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annotate planemo/lib/python3.7/site-packages/bioblend/galaxy/objects/wrappers.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 # pylint: disable=W0622,E1101
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2
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3 """
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4 A basic object-oriented interface for Galaxy entities.
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5 """
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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 Iterable,
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11 Mapping,
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12 Sequence,
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13 )
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14
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15 import bioblend
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16
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17
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18 __all__ = (
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19 'Wrapper',
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20 'Step',
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21 'Workflow',
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22 'ContentInfo',
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23 'LibraryContentInfo',
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24 'HistoryContentInfo',
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25 'DatasetContainer',
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26 'History',
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27 'Library',
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28 'Folder',
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29 'Dataset',
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30 'HistoryDatasetAssociation',
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31 'DatasetCollection',
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32 'HistoryDatasetCollectionAssociation',
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33 'LibraryDatasetDatasetAssociation',
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34 'LibraryDataset',
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35 'Tool',
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36 'Job',
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37 'Preview',
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38 'LibraryPreview',
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39 'HistoryPreview',
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40 'WorkflowPreview',
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41 )
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42
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43
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44 class Wrapper(object, metaclass=abc.ABCMeta):
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45 """
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46 Abstract base class for Galaxy entity wrappers.
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47
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48 Wrapper instances wrap deserialized JSON dictionaries such as the
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49 ones obtained by the Galaxy web API, converting key-based access to
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50 attribute-based access (e.g., ``library['name'] -> library.name``).
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51
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52 Dict keys that are converted to attributes are listed in the
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53 ``BASE_ATTRS`` class variable: this is the 'stable' interface.
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54 Note that the wrapped dictionary is accessible via the ``wrapped``
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55 attribute.
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56 """
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57 BASE_ATTRS = ('id', 'name')
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58
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59 @abc.abstractmethod
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60 def __init__(self, wrapped, parent=None, gi=None):
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61 """
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62 :type wrapped: dict
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63 :param wrapped: JSON-serializable dictionary
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64
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65 :type parent: :class:`Wrapper`
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66 :param parent: the parent of this wrapper
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67
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68 :type gi: :class:`GalaxyInstance`
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69 :param gi: the GalaxyInstance through which we can access this wrapper
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70 """
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71 if not isinstance(wrapped, Mapping):
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72 raise TypeError('wrapped object must be a mapping type')
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73 # loads(dumps(x)) is a bit faster than deepcopy and allows type checks
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74 try:
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75 dumped = json.dumps(wrapped)
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76 except (TypeError, ValueError):
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77 raise ValueError('wrapped object must be JSON-serializable')
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78 object.__setattr__(self, 'wrapped', json.loads(dumped))
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79 for k in self.BASE_ATTRS:
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80 object.__setattr__(self, k, self.wrapped.get(k))
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81 object.__setattr__(self, '_cached_parent', parent)
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82 object.__setattr__(self, 'is_modified', False)
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83 object.__setattr__(self, 'gi', gi)
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84
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85 @abc.abstractproperty
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86 def gi_module(self):
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87 """
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88 The GalaxyInstance module that deals with objects of this type.
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89 """
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90 pass
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91
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92 @property
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93 def parent(self):
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94 """
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95 The parent of this wrapper.
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96 """
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97 return self._cached_parent
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98
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99 @property
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100 def is_mapped(self):
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101 """
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102 ``True`` if this wrapper is mapped to an actual Galaxy entity.
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103 """
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104 return self.id is not None
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105
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106 def unmap(self):
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107 """
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108 Disconnect this wrapper from Galaxy.
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109 """
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110 object.__setattr__(self, 'id', None)
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111
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112 def clone(self):
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113 """
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114 Return an independent copy of this wrapper.
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115 """
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116 return self.__class__(self.wrapped)
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117
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118 def touch(self):
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119 """
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120 Mark this wrapper as having been modified since its creation.
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121 """
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122 object.__setattr__(self, 'is_modified', True)
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123 if self.parent:
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124 self.parent.touch()
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125
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126 def to_json(self):
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127 """
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128 Return a JSON dump of this wrapper.
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129 """
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130 return json.dumps(self.wrapped)
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131
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132 @classmethod
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133 def from_json(cls, jdef):
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134 """
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135 Build a new wrapper from a JSON dump.
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136 """
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137 return cls(json.loads(jdef))
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138
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139 # FIXME: things like self.x[0] = 'y' do NOT call self.__setattr__
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140 def __setattr__(self, name, value):
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141 if name not in self.wrapped:
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142 raise AttributeError("can't set attribute")
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143 else:
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144 self.wrapped[name] = value
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145 object.__setattr__(self, name, value)
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146 self.touch()
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147
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148 def __repr__(self):
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149 return "%s(%r)" % (self.__class__.__name__, self.wrapped)
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150
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151
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152 class Step(Wrapper):
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153 """
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154 Abstract base class for workflow steps.
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155
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156 Steps are the main building blocks of a Galaxy workflow. A step can be: an
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157 input (type ``data_collection_input``, ``data_input`` or
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158 ``parameter_input``), a computational tool (type ``tool``), a subworkflow
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159 (type ``subworkflow``) or a pause (type ``pause``).
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160 """
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161 BASE_ATTRS = Wrapper.BASE_ATTRS + (
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162 'input_steps', 'tool_id', 'tool_inputs', 'tool_version', 'type'
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163 )
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164
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165 def __init__(self, step_dict, parent):
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166 super().__init__(step_dict, parent=parent, gi=parent.gi)
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167 try:
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168 stype = step_dict['type']
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169 except KeyError:
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170 raise ValueError('not a step dict')
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171 if stype not in {'data_collection_input', 'data_input', 'parameter_input', 'pause', 'subworkflow', 'tool'}:
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172 raise ValueError('Unknown step type: %r' % stype)
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173
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174 @property
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175 def gi_module(self):
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176 return self.gi.workflows
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177
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178
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179 class Workflow(Wrapper):
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180 """
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181 Workflows represent ordered sequences of computations on Galaxy.
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182
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183 A workflow defines a sequence of steps that produce one or more
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184 results from an input dataset.
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185 """
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186 BASE_ATTRS = Wrapper.BASE_ATTRS + (
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187 'deleted', 'inputs', 'published', 'steps', 'tags'
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188 )
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189 POLLING_INTERVAL = 10 # for output state monitoring
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190
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191 def __init__(self, wf_dict, gi=None):
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192 super().__init__(wf_dict, gi=gi)
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193 missing_ids = []
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194 if gi:
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195 tools_list_by_id = [t.id for t in gi.tools.get_previews()]
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196 else:
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197 tools_list_by_id = []
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198 tool_labels_to_ids = {}
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199 for k, v in self.steps.items():
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200 # convert step ids to str for consistency with outer keys
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201 v['id'] = str(v['id'])
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202 for i in v['input_steps'].values():
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203 i['source_step'] = str(i['source_step'])
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204 step = Step(v, self)
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205 self.steps[k] = step
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206 if step.type == 'tool':
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207 if not step.tool_inputs or step.tool_id not in tools_list_by_id:
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208 missing_ids.append(k)
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209 tool_labels_to_ids.setdefault(step.tool_id, set()).add(step.id)
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210 input_labels_to_ids = {}
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211 for id_, d in self.inputs.items():
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212 input_labels_to_ids.setdefault(d['label'], set()).add(id_)
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213 object.__setattr__(self, 'input_labels_to_ids', input_labels_to_ids)
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214 object.__setattr__(self, 'tool_labels_to_ids', tool_labels_to_ids)
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215 dag, inv_dag = self._get_dag()
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216 heads, tails = set(dag), set(inv_dag)
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217 object.__setattr__(self, 'dag', dag)
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218 object.__setattr__(self, 'inv_dag', inv_dag)
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219 object.__setattr__(self, 'source_ids', heads - tails)
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220 assert set(self.inputs) == self.data_collection_input_ids | self.data_input_ids | self.parameter_input_ids, \
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221 "inputs is %r, while data_collection_input_ids is %r, data_input_ids is %r and parameter_input_ids is %r" % (
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222 self.inputs, self.data_collection_input_ids, self.data_input_ids, self.parameter_input_ids)
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223 object.__setattr__(self, 'sink_ids', tails - heads)
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224 object.__setattr__(self, 'missing_ids', missing_ids)
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225
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226 @property
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227 def gi_module(self):
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228 return self.gi.workflows
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229
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230 def _get_dag(self):
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231 """
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232 Return the workflow's DAG.
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233
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234 For convenience, this method computes a 'direct' (step =>
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235 successors) and an 'inverse' (step => predecessors)
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236 representation of the same DAG.
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237
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238 For instance, a workflow with a single tool *c*, two inputs
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239 *a, b* and three outputs *d, e, f* is represented by (direct)::
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240
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241 {'a': {'c'}, 'b': {'c'}, 'c': {'d', 'e', 'f'}}
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242
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243 and by (inverse)::
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244
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245 {'c': {'a', 'b'}, 'd': {'c'}, 'e': {'c'}, 'f': {'c'}}
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246 """
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247 dag, inv_dag = {}, {}
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248 for s in self.steps.values():
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249 for i in s.input_steps.values():
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250 head, tail = i['source_step'], s.id
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251 dag.setdefault(head, set()).add(tail)
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252 inv_dag.setdefault(tail, set()).add(head)
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253 return dag, inv_dag
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254
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255 def sorted_step_ids(self):
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256 """
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257 Return a topological sort of the workflow's DAG.
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258 """
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259 ids = []
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260 source_ids = self.source_ids.copy()
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261 inv_dag = dict((k, v.copy()) for k, v in self.inv_dag.items())
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262 while source_ids:
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263 head = source_ids.pop()
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264 ids.append(head)
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265 for tail in self.dag.get(head, []):
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266 incoming = inv_dag[tail]
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267 incoming.remove(head)
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268 if not incoming:
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269 source_ids.add(tail)
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270 return ids
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271
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272 @property
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273 def data_input_ids(self):
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274 """
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275 Return the ids of data input steps for this workflow.
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276 """
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277 return {id_ for id_, s in self.steps.items() if s.type == 'data_input'}
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278
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279 @property
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280 def data_collection_input_ids(self):
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281 """
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282 Return the ids of data collection input steps for this workflow.
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283 """
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284 return {id_ for id_, s in self.steps.items() if s.type == 'data_collection_input'}
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285
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286 @property
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287 def parameter_input_ids(self):
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288 """
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289 Return the ids of parameter input steps for this workflow.
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290 """
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291 return {id_ for id_, s in self.steps.items() if s.type == 'parameter_input'}
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292
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293 @property
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294 def tool_ids(self):
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295 """
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296 Return the ids of tool steps for this workflow.
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297 """
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298 return {id_ for id_, s in self.steps.items() if s.type == 'tool'}
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299
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300 @property
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301 def input_labels(self):
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302 """
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303 Return the labels of this workflow's input steps.
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304 """
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305 return set(self.input_labels_to_ids)
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306
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307 @property
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308 def is_runnable(self):
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309 """
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310 Return True if the workflow can be run on Galaxy.
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311
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312 A workflow is considered runnable on a Galaxy instance if all
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313 of the tools it uses are installed in that instance.
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314 """
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315 return not self.missing_ids
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316
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317 def convert_input_map(self, input_map):
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318 """
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319 Convert ``input_map`` to the format required by the Galaxy web API.
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320
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321 :type input_map: dict
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322 :param input_map: a mapping from input labels to datasets
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323
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324 :rtype: dict
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325 :return: a mapping from input slot ids to dataset ids in the
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326 format required by the Galaxy web API.
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327 """
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328 m = {}
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329 for label, slot_ids in self.input_labels_to_ids.items():
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330 datasets = input_map.get(label, [])
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331 if not isinstance(datasets, Iterable):
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332 datasets = [datasets]
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333 if len(datasets) < len(slot_ids):
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334 raise RuntimeError('not enough datasets for "%s"' % label)
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335 for id_, ds in zip(slot_ids, datasets):
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336 m[id_] = {'id': ds.id, 'src': ds.SRC}
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337 return m
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338
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339 def preview(self):
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340 getf = self.gi.workflows.get_previews
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341 try:
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342 p = [_ for _ in getf(published=True) if _.id == self.id][0]
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343 except IndexError:
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344 raise ValueError('no object for id %s' % self.id)
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345 return p
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346
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347 def run(self, input_map=None, history='', params=None, import_inputs=False,
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348 replacement_params=None, wait=False,
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349 polling_interval=POLLING_INTERVAL, break_on_error=True):
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350 """
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351 Run the workflow in the current Galaxy instance.
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352
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353 :type input_map: dict
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354 :param input_map: a mapping from workflow input labels to
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355 datasets, e.g.: ``dict(zip(workflow.input_labels,
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356 library.get_datasets()))``
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357
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358 :type history: :class:`History` or str
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359 :param history: either a valid history object (results will be
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360 stored there) or a string (a new history will be created with
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361 the given name).
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362
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363 :type params: dict
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364 :param params: a mapping of non-datasets tool parameters (see below)
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365
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366 :type import_inputs: bool
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367 :param import_inputs: If ``True``, workflow inputs will be imported into
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368 the history; if ``False``, only workflow outputs will be visible in
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369 the history.
