Addition of procedure parser in import.

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

@@ -2,7 +2,8 @@
 Contains all models for sqlalchemy
 """
 from __future__ import annotations
-import sys, logging
+
+import sys, logging, json
 
 from dateutil.parser import parse
 from pandas import DataFrame
@@ -565,15 +566,24 @@ class BaseClass(Base):
                 check = False
             if check:
                 continue
+            try:
                 value = getattr(self, k)
+            except AttributeError:
+                continue
             match value:
                 case datetime():
                     value = value.strftime("%Y-%m-%d %H:%M:%S")
                 case _:
                     pass
-            output[k] = value
+            output[k.strip("_")] = value
         return output
 
+    def show_details(self, obj):
+        logger.debug("Show Details")
+        from frontend.widgets.submission_details import SubmissionDetails
+        dlg = SubmissionDetails(parent=obj, sub=self)
+        if dlg.exec():
+            pass
 
 class LogMixin(Base):
     tracking_exclusion: ClassVar = ['artic_technician', 'clientsubmissionsampleassociation',

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

@@ -2,19 +2,16 @@
 All kittype and reagent related models
 """
 from __future__ import annotations
-import json, zipfile, yaml, logging, re, sys
+import zipfile, logging, re
 from operator import itemgetter
-from pprint import pformat
 
 import numpy as np
-from jinja2 import Template, TemplateNotFound
 from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, Interval, Table, FLOAT, BLOB
 from sqlalchemy.orm import relationship, validates, Query
 from sqlalchemy.ext.associationproxy import association_proxy
-from sqlalchemy.ext.hybrid import hybrid_property
 from datetime import date, datetime, timedelta
-from tools import check_authorization, setup_lookup, Report, Result, check_regex_match, yaml_regex_creator, timezone, \
+from tools import check_authorization, setup_lookup, Report, Result, check_regex_match, timezone, \
-    jinja_template_loading, ctx
+    jinja_template_loading
 from typing import List, Literal, Generator, Any, Tuple, TYPE_CHECKING
 from pandas import ExcelFile
 from pathlib import Path
@@ -632,7 +629,7 @@ class Reagent(BaseClass, LogMixin):
             missing=False
         )
         if full_data:
-            output['procedure'] = [sub.rsl_plate_num for sub in self.procedures]
+            output['procedure'] = [sub.rsl_plate_number for sub in self.procedures]
             output['excluded'] = ['missing', 'procedure', 'excluded', 'editable']
             output['editable'] = ['lot', 'expiry']
         return output
@@ -743,7 +740,7 @@ class Reagent(BaseClass, LogMixin):
                         role = ReagentRole.query(name=value, limit=1)
                     case _:
                         return
-                if role and role not in self.role:
+                if role and role not in self.reagentrole:
                     self.reagentrole.append(role)
                 return
             case "comment":
@@ -1097,9 +1094,13 @@ class ProcedureType(BaseClass):
     id = Column(INTEGER, primary_key=True)
     name = Column(String(64))
     reagent_map = Column(JSON)
+    info_map = Column(JSON)
+    sample_map = Column(JSON)
+    equipment_map = Column(JSON)
     plate_columns = Column(INTEGER, default=0)
     plate_rows = Column(INTEGER, default=0)
     allowed_result_methods = Column(JSON)
+    template_file = Column(BLOB)
 
     procedure = relationship("Procedure",
                              back_populates="proceduretype")  #: Concrete control of this type.
@@ -1218,6 +1219,15 @@ class ProcedureType(BaseClass):
             plate_columns=self.plate_columns
         )
 
+    def details_dict(self, **kwargs):
+        output = super().details_dict(**kwargs)
+        output['kittype'] = [item.details_dict() for item in output['kittype']]
+        # output['process'] = [item.details_dict() for item in output['process']]
+        output['equipment'] = [item.details_dict() for item in output['equipment']]
+        return output
+
+
+
     def construct_dummy_procedure(self, run: Run|None=None):
         from backend.validators.pydant import PydProcedure
         if run:
@@ -1277,6 +1287,7 @@ class Procedure(BaseClass):
     id = Column(INTEGER, primary_key=True)
     name = Column(String, unique=True)
     repeat = Column(INTEGER, nullable=False)
+
     technician = Column(String(64))  #: name of processing tech(s)
     results = relationship("Results", back_populates="procedure", uselist=True)
     proceduretype_id = Column(INTEGER, ForeignKey("_proceduretype.id", ondelete="SET NULL",
@@ -1372,7 +1383,7 @@ class Procedure(BaseClass):
 
     def add_results(self, obj, resultstype_name:str):
         logger.debug(f"Add Results! {resultstype_name}")
-        from frontend.widgets import results
+        from ...managers import results
         results_class = getattr(results, resultstype_name)
         rs = results_class(procedure=self, parent=obj)
 
@@ -1412,8 +1423,8 @@ class Procedure(BaseClass):
     def add_comment(self, obj):
         logger.debug("Add Comment!")
 
-    def show_details(self, obj):
+    # def show_details(self, obj):
-        logger.debug("Show Details!")
+    #     logger.debug("Show Details!")
 
     def delete(self, obj):
         logger.debug("Delete!")
@@ -1423,10 +1434,25 @@ class Procedure(BaseClass):
         output['kittype'] = output['kittype'].details_dict()
         output['proceduretype'] = output['proceduretype'].details_dict()
         output['results'] = [result.details_dict() for result in output['results']]
-        output['sample'] = [sample.details_dict() for sample in output['sample']]
+        run_samples = [sample for sample in self.run.sample]
+        active_samples = [sample.details_dict() for sample in output['proceduresampleassociation']
+                          if sample.sample.sample_id in [s.sample_id for s in run_samples]]
+        for sample in active_samples:
+            sample['active'] = True
+        inactive_samples = [sample.details_dict() for sample in run_samples if sample.name not in [s['sample_id'] for s in active_samples]]
+        # logger.debug(f"Inactive samples:{pformat(inactive_samples)}")
+        for sample in inactive_samples:
+            sample['active'] = False
+        # output['sample'] = [sample.details_dict() for sample in output['runsampleassociation']]
+        output['sample'] = active_samples + inactive_samples
+        # output['sample'] = [sample.details_dict() for sample in output['sample']]
         output['reagent'] = [reagent.details_dict() for reagent in output['procedurereagentassociation']]
         output['equipment'] = [equipment.details_dict() for equipment in output['procedureequipmentassociation']]
         output['tips'] = [tips.details_dict() for tips in output['proceduretipsassociation']]
+        output['repeat'] = bool(output['repeat'])
+        output['excluded'] = ['id', "results", "proceduresampleassociation", "sample", "procedurereagentassociation",
+                              "procedureequipmentassociation", "proceduretipsassociation", "reagent", "equipment", "tips",
+                              "excluded"]
         return output
 
 class ProcedureTypeKitTypeAssociation(BaseClass):
@@ -1814,7 +1840,7 @@ class ProcedureReagentAssociation(BaseClass):
             str: Representation of this RunReagentAssociation
         """
         try:
-            return f"<ProcedureReagentAssociation({self.procedure.procedure.rsl_plate_num} & {self.reagent.lot})>"
+            return f"<ProcedureReagentAssociation({self.procedure.procedure.rsl_plate_number} & {self.reagent.lot})>"
         except AttributeError:
             logger.error(f"Reagent {self.reagent.lot} procedure association {self.reagent_id} has no procedure!")
             return f"<ProcedureReagentAssociation(Unknown Submission & {self.reagent.lot})>"
@@ -1887,9 +1913,9 @@ class ProcedureReagentAssociation(BaseClass):
         # NOTE: Figure out how to merge the misc_info if doing .update instead.
         relevant = {k: v for k, v in output.items() if k not in ['reagent']}
         output = output['reagent'].details_dict()
-        misc = output['_misc_info']
+        misc = output['misc_info']
         output.update(relevant)
-        output['_misc_info'] = misc
+        output['misc_info'] = misc
         output['results'] = [result.details_dict() for result in output['results']]
         return output
 
