Qubit results parsing complete.

CHANGELOG.md

@@ -1,10 +1,15 @@
+# 202509.04
+
+- Qubit results parsing complete.
+
 # 202509.03
 
 - Sortable headers in treeview.
+- Added gitea remote.
 
 # 202509.02
 
-- First Useable updated version.
+- First usable updated version.
 
 # 202504.04
 
@@ -12,7 +17,7 @@
 
 # 202504.03
 
-- Split Concentration controls on the chart so they are individually selectable.
+- Split Concentration controls on the chart, so they are individually selectable.
 
 # 202504.02
 
@@ -315,7 +320,7 @@
 
 ## 202307.03
 
-- Auto-filling of some empty cells in Excel file.
+- Autofilling of some empty cells in Excel file.
 - Better pydantic validations of missing data.
 
 ## 202307.02

TODO.md

@@ -1,5 +1,5 @@
-- [ ] Add in database objects for rsl_run (submission -> run), procedure (run -> procedure), many more things will likely be associated with procedure.
+- [x] Add in database objects for rsl_run (submission -> run), procedure (run -> procedure), many more things will likely be associated with procedure.
-- [ ] Add in database object for client submission.
+- [x] Add in database object for client submission.
 - [ ] Add arbitrary pipette addition to equipment UI.
 - [ ] transfer details template rendering fully into sql objects
 - [x] Add in connecting links for tips.

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

@@ -18,7 +18,7 @@ from sqlalchemy.exc import ArgumentError
 from typing import Any, List, ClassVar
 from pathlib import Path
 from sqlalchemy.orm.relationships import _RelationshipDeclared
-from tools import report_result, list_sort_dict, jinja_template_loading, Report, Result, ctx
+from tools import report_result, list_sort_dict, jinja_template_loading, Report, Alert, ctx
 
 # NOTE: Load testing environment
 if 'pytest' in sys.modules:
@@ -364,7 +364,7 @@ class BaseClass(Base):
             logger.error(f"Error message: {type(e)}")
             logger.error(pformat(self.__dict__))
             self.__database_session__.rollback()
-            report.add_result(Result(msg=e, status="Critical"))
+            report.add_result(Alert(msg=e, status="Critical"))
             return report
 
     @property

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

@@ -4,13 +4,14 @@ All kittype and reagent related models
 from __future__ import annotations
 import zipfile, logging, re, numpy as np
 from operator import itemgetter
+from pathlib import Path
 from pprint import pformat
 from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, Interval, Table, FLOAT, func
 from sqlalchemy.ext.hybrid import hybrid_property
 from sqlalchemy.orm import relationship, validates, Query, declared_attr
 from sqlalchemy.ext.associationproxy import association_proxy
 from datetime import date, datetime, timedelta
-from tools import check_authorization, setup_lookup, Report, Result, check_regex_match, timezone, \
+from tools import check_authorization, setup_lookup, Report, Alert, check_regex_match, timezone, \
     jinja_template_loading, flatten_list
 from typing import List, Literal, Generator, Any, Tuple, TYPE_CHECKING
 from . import BaseClass, ClientLab, LogMixin
@@ -926,10 +927,13 @@ class Procedure(BaseClass):
         logger.info(f"Add Results! {resultstype_name}")
         from backend.managers import results
         results_manager = getattr(results, f"{resultstype_name}Manager")
-        rs = results_manager(procedure=self, parent=obj)
+        rs = results_manager(procedure=self, parent=obj, fname=Path("C:\\Users\lwark\Documents\Submission_Forms\QubitData_18-09-2025_13-43-53.csv"))
         procedure = rs.procedure_to_pydantic()
         samples = rs.samples_to_pydantic()
+        if procedure:
             procedure_sql = procedure.to_sql()
+        else:
+            return
         procedure_sql.save()
         for sample in samples:
             sample_sql = sample.to_sql()

