Added entry point to register align-and-merge processing results

Author: tieneupin

src/murfey/workflows/clem/register_align_and_merge_results.py

@@ -1,10 +1,17 @@
 from __future__ import annotations
 
+import json
 import logging
+import traceback
+from ast import literal_eval
 from pathlib import Path
 from typing import Optional
 
-from pydantic import BaseModel
+from pydantic import BaseModel, validator
+from sqlmodel import Session
+
+from murfey.util.db import CLEMImageSeries
+from murfey.workflows.clem import get_db_entry
 
 logger = logging.getLogger("murfey.workflows.clem.register_align_and_merge_results")
 
@@ -17,6 +24,97 @@ class AlignAndMergeResult(BaseModel):
     align_across: Optional[str] = None
     composite_image: Path
 
+    @validator(
+        "image_stacks",
+        pre=True,
+    )
+    def parse_stringified_list(cls, value):
+        if isinstance(value, str):
+            try:
+                eval_result = literal_eval(value)
+                if isinstance(eval_result, list):
+                    parent_tiffs = [Path(p) for p in eval_result]
+                    return parent_tiffs
+            except (SyntaxError, ValueError):
+                raise ValueError("Unable to parse input")
+        # Return value as-is; if it fails, it fails
+        return value
+
+
+def register_align_and_merge_result(
+    message: dict, db: Session, demo: bool = False
+) -> bool:
+    """
+    session_id (recipe)
+    register (wrapper)
+    result (wrapper)
+        key1
+        key2
+        ...
+    """
+
+    session_id: int = (
+        int(message["session_id"])
+        if not isinstance(message["session_id"], int)
+        else message["session_id"]
+    )
+
+    # Validate message and try and load results
+    if isinstance(message["result"], str):
+        try:
+            json_obj: dict = json.loads(message["result"])
+            result = AlignAndMergeResult(**json_obj)
+        except Exception:
+            logger.error(traceback.format_exc())
+            logger.error(
+                "Exception encountered when parsing align-and-merge processing result"
+            )
+            return False
+    elif isinstance(message["result"], dict):
+        try:
+            result = AlignAndMergeResult(**message["result"])
+        except Exception:
+            logger.error(traceback.format_exc())
+            logger.error(
+                "Exception encountered when parsing align-and-merge processing result"
+            )
+            return False
+    else:
+        logger.error(
+            "Invalid type for align-and-merge processing result: "
+            f"{type(message['result'])}"
+        )
+        return False
+
+    # Outer try-finally block for tidying up database-related section of function
+    try:
+        # Register items in database if not already present
+        try:
+            clem_img_series: CLEMImageSeries = get_db_entry(
+                db=db,
+                table=CLEMImageSeries,
+                session_id=session_id,
+                series_name=result.series_name,
+            )
+            clem_img_series.composite_image = str(result.composite_image)
+            clem_img_series.composite_created = True
+            db.add(clem_img_series)
+            db.commit()
+            db.refresh(clem_img_series)
+
+            logger.info(
+                "Align-and-merge processing result registered for "
+                f"{result.series_name!r} series"
+            )
+
+        except Exception:
+            logger.error(traceback.format_exc())
+            logger.error(
+                "Exception encountered when registering LIF preprocessing result for "
+                f"{result.series_name!r} {result.channel!r} image stack"
+            )
+            return False
 
-def register_align_and_merge_result():
-    return True
+        return True
+    finally:
+        db.close()