@@ -2087,9 +2113,9 @@ class Equipment(BaseClass, LogMixin):
             asset_number=self.asset_number
         )
         if full_data:
-            subs = [dict(plate=item.procedure.procedure.rsl_plate_num, process=item.process.name,
+            subs = [dict(plate=item.procedure.procedure.rsl_plate_number, process=item.process.name,
                          sub_date=item.procedure.procedure.start_date)
-                    if item.process else dict(plate=item.procedure.procedure.rsl_plate_num, process="NA")
+                    if item.process else dict(plate=item.procedure.procedure.rsl_plate_number, process="NA")
                     for item in self.equipmentprocedureassociation]
             output['procedure'] = sorted(subs, key=itemgetter("sub_date"), reverse=True)
             output['excluded'] = ['missing', 'procedure', 'excluded', 'editable']
@@ -2240,6 +2266,11 @@ class EquipmentRole(BaseClass):
         from backend.validators.omni_gui_objects import OmniEquipmentRole
         return OmniEquipmentRole(instance_object=self, name=self.name)
 
+    def details_dict(self, **kwargs):
+        output = super().details_dict(**kwargs)
+        output['equipment'] = [item.details_dict() for item in output['equipment']]
+        output['process'] = [item.details_dict() for item in output['process']]
+        return output
 
 class ProcedureEquipmentAssociation(BaseClass):
     """
@@ -2342,9 +2373,9 @@ class ProcedureEquipmentAssociation(BaseClass):
         # NOTE: Figure out how to merge the misc_info if doing .update instead.
         relevant = {k: v for k, v in output.items() if k not in ['equipment']}
         output = output['equipment'].details_dict()
-        misc = output['_misc_info']
+        misc = output['misc_info']
         output.update(relevant)
-        output['_misc_info'] = misc
+        output['misc_info'] = misc
         output['process'] = self.process.details_dict()
         return output
 
@@ -2530,12 +2561,25 @@ class Process(BaseClass):
             name=self.name,
         )
         if full_data:
-            subs = [dict(plate=sub.run.rsl_plate_num, equipment=sub.equipment.name,
+            subs = [dict(plate=sub.run.rsl_plate_number, equipment=sub.equipment.name,
                          submitted_date=sub.run.clientsubmission.submitted_date) for sub in self.procedure]
             output['procedure'] = sorted(subs, key=itemgetter("submitted_date"), reverse=True)
             output['excluded'] = ['missing', 'procedure', 'excluded', 'editable']
         return output
 
+    def to_pydantic(self):
+        from backend.validators.pydant import PydProcess
+        output = {}
+        for k, v in self.details_dict().items():
+            if isinstance(v, list):
+                output[k] = [item.name for item in v]
+            elif issubclass(v.__class__, BaseClass):
+                output[k] = v.name
+            else:
+                output[k] = v
+        return PydProcess(**output)
+
+
     # @classproperty
     # def details_template(cls) -> Template:
     #     """
@@ -2591,7 +2635,10 @@ class TipRole(BaseClass):
 
     @classmethod
     @setup_lookup
-    def query(cls, name: str | None = None, limit: int = 0, **kwargs) -> TipRole | List[TipRole]:
+    def query(cls,
+              name: str | None = None,
+              limit: int = 0,
+              **kwargs) -> TipRole | List[TipRole]:
         query = cls.__database_session__.query(cls)
         match name:
             case str():
@@ -2707,7 +2754,7 @@ class Tips(BaseClass, LogMixin):
         )
         if full_data:
             subs = [
-                dict(plate=item.procedure.procedure.rsl_plate_num, role=item.role_name,
+                dict(plate=item.procedure.procedure.rsl_plate_number, role=item.role_name,
                      sub_date=item.procedure.procedure.clientsubmission.submitted_date)
                 for item in self.tipsprocedureassociation]
             output['procedure'] = sorted(subs, key=itemgetter("sub_date"), reverse=True)
@@ -2819,15 +2866,16 @@ class ProcedureTipsAssociation(BaseClass):
         # NOTE: Figure out how to merge the misc_info if doing .update instead.
         relevant = {k: v for k, v in output.items() if k not in ['tips']}
         output = output['tips'].details_dict()
-        misc = output['_misc_info']
+        misc = output['misc_info']
         output.update(relevant)
-        output['_misc_info'] = misc
+        output['misc_info'] = misc
         return output
 
 
 class Results(BaseClass):
 
     id = Column(INTEGER, primary_key=True)
+    result_type = Column(String(32))
     result = Column(JSON)
     procedure_id = Column(INTEGER, ForeignKey("_procedure.id", ondelete='SET NULL',
                                                 name="fk_RES_procedure_id"))

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

@@ -26,7 +26,7 @@ from sqlite3 import OperationalError as SQLOperationalError, IntegrityError as S
 from openpyxl import Workbook
 from openpyxl.drawing.image import Image as OpenpyxlImage
 from tools import row_map, setup_lookup, jinja_template_loading, rreplace, row_keys, check_key_or_attr, Result, Report, \
-    report_result, create_holidays_for_year, check_dictionary_inclusion_equality
+    report_result, create_holidays_for_year, check_dictionary_inclusion_equality, is_power_user
 from datetime import datetime, date
 from typing import List, Any, Tuple, Literal, Generator, Type, TYPE_CHECKING
 from pathlib import Path
@@ -100,7 +100,7 @@ class ClientSubmission(BaseClass, LogMixin):
         Args:
             submission_type (str | models.SubmissionType | None, optional): Submission type of interest. Defaults to None.
             id (int | str | None, optional): Submission id in the database (limits results to 1). Defaults to None.
-            rsl_plate_num (str | None, optional): Submission name in the database (limits results to 1). Defaults to None.
+            rsl_plate_number (str | None, optional): Submission name in the database (limits results to 1). Defaults to None.
             start_date (date | str | int | None, optional): Beginning date to search by. Defaults to None.
             end_date (date | str | int | None, optional): Ending date to search by. Defaults to None.
             reagent (models.Reagent | str | None, optional): A reagent used in the procedure. Defaults to None.
@@ -304,7 +304,7 @@ class ClientSubmission(BaseClass, LogMixin):
         samples = [sample.to_pydantic() for sample in self.clientsubmissionsampleassociation]
         checker = SampleChecker(parent=None, title="Create Run", samples=samples, clientsubmission=self)
         if checker.exec():
-            run = Run(clientsubmission=self, rsl_plate_num=checker.rsl_plate_num)
+            run = Run(clientsubmission=self, rsl_plate_number=checker.rsl_plate_number)
             active_samples = [sample for sample in samples if sample.enabled]
             logger.debug(active_samples)
             for sample in active_samples:
@@ -323,8 +323,12 @@ class ClientSubmission(BaseClass, LogMixin):
     def add_comment(self, obj):
         logger.debug("Add Comment")
 
