- Skips /output cwd

Author: Alan Christie

src/python/pipelines_utils/file_utils.py

@@ -40,8 +40,11 @@ def pick(filename, directory=None):
     """
     if directory is None:
         directory = utils.get_undecorated_calling_module()
-        # Remove the CWD and the anticipated '/' from the front of the module
-        directory = directory[len(os.getcwd()) + 1:]
+        # If the 'cwd' is not '/output' (which indicates we're in a Container)
+        # then remove the CWD and the anticipated '/'
+        # from the front of the module
+        if os.getcwd() not in ['/output']:
+            directory = directory[len(os.getcwd()) + 1:]
 
     file_path = os.path.join(directory, filename)
     return file_path if os.path.isfile(file_path) else None
@@ -65,8 +68,11 @@ def pick_sdf(filename, directory=None):
     """
     if directory is None:
         directory = utils.get_undecorated_calling_module()
-        # Remove the CWD and the anticipated '/' from the front of the module
-        directory = directory[len(os.getcwd()) + 1:]
+        # If the 'cwd' is not '/output' (which indicates we're in a Container)
+        # then remove the CWD and the anticipated '/'
+        # from the front of the module
+        if os.getcwd() not in ['/output']:
+            directory = directory[len(os.getcwd()) + 1:]
 
     file_path = os.path.join(directory, filename)
     if os.path.isfile(file_path + '.sdf.gz'):

src/python/setup.py

@@ -22,7 +22,7 @@ def get_long_description():
 setup(
 
     name='im-pipelines-utils',
-    version='2.3.0',
+    version='2.3.1',
     author='Alan Christie',
     author_email='[email protected]',
     url='https://github.com/InformaticsMatters/pipelines-utils',