CoverageDr

><> from coverage_model import *

><> from coverage_model.recovery import CoverageDoctor

><> cov=SimplexCoverage.load('test_data/6eced7e8466f4d70a5d8febe0b9178f2')
---------------------------------------------------------------------------
IOError                                   Traceback (most recent call last)
/Users/cmueller/Development/OOI/Dev/code/coverage-model/extern/pyon/scripts/pycc.pyc in <module>()
----> 1 cov=SimplexCoverage.load('test_data/6eced7e8466f4d70a5d8febe0b9178f2')

/Users/cmueller/Development/OOI/Dev/code/coverage-model/coverage_model/coverage.pyc in load(cls, root_dir, persistence_guid, mode)
    104             raise ValueError('\'persistence_guid\' must be a string')
    105 
--> 106         return SimplexCoverage(root_dir, persistence_guid, mode=mode)
    107 
    108     @classmethod

/Users/cmueller/Development/OOI/Dev/code/coverage-model/coverage_model/coverage.pyc in __init__(self, root_dir, persistence_guid, name, parameter_dictionary, temporal_domain, spatial_domain, mode, in_memory_storage, bricking_scheme, inline_data_writes, auto_flush_values)
    270             if name is None or parameter_dictionary is None:
    271                 # This appears to be a load
--> 272                 _doload(self)
    273 
    274             else:

/Users/cmueller/Development/OOI/Dev/code/coverage-model/coverage_model/coverage.pyc in _doload(self)
    244 
    245                 # All appears well - load it up!
--> 246                 self._persistence_layer = PersistenceLayer(root_dir, persistence_guid, mode=self.mode)
    247 
    248                 self.name = self._persistence_layer.name

/Users/cmueller/Development/OOI/Dev/code/coverage-model/coverage_model/persistence.pyc in __init__(self, root, guid, name, tdom, sdom, mode, bricking_scheme, inline_data_writes, auto_flush_values, **kwargs)
     47         root = '.' if root is ('' or None) else root
     48 
---> 49         self.master_manager = MasterManager(root, guid, name=name, tdom=tdom, sdom=sdom, global_bricking_scheme=bricking_scheme)
     50 
     51         self.mode = mode

/Users/cmueller/Development/OOI/Dev/code/coverage-model/coverage_model/persistence_helpers.pyc in __init__(self, root_dir, guid, **kwargs)
    138 
    139     def __init__(self, root_dir, guid, **kwargs):
--> 140         BaseManager.__init__(self, root_dir=os.path.join(root_dir,guid), file_name='{0}_master.hdf5'.format(guid), **kwargs)
    141         self.guid = guid
    142 

/Users/cmueller/Development/OOI/Dev/code/coverage-model/coverage_model/persistence_helpers.pyc in __init__(self, root_dir, file_name, **kwargs)
     37 
     38         if os.path.exists(self.file_path):
---> 39             self._load()
     40 
     41         for k, v in kwargs.iteritems():

/Users/cmueller/Development/OOI/Dev/code/coverage-model/coverage_model/persistence_helpers.pyc in _load(self)
    148     def _load(self):
    149         with h5py.File(self.file_path, 'r') as f:
--> 150             self._base_load(f)
    151 
    152             self.param_groups = set()

/Users/cmueller/Development/OOI/Dev/code/coverage-model/coverage_model/persistence_helpers.pyc in _base_load(self, f)
     71 
     72     def _base_load(self, f):
---> 73         for key, val in f.attrs.iteritems():
     74             if val.startswith('DICTABLE'):
     75                 i = val.index('|', 9)

/Users/cmueller/Development/OOI/Dev/code/coverage-model/eggs/h5py-2.1.1a1-py2.7-macosx-10.6-intel.egg/h5py/_hl/base.pyc in iteritems(self)
    276             """ Get an iterator over (name, object) pairs """
    277             for x in self:
--> 278                 yield (x, self[x])
    279 
    280 

/Users/cmueller/Development/OOI/Dev/code/coverage-model/eggs/h5py-2.1.1a1-py2.7-macosx-10.6-intel.egg/h5py/_hl/attrs.pyc in __getitem__(self, name)
     41 
     42         arr = numpy.ndarray(attr.shape, dtype=rtdt, order='C')
---> 43         attr.read(arr)
     44 
     45         if len(arr.shape) == 0:

/Users/cmueller/Development/OOI/Dev/code/coverage-model/eggs/h5py-2.1.1a1-py2.7-macosx-10.6-intel.egg/h5py/h5a.so in h5py.h5a.AttrID.read (h5py/h5a.c:4125)()

/Users/cmueller/Development/OOI/Dev/code/coverage-model/eggs/h5py-2.1.1a1-py2.7-macosx-10.6-intel.egg/h5py/_proxy.so in h5py._proxy.attr_rw (h5py/_proxy.c:855)()

IOError: unable to read attribute (Attribute: Read failed)

><> cd=CoverageDoctor('test_data/6eced7e8466f4d70a5d8febe0b9178f2',None,None)

><> ar=cd.analyze()
h5dump(50629) malloc: *** error for object 0x100356e10: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug

><> ar.is_corrupt
--> True

><> cd.repair()
Fixed Master!  Original file moved to: test_data/6eced7e8466f4d70a5d8febe0b9178f2/6eced7e8466f4d70a5d8febe0b9178f2_master_orig.hdf5
--> True

><> cov=SimplexCoverage.load('test_data/6eced7e8466f4d70a5d8febe0b9178f2')

><> cov.num_timesteps
--> 9888

><> cov.list_parameters()
--> 
['conductivity',
 'density',
 'driver_timestamp',
 'internal_timestamp',
 'lat',
 'lon',
 'port_timestamp',
 'preferred_timestamp',
 'pressure',
 'quality_flag',
 'salinity',
 'temp',
 'time']