-    def show_details(self, obj):
+    # def show_details(self, obj):
-        logger.debug("Show Details")
+    #     logger.debug("Show Details")
+    #     from frontend.widgets.submission_details import SubmissionDetails
+    #     dlg = SubmissionDetails(parent=obj, sub=self)
+    #     if dlg.exec():
+    #         pass
 
     def details_dict(self, **kwargs):
         output = super().details_dict(**kwargs)
@@ -334,6 +338,11 @@ class ClientSubmission(BaseClass, LogMixin):
         output['run'] = [run.details_dict() for run in output['run']]
         output['sample'] = [sample.details_dict() for sample in output['clientsubmissionsampleassociation']]
         output['name'] = self.name
+        output['client_lab'] = output['clientlab']
+        output['submission_type'] = output['submissiontype']
+        output['excluded'] = ['run', "sample", "clientsubmissionsampleassociation", "excluded",
+                              "expanded", 'clientlab', 'submissiontype', 'id']
+        output['expanded'] = ["clientlab", "contact", "submissiontype"]
         return output
 
 
@@ -343,7 +352,7 @@ class Run(BaseClass, LogMixin):
     """
 
     id = Column(INTEGER, primary_key=True)  #: primary key
-    rsl_plate_num = Column(String(32), unique=True, nullable=False)  #: RSL name (e.g. RSL-22-0012)
+    rsl_plate_number = Column(String(32), unique=True, nullable=False)  #: RSL name (e.g. RSL-22-0012)
     clientsubmission_id = Column(INTEGER, ForeignKey("_clientsubmission.id", ondelete="SET NULL",
                                                      name="fk_BS_clientsub_id"))  #: client lab id from _organizations)
     clientsubmission = relationship("ClientSubmission", back_populates="run")
@@ -387,7 +396,7 @@ class Run(BaseClass, LogMixin):
 
     @hybrid_property
     def name(self):
-        return self.rsl_plate_num
+        return self.rsl_plate_number
 
     @classmethod
     def get_default_info(cls, *args, submissiontype: SubmissionType | None = None) -> dict:
@@ -593,8 +602,23 @@ class Run(BaseClass, LogMixin):
 
     def details_dict(self, **kwargs):
         output = super().details_dict()
-        output['sample'] = [sample.details_dict() for sample in output['runsampleassociation']]
+        submission_samples = [sample for sample in self.clientsubmission.sample]
+        # logger.debug(f"Submission samples:{pformat(submission_samples)}")
+        active_samples = [sample.details_dict() for sample in output['runsampleassociation']
+                          if sample.sample.sample_id in [s.sample_id for s in submission_samples]]
+        # logger.debug(f"Active samples:{pformat(active_samples)}")
+        for sample in active_samples:
+            sample['active'] = True
+        inactive_samples = [sample.details_dict() for sample in submission_samples if sample.name not in [s['sample_id'] for s in active_samples]]
+        # logger.debug(f"Inactive samples:{pformat(inactive_samples)}")
+        for sample in inactive_samples:
+            sample['active'] = False
+        # output['sample'] = [sample.details_dict() for sample in output['runsampleassociation']]
+        output['sample'] = active_samples + inactive_samples
         output['procedure'] = [procedure.details_dict() for procedure in output['procedure']]
+        output['permission'] = is_power_user()
+        output['excluded'] = ['procedure', "runsampleassociation", 'excluded', 'expanded', 'sample', 'id', 'custom', 'permission']
+
         return output
 
     @classmethod
@@ -890,10 +914,10 @@ class Run(BaseClass, LogMixin):
                     field_value = dict(value=self.__getattribute__(key).name, missing=missing)
                 case "plate_number":
                     key = 'name'
-                    field_value = dict(value=self.rsl_plate_num, missing=missing)
+                    field_value = dict(value=self.rsl_plate_number, missing=missing)
                 case "submitter_plate_number":
                     key = "submitter_plate_id"
-                    field_value = dict(value=self.submitter_plate_num, missing=missing)
+                    field_value = dict(value=self.submitter_plate_number, missing=missing)
                 case "id":
                     continue
                 case _:
@@ -1168,8 +1192,8 @@ class Run(BaseClass, LogMixin):
             e: SQLIntegrityError or SQLOperationalError if problem with commit.
         """
         from frontend.widgets.pop_ups import QuestionAsker
-        fname = self.__backup_path__.joinpath(f"{self.rsl_plate_num}-backup({date.today().strftime('%Y%m%d')})")
+        fname = self.__backup_path__.joinpath(f"{self.rsl_plate_number}-backup({date.today().strftime('%Y%m%d')})")
-        msg = QuestionAsker(title="Delete?", message=f"Are you sure you want to delete {self.rsl_plate_num}?\n")
+        msg = QuestionAsker(title="Delete?", message=f"Are you sure you want to delete {self.rsl_plate_number}?\n")
         if msg.exec():
             try:
                 # NOTE: backs up file as xlsx, same as export.
@@ -1187,17 +1211,17 @@ class Run(BaseClass, LogMixin):
             except AttributeError:
                 logger.error("App will not refresh data at this time.")
 
-    def show_details(self, obj):
+    # def show_details(self, obj):
-        """
+    #     """
-        Creates Widget for showing procedure details.
+    #     Creates Widget for showing procedure details.
-
+    #
-        Args:
+    #     Args:
-            obj (Widget): Parent widget
+    #         obj (Widget): Parent widget
-        """
+    #     """
-        from frontend.widgets.submission_details import SubmissionDetails
+    #     from frontend.widgets.submission_details import SubmissionDetails
-        dlg = SubmissionDetails(parent=obj, sub=self)
+    #     dlg = SubmissionDetails(parent=obj, sub=self)
-        if dlg.exec():
+    #     if dlg.exec():
-            pass
+    #         pass
 
     def edit(self, obj):
         """
@@ -1641,12 +1665,12 @@ class ClientSubmissionSampleAssociation(BaseClass):
         output = super().details_dict()
         # NOTE: Figure out how to merge the misc_info if doing .update instead.
         relevant = {k: v for k, v in output.items() if k not in ['sample']}
-        logger.debug(f"Relevant info from assoc output: {pformat(relevant)}")
+        # logger.debug(f"Relevant info from assoc output: {pformat(relevant)}")
         output = output['sample'].details_dict()
-        misc = output['_misc_info']
+        misc = output['misc_info']
-        logger.debug(f"Output from sample: {pformat(output)}")
+        # logger.debug(f"Output from sample: {pformat(output)}")
         output.update(relevant)
-        output['_misc_info'] = misc
+        output['misc_info'] = misc
         # output['sample'] = temp
         # output.update(output['sample'].details_dict())
         return output
@@ -1815,7 +1839,7 @@ class ClientSubmissionSampleAssociation(BaseClass):
             case ClientSubmission():
                 pass
             case str():
-                clientsubmission = ClientSubmission.query(rsl_plate_num=clientsubmission)
+                clientsubmission = ClientSubmission.query(rsl_plate_number=clientsubmission)
             case _:
                 raise ValueError()
         match sample:
@@ -1879,7 +1903,7 @@ class RunSampleAssociation(BaseClass):
 
     def __repr__(self) -> str:
         try:
-            return f"<{self.__class__.__name__}({self.run.rsl_plate_num} & {self.sample.sample_id})"
+            return f"<{self.__class__.__name__}({self.run.rsl_plate_number} & {self.sample.sample_id})"
         except AttributeError as e:
             logger.error(f"Unable to construct __repr__ due to: {e}")
             return super().__repr__()
@@ -1901,7 +1925,7 @@ class RunSampleAssociation(BaseClass):
         except KeyError as e:
             logger.error(f"Unable to find row {self.row} in row_map.")
             sample['Well'] = None
-        sample['plate_name'] = self.run.rsl_plate_num
+        sample['plate_name'] = self.run.rsl_plate_number
         sample['positive'] = False
         return sample
 
