Moved to error reporting framework.

src/submissions/backend/db/models/__init__.py

@@ -167,20 +167,20 @@ class BaseClass(Base):
         except Exception as e:
             logger.critical(f"Problem saving object: {e}")
             logger.error(f"Error message: {type(e)}")
-            match e:
-                case sqlalcIntegrityError():
-                    origin = e.orig.__str__().lower()
-                    logger.debug(f"Exception origin: {origin}")
-                    if "unique constraint failed:" in origin:
-                        field = origin.split(".")[1].replace("_", " ").upper()
-                        logger.debug(field)
-                        msg = f"{field} doesn't have a unique value.\nIt must be changed."
-                    else:
-                        msg = f"Got unknown integrity error: {e}"
-                case _:
-                    msg = f"Got generic error: {e}"
+            # match e:
+            #     case sqlalcIntegrityError():
+            #         origin = e.orig.__str__().lower()
+            #         logger.error(f"Exception origin: {origin}")
+            #         if "unique constraint failed:" in origin:
+            #             field = " ".join(origin.split(".")[1:]).replace("_", " ").upper()
+            #             # logger.debug(field)
+            #             msg = f"{field} doesn't have a unique value.\nIt must be changed."
+            #         else:
+            #             msg = f"Got unknown integrity error: {e}"
+            #     case _:
+            #         msg = f"Got generic error: {e}"
             self.__database_session__.rollback()
-            report.add_result(Result(msg=msg, status="Critical"))
+            report.add_result(Result(msg=e, status="Critical"))
             return report
 
 

src/submissions/backend/db/models/controls.py

@@ -9,7 +9,7 @@ from operator import itemgetter
 from . import BaseClass
 from tools import setup_lookup
 from datetime import date, datetime
-from typing import List
+from typing import List, Literal
 from dateutil.parser import parse
 from re import Pattern
 
@@ -53,7 +53,7 @@ class ControlType(BaseClass):
                 pass
         return cls.execute_query(query=query, limit=limit)
 
-    def get_subtypes(self, mode: str) -> List[str]:
+    def get_subtypes(self, mode: Literal['kraken', 'matches', 'contains']) -> List[str]:
         """
         Get subtypes associated with this controltype (currently used only for Kraken)
 
@@ -161,7 +161,7 @@ class Control(BaseClass):
         }
         return output
 
-    def convert_by_mode(self, mode: str) -> list[dict]:
+    def convert_by_mode(self, mode: Literal['kraken', 'matches', 'contains']) -> list[dict]:
         """
         split this instance into analysis types for controls graphs
 
@@ -195,7 +195,7 @@ class Control(BaseClass):
             output.append(_dict)
         # logger.debug("Have to triage kraken data to keep program from getting overwhelmed")
         if "kraken" in mode:
-            output = sorted(output, key=lambda d: d[f"{mode}_count"], reverse=True)[:49]
+            output = sorted(output, key=lambda d: d[f"{mode}_count"], reverse=True)[:50]
         return output
 
     @classmethod

src/submissions/backend/db/models/kits.py

@@ -7,6 +7,7 @@ import datetime
 import json
 from pprint import pprint, pformat
 
+import yaml
 from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, Interval, Table, FLOAT, BLOB
 from sqlalchemy.orm import relationship, validates, Query
 from sqlalchemy.ext.associationproxy import association_proxy
@@ -873,7 +874,12 @@ class SubmissionType(BaseClass):
             logging.critical(f"Given file could not be found.")
             return None
         with open(filepath, "r") as f:
-            import_dict = json.load(fp=f)
+            if filepath.suffix == ".json":
+                import_dict = json.load(fp=f)
+            elif filepath.suffix == ".yml":
+                import_dict = yaml.safe_load(stream=f)
+            else:
+                raise Exception(f"Filetype {filepath.suffix} not supported.")
         logger.debug(pformat(import_dict))
         submission_type = cls.query(name=import_dict['name'])
         if submission_type:

src/submissions/backend/db/models/submissions.py

@@ -2425,15 +2425,18 @@ class BasicSample(BaseClass):
             case _:
                 model = cls.find_polymorphic_subclass(attrs=kwargs)
             # logger.debug(f"Length of kwargs: {len(kwargs)}")
+        # logger.debug(f"Fuzzy search received sample type: {sample_type}")
         query: Query = cls.__database_session__.query(model)
+        # logger.debug(f"Queried model. Now running searches in {kwargs}")
         for k, v in kwargs.items():
+            # logger.debug(f"Running fuzzy search for attribute: {k} with value {v}")
             search = f"%{v}%"
             try:
                 attr = getattr(model, k)
                 query = query.filter(attr.like(search))
             except (ArgumentError, AttributeError) as e:
                 logger.error(f"Attribute {k} unavailable due to:\n\t{e}\nSkipping.")
-        return query.all()
+        return query.limit(50).all()
 
     def delete(self):
         raise AttributeError(f"Delete not implemented for {self.__class__}")