def make_progress() -> Progress:
_time = 0.0
def fake_time():
nonlocal _time
try:
return _time
finally:
_time += 1
console = Console(
file=io.StringIO(),
force_terminal=True,
color_system="truecolor",
width=80,
legacy_windows=False,
_environ={},
)
progress = Progress(console=console, get_time=fake_time, auto_refresh=False)
task1 = progress.add_task("foo")
task2 = progress.add_task("bar", total=30)
progress.advance(task2, 16)
task3 = progress.add_task("baz", visible=False)
task4 = progress.add_task("egg")
progress.remove_task(task4)
task4 = progress.add_task("foo2", completed=50, start=False)
progress.stop_task(task4)
progress.start_task(task4)
progress.update(
task4, total=200, advance=50, completed=200, visible=True, refresh=True
)
progress.stop_task(task4)
return progress
def singularity_download_image(self, container, out_path, cache_path,
progress):
"""Download a singularity image from the web.
Use native Python to download the file.
Args:
container (str): A pipeline's container name. Usually it is of similar format
to ``https://depot.galaxyproject.org/singularity/name:version``
out_path (str): The final target output path
cache_path (str, None): The NXF_SINGULARITY_CACHEDIR path if set, None if not
progress (Progress): Rich progress bar instance to add tasks to.
"""
log.debug(f"Downloading Singularity image: '{container}'")
# Set output path to save file to
output_path = cache_path or out_path
output_path_tmp = f"{output_path}.partial"
log.debug(f"Downloading to: '{output_path_tmp}'")
# Set up progress bar
nice_name = container.split("/")[-1][:50]
task = progress.add_task(nice_name,
start=False,
total=False,
progress_type="download")
try:
# Delete temporary file if it already exists
if os.path.exists(output_path_tmp):
os.remove(output_path_tmp)
# Open file handle and download
with open(output_path_tmp, "wb") as fh:
# Disable caching as this breaks streamed downloads
with requests_cache.disabled():
r = requests.get(container,
allow_redirects=True,
stream=True,
timeout=60 * 5)
filesize = r.headers.get("Content-length")
if filesize:
progress.update(task, total=int(filesize))
progress.start_task(task)
# Stream download
for data in r.iter_content(chunk_size=4096):
# Check that the user didn't hit ctrl-c
if self.kill_with_fire:
raise KeyboardInterrupt
progress.update(task, advance=len(data))
fh.write(data)
# Rename partial filename to final filename
os.rename(output_path_tmp, output_path)
output_path_tmp = None
# Copy cached download if we are using the cache
if cache_path:
log.debug("Copying {} from cache: '{}'".format(
container, os.path.basename(out_path)))
progress.update(
task, description="Copying from cache to target directory")
shutil.copyfile(cache_path, out_path)
progress.remove_task(task)
except:
# Kill the progress bars
for t in progress.task_ids:
progress.remove_task(t)
# Try to delete the incomplete download
log.debug(
f"Deleting incompleted singularity image download:\n'{output_path_tmp}'"
)
if output_path_tmp and os.path.exists(output_path_tmp):
os.remove(output_path_tmp)
if output_path and os.path.exists(output_path):
os.remove(output_path)
# Re-raise the caught exception
raise