been deleted
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206
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207 :rtype: list of :class:`~.wrappers.History`
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208 """
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209 dicts = self.gi.histories.get_histories(name=name, deleted=deleted)
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210 return [self.get(_['id']) for _ in dicts]
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211
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212 def delete(self, id_=None, name=None, purge=False):
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213 """
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214 Delete the history with the given id or name.
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215
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216 Note that the same name can map to multiple histories.
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217
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218 :type purge: bool
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219 :param purge: if ``True``, also purge (permanently delete) the history
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220
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221 .. note::
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222 For the purge option to work, the Galaxy instance must have the
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223 ``allow_user_dataset_purge`` option set to ``true`` in the
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224 ``config/galaxy.yml`` configuration file.
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225 """
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226 for id_ in self._select_ids(id_=id_, name=name):
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227 res = self.gi.histories.delete_history(id_, purge=purge)
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228 if not isinstance(res, Mapping):
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229 self._error('delete_history: unexpected reply: %r' % (res,))
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230
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231
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232 class ObjWorkflowClient(ObjClient):
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233 """
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234 Interacts with Galaxy workflows.
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235 """
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236
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237 def __init__(self, obj_gi):
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238 super().__init__(obj_gi)
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239
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240 def import_new(self, src, publish=False):
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241 """
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242 Imports a new workflow into Galaxy.
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243
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244 :type src: dict or str
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245 :param src: deserialized (dictionary) or serialized (str) JSON
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246 dump of the workflow (this is normally obtained by exporting
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247 a workflow from Galaxy).
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248
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249 :type publish: bool
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250 :param publish: if ``True`` the uploaded workflow will be published;
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251 otherwise it will be visible only by the user which uploads it (default).
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252
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253 :rtype: :class:`~.wrappers.Workflow`
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254 :return: the workflow just imported
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255 """
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256 if isinstance(src, Mapping):
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257 wf_dict = src
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258 else:
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259 try:
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260 wf_dict = json.loads(src)
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261 except (TypeError, ValueError):
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262 self._error('src not supported: %r' % (src,))
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263 wf_info = self.gi.workflows.import_workflow_dict(wf_dict, publish)
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264 return self.get(wf_info['id'])
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265
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266 def import_shared(self, id_):
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267 """
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268 Imports a shared workflow to the user's space.
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269
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270 :type id_: str
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271 :param id_: workflow id
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272
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273 :rtype: :class:`~.wrappers.Workflow`
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274 :return: the workflow just imported
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275 """
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276 wf_info = self.gi.workflows.import_shared_workflow(id_)
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277 return self.get(wf_info['id'])
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278
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279 def get(self, id_):
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280 """
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281 Retrieve the workflow corresponding to the given id.
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282
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283 :rtype: :class:`~.wrappers.Workflow`
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284 :return: the workflow corresponding to ``id_``
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285 """
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286 res = self.gi.workflows.show_workflow(id_)
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287 wf_dict = self._get_dict('show_workflow', res)
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288 return wrappers.Workflow(wf_dict, gi=self.obj_gi)
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289
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290 # the 'deleted' option is not available for workflows
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291 def get_previews(self, name=None, published=False):
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292 dicts = self.gi.workflows.get_workflows(name=name, published=published)
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293 return [wrappers.WorkflowPreview(_, gi=self.obj_gi) for _ in dicts]
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294
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295 # the 'deleted' option is not available for workflows
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296 def list(self, name=None, published=False):
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297 """
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298 Get workflows owned by the user of this Galaxy instance.
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299
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300 :type name: str
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301 :param name: return only workflows with this name
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302 :type published: bool
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303 :param published: if ``True``, return also published workflows
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304
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305 :rtype: list of :class:`~.wrappers.Workflow`
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306 """
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307 dicts = self.gi.workflows.get_workflows(name=name, published=published)
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308 return [self.get(_['id']) for _ in dicts]
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309
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310 def delete(self, id_=None, name=None):
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311 """
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312 Delete the workflow with the given id or name.
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313
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314 Note that the same name can map to multiple workflows.
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315
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316 .. warning::
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317 Deleting a workflow is irreversible - all of the data from
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318 the workflow will be permanently deleted.
