def __init__(self, dataDir):
super(FileSystemBackend, self).__init__()
self._dataDir = dataDir
# TODO this code is very ugly and should be regarded as a temporary
# stop-gap until we deal with iterating over the data tree properly.
# References
referencesDirName = "references"
referenceSetDir = os.path.join(self._dataDir, referencesDirName)
for referenceSetId in os.listdir(referenceSetDir):
relativePath = os.path.join(referenceSetDir, referenceSetId)
if os.path.isdir(relativePath):
referenceSet = references.HtslibReferenceSet(
referenceSetId, relativePath)
self._referenceSetIdMap[referenceSetId] = referenceSet
for reference in referenceSet.getReferences():
referenceId = reference.getId()
self._referenceIdMap[referenceId] = reference
self._referenceSetIds = sorted(self._referenceSetIdMap.keys())
self._referenceIds = sorted(self._referenceIdMap.keys())
# Datasets
datasetDirs = [
os.path.join(self._dataDir, directory)
for directory in os.listdir(self._dataDir)
if os.path.isdir(os.path.join(self._dataDir, directory)) and
directory != referencesDirName]
for datasetDir in datasetDirs:
dataset = datasets.FileSystemDataset(datasetDir)
self._datasetIdMap[dataset.getId()] = dataset
self._datasetIds = sorted(self._datasetIdMap.keys())
def __init__(self, dataDir):
super(FileSystemBackend, self).__init__()
self._dataDir = dataDir
# TODO this code is very ugly and should be regarded as a temporary
# stop-gap until we deal with iterating over the data tree properly.
# References
referencesDirName = "references"
referenceSetDir = os.path.join(self._dataDir, referencesDirName)
for referenceSetName in os.listdir(referenceSetDir):
relativePath = os.path.join(referenceSetDir, referenceSetName)
if os.path.isdir(relativePath):
referenceSet = references.HtslibReferenceSet(
referenceSetName, relativePath, self)
self.addReferenceSet(referenceSet)
# Datasets
datasetDirs = [
os.path.join(self._dataDir, directory)
for directory in os.listdir(self._dataDir)
if os.path.isdir(os.path.join(self._dataDir, directory))
and directory != referencesDirName
]
for datasetDir in datasetDirs:
dataset = datasets.FileSystemDataset(datasetDir, self)
self.addDataset(dataset)
def testBadReferenceDatasetMetadata(self):
localId = "bad_metadata"
path = self.getFullPath(localId)
localBackend = backend.EmptyBackend()
with self.assertRaises(exceptions.MissingDatasetMetadataException):
datasets.FileSystemDataset(localId, path, localBackend)