guppy_basecaller: env/lib/python3.7/site-packages/bioblend/galaxy/objects/wrappers.py annotate

annotate env/lib/python3.7/site-packages/bioblend/galaxy/objects/wrappers.py @ 4:79f47841a781 draft

"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"

author	shellac
date	Thu, 14 May 2020 16:47:39 -0400
parents	26e78fe6e8c4
children

rev	line source
0 26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1 # pylint: disable=W0622,E1101
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	2
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	3 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	4 A basic object-oriented interface for Galaxy entities.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	5 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	6
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	7 import abc
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	8 import collections
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	9 import json
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	10
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	11 import six
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	12
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	13 import bioblend
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	14
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	15 __all__ = (
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	16 'Wrapper',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	17 'Step',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	18 'Workflow',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	19 'ContentInfo',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	20 'LibraryContentInfo',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	21 'HistoryContentInfo',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	22 'DatasetContainer',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	23 'History',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	24 'Library',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	25 'Folder',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	26 'Dataset',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	27 'HistoryDatasetAssociation',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	28 'DatasetCollection',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	29 'HistoryDatasetCollectionAssociation',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	30 'LibraryDatasetDatasetAssociation',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	31 'LibraryDataset',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	32 'Tool',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	33 'Job',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	34 'Preview',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	35 'LibraryPreview',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	36 'HistoryPreview',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	37 'WorkflowPreview',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	38 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	39
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	40
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	41 @six.add_metaclass(abc.ABCMeta)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	42 class Wrapper(object):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	43 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	44 Abstract base class for Galaxy entity wrappers.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	45
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	46 Wrapper instances wrap deserialized JSON dictionaries such as the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	47 ones obtained by the Galaxy web API, converting key-based access to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	48 attribute-based access (e.g., ``library['name'] -> library.name``).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	49
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	50 Dict keys that are converted to attributes are listed in the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	51 ``BASE_ATTRS`` class variable: this is the 'stable' interface.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	52 Note that the wrapped dictionary is accessible via the ``wrapped``
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	53 attribute.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	54 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	55 BASE_ATTRS = ('id', 'name')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	56
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	57 @abc.abstractmethod
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	58 def __init__(self, wrapped, parent=None, gi=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	59 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	60 :type wrapped: dict
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	61 :param wrapped: JSON-serializable dictionary
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	62
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	63 :type parent: :class:`Wrapper`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	64 :param parent: the parent of this wrapper
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	65
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	66 :type gi: :class:`GalaxyInstance`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	67 :param gi: the GalaxyInstance through which we can access this wrapper
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	68 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	69 if not isinstance(wrapped, collections.Mapping):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	70 raise TypeError('wrapped object must be a mapping type')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	71 # loads(dumps(x)) is a bit faster than deepcopy and allows type checks
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	72 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	73 dumped = json.dumps(wrapped)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	74 except (TypeError, ValueError):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	75 raise ValueError('wrapped object must be JSON-serializable')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	76 object.__setattr__(self, 'wrapped', json.loads(dumped))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	77 for k in self.BASE_ATTRS:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	78 object.__setattr__(self, k, self.wrapped.get(k))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	79 object.__setattr__(self, '_cached_parent', parent)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	80 object.__setattr__(self, 'is_modified', False)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	81 object.__setattr__(self, 'gi', gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	82
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	83 @abc.abstractproperty
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	84 def gi_module(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	85 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	86 The GalaxyInstance module that deals with objects of this type.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	87 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	88 pass
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	89
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	90 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	91 def parent(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	92 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	93 The parent of this wrapper.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	94 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	95 return self._cached_parent
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	96
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	97 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	98 def is_mapped(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	99 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	100 ``True`` if this wrapper is mapped to an actual Galaxy entity.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	101 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	102 return self.id is not None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	103
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	104 def unmap(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	105 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	106 Disconnect this wrapper from Galaxy.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	107 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	108 object.__setattr__(self, 'id', None)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	109
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	110 def clone(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	111 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	112 Return an independent copy of this wrapper.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	113 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	114 return self.__class__(self.wrapped)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	115
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	116 def touch(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	117 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	118 Mark this wrapper as having been modified since its creation.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	119 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	120 object.__setattr__(self, 'is_modified', True)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	121 if self.parent:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	122 self.parent.touch()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	123
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	124 def to_json(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	125 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	126 Return a JSON dump of this wrapper.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	127 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	128 return json.dumps(self.wrapped)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	129
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	130 @classmethod
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	131 def from_json(cls, jdef):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	132 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	133 Build a new wrapper from a JSON dump.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	134 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	135 return cls(json.loads(jdef))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	136
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	137 # FIXME: things like self.x[0] = 'y' do NOT call self.__setattr__
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	138 def __setattr__(self, name, value):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	139 if name not in self.wrapped:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	140 raise AttributeError("can't set attribute")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	141 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	142 self.wrapped[name] = value
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	143 object.__setattr__(self, name, value)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	144 self.touch()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	145
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	146 def __repr__(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	147 return "%s(%r)" % (self.__class__.__name__, self.wrapped)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	148
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	149
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	150 class Step(Wrapper):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	151 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	152 Abstract base class for workflow steps.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	153
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	154 Steps are the main building blocks of a Galaxy workflow. A step can be: an
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	155 input (type 'data_collection_input` or 'data_input`), a computational tool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	156 (type 'tool`) or a pause (type 'pause`).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	157 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	158 BASE_ATTRS = Wrapper.BASE_ATTRS + (
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	159 'input_steps', 'tool_id', 'tool_inputs', 'tool_version', 'type'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	160 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	161
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	162 def __init__(self, step_dict, parent):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	163 super(Step, self).__init__(step_dict, parent=parent, gi=parent.gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	164 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	165 stype = step_dict['type']
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	166 except KeyError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	167 raise ValueError('not a step dict')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	168 if stype not in set(['data_collection_input', 'data_input', 'pause',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	169 'tool']):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	170 raise ValueError('Unknown step type: %r' % stype)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	171 if self.type == 'tool' and self.tool_inputs:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	172 for k, v in six.iteritems(self.tool_inputs):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	173 # In Galaxy before release_17.05, v is a JSON-encoded string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	174 if not isinstance(v, six.string_types):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	175 break
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	176 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	177 self.tool_inputs[k] = json.loads(v)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	178 except ValueError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	179 break
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	180
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	181 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	182 def gi_module(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	183 return self.gi.workflows
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	184
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	185
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	186 class Workflow(Wrapper):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	187 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	188 Workflows represent ordered sequences of computations on Galaxy.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	189
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	190 A workflow defines a sequence of steps that produce one or more
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	191 results from an input dataset.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	192 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	193 BASE_ATTRS = Wrapper.BASE_ATTRS + (
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	194 'deleted', 'inputs', 'published', 'steps', 'tags'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	195 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	196 POLLING_INTERVAL = 10 # for output state monitoring
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	197
