Bug fixes.

src/submissions/__main__.py

@@ -1,6 +1,6 @@
 import sys, os
 from tools import ctx, setup_logger, check_if_app
-
+from threading import Thread
 # environment variable must be set to enable qtwebengine in network path
 if check_if_app():
     os.environ['QTWEBENGINE_DISABLE_SANDBOX'] = "1"
@@ -23,12 +23,12 @@ def run_startup():
     for script in startup_scripts:
         try:
             func = getattr(scripts, script)
-            # func = modules[script]
         except AttributeError as e:
             logger.error(f"Couldn't run startup script {script} due to {e}")
             continue
         logger.info(f"Running startup script: {func.__name__}")
-        func.script(ctx)
+        thread = Thread(target=func.script, args=(ctx, ))
+        thread.start()
 
 
 def run_teardown():
@@ -45,7 +45,8 @@ def run_teardown():
             logger.error(f"Couldn't run teardown script {script} due to {e}")
             continue
         logger.info(f"Running teardown script: {func.__name__}")
-        func.script(ctx)
+        thread = Thread(target=func.script, args=(ctx,))
+        thread.start()
 
 if __name__ == '__main__':
     run_startup()

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

@@ -269,7 +269,7 @@ from .controls import *
 from .organizations import *
 from .kits import *
 from .submissions import *
-from .audit import AuditLog
+from .audit import *
 
 # NOTE: Add a creator to the submission for reagent association. Assigned here due to circular import constraints.
 # https://docs.sqlalchemy.org/en/20/orm/extensions/associationproxy.html#sqlalchemy.ext.associationproxy.association_proxy.params.creator

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

@@ -332,7 +332,6 @@ class KitType(BaseClass):
         return new_kit
 
 
-
 class ReagentRole(BaseClass):
     """
     Base of reagent type abstract

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

@@ -1265,7 +1265,9 @@ class BasicSubmission(BaseClass, LogMixin):
                     logger.error(f"Couldn't save association with {equip} due to {e}")
                 if equip.tips:
                     for tips in equip.tips:
+                        logger.debug(f"Attempting to add tips assoc: {tips} (pydantic)")
                         tassoc = tips.to_sql(submission=self)
+                        logger.debug(f"Attempting to add tips assoc: {tips.__dict__} (sql)")
                         if tassoc not in self.submission_tips_associations:
                             tassoc.save()
                         else:

src/submissions/backend/excel/__init__.py

@@ -2,6 +2,6 @@
 Contains pandas and openpyxl convenience functions for interacting with excel workbooks
 '''
 
-from .reports import *
 from .parser import *
+from .reports import *
 from .writer import *

src/submissions/backend/scripts/import_irida.py

@@ -4,20 +4,24 @@ from datetime import datetime
 from tools import Settings
 from backend import BasicSample
 from backend.db import IridaControl, ControlType
+from sqlalchemy.orm import Session
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
 
-def script(ctx:Settings):
+def script(ctx: Settings):
     """
     Grabs Irida controls from secondary database.
 
