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

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planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
author bcclaywell
date Mon, 12 Oct 2015 17:43:33 -0400
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1 # 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 collections
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9 import json
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10
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11 from six.moves import http_client
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12 import six
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13
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14 import bioblend
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15
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16 __all__ = [
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17 'Wrapper',
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18 'Step',
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19 'Workflow',
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20 'ContentInfo',
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21 'LibraryContentInfo',
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22 'HistoryContentInfo',
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23 'DatasetContainer',
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24 'History',
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25 'Library',
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26 'Folder',
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27 'Dataset',
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28 'HistoryDatasetAssociation',
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29 'LibraryDatasetDatasetAssociation',
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30 'LibraryDataset',
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31 'Tool',
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32 'Job',
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33 'Preview',
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34 'LibraryPreview',
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35 'HistoryPreview',
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36 'WorkflowPreview',
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37 ]
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38
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39
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40 @six.add_metaclass(abc.ABCMeta)
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41 class Wrapper(object):
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42 """
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43 Abstract base class for Galaxy entity wrappers.
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44
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45 Wrapper instances wrap deserialized JSON dictionaries such as the
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46 ones obtained by the Galaxy web API, converting key-based access to
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47 attribute-based access (e.g., ``library['name'] -> library.name``).
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48
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49 Dict keys that are converted to attributes are listed in the
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50 ``BASE_ATTRS`` class variable: this is the 'stable' interface.
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51 Note that the wrapped dictionary is accessible via the ``wrapped``
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52 attribute.
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53 """
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54 BASE_ATTRS = ('id', 'name')
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55
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56 @abc.abstractmethod
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57 def __init__(self, wrapped, parent=None, gi=None):
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58 """
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59 :type wrapped: dict
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60 :param wrapped: JSON-serializable dictionary
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61
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62 :type parent: :class:`Wrapper`
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63 :param parent: the parent of this wrapper
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64
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65 :type gi: :class:`GalaxyInstance`
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66 :param gi: the GalaxyInstance through which we can access this wrapper
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67 """
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68 if not isinstance(wrapped, collections.Mapping):
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69 raise TypeError('wrapped object must be a mapping type')
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70 # loads(dumps(x)) is a bit faster than deepcopy and allows type checks
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71 try:
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72 dumped = json.dumps(wrapped)
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73 except (TypeError, ValueError):
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74 raise ValueError('wrapped object must be JSON-serializable')
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75 object.__setattr__(self, 'wrapped', json.loads(dumped))
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76 for k in self.BASE_ATTRS:
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77 object.__setattr__(self, k, self.wrapped.get(k))
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78 object.__setattr__(self, '_cached_parent', parent)
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79 object.__setattr__(self, 'is_modified', False)
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80 object.__setattr__(self, 'gi', gi)
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81
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82 @abc.abstractproperty
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83 def gi_module(self):
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84 """
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85 The GalaxyInstance module that deals with objects of this type.
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86 """
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87 pass
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88
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89 @property
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90 def parent(self):
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91 """
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92 The parent of this wrapper.
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93 """
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94 return self._cached_parent
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95
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96 @property
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97 def is_mapped(self):
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98 """
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99 ``True`` if this wrapper is mapped to an actual Galaxy entity.
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100 """
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101 return self.id is not None
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102
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103 def unmap(self):
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104 """
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105 Disconnect this wrapper from Galaxy.
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106 """
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107 object.__setattr__(self, 'id', None)
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108
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109 def clone(self):
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110 """
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111 Return an independent copy of this wrapper.
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112 """
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113 return self.__class__(self.wrapped)
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114
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115 def touch(self):
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116 """
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117 Mark this wrapper as having been modified since its creation.
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118 """
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119 object.__setattr__(self, 'is_modified', True)
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120 if self.parent:
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121 self.parent.touch()
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122
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123 def to_json(self):
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124 """
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125 Return a JSON dump of this wrapper.
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126 """
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127 return json.dumps(self.wrapped)
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128
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129 @classmethod
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130 def from_json(cls, jdef):
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131 """
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132 Build a new wrapper from a JSON dump.
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133 """
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134 return cls(json.loads(jdef))
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135
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136 # FIXME: things like self.x[0] = 'y' do NOT call self.__setattr__
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137 def __setattr__(self, name, value):
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138 if name not in self.wrapped:
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139 raise AttributeError("can't set attribute")
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140 else:
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141 self.wrapped[name] = value
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142 object.__setattr__(self, name, value)
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143 self.touch()
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144
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145 def __repr__(self):
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146 return "%s(%r)" % (self.__class__.__name__, self.wrapped)
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147
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148
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149 class Step(Wrapper):
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150 """
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151 Abstract base class for workflow steps.
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152
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153 Steps are the main building blocks of a Galaxy workflow. A step
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154 can refer to either an input dataset (type 'data_input`) or a
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155 computational tool (type 'tool`).
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156 """
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157 BASE_ATTRS = Wrapper.BASE_ATTRS + (
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158 'input_steps', 'tool_id', 'tool_inputs', 'tool_version', 'type'
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159 )
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160
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161 def __init__(self, step_dict, parent):
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162 super(Step, self).__init__(step_dict, parent=parent, gi=parent.gi)
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163 if self.type == 'tool' and self.tool_inputs:
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164 for k, v in six.iteritems(self.tool_inputs):
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165 self.tool_inputs[k] = json.loads(v)
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166
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167 @property
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168 def gi_module(self):
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169 return self.gi.workflows
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170
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171
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172 class Workflow(Wrapper):
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173 """
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174 Workflows represent ordered sequences of computations on Galaxy.
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175
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176 A workflow defines a sequence of steps that produce one or more
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177 results from an input dataset.