@@ -1975,7 +1999,7 @@ class RunSampleAssociation(BaseClass):
             case Run():
                 query = query.filter(cls.run == run)
             case str():
-                query = query.join(Run).filter(Run.rsl_plate_num == run)
+                query = query.join(Run).filter(Run.rsl_plate_number == run)
             case _:
                 pass
         match sample:
@@ -2060,12 +2084,12 @@ class RunSampleAssociation(BaseClass):
         output = super().details_dict()
         # NOTE: Figure out how to merge the misc_info if doing .update instead.
         relevant = {k: v for k, v in output.items() if k not in ['sample']}
-        logger.debug(f"Relevant info from assoc output: {pformat(relevant)}")
+        # logger.debug(f"Relevant info from assoc output: {pformat(relevant)}")
         output = output['sample'].details_dict()
-        misc = output['_misc_info']
+        misc = output['misc_info']
-        logger.debug(f"Output from sample: {pformat(output)}")
+        # logger.debug(f"Output from sample: {pformat(output)}")
         output.update(relevant)
-        output['_misc_info'] = misc
+        output['misc_info'] = misc
         return output
 
 class ProcedureSampleAssociation(BaseClass):
@@ -2132,9 +2156,9 @@ class ProcedureSampleAssociation(BaseClass):
         # NOTE: Figure out how to merge the misc_info if doing .update instead.
         relevant = {k: v for k, v in output.items() if k not in ['sample']}
         output = output['sample'].details_dict()
-        misc = output['_misc_info']
+        misc = output['misc_info']
         output.update(relevant)
-        output['_misc_info'] = misc
+        output['misc_info'] = misc
         output['results'] = [result.details_dict() for result in output['results']]
         return output
 

src/submissions/backend/excel/__init__.py

@@ -3,6 +3,6 @@ Contains pandas and openpyxl convenience functions for interacting with excel wo
 '''
 
 from .parser import *
-from backend.excel.parsers.submission_parser import *
+from backend.excel.parsers.clientsubmission_parser import *
 from .reports import *
 from .writer import *

src/submissions/backend/excel/parser.py

@@ -630,12 +630,12 @@ class PCRParser(object):
                 return None
         if submission is None:
             self.submission_obj = Wastewater
-            rsl_plate_num = None
+            rsl_plate_number = None
         else:
             self.submission_obj = submission
-            rsl_plate_num = self.submission_obj.rsl_plate_num
+            rsl_plate_number = self.submission_obj.rsl_plate_number
-        self.samples = self.submission_obj.parse_pcr(xl=self.xl, rsl_plate_num=rsl_plate_num)
+        self.samples = self.submission_obj.parse_pcr(xl=self.xl, rsl_plate_number=rsl_plate_number)
-        self.controls = self.submission_obj.parse_pcr_controls(xl=self.xl, rsl_plate_num=rsl_plate_num)
+        self.controls = self.submission_obj.parse_pcr_controls(xl=self.xl, rsl_plate_number=rsl_plate_number)
 
     @property
     def pcr_info(self) -> dict:
@@ -675,11 +675,11 @@ class ConcentrationParser(object):
                 return None
         if run is None:
             self.submission_obj = Run()
-            rsl_plate_num = None
+            rsl_plate_number = None
         else:
             self.submission_obj = run
-            rsl_plate_num = self.submission_obj.rsl_plate_num
+            rsl_plate_number = self.submission_obj.rsl_plate_number
-        self.samples = self.submission_obj.parse_concentration(xl=self.xl, rsl_plate_num=rsl_plate_num)
+        self.samples = self.submission_obj.parse_concentration(xl=self.xl, rsl_plate_number=rsl_plate_number)
 
 # NOTE: Generified parsers below
 

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

@@ -1,14 +1,15 @@
 """
 
 """
+from __future__ import annotations
 import logging, re
 from pathlib import Path
-from typing import Generator, Tuple
+from typing import Generator, Tuple, TYPE_CHECKING
-from openpyxl import load_workbook
 from pandas import DataFrame
 from backend.validators import pydant
-from backend.db.models import Procedure
+if TYPE_CHECKING:
-from dataclasses import dataclass
+    from backend.db.models import ProcedureType
+
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -30,7 +31,7 @@ class DefaultParser(object):
         return instance
 
 
-    def __init__(self, filepath: Path | str, procedure: Procedure|None=None, range_dict: dict | None = None, *args, **kwargs):
+    def __init__(self, filepath: Path | str, proceduretype: ProcedureType|None=None, range_dict: dict | None = None, *args, **kwargs):
         """
 
         Args:
@@ -40,7 +41,7 @@ class DefaultParser(object):
             *args ():
             **kwargs ():
         """
-        self.procedure = procedure
+        self.proceduretype = proceduretype
         try:
             self._pyd_object = getattr(pydant, f"Pyd{self.__class__.__name__.replace('Parser', '')}")
         except AttributeError:
@@ -58,6 +59,13 @@ class DefaultParser(object):
         data['filepath'] = self.filepath
         return self._pyd_object(**data)
 
+    @classmethod
+    def correct_procedure_type(cls, proceduretype: str | "ProcedureType"):
+        from backend.db.models import ProcedureType
+        if isinstance(proceduretype, str):
+            proceduretype = ProcedureType.query(name=proceduretype)
+        return proceduretype
+
 
 class DefaultKEYVALUEParser(DefaultParser):
 
@@ -90,7 +98,6 @@ class DefaultTABLEParser(DefaultParser):
 
     default_range_dict = [dict(
         header_row=20,
-        end_row=116,
         sheet="Sample List"
     )]
 
@@ -98,15 +105,25 @@ class DefaultTABLEParser(DefaultParser):
     def parsed_info(self):
         for item in self.range_dict:
             list_worksheet = self.workbook[item['sheet']]
+            if "end_row" in item.keys():
+                list_df = DataFrame([item for item in list_worksheet.values][item['header_row'] - 1:item['end_row']-1])
+            else:
                 list_df = DataFrame([item for item in list_worksheet.values][item['header_row'] - 1:])
             list_df.columns = list_df.iloc[0]
             list_df = list_df[1:]
             list_df = list_df.dropna(axis=1, how='all')
             for ii, row in enumerate(list_df.iterrows()):
-                output = {key.lower().replace(" ", "_"): value for key, value in row[1].to_dict().items()}
+                output = {}
+                for key, value in row[1].to_dict().items():
+                    if isinstance(key, str):
+                        key = key.lower().replace(" ", "_")
+                        key = re.sub(r"_(\(.*\)|#)", "", key)
+                    logger.debug(f"Row {ii} values: {key}: {value}")
+                    output[key] = value
                 yield output
 
     def to_pydantic(self, **kwargs):
         return [self._pyd_object(**output) for output in self.parsed_info]
 
-from .submission_parser import *
+from .clientsubmission_parser import *
+from backend.excel.parsers.results_parsers.pcr_results_parser import *

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

@@ -1,6 +1,7 @@
 """
 
 """
+from __future__ import annotations
 import logging
 from pathlib import Path
 from string import ascii_lowercase
@@ -9,8 +10,9 @@ from typing import Generator
 from openpyxl.reader.excel import load_workbook
 
 from tools import row_keys
-from backend.db.models import SubmissionType
+# from backend.db.models import SubmissionType
 from . import DefaultKEYVALUEParser, DefaultTABLEParser
+from backend.managers import procedures as procedure_managers
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -34,6 +36,7 @@ class SubmissionTyperMixin(object):
 
     @classmethod
     def get_subtype_from_regex(cls, filepath: Path):
+        from backend.db.models import SubmissionType
         regex = SubmissionType.regex
         m = regex.search(filepath.__str__())
         try:
@@ -45,7 +48,8 @@ class SubmissionTyperMixin(object):
 
     @classmethod
     def get_subtype_from_preparse(cls, filepath: Path):
-        parser = ClientSubmissionParser(filepath)
+        from backend.db.models import SubmissionType
+        parser = ClientSubmissionInfoParser(filepath)
         sub_type = next((value for k, value in parser.parsed_info if k == "submissiontype"), None)
         sub_type = SubmissionType.query(name=sub_type)
         if isinstance(sub_type, list):
@@ -54,6 +58,7 @@ class SubmissionTyperMixin(object):
 
     @classmethod
     def get_subtype_from_properties(cls, filepath: Path):
+        from backend.db.models import SubmissionType
         wb = load_workbook(filepath)
         # NOTE: Gets first category in the metadata.
         categories = wb.properties.category.split(";")
@@ -64,7 +69,7 @@ class SubmissionTyperMixin(object):
         return sub_type
 
 
-class ClientSubmissionParser(DefaultKEYVALUEParser, SubmissionTyperMixin):
+class ClientSubmissionInfoParser(DefaultKEYVALUEParser, SubmissionTyperMixin):
     """
     Object for retrieving submitter info from "sample list" sheet
     """
@@ -78,13 +83,29 @@ class ClientSubmissionParser(DefaultKEYVALUEParser, SubmissionTyperMixin):
     )]
 
     def __init__(self, filepath: Path | str, *args, **kwargs):
+        from frontend.widgets.pop_ups import QuestionAsker
         self.submissiontype = self.retrieve_submissiontype(filepath=filepath)
         if "range_dict" not in kwargs:
             kwargs['range_dict'] = self.submissiontype.info_map
         super().__init__(filepath=filepath, **kwargs)
+        allowed_procedure_types = [item.name for item in self.submissiontype.proceduretype]
+        for name in allowed_procedure_types:
+            if name in self.workbook.sheetnames:
+                # TODO: check if run with name already exists
+                add_run = QuestionAsker(title="Add Run?", message="We've detected a sheet corresponding to an associated procedure type.\nWould you like to add a new run?")
+                if add_run.accepted:
 
 
-class ClientSampleParser(DefaultTABLEParser, SubmissionTyperMixin):
+                # NOTE: recruit parser.
+                    try:
+                        manager = getattr(procedure_managers, name)
+                    except AttributeError:
+                        manager = procedure_managers.DefaultManager
+                    self.manager = manager(proceduretype=name)
+                pass
+
+
+class ClientSubmissionSampleParser(DefaultTABLEParser, SubmissionTyperMixin):
     """
     Object for retrieving submitter samples from "sample list" sheet
     """

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

@@ -0,0 +1,119 @@
+from __future__ import annotations
+from pathlib import Path
+from typing import TYPE_CHECKING
+
+
+from backend.excel.parsers import DefaultTABLEParser, DefaultKEYVALUEParser
+if TYPE_CHECKING:
+    from backend.db.models import ProcedureType
+
+
+class DefaultInfoParser(DefaultKEYVALUEParser):
+
+    default_range_dict = [dict(
+        start_row=1,
+        end_row=14,
+        key_column=1,
+        value_column=2,
+        sheet=""
+    )]
+
+    def __init__(self, filepath: Path | str, proceduretype: "ProcedureType"|None=None, range_dict: dict | None = None, *args, **kwargs):
+        from backend.validators.pydant import PydProcedure
+        proceduretype = self.correct_procedure_type(proceduretype)
+        if not range_dict:
+            range_dict = proceduretype.info_map
+            if not range_dict:
+                range_dict = self.__class__.default_range_dict
+                for item in range_dict:
+                    item['sheet'] = proceduretype.name
+        super().__init__(filepath=filepath, proceduretype=proceduretype, range_dict=range_dict, *args, **kwargs)
+        self._pyd_object = PydProcedure
+
+
+class DefaultSampleParser(DefaultTABLEParser):
+
+    default_range_dict = [dict(
+        header_row=41,
+        sheet=""
+    )]
+
+    def __init__(self, filepath: Path | str, proceduretype: "ProcedureType"|None=None, range_dict: dict | None = None, *args, **kwargs):
+        from backend.validators.pydant import PydSample
+        proceduretype = self.correct_procedure_type(proceduretype)
+        if not range_dict:
+            range_dict = proceduretype.sample_map
+            if not range_dict:
+                range_dict = self.__class__.default_range_dict
+                for item in range_dict:
+                    item['sheet'] = proceduretype.name
+        super().__init__(filepath=filepath, procedure=proceduretype, range_dict=range_dict, *args, **kwargs)
+        self._pyd_object = PydSample
+
+
+class DefaultReagentParser(DefaultTABLEParser):
+
+    default_range_dict = [dict(
+        header_row=17,
+        end_row=29,
+        sheet=""
+    )]
+
+    def __init__(self, filepath: Path | str, proceduretype: "ProcedureType"|None=None, range_dict: dict | None = None, *args, **kwargs):
+        from backend.validators.pydant import PydReagent
+        proceduretype = self.correct_procedure_type(proceduretype)
+        if not range_dict:
+            range_dict = proceduretype.sample_map
+            if not range_dict:
+                range_dict = self.__class__.default_range_dict
+                for item in range_dict:
+                    item['sheet'] = proceduretype.name
+        super().__init__(filepath=filepath, proceduretype=proceduretype, range_dict=range_dict, *args, **kwargs)
+        self._pyd_object = PydReagent
+
+    @property
+    def parsed_info(self):
+        output = super().parsed_info
+        for item in output:
+            if not item['lot']:
+                continue
+            item['reagentrole'] = item['reagent_role']
+            yield item
+
+class DefaultEquipmentParser(DefaultTABLEParser):
+
+    default_range_dict = [dict(
+        header_row=32,
+        end_row=39,
+        sheet=""
+    )]
+
+    def __init__(self, filepath: Path | str, proceduretype: "ProcedureType"|None=None, range_dict: dict | None = None, *args, **kwargs):
+        from backend.validators.pydant import PydEquipment
+        proceduretype = self.correct_procedure_type(proceduretype)
+        if not range_dict:
+            range_dict = proceduretype.sample_map
+            if not range_dict:
+                range_dict = self.__class__.default_range_dict
+                for item in range_dict:
+                    item['sheet'] = proceduretype.name
+        super().__init__(filepath=filepath, proceduretype=proceduretype, range_dict=range_dict, *args, **kwargs)
+        self._pyd_object = PydEquipment
+
+    @property
+    def parsed_info(self):
+        output = super().parsed_info
+        for item in output:
+            if not item['name']:
+                continue
+            from backend.db.models import Equipment, Process
+            from backend.validators.pydant import PydTips, PydProcess
+            eq = Equipment.query(name=item['name'])
+            item['asset_number'] = eq.asset_number
+            item['nickname'] = eq.nickname
+            process = Process.query(name=item['process'])
+
+            if item['tips']:
+                item['tips'] = [PydTips(name=item['tips'], tiprole=process.tiprole[0].name)]
+            item['equipmentrole'] = item['equipment_role']
+            yield item