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370
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371 :type replacement_params: dict
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372 :param replacement_params: pattern-based replacements for
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373 post-job actions (see the docs for
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374 :meth:`~bioblend.galaxy.workflows.WorkflowClient.invoke_workflow`)
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375
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376 :type wait: bool
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377 :param wait: whether to wait while the returned datasets are
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378 in a pending state
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379
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380 :type polling_interval: float
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381 :param polling_interval: polling interval in seconds
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382
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383 :type break_on_error: bool
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384 :param break_on_error: whether to break as soon as at least one
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385 of the returned datasets is in the 'error' state
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386
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387 :rtype: tuple
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388 :return: list of output datasets, output history
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389
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390 The ``params`` dict should be specified as follows::
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391
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392 {STEP_ID: PARAM_DICT, ...}
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393
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394 where PARAM_DICT is::
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395
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396 {PARAM_NAME: VALUE, ...}
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397
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398 For backwards compatibility, the following (deprecated) format is
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399 also supported for ``params``::
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400
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401 {TOOL_ID: PARAM_DICT, ...}
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diff changeset
402
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403 in which case PARAM_DICT affects all steps with the given tool id.
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404 If both by-tool-id and by-step-id specifications are used, the
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405 latter takes precedence.
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406
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407 Finally (again, for backwards compatibility), PARAM_DICT can also
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408 be specified as::
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409
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410 {'param': PARAM_NAME, 'value': VALUE}
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411
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412 Note that this format allows only one parameter to be set per step.
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413
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414 Example: set 'a' to 1 for the third workflow step::
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415
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416 params = {workflow.steps[2].id: {'a': 1}}
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417
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418 .. warning::
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419
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420 This is a blocking operation that can take a very long time. If
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421 ``wait`` is set to ``False``, the method will return as soon as the
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422 workflow has been *scheduled*, otherwise it will wait until the
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423 workflow has been *run*. With a large number of steps, however, the
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424 delay may not be negligible even in the former case (e.g. minutes for
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425 100 steps).
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426 """
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427 if not self.is_mapped:
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428 raise RuntimeError('workflow is not mapped to a Galaxy object')
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429 if not self.is_runnable:
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430 raise RuntimeError('workflow has missing tools: %s' % ', '.join(
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431 '%s[%s]' % (self.steps[_].tool_id, _)
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432 for _ in self.missing_ids))
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433 kwargs = {
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434 'dataset_map': self.convert_input_map(input_map or {}),
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435 'params': params,
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436 'import_inputs_to_history': import_inputs,
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437 'replacement_params': replacement_params,
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438 }
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439 if isinstance(history, History):
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440 try:
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441 kwargs['history_id'] = history.id
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442 except AttributeError:
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443 raise RuntimeError('history does not have an id')
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444 elif isinstance(history, str):
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445 kwargs['history_name'] = history
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446 else:
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447 raise TypeError(
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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448 'history must be either a history wrapper or a string')
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449 res = self.gi.gi.workflows.run_workflow(self.id, **kwargs)
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450 # res structure: {'history': HIST_ID, 'outputs': [CI_ID, CI_ID, ...]}
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451 out_hist = self.gi.histories.get(res['history'])
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452 content_infos_dict = dict()
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453 for ci in out_hist.content_infos:
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454 content_infos_dict[ci.id] = ci
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455 outputs = []
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456 for output_id in res['outputs']:
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457 if content_infos_dict[output_id].type == 'file':
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458 outputs.append(out_hist.get_dataset(output_id))
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459 elif content_infos_dict[output_id].type == 'collection':
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460 outputs.append(out_hist.get_dataset_collection(output_id))
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461
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462 if wait:
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463 self.gi._wait_datasets(outputs, polling_interval=polling_interval,
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464 break_on_error=break_on_error)
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465 return outputs, out_hist
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466
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467 def export(self):
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468 """
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469 Export a re-importable representation of the workflow.
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470
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471 :rtype: dict
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472 :return: a JSON-serializable dump of the workflow
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473 """
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474 return self.gi.gi.workflows.export_workflow_dict(self.id)
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475
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476 def delete(self):
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477 """
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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478 Delete this workflow.
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479
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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480 .. warning::
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481 Deleting a workflow is irreversible - all of the data from
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482 the workflow will be permanently deleted.
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483 """
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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484 self.gi.workflows.delete(id_=self.id)
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485 self.unmap()
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486
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487
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488 class Dataset(Wrapper, metaclass=abc.ABCMeta):
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489 """
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490 Abstract base class for Galaxy datasets.
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491 """
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492 BASE_ATTRS = Wrapper.BASE_ATTRS + (
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493 'data_type', 'file_ext', 'file_name', 'file_size', 'genome_build', 'misc_info', 'state'
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494 )
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495 POLLING_INTERVAL = 1 # for state monitoring
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496
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497 @abc.abstractmethod
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498 def __init__(self, ds_dict, container, gi=None):
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499 super().__init__(ds_dict, gi=gi)
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500 object.__setattr__(self, 'container', container)
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501
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502 @property
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503 def container_id(self):
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504 """
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505 Deprecated property.
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506
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507 Id of the dataset container. Use :attr:`.container.id` instead.
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508 """
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509 return self.container.id
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510
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511 @abc.abstractproperty
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512 def _stream_url(self):
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513 """
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514 Return the URL to stream this dataset.
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515 """
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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516 pass
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517
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518 def get_stream(self, chunk_size=bioblend.CHUNK_SIZE):
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519 """
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520 Open dataset for reading and return an iterator over its contents.
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521
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522 :type chunk_size: int
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523 :param chunk_size: read this amount of bytes at a time
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524 """
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525 kwargs = {'stream': True}
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526 if isinstance(self, LibraryDataset):
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527 kwargs['params'] = {'ld_ids%5B%5D': self.id}
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528 r = self.gi.gi.make_get_request(self._stream_url, **kwargs)
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529 if isinstance(self, LibraryDataset) and r.status_code == 500:
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530 # compatibility with older Galaxy releases
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531 kwargs['params'] = {'ldda_ids%5B%5D': self.id}
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532 r = self.gi.gi.make_get_request(self._stream_url, **kwargs)
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533 r.raise_for_status()
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534 return r.iter_content(chunk_size) # FIXME: client can't close r
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535
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536 def peek(self, chunk_size=bioblend.CHUNK_SIZE):
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537 """
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538 Open dataset for reading and return the first chunk.
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539
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540 See :meth:`.get_stream` for param info.
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541 """
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542 try:
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543 return next(self.get_stream(chunk_size=chunk_size))
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544 except StopIteration:
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545 return b''
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546
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547 def download(self, file_object, chunk_size=bioblend.CHUNK_SIZE):
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548 """
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549 Open dataset for reading and save its contents to ``file_object``.
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550
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551 :type file_object: file
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552 :param file_object: output file object
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553
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554 See :meth:`.get_stream` for info on other params.
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555 """
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556 for chunk in self.get_stream(chunk_size=chunk_size):
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557 file_object.write(chunk)
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558
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559 def get_contents(self, chunk_size=bioblend.CHUNK_SIZE):
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560 """
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561 Open dataset for reading and return its **full** contents.
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562
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563 See :meth:`.get_stream` for param info.
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564 """
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565 return b''.join(self.get_stream(chunk_size=chunk_size))
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566
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567 def refresh(self):
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568 """
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569 Re-fetch the attributes pertaining to this object.