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178 """
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179 BASE_ATTRS = Wrapper.BASE_ATTRS + (
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180 'deleted', 'inputs', 'published', 'steps', 'tags'
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181 )
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182 POLLING_INTERVAL = 10 # for output state monitoring
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183
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184 def __init__(self, wf_dict, gi=None):
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185 super(Workflow, self).__init__(wf_dict, gi=gi)
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186 missing_ids = []
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187 if gi:
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188 tools_list_by_id = [t.id for t in gi.tools.get_previews()]
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189 else:
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190 tools_list_by_id = []
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191 for k, v in six.iteritems(self.steps):
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192 # convert step ids to str for consistency with outer keys
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193 v['id'] = str(v['id'])
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194 for i in six.itervalues(v['input_steps']):
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195 i['source_step'] = str(i['source_step'])
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196 step = self._build_step(v, self)
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197 self.steps[k] = step
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198 if step.type == 'tool':
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199 if not step.tool_inputs or step.tool_id not in tools_list_by_id:
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200 missing_ids.append(k)
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201 input_labels_to_ids = {}
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202 for id_, d in six.iteritems(self.inputs):
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203 input_labels_to_ids.setdefault(d['label'], set()).add(id_)
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204 tool_labels_to_ids = {}
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205 for s in six.itervalues(self.steps):
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206 if s.type == 'tool':
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207 tool_labels_to_ids.setdefault(s.tool_id, set()).add(s.id)
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208 object.__setattr__(self, 'input_labels_to_ids', input_labels_to_ids)
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209 object.__setattr__(self, 'tool_labels_to_ids', tool_labels_to_ids)
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210 dag, inv_dag = self._get_dag()
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211 heads, tails = set(dag), set(inv_dag)
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212 object.__setattr__(self, 'dag', dag)
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213 object.__setattr__(self, 'inv_dag', inv_dag)
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214 object.__setattr__(self, 'source_ids', heads - tails)
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215 assert self.data_input_ids == set(self.inputs)
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216 object.__setattr__(self, 'sink_ids', tails - heads)
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217 object.__setattr__(self, 'missing_ids', missing_ids)
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218
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219 @property
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220 def gi_module(self):
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221 return self.gi.workflows
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222
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223 def _get_dag(self):
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224 """
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225 Return the workflow's DAG.
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226
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227 For convenience, this method computes a 'direct' (step =>
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228 successors) and an 'inverse' (step => predecessors)
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229 representation of the same DAG.
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230
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231 For instance, a workflow with a single tool *c*, two inputs
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232 *a, b* and three outputs *d, e, f* is represented by (direct)::
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233
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234 {'a': {'c'}, 'b': {'c'}, 'c': set(['d', 'e', 'f'])}
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235
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236 and by (inverse)::
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237
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238 {'c': set(['a', 'b']), 'd': {'c'}, 'e': {'c'}, 'f': {'c'}}
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239 """
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240 dag, inv_dag = {}, {}
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241 for s in six.itervalues(self.steps):
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242 for i in six.itervalues(s.input_steps):
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243 head, tail = i['source_step'], s.id
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244 dag.setdefault(head, set()).add(tail)
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245 inv_dag.setdefault(tail, set()).add(head)
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246 return dag, inv_dag
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247
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248 def sorted_step_ids(self):
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249 """
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250 Return a topological sort of the workflow's DAG.
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251 """
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252 ids = []
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253 source_ids = self.source_ids.copy()
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254 inv_dag = dict((k, v.copy()) for k, v in six.iteritems(self.inv_dag))
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255 while source_ids:
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256 head = source_ids.pop()
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257 ids.append(head)
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258 for tail in self.dag.get(head, []):
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259 incoming = inv_dag[tail]
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260 incoming.remove(head)
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261 if not incoming:
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262 source_ids.add(tail)
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263 return ids
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264
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265 @staticmethod
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266 def _build_step(step_dict, parent):
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267 """
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268 Return a Step object for the given parameters.
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269 """
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270 try:
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271 stype = step_dict['type']
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272 except KeyError:
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273 raise ValueError('not a step dict')
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274 if stype not in set(['data_input', 'tool']):
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275 raise ValueError('unknown step type: %r' % (stype,))
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276 return Step(step_dict, parent)
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277
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278 @property
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279 def data_input_ids(self):
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280 """
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281 Return the list of data input steps for this workflow.
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282 """
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283 return set(id_ for id_, s in six.iteritems(self.steps)
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284 if s.type == 'data_input')
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285
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286 @property
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287 def tool_ids(self):
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288 """
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289 Return the list of tool steps for this workflow.
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290 """
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291 return set(id_ for id_, s in six.iteritems(self.steps)
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292 if s.type == 'tool')
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293
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294 @property
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295 def input_labels(self):
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296 """
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297 Return the labels of this workflow's input steps.
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298 """
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299 return set(self.input_labels_to_ids)
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300
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301 @property
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302 def is_runnable(self):
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303 """
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304 Return True if the workflow can be run on Galaxy.
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305
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306 A workflow is considered runnable on a Galaxy instance if all
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307 of the tools it uses are installed in that instance.
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308 """
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309 return not self.missing_ids
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310
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311 def convert_input_map(self, input_map):
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312 """
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313 Convert ``input_map`` to the format required by the Galaxy web API.
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314
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315 :type input_map: dict
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316 :param input_map: a mapping from input labels to datasets
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317
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318 :rtype: dict
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319 :return: a mapping from input slot ids to dataset ids in the
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320 format required by the Galaxy web API.
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321 """
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322 m = {}
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323 for label, slot_ids in six.iteritems(self.input_labels_to_ids):
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324 datasets = input_map.get(label, [])
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325 if not isinstance(datasets, collections.Iterable):
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326 datasets = [datasets]
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327 if len(datasets) < len(slot_ids):
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328 raise RuntimeError('not enough datasets for "%s"' % label)
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329 for id_, ds in zip(slot_ids, datasets):
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330 m[id_] = {'id': ds.id, 'src': ds.SRC}
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331 return m
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332
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333 def preview(self):
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334 getf = self.gi.workflows.get_previews
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335 try:
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336 p = [_ for _ in getf(published=True) if _.id == self.id][0]
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337 except IndexError:
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338 raise ValueError('no object for id %s' % self.id)
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339 return p
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340
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341 def run(self, input_map=None, history='', params=None, import_inputs=False,
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342 replacement_params=None, wait=False,
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343 polling_interval=POLLING_INTERVAL, break_on_error=True):
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344 """
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345 Run the workflow in the current Galaxy instance.
