Coverage for src/hdmf/backends/io.py: 97%

79 statements  

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1from abc import ABCMeta, abstractmethod 

2import os 

3from pathlib import Path 

4 

5from ..build import BuildManager, GroupBuilder 

6from ..container import Container, ExternalResourcesManager 

7from .errors import UnsupportedOperation 

8from ..utils import docval, getargs, popargs 

9from warnings import warn 

10 

11 

12class HDMFIO(metaclass=ABCMeta): 

13 

14 @staticmethod 

15 @abstractmethod 

16 def can_read(path): 

17 """Determines whether a given path is readable by this HDMFIO class""" 

18 pass 

19 

20 @docval({'name': 'manager', 'type': BuildManager, 

21 'doc': 'the BuildManager to use for I/O', 'default': None}, 

22 {"name": "source", "type": (str, Path), 

23 "doc": "the source of container being built i.e. file path", 'default': None}, 

24 {'name': 'external_resources_path', 'type': str, 

25 'doc': 'The path to the ExternalResources', 'default': None},) 

26 def __init__(self, **kwargs): 

27 manager, source, external_resources_path = getargs('manager', 'source', 'external_resources_path', kwargs) 

28 if isinstance(source, Path): 28 ↛ 29line 28 didn't jump to line 29, because the condition on line 28 was never true

29 source = source.resolve() 

30 elif (isinstance(source, str) and 

31 not (source.lower().startswith("http://") or 

32 source.lower().startswith("https://") or 

33 source.lower().startswith("s3://"))): 

34 source = os.path.abspath(source) 

35 

36 self.__manager = manager 

37 self.__built = dict() 

38 self.__source = source 

39 self.external_resources_path = external_resources_path 

40 self.external_resources = None 

41 self.open() 

42 

43 @property 

44 def manager(self): 

45 '''The BuildManager this instance is using''' 

46 return self.__manager 

47 

48 @property 

49 def source(self): 

50 '''The source of the container being read/written i.e. file path''' 

51 return self.__source 

52 

53 @docval(returns='the Container object that was read in', rtype=Container) 

54 def read(self, **kwargs): 

55 """Read a container from the IO source.""" 

56 f_builder = self.read_builder() 

57 if all(len(v) == 0 for v in f_builder.values()): 

58 # TODO also check that the keys are appropriate. print a better error message 

59 raise UnsupportedOperation('Cannot build data. There are no values.') 

60 container = self.__manager.construct(f_builder) 

61 container.read_io = self 

62 if self.external_resources_path is not None: 

63 from hdmf.common import ExternalResources 

64 try: 

65 self.external_resources = ExternalResources.from_norm_tsv(path=self.external_resources_path) 

66 if isinstance(container, ExternalResourcesManager): 66 ↛ 75line 66 didn't jump to line 75, because the condition on line 66 was never false

67 container.link_resources(external_resources=self.external_resources) 

68 except FileNotFoundError: 

69 msg = "File not found at {}. ExternalResources not added.".format(self.external_resources_path) 

70 warn(msg) 

71 except ValueError: 

72 msg = "Check ExternalResources separately for alterations. ExternalResources not added." 

73 warn(msg) 

74 

75 return container 

76 

77 @docval({'name': 'container', 'type': Container, 'doc': 'the Container object to write'}, 

78 allow_extra=True) 

79 def write(self, **kwargs): 

80 """Write a container to the IO source.""" 

81 container = popargs('container', kwargs) 

82 f_builder = self.__manager.build(container, source=self.__source, root=True) 

83 self.write_builder(f_builder, **kwargs) 

84 

85 @docval({'name': 'src_io', 'type': 'HDMFIO', 'doc': 'the HDMFIO object for reading the data to export'}, 

86 {'name': 'container', 'type': Container, 

87 'doc': ('the Container object to export. If None, then the entire contents of the HDMFIO object will be ' 

88 'exported'), 

89 'default': None}, 

90 {'name': 'write_args', 'type': dict, 'doc': 'arguments to pass to :py:meth:`write_builder`', 

91 'default': dict()}, 

92 {'name': 'clear_cache', 'type': bool, 'doc': 'whether to clear the build manager cache', 

93 'default': False}) 

94 def export(self, **kwargs): 

95 """Export from one backend to the backend represented by this class. 

