Mercurial > repos > bcclaywell > argo_navis

annotate venv/lib/python2.7/site-packages/bioblend/galaxy/objects/client.py @ 0:d67268158946 draft

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planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
author bcclaywell
date Mon, 12 Oct 2015 17:43:33 -0400
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1 """
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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 collections
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9 import json
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10
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11 import six
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12
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13 import bioblend
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14 from . import wrappers
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15
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16
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17 @six.add_metaclass(abc.ABCMeta)
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18 class ObjClient(object):
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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, collections.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, collections.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 def __init__(self, obj_gi):
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103 super(ObjLibraryClient, self).__init__(obj_gi)
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104
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105 def create(self, name, description=None, synopsis=None):
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106 """
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107 Create a data library with the properties defined in the arguments.
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108
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109 :rtype: :class:`~.wrappers.Library`
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110 :return: the library just created
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111 """
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112 res = self.gi.libraries.create_library(name, description, synopsis)
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113 lib_info = self._get_dict('create_library', res)
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114 return self.get(lib_info['id'])
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115
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116 def get(self, id_):
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117 """
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118 Retrieve the data library corresponding to the given id.
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119
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120 :rtype: :class:`~.wrappers.Library`
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121 :return: the library corresponding to ``id_``
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122 """
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123 return self._get_container(id_, wrappers.Library)
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124
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125 def get_previews(self, name=None, deleted=False):
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126 dicts = self.gi.libraries.get_libraries(name=name, deleted=deleted)
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127 return [wrappers.LibraryPreview(_, gi=self.obj_gi) for _ in dicts]
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128
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129 def list(self, name=None, deleted=False):
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130 """
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131 Get libraries owned by the user of this Galaxy instance.
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132
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133 :type name: str
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134 :param name: return only libraries with this name
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135 :type deleted: bool
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136 :param deleted: if ``True``, return libraries that have been deleted
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137
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138 :rtype: list of :class:`~.wrappers.Library`
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139 """
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140 dicts = self.gi.libraries.get_libraries(name=name, deleted=deleted)
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141 if not deleted:
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142 # return Library objects only for not-deleted libraries since Galaxy
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143 # does not filter them out and Galaxy release_14.08 and earlier
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144 # crashes when trying to get a deleted library
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145 return [self.get(_['id']) for _ in dicts if not _['deleted']]
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146 else:
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147 return [self.get(_['id']) for _ in dicts]
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148
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149 def delete(self, id_=None, name=None):
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150 """
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151 Delete the library with the given id or name.
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152
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153 Note that the same name can map to multiple libraries.
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154
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155 .. warning::
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156 Deleting a data library is irreversible - all of the data from
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157 the library will be permanently deleted.
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158 """
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159 for id_ in self._select_ids(id_=id_, name=name):
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160 res = self.gi.libraries.delete_library(id_)
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161 if not isinstance(res, collections.Mapping):
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162 self._error('delete_library: unexpected reply: %r' % (res,))
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163
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164
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165 class ObjHistoryClient(ObjDatasetContainerClient):
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166 """
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167 Interacts with Galaxy histories.
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168 """
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169
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170 def __init__(self, obj_gi):
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171 super(ObjHistoryClient, self).__init__(obj_gi)
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172
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173 def create(self, name=None):
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174 """
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175 Create a new Galaxy history, optionally setting its name.
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176
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177 :rtype: :class:`~.wrappers.History`
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178 :return: the history just created
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179 """
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180 res = self.gi.histories.create_history(name=name)
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181 hist_info = self._get_dict('create_history', res)
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182 return self.get(hist_info['id'])
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183
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184 def get(self, id_):
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185 """
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186 Retrieve the history corresponding to the given id.
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187
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188 :rtype: :class:`~.wrappers.History`
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189 :return: the history corresponding to ``id_``
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190 """
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191 return self._get_container(id_, wrappers.History)
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192
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193 def get_previews(self, name=None, deleted=False):
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194 dicts = self.gi.histories.get_histories(name=name, deleted=deleted)
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195 return [wrappers.HistoryPreview(_, gi=self.obj_gi) for _ in dicts]
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196
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197 def list(self, name=None, deleted=False):
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198 """
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199 Get histories owned by the user of this Galaxy instance.