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346
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347 :type input_map: dict
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348 :param input_map: a mapping from workflow input labels to
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349 datasets, e.g.: ``dict(zip(workflow.input_labels,
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350 library.get_datasets()))``
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351
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352 :type history: :class:`History` or str
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353 :param history: either a valid history object (results will be
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354 stored there) or a string (a new history will be created with
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355 the given name).
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356
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357 :type params: :class:`~collections.Mapping`
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358 :param params: parameter settings for workflow steps (see below)
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359
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360 :type import_inputs: bool
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361 :param import_inputs: If ``True``, workflow inputs will be imported into
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362 the history; if ``False``, only workflow outputs will be visible in
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363 the history.
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364
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365 :type replacement_params: :class:`~collections.Mapping`
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366 :param replacement_params: pattern-based replacements for
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367 post-job actions (see the docs for
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368 :meth:`~bioblend.galaxy.workflows.WorkflowClient.run_workflow`)
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369
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370 :type wait: bool
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371 :param wait: whether to wait while the returned datasets are
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372 in a pending state
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373
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374 :type polling_interval: float
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375 :param polling_interval: polling interval in seconds
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376
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377 :type break_on_error: bool
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378 :param break_on_error: whether to break as soon as at least one
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379 of the returned datasets is in the 'error' state
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380
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381 :rtype: tuple
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382 :return: list of output datasets, output history
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383
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384 The ``params`` dict should be structured as follows::
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385
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386 PARAMS = {STEP_ID: PARAM_DICT, ...}
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387 PARAM_DICT = {NAME: VALUE, ...}
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388
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389 For backwards compatibility, the following (deprecated) format is
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390 also supported::
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391
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392 PARAMS = {TOOL_ID: PARAM_DICT, ...}
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393
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394 in which case PARAM_DICT affects all steps with the given tool id.
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395 If both by-tool-id and by-step-id specifications are used, the
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396 latter takes precedence.
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397
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398 Finally (again, for backwards compatibility), PARAM_DICT can also
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399 be specified as::
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400
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401 PARAM_DICT = {'param': NAME, 'value': VALUE}
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402
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403 Note that this format allows only one parameter to be set per step.
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404
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405 Example: set 'a' to 1 for the third workflow step::
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406
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407 params = {workflow.steps[2].id: {'a': 1}}
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408
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409 .. warning::
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410
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411 This is a blocking operation that can take a very long time. If
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412 ``wait`` is set to ``False``, the method will return as soon as the
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413 workflow has been *scheduled*, otherwise it will wait until the
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414 workflow has been *run*. With a large number of steps, however, the
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415 delay may not be negligible even in the former case (e.g. minutes for
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416 100 steps).
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417 """
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418 if not self.is_mapped:
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419 raise RuntimeError('workflow is not mapped to a Galaxy object')
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420 if not self.is_runnable:
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421 raise RuntimeError('workflow has missing tools: %s' % ', '.join(
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422 '%s[%s]' % (self.steps[_].tool_id, _)
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423 for _ in self.missing_ids))
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424 kwargs = {
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425 'dataset_map': self.convert_input_map(input_map or {}),
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426 'params': params,
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427 'import_inputs_to_history': import_inputs,
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428 'replacement_params': replacement_params,
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429 }
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430 if isinstance(history, History):
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431 try:
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432 kwargs['history_id'] = history.id
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433 except AttributeError:
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434 raise RuntimeError('history does not have an id')
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435 elif isinstance(history, six.string_types):
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436 kwargs['history_name'] = history
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437 else:
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438 raise TypeError(
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439 'history must be either a history wrapper or a string')
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440 res = self.gi.gi.workflows.run_workflow(self.id, **kwargs)
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441 # res structure: {'history': HIST_ID, 'outputs': [DS_ID, DS_ID, ...]}
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442 out_hist = self.gi.histories.get(res['history'])
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443 assert set(res['outputs']).issubset(out_hist.dataset_ids)
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444 outputs = [out_hist.get_dataset(_) for _ in res['outputs']]
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445
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446 if wait:
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447 self.gi._wait_datasets(outputs, polling_interval=polling_interval,
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448 break_on_error=break_on_error)
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449 return outputs, out_hist
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450
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451 def export(self):
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452 """
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453 Export a re-importable representation of the workflow.
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454
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455 :rtype: dict
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456 :return: a JSON-serializable dump of the workflow
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457 """
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458 return self.gi.gi.workflows.export_workflow_json(self.id)
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459
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460 def delete(self):
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461 """
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462 Delete this workflow.
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463
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464 .. warning::
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465 Deleting a workflow is irreversible - all of the data from
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466 the workflow will be permanently deleted.
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467 """
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468 self.gi.workflows.delete(id_=self.id)
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469 self.unmap()
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470
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471
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472 @six.add_metaclass(abc.ABCMeta)
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473 class Dataset(Wrapper):
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474 """
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475 Abstract base class for Galaxy datasets.
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476 """
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477 BASE_ATTRS = Wrapper.BASE_ATTRS + (
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478 'data_type', 'file_name', 'file_size', 'state', 'deleted', 'file_ext'
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479 )
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480 POLLING_INTERVAL = 1 # for state monitoring
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481
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482 @abc.abstractmethod
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483 def __init__(self, ds_dict, container, gi=None):
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484 super(Dataset, self).__init__(ds_dict, gi=gi)
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485 object.__setattr__(self, 'container', container)
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486
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487 @property
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488 def container_id(self):
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489 """
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490 Deprecated property.
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491
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492 Id of the dataset container. Use :attr:`.container.id` instead.
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493 """
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494 return self.container.id
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495
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496 @abc.abstractproperty
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497 def _stream_url(self):
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498 """
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499 Return the URL to stream this dataset.
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500 """
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501 pass
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502
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503 def get_stream(self, chunk_size=bioblend.CHUNK_SIZE):
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504 """
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505 Open dataset for reading and return an iterator over its contents.
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506
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507 :type chunk_size: int
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508 :param chunk_size: read this amount of bytes at a time
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509
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510 .. warning::
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511
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512 Due to a change in the Galaxy API endpoint, this method does
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513 not work on :class:`LibraryDataset` instances with Galaxy
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514 ``release_2014.06.02``. Methods that delegate work to this one
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515 are also affected: :meth:`peek`, :meth:`download` and
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516 :meth:`get_contents`.
