Progress update for pizza tracker

app/ms1/nta_task.py

@@ -175,6 +175,12 @@ def __init__(
         self.qnta_samples = None
         self.val_df = val_df
         self.spectra_inputs = ms2_inputs
+
+        # Build workflow steps dynamically based on parameters
+        self.workflow_steps = self._build_workflow_steps()
+        self.current_step_index = 0
+        self.current_step_progress = 0  # 0-100 within current step
+        self.total_workflow_weight = sum(step["weight"] for step in self.workflow_steps)
         self.qnta_dfs_out = None
         self.ests_out = [None, None]
         self.qnta_occ_input = None
@@ -215,6 +221,45 @@ def __init__(
         self.aq_plots = []
         self.ecdf_plots = []
 
+    def _build_workflow_steps(self):
+        steps = [
+            {"name": "Processing", "weight": 2},
+            {"name": "Check for existence of required columns", "weight": 3},
+            {"name": "Flagging duplicates", "weight": 8},
+            {"name": "Calculating statistics", "weight": 10},
+            {"name": "Create heatmap", "weight": 5},
+            {"name": "Checking tracers", "weight": 7},
+            {"name": "Create scatterplot", "weight": 5},
+        ]
+
+        # Add optional qNTA step if enabled
+        if self.parameters and self.parameters.get("do_qnta", [None, "no"])[1] == "yes":
+            steps.append({"name": "Performing qNTA", "weight": 12})
+
+        steps.extend([
+            {"name": "Cleaning features", "weight": 8},
+            {"name": "Merge detection counts onto tracers", "weight": 3},
+            {"name": "Combining modes", "weight": 5},
+        ])
+
+        # Add optional database search steps if enabled
+        if self.parameters and self.parameters.get("search_dsstox", [None, "no"])[1] == "yes":
+            steps.append({"name": "Searching dsstox database", "weight": 20})
+
+        if self.parameters and self.parameters.get("search_hcd", [None, "no"])[1] == "yes":
+            steps.append({"name": "Searching Cheminformatics Hazard Module database", "weight": 10})
+
+        # Add optional MS2 step if enabled
+        if self.parameters and self.parameters.get("do_ms2", [None, "no"])[1] == "yes":
+            steps.append({"name": "Performing MS2", "weight": 15})
+
+        steps.extend([
+            {"name": "Storing data", "weight": 5},
+            {"name": "Displaying results", "weight": 2}
+        ])
+
+        return steps
+
     def log_memory_usage(self, step_name):
         """Logs the current memory usage."""
         process = psutil.Process()
@@ -561,44 +606,100 @@ def create_run_sequence_sheets(self):
 
         return
 
-    def set_status(self, status, create=False):
+    def set_status(self, status, create=False, step_progress=0):
         """
         Accepts a string (e.g., "Processing", or "Step Completed") and, if create is TRUE,
         post status to the logger with the Job ID and timestamp.
 
         Args:
             status (string)
             create (Boolean)
+            step_progress (int): Progress within current step (0-100)
         Notes:
-            In a future version, we would like to display status on the UI
+            Enhanced with step-based progress tracking
         Returns:
             None
         """
+        # Find step index and update progress tracking
+        step_index = next((i for i, step in enumerate(self.workflow_steps) 
+                          if step["name"] == status), self.current_step_index)
+
+        self.current_step_index = step_index
+        self.current_step_progress = step_progress
+
+        # Calculate overall percentage
+        total_weight = sum(step["weight"] for step in self.workflow_steps)
+
+        completed_weight = 0
+        current_step_weight = 0
+
+        for i, step in enumerate(self.workflow_steps):
+            if step["name"] == status:
+                current_step_weight = step["weight"]
+                break
+            completed_weight += step["weight"]
+
+        overall_percentage = ((completed_weight + (current_step_weight * step_progress / 100)) 
+                             / total_weight * 100) if total_weight > 0 else 0
+
         posts = self.mongo.posts
         # Get time stamp
         time_stamp = datetime.utcnow()
         # Generate ID with status
         post_id = self.jobid + "_" + "status"
+
+        base_data = {
+            "_id": post_id,
+            "status": status,
+            "current_step_index": step_index,
+            "current_step_progress": step_progress,
+            "overall_percentage": f"{overall_percentage:.1f}",
+            "total_steps": len(self.workflow_steps),
+            "workflow_steps": [step["name"] for step in self.workflow_steps],
+        }
+
         # If create, post update
         if create:
-            posts.update_one(
-                {"_id": post_id},
-                {
-                    "$set": {
-                        "_id": post_id,
-                        "date": time_stamp,
-                        "status": status,
-                        "error_info": "",
-                    }
-                },
-                upsert=True,
-            )
-        else:
-            posts.update_one(
-                {"_id": post_id},
-                {"$set": {"_id": post_id, "status": status}},
-                upsert=True,
-            )
+            base_data.update({
+                "date": time_stamp,
+                "error_info": "",
+            })
+
+        posts.update_one(
+            {"_id": post_id},
+            {"$set": base_data},
+            upsert=True,
+        )
+
+    def update_step_progress(self, progress_percentage):
+        """Update progress within the current step (0-100)"""
+        self.current_step_progress = progress_percentage
+
+        # Calculate overall percentage
+        total_weight = sum(step["weight"] for step in self.workflow_steps)
+
+        completed_weight = 0
+        current_step_weight = 0
+
+        for step in self.workflow_steps:
+            if step["name"] == self.step:
+                current_step_weight = step["weight"]
+                break
+            completed_weight += step["weight"]
+
+        overall_percentage = ((completed_weight + (current_step_weight * progress_percentage / 100)) 
+                             / total_weight * 100) if total_weight > 0 else 0
+
+        posts = self.mongo.posts
+        post_id = self.jobid + "_" + "status"
+        posts.update_one(
+            {"_id": post_id},
+            {"$set": {
+                "current_step_progress": progress_percentage,
+                "overall_percentage": f"{overall_percentage:.1f}",
+            }},
+            upsert=True,
+        )
 
     def set_except_message(self, e):
         """
@@ -1654,7 +1755,7 @@ def perform_MS2(self):
                 self.spectra_inputs[0],
                 self.search_results,
                 mode="pos",
-                parameters=parameters,
+                parameters=self.parameters,
             )
             # Run execute function
             ms2_pos.execute()
@@ -1675,7 +1776,7 @@ def perform_MS2(self):
                 self.spectra_inputs[1],
                 self.search_results,
                 mode="neg",
-                parameters=parameters,
+                parameters=self.parameters,
             )
             # Run execute function
             ms2_neg.execute()