Pre-fixing JSON update bug.

CHANGELOG.md

@@ -2,6 +2,7 @@
 
 - Various bug fixes.
 - Move import PCR results to context menu.
+- Automated backup of database.
 - Added ability to sign off on submission in submission details.
 
 ## 202403.03

TODO.md

@@ -1,5 +1,11 @@
+- [ ] Appending of qPCR results to WW not saving. Find out why.
+    - Possibly due to immutable JSON? But... it's worked before... Right?
+    - Based on research, if a top-level JSON field is not changed, SQLalchemy will not detect changes.
+    - May have to use a special class: [link](https://docs.sqlalchemy.org/en/14/orm/extensions/mutable.html#establishing-mutability-on-scalar-column-values)
+- [ ] Add Bead basher and Assit to DB.
+- [x] Artic not creating right plate name.
 - [ ] Merge BasicSubmission.find_subclasses and BasicSubmission.find_polymorphic_subclass
-- [ ] Fix updating of Extraction Kit in submission form widget.
+- [x] Fix updating of Extraction Kit in submission form widget.
 - [x] Fix cropping of gel image.
 - [ ] Create Tips ... *sigh*.
 - [x] Create platemap image from html for export to pdf.

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

@@ -86,6 +86,7 @@ class BaseClass(Base):
         """
         Add the object to the database and commit
         """        
+        logger.debug(f"Saving object: {pformat(self.__dict__)}")
         try:
             self.__database_session__.add(self)
             self.__database_session__.commit()