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

@@ -1,19 +1,14 @@
 """
 
 """
-import logging, re, sys
+import logging
-from pprint import pformat
-from pathlib import Path
-from typing import Generator, Tuple
-
-from openpyxl import load_workbook
-
 from backend.db.models import Run, Sample, Procedure, ProcedureSampleAssociation
-from . import DefaultKEYVALUEParser, DefaultTABLEParser
+from backend.excel.parsers import DefaultKEYVALUEParser, DefaultTABLEParser
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
-
+# class PCRResultsParser(DefaultParser):
+#     pass
 
 class PCRInfoParser(DefaultKEYVALUEParser):
     default_range_dict = [dict(

src/submissions/backend/excel/reports.py

@@ -191,7 +191,7 @@ class TurnaroundMaker(ReportArchetype):
             tat_ok = days <= tat
         except TypeError:
             return {}
-        return dict(name=str(sub.rsl_plate_num), days=days, submitted_date=sub.submitted_date,
+        return dict(name=str(sub.rsl_plate_number), days=days, submitted_date=sub.submitted_date,
                     completed_date=sub.completed_date, acceptable=tat_ok)
 
 

src/submissions/backend/managers/__init__.py

@@ -0,0 +1,22 @@
+import logging
+from pathlib import Path
+from backend.db.models import ProcedureType
+from frontend.widgets.functions import select_open_file
+from tools import get_application_from_parent
+
+logger = logging.getLogger(f"submissions.{__name__}")
+
+class DefaultManager(object):
+
+    def __init__(self, proceduretype: ProcedureType, parent, fname: Path | str | None = None):
+        logger.debug(f"FName before correction: {fname}")
+        if isinstance(proceduretype, str):
+            proceduretype = ProcedureType.query(name=proceduretype)
+        self.proceduretype = proceduretype
+        if fname != "no_file":
+            if not fname:
+                self.fname = select_open_file(file_extension="xlsx", obj=get_application_from_parent(parent))
+            elif isinstance(fname, str):
+                self.fname = Path(fname)
+        logger.debug(f"FName after correction: {fname}")
+

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

@@ -0,0 +1,44 @@
+from __future__ import annotations
+import logging
+from backend.managers import DefaultManager
+from typing import TYPE_CHECKING
+from pathlib import Path
+from backend.excel.parsers import procedure_parsers
+if TYPE_CHECKING:
+    from backend.db.models import ProcedureType
+
+logger = logging.getLogger(f"submissions.{__name__}")
+
+
+class DefaultProcedure(DefaultManager):
+
+    def __init__(self, proceduretype: "ProcedureType"|str, parent, fname: Path | str | None = None):
+
+        super().__init__(proceduretype=proceduretype, parent=parent, fname=fname)
+        try:
+            info_parser = getattr(procedure_parsers, f"{self.proceduretype.name.replace(' ', '')}InfoParser")
+        except AttributeError:
+            info_parser = procedure_parsers.DefaultInfoParser
+        self.info_parser = info_parser(filepath=fname, proceduretype=proceduretype)
+        try:
+            reagent_parser = getattr(procedure_parsers, f"{self.proceduretype.name.replace(' ', '')}ReagentParser")
+        except AttributeError:
+            reagent_parser = procedure_parsers.DefaultReagentParser
+        self.reagent_parser = reagent_parser(filepath=fname, proceduretype=proceduretype)
+        try:
+            sample_parser = getattr(procedure_parsers, f"{self.proceduretype.name.replace(' ', '')}SampleParser")
+        except AttributeError:
+            sample_parser = procedure_parsers.DefaultSampleParser
+        self.sample_parser = sample_parser(filepath=fname, proceduretype=proceduretype)
+        try:
+            equipment_parser = getattr(procedure_parsers, f"{self.proceduretype.name.replace(' ', '')}EquipmentParser")
+        except AttributeError:
+            equipment_parser = procedure_parsers.DefaultEquipmentParser
+        self.equipment_parser = equipment_parser(filepath=fname, proceduretype=proceduretype)
+        self.to_pydantic()
+
+    def to_pydantic(self):
+        self.procedure = self.info_parser.to_pydantic()
+        self.reagents = self.reagent_parser.to_pydantic()
+        self.samples = self.sample_parser.to_pydantic()
+        self.equipment = self.equipment_parser.to_pydantic()

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

@@ -0,0 +1,21 @@
+import logging
+from .. import DefaultManager
+from backend.db.models import Procedure
+from pathlib import Path
+from frontend.widgets.functions import select_open_file
+from tools import get_application_from_parent
+
+logger = logging.getLogger(f"submission.{__name__}")
+
+class DefaultResults(DefaultManager):
+
+    def __init__(self, procedure: Procedure, parent, fname: Path | str | None = None):
+        logger.debug(f"FName before correction: {fname}")
+        self.procedure = procedure
+        if not fname:
+            self.fname = select_open_file(file_extension="xlsx", obj=get_application_from_parent(parent))
+        elif isinstance(fname, str):
+            self.fname = Path(fname)
+        logger.debug(f"FName after correction: {fname}")
+
+from .pcr_results_manager import PCR

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

@@ -3,11 +3,8 @@
 """
 import logging
 from pathlib import Path
-from backend.validators import PydResults
+from backend.db.models import Procedure
-from backend.db.models import Procedure, Results
+from backend.excel.parsers.results_parsers.pcr_results_parser import PCRSampleParser, PCRInfoParser
-from backend.excel.parsers.pcr_parser import PCRSampleParser, PCRInfoParser
-from frontend.widgets.functions import select_open_file
-from tools import get_application_from_parent
 from . import DefaultResults
 
 logger = logging.getLogger(f"submissions.{__name__}")
@@ -15,25 +12,21 @@ logger = logging.getLogger(f"submissions.{__name__}")
 class PCR(DefaultResults):
 
     def __init__(self, procedure: Procedure, parent, fname:Path|str|None=None):
-        logger.debug(f"FName before correction: {fname}")
+        super().__init__(procedure=procedure, parent=parent, fname=fname)
-        self.procedure = procedure
-        if not fname:
-            self.fname = select_open_file(file_extension="xlsx", obj=get_application_from_parent(parent))
-        elif isinstance(fname, str):
-            self.fname = Path(fname)
-        logger.debug(f"FName after correction: {fname}")
         self.info_parser = PCRInfoParser(filepath=self.fname, procedure=self.procedure)
         self.sample_parser = PCRSampleParser(filepath=self.fname, procedure=self.procedure)
-        self.build_procedure()
+        self.build_info()
         self.build_samples()
 