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	198 def __init__(self, wf_dict, gi=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	199 super(Workflow, self).__init__(wf_dict, gi=gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	200 missing_ids = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	201 if gi:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	202 tools_list_by_id = [t.id for t in gi.tools.get_previews()]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	203 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	204 tools_list_by_id = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	205 tool_labels_to_ids = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	206 for k, v in six.iteritems(self.steps):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	207 # convert step ids to str for consistency with outer keys
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	208 v['id'] = str(v['id'])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	209 for i in six.itervalues(v['input_steps']):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	210 i['source_step'] = str(i['source_step'])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	211 step = Step(v, self)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	212 self.steps[k] = step
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	213 if step.type == 'tool':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	214 if not step.tool_inputs or step.tool_id not in tools_list_by_id:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	215 missing_ids.append(k)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	216 tool_labels_to_ids.setdefault(step.tool_id, set()).add(step.id)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	217 input_labels_to_ids = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	218 for id_, d in six.iteritems(self.inputs):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	219 input_labels_to_ids.setdefault(d['label'], set()).add(id_)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	220 object.__setattr__(self, 'input_labels_to_ids', input_labels_to_ids)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	221 object.__setattr__(self, 'tool_labels_to_ids', tool_labels_to_ids)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	222 dag, inv_dag = self._get_dag()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	223 heads, tails = set(dag), set(inv_dag)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	224 object.__setattr__(self, 'dag', dag)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	225 object.__setattr__(self, 'inv_dag', inv_dag)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	226 object.__setattr__(self, 'source_ids', heads - tails)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	227 assert set(self.inputs) == self.data_collection_input_ids \| self.data_input_ids, \
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	228 "inputs is %r, while data_collection_input_ids is %r and data_input_ids is %r" % (self.inputs, self.data_collection_input_ids, self.data_input_ids)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	229 object.__setattr__(self, 'sink_ids', tails - heads)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	230 object.__setattr__(self, 'missing_ids', missing_ids)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	231
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	232 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	233 def gi_module(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	234 return self.gi.workflows
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	235
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	236 def _get_dag(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	237 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	238 Return the workflow's DAG.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	239
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	240 For convenience, this method computes a 'direct' (step =>
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	241 successors) and an 'inverse' (step => predecessors)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	242 representation of the same DAG.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	243
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	244 For instance, a workflow with a single tool c, two inputs
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	245 a, b and three outputs d, e, f is represented by (direct)::
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	246
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	247 {'a': {'c'}, 'b': {'c'}, 'c': set(['d', 'e', 'f'])}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	248
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	249 and by (inverse)::
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	250
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	251 {'c': set(['a', 'b']), 'd': {'c'}, 'e': {'c'}, 'f': {'c'}}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	252 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	253 dag, inv_dag = {}, {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	254 for s in six.itervalues(self.steps):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	255 for i in six.itervalues(s.input_steps):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	256 head, tail = i['source_step'], s.id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	257 dag.setdefault(head, set()).add(tail)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	258 inv_dag.setdefault(tail, set()).add(head)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	259 return dag, inv_dag
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	260
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	261 def sorted_step_ids(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	262 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	263 Return a topological sort of the workflow's DAG.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	264 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	265 ids = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	266 source_ids = self.source_ids.copy()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	267 inv_dag = dict((k, v.copy()) for k, v in six.iteritems(self.inv_dag))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	268 while source_ids:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	269 head = source_ids.pop()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	270 ids.append(head)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	271 for tail in self.dag.get(head, []):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	272 incoming = inv_dag[tail]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	273 incoming.remove(head)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	274 if not incoming:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	275 source_ids.add(tail)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	276 return ids
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	277
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	278 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	279 def data_input_ids(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	280 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	281 Return the ids of data input steps for this workflow.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	282 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	283 return set(id_ for id_, s in six.iteritems(self.steps)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	284 if s.type == 'data_input')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	285
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	286 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	287 def data_collection_input_ids(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	288 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	289 Return the ids of data collection input steps for this workflow.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	290 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	291 return set(id_ for id_, s in six.iteritems(self.steps)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	292 if s.type == 'data_collection_input')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	293
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	294 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	295 def tool_ids(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	296 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	297 Return the ids of tool steps for this workflow.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	298 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	299 return set(id_ for id_, s in six.iteritems(self.steps)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	300 if s.type == 'tool')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	301
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	302 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	303 def input_labels(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	304 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	305 Return the labels of this workflow's input steps.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	306 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	307 return set(self.input_labels_to_ids)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	308
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	309 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	310 def is_runnable(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	311 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	312 Return True if the workflow can be run on Galaxy.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	313
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	314 A workflow is considered runnable on a Galaxy instance if all
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	315 of the tools it uses are installed in that instance.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	316 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	317 return not self.missing_ids
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	318
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	319 def convert_input_map(self, input_map):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	320 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	321 Convert ``input_map`` to the format required by the Galaxy web API.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	322
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	323 :type input_map: dict
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	324 :param input_map: a mapping from input labels to datasets
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	325
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	326 :rtype: dict
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	327 :return: a mapping from input slot ids to dataset ids in the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	328 format required by the Galaxy web API.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	329 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	330 m = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	331 for label, slot_ids in six.iteritems(self.input_labels_to_ids):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	332 datasets = input_map.get(label, [])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	333 if not isinstance(datasets, collections.Iterable):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	334 datasets = [datasets]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	335 if len(datasets) < len(slot_ids):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	336 raise RuntimeError('not enough datasets for "%s"' % label)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	337 for id_, ds in zip(slot_ids, datasets):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	338 m[id_] = {'id': ds.id, 'src': ds.SRC}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	339 return m
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	340
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	341 def preview(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	342 getf = self.gi.workflows.get_previews
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	343 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	344 p = [_ for _ in getf(published=True) if _.id == self.id][0]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	345 except IndexError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	346 raise ValueError('no object for id %s' % self.id)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	347 return p
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	348
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	349 def run(self, input_map=None, history='', params=None, import_inputs=False,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	350 replacement_params=None, wait=False,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	351 polling_interval=POLLING_INTERVAL, break_on_error=True):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	352 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	353 Run the workflow in the current Galaxy instance.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	354
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	355 :type input_map: dict
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	356 :param input_map: a mapping from workflow input labels to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	357 datasets, e.g.: ``dict(zip(workflow.input_labels,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	358 library.get_datasets()))``
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	359
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	360 :type history: :class:`History` or str
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	361 :param history: either a valid history object (results will be
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	362 stored there) or a string (a new history will be created with
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	363 the given name).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	364
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	365 :type params: dict
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	366 :param params: a mapping of non-datasets tool parameters (see below)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	367
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	368 :type import_inputs: bool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	369 :param import_inputs: If ``True``, workflow inputs will be imported into
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	370 the history; if ``False``, only workflow outputs will be visible in
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	371 the history.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	372
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	373 :type replacement_params: dict
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	374 :param replacement_params: pattern-based replacements for
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	375 post-job actions (see the docs for
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	376 :meth:`~bioblend.galaxy.workflows.WorkflowClient.invoke_workflow`)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	377
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	378 :type wait: bool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	379 :param wait: whether to wait while the returned datasets are
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	380 in a pending state
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	381
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	382 :type polling_interval: float