     Args:
         ctx (Settings): Settings inherited from app.
-
     """
-    ct = ControlType.query(name="Irida Control")
+    # NOTE: Because the main session will be busy in another thread, this requires a new session.
-    existing_controls = [item.name for item in IridaControl.query()]
+    new_session = Session(ctx.database_session.get_bind())
+    # ct = ControlType.query(name="Irida Control")
+    ct = new_session.query(ControlType).filter(ControlType.name == "Irida Control").first()
+    # existing_controls = [item.name for item in IridaControl.query()]
+    existing_controls = [item.name for item in new_session.query(IridaControl)]
     prm_list = ", ".join([f"'{thing}'" for thing in existing_controls])
     ctrl_db_path = ctx.directory_path.joinpath("submissions_parser_output", "submissions.db")
     try:
@@ -25,29 +29,39 @@ def script(ctx:Settings):
     except AttributeError as e:
         logger.error(f"Error, could not import from irida due to {e}")
         return
-    sql = f"SELECT name, submitted_date, submission_id, contains, matches, kraken, subtype, refseq_version, " \
+    sql = "SELECT name, submitted_date, submission_id, contains, matches, kraken, subtype, refseq_version, " \
-          f"kraken2_version, kraken2_db_version, sample_id FROM _iridacontrol INNER JOIN _control on _control.id " \
+          "kraken2_version, kraken2_db_version, sample_id FROM _iridacontrol INNER JOIN _control on _control.id " \
           f"= _iridacontrol.id WHERE _control.name NOT IN ({prm_list})"
     cursor = conn.execute(sql)
-    records = [dict(name=row[0], submitted_date=row[1], submission_id=row[2], contains=row[3], matches=row[4], kraken=row[5],
+    records = [
-                    subtype=row[6], refseq_version=row[7], kraken2_version=row[8], kraken2_db_version=row[9],
+        dict(name=row[0], submitted_date=row[1], submission_id=row[2], contains=row[3], matches=row[4], kraken=row[5],
-                    sample_id=row[10]) for row in cursor]
+             subtype=row[6], refseq_version=row[7], kraken2_version=row[8], kraken2_db_version=row[9],
+             sample_id=row[10]) for row in cursor]
     for record in records:
-        instance = IridaControl.query(name=record['name'])
+        # instance = IridaControl.query(name=record['name'])
+        instance = new_session.query(IridaControl).filter(IridaControl.name == record['name']).first()
         if instance:
             logger.warning(f"Irida Control {instance.name} already exists, skipping.")
             continue
-        record['contains'] = json.loads(record['contains'])
+        for thing in ['contains', 'matches', 'kraken']:
-        assert isinstance(record['contains'], dict)
+            if record[thing]:
-        record['matches'] = json.loads(record['matches'])
+                record[thing] = json.loads(record[thing])
-        assert isinstance(record['matches'], dict)
+                assert isinstance(record[thing], dict)
-        record['kraken'] = json.loads(record['kraken'])
+            else:
-        assert isinstance(record['kraken'], dict)
+                record[thing] = {}
+        # record['matches'] = json.loads(record['matches'])
+        # assert isinstance(record['matches'], dict)
+        # record['kraken'] = json.loads(record['kraken'])
+        # assert isinstance(record['kraken'], dict)
         record['submitted_date'] = datetime.strptime(record['submitted_date'], "%Y-%m-%d %H:%M:%S.%f")
         assert isinstance(record['submitted_date'], datetime)
         instance = IridaControl(controltype=ct, **record)
-        sample = BasicSample.query(submitter_id=instance.name)
+        # sample = BasicSample.query(submitter_id=instance.name)
+        sample = new_session.query(BasicSample).filter(BasicSample.submitter_id == instance.name).first()
         if sample:
             instance.sample = sample
             instance.submission = sample.submissions[0]
-        instance.save()
+        # instance.save()
+        new_session.add(instance)
+    new_session.commit()
+    new_session.close()

src/submissions/backend/validators/pydant.py

@@ -295,7 +295,8 @@ class PydTips(BaseModel):
         Returns:
             SubmissionTipsAssociation: Association between queried tips and submission
         """
-        tips = Tips.query(name=self.name, lot=self.lot, limit=1)
+        tips = Tips.query(name=self.name, limit=1)
+        logger.debug(f"Tips query has yielded: {tips}")
         assoc = SubmissionTipsAssociation.query(tip_id=tips.id, submission_id=submission.id, role=self.role, limit=1)
         if assoc is None:
             assoc = SubmissionTipsAssociation(submission=submission, tips=tips, role_name=self.role)
@@ -900,17 +901,20 @@ class PydSubmission(BaseModel, extra='allow'):
         return render
 
     # @report_result
-    def check_kit_integrity(self, extraction_kit: str | dict | None = None) -> Tuple[List[PydReagent], Report]:
+    def check_kit_integrity(self, extraction_kit: str | dict | None = None, exempt:List[PydReagent]=[]) -> Tuple[
+        List[PydReagent], Report]:
         """
         Ensures all reagents expected in kit are listed in Submission
        
         Args:
-            reagenttypes (list | None, optional): List to check against complete list. Defaults to None.
+            extraction_kit (str | dict | None, optional): kit to be checked. Defaults to None.
+            exempt (List[PydReagent], optional): List of reagents that don't need to be checked. Defaults to []
 