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

@@ -436,6 +436,7 @@ class BasicSubmission(BaseClass):
         Args:
             original (bool, optional): Is this the first save. Defaults to True.
         """        
+        logger.debug("Saving submission.")
         if original:
             self.uploaded_by = getuser()
         super().save()
@@ -605,12 +606,15 @@ class BasicSubmission(BaseClass):
         # logger.info(f"Hello from {cls.__mapper_args__['polymorphic_identity']} Enforcer!")
         # return instr
         from backend.validators import RSLNamer
+        logger.debug(f"instr coming into {cls}: {instr}")
+        logger.debug(f"data coming into {cls}: {data}")
         defaults = cls.get_default_info()
         data['abbreviation'] = defaults['abbreviation']
         if 'submission_type' not in data.keys() or data['submission_type'] in [None, ""]:
             data['submission_type'] = defaults['submission_type']
         # outstr = super().enforce_name(instr=instr, data=data)
         if instr in [None, ""]:
+            logger.debug("Sending to RSLNamer to make new plate name.")
             outstr = RSLNamer.construct_new_plate_name(data=data)
         else:
             outstr = instr
@@ -620,6 +624,7 @@ class BasicSubmission(BaseClass):
             outstr = re.sub(r"(\d{4})-(\d{2})-(\d{2})", r"\1\2\3", outstr)
             outstr = re.sub(rf"{data['abbreviation']}(\d{6})", rf"{data['abbreviation']}-\1", outstr, flags=re.IGNORECASE).upper()
         except (AttributeError, TypeError) as e:
+            logger.error(f"Error making outstr: {e}, sending to RSLNamer to make new plate name.")
             outstr = RSLNamer.construct_new_plate_name(data=data)
         try:
             plate_number = re.search(r"(?:(-|_)\d)(?!\d)", outstr).group().strip("_").strip("-")
@@ -1281,28 +1286,32 @@ class Wastewater(BasicSubmission):
         if hasattr(self, 'pcr_info') and self.pcr_info != None:
             # existing = json.loads(sub.pcr_info)
             existing = self.pcr_info
+            logger.debug(f"Found existing pcr info: {pformat(self.pcr_info)}")
         else:
             existing = None
         if existing != None:
             # update pcr_info
             try:
-                logger.debug(f"Updating {type(existing)}: {existing} with {type(parser.pcr)}: {parser.pcr}")
+                logger.debug(f"Updating {type(existing)}:\n {pformat(existing)} with {type(parser.pcr)}:\n {pformat(parser.pcr)}")
                 # if json.dumps(parser.pcr) not in sub.pcr_info:
                 if parser.pcr not in self.pcr_info:
+                    logger.debug(f"This is new pcr info, appending to existing")
                     existing.append(parser.pcr)
-                logger.debug(f"Setting: {existing}")
+                else:
+                    logger.debug("This info already exists, skipping.")
+                # logger.debug(f"Setting {self.rsl_plate_num} PCR to:\n {pformat(existing)}")
                 # sub.pcr_info = json.dumps(existing)
                 self.pcr_info = existing
             except TypeError:
                 logger.error(f"Error updating!")
                 # sub.pcr_info = json.dumps([parser.pcr])
                 self.pcr_info = [parser.pcr]
-            logger.debug(f"Final pcr info for {self.rsl_plate_num}: {self.pcr_info}")
+            logger.debug(f"Final pcr info for {self.rsl_plate_num}:\n {pformat(self.pcr_info)}")
         else:
             # sub.pcr_info = json.dumps([parser.pcr])
             self.pcr_info = [parser.pcr]
-        logger.debug(f"Existing {type(self.pcr_info)}: {self.pcr_info}")
+        # logger.debug(f"Existing {type(self.pcr_info)}: {self.pcr_info}")
-        logger.debug(f"Inserting {type(parser.pcr)}: {parser.pcr}")
+        # logger.debug(f"Inserting {type(parser.pcr)}: {parser.pcr}")
         self.save(original=False)
         logger.debug(f"Got {len(parser.samples)} samples to update!")
         logger.debug(f"Parser samples: {parser.samples}")
@@ -1383,15 +1392,15 @@ class WastewaterArtic(BasicSubmission):
             instr = re.sub(r"Artic", "", instr, flags=re.IGNORECASE)
         except (AttributeError, TypeError) as e:
             logger.error(f"Problem using regex: {e}")
-        try:
+        # try:
-            check = instr.startswith("RSL")
+        #     check = instr.startswith("RSL")
-        except AttributeError:
+        # except AttributeError:
-            check = False
+        #     check = False
-        if not check:
+        # if not check:
-            try:
+        #     try:
-                instr = "RSL" + instr
+        #         instr = "RSL" + instr
-            except:
+        #     except TypeError:
-                instr = "RSL"
+        #         instr = "RSL"
         outstr = super().enforce_name(instr=instr, data=data)
         return outstr
 
@@ -1540,7 +1549,8 @@ class WastewaterArtic(BasicSubmission):
             df.sort_values(by=['destination_column', 'destination_row'], inplace=True)
         except AttributeError as e:
             logger.error(f"Couldn't construct df due to {e}")
-        input_dict['csv'] = df
+        # input_dict['csv'] = df
+        input_dict['csv'] = xl.parse("hitpicks_csv_to_export")
         return input_dict
 
     @classmethod

src/submissions/backend/excel/parser.py

@@ -266,7 +266,11 @@ class ReagentParser(object):
                 # logger.debug(f"Got lot for {item}-{name}: {lot} as {type(lot)}")
                 lot = str(lot)
                 logger.debug(f"Going into pydantic: name: {name}, lot: {lot}, expiry: {expiry}, type: {item.strip()}, comment: {comment}")
-                if name.lower() != "not applicable":
+                try:
+                    check = name.lower() != "not applicable"
+                except AttributeError:
+                    check = True
+                if check:
                     listo.append(PydReagent(type=item.strip(), lot=lot, expiry=expiry, name=name, comment=comment, missing=missing))
         return listo
 