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	383 :param polling_interval: polling interval in seconds
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	384
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	385 :type break_on_error: bool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	386 :param break_on_error: whether to break as soon as at least one
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	387 of the returned datasets is in the 'error' state
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	388
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	389 :rtype: tuple
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	390 :return: list of output datasets, output history
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	391
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	392 The ``params`` dict should be specified as follows::
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	393
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	394 {STEP_ID: PARAM_DICT, ...}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	395
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	396 where PARAM_DICT is::
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	397
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	398 {PARAM_NAME: VALUE, ...}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	399
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	400 For backwards compatibility, the following (deprecated) format is
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	401 also supported for ``params``::
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	402
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	403 {TOOL_ID: PARAM_DICT, ...}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	404
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	405 in which case PARAM_DICT affects all steps with the given tool id.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	406 If both by-tool-id and by-step-id specifications are used, the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	407 latter takes precedence.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	408
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	409 Finally (again, for backwards compatibility), PARAM_DICT can also
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	410 be specified as::
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	411
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	412 {'param': PARAM_NAME, 'value': VALUE}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	413
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	414 Note that this format allows only one parameter to be set per step.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	415
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	416 Example: set 'a' to 1 for the third workflow step::
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	417
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	418 params = {workflow.steps[2].id: {'a': 1}}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	419
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	420 .. warning::
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	421
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	422 This is a blocking operation that can take a very long time. If
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	423 ``wait`` is set to ``False``, the method will return as soon as the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	424 workflow has been scheduled, otherwise it will wait until the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	425 workflow has been run. With a large number of steps, however, the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	426 delay may not be negligible even in the former case (e.g. minutes for
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	427 100 steps).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	428 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	429 if not self.is_mapped:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	430 raise RuntimeError('workflow is not mapped to a Galaxy object')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	431 if not self.is_runnable:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	432 raise RuntimeError('workflow has missing tools: %s' % ', '.join(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	433 '%s[%s]' % (self.steps[_].tool_id, _)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	434 for _ in self.missing_ids))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	435 kwargs = {
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	436 'dataset_map': self.convert_input_map(input_map or {}),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	437 'params': params,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	438 'import_inputs_to_history': import_inputs,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	439 'replacement_params': replacement_params,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	440 }
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	441 if isinstance(history, History):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	442 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	443 kwargs['history_id'] = history.id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	444 except AttributeError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	445 raise RuntimeError('history does not have an id')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	446 elif isinstance(history, six.string_types):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	447 kwargs['history_name'] = history
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	448 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	449 raise TypeError(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	450 'history must be either a history wrapper or a string')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	451 res = self.gi.gi.workflows.run_workflow(self.id, **kwargs)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	452 # res structure: {'history': HIST_ID, 'outputs': [CI_ID, CI_ID, ...]}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	453 out_hist = self.gi.histories.get(res['history'])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	454 content_infos_dict = dict()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	455 for ci in out_hist.content_infos:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	456 content_infos_dict[ci.id] = ci
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	457 outputs = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	458 for output_id in res['outputs']:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	459 if content_infos_dict[output_id].type == 'file':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	460 outputs.append(out_hist.get_dataset(output_id))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	461 elif content_infos_dict[output_id].type == 'collection':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	462 outputs.append(out_hist.get_dataset_collection(output_id))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	463
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	464 if wait:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	465 self.gi._wait_datasets(outputs, polling_interval=polling_interval,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	466 break_on_error=break_on_error)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	467 return outputs, out_hist
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	468
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	469 def export(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	470 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	471 Export a re-importable representation of the workflow.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	472
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	473 :rtype: dict
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	474 :return: a JSON-serializable dump of the workflow
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	475 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	476 return self.gi.gi.workflows.export_workflow_dict(self.id)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	477
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	478 def delete(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	479 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	480 Delete this workflow.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	481
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	482 .. warning::
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	483 Deleting a workflow is irreversible - all of the data from
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	484 the workflow will be permanently deleted.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	485 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	486 self.gi.workflows.delete(id_=self.id)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	487 self.unmap()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	488
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	489
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	490 @six.add_metaclass(abc.ABCMeta)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	491 class Dataset(Wrapper):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	492 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	493 Abstract base class for Galaxy datasets.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	494 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	495 BASE_ATTRS = Wrapper.BASE_ATTRS + (
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	496 'data_type', 'file_ext', 'file_name', 'file_size', 'genome_build', 'misc_info', 'state'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	497 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	498 POLLING_INTERVAL = 1 # for state monitoring
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	499
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	500 @abc.abstractmethod
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	501 def __init__(self, ds_dict, container, gi=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	502 super(Dataset, self).__init__(ds_dict, gi=gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	503 object.__setattr__(self, 'container', container)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	504
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	505 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	506 def container_id(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	507 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	508 Deprecated property.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	509
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	510 Id of the dataset container. Use :attr:`.container.id` instead.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	511 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	512 return self.container.id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	513
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	514 @abc.abstractproperty
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	515 def _stream_url(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	516 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	517 Return the URL to stream this dataset.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	518 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	519 pass
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	520
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	521 def get_stream(self, chunk_size=bioblend.CHUNK_SIZE):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	522 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	523 Open dataset for reading and return an iterator over its contents.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	524
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	525 :type chunk_size: int
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	526 :param chunk_size: read this amount of bytes at a time
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	527 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	528 kwargs = {'stream': True}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	529 if isinstance(self, LibraryDataset):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	530 kwargs['params'] = {'ld_ids%5B%5D': self.id}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	531 r = self.gi.gi.make_get_request(self._stream_url, **kwargs)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	532 if isinstance(self, LibraryDataset) and r.status_code == 500:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	533 # compatibility with older Galaxy releases
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	534 kwargs['params'] = {'ldda_ids%5B%5D': self.id}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	535 r = self.gi.gi.make_get_request(self._stream_url, **kwargs)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	536 r.raise_for_status()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	537 return r.iter_content(chunk_size) # FIXME: client can't close r
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	538
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	539 def peek(self, chunk_size=bioblend.CHUNK_SIZE):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	540 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	541 Open dataset for reading and return the first chunk.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	542
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	543 See :meth:`.get_stream` for param info.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	544 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	545 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	546 return next(self.get_stream(chunk_size=chunk_size))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	547 except StopIteration:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	548 return b''
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	549
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	550 def download(self, file_object, chunk_size=bioblend.CHUNK_SIZE):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	551 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	552 Open dataset for reading and save its contents to ``file_object``.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	553
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	554 :type file_object: file
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	555 :param file_object: output file object
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	556
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	557 See :meth:`.get_stream` for info on other params.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	558 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	559 for chunk in self.get_stream(chunk_size=chunk_size):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	560 file_object.write(chunk)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	561
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	562 def get_contents(self, chunk_size=bioblend.CHUNK_SIZE):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	563 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	564 Open dataset for reading and return its full contents.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	565
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	566 See :meth:`.get_stream` for param info.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	567 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	568 return b''.join(self.get_stream(chunk_size=chunk_size))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	569