-    def build_procedure(self):
+    def build_info(self):
         procedure_info = self.info_parser.to_pydantic()
+        procedure_info.results_type = self.__class__.__name__
         procedure_sql = procedure_info.to_sql()
         procedure_sql.save()
 
     def build_samples(self):
         samples = self.sample_parser.to_pydantic()
         for sample in samples:
+            sample.results_type = self.__class__.__name__
             sql = sample.to_sql()
             sql.save()

src/submissions/backend/validators/__init__.py

@@ -59,8 +59,8 @@ class ClientSubmissionNamer(DefaultNamer):
 
 
     def get_subtype_from_preparse(self):
-        from backend.excel.parsers.submission_parser import ClientSubmissionParser
+        from backend.excel.parsers.clientsubmission_parser import ClientSubmissionInfoParser
-        parser = ClientSubmissionParser(self.filepath)
+        parser = ClientSubmissionInfoParser(self.filepath)
         sub_type = next((value for k, value in parser.parsed_info if k == "submissiontype"), None)
         sub_type = SubmissionType.query(name=sub_type)
         if isinstance(sub_type, list):

src/submissions/backend/validators/pydant.py

@@ -262,6 +262,12 @@ class PydSample(PydBaseClass):
                 pass
         return value
 
+    @field_validator("row", mode="before")
+    @classmethod
+    def str_to_int(cls, value):
+        if isinstance(value, str):
+            value = row_keys[value]
+        return value
 
 class PydTips(BaseModel):
     name: str
@@ -298,7 +304,7 @@ class PydEquipment(BaseModel, extra='ignore'):
     asset_number: str
     name: str
     nickname: str | None
-    processes: List[str] | None
+    process: List[str] | None
     equipmentrole: str | None
     tips: List[PydTips] | None = Field(default=None)
 
@@ -309,7 +315,7 @@ class PydEquipment(BaseModel, extra='ignore'):
             value = value.name
         return value
 
-    @field_validator('processes', mode='before')
+    @field_validator('process', mode='before')
     @classmethod
     def make_empty_list(cls, value):
         # if isinstance(value, dict):
@@ -397,7 +403,7 @@ class PydSubmission(BaseModel, extra='allow'):
     filepath: Path
     submissiontype: dict | None
     submitter_plate_id: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
-    rsl_plate_num: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
+    rsl_plate_number: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
     submitted_date: dict | None = Field(default=dict(value=date.today(), missing=True), validate_default=True)
     clientlab: dict | None
     sample_count: dict | None
@@ -517,14 +523,14 @@ class PydSubmission(BaseModel, extra='allow'):
                 value['value'] = None
         return value
 
-    @field_validator("rsl_plate_num", mode='before')
+    @field_validator("rsl_plate_number", mode='before')
     @classmethod
     def rescue_rsl_number(cls, value):
         if value is None:
             return dict(value=None, missing=True)
         return value
 
-    @field_validator("rsl_plate_num")
+    @field_validator("rsl_plate_number")
     @classmethod
     def rsl_from_file(cls, value, values):
         sub_type = values.data['proceduretype']['value']
@@ -689,7 +695,7 @@ class PydSubmission(BaseModel, extra='allow'):
         # NOTE: this could also be done with default_factory
         self.submission_object = Run.find_polymorphic_subclass(
             polymorphic_identity=self.submission_type['value'])
-        self.namer = RSLNamer(self.rsl_plate_num['value'], submission_type=self.submission_type['value'])
+        self.namer = RSLNamer(self.rsl_plate_number['value'], submission_type=self.submission_type['value'])
         if run_custom:
             self.submission_object.custom_validation(pyd=self)
 
@@ -796,7 +802,7 @@ class PydSubmission(BaseModel, extra='allow'):
         # logger.debug(f"Pydantic procedure type: {self.proceduretype['value']}")
         # logger.debug(f"Pydantic improved_dict: {pformat(dicto)}")
         instance, result = Run.query_or_create(submissiontype=self.submission_type['value'],
-                                                    rsl_plate_num=self.rsl_plate_num['value'])
+                                               rsl_plate_number=self.rsl_plate_number['value'])
         # logger.debug(f"Created or queried instance: {instance}")
         if instance is None:
             report.add_result(Result(msg="Overwrite Cancelled."))
@@ -1266,13 +1272,13 @@ class PydEquipmentRole(BaseModel):
 class PydProcess(BaseModel, extra="allow"):
     name: str
     version: str = Field(default="1")
-    submissiontype: List[str]
+    proceduretype: List[str]
     equipment: List[str]
     equipmentrole: List[str]
     kittype: List[str]
     tiprole: List[str]
 
-    @field_validator("submissiontype", "equipment", "equipmentrole", "kittype", "tiprole", mode="before")
+    @field_validator("proceduretype", "equipment", "equipmentrole", "kittype", "tiprole", mode="before")
     @classmethod
     def enforce_list(cls, value):
         if not isinstance(value, list):
@@ -1361,10 +1367,10 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
             else:
                 procedure_type = None
             if values.data['run']:
-                run = values.data['run'].rsl_plate_num
+                run = values.data['run'].rsl_plate_number
             else:
                 run = None
-            value['value'] = f"{procedure_type}-{run}"
+            value['value'] = f"{run}-{procedure_type}"
             value['missing'] = True
         return value
 
@@ -1391,7 +1397,7 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
         if not value:
             if values.data['kittype']['value'] != cls.model_fields['kittype'].default['value']:
                 kittype = KitType.query(name=values.data['kittype']['value'])
-                value = {item.name: item.reagents for item in kittype.reagentrole}
+                value = {item.name: item.reagent for item in kittype.reagentrole}
         return value
 
     def update_kittype_reagentroles(self, kittype: str | KitType):
@@ -1545,11 +1551,13 @@ class PydClientSubmission(PydBaseClass):
 class PydResults(PydBaseClass, arbitrary_types_allowed=True):
 
     results: dict = Field(default={})
-    img: None = Field(default=None)
+    results_type: str = Field(default="NA")
+    img: None | bytes = Field(default=None)
     parent: Procedure|ProcedureSampleAssociation|None = Field(default=None)
 
     def to_sql(self):
-        sql = Results(result=self.results)
+        sql = Results(results_type=self.results_type, result=self.results)
+        sql.image = self.img
         match self.parent:
             case ProcedureSampleAssociation():
                 sql.sampleprocedureassociation = self.parent

src/submissions/frontend/widgets/pop_ups.py

@@ -8,8 +8,8 @@ from PyQt6.QtWidgets import (
 from PyQt6.QtWebEngineWidgets import QWebEngineView
 from tools import jinja_template_loading
 import logging
-from backend.db import models
+
-from typing import Literal
+from typing import Literal, Any
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -70,7 +70,8 @@ class ObjectSelector(QDialog):
     dialog to input BaseClass type manually
     """
 
