mirror of
https://github.com/chanzuckerberg/cellxgene.git
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a593e95ab3
* rename config param label-file * annotations rework - CLI params, file naming and backups * lint * improve cli option error checks * enable session cookies * enable session cookies * add session id * name annotations file in multi-dataset and multi-user safe manner * pass data user hash to front-end * add annotation collection name support to front-end * add constant for annotation data collection name * parameterize annotation collection name; make it sticky in the session * clarify comments * hard wire a temporary data collection name for testing * prettier * test comment * package command * set annotations filename dialog * name and hash are visible * wire up data collection capture
104 lines
3.2 KiB
Python
104 lines
3.2 KiB
Python
import os
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import tempfile
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import fsspec
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from datetime import datetime
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class DataLocator():
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"""
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DataLocator is a simple wrapper around fsspec functionality, and provides a
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set of functions to encapsulate a data location (URI or path), interogate
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metadata about the object at that location (size, existance, etc) and
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access the underlying data.
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https://filesystem-spec.readthedocs.io/en/latest/index.html
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Example:
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dl = DataLocator("/tmp/foo.h5ad")
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if dl.exists():
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print(dl.size())
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with dl.open() as f:
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thecontents = f.read()
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DataLocator will accept a URI or native path. Error handling is as defined
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in fsspec.
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"""
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def __init__(self, uri_or_path):
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self.uri_or_path = uri_or_path
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self.protocol, self.path = DataLocator._get_protocol_and_path(uri_or_path)
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# work-around for LocalFileSystem not treating file: and None as the same scheme/protocol
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self.cname = self.path if self.protocol == 'file' else self.uri_or_path
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# will throw RuntimeError if the protocol is unsupported
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self.fs = fsspec.filesystem(self.protocol)
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@staticmethod
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def _get_protocol_and_path(uri_or_path):
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if "://" in uri_or_path:
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protocol, path = uri_or_path.split("://", 1)
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# windows!!! Ignore single letter drive identifiers,
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# eg, G:\foo.txt
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if len(protocol) > 1:
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return protocol, path
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return None, uri_or_path
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def exists(self):
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return self.fs.exists(self.cname)
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def size(self):
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return self.fs.size(self.cname)
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def lastmodtime(self):
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""" return datetime object representing last modification time, or None if unavailable """
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info = self.fs.info(self.cname)
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if self.islocal() and info is not None:
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return datetime.fromtimestamp(info['mtime'])
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else:
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return getattr(info, 'LastModified', None)
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def abspath(self):
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"""
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return the absolute path for the locator - only really does something
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for file: protocol, as all others are already absolute
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"""
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if self.islocal():
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return os.path.abspath(self.path)
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else:
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return self.uri_or_path
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def isfile(self):
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return self.fs.isfile(self.cname)
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def open(self, *args):
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return self.fs.open(self.uri_or_path, *args)
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def islocal(self):
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return self.protocol is None or self.protocol == 'file'
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def local_handle(self):
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if self.islocal():
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return LocalFilePath(self.path)
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# if not local, create a tmp file system object to contain the data,
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# and clean it up when done.
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with self.open() as src, tempfile.NamedTemporaryFile(prefix="cellxgene_", delete=False) as tmp:
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tmp.write(src.read())
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tmp.close()
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src.close()
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tmp_path = tmp.name
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return LocalFilePath(tmp_path, delete=True)
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class LocalFilePath():
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def __init__(self, tmp_path, delete=False):
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self.tmp_path = tmp_path
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self.delete = delete
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def __enter__(self):
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return self.tmp_path
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def __exit__(self, *args):
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if self.delete:
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os.unlink(self.tmp_path)
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