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	570 def refresh(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	571 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	572 Re-fetch the attributes pertaining to this object.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	573
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	574 Returns: self
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	575 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	576 gi_client = getattr(self.gi.gi, self.container.API_MODULE)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	577 ds_dict = gi_client.show_dataset(self.container.id, self.id)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	578 self.__init__(ds_dict, self.container, self.gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	579 return self
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	580
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	581 def wait(self, polling_interval=POLLING_INTERVAL, break_on_error=True):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	582 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	583 Wait for this dataset to come out of the pending states.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	584
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	585 :type polling_interval: float
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	586 :param polling_interval: polling interval in seconds
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	587
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	588 :type break_on_error: bool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	589 :param break_on_error: if ``True``, raise a RuntimeError exception if
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	590 the dataset ends in the 'error' state.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	591
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	592 .. warning::
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	593
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	594 This is a blocking operation that can take a very long time. Also,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	595 note that this method does not return anything; however, this dataset
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	596 is refreshed (possibly multiple times) during the execution.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	597 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	598 self.gi._wait_datasets([self], polling_interval=polling_interval,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	599 break_on_error=break_on_error)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	600
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	601
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	602 class HistoryDatasetAssociation(Dataset):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	603 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	604 Maps to a Galaxy ``HistoryDatasetAssociation``.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	605 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	606 BASE_ATTRS = Dataset.BASE_ATTRS + ('annotation', 'deleted', 'purged', 'tags', 'visible')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	607 SRC = 'hda'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	608
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	609 def __init__(self, ds_dict, container, gi=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	610 super(HistoryDatasetAssociation, self).__init__(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	611 ds_dict, container, gi=gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	612
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	613 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	614 def gi_module(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	615 return self.gi.histories
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	616
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	617 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	618 def _stream_url(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	619 base_url = self.gi.gi._make_url(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	620 self.gi.gi.histories, module_id=self.container.id, contents=True)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	621 return "%s/%s/display" % (base_url, self.id)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	622
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	623 def update(self, **kwds):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	624 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	625 Update this history dataset metadata. Some of the attributes that can be
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	626 modified are documented below.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	627
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	628 :type name: str
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	629 :param name: Replace history dataset name with the given string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	630
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	631 :type genome_build: str
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	632 :param genome_build: Replace history dataset genome build (dbkey)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	633
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	634 :type annotation: str
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	635 :param annotation: Replace history dataset annotation with given string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	636
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	637 :type deleted: bool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	638 :param deleted: Mark or unmark history dataset as deleted
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	639
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	640 :type visible: bool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	641 :param visible: Mark or unmark history dataset as visible
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	642 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	643 res = self.gi.gi.histories.update_dataset(self.container.id, self.id, **kwds)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	644 # Refresh also the history because the dataset may have been (un)deleted
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	645 self.container.refresh()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	646 if 'id' in res:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	647 self.__init__(res, self.container, gi=self.gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	648 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	649 # for Galaxy < release_15.03 res contains only the updated fields
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	650 self.refresh()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	651 return self
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	652
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	653 def delete(self, purge=False):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	654 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	655 Delete this history dataset.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	656
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	657 :type purge: bool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	658 :param purge: if ``True``, also purge (permanently delete) the dataset
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	659
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	660 .. note::
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	661 For the purge option to work, the Galaxy instance must have the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	662 ``allow_user_dataset_purge`` option set to ``true`` in the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	663 ``config/galaxy.yml`` configuration file.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	664
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	665 .. warning::
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	666 If you purge a dataset which has not been previously deleted,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	667 Galaxy from release_15.03 to release_17.01 does not set the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	668 ``deleted`` attribute of the dataset to ``True``, see
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	669 https://github.com/galaxyproject/galaxy/issues/3548
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	670 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	671 self.gi.gi.histories.delete_dataset(self.container.id, self.id, purge=purge)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	672 self.container.refresh()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	673 self.refresh()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	674
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	675
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	676 @six.add_metaclass(abc.ABCMeta)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	677 class DatasetCollection(Wrapper):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	678 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	679 Abstract base class for Galaxy dataset collections.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	680 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	681 BASE_ATTRS = Wrapper.BASE_ATTRS + (
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	682 'state', 'deleted', 'collection_type'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	683 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	684
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	685 @abc.abstractmethod
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	686 def __init__(self, dsc_dict, container, gi=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	687 super(DatasetCollection, self).__init__(dsc_dict, gi=gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	688 object.__setattr__(self, 'container', container)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	689
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	690 def refresh(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	691 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	692 Re-fetch the attributes pertaining to this object.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	693
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	694 Returns: self
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	695 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	696 gi_client = getattr(self.gi.gi, self.container.API_MODULE)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	697 dsc_dict = gi_client.show_dataset_collection(self.container.id, self.id)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	698 self.__init__(dsc_dict, self.container, self.gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	699 return self
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	700
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	701
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	702 class HistoryDatasetCollectionAssociation(DatasetCollection):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	703 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	704 Maps to a Galaxy ``HistoryDatasetCollectionAssociation``.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	705 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	706 BASE_ATTRS = DatasetCollection.BASE_ATTRS + ('tags', 'visible', 'elements')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	707 SRC = 'hdca'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	708
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	709 def __init__(self, dsc_dict, container, gi=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	710 super(HistoryDatasetCollectionAssociation, self).__init__(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	711 dsc_dict, container, gi=gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	712
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	713 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	714 def gi_module(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	715 return self.gi.histories
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	716
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	717 def delete(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	718 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	719 Delete this dataset collection.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	720 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	721 self.gi.gi.histories.delete_dataset_collection(self.container.id, self.id)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	722 self.container.refresh()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	723 self.refresh()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	724
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	725
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	726 class LibRelatedDataset(Dataset):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	727 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	728 Base class for LibraryDatasetDatasetAssociation and LibraryDataset classes.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	729 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	730
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	731 def __init__(self, ds_dict, container, gi=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	732 super(LibRelatedDataset, self).__init__(ds_dict, container, gi=gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	733
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	734 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	735 def gi_module(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	736 return self.gi.libraries
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	737
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	738 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	739 def _stream_url(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	740 base_url = self.gi.gi._make_url(self.gi.gi.libraries)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	741 return "%s/datasets/download/uncompressed" % base_url
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	742
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	743
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	744 class LibraryDatasetDatasetAssociation(LibRelatedDataset):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	745 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	746 Maps to a Galaxy ``LibraryDatasetDatasetAssociation``.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	747 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	748 BASE_ATTRS = LibRelatedDataset.BASE_ATTRS + ('deleted',)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	749 SRC = 'ldda'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	750
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	751
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	752 class LibraryDataset(LibRelatedDataset):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	753 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	754 Maps to a Galaxy ``LibraryDataset``.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	755 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	756 SRC = 'ld'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	757
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	758 def delete(self, purged=False):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	759 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	760 Delete this library dataset.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	761