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570
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571 Returns: self
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572 """
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573 gi_client = getattr(self.gi.gi, self.container.API_MODULE)
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574 ds_dict = gi_client.show_dataset(self.container.id, self.id)
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575 self.__init__(ds_dict, self.container, self.gi)
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576 return self
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577
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578 def wait(self, polling_interval=POLLING_INTERVAL, break_on_error=True):
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579 """
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580 Wait for this dataset to come out of the pending states.
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581
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582 :type polling_interval: float
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583 :param polling_interval: polling interval in seconds
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584
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585 :type break_on_error: bool
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586 :param break_on_error: if ``True``, raise a RuntimeError exception if
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587 the dataset ends in the 'error' state.
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588
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589 .. warning::
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590
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591 This is a blocking operation that can take a very long time. Also,
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592 note that this method does not return anything; however, this dataset
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593 is refreshed (possibly multiple times) during the execution.
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594 """
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595 self.gi._wait_datasets([self], polling_interval=polling_interval,
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596 break_on_error=break_on_error)
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597
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598
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599 class HistoryDatasetAssociation(Dataset):
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600 """
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601 Maps to a Galaxy ``HistoryDatasetAssociation``.
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602 """
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603 BASE_ATTRS = Dataset.BASE_ATTRS + ('annotation', 'deleted', 'purged', 'tags', 'visible')
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604 SRC = 'hda'
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605
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606 def __init__(self, ds_dict, container, gi=None):
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607 super().__init__(ds_dict, container, gi=gi)
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608
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609 @property
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610 def gi_module(self):
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611 return self.gi.histories
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612
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613 @property
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614 def _stream_url(self):
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615 base_url = self.gi.gi.histories._make_url(module_id=self.container.id, contents=True)
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616 return "%s/%s/display" % (base_url, self.id)
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617
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618 def update(self, **kwds):
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619 """
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620 Update this history dataset metadata. Some of the attributes that can be
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621 modified are documented below.
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622
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623 :type name: str
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624 :param name: Replace history dataset name with the given string
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625
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626 :type genome_build: str
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627 :param genome_build: Replace history dataset genome build (dbkey)
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628
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629 :type annotation: str
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630 :param annotation: Replace history dataset annotation with given string
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631
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632 :type deleted: bool
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633 :param deleted: Mark or unmark history dataset as deleted
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634
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635 :type visible: bool
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636 :param visible: Mark or unmark history dataset as visible
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637 """
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638 res = self.gi.gi.histories.update_dataset(self.container.id, self.id, **kwds)
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639 # Refresh also the history because the dataset may have been (un)deleted
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640 self.container.refresh()
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641 self.__init__(res, self.container, gi=self.gi)
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642 return self
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643
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644 def delete(self, purge=False):
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645 """
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646 Delete this history dataset.
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647
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648 :type purge: bool
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649 :param purge: if ``True``, also purge (permanently delete) the dataset
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650
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651 .. note::
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652 For the purge option to work, the Galaxy instance must have the
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653 ``allow_user_dataset_purge`` option set to ``true`` in the
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654 ``config/galaxy.yml`` configuration file.
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655 """
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656 self.gi.gi.histories.delete_dataset(self.container.id, self.id, purge=purge)
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657 self.container.refresh()
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658 self.refresh()
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659
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660
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661 class DatasetCollection(Wrapper, metaclass=abc.ABCMeta):
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662 """
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663 Abstract base class for Galaxy dataset collections.
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664 """
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665 BASE_ATTRS = Wrapper.BASE_ATTRS + (
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666 'state', 'deleted', 'collection_type'
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667 )
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668
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669 @abc.abstractmethod
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670 def __init__(self, dsc_dict, container, gi=None):
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671 super().__init__(dsc_dict, gi=gi)
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672 object.__setattr__(self, 'container', container)
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673
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674 def refresh(self):
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675 """
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676 Re-fetch the attributes pertaining to this object.
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677
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678 Returns: self
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679 """
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680 gi_client = getattr(self.gi.gi, self.container.API_MODULE)
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681 dsc_dict = gi_client.show_dataset_collection(self.container.id, self.id)
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682 self.__init__(dsc_dict, self.container, self.gi)
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683 return self
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684
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685
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686 class HistoryDatasetCollectionAssociation(DatasetCollection):
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687 """
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688 Maps to a Galaxy ``HistoryDatasetCollectionAssociation``.
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689 """
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690 BASE_ATTRS = DatasetCollection.BASE_ATTRS + ('tags', 'visible', 'elements')
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691 SRC = 'hdca'
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692
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693 def __init__(self, dsc_dict, container, gi=None):
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694 super().__init__(dsc_dict, container, gi=gi)
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695
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696 @property
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697 def gi_module(self):
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698 return self.gi.histories
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699
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700 def delete(self):
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701 """
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702 Delete this dataset collection.
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703 """
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704 self.gi.gi.histories.delete_dataset_collection(self.container.id, self.id)
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705 self.container.refresh()
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706 self.refresh()
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707
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708
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709 class LibRelatedDataset(Dataset):
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710 """
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711 Base class for LibraryDatasetDatasetAssociation and LibraryDataset classes.
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712 """
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713
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714 def __init__(self, ds_dict, container, gi=None):
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715 super().__init__(ds_dict, container, gi=gi)
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716
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717 @property
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718 def gi_module(self):
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719 return self.gi.libraries
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720
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721 @property
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722 def _stream_url(self):
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723 base_url = self.gi.gi.libraries._make_url()
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724 return "%s/datasets/download/uncompressed" % base_url
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725
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726
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727 class LibraryDatasetDatasetAssociation(LibRelatedDataset):
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728 """
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729 Maps to a Galaxy ``LibraryDatasetDatasetAssociation``.
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730 """
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731 BASE_ATTRS = LibRelatedDataset.BASE_ATTRS + ('deleted',)
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732 SRC = 'ldda'
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733
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734
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735 class LibraryDataset(LibRelatedDataset):
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736 """
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737 Maps to a Galaxy ``LibraryDataset``.
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738 """
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739 SRC = 'ld'
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740
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741 def delete(self, purged=False):
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742 """
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743 Delete this library dataset.
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744
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745 :type purged: bool
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746 :param purged: if ``True``, also purge (permanently delete) the dataset
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747 """
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748 self.gi.gi.libraries.delete_library_dataset(
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749 self.container.id, self.id, purged=purged)
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750 self.container.refresh()
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751 self.refresh()
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752
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753 def update(self, **kwds):
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754 """
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755 Update this library dataset metadata. Some of the attributes that can be
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756 modified are documented below.
