Coverage for src/hdmf/backends/io.py: 98%

85 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, HERDManager 

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': 'herd_path', 'type': str, 

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

26 def __init__(self, **kwargs): 

27 manager, source, herd_path = getargs('manager', 'source', 'herd_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.herd_path = herd_path 

40 self.herd = 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.herd_path is not None: 

63 from hdmf.common import HERD 

64 try: 

65 self.herd = HERD.from_zip(path=self.herd_path) 

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

67 container.link_resources(herd=self.herd) 

68 except FileNotFoundError: 

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

70 warn(msg) 

71 except ValueError: 

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

73 warn(msg) 

74 

75 return container 

76 

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

78 def write(self, **kwargs): 

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

80 container = popargs('container', kwargs) 

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

82 self.write_builder(f_builder, **kwargs) 

83 

84 if self.herd_path is not None: 

85 herd = container.get_linked_resources() 

86 if herd is not None: 

87 herd.to_zip(path=self.herd_path) 

88 else: 

89 msg = "Could not find linked HERD. Container was still written to IO source." 

90 warn(msg) 

91 

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

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

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

95 'exported'), 

96 'default': None}, 

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

98 'default': dict()}, 

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

100 'default': False}) 

101 def export(self, **kwargs): 

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

103 

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

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

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

107 backend. 

108 

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

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

111 

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

113 supported during export. 

114 

115 Example usage: 

116 

117 .. code-block:: python 

118 

119 old_io = HDF5IO('old.nwb', 'r') 

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

121 new_io.export(old_io) 

122 

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

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

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

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

127 """ 

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

129 if container is None and clear_cache: 

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

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

132 # rebuild of src_io with new source. 

133 container = src_io.read() 

134 if container is not None: 

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

136 if src_io.manager is None: 

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

138 'property.') 

139 old_bldr = src_io.manager.get_builder(container) 

140 if old_bldr is None: 

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

142 if old_bldr.parent is not None: 

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

144 'source used to read the container.') 

145 

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

147 if clear_cache: 

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

149 src_io.manager.clear_cache() 

150 else: 

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

152 src_io.manager.purge_outdated() 

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

154 else: 

155 bldr = src_io.read_builder() 

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

157 

158 @abstractmethod 

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

160 def read_builder(self): 

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

162 pass 

163 

164 @abstractmethod 

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

166 allow_extra=True) 

167 def write_builder(self, **kwargs): 

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

169 pass 

170 

171 @abstractmethod 

172 def open(self): 

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

174 pass 

175 

176 @abstractmethod 

177 def close(self): 

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

179 pass 

180 

181 def __enter__(self): 

182 return self 

183 

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

185 self.close() 

186 

187 def __del__(self): 

188 self.close()