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	762 :type purged: bool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	763 :param purged: if ``True``, also purge (permanently delete) the dataset
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	764 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	765 self.gi.gi.libraries.delete_library_dataset(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	766 self.container.id, self.id, purged=purged)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	767 self.container.refresh()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	768 self.refresh()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	769
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	770 def update(self, **kwds):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	771 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	772 Update this library dataset metadata. Some of the attributes that can be
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	773 modified are documented below.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	774
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	775 :type name: str
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	776 :param name: Replace history dataset name with the given string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	777
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	778 :type genome_build: str
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	779 :param genome_build: Replace history dataset genome build (dbkey)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	780 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	781 res = self.gi.gi.libraries.update_library_dataset(self.id, **kwds)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	782 self.container.refresh()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	783 self.__init__(res, self.container, gi=self.gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	784 return self
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	785
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	786
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	787 @six.add_metaclass(abc.ABCMeta)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	788 class ContentInfo(Wrapper):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	789 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	790 Instances of this class wrap dictionaries obtained by getting
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	791 ``/api/{histories,libraries}/<ID>/contents`` from Galaxy.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	792 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	793 BASE_ATTRS = Wrapper.BASE_ATTRS + ('type',)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	794
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	795 @abc.abstractmethod
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	796 def __init__(self, info_dict, gi=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	797 super(ContentInfo, self).__init__(info_dict, gi=gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	798
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	799
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	800 class LibraryContentInfo(ContentInfo):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	801 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	802 Instances of this class wrap dictionaries obtained by getting
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	803 ``/api/libraries/<ID>/contents`` from Galaxy.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	804 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	805 def __init__(self, info_dict, gi=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	806 super(LibraryContentInfo, self).__init__(info_dict, gi=gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	807
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	808 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	809 def gi_module(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	810 return self.gi.libraries
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	811
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	812
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	813 class HistoryContentInfo(ContentInfo):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	814 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	815 Instances of this class wrap dictionaries obtained by getting
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	816 ``/api/histories/<ID>/contents`` from Galaxy.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	817 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	818 BASE_ATTRS = ContentInfo.BASE_ATTRS + ('deleted', 'state', 'visible')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	819
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	820 def __init__(self, info_dict, gi=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	821 super(HistoryContentInfo, self).__init__(info_dict, gi=gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	822
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	823 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	824 def gi_module(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	825 return self.gi.histories
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	826
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	827
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	828 @six.add_metaclass(abc.ABCMeta)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	829 class DatasetContainer(Wrapper):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	830 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	831 Abstract base class for dataset containers (histories and libraries).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	832 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	833 BASE_ATTRS = Wrapper.BASE_ATTRS + ('deleted',)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	834
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	835 @abc.abstractmethod
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	836 def __init__(self, c_dict, content_infos=None, gi=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	837 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	838 :type content_infos: list of :class:`ContentInfo`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	839 :param content_infos: info objects for the container's contents
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	840 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	841 super(DatasetContainer, self).__init__(c_dict, gi=gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	842 if content_infos is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	843 content_infos = []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	844 object.__setattr__(self, 'content_infos', content_infos)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	845
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	846 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	847 def dataset_ids(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	848 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	849 Return the ids of the contained datasets.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	850 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	851 return [_.id for _ in self.content_infos if _.type == 'file']
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	852
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	853 def preview(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	854 getf = self.gi_module.get_previews
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	855 # self.state could be stale: check both regular and deleted containers
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	856 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	857 p = [_ for _ in getf() if _.id == self.id][0]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	858 except IndexError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	859 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	860 p = [_ for _ in getf(deleted=True) if _.id == self.id][0]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	861 except IndexError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	862 raise ValueError('no object for id %s' % self.id)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	863 return p
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	864
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	865 def refresh(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	866 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	867 Re-fetch the attributes pertaining to this object.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	868
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	869 Returns: self
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	870 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	871 fresh = self.gi_module.get(self.id)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	872 self.__init__(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	873 fresh.wrapped, content_infos=fresh.content_infos, gi=self.gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	874 return self
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	875
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	876 def get_dataset(self, ds_id):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	877 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	878 Retrieve the dataset corresponding to the given id.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	879
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	880 :type ds_id: str
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	881 :param ds_id: dataset id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	882
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	883 :rtype: :class:`~.HistoryDatasetAssociation` or
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	884 :class:`~.LibraryDataset`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	885 :return: the dataset corresponding to ``ds_id``
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	886 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	887 gi_client = getattr(self.gi.gi, self.API_MODULE)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	888 ds_dict = gi_client.show_dataset(self.id, ds_id)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	889 return self.DS_TYPE(ds_dict, self, gi=self.gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	890
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	891 def get_datasets(self, name=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	892 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	893 Get all datasets contained inside this dataset container.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	894
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	895 :type name: str
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	896 :param name: return only datasets with this name
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	897
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	898 :rtype: list of :class:`~.HistoryDatasetAssociation` or list of
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	899 :class:`~.LibraryDataset`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	900 :return: datasets with the given name contained inside this
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	901 container
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	902
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	903 .. note::
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	904
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	905 when filtering library datasets by name, specify their full
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	906 paths starting from the library's root folder, e.g.,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	907 ``/seqdata/reads.fastq``. Full paths are available through
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	908 the ``content_infos`` attribute of
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	909 :class:`~.Library` objects.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	910 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	911 if name is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	912 ds_ids = self.dataset_ids
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	913 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	914 ds_ids = [_.id for _ in self.content_infos if _.name == name]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	915 return [self.get_dataset(_) for _ in ds_ids]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	916
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	917
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	918 class History(DatasetContainer):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	919 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	920 Maps to a Galaxy history.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	921 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	922 BASE_ATTRS = DatasetContainer.BASE_ATTRS + ('annotation', 'published', 'state', 'state_ids', 'state_details', 'tags')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	923 DS_TYPE = HistoryDatasetAssociation
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	924 DSC_TYPE = HistoryDatasetCollectionAssociation
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	925 CONTENT_INFO_TYPE = HistoryContentInfo
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	926 API_MODULE = 'histories'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	927
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	928 def __init__(self, hist_dict, content_infos=None, gi=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	929 super(History, self).__init__(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	930 hist_dict, content_infos=content_infos, gi=gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	931
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	932 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	933 def gi_module(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	934 return self.gi.histories
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	935
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	936 def update(self, **kwds):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	937 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	938 Update history metadata information. Some of the attributes that can be
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	939 modified are documented below.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	940
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	941 :type name: str
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	942 :param name: Replace history name with the given string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	943
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	944 :type annotation: str
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	945 :param annotation: Replace history annotation with the given string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	946
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	947 :type deleted: bool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	948 :param deleted: Mark or unmark history as deleted
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	949
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	950 :type purged: bool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	951 :param purged: If True, mark history as purged (permanently deleted).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	952 Ignored on Galaxy release_15.01 and earlier
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	953
