Improved error messaging when saving submissions.

CHANGELOG.md

@@ -1,4 +1,12 @@
-## 202408-05
+## 202409.03
+
+- Improved error messaging when saving submissions.
+
+## 202409.02
+
+- Creation of generic submissions using only database is now supported.
+
+## 202408.05
 
 - Improved scraping for gel info of Artic submissions.
 

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

@@ -6,10 +6,11 @@ import sys, logging
 from sqlalchemy import Column, INTEGER, String, JSON
 from sqlalchemy.orm import DeclarativeMeta, declarative_base, Query, Session
 from sqlalchemy.ext.declarative import declared_attr
-from sqlalchemy.exc import ArgumentError
+from sqlalchemy.exc import ArgumentError, IntegrityError as sqlalcIntegrityError
 from typing import Any, List
 from pathlib import Path
 from tools import report_result
+# from sqlite3 import IntegrityError as sqliteIntegrityError
 
 # Load testing environment
 if 'pytest' in sys.modules:
@@ -165,8 +166,21 @@ class BaseClass(Base):
             self.__database_session__.commit()
         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}"
             self.__database_session__.rollback()
-            report.add_result(Result(msg=f"Problem saving object {e}", status="Critical"))
+            report.add_result(Result(msg=msg, status="Critical"))
             return report
 
 

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

@@ -142,20 +142,22 @@ class Control(BaseClass):
         kraken_cnt_total = sum([kraken[item]['kraken_count'] for item in kraken])
         # logger.debug("Creating new kraken.")
         new_kraken = [dict(name=item, kraken_count=kraken[item]['kraken_count'],
-                           kraken_percent="{0:.0%}".format(kraken[item]['kraken_count'] / kraken_cnt_total)) for item in
+                           kraken_percent="{0:.0%}".format(kraken[item]['kraken_count'] / kraken_cnt_total),
-                      kraken]
+                           target=item in self.controltype.targets)
+                      for item in kraken]
+        # logger.debug(f"New kraken before sort: {new_kraken}")
         new_kraken = sorted(new_kraken, key=itemgetter('kraken_count'), reverse=True)
         # logger.debug("setting targets")
-        if not self.controltype.targets:
+        if self.controltype.targets:
-            targets = ["None"]
-        else:
             targets = self.controltype.targets
+        else:
+            targets = ["None"]
         # logger.debug("constructing output dictionary")
         output = {
             "name": self.name,
             "type": self.controltype.name,
             "targets": ", ".join(targets),
-            "kraken": new_kraken[0:5]
+            "kraken": new_kraken[0:10]
         }
         return output
 

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

@@ -645,7 +645,7 @@ class BasicSubmission(BaseClass):
         # logger.debug("Saving submission.")
         if original:
             self.uploaded_by = getuser()
-        super().save()
+        return super().save()
 
     @classmethod
     def get_regex(cls, submission_type:SubmissionType|str|None=None):

src/submissions/frontend/widgets/submission_widget.py

@@ -377,11 +377,18 @@ class SubmissionFormWidget(QWidget):
             # logger.debug(f"Updating: {reagent} with {reagent.lot}")
             reagent.update_last_used(kit=base_submission.extraction_kit)
         # logger.debug(f"Final reagents: {pformat(base_submission.reagents)}")
-        base_submission.save()
+        save_output = base_submission.save()
+        # logger.debug(f"Save output: {save_output}")
         # NOTE: update summary sheet
         self.app.table_widget.sub_wid.setData()
         # NOTE: reset form
-        self.setParent(None)
+        try:
+            check = save_output.results == []
+        except AttributeError:
+            logger.error(f"No save output, check passes")
+            check = True
+        if check:
+            self.setParent(None)
         # logger.debug(f"All attributes of obj: {pformat(self.__dict__)}")
         return report
 

src/submissions/templates/bacterialculture_details.html

@@ -14,7 +14,7 @@
         {% for item in sub['controls'] %}
             <p>&nbsp;&nbsp;&nbsp;<b>{{ item['name'] }}:</b> {{ item['type'] }} (Targets: {{ item['targets'] }})</p>
             {% if item['kraken'] %}
-                <p>&nbsp;&nbsp;&nbsp;{{ item['name'] }} Top 5 Kraken Results:</p>
+                <p>&nbsp;&nbsp;&nbsp;{{ item['name'] }} Top 10 Kraken Results:</p>
                 <p>{% for genera in item['kraken'] %}
                     &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;{{ genera['name'] }}: {{ genera['kraken_count'] }} ({{ genera['kraken_percent'] }})<br>
                 {% endfor %}</p>