Merge pull request #183 from daichengxin/dev

ignore case in original extension

sdrf_pipelines/__init__.py

@@ -1 +1 @@
-__version__ = "0.0.31"
+__version__ = "0.0.32"

sdrf_pipelines/openms/openms.py

@@ -42,8 +42,9 @@ def _removesuffix(x: str, suffix: str, /) -> str:
         # This is a backport of the function, remove it and use the
         # built-in function when we drop support for python 3.8
         # https://peps.python.org/pep-0616/
-        if suffix and x.endswith(suffix):
-            return x[: -len(suffix)]
+        if suffix and x.lower().endswith(suffix.lower()):
+            res = re.sub(suffix + "$", "", x, flags=re.I)
+            return res
         else:
             return x[:]
 
@@ -59,7 +60,7 @@ def _removesuffix(x: str, suffix: str, /) -> str:
 
     raw_bkp = raw
     for current_extension, target_extension in extension_convert_dict.items():
-        if raw.endswith(current_extension):
+        if raw.lower().endswith(current_extension.lower()):
             raw = _removesuffix(raw, current_extension)
             raw += target_extension
             if not any(raw.endswith(x) for x in possible_extension):

sdrf_pipelines/parse_sdrf.py

@@ -45,7 +45,7 @@ def cli():
 @click.option(
     "--extension_convert",
     "-e",
-    help="convert extensions of files from one type to other 'raw:mzML,mzml:MZML,mzML:mzML,d:d'",
+    help="convert extensions of files from one type to other 'raw:mzML,mzml:MZML,d:d'. The original extensions are case insensitive",
 )
 @click.pass_context
 def openms_from_sdrf(