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	954 :type published: bool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	955 :param published: Mark or unmark history as published
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	956
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	957 :type importable: bool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	958 :param importable: Mark or unmark history as importable
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	959
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	960 :type tags: list
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	961 :param tags: Replace history tags with the given list
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	962 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	963 # TODO: wouldn't it be better if name and annotation were attributes?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	964 self.gi.gi.histories.update_history(self.id, **kwds)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	965 self.refresh()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	966 return self
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	967
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	968 def delete(self, purge=False):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	969 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	970 Delete this history.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	971
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	972 :type purge: bool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	973 :param purge: if ``True``, also purge (permanently delete) the history
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	974
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	975 .. note::
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	976 For the purge option to work, the Galaxy instance must have the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	977 ``allow_user_dataset_purge`` option set to ``true`` in the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	978 ``config/galaxy.yml`` configuration file.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	979 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	980 self.gi.histories.delete(id_=self.id, purge=purge)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	981 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	982 self.refresh()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	983 except Exception:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	984 # Galaxy release_15.01 and earlier requires passing 'deleted=False'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	985 # when getting the details of a deleted history
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	986 pass
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	987 self.unmap()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	988
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	989 def import_dataset(self, lds):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	990 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	991 Import a dataset into the history from a library.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	992
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	993 :type lds: :class:`~.LibraryDataset`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	994 :param lds: the library dataset to import
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	995
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	996 :rtype: :class:`~.HistoryDatasetAssociation`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	997 :return: the imported history dataset
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	998 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	999 if not self.is_mapped:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1000 raise RuntimeError('history is not mapped to a Galaxy object')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1001 if not isinstance(lds, LibraryDataset):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1002 raise TypeError('lds is not a LibraryDataset')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1003 res = self.gi.gi.histories.upload_dataset_from_library(self.id, lds.id)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1004 if not isinstance(res, collections.Mapping):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1005 raise RuntimeError(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1006 'upload_dataset_from_library: unexpected reply: %r' % res)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1007 self.refresh()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1008 return self.get_dataset(res['id'])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1009
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1010 def upload_file(self, path, **kwargs):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1011 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1012 Upload the file specified by ``path`` to this history.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1013
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1014 :type path: str
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1015 :param path: path of the file to upload
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1016
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1017 See :meth:`~bioblend.galaxy.tools.ToolClient.upload_file` for
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1018 the optional parameters.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1019
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1020 :rtype: :class:`~.HistoryDatasetAssociation`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1021 :return: the uploaded dataset
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1022 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1023 out_dict = self.gi.gi.tools.upload_file(path, self.id, **kwargs)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1024 self.refresh()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1025 return self.get_dataset(out_dict['outputs'][0]['id'])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1026
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1027 upload_dataset = upload_file
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1028
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1029 def upload_from_ftp(self, path, **kwargs):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1030 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1031 Upload the file specified by ``path`` from the user's FTP directory to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1032 this history.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1033
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1034 :type path: str
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1035 :param path: path of the file in the user's FTP directory
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1036
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1037 See :meth:`~bioblend.galaxy.tools.ToolClient.upload_file` for
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1038 the optional parameters.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1039
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1040 :rtype: :class:`~.HistoryDatasetAssociation`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1041 :return: the uploaded dataset
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1042 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1043 out_dict = self.gi.gi.tools.upload_from_ftp(path, self.id, **kwargs)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1044 self.refresh()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1045 return self.get_dataset(out_dict['outputs'][0]['id'])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1046
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1047 def paste_content(self, content, **kwargs):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1048 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1049 Upload a string to a new dataset in this history.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1050
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1051 :type content: str
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1052 :param content: content of the new dataset to upload
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1053
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1054 See :meth:`~bioblend.galaxy.tools.ToolClient.upload_file` for
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1055 the optional parameters (except file_name).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1056
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1057 :rtype: :class:`~.HistoryDatasetAssociation`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1058 :return: the uploaded dataset
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1059 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1060 out_dict = self.gi.gi.tools.paste_content(content, self.id, **kwargs)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1061 self.refresh()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1062 return self.get_dataset(out_dict['outputs'][0]['id'])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1063
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1064 def export(self, gzip=True, include_hidden=False, include_deleted=False,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1065 wait=False, maxwait=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1066 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1067 Start a job to create an export archive for this history. See
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1068 :meth:`~bioblend.galaxy.histories.HistoryClient.export_history`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1069 for parameter and return value info.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1070 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1071 return self.gi.gi.histories.export_history(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1072 self.id, gzip=gzip, include_hidden=include_hidden,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1073 include_deleted=include_deleted, wait=wait, maxwait=maxwait)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1074
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1075 def download(self, jeha_id, outf, chunk_size=bioblend.CHUNK_SIZE):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1076 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1077 Download an export archive for this history. Use :meth:`export`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1078 to create an export and get the required ``jeha_id``. See
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1079 :meth:`~bioblend.galaxy.histories.HistoryClient.download_history`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1080 for parameter and return value info.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1081 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1082 return self.gi.gi.histories.download_history(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1083 self.id, jeha_id, outf, chunk_size=chunk_size)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1084
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1085 def create_dataset_collection(self, collection_description):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1086 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1087 Create a new dataset collection in the history by providing a collection description.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1088
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1089 :type collection_description: bioblend.galaxy.dataset_collections.CollectionDescription
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1090 :param collection_description: a description of the dataset collection
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1091
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1092 :rtype: :class:`~.HistoryDatasetCollectionAssociation`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1093 :return: the new dataset collection
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1094 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1095 dataset_collection = self.gi.gi.histories.create_dataset_collection(self.id, collection_description)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1096 self.refresh()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1097 return self.get_dataset_collection(dataset_collection['id'])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1098
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1099 def get_dataset_collection(self, dsc_id):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1100 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1101 Retrieve the dataset collection corresponding to the given id.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1102
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1103 :type dsc_id: str
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1104 :param dsc_id: dataset collection id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1105
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1106 :rtype: :class:`~.HistoryDatasetCollectionAssociation`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1107 :return: the dataset collection corresponding to ``dsc_id``
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1108 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1109 dsc_dict = self.gi.gi.histories.show_dataset_collection(self.id, dsc_id)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1110 return self.DSC_TYPE(dsc_dict, self, gi=self.gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1111
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1112
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1113 class Library(DatasetContainer):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1114 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1115 Maps to a Galaxy library.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1116 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1117 BASE_ATTRS = DatasetContainer.BASE_ATTRS + ('description', 'synopsis')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1118 DS_TYPE = LibraryDataset
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1119 CONTENT_INFO_TYPE = LibraryContentInfo
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1120 API_MODULE = 'libraries'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1121
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1122 def __init__(self, lib_dict, content_infos=None, gi=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1123 super(Library, self).__init__(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1124 lib_dict, content_infos=content_infos, gi=gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1125
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1126 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1127 def gi_module(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1128 return self.gi.libraries
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1129
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1130 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1131 def folder_ids(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1132 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1133 Return the ids of the contained folders.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1134 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1135 return [_.id for _ in self.content_infos if _.type == 'folder']
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1136