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517 """
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518 kwargs = {'stream': True}
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519 if isinstance(self, LibraryDataset):
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520 kwargs['params'] = {'ld_ids%5B%5D': self.id}
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521 r = self.gi.gi.make_get_request(self._stream_url, **kwargs)
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522 if isinstance(self, LibraryDataset) and r.status_code == 500:
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523 # compatibility with older Galaxy releases
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524 kwargs['params'] = {'ldda_ids%5B%5D': self.id}
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525 r = self.gi.gi.make_get_request(self._stream_url, **kwargs)
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526 r.raise_for_status()
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527 return r.iter_content(chunk_size) # FIXME: client can't close r
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528
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529 def peek(self, chunk_size=bioblend.CHUNK_SIZE):
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530 """
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531 Open dataset for reading and return the first chunk.
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532
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533 See :meth:`.get_stream` for param info.
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534 """
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535 try:
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536 return next(self.get_stream(chunk_size=chunk_size))
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537 except StopIteration:
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538 return b''
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539
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540 def download(self, file_object, chunk_size=bioblend.CHUNK_SIZE):
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541 """
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542 Open dataset for reading and save its contents to ``file_object``.
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543
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544 :type file_object: file
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545 :param file_object: output file object
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546
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547 See :meth:`.get_stream` for info on other params.
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548 """
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549 for chunk in self.get_stream(chunk_size=chunk_size):
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550 file_object.write(chunk)
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551
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552 def get_contents(self, chunk_size=bioblend.CHUNK_SIZE):
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553 """
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554 Open dataset for reading and return its **full** contents.
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555
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556 See :meth:`.get_stream` for param info.
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557 """
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558 return b''.join(self.get_stream(chunk_size=chunk_size))
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559
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560 def refresh(self):
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561 """
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562 Re-fetch the attributes pertaining to this object.
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563
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564 Returns: self
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565 """
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566 gi_client = getattr(self.gi.gi, self.container.API_MODULE)
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567 ds_dict = gi_client.show_dataset(self.container.id, self.id)
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568 self.__init__(ds_dict, self.container, self.gi)
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569 return self
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570
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571 def wait(self, polling_interval=POLLING_INTERVAL, break_on_error=True):
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572 """
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573 Wait for this dataset to come out of the pending states.
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574
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575 :type polling_interval: float
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576 :param polling_interval: polling interval in seconds
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577
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578 :type break_on_error: bool
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579 :param break_on_error: if ``True``, raise a RuntimeError exception if
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580 the dataset ends in the 'error' state.
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581
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582 .. warning::
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583
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584 This is a blocking operation that can take a very long time. Also,
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585 note that this method does not return anything; however, this dataset
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586 is refreshed (possibly multiple times) during the execution.
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587 """
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588 self.gi._wait_datasets([self], polling_interval=polling_interval,
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589 break_on_error=break_on_error)
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590
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591
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592 class HistoryDatasetAssociation(Dataset):
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593 """
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594 Maps to a Galaxy ``HistoryDatasetAssociation``.
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595 """
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596 BASE_ATTRS = Dataset.BASE_ATTRS + ('tags', 'visible')
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597 SRC = 'hda'
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598
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599 def __init__(self, ds_dict, container, gi=None):
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600 super(HistoryDatasetAssociation, self).__init__(
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601 ds_dict, container, gi=gi)
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602
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603 @property
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604 def gi_module(self):
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605 return self.gi.histories
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606
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607 @property
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608 def _stream_url(self):
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609 base_url = self.gi.gi._make_url(
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610 self.gi.gi.histories, module_id=self.container.id, contents=True)
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611 return "%s/%s/display" % (base_url, self.id)
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612
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613 def delete(self):
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614 """
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615 Delete this dataset.
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616 """
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617 self.gi.gi.histories.delete_dataset(self.container.id, self.id)
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618 self.container.refresh()
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619 self.refresh()
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620
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621
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622 class LibRelatedDataset(Dataset):
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623 """
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624 Base class for LibraryDatasetDatasetAssociation and LibraryDataset classes.
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625 """
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626
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627 def __init__(self, ds_dict, container, gi=None):
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628 super(LibRelatedDataset, self).__init__(ds_dict, container, gi=gi)
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629
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630 @property
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631 def gi_module(self):
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632 return self.gi.libraries
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633
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634 @property
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635 def _stream_url(self):
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636 base_url = self.gi.gi._make_url(self.gi.gi.libraries)
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637 return "%s/datasets/download/uncompressed" % base_url
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638
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639
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640 class LibraryDatasetDatasetAssociation(LibRelatedDataset):
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641 """
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642 Maps to a Galaxy ``LibraryDatasetDatasetAssociation``.
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643 """
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644 SRC = 'ldda'
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645
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646
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647 class LibraryDataset(LibRelatedDataset):
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648 """
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649 Maps to a Galaxy ``LibraryDataset``.
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650 """
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651 SRC = 'ld'
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652
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653 def delete(self, purged=False):
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654 """
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655 Delete this library dataset.
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656
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657 :type purged: bool
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658 :param purged: if ``True``, also purge (permanently delete) the dataset
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659 """
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660 self.gi.gi.libraries.delete_library_dataset(
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661 self.container.id, self.id, purged=purged)
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662 self.container.refresh()
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663 self.refresh()
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664
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665
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666 @six.add_metaclass(abc.ABCMeta)
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667 class ContentInfo(Wrapper):
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668 """
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669 Instances of this class wrap dictionaries obtained by getting
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670 ``/api/{histories,libraries}/<ID>/contents`` from Galaxy.
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671 """
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672 BASE_ATTRS = Wrapper.BASE_ATTRS + ('type',)
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673
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674 @abc.abstractmethod
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675 def __init__(self, info_dict, gi=None):
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676 super(ContentInfo, self).__init__(info_dict, gi=gi)
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677
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678
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679 class LibraryContentInfo(ContentInfo):
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680 """
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681 Instances of this class wrap dictionaries obtained by getting
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682 ``/api/libraries/<ID>/contents`` from Galaxy.