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

@@ -18,7 +18,8 @@ from sqlalchemy.orm.attributes import flag_modified
 from sqlalchemy.ext.associationproxy import association_proxy
 from sqlalchemy.exc import OperationalError as AlcOperationalError, IntegrityError as AlcIntegrityError, StatementError
 from sqlite3 import OperationalError as SQLOperationalError, IntegrityError as SQLIntegrityError
-from tools import setup_lookup, jinja_template_loading, create_holidays_for_year, check_dictionary_inclusion_equality, is_power_user
+from tools import (setup_lookup, jinja_template_loading, create_holidays_for_year,
+                   check_dictionary_inclusion_equality, is_power_user, row_map)
 from datetime import datetime, date
 from typing import List, Literal, Generator, TYPE_CHECKING
 from pathlib import Path
@@ -1865,6 +1866,16 @@ class ProcedureSampleAssociation(BaseClass):
 
     results = relationship("Results", back_populates="sampleprocedureassociation")  #: associated results
 
+    @property
+    def well(self):
+        if self.row > 0:
+            if self.column > 0:
+                return f"{row_map[self.row]}{self.column}"
+            else:
+                return self.row
+        else:
+            return None
+
     @classmethod
     def query(cls, sample: Sample | str | None = None, procedure: Procedure | str | None = None, limit: int = 0,
               **kwargs):

src/submissions/backend/excel/parsers/__init__.py

@@ -2,11 +2,13 @@
 Default Parser archetypes.
 """
 from __future__ import annotations
-import logging, re
+import logging, re, csv
 from pathlib import Path
+from pprint import pformat
 from typing import Generator, TYPE_CHECKING
 from openpyxl.cell import MergedCell
 from openpyxl.reader.excel import load_workbook
+from openpyxl.workbook import Workbook
 from pandas import DataFrame
 from backend.validators import pydant
 if TYPE_CHECKING:
@@ -44,6 +46,8 @@ class DefaultParser(object):
             **kwargs ():
         """
         logger.info(f"\n\nHello from {self.__class__.__name__}\n\n")
+        if isinstance(filepath, str):
+            filepath = Path(filepath)
         self.filepath = filepath
         self.proceduretype = proceduretype
         try:
@@ -58,13 +62,27 @@ class DefaultParser(object):
         self.sheet = sheet
         if not start_row:
             start_row = self.__class__.start_row
+        if self.filepath.suffix == ".xslx":
             self.workbook = load_workbook(self.filepath, data_only=True)
             self.worksheet = self.workbook[self.sheet]
+        elif self.filepath.suffix == ".csv":
+            self.workbook, self.worksheet = self.csv2xlsx(self.filepath)
         self.start_row = self.delineate_start_row(start_row=start_row)
         self.end_row = self.delineate_end_row(start_row=self.start_row)
 
+    @classmethod
+    def csv2xlsx(cls, filepath):
+        wb = Workbook()
+        ws = wb.active
+        with open(filepath, "r") as f:
+            reader = csv.reader(f, delimiter=",")
+            for row in reader:
+                ws.append(row)
+        return wb, ws
+
     def to_pydantic(self):
         data = self.parsed_info
+        logger.debug(f"Data for {self.__class__.__name__}: {pformat(data)}")
         data['filepath'] = self.filepath
         return self._pyd_object(**data)
 
@@ -85,7 +103,7 @@ class DefaultParser(object):
         for iii, row in enumerate(self.worksheet.iter_rows(min_row=start_row), start=start_row):
             if all([item.value is None for item in row]):
                 return iii
-        return self.worksheet.max_row
+        return self.worksheet.max_row + 1
 
 
 class DefaultKEYVALUEParser(DefaultParser):

src/submissions/backend/excel/parsers/results_parsers/__init__.py

@@ -12,12 +12,22 @@ logger = logging.getLogger(f"submissions.{__name__}")
 class DefaultResultsInfoParser(DefaultKEYVALUEParser):
     pyd_name = "PydResults"
 