src/submissions/backend/validators/pydant.py

@@ -192,7 +192,7 @@ class PydSample(BaseModel, extra='allow'):
                                                                             row=row, column=column, id=id)
                 # logger.debug(f"Using submission_sample_association: {association}")
                 try:
-                    instance.sample_submission_associations.append(association)
+                    # instance.sample_submission_associations.append(association)
                     out_associations.append(association)
                 except IntegrityError as e:
                     logger.error(f"Could not attach submission sample association due to: {e}")
@@ -809,7 +809,8 @@ class PydSubmission(BaseModel, extra='allow'):
         # # what reagent types are in both lists?
         # missing = list(set(ext_kit_rtypes).difference(reagenttypes))
         missing = []
-        output_reagents = self.reagents
+        # output_reagents = self.reagents
+        output_reagents = ext_kit_rtypes
         logger.debug(f"Already have these reagent types: {reagenttypes}")
         for rt in ext_kit_rtypes:
             if rt.type not in reagenttypes:

src/submissions/frontend/widgets/app.py

@@ -9,9 +9,10 @@ from PyQt6.QtWidgets import (
 from PyQt6.QtGui import QAction
 from pathlib import Path
 from tools import check_if_app, Settings, Report
+from datetime import date
 from .pop_ups import  AlertPop
 from .misc import LogParser
-import logging, webbrowser, sys
+import logging, webbrowser, sys, shutil
 from .submission_table import SubmissionsSheet
 from .submission_widget import SubmissionFormContainer
 from .controls_chart import ControlsViewer
@@ -51,6 +52,7 @@ class App(QMainWindow):
         self._connectActions()
         self.show()
         self.statusBar().showMessage('Ready', 5000)
+        self.backup_database()
         
     def _createMenuBar(self):
         """
@@ -159,6 +161,16 @@ class App(QMainWindow):
         dlg = LogParser(self)
         dlg.exec()
 
+    def backup_database(self):
+        month = date.today().strftime("%Y-%m")
+        # day = date.today().strftime("%Y-%m-%d")
+        logger.debug(f"Here is the db directory: {self.ctx.database_path}")
+        logger.debug(f"Here is the backup directory: {self.ctx.backup_path}")
+        current_month_bak = Path(self.ctx.backup_path).joinpath(f"submissions_backup-{month}").resolve().with_suffix(".db")
+        if not current_month_bak.exists() and "demo" not in self.ctx.database_path.__str__():
+            logger.debug("No backup found for this month, backing up database.")
+            shutil.copyfile(self.ctx.database_path, current_month_bak)
+
 class AddSubForm(QWidget):
     
     def __init__(self, parent:QWidget):

src/submissions/frontend/widgets/submission_widget.py

@@ -5,7 +5,7 @@ from PyQt6.QtWidgets import (
 from PyQt6.QtCore import pyqtSignal
 from pathlib import Path
 from . import select_open_file, select_save_file
-import logging, difflib, inspect, json
+import logging, difflib, inspect, pickle
 from pathlib import Path
 from tools import Report, Result, check_not_nan
 from backend.excel.parser import SheetParser, PCRParser
@@ -147,7 +147,7 @@ class SubmissionFormWidget(QWidget):
 
     def __init__(self, parent: QWidget, submission:PydSubmission) -> None:
         super().__init__(parent)
-        self.report = Report()
+        # self.report = Report()
         self.app = parent.app
         self.pyd = submission
         # self.input = [{k:v} for k,v in kwargs.items()]
@@ -177,18 +177,18 @@ class SubmissionFormWidget(QWidget):
         self.scrape_reagents(self.pyd.extraction_kit)
         # extraction kit must be added last so widget order makes sense.
         # self.layout.addWidget(self.create_widget(key="extraction_kit", value=self.extraction_kit, submission_type=self.submission_type))
-        if hasattr(self.pyd, "csv"):
+        # if hasattr(self.pyd, "csv"):
-            export_csv_btn = QPushButton("Export CSV")
+        #     export_csv_btn = QPushButton("Export CSV")
-            export_csv_btn.setObjectName("export_csv_btn")
+        #     export_csv_btn.setObjectName("export_csv_btn")
-            self.layout.addWidget(export_csv_btn)
+        #     self.layout.addWidget(export_csv_btn)
-            export_csv_btn.clicked.connect(self.export_csv_function)
+        #     export_csv_btn.clicked.connect(self.export_csv_function)
-        submit_btn = QPushButton("Submit")
+        # submit_btn = QPushButton("Submit")
-        submit_btn.setObjectName("submit_btn")
+        # submit_btn.setObjectName("submit_btn")
-        self.layout.addWidget(submit_btn)
+        # self.layout.addWidget(submit_btn)
-        submit_btn.clicked.connect(self.submit_new_sample_function)
+        # submit_btn.clicked.connect(self.submit_new_sample_function)
-        self.setLayout(self.layout)
+        # self.setLayout(self.layout)
-        self.app.report.add_result(self.report)
+        # self.app.report.add_result(self.report)
-        self.app.result_reporter()
+        # self.app.result_reporter()
 