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683 """
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684 def __init__(self, info_dict, gi=None):
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685 super(LibraryContentInfo, self).__init__(info_dict, gi=gi)
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686
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687 @property
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688 def gi_module(self):
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689 return self.gi.libraries
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690
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691
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692 class HistoryContentInfo(ContentInfo):
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693 """
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694 Instances of this class wrap dictionaries obtained by getting
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695 ``/api/histories/<ID>/contents`` from Galaxy.
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696 """
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697 BASE_ATTRS = ContentInfo.BASE_ATTRS + ('deleted', 'state', 'visible')
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698
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699 def __init__(self, info_dict, gi=None):
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700 super(HistoryContentInfo, self).__init__(info_dict, gi=gi)
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701
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702 @property
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703 def gi_module(self):
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704 return self.gi.histories
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705
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706
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707 @six.add_metaclass(abc.ABCMeta)
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708 class DatasetContainer(Wrapper):
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709 """
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710 Abstract base class for dataset containers (histories and libraries).
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711 """
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712 BASE_ATTRS = Wrapper.BASE_ATTRS + ('deleted',)
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713
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714 @abc.abstractmethod
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715 def __init__(self, c_dict, content_infos=None, gi=None):
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716 """
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717 :type content_infos: list of :class:`ContentInfo`
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718 :param content_infos: info objects for the container's contents
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719 """
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720 super(DatasetContainer, self).__init__(c_dict, gi=gi)
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721 if content_infos is None:
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722 content_infos = []
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723 object.__setattr__(self, 'content_infos', content_infos)
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724
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725 @property
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726 def dataset_ids(self):
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727 """
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728 Return the ids of the contained datasets.
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729 """
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730 return [_.id for _ in self.content_infos if _.type == 'file']
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731
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732 def preview(self):
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733 getf = self.gi_module.get_previews
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734 # self.state could be stale: check both regular and deleted containers
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735 try:
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736 p = [_ for _ in getf() if _.id == self.id][0]
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737 except IndexError:
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738 try:
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739 p = [_ for _ in getf(deleted=True) if _.id == self.id][0]
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740 except IndexError:
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741 raise ValueError('no object for id %s' % self.id)
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742 return p
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743
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744 def refresh(self):
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745 """
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746 Re-fetch the attributes pertaining to this object.
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747
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748 Returns: self
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749 """
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750 fresh = self.gi_module.get(self.id)
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751 self.__init__(
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752 fresh.wrapped, content_infos=fresh.content_infos, gi=self.gi)
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753 return self
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754
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755 def get_dataset(self, ds_id):
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756 """
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757 Retrieve the dataset corresponding to the given id.
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758
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759 :type ds_id: str
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760 :param ds_id: dataset id
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761
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762 :rtype: :class:`~.HistoryDatasetAssociation` or
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763 :class:`~.LibraryDataset`
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764 :return: the dataset corresponding to ``ds_id``
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765 """
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766 gi_client = getattr(self.gi.gi, self.API_MODULE)
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767 ds_dict = gi_client.show_dataset(self.id, ds_id)
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768 return self.DS_TYPE(ds_dict, self, gi=self.gi)
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769
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770 def get_datasets(self, name=None):
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771 """
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772 Get all datasets contained inside this dataset container.
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diff changeset
773
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774 :type name: str
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775 :param name: return only datasets with this name
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776
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777 :rtype: list of :class:`~.HistoryDatasetAssociation` or list of
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778 :class:`~.LibraryDataset`
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779 :return: datasets with the given name contained inside this
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780 container
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diff changeset
781
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782 .. note::
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783
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784 when filtering library datasets by name, specify their full
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785 paths starting from the library's root folder, e.g.,
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786 ``/seqdata/reads.fastq``. Full paths are available through
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787 the ``content_infos`` attribute of
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788 :class:`~.Library` objects.
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789 """
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790 if name is None:
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791 ds_ids = self.dataset_ids
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792 else:
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793 ds_ids = [_.id for _ in self.content_infos if _.name == name]
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794 return [self.get_dataset(_) for _ in ds_ids]
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795
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796
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797 class History(DatasetContainer):
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798 """
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799 Maps to a Galaxy history.
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800 """
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801 BASE_ATTRS = DatasetContainer.BASE_ATTRS + ('annotation', 'state', 'state_ids', 'state_details', 'tags')
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802 DS_TYPE = HistoryDatasetAssociation
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803 CONTENT_INFO_TYPE = HistoryContentInfo
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804 API_MODULE = 'histories'
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805
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806 def __init__(self, hist_dict, content_infos=None, gi=None):
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807 super(History, self).__init__(
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808 hist_dict, content_infos=content_infos, gi=gi)
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809
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810 @property
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811 def gi_module(self):
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812 return self.gi.histories
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813
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814 def update(self, name=None, annotation=None, **kwds):
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815 """
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816 Update history metadata information. Some of the attributes that can be
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817 modified are documented below.
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818
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819 :type name: str
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820 :param name: Replace history name with the given string
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821
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822 :type annotation: str
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823 :param annotation: Replace history annotation with the given string
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824
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825 :type deleted: bool
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826 :param deleted: Mark or unmark history as deleted
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827
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828 :type published: bool
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829 :param published: Mark or unmark history as published
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830
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831 :type importable: bool
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832 :param importable: Mark or unmark history as importable
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833
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834 :type tags: list
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835 :param tags: Replace history tags with the given list
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836 """
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837 # TODO: wouldn't it be better if name and annotation were attributes?
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838 # TODO: do we need to ensure the attributes of `self` are the same as
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839 # the ones returned by the call to `update_history` below?
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840 res = self.gi.gi.histories.update_history(
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841 self.id, name=name, annotation=annotation, **kwds)
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842 if res != http_client.OK:
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843 raise RuntimeError('failed to update history')
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844 self.refresh()
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845 return self
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846
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847 def delete(self, purge=False):
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848 """
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849 Delete this history.
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850
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851 :type purge: bool
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852 :param purge: if ``True``, also purge (permanently delete) the history
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853
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854 .. note::
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855 For the purge option to work, the Galaxy instance must have the
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856 ``allow_user_dataset_purge`` option set to ``True`` in the
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857 ``config/galaxy.ini`` configuration file.