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757
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758 :type name: str
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759 :param name: Replace history dataset name with the given string
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760
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761 :type genome_build: str
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762 :param genome_build: Replace history dataset genome build (dbkey)
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763 """
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764 res = self.gi.gi.libraries.update_library_dataset(self.id, **kwds)
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765 self.container.refresh()
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766 self.__init__(res, self.container, gi=self.gi)
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767 return self
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768
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769
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770 class ContentInfo(Wrapper, metaclass=abc.ABCMeta):
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771 """
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772 Instances of this class wrap dictionaries obtained by getting
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773 ``/api/{histories,libraries}/<ID>/contents`` from Galaxy.
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774 """
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775 BASE_ATTRS = Wrapper.BASE_ATTRS + ('type',)
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776
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777 @abc.abstractmethod
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778 def __init__(self, info_dict, gi=None):
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779 super().__init__(info_dict, gi=gi)
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780
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781
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782 class LibraryContentInfo(ContentInfo):
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783 """
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784 Instances of this class wrap dictionaries obtained by getting
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785 ``/api/libraries/<ID>/contents`` from Galaxy.
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786 """
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787 def __init__(self, info_dict, gi=None):
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788 super().__init__(info_dict, gi=gi)
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789
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790 @property
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791 def gi_module(self):
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diff changeset
792 return self.gi.libraries
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793
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794
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795 class HistoryContentInfo(ContentInfo):
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796 """
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797 Instances of this class wrap dictionaries obtained by getting
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diff changeset
798 ``/api/histories/<ID>/contents`` from Galaxy.
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parents:
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799 """
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800 BASE_ATTRS = ContentInfo.BASE_ATTRS + ('deleted', 'state', 'visible')
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801
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802 def __init__(self, info_dict, gi=None):
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diff changeset
803 super().__init__(info_dict, gi=gi)
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804
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805 @property
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diff changeset
806 def gi_module(self):
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807 return self.gi.histories
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parents:
diff changeset
808
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diff changeset
809
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810 class DatasetContainer(Wrapper, metaclass=abc.ABCMeta):
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811 """
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diff changeset
812 Abstract base class for dataset containers (histories and libraries).
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813 """
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814 BASE_ATTRS = Wrapper.BASE_ATTRS + ('deleted',)
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815
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816 @abc.abstractmethod
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817 def __init__(self, c_dict, content_infos=None, gi=None):
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818 """
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819 :type content_infos: list of :class:`ContentInfo`
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820 :param content_infos: info objects for the container's contents
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821 """
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822 super().__init__(c_dict, gi=gi)
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823 if content_infos is None:
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824 content_infos = []
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825 object.__setattr__(self, 'content_infos', content_infos)
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826
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827 @property
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828 def dataset_ids(self):
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829 """
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830 Return the ids of the contained datasets.
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831 """
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832 return [_.id for _ in self.content_infos if _.type == 'file']
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833
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834 def preview(self):
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835 getf = self.gi_module.get_previews
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diff changeset
836 # self.state could be stale: check both regular and deleted containers
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837 try:
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838 p = [_ for _ in getf() if _.id == self.id][0]
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839 except IndexError:
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840 try:
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841 p = [_ for _ in getf(deleted=True) if _.id == self.id][0]
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842 except IndexError:
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843 raise ValueError('no object for id %s' % self.id)
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844 return p
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845
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846 def refresh(self):
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847 """
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848 Re-fetch the attributes pertaining to this object.
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849
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850 Returns: self
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851 """
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852 fresh = self.gi_module.get(self.id)
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853 self.__init__(
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diff changeset
854 fresh.wrapped, content_infos=fresh.content_infos, gi=self.gi)
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855 return self
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856
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857 def get_dataset(self, ds_id):
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858 """
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859 Retrieve the dataset corresponding to the given id.
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860
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861 :type ds_id: str
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862 :param ds_id: dataset id
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863
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864 :rtype: :class:`~.HistoryDatasetAssociation` or
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865 :class:`~.LibraryDataset`
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866 :return: the dataset corresponding to ``ds_id``
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867 """
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868 gi_client = getattr(self.gi.gi, self.API_MODULE)
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diff changeset
869 ds_dict = gi_client.show_dataset(self.id, ds_id)
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870 return self.DS_TYPE(ds_dict, self, gi=self.gi)
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871
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872 def get_datasets(self, name=None):
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873 """
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874 Get all datasets contained inside this dataset container.
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875
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876 :type name: str
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877 :param name: return only datasets with this name
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878
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879 :rtype: list of :class:`~.HistoryDatasetAssociation` or list of
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880 :class:`~.LibraryDataset`
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881 :return: datasets with the given name contained inside this
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882 container
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883
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884 .. note::
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885
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886 when filtering library datasets by name, specify their full
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diff changeset
887 paths starting from the library's root folder, e.g.,
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diff changeset
888 ``/seqdata/reads.fastq``. Full paths are available through
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diff changeset
889 the ``content_infos`` attribute of
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890 :class:`~.Library` objects.
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891 """
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892 if name is None:
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893 ds_ids = self.dataset_ids
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894 else:
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diff changeset
895 ds_ids = [_.id for _ in self.content_infos if _.name == name]
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896 return [self.get_dataset(_) for _ in ds_ids]
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897
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898
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899 class History(DatasetContainer):
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900 """
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901 Maps to a Galaxy history.
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902 """
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903 BASE_ATTRS = DatasetContainer.BASE_ATTRS + ('annotation', 'published', 'state', 'state_ids', 'state_details', 'tags')
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904 DS_TYPE = HistoryDatasetAssociation
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905 DSC_TYPE = HistoryDatasetCollectionAssociation
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906 CONTENT_INFO_TYPE = HistoryContentInfo
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907 API_MODULE = 'histories'
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908
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909 def __init__(self, hist_dict, content_infos=None, gi=None):
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910 super().__init__(hist_dict, content_infos=content_infos, gi=gi)
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911
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912 @property
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913 def gi_module(self):
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914 return self.gi.histories
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915
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916 def update(self, **kwds):
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917 """
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918 Update history metadata information. Some of the attributes that can be
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diff changeset
919 modified are documented below.
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920
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921 :type name: str
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922 :param name: Replace history name with the given string
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923
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diff changeset
924 :type annotation: str
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diff changeset
925 :param annotation: Replace history annotation with the given string
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diff changeset
926
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diff changeset
927 :type deleted: bool
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diff changeset
928 :param deleted: Mark or unmark history as deleted
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diff changeset
929
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diff changeset
930 :type purged: bool
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diff changeset
931 :param purged: If True, mark history as purged (permanently deleted).
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diff changeset
932
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diff changeset
933 :type published: bool
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diff changeset
934 :param published: Mark or unmark history as published
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diff changeset
935
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diff changeset
936 :type importable: bool
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diff changeset
937 :param importable: Mark or unmark history as importable
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diff changeset
938
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diff changeset
939 :type tags: list
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diff changeset
940 :param tags: Replace history tags with the given list
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diff changeset
941 """
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diff changeset
942 # TODO: wouldn't it be better if name and annotation were attributes?
