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Solve macOS issue with ~/.docker/config.json file when pulling the co…
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…ntainer
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@danifranco
danifranco committed May 23, 2024
1 parent a11945f commit b880ade
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Showing 2 changed files with 89 additions and 20 deletions.
107 changes: 88 additions & 19 deletions run_functions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,8 @@
import numpy as np
from datetime import datetime, timedelta
import multiprocessing
import json
from pathlib import Path

from PySide2 import QtCore, QtGui, QtWidgets
from PySide2.QtCore import Qt, QObject, QUrl
Expand Down Expand Up @@ -250,25 +252,92 @@ def run(self):
self.process_steps = "pulling"
# Collect the output of the container and update the GUI
self.total_layers = {}
for item in self.docker_client.api.pull(self.main_gui.cfg.settings['biapy_container_name'], stream=True, decode=True):
self.main_gui.logger.info(item)
if item["status"] == 'Pulling fs layer':
self.total_layers[item["id"]+"_download"] = 0
self.total_layers[item["id"]+"_extract"] = 0
elif item["status"] == "Downloading":
self.total_layers[item["id"]+"_download"] = item["progressDetail"]['current']/item["progressDetail"]['total']
elif item["status"] == "Extracting":
self.total_layers[item["id"]+"_extract"] = item["progressDetail"]['current']/item["progressDetail"]['total']
elif item["status"] == "Pull complete":
self.total_layers[item["id"]+"_download"] = 1
self.total_layers[item["id"]+"_extract"] = 1

if self.break_pulling:
self.main_gui.logger.info("Stopping pulling process . . .")
return
# Update GUI
steps = np.sum([int(float(x)*10) for x in self.total_layers.values()])
self.update_pulling_progress_signal.emit(steps)
problem_attempts = 0
json_orig_data = None
while problem_attempts < 4:
try:
self.main_gui.logger.info("Pulling container . . .")
self.docker_client = docker.from_env() # Necessary
for item in self.docker_client.api.pull(self.main_gui.cfg.settings['biapy_container_name'], stream=True, decode=True):
self.main_gui.logger.info(item)
if item["status"] == 'Pulling fs layer':
self.total_layers[item["id"]+"_download"] = 0
self.total_layers[item["id"]+"_extract"] = 0
elif item["status"] == "Downloading":
self.total_layers[item["id"]+"_download"] = item["progressDetail"]['current']/item["progressDetail"]['total']
elif item["status"] == "Extracting":
self.total_layers[item["id"]+"_extract"] = item["progressDetail"]['current']/item["progressDetail"]['total']
elif item["status"] == "Pull complete":
self.total_layers[item["id"]+"_download"] = 1
self.total_layers[item["id"]+"_extract"] = 1

if self.break_pulling:
self.main_gui.logger.info("Stopping pulling process . . .")
return
# Update GUI
steps = np.sum([int(float(x)*10) for x in self.total_layers.values()])
self.update_pulling_progress_signal.emit(steps)
except Exception as e:
problem_attempts += 1
self.main_gui.logger.error(f"Error pulling the container: {e}")
self.main_gui.logger.info(f"Trying to modify ~/.docker/config.json - (attempt {problem_attempts})")

# Attempt 1: trying to change the values of "credsStore" and some possible typos as documented in
# the issue: https://github.com/docker/for-mac/issues/3785#issuecomment-518328553
if problem_attempts == 1:
try:
with open(Path.home() / ".docker" / "config.json", "r") as jsonFile:
data = json.load(jsonFile)
json_orig_data = data.copy()

# Possible typo
if "credSstore" in data:
val = data["credSstore"]
del data["credSstore"]
data["credsStore"] = val

# Change credsStore value
if "credsStore" in data:
val = data["credsStore"]
data["credsStore"] = "osxkeychain" if "desktop" in val else "desktop"

with open(Path.home() / ".docker" / "config.json", "w") as jsonFile:
json.dump(data, jsonFile, indent=4)
except Exception as e:
self.main_gui.logger.error(f"Error modifying ~/.docker/config.json file (attempt 1): {e}")

# Attempt 2: remove "credsStore" key
elif problem_attempts == 2:
try:
with open(Path.home() / ".docker" / "config.json", "r") as jsonFile:
data = json.load(jsonFile)

# Delete credsStore directly
if "credsStore" in data:
del data["credsStore"]

with open(Path.home() / ".docker" / "config.json", "w") as jsonFile:
json.dump(data, jsonFile, indent=4)

except Exception as e:
self.main_gui.logger.error(f"Error modifying ~/.docker/config.json file (attempt 2): {e}")

# Attempt 3: rename the file
else:
try:
os.rename(Path.home() / ".docker" / "config.json", Path.home() / ".docker" / "config.json.backup")
except Exception as e:
self.main_gui.logger.error(f"Error modifying ~/.docker/config.json file (attempt 3): {e}")
else:
self.main_gui.logger.info(f"No errors pulling, continuing . . .")
problem_attempts = 10 # break the loop

# Revert configuration ~/.docker/config.json configuration
if json_orig_data is not None:
if os.path.exists(Path.home() / ".docker" / "config.json.backup"):
os.rename(Path.home() / ".docker" / "config.json.backup", Path.home() / ".docker" / "config.json")
with open(Path.home() / ".docker" / "config.json", "w") as jsonFile:
json.dump(json_orig_data, jsonFile, indent=4)

self.update_pulling_signal.emit(1)

Expand Down
2 changes: 1 addition & 1 deletion settings.py
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ def init_default_settings(self):
# BiaPy
self.settings['biapy_code_version'] = "v3.4.4"
self.settings['biapy_code_github'] = "https://github.com/BiaPyX/BiaPy"
self.settings['biapy_gui_version'] = "v1.0.7"
self.settings['biapy_gui_version'] = "v1.0.8"
self.settings['biapy_gui_github'] = "https://github.com/BiaPyX/BiaPy-GUI"
self.settings['biapy_container_basename'] = "biapyx/biapy"
self.settings['biapy_container_name'] = self.settings['biapy_container_basename']+":latest-"+str(self.settings['CUDA_version'][-1])
Expand Down

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