-    def __init__(self, filepath: Path | str, proceduretype: "ProcedureType" | None = None,
+    def __init__(self, filepath: Path | str, results_type: str, proceduretype: "ProcedureType" | None = None,
-                 results_type: str | None = "PCR", *args, **kwargs):
+                  *args, **kwargs):
         if results_type:
             self.results_type = results_type
+        try:
             sheet = proceduretype.allowed_result_methods[results_type]['info']['sheet']
+        except KeyError:
+            sheet = 1
+        if "start_row" not in kwargs:
+            try:
                 start_row = proceduretype.allowed_result_methods[results_type]['info']['start_row']
+            except KeyError:
+                start_row = 1
+        else:
+            start_row = kwargs.pop('start_row')
+        # start_row = proceduretype.allowed_result_methods[results_type]['info']['start_row']
         super().__init__(filepath=filepath, proceduretype=proceduretype, sheet=sheet, start_row=start_row, *args,
                          **kwargs)
 
@@ -25,14 +35,24 @@ class DefaultResultsInfoParser(DefaultKEYVALUEParser):
 class DefaultResultsSampleParser(DefaultTABLEParser):
     pyd_name = "PydResults"
 
-    def __init__(self, filepath: Path | str, proceduretype: "ProcedureType" | None = None,
+    def __init__(self, filepath: Path | str, results_type: str, proceduretype: "ProcedureType" | None = None,
-                 results_type: str | None = "PCR", *args, **kwargs):
+                 *args, **kwargs):
         if results_type:
             self.results_type = results_type
+        try:
             sheet = proceduretype.allowed_result_methods[results_type]['sample']['sheet']
+        except KeyError:
+            sheet = 1
+        if "start_row" not in kwargs:
+            try:
                 start_row = proceduretype.allowed_result_methods[results_type]['sample']['start_row']
+            except KeyError:
+                start_row = 1
+        else:
+            start_row = kwargs.pop('start_row')
         super().__init__(filepath=filepath, proceduretype=proceduretype, sheet=sheet, start_row=start_row, *args,
                          **kwargs)
 
 
 from .pcr_results_parser import PCRInfoParser, PCRSampleParser
+from .qubit_results_parser import QubitInfoParser, QubitSampleParser

src/submissions/backend/managers/results/__init__.py

@@ -17,15 +17,19 @@ logger = logging.getLogger(f"submission.{__name__}")
 
 class DefaultResultsManager(DefaultManager):
 
-    def __init__(self, procedure: Procedure, parent, fname: Path | str | None = None):
+    def __init__(self, procedure: Procedure, parent, fname: Path | str | None = None, extension: str|None="xlsx"):
         self.procedure = procedure
         if not fname:
-            self.fname = select_open_file(file_extension="xlsx", obj=get_application_from_parent(parent))
+            fname = select_open_file(file_extension=extension, obj=get_application_from_parent(parent))
         elif isinstance(fname, str):
-            self.fname = Path(fname)
+            fname = Path(fname)
+        self.fname = fname
+
 
     def procedure_to_pydantic(self) -> PydResults:
+        logger.debug(f"Info parser: {self.info_parser}")
         info = self.info_parser.to_pydantic()
+        if info:
             info.parent = self.procedure
         return info
 
@@ -34,3 +38,4 @@ class DefaultResultsManager(DefaultManager):
         return sample
 
 from .pcr_results_manager import PCRManager
+from .qubit_results_manager import QubitManager

src/submissions/backend/validators/pydant.py

@@ -12,7 +12,7 @@ from typing import List, Tuple, Literal, Generator
 from types import GeneratorType
 from . import RSLNamer
 from pathlib import Path
-from tools import check_not_nan, convert_nans_to_nones, Report, Result, timezone, sort_dict_by_list, row_keys, flatten_list
+from tools import check_not_nan, convert_nans_to_nones, Report, Alert, timezone, sort_dict_by_list, row_keys, flatten_list
 from backend.db import models
 from backend.db.models import *
 from sqlalchemy.orm.properties import ColumnProperty
@@ -1397,14 +1397,14 @@ class PydRun(PydBaseClass):  #, extra='allow'):
         Converts this instance into a backend.db.models.procedure.BasicRun instance
 