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diff changeset
943 self.gi.gi.histories.update_history(self.id, **kwds)
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diff changeset
944 self.refresh()
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diff changeset
945 return self
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diff changeset
946
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947 def delete(self, purge=False):
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diff changeset
948 """
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diff changeset
949 Delete this history.
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diff changeset
950
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951 :type purge: bool
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diff changeset
952 :param purge: if ``True``, also purge (permanently delete) the history
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diff changeset
953
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954 .. note::
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955 For the purge option to work, the Galaxy instance must have the
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diff changeset
956 ``allow_user_dataset_purge`` option set to ``true`` in the
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diff changeset
957 ``config/galaxy.yml`` configuration file.
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diff changeset
958 """
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diff changeset
959 self.gi.histories.delete(id_=self.id, purge=purge)
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diff changeset
960 self.refresh()
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961 self.unmap()
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962
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963 def import_dataset(self, lds):
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964 """
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diff changeset
965 Import a dataset into the history from a library.
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diff changeset
966
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967 :type lds: :class:`~.LibraryDataset`
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diff changeset
968 :param lds: the library dataset to import
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969
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970 :rtype: :class:`~.HistoryDatasetAssociation`
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diff changeset
971 :return: the imported history dataset
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972 """
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973 if not self.is_mapped:
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diff changeset
974 raise RuntimeError('history is not mapped to a Galaxy object')
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975 if not isinstance(lds, LibraryDataset):
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976 raise TypeError('lds is not a LibraryDataset')
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977 res = self.gi.gi.histories.upload_dataset_from_library(self.id, lds.id)
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978 if not isinstance(res, Mapping):
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979 raise RuntimeError(
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980 'upload_dataset_from_library: unexpected reply: %r' % res)
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981 self.refresh()
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982 return self.get_dataset(res['id'])
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983
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984 def upload_file(self, path, **kwargs):
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985 """
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986 Upload the file specified by ``path`` to this history.
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987
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988 :type path: str
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989 :param path: path of the file to upload
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990
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991 See :meth:`~bioblend.galaxy.tools.ToolClient.upload_file` for
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992 the optional parameters.
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993
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994 :rtype: :class:`~.HistoryDatasetAssociation`
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995 :return: the uploaded dataset
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996 """
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997 out_dict = self.gi.gi.tools.upload_file(path, self.id, **kwargs)
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998 self.refresh()
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999 return self.get_dataset(out_dict['outputs'][0]['id'])
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diff changeset
1000
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1001 upload_dataset = upload_file
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1002
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1003 def upload_from_ftp(self, path, **kwargs):
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1004 """
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diff changeset
1005 Upload the file specified by ``path`` from the user's FTP directory to
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diff changeset
1006 this history.
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diff changeset
1007
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1008 :type path: str
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1009 :param path: path of the file in the user's FTP directory
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diff changeset
1010
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1011 See :meth:`~bioblend.galaxy.tools.ToolClient.upload_file` for
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1012 the optional parameters.
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1013
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1014 :rtype: :class:`~.HistoryDatasetAssociation`
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1015 :return: the uploaded dataset
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1016 """
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1017 out_dict = self.gi.gi.tools.upload_from_ftp(path, self.id, **kwargs)
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1018 self.refresh()
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1019 return self.get_dataset(out_dict['outputs'][0]['id'])
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1020
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1021 def paste_content(self, content, **kwargs):
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1022 """
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1023 Upload a string to a new dataset in this history.
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1024
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1025 :type content: str
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1026 :param content: content of the new dataset to upload
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diff changeset
1027
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diff changeset
1028 See :meth:`~bioblend.galaxy.tools.ToolClient.upload_file` for
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1029 the optional parameters (except file_name).
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1030
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1031 :rtype: :class:`~.HistoryDatasetAssociation`
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1032 :return: the uploaded dataset
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1033 """
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diff changeset
1034 out_dict = self.gi.gi.tools.paste_content(content, self.id, **kwargs)
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diff changeset
1035 self.refresh()
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diff changeset
1036 return self.get_dataset(out_dict['outputs'][0]['id'])
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diff changeset
1037
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1038 def export(self, gzip=True, include_hidden=False, include_deleted=False,
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1039 wait=False, maxwait=None):
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1040 """
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1041 Start a job to create an export archive for this history. See
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diff changeset
1042 :meth:`~bioblend.galaxy.histories.HistoryClient.export_history`
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diff changeset
1043 for parameter and return value info.
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1044 """
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diff changeset
1045 return self.gi.gi.histories.export_history(
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diff changeset
1046 self.id, gzip=gzip, include_hidden=include_hidden,
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diff changeset
1047 include_deleted=include_deleted, wait=wait, maxwait=maxwait)
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1048
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1049 def download(self, jeha_id, outf, chunk_size=bioblend.CHUNK_SIZE):
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1050 """
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1051 Download an export archive for this history. Use :meth:`export`
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diff changeset
1052 to create an export and get the required ``jeha_id``. See
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diff changeset
1053 :meth:`~bioblend.galaxy.histories.HistoryClient.download_history`
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diff changeset
1054 for parameter and return value info.
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1055 """
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1056 return self.gi.gi.histories.download_history(
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1057 self.id, jeha_id, outf, chunk_size=chunk_size)
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1058
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1059 def create_dataset_collection(self, collection_description):
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1060 """
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diff changeset
1061 Create a new dataset collection in the history by providing a collection description.
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1062
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1063 :type collection_description: bioblend.galaxy.dataset_collections.CollectionDescription
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1064 :param collection_description: a description of the dataset collection
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1065
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1066 :rtype: :class:`~.HistoryDatasetCollectionAssociation`
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1067 :return: the new dataset collection
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1068 """
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1069 dataset_collection = self.gi.gi.histories.create_dataset_collection(self.id, collection_description)
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1070 self.refresh()
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1071 return self.get_dataset_collection(dataset_collection['id'])
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1072
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1073 def get_dataset_collection(self, dsc_id):
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1074 """
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1075 Retrieve the dataset collection corresponding to the given id.
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1076
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1077 :type dsc_id: str
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1078 :param dsc_id: dataset collection id
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1079
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1080 :rtype: :class:`~.HistoryDatasetCollectionAssociation`
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1081 :return: the dataset collection corresponding to ``dsc_id``
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1082 """
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1083 dsc_dict = self.gi.gi.histories.show_dataset_collection(self.id, dsc_id)
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1084 return self.DSC_TYPE(dsc_dict, self, gi=self.gi)
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1085
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1086
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1087 class Library(DatasetContainer):
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1088 """
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1089 Maps to a Galaxy library.
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1090 """
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1091 BASE_ATTRS = DatasetContainer.BASE_ATTRS + ('description', 'synopsis')
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1092 DS_TYPE = LibraryDataset
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1093 CONTENT_INFO_TYPE = LibraryContentInfo
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1094 API_MODULE = 'libraries'
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1095
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1096 def __init__(self, lib_dict, content_infos=None, gi=None):
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1097 super().__init__(lib_dict, content_infos=content_infos, gi=gi)
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1098
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1099 @property
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1100 def gi_module(self):
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1101 return self.gi.libraries
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1102
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1103 @property
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1104 def folder_ids(self):
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1105 """
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1106 Return the ids of the contained folders.