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1137 def delete(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1138 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1139 Delete this library.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1140 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1141 self.gi.libraries.delete(id_=self.id)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1142 self.refresh()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1143 self.unmap()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1144
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1145 def _pre_upload(self, folder):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1146 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1147 Return the id of the given folder, after sanity checking.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1148 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1149 if not self.is_mapped:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1150 raise RuntimeError('library is not mapped to a Galaxy object')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1151 return None if folder is None else folder.id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1152
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1153 def upload_data(self, data, folder=None, **kwargs):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1154 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1155 Upload data to this library.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1156
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1157 :type data: str
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1158 :param data: dataset contents
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1159
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1160 :type folder: :class:`~.Folder`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1161 :param folder: a folder object, or ``None`` to upload to the root folder
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1162
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1163 :rtype: :class:`~.LibraryDataset`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1164 :return: the dataset object that represents the uploaded content
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1165
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1166 Optional keyword arguments: ``file_type``, ``dbkey``.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1167 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1168 fid = self._pre_upload(folder)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1169 res = self.gi.gi.libraries.upload_file_contents(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1170 self.id, data, folder_id=fid, **kwargs)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1171 self.refresh()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1172 return self.get_dataset(res[0]['id'])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1173
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1174 def upload_from_url(self, url, folder=None, **kwargs):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1175 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1176 Upload data to this library from the given URL.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1177
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1178 :type url: str
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1179 :param url: URL from which data should be read
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1180
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1181 See :meth:`.upload_data` for info on other params.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1182 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1183 fid = self._pre_upload(folder)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1184 res = self.gi.gi.libraries.upload_file_from_url(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1185 self.id, url, folder_id=fid, **kwargs)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1186 self.refresh()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1187 return self.get_dataset(res[0]['id'])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1188
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1189 def upload_from_local(self, path, folder=None, **kwargs):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1190 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1191 Upload data to this library from a local file.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1192
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1193 :type path: str
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1194 :param path: local file path from which data should be read
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1195
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1196 See :meth:`.upload_data` for info on other params.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1197 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1198 fid = self._pre_upload(folder)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1199 res = self.gi.gi.libraries.upload_file_from_local_path(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1200 self.id, path, folder_id=fid, **kwargs)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1201 self.refresh()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1202 return self.get_dataset(res[0]['id'])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1203
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1204 def upload_from_galaxy_fs(self, paths, folder=None, link_data_only=None, **kwargs):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1205 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1206 Upload data to this library from filesystem paths on the server.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1207
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1208 .. note::
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1209 For this method to work, the Galaxy instance must have the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1210 ``allow_path_paste`` (``allow_library_path_paste`` in Galaxy
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1211 ``release_17.05`` and earlier) option set to ``true`` in the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1212 ``config/galaxy.yml`` configuration file.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1213
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1214 :type paths: str or :class:`~collections.Iterable` of str
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1215 :param paths: server-side file paths from which data should be read
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1216
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1217 :type link_data_only: str
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1218 :param link_data_only: either 'copy_files' (default) or
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1219 'link_to_files'. Setting to 'link_to_files' symlinks instead of
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1220 copying the files
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1221
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1222 :rtype: list of :class:`~.LibraryDataset`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1223 :return: the dataset objects that represent the uploaded content
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1224
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1225 See :meth:`.upload_data` for info on other params.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1226 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1227 fid = self._pre_upload(folder)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1228 if isinstance(paths, six.string_types):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1229 paths = (paths,)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1230 paths = '\n'.join(paths)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1231 res = self.gi.gi.libraries.upload_from_galaxy_filesystem(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1232 self.id, paths, folder_id=fid, link_data_only=link_data_only,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1233 **kwargs)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1234 if res is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1235 raise RuntimeError('upload_from_galaxy_filesystem: no reply')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1236 if not isinstance(res, collections.Sequence):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1237 raise RuntimeError(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1238 'upload_from_galaxy_filesystem: unexpected reply: %r' % res)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1239 new_datasets = [
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1240 self.get_dataset(ds_info['id']) for ds_info in res
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1241 ]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1242 self.refresh()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1243 return new_datasets
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1244
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1245 def copy_from_dataset(self, hda, folder=None, message=''):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1246 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1247 Copy a history dataset into this library.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1248
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1249 :type hda: :class:`~.HistoryDatasetAssociation`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1250 :param hda: history dataset to copy into the library
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1251
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1252 See :meth:`.upload_data` for info on other params.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1253 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1254 fid = self._pre_upload(folder)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1255 res = self.gi.gi.libraries.copy_from_dataset(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1256 self.id, hda.id, folder_id=fid, message=message)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1257 self.refresh()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1258 return self.get_dataset(res['library_dataset_id'])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1259
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1260 def create_folder(self, name, description=None, base_folder=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1261 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1262 Create a folder in this library.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1263
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1264 :type name: str
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1265 :param name: folder name
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1266
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1267 :type description: str
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1268 :param description: optional folder description
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1269
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1270 :type base_folder: :class:`~.Folder`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1271 :param base_folder: parent folder, or ``None`` to create in the root
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1272 folder
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1273
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1274 :rtype: :class:`~.Folder`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1275 :return: the folder just created
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1276 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1277 bfid = None if base_folder is None else base_folder.id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1278 res = self.gi.gi.libraries.create_folder(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1279 self.id, name, description=description, base_folder_id=bfid)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1280 self.refresh()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1281 return self.get_folder(res[0]['id'])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1282
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1283 def get_folder(self, f_id):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1284 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1285 Retrieve the folder corresponding to the given id.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1286
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1287 :rtype: :class:`~.Folder`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1288 :return: the folder corresponding to ``f_id``
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1289 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1290 f_dict = self.gi.gi.libraries.show_folder(self.id, f_id)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1291 return Folder(f_dict, self, gi=self.gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1292
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1293 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1294 def root_folder(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1295 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1296 The root folder of this library.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1297
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1298 :rtype: :class:`~.Folder`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1299 :return: the root folder of this library
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1300 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1301 return self.get_folder(self.gi.gi.libraries._get_root_folder_id(self.id))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1302
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1303
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1304 class Folder(Wrapper):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1305 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1306 Maps to a folder in a Galaxy library.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1307 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1308 BASE_ATTRS = Wrapper.BASE_ATTRS + ('description', 'deleted', 'item_count')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1309
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1310 def __init__(self, f_dict, container, gi=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1311 super(Folder, self).__init__(f_dict, gi=gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1312 object.__setattr__(self, 'container', container)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1313
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1314 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1315 def parent(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1316 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1317 The parent folder of this folder. The parent of the root folder is
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1318 ``None``.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1319
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1320 :rtype: :class:`~.Folder`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1321 :return: the parent of this folder
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1322 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1323 if self._cached_parent is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1324 object.__setattr__(self,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1325 '_cached_parent',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1326 self._get_parent())
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1327 return self._cached_parent
