Merge pull request #42 from AdebayoBraimah/dev5

Dev5

CHANGES.rst

@@ -1,6 +1,14 @@
 CHANGES
 =========
 
+0.2.0a10
+---------
+
+This version is an alpha release that contains several bug fixes and updates.
+
+* BUG FIX: Removed gzip/gunzip file checks, as this caused file and BIDS validation issues.
+* BUG FIX: Added support for all caps BIDS metadata, and exclusion of non-BIDS metadata rather than raising exceptions.
+
 0.2.0a9
 ---------
 

convert_source/cs_utils/bids_info.py

@@ -62,12 +62,13 @@ def is_camel_case(s: str,
         Boolean.
     """
     if bids_case:
-        return s != s.lower() and s != s.upper() and s[0].isupper() and "_" not in s
+        return (s != s.lower() and s != s.upper() and s[0].isupper() and "_" not in s) or (s == s.upper())
     else:
         return s != s.lower() and s != s.upper() and "_" not in s
 
 def construct_bids_dict(meta_dict: Optional[Dict] = None,
                         json_dict: Optional[Dict] = None,
+                        raise_exec: Optional[bool] = False
                         ) -> Dict:
     """Constructs dictionary of relevant BIDS related information that includes subject and session IDs, in addition
     to various metadata. Custom BIDS fields can also be added through the metadata dictionary.
@@ -83,12 +84,14 @@ def construct_bids_dict(meta_dict: Optional[Dict] = None,
     Arguments:
         meta_dict: Metadata dictionary that contains the relevant BIDS metadata.
         json_dict: Dictionary constructed from the BIDS JSON file, or some secondary dictionary.
+        raise_exec: Raises exception in the case that BIDS Metadata is not ``CamelCase``.
 
     Returns:
         Dictionary containing BIDS related metadata.
     
     Raises:
         IndexError: Error that arises if constant variables ``BIDS_INFO``'s keys and ``BIDS_ORD_ARR`` are of different lengths.
+        BIDSMetaDataError: Exception that is raised in the case that the one of the metadata fields are not ``CamelCase``.
     """
     # BIDS informatino dictionary
     bids_info: Dict = deepcopy(BIDS_INFO)
@@ -127,7 +130,10 @@ def construct_bids_dict(meta_dict: Optional[Dict] = None,
         if is_camel_case(word,bids_case=True):
             pass
         else:
-            raise BIDSMetaDataError(f"Input metadata: {word} is not BIDS compliant.")
+            if raise_exec:
+                raise BIDSMetaDataError(f"Input metadata: {word} is not BIDS compliant.")
+            else:
+                continue
 
         # Add field to ordered array
         if word in ordered_list:

convert_source/cs_utils/utils.py

@@ -392,19 +392,22 @@ def gzip_file(file: str,
     elif os.path.exists(file[:-3]):
         file: str = file[:-3]
 
-    # Check if the file is already gzipped
-    if _is_gzipped(file=file) and ('.gz' in file.lower()):
-        return file
-    elif _is_gzipped(file=file) and ('.gz' not in file.lower()):
-        file_tmp: str = file + ".gz"
-        os.rename(file,file_tmp)
-        return file_tmp
-    elif (not _is_gzipped(file=file)) and ('.gz' in file.lower()):
-        file_tmp: str = file[:-3]
-        os.rename(file,file_tmp)
-        file: str = file_tmp
-    elif (not _is_gzipped(file=file)) and ('.gz' not in file.lower()):
-        pass
+    # NOTE: Removing gzip file checks as this caused
+    #   file and BIDS validation issues.
+    # 
+    # # Check if the file is already gzipped
+    # if _is_gzipped(file=file) and ('.gz' in file.lower()):
+    #     return file
+    # elif _is_gzipped(file=file) and ('.gz' not in file.lower()):
+    #     file_tmp: str = file + ".gz"
+    #     os.rename(file,file_tmp)
+    #     return file_tmp
+    # elif (not _is_gzipped(file=file)) and ('.gz' in file.lower()):
+    #     file_tmp: str = file[:-3]
+    #     os.rename(file,file_tmp)
+    #     file: str = file_tmp
+    # elif (not _is_gzipped(file=file)) and ('.gz' not in file.lower()):
+    #     pass
 
     if native:
         # Native implementation
@@ -466,19 +469,22 @@ def gunzip_file(file: str,
     elif os.path.exists(file[:-3]):
         file: str = file[:-3]
 