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1107 """
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1108 return [_.id for _ in self.content_infos if _.type == 'folder']
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1109
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1110 def delete(self):
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1111 """
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1112 Delete this library.
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1113 """
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1114 self.gi.libraries.delete(id_=self.id)
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1115 self.refresh()
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1116 self.unmap()
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1117
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1118 def _pre_upload(self, folder):
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1119 """
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1120 Return the id of the given folder, after sanity checking.
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1121 """
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1122 if not self.is_mapped:
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1123 raise RuntimeError('library is not mapped to a Galaxy object')
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1124 return None if folder is None else folder.id
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1125
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1126 def upload_data(self, data, folder=None, **kwargs):
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1127 """
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1128 Upload data to this library.
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1129
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1130 :type data: str
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1131 :param data: dataset contents
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1132
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1133 :type folder: :class:`~.Folder`
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1134 :param folder: a folder object, or ``None`` to upload to the root folder
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1135
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1136 :rtype: :class:`~.LibraryDataset`
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1137 :return: the dataset object that represents the uploaded content
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1138
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1139 Optional keyword arguments: ``file_type``, ``dbkey``.
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1140 """
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1141 fid = self._pre_upload(folder)
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1142 res = self.gi.gi.libraries.upload_file_contents(
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1143 self.id, data, folder_id=fid, **kwargs)
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1144 self.refresh()
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1145 return self.get_dataset(res[0]['id'])
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1146
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1147 def upload_from_url(self, url, folder=None, **kwargs):
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1148 """
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1149 Upload data to this library from the given URL.
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1150
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1151 :type url: str
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1152 :param url: URL from which data should be read
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diff changeset
1153
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1154 See :meth:`.upload_data` for info on other params.
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1155 """
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1156 fid = self._pre_upload(folder)
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diff changeset
1157 res = self.gi.gi.libraries.upload_file_from_url(
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1158 self.id, url, folder_id=fid, **kwargs)
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1159 self.refresh()
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1160 return self.get_dataset(res[0]['id'])
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1161
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1162 def upload_from_local(self, path, folder=None, **kwargs):
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1163 """
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1164 Upload data to this library from a local file.
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diff changeset
1165
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1166 :type path: str
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1167 :param path: local file path from which data should be read
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1168
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1169 See :meth:`.upload_data` for info on other params.
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1170 """
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1171 fid = self._pre_upload(folder)
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1172 res = self.gi.gi.libraries.upload_file_from_local_path(
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1173 self.id, path, folder_id=fid, **kwargs)
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1174 self.refresh()
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1175 return self.get_dataset(res[0]['id'])
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diff changeset
1176
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1177 def upload_from_galaxy_fs(self, paths, folder=None, link_data_only=None, **kwargs):
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1178 """
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1179 Upload data to this library from filesystem paths on the server.
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1180
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1181 .. note::
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1182 For this method to work, the Galaxy instance must have the
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1183 ``allow_path_paste`` option set to ``true`` in the
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1184 ``config/galaxy.yml`` configuration file.
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1185
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1186 :type paths: str or :class:`~collections.abc.Iterable` of str
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1187 :param paths: server-side file paths from which data should be read
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1188
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1189 :type link_data_only: str
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1190 :param link_data_only: either 'copy_files' (default) or
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1191 'link_to_files'. Setting to 'link_to_files' symlinks instead of
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1192 copying the files
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1193
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1194 :rtype: list of :class:`~.LibraryDataset`
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1195 :return: the dataset objects that represent the uploaded content
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1196
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1197 See :meth:`.upload_data` for info on other params.
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1198 """
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1199 fid = self._pre_upload(folder)
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1200 if isinstance(paths, str):
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1201 paths = (paths,)
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1202 paths = '\n'.join(paths)
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1203 res = self.gi.gi.libraries.upload_from_galaxy_filesystem(
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1204 self.id, paths, folder_id=fid, link_data_only=link_data_only,
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1205 **kwargs)
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1206 if res is None:
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1207 raise RuntimeError('upload_from_galaxy_filesystem: no reply')
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1208 if not isinstance(res, Sequence):
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1209 raise RuntimeError(
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1210 'upload_from_galaxy_filesystem: unexpected reply: %r' % res)
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1211 new_datasets = [
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1212 self.get_dataset(ds_info['id']) for ds_info in res
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1213 ]
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1214 self.refresh()
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1215 return new_datasets
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1216
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1217 def copy_from_dataset(self, hda, folder=None, message=''):
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1218 """
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1219 Copy a history dataset into this library.
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1220
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1221 :type hda: :class:`~.HistoryDatasetAssociation`
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1222 :param hda: history dataset to copy into the library
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1223
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1224 See :meth:`.upload_data` for info on other params.
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1225 """
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1226 fid = self._pre_upload(folder)
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1227 res = self.gi.gi.libraries.copy_from_dataset(
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1228 self.id, hda.id, folder_id=fid, message=message)
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1229 self.refresh()
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1230 return self.get_dataset(res['library_dataset_id'])
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1231
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1232 def create_folder(self, name, description=None, base_folder=None):
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1233 """
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1234 Create a folder in this library.
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1235
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1236 :type name: str
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1237 :param name: folder name
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1238
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1239 :type description: str
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1240 :param description: optional folder description
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1241
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1242 :type base_folder: :class:`~.Folder`
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1243 :param base_folder: parent folder, or ``None`` to create in the root
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1244 folder
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1245
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1246 :rtype: :class:`~.Folder`
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1247 :return: the folder just created
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1248 """
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1249 bfid = None if base_folder is None else base_folder.id
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1250 res = self.gi.gi.libraries.create_folder(
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1251 self.id, name, description=description, base_folder_id=bfid)
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1252 self.refresh()
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1253 return self.get_folder(res[0]['id'])
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1254
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1255 def get_folder(self, f_id):
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1256 """
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1257 Retrieve the folder corresponding to the given id.
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1258
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1259 :rtype: :class:`~.Folder`
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1260 :return: the folder corresponding to ``f_id``
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1261 """
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1262 f_dict = self.gi.gi.libraries.show_folder(self.id, f_id)
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1263 return Folder(f_dict, self, gi=self.gi)
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1264
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1265 @property
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1266 def root_folder(self):
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1267 """
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1268 The root folder of this library.
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1269
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1270 :rtype: :class:`~.Folder`
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1271 :return: the root folder of this library
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1272 """
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1273 return self.get_folder(self.gi.gi.libraries._get_root_folder_id(self.id))
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1274
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1275
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1276 class Folder(Wrapper):
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1277 """
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1278 Maps to a folder in a Galaxy library.
