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 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 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