Merge pull request #54 from jjjermiah/organize_project_todo

Organize project todo

setup.py

@@ -3,7 +3,7 @@
 __version__ = "0.10.7"
 
 setup(
-   name="nbiatoolkit",
-   version=__version__,
-   # And so on...
-)
+    name="nbiatoolkit",
+    version=__version__,
+    # And so on...
+)

src/nbiatoolkit/__init__.py

@@ -1,7 +1,7 @@
 ## __init__.py
 # Path: projects/nbia-toolkit/src/__init__.py
 
-# this is the __init__.py file 
+# this is the __init__.py file
 # this file is run when the package is imported
 # this file is used to import all the modules in the package
 # this file is used to define the __all__ variable
@@ -16,10 +16,4 @@
 from .utils.nbia_endpoints import NBIA_ENDPOINTS
 
 # define the __all__ variable
-__all__ = [
-    'NBIAClient',
-    'OAuth2',
-    'setup_logger',
-    'NBIA_ENDPOINTS',
-    '__version__'
-]
+__all__ = ["NBIAClient", "OAuth2", "setup_logger", "NBIA_ENDPOINTS", "__version__"]

src/nbiatoolkit/auth.py

@@ -2,18 +2,19 @@
 import time
 from typing import Union
 
+
 class OAuth2:
     """
     OAuth2 class for handling authentication and access token retrieval.
 
     This class provides methods to authenticate with the NBIA API using OAuth2
     and retrieve the access token required for accessing the API.
-    
+
     Defaults to using the NBIA Guest for accessing public collections.
     If you have a username and password which has been granted access
     to the collections tagged with "limited access" you can use those
     credentials to access those collections.
-    
+
 
     Attributes
     ----------
@@ -39,7 +40,7 @@ class OAuth2:
     Methods
     -------
     getToken()
-        Authenticates with the API. Returns API headers containing the 
+        Authenticates with the API. Returns API headers containing the
         access token.
 
     Example Usage
@@ -66,7 +67,9 @@ class OAuth2:
     this class, please open an issue on the GitHub repository.
     """
 
-    def __init__(self, username: str = "nbia_guest", password: str = "", client_id: str = "NBIA"):
+    def __init__(
+        self, username: str = "nbia_guest", password: str = "", client_id: str = "NBIA"
+    ):
         """
         Initialize the OAuth2 class.
 
@@ -104,7 +107,7 @@ def getToken(self) -> Union[dict, int]:
         >>> from nbiatoolkit import OAuth2
         >>> oauth = OAuth2()
         >>> api_headers = oauth.getToken()
-        
+
         >>> requests.get(url=query_url, headers=api_headers)
         """
         # Check if the access token is valid and not expired
@@ -113,37 +116,35 @@ def getToken(self) -> Union[dict, int]:
 
         # Prepare the request data
         data = {
-            'username': self.username,
-            'password': self.password,
-            'client_id': self.client_id,
-            'grant_type': 'password'
+            "username": self.username,
+            "password": self.password,
+            "client_id": self.client_id,
+            "grant_type": "password",
         }
-        token_url = 'https://services.cancerimagingarchive.net/nbia-api/oauth/token'
+        token_url = "https://services.cancerimagingarchive.net/nbia-api/oauth/token"
 
         response = requests.post(token_url, data=data)
 
-
         try:
             response = requests.post(token_url, data=data)
             response.raise_for_status()  # Raise an HTTPError for bad responses
         except requests.exceptions.RequestException as e:
             self.access_token = -1
-            raise requests.exceptions.RequestException(\
-                f'Failed to get access token. Status code:\
-                    {response.status_code}') from e
+            raise requests.exceptions.RequestException(
+                f"Failed to get access token. Status code:\
+                    {response.status_code}"
+            ) from e
         else:
             # Code to execute if there is no exception
             token_data = response.json()
-            self.access_token = token_data.get('access_token')
+            self.access_token = token_data.get("access_token")
 
-            self.api_headers = {
-                'Authorization': f'Bearer {self.access_token}'
-            }
+            self.api_headers = {"Authorization": f"Bearer {self.access_token}"}
 