96 

97 If `container` is provided, then the build manager of `src_io` is used to build the container, and the resulting 

98 builder will be exported to the new backend. So if `container` is provided, `src_io` must have a non-None 

99 manager property. If `container` is None, then the contents of `src_io` will be read and exported to the new 

100 backend. 

101 

102 The provided container must be the root of the hierarchy of the source used to read the container (i.e., you 

103 cannot read a file and export a part of that file. 

104 

105 Arguments can be passed in for the `write_builder` method using `write_args`. Some arguments may not be 

106 supported during export. 

107 

108 Example usage: 

109 

110 .. code-block:: python 

111 

112 old_io = HDF5IO('old.nwb', 'r') 

113 with HDF5IO('new_copy.nwb', 'w') as new_io: 

114 new_io.export(old_io) 

115 

116 NOTE: When implementing export support on custom backends. Export does not update the Builder.source 

117 on the Builders. As such, when writing LinkBuilders we need to determine if LinkBuilder.source 

118 and LinkBuilder.builder.source are the same, and if so the link should be internal to the 

119 current file (even if the Builder.source points to a different location). 

120 """ 

121 src_io, container, write_args, clear_cache = getargs('src_io', 'container', 'write_args', 'clear_cache', kwargs) 

122 if container is None and clear_cache: 

123 # clear all containers and builders from cache so that they can all get rebuilt with export=True. 

124 # constructing the container is not efficient but there is no elegant way to trigger a 

125 # rebuild of src_io with new source. 

126 container = src_io.read() 

127 if container is not None: 

128 # check that manager exists, container was built from manager, and container is root of hierarchy 

129 if src_io.manager is None: 

130 raise ValueError('When a container is provided, src_io must have a non-None manager (BuildManager) ' 

131 'property.') 

132 old_bldr = src_io.manager.get_builder(container) 

133 if old_bldr is None: 

134 raise ValueError('The provided container must have been read by the provided src_io.') 

135 if old_bldr.parent is not None: 

136 raise ValueError('The provided container must be the root of the hierarchy of the ' 

137 'source used to read the container.') 

138 

139 # NOTE in HDF5IO, clear_cache is set to True when link_data is False 

140 if clear_cache: 

141 # clear all containers and builders from cache so that they can all get rebuilt with export=True 

142 src_io.manager.clear_cache() 

143 else: 

144 # clear only cached containers and builders where the container was modified 

145 src_io.manager.purge_outdated() 

146 bldr = src_io.manager.build(container, source=self.__source, root=True, export=True) 

147 else: 

148 bldr = src_io.read_builder() 

149 self.write_builder(builder=bldr, **write_args) 

150 

151 @abstractmethod 

152 @docval(returns='a GroupBuilder representing the read data', rtype='GroupBuilder') 

153 def read_builder(self): 

154 ''' Read data and return the GroupBuilder representing it ''' 

155 pass 

156 

157 @abstractmethod 

158 @docval({'name': 'builder', 'type': GroupBuilder, 'doc': 'the GroupBuilder object representing the Container'}, 

159 allow_extra=True) 

160 def write_builder(self, **kwargs): 

161 ''' Write a GroupBuilder representing an Container object ''' 

162 pass 

163 

164 @abstractmethod 

165 def open(self): 

166 ''' Open this HDMFIO object for writing of the builder ''' 

167 pass 

168 

169 @abstractmethod 

170 def close(self): 

171 ''' Close this HDMFIO object to further reading/writing''' 

172 pass 

173 

174 def __enter__(self): 

175 return self 

176 

177 def __exit__(self, type, value, traceback): 

178 self.close() 

179 

180 def __del__(self): 

181 self.close()