         Returns:
-            Report: Result object containing a message and any missing components.
+            Tuple[List[PydReagent], Report]: List of reagents and Result object containing a message and any missing components.
         """
         report = Report()
+        # logger.debug(f"The following reagents are exempt from the kit integrity check:\n{exempt}")
         if isinstance(extraction_kit, str):
             extraction_kit = dict(value=extraction_kit)
         if extraction_kit is not None and extraction_kit != self.extraction_kit['value']:
@@ -922,7 +926,8 @@ class PydSubmission(BaseModel, extra='allow'):
         expected_check = [item.role for item in ext_kit_rtypes]
         output_reagents = [rt for rt in self.reagents if rt.role in expected_check]
         missing_check = [item.role for item in output_reagents]
-        missing_reagents = [rt for rt in ext_kit_rtypes if rt.role not in missing_check]
+        missing_reagents = [rt for rt in ext_kit_rtypes if rt.role not in missing_check and rt.role not in exempt]
+        # logger.debug(f"Missing reagents: {missing_reagents}")
         missing_reagents += [rt for rt in output_reagents if rt.missing]
         output_reagents += [rt for rt in missing_reagents if rt not in output_reagents]
         # NOTE: if lists are equal return no problem
@@ -930,8 +935,8 @@ class PydSubmission(BaseModel, extra='allow'):
             result = None
         else:
             result = Result(
-                msg=f"The excel sheet you are importing is missing some reagents expected by the kit.\n\nIt looks like you are missing: {[item.role.upper() for item in missing_reagents]}\n\nAlternatively, you may have set the wrong extraction kit.\n\nThe program will populate lists using existing reagents.\n\nPlease make sure you check the lots carefully!",
+                    msg=f"The excel sheet you are importing is missing some reagents expected by the kit.\n\nIt looks like you are missing: {[item.role.upper() for item in missing_reagents]}\n\nAlternatively, you may have set the wrong extraction kit.\n\nThe program will populate lists using existing reagents.\n\nPlease make sure you check the lots carefully!",
-                status="Warning")
+                    status="Warning")
         report.add_result(result)
         return output_reagents, report
 

src/submissions/frontend/widgets/__init__.py

@@ -2,15 +2,17 @@
 Contains all custom generated PyQT6 derivative widgets.
 """
 
+from .app import App
+from .controls_chart import *
+from .equipment_usage import *
 from .functions import *
+from .gel_checker import *
+from .info_tab import *
 from .misc import *
+from .omni_search import *
 from .pop_ups import *
+from .submission_details import *
 from .submission_table import *
 from .submission_widget import *
-from .controls_chart import *
+from .summary import *
-from .submission_details import *
+from .turnaround import *
-from .equipment_usage import *
-from .gel_checker import *
-from .summary import Summary
-from .turnaround import TurnaroundTime
-from .app import App

src/submissions/frontend/widgets/equipment_usage.py

@@ -160,7 +160,7 @@ class RoleComboBox(QWidget):
             PydEquipment|None: PydEquipment matching form
         """
         eq = Equipment.query(name=self.box.currentText())
-        tips = [PydTips(name=item.currentText(), role=item.objectName().lstrip("tips").lstrip("_")) for item in
+        tips = [PydTips(name=item.currentText(), role=item.objectName().lstrip("tips").lstrip("_"), lot="") for item in
                 self.findChildren(QComboBox) if item.objectName().startswith("tips")]
         try:
             return PydEquipment(

src/submissions/frontend/widgets/submission_widget.py

@@ -6,7 +6,7 @@ from PyQt6.QtWidgets import (
     QComboBox, QDateEdit, QLineEdit, QLabel, QCheckBox, QHBoxLayout, QGridLayout
 )
 from PyQt6.QtCore import pyqtSignal, Qt, QSignalBlocker
-from . import select_open_file, select_save_file
+from .functions import select_open_file, select_save_file
 import logging
 from pathlib import Path
 from tools import Report, Result, check_not_nan, main_form_style, report_result
@@ -338,11 +338,15 @@ class SubmissionFormWidget(QWidget):
         report = Report()
         result = self.parse_form()
         report.add_result(result)
+        # allow = not all([item.lot.isEnabled() for item in self.findChildren(self.ReagentFormWidget)])
+        exempt = [item.reagent.role for item in self.findChildren(self.ReagentFormWidget) if not item.lot.isEnabled()]
+        # if allow:
+        #     logger.warning(f"Some reagents are disabled, allowing incomplete kit.")
         if self.disabler.checkbox.isChecked():
-            _, result = self.pyd.check_kit_integrity()
+            _, result = self.pyd.check_kit_integrity(exempt=exempt)
             report.add_result(result)
         if len(result.results) > 0:
-            return
+            return report
         base_submission, result = self.pyd.to_sql()
         # NOTE: check output message for issues
         try: