Move debug statements to info

biorack · Feb 7, 2025 · c11c5b4 · c11c5b4
1 parent 64e5dbb
commit c11c5b4
Show file tree

Hide file tree

Showing 4 changed files with 12 additions and 12 deletions.
diff --git a/metatlas/datastructures/groups.py b/metatlas/datastructures/groups.py
@@ -63,8 +63,8 @@ def filter_lcmsruns(
         )
     else:
         post_exclude = post_include
-    #for run in post_exclude:
-        #logger.debug("Run: %s", run.name)
+    for run in post_exclude:
+        logger.debug("Run: %s", run.name)
     logger.debug("After filtering, %s LCMS output files remain.", len(post_exclude))
     try:
         if len(post_exclude) == 0:

diff --git a/metatlas/datastructures/metatlas_objects.py b/metatlas/datastructures/metatlas_objects.py
@@ -116,9 +116,9 @@ def store(objects, **kwargs):
     workspace = Workspace.get_instance()
     if isinstance(objects, list):
         for obj in objects:
-            logger.debug('Depositing %s to database', obj.name)
+            logger.info('Depositing %s to database', obj.name)
     else:
-        logger.debug('Depositing %s to database', objects.name)
+        logger.info('Depositing %s to database', objects.name)
     workspace.save_objects(objects, **kwargs)
 
 
@@ -186,7 +186,7 @@ def clone(self, recursive=False):
         obj: MetatlasObject
             Cloned object.
         """
-        logger.debug('Cloning instance of %s with recursive=%s', self.__class__.__name__, recursive)
+        logger.info('Cloning instance of %s with recursive=%s', self.__class__.__name__, recursive)
         obj = self.__class__()
         for (tname, trait) in self.traits().items():
             if tname.startswith('_') or trait.metadata.get('readonly', False):
@@ -200,6 +200,7 @@ def clone(self, recursive=False):
         obj.prev_uid = self.unique_id
         obj.head_id = self.unique_id
         obj.unique_id = uuid.uuid4().hex
+        logger.info('Finished cloning %s object %s to %s', self.__class__.__name__, self.unique_id, obj.unique_id)
         return obj
 
     def show_diff(self, unique_id=None):

diff --git a/metatlas/datastructures/object_helpers.py b/metatlas/datastructures/object_helpers.py
@@ -197,7 +197,7 @@ def convert_to_double(self, table, entry):
 
     def save_objects(self, objects, _override=False):
         """Save objects to the database"""
-        logger.debug('Entering Workspace.save_objects')
+        logger.info('Entering Workspace.save_objects')
         if not isinstance(objects, (list, set)):
             objects = [objects]
         self._seen = dict()
@@ -209,17 +209,17 @@ def save_objects(self, objects, _override=False):
         if self._inserts:
             logger.debug('Workspace._inserts=%s', self._inserts)
         if self._updates:
-            logger.debug('Workspace._updates=%s', self._updates)
+            logger.info('Workspace._updates=%s', self._updates)
         if self._link_updates:
-            logger.debug('Workspace._link_updates=%s', self._link_updates)
+            logger.info('Workspace._link_updates=%s', self._link_updates)
         db = self.get_connection()
         db.begin()
         try:
             for (table_name, updates) in self._link_updates.items():
                 if table_name not in db:
                     continue
                 for (uid, prev_uid) in updates:
-                    logger.debug('QUERY: update `%s` set source_id = "%s" where source_id = "%s"' %
+                    logger.info('QUERY: update `%s` set source_id = "%s" where source_id = "%s"' %
                              (table_name, prev_uid, uid))
                     db.query('update `%s` set source_id = "%s" where source_id = "%s"' %
                              (table_name, prev_uid, uid))
@@ -229,7 +229,7 @@ def save_objects(self, objects, _override=False):
                     if 'sqlite' not in self.path:
                         self.fix_table(table_name)
                 for (uid, prev_uid) in updates:
-                    logger.debug('QUERY: update `%s` set unique_id = "%s" where unique_id = "%s"' %
+                    logger.info('QUERY: update `%s` set unique_id = "%s" where unique_id = "%s"' %
                              (table_name, prev_uid, uid))
                     db.query('update `%s` set unique_id = "%s" where unique_id = "%s"' %
                              (table_name, prev_uid, uid))

diff --git a/metatlas/targeted/rt_alignment.py b/metatlas/targeted/rt_alignment.py
@@ -129,7 +129,7 @@ def generate_rt_alignment_models(
     return (linear, poly, offset)
 
 
-def generate_outputs(data: MetatlasDataset, workflow: Workflow, set_parameters: dict) -> list:
+def generate_outputs(data: MetatlasDataset, workflow: Workflow, set_parameters: dict) -> None:
     """
     Generate the RT alignment models, associated atlases with relative RT values, follow up notebooks
     set_parameters contains the parameters set in the RT-Alignment notebook, before config file processing
@@ -161,7 +161,6 @@ def generate_outputs(data: MetatlasDataset, workflow: Workflow, set_parameters:
                 papermill.execute_notebook(in_file_name, out_file_name, {}, kernel_name="papermill")
     copy_outputs_to_google_drive(ids)
     logger.info("RT-Alignment notebook complete. Switch to an analysis notebook to continue.")
-    return atlases
 
 def get_rts(metatlas_dataset: MetatlasDataset, include_atlas_rt_peak: bool = True) -> pd.DataFrame:
     """Returns RT values in DataFrame format"""