     def create_widget(self, key:str, value:dict|PydReagent, submission_type:str|None=None, extraction_kit:str|None=None) -> "self.InfoItem":
         """
@@ -230,7 +230,7 @@ class SubmissionFormWidget(QWidget):
         caller = inspect.stack()[1].function.__repr__().replace("'", "")
         # self.reagents = []
         # logger.debug(f"Self.reagents: {self.reagents}")
-        # logger.debug(f"\n\n{caller}\n\n")
+        logger.debug(f"\n\n{pformat(caller)}\n\n")
         # logger.debug(f"SubmissionType: {self.submission_type}")
         report = Report()
         logger.debug(f"Extraction kit: {extraction_kit}")
@@ -257,13 +257,25 @@ class SubmissionFormWidget(QWidget):
         # self.pyd.reagents = already_have + reagents
         # logger.debug(f"Reagents: {self.reagents}")
         # self.kit_integrity_completion_function(extraction_kit=extraction_kit)
-        reagents, report = self.pyd.check_kit_integrity(extraction_kit=extraction_kit)
+        reagents, integrity_report = self.pyd.check_kit_integrity(extraction_kit=extraction_kit)
         # logger.debug(f"Missing reagents: {obj.missing_reagents}")
         for reagent in reagents:
             add_widget = self.ReagentFormWidget(parent=self, reagent=reagent, extraction_kit=self.pyd.extraction_kit)
             self.layout.addWidget(add_widget)
-        self.report.add_result(report)
+        report.add_result(integrity_report)
-        logger.debug(f"Outgoing report: {self.report.results}")
+        logger.debug(f"Outgoing report: {report.results}")
+        if hasattr(self.pyd, "csv"):
+            export_csv_btn = QPushButton("Export CSV")
+            export_csv_btn.setObjectName("export_csv_btn")
+            self.layout.addWidget(export_csv_btn)
+            export_csv_btn.clicked.connect(self.export_csv_function)
+        submit_btn = QPushButton("Submit")
+        submit_btn.setObjectName("submit_btn")
+        self.layout.addWidget(submit_btn)
+        submit_btn.clicked.connect(self.submit_new_sample_function)
+        self.setLayout(self.layout)
+        self.app.report.add_result(report)
+        self.app.result_reporter()
 
     def kit_integrity_completion_function(self, extraction_kit:str|None=None):
         """
@@ -302,7 +314,6 @@ class SubmissionFormWidget(QWidget):
                             Alternatively, 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!""".replace("  ", ""), status="Warning")
             report.add_result(result)
-        
         self.report.add_result(report)
         logger.debug(f"Outgoing report: {self.report.results}")
         

src/submissions/tools.py

@@ -538,7 +538,11 @@ def rreplace(s, old, new):
 ctx = get_config(None)
 
 def is_power_user() -> bool:
-    return getpass.getuser() in ctx.power_users
+    try:
+        check = getpass.getuser() in ctx.power_users
+    except:
+        check = False
+    return check
 
 def check_authorization(func):
     """