def wrapNewResource(path):
# filter out non-resource file types:
for ext in FILE_INDICES.keys():
if path.endswith(ext):
log.debug('Index file {f} given as regular file, will be treated '
' as an index file instead'.format(f=path))
return
extRes = ExternalResource()
path = resolveLocation(path)
extRes.resourceId = path
index_files = [
path + ext for ext in FILE_INDICES.keys() if os.path.exists(path + ext)
]
if index_files:
extRes.addIndices(index_files)
# Check for sub resources:
for ext in SUB_RESOURCES:
filen = '.'.join(path.split('.')[:-2]) + ext
# don't want to add e.g. scraps to scraps:
if os.path.exists(filen) and path.endswith('subreads.bam'):
log.debug("Adding {} as a subresource".format(filen))
subres = wrapNewResource(filen)
setattr(extRes, ext.split('.')[1], subres)
return extRes
def test_addExternalResources(self):
ds = DataSet()
er1 = ExternalResource()
er1.resourceId = "test1.bam"
er2 = ExternalResource()
er2.resourceId = "test2.bam"
er3 = ExternalResource()
er3.resourceId = "test1.bam"
ds.addExternalResources([er1], updateCount=False)
self.assertEquals(ds.numExternalResources, 1)
# different resourceId: succeeds
ds.addExternalResources([er2], updateCount=False)
self.assertEquals(ds.numExternalResources, 2)
# same resourceId: fails
ds.addExternalResources([er3], updateCount=False)
self.assertEquals(ds.numExternalResources, 2)
for extRef in ds.externalResources:
self.assertEqual(type(extRef).__name__, "ExternalResource")
extRef = ds.externalResources[0]
self.assertEqual(type(extRef).__name__, "ExternalResource")
self.assertEqual(extRef.resourceId, 'test1.bam')
extRef = ds.externalResources[1]
self.assertEqual(type(extRef).__name__, "ExternalResource")
self.assertEqual(extRef.resourceId, 'test2.bam')
def wrapNewResource(path):
possible_indices = [".fai", ".pbi", ".bai", ".metadata.xml"]
for ext in possible_indices:
if path.endswith(ext):
log.debug(
"Index file {f} given as regular file, will be treated " " as an index file instead".format(f=path)
)
return
extRes = ExternalResource()
path = resolveLocation(path)
extRes.resourceId = path
index_files = [path + ext for ext in possible_indices if os.path.exists(path + ext)]
if index_files:
extRes.addIndices(index_files)
return extRes
def wrapNewResource(path):
possible_indices = ['.fai', '.pbi', '.bai', '.metadata.xml']
for ext in possible_indices:
if path.endswith(ext):
log.debug('Index file {f} given as regular file, will be treated '
' as an index file instead'.format(f=path))
return
extRes = ExternalResource()
path = resolveLocation(path)
extRes.resourceId = path
index_files = [
path + ext for ext in possible_indices if os.path.exists(path + ext)
]
if index_files:
extRes.addIndices(index_files)
return extRes
def test_addExternalResources(self):
ds = DataSet()
er1 = ExternalResource()
er1.resourceId = "test1.bam"
er2 = ExternalResource()
er2.resourceId = "test2.bam"
er3 = ExternalResource()
er3.resourceId = "test1.bam"
ds.addExternalResources([er1], updateCount=False)
self.assertEquals(ds.numExternalResources, 1)
# different resourceId: succeeds
ds.addExternalResources([er2], updateCount=False)
self.assertEquals(ds.numExternalResources, 2)
# same resourceId: fails
ds.addExternalResources([er3], updateCount=False)
self.assertEquals(ds.numExternalResources, 2)
for extRef in ds.externalResources:
self.assertEqual(type(extRef).__name__, "ExternalResource")
extRef = ds.externalResources[0]
self.assertEqual(type(extRef).__name__, "ExternalResource")
self.assertEqual(extRef.resourceId, 'test1.bam')
extRef = ds.externalResources[1]
self.assertEqual(type(extRef).__name__, "ExternalResource")
self.assertEqual(extRef.resourceId, 'test2.bam')
def wrapNewResource(path):
# filter out non-resource file types:
for ext in FILE_INDICES:
if path.endswith(ext):
log.debug('Index file {f} given as regular file, will be treated '
' as an index file instead'.format(f=path))
return
extRes = ExternalResource()
path = resolveLocation(path)
extRes.resourceId = path
index_files = [path + ext for ext in FILE_INDICES if
os.path.exists(path + ext)]
if index_files:
extRes.addIndices(index_files)
# Check for sub resources:
for ext in SUB_RESOURCES:
filen = '.'.join(path.split('.')[:-2]) + ext
# don't want to add e.g. scraps to scraps:
if os.path.exists(filen) and path.endswith('subreads.bam'):
subres = wrapNewResource(filen)
setattr(extRes, ext.split('.')[1], subres)
return extRes