def fetch_version(self, version: str, target_filename: Path) -> None:
"""
Takes care of the tool download.
Overrides the ExternalAlgorithm methood. Downloads the VEP cache
to the prebuild location specified by the corresponding
ExternalAlgorithmStore and packs it into a tar.gz file.
Parameters
----------
version : str
The tool version to be used.
target_filename : Path
The path to the local tar.gz file.
"""
url = f"ftp://ftp.ensembl.org/pub/release-{self.revision}/variation/indexed_vep_cache/{self.species}_vep_{self.revision}_{self.grch}.tar.gz"
download_file(url, target_filename.open("wb"))
def download_gunzip_and_attach(url, unzipped_filename, files_to_attach):
import shutil
import gzip
import tempfile
tf = tempfile.NamedTemporaryFile(suffix=".gz")
download_file(url, tf)
tf.flush()
attach = b""
for f in files_to_attach:
attach += Path(f).read_bytes()
with gzip.GzipFile(tf.name, "rb") as gz_in:
with open(unzipped_filename, "wb") as op:
shutil.copyfileobj(gz_in, op)
op.write(attach)
def df(url, filename):
with open(filename, "wb") as op:
download_file(url, op)
def download(url=url, target_fn=target_fn):
Path(target_fn).parent.mkdir(exist_ok=True, parents=True)
target_fn.with_name(target_fn.name + ".url").write_text(url)
with open(str(target_fn) + "_temp", "wb") as op:
download_file(url, op)
shutil.move(str(target_fn) + "_temp", target_fn)
def __dump():
download_file(self.url, outfile.open("wb"))
def __dump():
download_file(self.url, self.input_file.open("wb"))
def get_set_from_url(self):
url = f"https://data.broadinstitute.org/gsea-msigdb/msigdb/release/{self.version}/{self.name}.symbols.gmt"
download_file(url, self._gmt.open("wb"))
def test_download_file_with_filename_raises(self):
from mbf_externals.util import download_file
with pytest.raises(ValueError):
download_file("http://ftp.ensembl.org", "out.file")