Source code for

import logging
import os
import tarfile
import tempfile

import h5py
import numpy

logger = logging.getLogger("")


from import database

[docs]def filter_missing_files( file_names, split_by_client=False, allow_missing_files=True ): """This function filters out files that do not exist, but only if ``allow_missing_files`` is set to ``True``, otherwise the list of ``file_names`` is returned unaltered.""" if not allow_missing_files: return file_names if split_by_client: # filter out missing files and empty clients existing_files = [ [f for f in client_files if os.path.exists(f)] for client_files in file_names ] existing_files = [ client_files for client_files in existing_files if client_files ] else: # filter out missing files existing_files = [f for f in file_names if os.path.exists(f)] return existing_files
[docs]def filter_none(data, split_by_client=False): """This function filters out ``None`` values from the given list (or list of lists, when ``split_by_client`` is enabled).""" if split_by_client: # filter out missing files and empty clients existing_data = [ [d for d in client_data if d is not None] for client_data in data ] existing_data = [ client_data for client_data in existing_data if client_data ] else: # filter out missing files existing_data = [d for d in data if d is not None] return existing_data
[docs]def check_file(filename, force, expected_file_size=1): """Checks if the file with the given ``filename`` exists and has size greater or equal to ``expected_file_size``. If the file is to small, **or** if the ``force`` option is set to ``True``, the file is removed. This function returns ``True`` is the file exists (and has not been removed), otherwise ``False``""" if os.path.exists(filename): if force or os.path.getsize(filename) < expected_file_size: logger.debug(" .. Removing old file '%s'.", filename) os.remove(filename) return False else: return True return False
[docs]def read_original_data(biofile, directory, extension): """This function reads the original data using the given ``biofile`` instance. It simply calls ``load(directory, extension)`` from :py:class:`` or one of its derivatives. Parameters ---------- biofile : :py:class:`` or one of its derivatives The file to read the original data. directory : str The base directory of the database. extension : str or ``None`` The extension of the original data. Might be ``None`` if the ``biofile`` itself has the extension stored. Returns ------- object Whatver ``biofile.load`` returns; usually a :py:class:`numpy.ndarray` """ assert isinstance(biofile, database.BioFile) return biofile.load(directory, extension)
[docs]def load(file): """Loads data from file. The given file might be an HDF5 file open for reading or a string.""" if isinstance(file, h5py.File): return numpy.array(file["array"]) else: return
[docs]def save(data, file, compression=0): """Saves the data to file using HDF5. The given file might be an HDF5 file open for writing, or a string. If the given data contains a ``save`` method, this method is called with the given HDF5 file. Otherwise the data is written to the HDF5 file using the given compression.""" f = file if isinstance(file, h5py.File) else h5py.File(file, "w") if hasattr(data, "save"): else: f["array"] = data
[docs]def open_compressed(filename, open_flag="r", compression_type="bz2"): """Opens a compressed HDF5File with the given opening flags. For the 'r' flag, the given compressed file will be extracted to a local space. For 'w', an empty HDF5File is created. In any case, the opened HDF5File is returned, which needs to be closed using the close_compressed() function. """ # create temporary HDF5 file name hdf5_file_name = tempfile.mkstemp(".hdf5", "bob_")[1] if open_flag == "r": # extract the HDF5 file from the given file name into a temporary file name tar =, mode="r:" + compression_type) memory_file = tar.extractfile( real_file = open(hdf5_file_name, "wb") real_file.write( del memory_file real_file.close() tar.close() return h5py.File(hdf5_file_name, open_flag)
[docs]def close_compressed( filename, hdf5_file, compression_type="bz2", create_link=False ): """Closes the compressed hdf5_file that was opened with open_compressed. When the file was opened for writing (using the 'w' flag in open_compressed), the created HDF5 file is compressed into the given file name. To be able to read the data using the real tools, a link with the correct extension might is created, when create_link is set to True. """ hdf5_file_name = hdf5_file.filename is_writable = hdf5_file.writable hdf5_file.close() if is_writable: # create compressed tar file tar =, mode="w:" + compression_type) tar.add(hdf5_file_name, os.path.basename(filename)) tar.close() if create_link: extension = {"": ".tar", "bz2": ".tar.bz2", "gz": "tar.gz"}[ compression_type ] link_file = filename + extension if not os.path.exists(link_file): os.symlink(os.path.basename(filename), link_file) # clean up locally generated files os.remove(hdf5_file_name)
[docs]def load_compressed(filename, compression_type="bz2"): """Extracts the data to a temporary HDF5 file using HDF5 and reads its contents. Note that, though the file name is .hdf5, it contains compressed data! Accepted compression types are 'gz', 'bz2', ''""" # read from compressed HDF5 hdf5 = open_compressed(filename, "r") data = numpy.array(hdf5["array"]) close_compressed(filename, hdf5) return data
[docs]def save_compressed(data, filename, compression_type="bz2", create_link=False): """Saves the data to a temporary file using HDF5. Afterwards, the file is compressed using the given compression method and saved using the given file name. Note that, though the file name will be .hdf5, it will contain compressed data! Accepted compression types are 'gz', 'bz2', ''""" # write to compressed HDF5 file hdf5 = open_compressed(filename, "w") save(data, hdf5) close_compressed(filename, hdf5, compression_type, create_link)