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Pre-fixing JSON update bug.

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This commit is contained in:
Landon Wark
2024-04-15 08:12:36 -05:00
parent f994f81d11
commit 7c46578d21
9 changed files with 90 additions and 40 deletions
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1
CHANGELOG.md
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@@ -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

8
TODO.md
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@@ -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.

1
src/submissions/backend/db/models/__init__.py
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@@ -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()

40
src/submissions/backend/db/models/submissions.py
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@@ -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"Inserting {type(parser.pcr)}: {parser.pcr}")
# logger.debug(f"Existing {type(self.pcr_info)}: {self.pcr_info}")
# 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:
check = instr.startswith("RSL")
except AttributeError:
check = False
if not check:
try:
instr = "RSL" + instr
except:
instr = "RSL"
# try:
# check = instr.startswith("RSL")
# except AttributeError:
# check = False
# if not check:
# try:
# instr = "RSL" + instr
# except TypeError:
# 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

6
src/submissions/backend/excel/parser.py
View File

@@ -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

5
src/submissions/backend/validators/pydant.py
View File

@@ -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:

14
src/submissions/frontend/widgets/app.py
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@@ -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):

49
src/submissions/frontend/widgets/submission_widget.py
View File

@@ -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"):
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(self.report)
self.app.result_reporter()
# 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(self.report)
# 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)
logger.debug(f"Outgoing report: {self.report.results}")
report.add_result(integrity_report)
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}")

6
src/submissions/tools.py
View File

@@ -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):
"""