-            self.expiry_time = time.ctime(time.time() + token_data.get('expires_in'))
-            self.refresh_token = token_data.get('refresh_token')
-            self.refresh_expiry = token_data.get('refresh_expires_in')
-            self.scope = token_data.get('scope')
+            self.expiry_time = time.ctime(time.time() + token_data.get("expires_in"))
+            self.refresh_token = token_data.get("refresh_token")
+            self.refresh_expiry = token_data.get("refresh_expires_in")
+            self.scope = token_data.get("scope")
 
             return self.api_headers
 
@@ -169,4 +170,4 @@ def headers(self):
         api_headers : dict or None
             The authentication headers containing the access token.
         """
-        return self.api_headers
+        return self.api_headers

src/nbiatoolkit/dicomsort/__init__.py

@@ -10,9 +10,4 @@
 from .dicomsort import DICOMSorter
 from .helper_functions import parseDICOMKeysFromFormat, sanitizeFileName, truncateUID
 
-__all__ = [
-    "DICOMSorter",
-    "parseDICOMKeysFromFormat",
-    "sanitizeFileName",
-    "truncateUID"
-]
+__all__ = ["DICOMSorter", "parseDICOMKeysFromFormat", "sanitizeFileName", "truncateUID"]

src/nbiatoolkit/dicomsort/dicomsort.py

@@ -1,25 +1,28 @@
 import re, os, sys, shutil
-import pydicom 
+import pydicom
 
 from pydicom.filereader import InvalidDicomError
 
 from .helper_functions import parseDICOMKeysFromFormat, sanitizeFileName, truncateUID
-    
+
 
 class DICOMSorter:
-
     def __init__(
-        self, sourceDir: str, destinationDir: str, targetPattern: str = None,
-        truncateUID: bool = True, sanitizeFilename: bool = True
-        ):
+        self,
+        sourceDir: str,
+        destinationDir: str,
+        targetPattern: str = None,
+        truncateUID: bool = True,
+        sanitizeFilename: bool = True,
+    ):
         """
         Initialize the DICOMSorter with a target pattern.
         """
         self.targetPattern = targetPattern
         self.sourceDir = sourceDir
         self.destinationDir = destinationDir
-        self.truncateUID=truncateUID
-        self.sanitizeFilename=sanitizeFilename        
+        self.truncateUID = truncateUID
+        self.sanitizeFilename = sanitizeFilename
 
     def generateFilePathFromDICOMAttributes(
         self, dataset: pydicom.dataset.FileDataset
@@ -33,30 +36,37 @@ def generateFilePathFromDICOMAttributes(
         # Prepare the replacements dictionary with sanitized attribute values
         for key in keys:
             # Retrieve the attribute value if it exists or default to a placeholder string
-            value = str(getattr(dataset, key, 'Unknown' + key))
-
-            value = truncateUID(value) if key.endswith("UID") and self.truncateUID else value
-
-            replacements[key] = sanitizeFileName(value) if self.sanitizeFilename else value
+            value = str(getattr(dataset, key, "Unknown" + key))
+
+            value = (
+                truncateUID(value)
+                if key.endswith("UID") and self.truncateUID
+                else value
+            )
+
+            replacements[key] = (
+                sanitizeFileName(value) if self.sanitizeFilename else value
+            )
 
         # Build the target path by interpolating the replacement values
         return fmt % replacements
-
-
+
     def sortSingleDICOMFile(
         self, filePath: str, option: str, overwrite: bool = False
     ) -> bool:
         assert option in ["copy", "move"], "Invalid option: symlink not implemented yet"
-        
-        try: 
+
+        try:
             dataset = pydicom.dcmread(filePath, stop_before_pixels=True)
         except InvalidDicomError as e:
             print(f"Error reading file {filePath}: {e}")
             return False
         except TypeError as e:
-            print(f"Error reading file {filePath}: is ``None`` or of an unsupported type.")
-            return False    
-
+            print(
+                f"Error reading file {filePath}: is ``None`` or of an unsupported type."
+            )
+            return False
+
         name = self.generateFilePathFromDICOMAttributes(dataset)
         assert name is not None and isinstance(name, str)
 
@@ -65,53 +75,52 @@ def sortSingleDICOMFile(
         if os.path.exists(targetFilename) and not overwrite:
             print(f"Source File: {filePath}\n")
             print(f"File {targetFilename} already exists. ")
-            sys.exit("Pattern is probably not unique or overwrite is set to False. Exiting.")
-
+            sys.exit(
+                "Pattern is probably not unique or overwrite is set to False. Exiting."
+            )
+
         os.makedirs(os.path.dirname(targetFilename), exist_ok=True)
-        
+
         match option:
             case "copy":
-                shutil.copyfile(src = filePath, dst=targetFilename)
+                shutil.copyfile(src=filePath, dst=targetFilename)
             case "move":
-                shutil.move(src = filePath, dst=targetFilename)
+                shutil.move(src=filePath, dst=targetFilename)
 
         return True
-
-    def sortDICOMFiles(
-        self, option: str = "copy", overwrite: bool = False
-    ) -> bool:
 
+    def sortDICOMFiles(self, option: str = "copy", overwrite: bool = False) -> bool:
         dicom_file_paths = self._get_dicom_files()
 
-        results = [self.sortSingleDICOMFile(file, option, overwrite) for file in dicom_file_paths]
+        results = [
+            self.sortSingleDICOMFile(file, option, overwrite)
+            for file in dicom_file_paths
+        ]
 
         return all(results)
 
-
     def _get_dicom_files(self) -> list[str]:
         dicom_file_paths = []
         # Iterate over all files in the source directory
         for root, dirs, files in os.walk(self.sourceDir):
             for f in files:
-                dicom_file_paths.append(os.path.join(root, f)) if f.endswith(".dcm") else None
+                dicom_file_paths.append(os.path.join(root, f)) if f.endswith(
+                    ".dcm"
+                ) else None
 
         return dicom_file_paths
 
+
 # Test case
 # if __name__ == "__main__":
 
-    # sorter = DICOMSorter(
-    #     sourceDir = sourceDir,
-    #     destinationDir=destinationDir,
-    #     targetPattern=pattern,
-    #     truncateUID=True,
-    #     sanitizeFilename=True,
-    #     overwrite=True
-    #     )
-
-    # sorter.sortDICOMFiles(option="move")
-
-
-
-
+# sorter = DICOMSorter(
+#     sourceDir = sourceDir,
+#     destinationDir=destinationDir,
+#     targetPattern=pattern,
+#     truncateUID=True,
+#     sanitizeFilename=True,
+#     overwrite=True
+#     )
 
+# sorter.sortDICOMFiles(option="move")

src/nbiatoolkit/dicomsort/helper_functions.py

@@ -1,5 +1,7 @@
 import re
 from typing import Tuple, List
+
+
 def parseDICOMKeysFromFormat(targetPattern: str) -> Tuple[str, List[str]]:
     """
     Parse the target pattern to create a format string with named placeholders
@@ -19,13 +21,14 @@ def parseDICOMKeysFromFormat(targetPattern: str) -> Tuple[str, List[str]]:
     """
 
     # Compile the regex pattern for efficiency
-    dicom_key_pattern = re.compile(r'%([A-Za-z]+)')
+    dicom_key_pattern = re.compile(r"%([A-Za-z]+)")
     keys = dicom_key_pattern.findall(targetPattern)
     # Use the same compiled pattern for replacing
-    formatted_pattern = dicom_key_pattern.sub(r'%(\1)s', targetPattern)
+    formatted_pattern = dicom_key_pattern.sub(r"%(\1)s", targetPattern)
 
     return formatted_pattern, keys
 
+
 def sanitizeFileName(fileName: str) -> str:
     """
     Sanitize the file name by replacing potentially dangerous characters.
@@ -35,14 +38,14 @@ def sanitizeFileName(fileName: str) -> str:
     # Define a pattern for disallowed filename characters and their replacements
     disallowed_characters_pattern = re.compile(r'[<>:"/\\|?*\x00-\x1f]')
     # Replace disallowed characters with an underscore
-    sanitized_name = disallowed_characters_pattern.sub('_', fileName)
-    
+    sanitized_name = disallowed_characters_pattern.sub("_", fileName)
+
     # replace spaces with underscores
     sanitized_name = sanitized_name.replace(" ", "_")
-    
+
     # Remove subsequent underscores
-    sanitized_name = re.sub(r'(_{2,})', '_', sanitized_name)
-    
+    sanitized_name = re.sub(r"(_{2,})", "_", sanitized_name)
+
     return sanitized_name
 
 

src/nbiatoolkit/logger/__init__.py

@@ -1,5 +1,3 @@
 from .logger import setup_logger
 
-__all__ = [
-    'setup_logger'
-]
+__all__ = ["setup_logger"]