Solve macOS issue with ~/.docker/config.json file when pulling the container

Author: danifranco

run_functions.py

@@ -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
@@ -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)     
 

settings.py

@@ -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])