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200
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201 :type name: str
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202 :param name: return only histories with this name
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203 :type deleted: bool
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204 :param deleted: if ``True``, return histories that have been deleted
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205
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206 :rtype: list of :class:`~.wrappers.History`
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207 """
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208 dicts = self.gi.histories.get_histories(name=name, deleted=deleted)
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209 return [self.get(_['id']) for _ in dicts]
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210
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211 def delete(self, id_=None, name=None, purge=False):
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212 """
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213 Delete the history with the given id or name.
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214
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215 Note that the same name can map to multiple histories.
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216
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217 :type purge: bool
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218 :param purge: if ``True``, also purge (permanently delete) the history
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219
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220 .. note::
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221 For the purge option to work, the Galaxy instance must have the
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222 ``allow_user_dataset_purge`` option set to ``True`` in the
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223 ``config/galaxy.ini`` configuration file.
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224 """
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225 for id_ in self._select_ids(id_=id_, name=name):
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226 res = self.gi.histories.delete_history(id_, purge=purge)
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227 if not isinstance(res, collections.Mapping):
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228 self._error('delete_history: unexpected reply: %r' % (res,))
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229
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230
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231 class ObjWorkflowClient(ObjClient):
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232 """
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233 Interacts with Galaxy workflows.
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234 """
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235
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236 def __init__(self, obj_gi):
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237 super(ObjWorkflowClient, self).__init__(obj_gi)
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238
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239 def import_new(self, src):
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240 """
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241 Imports a new workflow into Galaxy.
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242
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243 :type src: dict or str
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244 :param src: deserialized (dictionary) or serialized (str) JSON
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245 dump of the workflow (this is normally obtained by exporting
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246 a workflow from Galaxy).
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247
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248 :rtype: :class:`~.wrappers.Workflow`
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249 :return: the workflow just imported
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250 """
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251 if isinstance(src, collections.Mapping):
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252 wf_dict = src
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253 else:
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254 try:
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255 wf_dict = json.loads(src)
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256 except (TypeError, ValueError):
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257 self._error('src not supported: %r' % (src,))
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258 wf_info = self.gi.workflows.import_workflow_json(wf_dict)
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259 return self.get(wf_info['id'])
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260
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261 def import_shared(self, id_):
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262 """
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263 Imports a shared workflow to the user's space.
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264
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265 :type id_: str
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266 :param id_: workflow id
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267
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268 :rtype: :class:`~.wrappers.Workflow`
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269 :return: the workflow just imported
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270 """
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271 wf_info = self.gi.workflows.import_shared_workflow(id_)
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272 return self.get(wf_info['id'])
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273
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274 def get(self, id_):
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275 """
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276 Retrieve the workflow corresponding to the given id.
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277
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278 :rtype: :class:`~.wrappers.Workflow`
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279 :return: the workflow corresponding to ``id_``
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280 """
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281 res = self.gi.workflows.show_workflow(id_)
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282 wf_dict = self._get_dict('show_workflow', res)
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283 return wrappers.Workflow(wf_dict, gi=self.obj_gi)
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284
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285 # the 'deleted' option is not available for workflows
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286 def get_previews(self, name=None, published=False):
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287 dicts = self.gi.workflows.get_workflows(name=name, published=published)
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288 return [wrappers.WorkflowPreview(_, gi=self.obj_gi) for _ in dicts]
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289
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290 # the 'deleted' option is not available for workflows
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291 def list(self, name=None, published=False):
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292 """
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293 Get workflows owned by the user of this Galaxy instance.
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294
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295 :type name: str
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296 :param name: return only workflows with this name
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297 :type published: bool
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298 :param published: if ``True``, return also published workflows
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299
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300 :rtype: list of :class:`~.wrappers.Workflow`
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301 """
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302 dicts = self.gi.workflows.get_workflows(name=name, published=published)
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303 return [self.get(_['id']) for _ in dicts]
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304
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305 def delete(self, id_=None, name=None):
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306 """
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307 Delete the workflow with the given id or name.
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308
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309 Note that the same name can map to multiple workflows.
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310
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311 .. warning::
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312 Deleting a workflow is irreversible - all of the data from
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313 the workflow will be permanently deleted.
