Add sanitization of pipeline dumps, handle invalid dump version parameter (#53)

Author: David Stirling

cellprofiler_core/pipeline/_pipeline.py

@@ -592,8 +592,8 @@ def setup_module(
 
         return module
 
-    def dump(self, fp, save_image_plane_details=True):
-        dumpit(self, fp, save_image_plane_details)
+    def dump(self, fp, save_image_plane_details=True, sanitize=False):
+        dumpit(self, fp, save_image_plane_details, sanitize=sanitize)
 
     def save_pipeline_notes(self, fd, indent=2):
         """Save pipeline notes to a text file

cellprofiler_core/pipeline/io/__init__.py

@@ -9,8 +9,10 @@
 from ._v6 import dump as dump_v6
 
 
-def dump(pipeline, fp, save_image_plane_details=True, version=5):
+def dump(pipeline, fp, save_image_plane_details=True, version=5, sanitize=False):
     if version == 5:
-        dump_v5(pipeline, fp, save_image_plane_details)
+        dump_v5(pipeline, fp, save_image_plane_details, sanitize)
     elif version == 6:
         dump_v6(pipeline, fp, save_image_plane_details)
+    else:
+        raise NotImplementedError("Invalid pipeline version")

cellprofiler_core/pipeline/io/_v5.py

@@ -6,7 +6,7 @@
 import cellprofiler_core.utilities.core.pipeline
 
 
-def dump(pipeline, fp, save_image_plane_details):
+def dump(pipeline, fp, save_image_plane_details, sanitize=False):
     if len(pipeline.file_list) == 0:
         save_image_plane_details = False
 
@@ -44,6 +44,11 @@ def dump(pipeline, fp, save_image_plane_details):
         fp.write(f"{module.module_name}:[{'|'.join(module_attributes)}]\n")
 
         for setting in module.settings():
+            if sanitize and any(
+                phrase in setting.text.lower()
+                for phrase in ("username", "password", "host")
+            ):
+                setting.unicode_value = "*****"
             fp.write(f"    {setting.text}:{setting.unicode_value}\n")
 
     if save_image_plane_details: