def download_test_model(output_dir, overwrite=False) -> None:
os.makedirs(os.path.abspath(output_dir), exist_ok=True)
urls = [
("demo_ilastik_model.zip", "demo.ilp", DEMO_ILASTIK_MODEL),
]
for zipfln, fln, url in urls:
zipfln = pjoin(output_dir, zipfln)
fln = pjoin(output_dir, fln)
if os.path.exists(fln) and not overwrite:
log.debug("File exists, skipping: '%s'", url)
continue
log.info("Downloading test model: '%s'", url)
request.urlretrieve(url, zipfln)
log.info("Unzipping test model: '%s'", url)
run_shell_command(f"unzip -d {output_dir} {zipfln}")
def download_test_data(output_dir, overwrite=False) -> None:
os.makedirs(os.path.abspath(output_dir), exist_ok=True)
urls = [
("imcpipeline-example_pannel.csv", DEMO_CSV),
("imcpipeline-demo_data.zip", DEMO_DATA),
]
for fln, url in urls:
fln = pjoin(output_dir, fln)
if os.path.exists(fln) and not overwrite:
log.debug("File exists, skipping: '%s'", url)
continue
log.info("Downloading test file: '%s'", url)
if not os.path.exists(fln):
request.urlretrieve(url, fln)
def get_docker_image_or_build() -> None:
"""Pull docker image to use or build it if not existing."""
def check_image() -> bool:
try:
# check if exists
out = (subprocess.check_output(
"docker images".split(" ")).decode().strip())
for line in out.split("\n")[1:]:
if line.split(" ")[0] == DOCKER_IMAGE:
return True
except FileNotFoundError:
log.error("Docker installation not detected.")
raise
except IndexError:
pass
return False
if not check_image():
log.debug("Did not find cellprofiler docker image. Will build.")
build_docker_image()
else:
log.debug("Found docker image.")
cfg.args.container_image = DOCKER_IMAGE
def run_shell_command(cmd) -> int:
"""
Run a system command.
Will detect whether a separate shell is required.
"""
# in case the command has unix pipes or bash builtins,
# the subprocess call must have its own shell
# this should only occur if cellprofiler is being run uncontainerized
# and needs a command to be called prior such as conda activate, etc
symbol = any([x in cmd for x in ["&", "&&", "|"]])
source = cmd.startswith("source")
shell = bool(symbol or source)
log.debug(
"Running command%s:\n%s",
" in shell" if shell else "",
textwrap.dedent(cmd) + "\n",
)
c = re.findall(r"\S+", cmd.replace("\\\n", ""))
if not cfg.args.dry_run:
if shell:
log.debug("Running command in shell.")
code = subprocess.call(cmd, shell=shell)
else:
code = subprocess.call(c, shell=shell)
if code != 0:
log.error(
"Process for command below failed with error:\n'%s'\nTerminating pipeline.\n",
textwrap.dedent(cmd),
)
sys.exit(code)
if not shell:
usage = resource.getrusage(resource.RUSAGE_SELF)
log.debug("Maximum used memory so far: {:.2f}Gb".format(
usage.ru_maxrss / 1e6))
return code