mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-19 10:58:10 +08:00
20317fd08f
* initial commit of URL support for launch * lint * modify tests to use new data locator * add locator unit tests * fix typo in faq * more lint * update faq per PR review
85 lines
2.6 KiB
Python
85 lines
2.6 KiB
Python
import os
|
|
import tempfile
|
|
import fsspec
|
|
|
|
|
|
class DataLocator():
|
|
"""
|
|
DataLocator is a simple wrapper around fsspec functionality, and provides a
|
|
set of functions to encapsulate a data location (URI or path), interogate
|
|
metadata about the object at that location (size, existance, etc) and
|
|
access the underlying data.
|
|
|
|
https://filesystem-spec.readthedocs.io/en/latest/index.html
|
|
|
|
Example:
|
|
dl = DataLocator("/tmp/foo.h5ad")
|
|
if dl.exists():
|
|
print(dl.size())
|
|
with dl.open() as f:
|
|
thecontents = f.read()
|
|
|
|
DataLocator will accept a URI or native path. Error handling is as defined
|
|
in fsspec.
|
|
|
|
"""
|
|
|
|
def __init__(self, uri_or_path):
|
|
self.uri_or_path = uri_or_path
|
|
self.protocol, self.path = DataLocator._get_protocol_and_path(uri_or_path)
|
|
# work-around for LocalFileSystem not treating file: and None as the same scheme/protocol
|
|
self.cname = self.path if self.protocol == 'file' else self.uri_or_path
|
|
# will throw RuntimeError if the protocol is unsupported
|
|
self.fs = fsspec.filesystem(self.protocol)
|
|
|
|
@staticmethod
|
|
def _get_protocol_and_path(uri_or_path):
|
|
if "://" in uri_or_path:
|
|
protocol, path = uri_or_path.split("://", 1)
|
|
# windows!!! Ignore single letter drive identifiers,
|
|
# eg, G:\foo.txt
|
|
if len(protocol) > 1:
|
|
return protocol, path
|
|
return None, uri_or_path
|
|
|
|
def exists(self):
|
|
return self.fs.exists(self.cname)
|
|
|
|
def size(self):
|
|
return self.fs.size(self.cname)
|
|
|
|
def isfile(self):
|
|
return self.fs.isfile(self.cname)
|
|
|
|
def open(self, *args):
|
|
return self.fs.open(self.uri_or_path, *args)
|
|
|
|
def islocal(self):
|
|
return self.protocol is None or self.protocol == 'file'
|
|
|
|
def local_handle(self):
|
|
if self.islocal():
|
|
return LocalFilePath(self.path)
|
|
|
|
# if not local, create a tmp file system object to contain the data,
|
|
# and clean it up when done.
|
|
with self.open() as src, tempfile.NamedTemporaryFile(prefix="cellxgene_", delete=False) as tmp:
|
|
tmp.write(src.read())
|
|
tmp.close()
|
|
src.close()
|
|
tmp_path = tmp.name
|
|
return LocalFilePath(tmp_path, delete=True)
|
|
|
|
|
|
class LocalFilePath():
|
|
def __init__(self, tmp_path, delete=False):
|
|
self.tmp_path = tmp_path
|
|
self.delete = delete
|
|
|
|
def __enter__(self):
|
|
return self.tmp_path
|
|
|
|
def __exit__(self, *args):
|
|
if self.delete:
|
|
os.unlink(self.tmp_path)
|