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314 """
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315 for id_ in self._select_ids(id_=id_, name=name):
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316 res = self.gi.workflows.delete_workflow(id_)
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317 if not isinstance(res, six.string_types):
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318 self._error('delete_workflow: unexpected reply: %r' % (res,))
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319
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320
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321 class ObjToolClient(ObjClient):
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322 """
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323 Interacts with Galaxy tools.
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324 """
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325 def __init__(self, obj_gi):
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326 super(ObjToolClient, self).__init__(obj_gi)
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327
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328 def get(self, id_, io_details=False, link_details=False):
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329 """
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330 Retrieve the tool corresponding to the given id.
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331
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332 :type io_details: bool
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333 :param io_details: if True, get also input and output details
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334
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335 :type link_details: bool
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336 :param link_details: if True, get also link details
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337
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338 :rtype: :class:`~.wrappers.Tool`
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339 :return: the tool corresponding to ``id_``
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340 """
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341 res = self.gi.tools.show_tool(id_, io_details=io_details,
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342 link_details=link_details)
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343 tool_dict = self._get_dict('show_tool', res)
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344 return wrappers.Tool(tool_dict, gi=self.obj_gi)
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345
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346 def get_previews(self, name=None, trackster=None):
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347 """
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348 Get the list of tools installed on the Galaxy instance.
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349
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350 :type name: str
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351 :param name: return only tools with this name
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352
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353 :type trackster: bool
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354 :param trackster: if True, only tools that are compatible with
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355 Trackster are returned
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356
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357 :rtype: list of :class:`~.wrappers.Tool`
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358 """
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359 dicts = self.gi.tools.get_tools(name=name, trackster=trackster)
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360 return [wrappers.Tool(_, gi=self.obj_gi) for _ in dicts]
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361
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362 # the 'deleted' option is not available for tools
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363 def list(self, name=None, trackster=None):
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364 """
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365 Get the list of tools installed on the Galaxy instance.
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366
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367 :type name: str
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368 :param name: return only tools with this name
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369
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370 :type trackster: bool
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371 :param trackster: if True, only tools that are compatible with
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372 Trackster are returned
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373
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374 :rtype: list of :class:`~.wrappers.Tool`
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375 """
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376 # dicts = self.gi.tools.get_tools(name=name, trackster=trackster)
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377 # return [self.get(_['id']) for _ in dicts]
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378 # As of 2015/04/15, GET /api/tools returns also data manager tools for
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379 # non-admin users, see
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380 # https://trello.com/c/jyl0cvFP/2633-api-tool-list-filtering-doesn-t-filter-data-managers-for-non-admins
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381 # Trying to get() a data manager tool would then return a 404 Not Found
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382 # error.
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383 # Moreover, the dicts returned by gi.tools.get_tools() are richer than
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384 # those returned by get(), so make this an alias for get_previews().
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385 return self.get_previews(name, trackster)
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386
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387
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388 class ObjJobClient(ObjClient):
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389 """
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390 Interacts with Galaxy jobs.
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391 """
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392 def __init__(self, obj_gi):
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393 super(ObjJobClient, self).__init__(obj_gi)
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394
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395 def get(self, id_, full_details=False):
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396 """
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397 Retrieve the job corresponding to the given id.
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398
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399 :type full_details: bool
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400 :param full_details: if ``True``, return the complete list of details
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401 for the given job.
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402
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403 :rtype: :class:`~.wrappers.Job`
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404 :return: the job corresponding to ``id_``
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405 """
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406 res = self.gi.jobs.show_job(id_, full_details)
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407 job_dict = self._get_dict('job_tool', res)
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408 return wrappers.Job(job_dict, gi=self.obj_gi)
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409
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410 def get_previews(self):
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411 dicts = self.gi.jobs.get_jobs()
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412 return [wrappers.JobPreview(_, gi=self.obj_gi) for _ in dicts]
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413
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414 def list(self):
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415 """
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416 Get the list of jobs of the current user.
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417
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418 :rtype: list of :class:`~.wrappers.Job`
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419 """
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420 dicts = self.gi.jobs.get_jobs()
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421 return [self.get(_['id']) for _ in dicts]