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319 """
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320 for id_ in self._select_ids(id_=id_, name=name):
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321 res = self.gi.workflows.delete_workflow(id_)
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322 if not isinstance(res, str):
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323 self._error('delete_workflow: unexpected reply: %r' % res)
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324
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325
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326 class ObjToolClient(ObjClient):
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327 """
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328 Interacts with Galaxy tools.
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329 """
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330
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331 def __init__(self, obj_gi):
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332 super().__init__(obj_gi)
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333
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334 def get(self, id_, io_details=False, link_details=False):
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335 """
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336 Retrieve the tool corresponding to the given id.
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337
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338 :type io_details: bool
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339 :param io_details: if True, get also input and output details
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340
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341 :type link_details: bool
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342 :param link_details: if True, get also link details
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343
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344 :rtype: :class:`~.wrappers.Tool`
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345 :return: the tool corresponding to ``id_``
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346 """
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347 res = self.gi.tools.show_tool(id_, io_details=io_details,
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348 link_details=link_details)
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349 tool_dict = self._get_dict('show_tool', res)
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350 return wrappers.Tool(tool_dict, gi=self.obj_gi)
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351
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352 def get_previews(self, name=None, trackster=None):
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353 """
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354 Get the list of tools installed on the Galaxy instance.
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355
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356 :type name: str
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357 :param name: return only tools with this name
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358
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359 :type trackster: bool
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360 :param trackster: if True, only tools that are compatible with
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361 Trackster are returned
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362
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363 :rtype: list of :class:`~.wrappers.Tool`
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364 """
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365 dicts = self.gi.tools.get_tools(name=name, trackster=trackster)
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366 return [wrappers.Tool(_, gi=self.obj_gi) for _ in dicts]
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367
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368 # the 'deleted' option is not available for tools
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369 def list(self, name=None, trackster=None):
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370 """
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371 Get the list of tools installed on the Galaxy instance.
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372
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373 :type name: str
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374 :param name: return only tools with this name
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375
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376 :type trackster: bool
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377 :param trackster: if True, only tools that are compatible with
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378 Trackster are returned
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379
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380 :rtype: list of :class:`~.wrappers.Tool`
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381 """
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382 # dicts = self.gi.tools.get_tools(name=name, trackster=trackster)
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383 # return [self.get(_['id']) for _ in dicts]
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384 # As of 2015/04/15, GET /api/tools returns also data manager tools for
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385 # non-admin users, see
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386 # https://trello.com/c/jyl0cvFP/2633-api-tool-list-filtering-doesn-t-filter-data-managers-for-non-admins
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387 # Trying to get() a data manager tool would then return a 404 Not Found
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388 # error.
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389 # Moreover, the dicts returned by gi.tools.get_tools() are richer than
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390 # those returned by get(), so make this an alias for get_previews().
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391 return self.get_previews(name, trackster)
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392
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393
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394 class ObjJobClient(ObjClient):
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395 """
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396 Interacts with Galaxy jobs.
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397 """
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398
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399 def __init__(self, obj_gi):
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400 super().__init__(obj_gi)
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401
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402 def get(self, id_, full_details=False):
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403 """
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404 Retrieve the job corresponding to the given id.
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405
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406 :type full_details: bool
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407 :param full_details: if ``True``, return the complete list of details
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408 for the given job.
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409
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410 :rtype: :class:`~.wrappers.Job`
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411 :return: the job corresponding to ``id_``
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412 """
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413 res = self.gi.jobs.show_job(id_, full_details)
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414 job_dict = self._get_dict('job_tool', res)
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415 return wrappers.Job(job_dict, gi=self.obj_gi)
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416
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417 def get_previews(self):
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418 dicts = self.gi.jobs.get_jobs()
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419 return [wrappers.JobPreview(_, gi=self.obj_gi) for _ in dicts]
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420
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421 def list(self):
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422 """
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423 Get the list of jobs of the current user.
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424
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425 :rtype: list of :class:`~.wrappers.Job`
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426 """
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427 dicts = self.gi.jobs.get_jobs()
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428 return [self.get(_['id']) for _ in dicts]