         Returns:
-            Tuple[BasicRun, Result]: BasicRun instance, result object
+            Tuple[BasicRun, Alert]: BasicRun instance, result object
         """
         report = Report()
         dicto = self.improved_dict()
         instance, result = Run.query_or_create(submissiontype=self.submission_type['value'],
                                                rsl_plate_number=self.rsl_plate_number['value'])
         if instance is None:
-            report.add_result(Result(msg="Overwrite Cancelled."))
+            report.add_result(Alert(msg="Overwrite Cancelled."))
             return None, report
         report.add_result(result)
         self.handle_duplicate_samples()
@@ -1585,7 +1585,7 @@ class PydRun(PydBaseClass):  #, extra='allow'):
                     expired.append(f"{reagent.role}, {reagent.lot}: {reagent.expiry.date()} + {role_eol.days}")
         if expired:
             output = '\n'.join(expired)
-            result = Result(status="Warning",
+            result = Alert(status="Warning",
                             msg=f"The following reagents are expired:\n\n{output}"
                             )
             report.add_result(result)

src/submissions/frontend/widgets/info_tab.py

@@ -5,7 +5,7 @@ from datetime import date
 from PyQt6.QtCore import QSignalBlocker
 from PyQt6.QtWebEngineWidgets import QWebEngineView
 from PyQt6.QtWidgets import QWidget, QGridLayout
-from tools import Report, report_result, Result
+from tools import Report, report_result, Alert
 from .misc import StartEndDatePicker
 from .functions import select_save_file, save_pdf
 import logging
@@ -42,7 +42,7 @@ class InfoPane(QWidget):
             with QSignalBlocker(self.datepicker.start_date) as blocker:
                 self.datepicker.start_date.setDate(lastmonth)
             self.update_data()
-            report.add_result(Result(owner=self.__str__(), msg=msg, status="Warning"))
+            report.add_result(Alert(owner=self.__str__(), msg=msg, status="Warning"))
             return report
 
     @classmethod

src/submissions/frontend/widgets/submission_table.py

@@ -109,9 +109,7 @@ class SubmissionsTree(QTreeView):
         sets data in model
         """
         self.clear()
-        self.data = [item.to_dict(full_data=True) for item in
+        self.data = [item.to_dict(full_data=True) for item in ClientSubmission.query(chronologic=True, page=page, page_size=page_size)]
-        # self.data = [item.details_dict() for item in
-                     ClientSubmission.query(chronologic=True, page=page, page_size=page_size)]
         root = self.model.invisibleRootItem()
         for submission in self.data:
             group_str = f"{submission['submissiontype']}-{submission['submitter_plate_id']}-{submission['submitted_date']}"

src/submissions/frontend/widgets/submission_widget.py

@@ -9,7 +9,7 @@ from PyQt6.QtWidgets import (
 from PyQt6.QtCore import pyqtSignal, Qt, QSignalBlocker
 from .functions import select_open_file, select_save_file
 from pathlib import Path
-from tools import Report, Result, check_not_nan, main_form_style, report_result, get_application_from_parent
+from tools import Report, Alert, check_not_nan, main_form_style, report_result, get_application_from_parent
 from backend.validators import PydReagent, PydClientSubmission, PydSample
 from backend.db.models import (
     ClientLab, SubmissionType, Reagent, ReagentLot,
@@ -116,7 +116,7 @@ class SubmissionFormContainer(QWidget):
         if isinstance(fname, bool) or fname is None:
             fname = select_open_file(self, file_extension="xlsx")
         if not fname:
-            report.add_result(Result(msg=f"File {fname.__str__()} not found.", status="critical"))
+            report.add_result(Alert(msg=f"File {fname.__str__()} not found.", status="critical"))
             return report
         # NOTE: create sheetparser using excel sheet and context from gui
         self.clientsubmission_manager = DefaultClientSubmissionManager(parent=self, input_object=fname)
@@ -133,7 +133,7 @@ class SubmissionFormContainer(QWidget):
         else:
             message = "Submission cancelled."
             logger.warning(message)
-            report.add_result(Result(msg=message, owner=self.__class__.__name__, status="Warning"))
+            report.add_result(Alert(msg=message, owner=self.__class__.__name__, status="Warning"))
         return report
 