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1328
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1329 def _get_parent(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1330 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1331 Return the parent folder of this folder.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1332 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1333 # Galaxy release_13.04 and earlier does not have parent_id in the folder
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1334 # dictionary, may be implemented by searching for the folder with the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1335 # correct name
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1336 if 'parent_id' not in self.wrapped:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1337 raise NotImplementedError('This method has not been implemented for Galaxy release_13.04 and earlier')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1338 parent_id = self.wrapped['parent_id']
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1339 if parent_id is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1340 return None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1341 # Galaxy from release_14.02 to release_15.01 returns a dummy parent_id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1342 # for the root folder instead of None, so check if this is the root
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1343 if self.id == self.gi.gi.libraries._get_root_folder_id(self.container.id):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1344 return None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1345 # Galaxy release_13.11 and earlier returns a parent_id without the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1346 # initial 'F'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1347 if not parent_id.startswith('F'):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1348 parent_id = 'F' + parent_id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1349 return self.container.get_folder(parent_id)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1350
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1351 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1352 def gi_module(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1353 return self.gi.libraries
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1354
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1355 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1356 def container_id(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1357 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1358 Deprecated property.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1359
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1360 Id of the folder container. Use :attr:`.container.id` instead.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1361 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1362 return self.container.id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1363
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1364 def refresh(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1365 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1366 Re-fetch the attributes pertaining to this object.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1367
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1368 Returns: self
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1369 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1370 f_dict = self.gi.gi.libraries.show_folder(self.container.id, self.id)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1371 self.__init__(f_dict, self.container, gi=self.gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1372 return self
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1373
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1374
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1375 class Tool(Wrapper):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1376 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1377 Maps to a Galaxy tool.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1378 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1379 BASE_ATTRS = Wrapper.BASE_ATTRS + ('version',)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1380 POLLING_INTERVAL = 10 # for output state monitoring
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1381
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1382 def __init__(self, t_dict, gi=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1383 super(Tool, self).__init__(t_dict, gi=gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1384
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1385 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1386 def gi_module(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1387 return self.gi.tools
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1388
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1389 def run(self, inputs, history, wait=False,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1390 polling_interval=POLLING_INTERVAL):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1391 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1392 Execute this tool in the given history with inputs from dict
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1393 ``inputs``.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1394
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1395 :type inputs: dict
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1396 :param inputs: dictionary of input datasets and parameters for
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1397 the tool (see below)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1398
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1399 :type history: :class:`History`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1400 :param history: the history where to execute the tool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1401
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1402 :type wait: bool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1403 :param wait: whether to wait while the returned datasets are
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1404 in a pending state
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1405
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1406 :type polling_interval: float
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1407 :param polling_interval: polling interval in seconds
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1408
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1409 :rtype: list of :class:`HistoryDatasetAssociation`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1410 :return: list of output datasets
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1411
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1412 The ``inputs`` dict should contain input datasets and parameters
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1413 in the (largely undocumented) format used by the Galaxy API.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1414 Some examples can be found in `Galaxy's API test suite
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1415 <https://github.com/galaxyproject/galaxy/blob/dev/test/api/test_tools.py>`_.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1416 The value of an input dataset can also be a :class:`Dataset`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1417 object, which will be automatically converted to the needed
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1418 format.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1419 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1420 for k, v in six.iteritems(inputs):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1421 if isinstance(v, Dataset):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1422 inputs[k] = {'src': v.SRC, 'id': v.id}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1423 out_dict = self.gi.gi.tools.run_tool(history.id, self.id, inputs)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1424 outputs = [history.get_dataset(_['id']) for _ in out_dict['outputs']]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1425 if wait:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1426 self.gi._wait_datasets(outputs, polling_interval=polling_interval)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1427 return outputs
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1428
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1429
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1430 class Job(Wrapper):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1431 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1432 Maps to a Galaxy job.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1433 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1434 BASE_ATTRS = ('id', 'state')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1435
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1436 def __init__(self, j_dict, gi=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1437 super(Job, self).__init__(j_dict, gi=gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1438
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1439 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1440 def gi_module(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1441 return self.gi.jobs
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1442
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1443
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1444 @six.add_metaclass(abc.ABCMeta)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1445 class Preview(Wrapper):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1446 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1447 Abstract base class for Galaxy entity 'previews'.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1448
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1449 Classes derived from this one model the short summaries returned
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1450 by global getters such as ``/api/libraries``.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1451 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1452 BASE_ATTRS = Wrapper.BASE_ATTRS + ('deleted',)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1453
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1454 @abc.abstractmethod
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1455 def __init__(self, pw_dict, gi=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1456 super(Preview, self).__init__(pw_dict, gi=gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1457
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1458
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1459 class LibraryPreview(Preview):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1460 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1461 Models Galaxy library 'previews'.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1462
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1463 Instances of this class wrap dictionaries obtained by getting
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1464 ``/api/libraries`` from Galaxy.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1465 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1466 def __init__(self, pw_dict, gi=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1467 super(LibraryPreview, self).__init__(pw_dict, gi=gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1468
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1469 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1470 def gi_module(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1471 return self.gi.libraries
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1472
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1473
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1474 class HistoryPreview(Preview):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1475 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1476 Models Galaxy history 'previews'.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1477
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1478 Instances of this class wrap dictionaries obtained by getting
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1479 ``/api/histories`` from Galaxy.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1480 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1481 BASE_ATTRS = Preview.BASE_ATTRS + ('tags',)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1482
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1483 def __init__(self, pw_dict, gi=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1484 super(HistoryPreview, self).__init__(pw_dict, gi=gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1485
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1486 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1487 def gi_module(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1488 return self.gi.histories
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1489
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1490
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1491 class WorkflowPreview(Preview):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1492 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1493 Models Galaxy workflow 'previews'.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1494
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1495 Instances of this class wrap dictionaries obtained by getting
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1496 ``/api/workflows`` from Galaxy.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1497 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1498 BASE_ATTRS = Preview.BASE_ATTRS + ('published', 'tags')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1499
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1500 def __init__(self, pw_dict, gi=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1501 super(WorkflowPreview, self).__init__(pw_dict, gi=gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1502
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1503 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1504 def gi_module(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1505 return self.gi.workflows
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1506
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1507
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1508 class JobPreview(Preview):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1509 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1510 Models Galaxy job 'previews'.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1511
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1512 Instances of this class wrap dictionaries obtained by getting
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1513 ``/api/jobs`` from Galaxy.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1514 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1515 BASE_ATTRS = ('id', 'state')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1516
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1517 def __init__(self, pw_dict, gi=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1518 super(JobPreview, self).__init__(pw_dict, gi=gi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1519
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1520 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1521 def gi_module(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1522 return self.gi.jobs

Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/bioblend/galaxy/objects/wrappers.py @ 4:79f47841a781 draft