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858 """
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859 self.gi.histories.delete(id_=self.id, purge=purge)
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860 self.unmap()
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861
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862 def import_dataset(self, lds):
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863 """
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864 Import a dataset into the history from a library.
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865
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866 :type lds: :class:`~.LibraryDataset`
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867 :param lds: the library dataset to import
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868
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869 :rtype: :class:`~.HistoryDatasetAssociation`
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870 :return: the imported history dataset
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871 """
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872 if not self.is_mapped:
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873 raise RuntimeError('history is not mapped to a Galaxy object')
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874 if not isinstance(lds, LibraryDataset):
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875 raise TypeError('lds is not a LibraryDataset')
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876 res = self.gi.gi.histories.upload_dataset_from_library(self.id, lds.id)
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877 if not isinstance(res, collections.Mapping):
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878 raise RuntimeError(
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879 'upload_dataset_from_library: unexpected reply: %r' % res)
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880 self.refresh()
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881 return self.get_dataset(res['id'])
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882
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883 def upload_file(self, path, **kwargs):
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884 """
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885 Upload the file specified by path to this history.
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886
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887 :type path: str
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888 :param path: path of the file to upload
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889
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890 See :meth:`~bioblend.galaxy.tools.ToolClient.upload_file` for
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891 the optional parameters.
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892
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893 :rtype: :class:`~.HistoryDatasetAssociation`
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894 :return: the uploaded dataset
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895 """
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896 out_dict = self.gi.gi.tools.upload_file(path, self.id, **kwargs)
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897 self.refresh()
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898 return self.get_dataset(out_dict['outputs'][0]['id'])
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899
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900 upload_dataset = upload_file
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901
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902 def paste_content(self, content, **kwargs):
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903 """
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904 Upload a string to a new dataset in this history.
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905
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906 :type content: str
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907 :param content: content of the new dataset to upload
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908
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909 See :meth:`~bioblend.galaxy.tools.ToolClient.upload_file` for
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910 the optional parameters (except file_name).
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911
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912 :rtype: :class:`~.HistoryDatasetAssociation`
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913 :return: the uploaded dataset
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914 """
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915 out_dict = self.gi.gi.tools.paste_content(content, self.id, **kwargs)
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916 self.refresh()
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917 return self.get_dataset(out_dict['outputs'][0]['id'])
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918
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919 def export(self, gzip=True, include_hidden=False, include_deleted=False,
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920 wait=False):
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921 """
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922 Start a job to create an export archive for this history. See
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923 :meth:`~bioblend.galaxy.histories.HistoryClient.export_history`
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924 for parameter and return value info.
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925 """
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926 return self.gi.gi.histories.export_history(
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927 self.id,
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928 gzip=gzip,
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929 include_hidden=include_hidden,
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930 include_deleted=include_deleted,
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931 wait=wait)
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932
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933 def download(self, jeha_id, outf, chunk_size=bioblend.CHUNK_SIZE):
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934 """
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935 Download an export archive for this history. Use :meth:`export`
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936 to create an export and get the required ``jeha_id``. See
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937 :meth:`~bioblend.galaxy.histories.HistoryClient.download_history`
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938 for parameter and return value info.
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939 """
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940 return self.gi.gi.histories.download_history(
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941 self.id, jeha_id, outf, chunk_size=chunk_size)
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942
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943
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944 class Library(DatasetContainer):
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945 """
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946 Maps to a Galaxy library.
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947 """
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948 BASE_ATTRS = DatasetContainer.BASE_ATTRS + ('description', 'synopsis')
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949 DS_TYPE = LibraryDataset
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950 CONTENT_INFO_TYPE = LibraryContentInfo
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951 API_MODULE = 'libraries'
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952
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953 def __init__(self, lib_dict, content_infos=None, gi=None):
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954 super(Library, self).__init__(
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955 lib_dict, content_infos=content_infos, gi=gi)
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956
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957 @property
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958 def gi_module(self):
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959 return self.gi.libraries
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960
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961 @property
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962 def folder_ids(self):
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963 """
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964 Return the ids of the contained folders.
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965 """
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966 return [_.id for _ in self.content_infos if _.type == 'folder']
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967
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968 def delete(self):
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969 """
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970 Delete this library.
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971 """
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972 self.gi.libraries.delete(id_=self.id)
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973 self.unmap()
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974
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975 def __pre_upload(self, folder):
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976 """
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977 Return the id of the given folder, after sanity checking.
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978 """
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979 if not self.is_mapped:
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980 raise RuntimeError('library is not mapped to a Galaxy object')
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981 return None if folder is None else folder.id
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982
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983 def upload_data(self, data, folder=None, **kwargs):
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984 """
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985 Upload data to this library.
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986
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987 :type data: str
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988 :param data: dataset contents
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989
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990 :type folder: :class:`~.Folder`
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991 :param folder: a folder object, or ``None`` to upload to the root folder
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992
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993 :rtype: :class:`~.LibraryDataset`
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994 :return: the dataset object that represents the uploaded content
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995
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996 Optional keyword arguments: ``file_type``, ``dbkey``.
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997 """
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998 fid = self.__pre_upload(folder)
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999 res = self.gi.gi.libraries.upload_file_contents(
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1000 self.id, data, folder_id=fid, **kwargs)
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1001 self.refresh()
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1002 return self.get_dataset(res[0]['id'])
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1003
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1004 def upload_from_url(self, url, folder=None, **kwargs):
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1005 """
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1006 Upload data to this library from the given URL.
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1007
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1008 :type url: str
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1009 :param url: URL from which data should be read
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1010
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1011 See :meth:`.upload_data` for info on other params.
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1012 """
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1013 fid = self.__pre_upload(folder)
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1014 res = self.gi.gi.libraries.upload_file_from_url(
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1015 self.id, url, folder_id=fid, **kwargs)
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1016 self.refresh()
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1017 return self.get_dataset(res[0]['id'])
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1018
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1019 def upload_from_local(self, path, folder=None, **kwargs):
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1020 """
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1021 Upload data to this library from a local file.
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1022
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1023 :type path: str
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1024 :param path: local file path from which data should be read
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1025
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1026 See :meth:`.upload_data` for info on other params.