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1279 """
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1280 BASE_ATTRS = Wrapper.BASE_ATTRS + ('description', 'deleted', 'item_count')
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1281
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1282 def __init__(self, f_dict, container, gi=None):
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1283 super().__init__(f_dict, gi=gi)
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diff changeset
1284 object.__setattr__(self, 'container', container)
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diff changeset
1285
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1286 @property
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1287 def parent(self):
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1288 """
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1289 The parent folder of this folder. The parent of the root folder is
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diff changeset
1290 ``None``.
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1291
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1292 :rtype: :class:`~.Folder`
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1293 :return: the parent of this folder
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1294 """
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1295 if self._cached_parent is None:
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1296 object.__setattr__(self,
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1297 '_cached_parent',
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1298 self._get_parent())
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1299 return self._cached_parent
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1300
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1301 def _get_parent(self):
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1302 """
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1303 Return the parent folder of this folder.
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1304 """
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1305 parent_id = self.wrapped['parent_id']
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1306 if parent_id is None:
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1307 return None
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1308 return self.container.get_folder(parent_id)
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1309
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1310 @property
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1311 def gi_module(self):
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1312 return self.gi.libraries
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1313
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1314 @property
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1315 def container_id(self):
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1316 """
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1317 Deprecated property.
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1318
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1319 Id of the folder container. Use :attr:`.container.id` instead.
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1320 """
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1321 return self.container.id
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1322
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1323 def refresh(self):
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1324 """
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1325 Re-fetch the attributes pertaining to this object.
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1326
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1327 Returns: self
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1328 """
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1329 f_dict = self.gi.gi.libraries.show_folder(self.container.id, self.id)
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1330 self.__init__(f_dict, self.container, gi=self.gi)
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1331 return self
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1332
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1333
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1334 class Tool(Wrapper):
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1335 """
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1336 Maps to a Galaxy tool.
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1337 """
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1338 BASE_ATTRS = Wrapper.BASE_ATTRS + ('version',)
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1339 POLLING_INTERVAL = 10 # for output state monitoring
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1340
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1341 def __init__(self, t_dict, gi=None):
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1342 super().__init__(t_dict, gi=gi)
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1343
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1344 @property
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1345 def gi_module(self):
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1346 return self.gi.tools
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1347
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1348 def run(self, inputs, history, wait=False,
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1349 polling_interval=POLLING_INTERVAL):
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1350 """
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1351 Execute this tool in the given history with inputs from dict
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1352 ``inputs``.
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1353
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1354 :type inputs: dict
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1355 :param inputs: dictionary of input datasets and parameters for
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1356 the tool (see below)
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1357
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1358 :type history: :class:`History`
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1359 :param history: the history where to execute the tool
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1360
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1361 :type wait: bool
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1362 :param wait: whether to wait while the returned datasets are
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1363 in a pending state
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1364
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1365 :type polling_interval: float
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1366 :param polling_interval: polling interval in seconds
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1367
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1368 :rtype: list of :class:`HistoryDatasetAssociation`
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1369 :return: list of output datasets
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1370
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1371 The ``inputs`` dict should contain input datasets and parameters
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1372 in the (largely undocumented) format used by the Galaxy API.
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1373 Some examples can be found in `Galaxy's API test suite
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1374 <https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy_test/api/test_tools.py>`_.
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1375 The value of an input dataset can also be a :class:`Dataset`
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1376 object, which will be automatically converted to the needed
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1377 format.
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1378 """
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1379 for k, v in inputs.items():
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1380 if isinstance(v, Dataset):
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1381 inputs[k] = {'src': v.SRC, 'id': v.id}
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1382 out_dict = self.gi.gi.tools.run_tool(history.id, self.id, inputs)
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1383 outputs = [history.get_dataset(_['id']) for _ in out_dict['outputs']]
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1384 if wait:
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1385 self.gi._wait_datasets(outputs, polling_interval=polling_interval)
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1386 return outputs
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1387
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1388
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1389 class Job(Wrapper):
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1390 """
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1391 Maps to a Galaxy job.
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1392 """
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1393 BASE_ATTRS = ('id', 'state')
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1394
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1395 def __init__(self, j_dict, gi=None):
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1396 super().__init__(j_dict, gi=gi)
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1397
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1398 @property
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1399 def gi_module(self):
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1400 return self.gi.jobs
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1401
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1402
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1403 class Preview(Wrapper, metaclass=abc.ABCMeta):
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1404 """
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1405 Abstract base class for Galaxy entity 'previews'.
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1406
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1407 Classes derived from this one model the short summaries returned
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1408 by global getters such as ``/api/libraries``.
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1409 """
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1410 BASE_ATTRS = Wrapper.BASE_ATTRS + ('deleted',)
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1411
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1412 @abc.abstractmethod
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1413 def __init__(self, pw_dict, gi=None):
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1414 super().__init__(pw_dict, gi=gi)
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1415
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1416
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1417 class LibraryPreview(Preview):
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1418 """
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1419 Models Galaxy library 'previews'.
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1420
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1421 Instances of this class wrap dictionaries obtained by getting
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1422 ``/api/libraries`` from Galaxy.
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1423 """
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1424 def __init__(self, pw_dict, gi=None):
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1425 super().__init__(pw_dict, gi=gi)
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1426
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1427 @property
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1428 def gi_module(self):
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1429 return self.gi.libraries
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1430
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1431
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1432 class HistoryPreview(Preview):
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1433 """
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1434 Models Galaxy history 'previews'.
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1435
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1436 Instances of this class wrap dictionaries obtained by getting
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1437 ``/api/histories`` from Galaxy.
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1438 """
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1439 BASE_ATTRS = Preview.BASE_ATTRS + ('tags',)
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1440
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1441 def __init__(self, pw_dict, gi=None):
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1442 super().__init__(pw_dict, gi=gi)
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1443
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1444 @property
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1445 def gi_module(self):
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1446 return self.gi.histories
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1447
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1448
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1449 class WorkflowPreview(Preview):
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1450 """
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1451 Models Galaxy workflow 'previews'.
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1452
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1453 Instances of this class wrap dictionaries obtained by getting
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1454 ``/api/workflows`` from Galaxy.
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1455 """
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1456 BASE_ATTRS = Preview.BASE_ATTRS + ('published', 'tags')
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1457
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1458 def __init__(self, pw_dict, gi=None):
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1459 super().__init__(pw_dict, gi=gi)
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1460
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1461 @property
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1462 def gi_module(self):
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1463 return self.gi.workflows
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1464
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1465
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1466 class JobPreview(Preview):
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1467 """
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1468 Models Galaxy job 'previews'.
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1469
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1470 Instances of this class wrap dictionaries obtained by getting
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1471 ``/api/jobs`` from Galaxy.
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1472 """
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1473 BASE_ATTRS = ('id', 'state')
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1474
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1475 def __init__(self, pw_dict, gi=None):
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1476 super().__init__(pw_dict, gi=gi)
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1477
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1478 @property
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1479 def gi_module(self):
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1480 return self.gi.jobs