-    # Check if the file is alrady gunzipped
-    if _is_gzipped(file=file) and ('.gz' in file.lower()):
-        pass
-    elif _is_gzipped(file=file) and ('.gz' not in file.lower()):
-        file_tmp: str = file + ".gz"
-        os.rename(file,file_tmp)
-        file: str = file_tmp
-    elif (not _is_gzipped(file=file)) and ('.gz' in file.lower()):
-        file_tmp: str = file[:-3]
-        os.rename(file,file_tmp)
-        return file_tmp
-    elif (not _is_gzipped(file=file)) and ('.gz' not in file.lower()):
-        return file
+    # NOTE: Removing gunzip file checks as this caused
+    #   file and BIDS validation issues.
+    # 
+    # # Check if the file is alrady gunzipped
+    # if _is_gzipped(file=file) and ('.gz' in file.lower()):
+    #     pass
+    # elif _is_gzipped(file=file) and ('.gz' not in file.lower()):
+    #     file_tmp: str = file + ".gz"
+    #     os.rename(file,file_tmp)
+    #     file: str = file_tmp
+    # elif (not _is_gzipped(file=file)) and ('.gz' in file.lower()):
+    #     file_tmp: str = file[:-3]
+    #     os.rename(file,file_tmp)
+    #     return file_tmp
+    # elif (not _is_gzipped(file=file)) and ('.gz' not in file.lower()):
+    #     return file
 
     if native:
         # Native implementation
@@ -1679,28 +1685,31 @@ def list_dir_files(pathname: str,
         file_dir_list.sort()
         return file_dir_list
 
-def _is_gzipped(file: str) -> bool:
-    """Helper function that determines if a file is actually gzipped or not.
-    The file extension is ignored as the file itself is checked.
-
-    Usage example:
-        >>> _is_gzipped(file='MR0001.nii.gz')
-        'True'
-
-    Arguments:
-        file: Input file name.
-
-    Returns:
-        Boolean - ``True`` if the file is gzipped, and ``false`` otherwise.
-    """
-    GZIP_MAGIC_NUMBER = "1f8b"
-    with open(file=file,mode='r') as f:
-        try:
-            # This should fail if the file is actually gzipped, as the 
-            #   'utf-8' codec cannot decode byte 0x8b in position 1.
-            return f.read(2).encode("utf-8").hex() == GZIP_MAGIC_NUMBER
-        except UnicodeDecodeError:
-            return True
+# NOTE: Commenting out this helper function as no other function depends on this
+#   helper function.
+# 
+# def _is_gzipped(file: str) -> bool:
+#     """Helper function that determines if a file is actually gzipped or not.
+#     The file extension is ignored as the file itself is checked.
+# 
+#     Usage example:
+#         >>> _is_gzipped(file='MR0001.nii.gz')
+#         'True'
+# 
+#     Arguments:
+#         file: Input file name.
+# 
+#     Returns:
+#         Boolean - ``True`` if the file is gzipped, and ``false`` otherwise.
+#     """
+#     GZIP_MAGIC_NUMBER = "1f8b"
+#     with open(file=file,mode='r') as f:
+#         try:
+#             # This should fail if the file is actually gzipped, as the 
+#             #   'utf-8' codec cannot decode byte 0x8b in position 1.
+#             return f.read(2).encode("utf-8").hex() == GZIP_MAGIC_NUMBER
+#         except UnicodeDecodeError:
+#             return True
 
 def sym_link(src: str,
              tar: str,

convert_source/version.txt

@@ -1 +1 @@
-0.2.0a9
+0.2.0a10