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1027 """
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1028 fid = self.__pre_upload(folder)
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1029 res = self.gi.gi.libraries.upload_file_from_local_path(
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1030 self.id, path, folder_id=fid, **kwargs)
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1031 self.refresh()
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1032 return self.get_dataset(res[0]['id'])
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1033
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1034 def upload_from_galaxy_fs(self, paths, folder=None, link_data_only=None, **kwargs):
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1035 """
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1036 Upload data to this library from filesystem paths on the server.
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1037
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1038 .. note::
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1039 For this method to work, the Galaxy instance must have the
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1040 ``allow_library_path_paste`` option set to ``True`` in the
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1041 ``config/galaxy.ini`` configuration file.
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1042
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1043 :type paths: str or :class:`~collections.Iterable` of str
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1044 :param paths: server-side file paths from which data should be read
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1045
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1046 :type link_data_only: str
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1047 :param link_data_only: either 'copy_files' (default) or
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1048 'link_to_files'. Setting to 'link_to_files' symlinks instead of
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1049 copying the files
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1050
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1051 :rtype: list of :class:`~.LibraryDataset`
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1052 :return: the dataset objects that represent the uploaded content
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1053
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1054 See :meth:`.upload_data` for info on other params.
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1055 """
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1056 fid = self.__pre_upload(folder)
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1057 if isinstance(paths, six.string_types):
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1058 paths = (paths,)
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1059 paths = '\n'.join(paths)
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1060 res = self.gi.gi.libraries.upload_from_galaxy_filesystem(
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1061 self.id, paths, folder_id=fid, link_data_only=link_data_only,
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1062 **kwargs)
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1063 if res is None:
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1064 raise RuntimeError('upload_from_galaxy_filesystem: no reply')
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1065 if not isinstance(res, collections.Sequence):
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1066 raise RuntimeError(
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1067 'upload_from_galaxy_filesystem: unexpected reply: %r' % res)
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1068 new_datasets = [
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1069 self.get_dataset(ds_info['id']) for ds_info in res
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1070 ]
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1071 self.refresh()
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1072 return new_datasets
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1073
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1074 def copy_from_dataset(self, hda, folder=None, message=''):
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1075 """
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1076 Copy a history dataset into this library.
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1077
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1078 :type hda: :class:`~.HistoryDatasetAssociation`
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1079 :param hda: history dataset to copy into the library
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1080
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1081 See :meth:`.upload_data` for info on other params.
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1082 """
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1083 fid = self.__pre_upload(folder)
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1084 res = self.gi.gi.libraries.copy_from_dataset(
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1085 self.id, hda.id, folder_id=fid, message=message)
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1086 self.refresh()
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1087 return self.get_dataset(res['library_dataset_id'])
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1088
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1089 def create_folder(self, name, description=None, base_folder=None):
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1090 """
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1091 Create a folder in this library.
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1092
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1093 :type name: str
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1094 :param name: folder name
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1095
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1096 :type description: str
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1097 :param description: optional folder description
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1098
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1099 :type base_folder: :class:`~.Folder`
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1100 :param base_folder: parent folder, or ``None`` to create in the root
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1101 folder
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1102
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1103 :rtype: :class:`~.Folder`
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1104 :return: the folder just created
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1105 """
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1106 bfid = None if base_folder is None else base_folder.id
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1107 res = self.gi.gi.libraries.create_folder(
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1108 self.id, name, description=description, base_folder_id=bfid)
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1109 self.refresh()
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1110 return self.get_folder(res[0]['id'])
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1111
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1112 def get_folder(self, f_id):
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1113 """
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1114 Retrieve the folder corresponding to the given id.
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1115
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1116 :rtype: :class:`~.Folder`
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1117 :return: the folder corresponding to ``f_id``
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1118 """
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1119 f_dict = self.gi.gi.libraries.show_folder(self.id, f_id)
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1120 return Folder(f_dict, self, gi=self.gi)
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1121
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1122 @property
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1123 def root_folder(self):
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1124 """
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1125 The root folder of this library.
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1126
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1127 :rtype: :class:`~.Folder`
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1128 :return: the root folder of this library
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1129 """
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1130 return self.get_folder(self.gi.gi.libraries._get_root_folder_id(self.id))
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1131
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1132
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1133 class Folder(Wrapper):
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1134 """
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1135 Maps to a folder in a Galaxy library.
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1136 """
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1137 BASE_ATTRS = Wrapper.BASE_ATTRS + ('description', 'deleted', 'item_count')
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1138
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1139 def __init__(self, f_dict, container, gi=None):
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1140 super(Folder, self).__init__(f_dict, gi=gi)
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1141 object.__setattr__(self, 'container', container)
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1142
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1143 @property
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1144 def parent(self):
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1145 """
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parents:
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1146 The parent folder of this folder. The parent of the root folder is
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1147 ``None``.
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1148
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1149 :rtype: :class:`~.Folder`
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1150 :return: the parent of this folder
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1151 """
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1152 if self._cached_parent is None:
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1153 object.__setattr__(self,
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1154 '_cached_parent',
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1155 self._get_parent())
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1156 return self._cached_parent
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1157
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1158 def _get_parent(self):
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1159 """
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1160 Return the parent folder of this folder.
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1161 """
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1162 # Galaxy release_13.04 and earlier does not have parent_id in the folder
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1163 # dictionary, may be implemented by searching for the folder with the
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1164 # correct name
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1165 if 'parent_id' not in self.wrapped:
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1166 raise NotImplementedError('This method has not been implemented for Galaxy release_13.04 and earlier')
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1167 parent_id = self.wrapped['parent_id']
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1168 if parent_id is None:
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1169 return None
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1170 # Galaxy from release_14.02 to release_15.01 returns a dummy parent_id
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1171 # for the root folder instead of None, so check if this is the root
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1172 if self.id == self.gi.gi.libraries._get_root_folder_id(self.container.id):
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1173 return None
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1174 # Galaxy release_13.11 and earlier returns a parent_id without the
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1175 # initial 'F'
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1176 if not parent_id.startswith('F'):
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1177 parent_id = 'F' + parent_id
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1178 return self.container.get_folder(parent_id)
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1179
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1180 @property
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1181 def gi_module(self):
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1182 return self.gi.libraries
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1183
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1184 @property
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1185 def container_id(self):
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1186 """
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1187 Deprecated property.