     @report_result
@@ -157,7 +157,7 @@ class SubmissionFormContainer(QWidget):
             # NOTE: send reagent to db
             sqlobj = reagent.to_sql()
             sqlobj.save()
-            report.add_result(Result(owner=__name__, code=0, msg="New reagent created.", status="Information"))
+            report.add_result(Alert(owner=__name__, code=0, msg="New reagent created.", status="Information"))
             return reagent, report
 
 
@@ -386,7 +386,7 @@ class SubmissionFormWidget(QWidget):
                     if reagent is not None:
                         reagents.append(reagent)
                     else:
-                        report.add_result(Result(msg="Failed integrity check", status="Critical"))
+                        report.add_result(Alert(msg="Failed integrity check", status="Critical"))
                         return report
                 case self.InfoItem():
                     field, value = widget.parse_form()
@@ -779,7 +779,7 @@ class ClientSubmissionFormWidget(SubmissionFormWidget):
                     if reagent is not None:
                         reagents.append(reagent)
                     else:
-                        report.add_result(Result(msg="Failed integrity check", status="Critical"))
+                        report.add_result(Alert(msg="Failed integrity check", status="Critical"))
                         return report
                 case self.InfoItem():
                     field, value = widget.parse_form()

src/submissions/templates/css/styles.css

@@ -104,8 +104,6 @@ div.gallery {
   padding: 5px;
 }
 
-
-
 .plate {
     display: inline-grid;
     grid-auto-flow: column;
@@ -189,3 +187,9 @@ ul.no-bullets {
           display: grid;
           grid-auto-flow: column;
         }
+
+.disable_section {
+  pointer-events: none;
+  opacity: 0.4;
+}
+

src/submissions/templates/details.html

@@ -25,7 +25,7 @@
 {% block script %}
 {% if not child %}
 
-{% for j in js%}
+{% for j in js %}
 
 <script>
     {{ j }}

src/submissions/tools/__init__.py

@@ -458,7 +458,6 @@ def render_details_template(template_name: str, css_in: List[str] | str = [], js
     js_in = ["details"] + js_in
     js_in = [html_folder.joinpath("js", f"{j}.js") for j in js_in]
     template = env.get_template(f"{template_name}.html")
-    # template_path = Path(template.environment.loader.__getattribute__("searchpath")[0])
     css_out = []
     for css in css_in:
         with open(css, "r") as f:
@@ -645,7 +644,7 @@ def get_application_from_parent(widget):
     return widget
 
 
-class Result(BaseModel, arbitrary_types_allowed=True):
+class Alert(BaseModel, arbitrary_types_allowed=True):
     owner: str = Field(default="", validate_default=True)
     code: int = Field(default=0)
     msg: str | Exception
@@ -704,7 +703,7 @@ class Result(BaseModel, arbitrary_types_allowed=True):
 
 
 class Report(BaseModel):
-    results: List[Result] = Field(default=[])
+    results: List[Alert] = Field(default=[])
 
     def __repr__(self):
         return f"<Report(result_count:{len(self.results)})>"
@@ -717,10 +716,10 @@ class Report(BaseModel):
         Takes a result object or all results in another report and adds them to this one.
 
         Args:
-            result (Result | Report | None): Results to be added.
+            result (Alert | Report | None): Results to be added.
         """
         match result:
-            case Result():
+            case Alert():
                 logger.info(f"Adding {result} to results.")
                 try:
                     self.results.append(result)
@@ -853,7 +852,7 @@ def check_authorization(func):
             logger.error(error_msg)
             report = Report()
             report.add_result(
-                Result(owner=func.__str__(), code=1, msg=error_msg, status="warning"))
+                Alert(owner=func.__str__(), code=1, msg=error_msg, status="warning"))
             return report, kwargs
     return wrapper
 
@@ -877,7 +876,7 @@ def under_development(func):
             logger.error(error_msg)
             report = Report()
             report.add_result(
-                Result(owner=func.__str__(), code=1, msg=error_msg,
+                Alert(owner=func.__str__(), code=1, msg=error_msg,
                        status="warning"))
             return report
     return wrapper