Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

[FIX] Add a timeout when trying to retrieve dcm2bids version #154

Merged
merged 9 commits into from
May 30, 2022
Merged

[FIX] Add a timeout when trying to retrieve dcm2bids version #154

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
08bc4b1
Remove internet() function and add timeout in check_github_latest()
po09i Apr 11, 2022
a82a836
Remove testing of the internet() function
po09i Apr 11, 2022
d285794
Split logging into info and debug
po09i Apr 25, 2022
3fa7f4b
Add exception names in the except clause
po09i Apr 28, 2022
710529b
Merge branch 'master' into ad/internet
po09i May 26, 2022
9060400
Remove unused import
po09i May 27, 2022
6e7cf4a
Check versions after initializing the logger
po09i May 27, 2022
357c401
Add ability for curl to follow redirect links
po09i May 27, 2022
e4ad28b
Restrict version to 5 charaters
po09i May 27, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 4 additions & 3 deletions dcm2bids/dcm2bids.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -103,6 +103,10 @@ def run(self):
self.participant,
self.config.get("dcm2niixOptions", DEFAULT.dcm2niixOptions),
)

check_latest()
check_latest("dcm2niix")

dcm2niix.run(self.forceDcm2niix)

sidecars = []
Expand Down Expand Up @@ -236,9 +240,6 @@ def main():
parser = _build_arg_parser()
args = parser.parse_args()

check_latest()
check_latest("dcm2niix")

app = Dcm2bids(**vars(args))
return app.run()

Expand Down
59 changes: 19 additions & 40 deletions dcm2bids/version.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,38 +8,14 @@

import logging
import shlex
import socket
from distutils.version import LooseVersion
from subprocess import check_output
from subprocess import check_output, CalledProcessError, TimeoutExpired
from shutil import which


logger = logging.getLogger(__name__)


def internet(host="8.8.8.8", port=53, timeout=3):
""" Check if user has internet

Args:
host (string): 8.8.8.8 (google-public-dns-a.google.com)
port (int): OpenPort 53/tcp
Service: domain (DNS/TCP)
timeout (int): default=3

Returns:
boolean

Source: https://stackoverflow.com/a/33117579
"""
try:
socket.setdefaulttimeout(timeout)
socket.socket(socket.AF_INET, socket.SOCK_STREAM).connect((host, port))
return True

except:
return False


def is_tool(name):
""" Check if a program is in PATH

Expand All @@ -51,33 +27,36 @@ def is_tool(name):
return which(name) is not None


def check_github_latest(githubRepo):
def check_github_latest(githubRepo, timeout=3):
""" Check the latest version of a github repository

Args:
githubRepo (string): a github repository ("username/repository")
timeout (int): time in seconds

Returns:
A string of the version
"""
url = "https://github.com/{}/releases/latest".format(githubRepo)
try:
output = check_output(shlex.split("curl --silent " + url))
except:
logger.debug(
"Checking latest version of %s was not possible", githubRepo,
exc_info=True,
)
output = check_output(shlex.split("curl -L --silent " + url), timeout=timeout)
except CalledProcessError:
logger.info(f"Checking latest version of {githubRepo} was not possible")
logger.debug(f"Error while 'curl --silent {url}'", exc_info=True)
return
except TimeoutExpired:
logger.info(f"Checking latest version of {githubRepo} was not possible")
logger.debug(f"Command 'curl --silent {url}' timed out after {timeout}s")
return

# The output should have this format
# <html><body>You are being <a href="https://github.com/{gitRepo}/releases/tag/{version}">redirected</a>.</body></html>
try:
return (
output.decode()
.split("{}/releases/tag/".format(githubRepo))[1]
.split('"')[0]
)
version = output.decode().split("{}/releases/tag/".format(githubRepo))[1].split('"')[0]

# Versions are X.X.X
if len(version) > 5:
version = version[:5]
return version
except:
logger.debug(
"Checking latest version of %s was not possible", githubRepo,
Expand Down Expand Up @@ -109,7 +88,7 @@ def check_latest(name="dcm2bids"):
},
}

if internet() and is_tool("curl"):
if is_tool("curl"):
host = data.get(name)["host"]

if host == "https://github.com":
Expand All @@ -122,7 +101,7 @@ def check_latest(name="dcm2bids"):

else:
logger.debug("Checking latest version of %s was not possible", name)
logger.debug("internet: %s, curl: %s", internet(), is_tool("curl"))
logger.debug("curl: %s", is_tool("curl"))
return

current = data.get(name)["current"]
Expand Down
6 changes: 1 addition & 5 deletions tests/test_version.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,11 +1,7 @@
# -*- coding: utf-8 -*-


from dcm2bids.version import internet, is_tool, check_github_latest, __version__


def test_internet():
assert internet(port=1234) is False
from dcm2bids.version import is_tool, check_github_latest, __version__


def test_is_tool():
Expand Down