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1188
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1189 Id of the folder container. Use :attr:`.container.id` instead.
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1190 """
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1191 return self.container.id
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1192
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1193 def refresh(self):
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1194 """
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1195 Re-fetch the attributes pertaining to this object.
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1196
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1197 Returns: self
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1198 """
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1199 f_dict = self.gi.gi.libraries.show_folder(self.container.id, self.id)
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1200 self.__init__(f_dict, self.container, gi=self.gi)
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1201 return self
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1202
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1203
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1204 class Tool(Wrapper):
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1205 """
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1206 Maps to a Galaxy tool.
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1207 """
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1208 BASE_ATTRS = Wrapper.BASE_ATTRS + ('version',)
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1209 POLLING_INTERVAL = 10 # for output state monitoring
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1210
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1211 def __init__(self, t_dict, gi=None):
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1212 super(Tool, self).__init__(t_dict, gi=gi)
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1213
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1214 @property
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1215 def gi_module(self):
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1216 return self.gi.tools
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1217
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1218 def run(self, inputs, history, wait=False,
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1219 polling_interval=POLLING_INTERVAL):
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1220 """
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1221 Execute this tool in the given history with inputs from dict
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1222 ``inputs``.
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1223
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1224 :type inputs: dict
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1225 :param inputs: dictionary of input datasets and parameters for
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1226 the tool (see below)
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1227
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1228 :type history: :class:`History`
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1229 :param history: the history where to execute the tool
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1230
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1231 :type wait: bool
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1232 :param wait: whether to wait while the returned datasets are
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1233 in a pending state
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1234
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1235 :type polling_interval: float
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1236 :param polling_interval: polling interval in seconds
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1237
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1238 :rtype: list of :class:`HistoryDatasetAssociation`
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1239 :return: list of output datasets
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1240
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1241 The ``inputs`` dict should contain input datasets and parameters
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1242 in the (largely undocumented) format used by the Galaxy API.
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1243 Some examples can be found in `Galaxy's API test suite
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1244 <https://bitbucket.org/galaxy/galaxy-central/src/tip/test/api/test_tools.py>`_.
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1245 The value of an input dataset can also be a :class:`Dataset`
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1246 object, which will be automatically converted to the needed
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1247 format.
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1248 """
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1249 for k, v in six.iteritems(inputs):
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1250 if isinstance(v, Dataset):
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1251 inputs[k] = {'src': v.SRC, 'id': v.id}
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1252 out_dict = self.gi.gi.tools.run_tool(history.id, self.id, inputs)
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1253 outputs = [history.get_dataset(_['id']) for _ in out_dict['outputs']]
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1254 if wait:
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1255 self.gi._wait_datasets(outputs, polling_interval=polling_interval)
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1256 return outputs
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1257
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1258
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1259 class Job(Wrapper):
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1260 """
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1261 Maps to a Galaxy job.
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1262 """
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1263 BASE_ATTRS = ('id', 'state')
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1264
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1265 def __init__(self, j_dict, gi=None):
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1266 super(Job, self).__init__(j_dict, gi=gi)
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1267
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1268 @property
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1269 def gi_module(self):
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1270 return self.gi.jobs
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1271
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1272
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1273 @six.add_metaclass(abc.ABCMeta)
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1274 class Preview(Wrapper):
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1275 """
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1276 Abstract base class for Galaxy entity 'previews'.
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1277
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1278 Classes derived from this one model the short summaries returned
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1279 by global getters such as ``/api/libraries``.
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1280 """
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1281 BASE_ATTRS = Wrapper.BASE_ATTRS + ('deleted',)
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1282
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1283 @abc.abstractmethod
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1284 def __init__(self, pw_dict, gi=None):
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1285 super(Preview, self).__init__(pw_dict, gi=gi)
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1286
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1287
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1288 class LibraryPreview(Preview):
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1289 """
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1290 Models Galaxy library 'previews'.
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1291
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1292 Instances of this class wrap dictionaries obtained by getting
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1293 ``/api/libraries`` from Galaxy.
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1294 """
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1295 def __init__(self, pw_dict, gi=None):
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1296 super(LibraryPreview, self).__init__(pw_dict, gi=gi)
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1297
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1298 @property
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1299 def gi_module(self):
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1300 return self.gi.libraries
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1301
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1302
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1303 class HistoryPreview(Preview):
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1304 """
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1305 Models Galaxy history 'previews'.
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1306
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1307 Instances of this class wrap dictionaries obtained by getting
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1308 ``/api/histories`` from Galaxy.
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1309 """
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1310 BASE_ATTRS = Preview.BASE_ATTRS + ('tags',)
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1311
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1312 def __init__(self, pw_dict, gi=None):
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1313 super(HistoryPreview, self).__init__(pw_dict, gi=gi)
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1314
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1315 @property
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1316 def gi_module(self):
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1317 return self.gi.histories
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1318
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1319
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1320 class WorkflowPreview(Preview):
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1321 """
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1322 Models Galaxy workflow 'previews'.
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1323
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1324 Instances of this class wrap dictionaries obtained by getting
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1325 ``/api/workflows`` from Galaxy.
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1326 """
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1327 BASE_ATTRS = Preview.BASE_ATTRS + ('published', 'tags')
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1328
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1329 def __init__(self, pw_dict, gi=None):
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1330 super(WorkflowPreview, self).__init__(pw_dict, gi=gi)
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1331
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1332 @property
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1333 def gi_module(self):
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1334 return self.gi.workflows
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1335
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1336
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1337 class JobPreview(Preview):
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1338 """
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1339 Models Galaxy job 'previews'.
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1340
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1341 Instances of this class wrap dictionaries obtained by getting
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1342 ``/api/jobs`` from Galaxy.
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1343 """
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1344 BASE_ATTRS = ('id', 'state')
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1345
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1346 def __init__(self, pw_dict, gi=None):
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1347 super(JobPreview, self).__init__(pw_dict, gi=gi)
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1348
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1349 @property
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1350 def gi_module(self):
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1351 return self.gi.jobs