-    def __init__(self, title: str, message: str, obj_type: str | type[models.BaseClass], values: list | None = None):
+    def __init__(self, title: str, message: str, obj_type: str | Any, values: list | None = None):
+        from backend.db import models
         super().__init__()
         self.setWindowTitle(title)
         self.widget = QComboBox()

src/submissions/frontend/widgets/procedure_creation.py

@@ -29,7 +29,7 @@ class ProcedureCreation(QDialog):
         super().__init__(parent)
         self.run = run
         self.proceduretype = proceduretype
-        self.setWindowTitle(f"New {proceduretype.name} for { run.rsl_plate_num }")
+        self.setWindowTitle(f"New {proceduretype.name} for { run.rsl_plate_number }")
         self.created_procedure = self.proceduretype.construct_dummy_procedure(run=self.run)
         self.created_procedure.update_kittype_reagentroles(kittype=self.created_procedure.possible_kits[0])
         self.created_procedure.samples = self.run.constuct_sample_dicts_for_proceduretype(proceduretype=self.proceduretype)
@@ -65,8 +65,8 @@ class ProcedureCreation(QDialog):
             template_name="procedure_creation",
             # css_in=['new_context_menu'],
             js_in=["procedure_form", "grid_drag", "context_menu"],
-            proceduretype=self.proceduretype.as_dict,
+            proceduretype=self.proceduretype.details_dict(),
-            run=self.run.to_dict(),
+            run=self.run.details_dict(),
             procedure=self.created_procedure.__dict__,
             plate_map=self.plate_map
         )

src/submissions/frontend/widgets/results/__init__.py

@@ -1,7 +0,0 @@
-
-
-class DefaultResults(object):
-
-    pass
-
-from .pcr import PCR

src/submissions/frontend/widgets/sample_checker.py

@@ -21,9 +21,9 @@ class SampleChecker(QDialog):
     def __init__(self, parent, title: str, samples: List[PydSample], clientsubmission: ClientSubmission|None=None):
         super().__init__(parent)
         if clientsubmission:
-            self.rsl_plate_num = RSLNamer.construct_new_plate_name(clientsubmission.to_dict())
+            self.rsl_plate_number = RSLNamer.construct_new_plate_name(clientsubmission.to_dict())
         else:
-            self.rsl_plate_num = clientsubmission
+            self.rsl_plate_number = clientsubmission
         self.samples = samples
         self.setWindowTitle(title)
         self.app = get_application_from_parent(parent)
@@ -45,7 +45,7 @@ class SampleChecker(QDialog):
         except AttributeError as e:
             logger.error(f"Problem getting sample list: {e}")
             samples = []
-        html = template.render(samples=samples, css=css, rsl_plate_num=self.rsl_plate_num)
+        html = template.render(samples=samples, css=css, rsl_plate_number=self.rsl_plate_number)
         self.webview.setHtml(html)
         QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
         self.buttonBox = QDialogButtonBox(QBtn)
@@ -76,9 +76,9 @@ class SampleChecker(QDialog):
         item.__setattr__("enabled", enabled)
 
     @pyqtSlot(str)
-    def set_rsl_plate_num(self, rsl_plate_num: str):
+    def set_rsl_plate_number(self, rsl_plate_number: str):
-        logger.debug(f"RSL plate num: {rsl_plate_num}")
+        logger.debug(f"RSL plate num: {rsl_plate_number}")
-        self.rsl_plate_num = rsl_plate_num
+        self.rsl_plate_number = rsl_plate_number
 
     @property
     def formatted_list(self) -> List[dict]:

src/submissions/frontend/widgets/submission_details.py

@@ -50,17 +50,33 @@ class SubmissionDetails(QDialog):
         # NOTE: setup channel
         self.channel = QWebChannel()
         self.channel.registerObject('backend', self)
-        match sub:
+        # match sub:
-            case Run():
+        #     case Run():
-                self.run_details(run=sub)
+        #         self.run_details(run=sub)
-                self.rsl_plate_num = sub.rsl_plate_num
+        #         self.rsl_plate_number = sub.rsl_plate_number
-            case Sample():
+        #     case Sample():
-                self.sample_details(sample=sub)
+        #         self.sample_details(sample=sub)
-            case Reagent():
+        #     case Reagent():
-                self.reagent_details(reagent=sub)
+        #         self.reagent_details(reagent=sub)
         # NOTE: Used to maintain javascript functions.
+        self.object_details(object=sub)
         self.webview.page().setWebChannel(self.channel)
 
+    def object_details(self, object):
+        details = object.details_dict()
+        template = object.details_template
+        template_path = Path(template.environment.loader.__getattribute__("searchpath")[0])
+        with open(template_path.joinpath("css", "styles.css"), "r") as f:
+            css = f.read()
+        key = object.__class__.__name__.lower()
+        d = {key: details}
+        logger.debug(f"Using details: {d}")
+        html = template.render(**d, css=css)
+        self.webview.setHtml(html)
+        self.setWindowTitle(f"{object.__class__.__name__} Details - {object.name}")
+
+
+
     def activate_export(self) -> None:
         """
         Determines if export pdf should be active.
@@ -213,7 +229,7 @@ class SubmissionDetails(QDialog):
         logger.debug(f"Submission details.")
         if isinstance(run, str):
             run = Run.query(name=run)
-        self.rsl_plate_num = run.rsl_plate_num
+        self.rsl_plate_number = run.rsl_plate_number
         self.base_dict = run.to_dict(full_data=True)
         # NOTE: don't want id
         self.base_dict['platemap'] = run.make_plate_map(sample_list=run.hitpicked)
@@ -244,7 +260,7 @@ class SubmissionDetails(QDialog):
         run.completed_date = datetime.now()
         run.completed_date.replace(tzinfo=timezone)
         run.save()
-        self.run_details(run=self.rsl_plate_num)
+        self.run_details(run=self.rsl_plate_number)
 
     def save_pdf(self):
         """
@@ -264,7 +280,7 @@ class SubmissionComment(QDialog):
         super().__init__(parent)
         self.app = get_application_from_parent(parent)
         self.submission = submission
-        self.setWindowTitle(f"{self.submission.rsl_plate_num} Submission Comment")
+        self.setWindowTitle(f"{self.submission.rsl_plate_number} Submission Comment")
         # NOTE: create text field
         self.txt_editor = QTextEdit(self)
         self.txt_editor.setReadOnly(False)

src/submissions/frontend/widgets/submission_table.py

@@ -161,7 +161,7 @@ class SubmissionsSheet(QTableView):
         for run in runs:
             new_run = dict(
                 start_time=run[0].strip(),
-                rsl_plate_num=run[1].strip(),
+                rsl_plate_number=run[1].strip(),
                 sample_count=run[2].strip(),
                 status=run[3].strip(),
                 experiment_name=run[4].strip(),
@@ -213,7 +213,7 @@ class SubmissionsSheet(QTableView):
         for run in runs:
             new_run = dict(
                 start_time=run[0].strip(),
-                rsl_plate_num=run[1].strip(),
+                rsl_plate_number=run[1].strip(),
                 biomek_status=run[2].strip(),
                 quant_status=run[3].strip(),
                 experiment_name=run[4].strip(),
@@ -379,7 +379,7 @@ class SubmissionsTree(QTreeView):
                 query_str=submission['submitter_plate_id'],
                 item_type=ClientSubmission
             ))
-            logger.debug(f"Added {submission_item}")
+            # logger.debug(f"Added {submission_item}")
             for run in submission['run']:
                 # self.model.append_element_to_group(group_item=group_item, element=run)
                 run_item = self.model.add_child(parent=submission_item, child=dict(
@@ -387,14 +387,14 @@ class SubmissionsTree(QTreeView):
                     query_str=run['plate_number'],
                     item_type=Run
                 ))
-                logger.debug(f"Added {run_item}")
+                # logger.debug(f"Added {run_item}")
                 for procedure in run['procedures']:
                     procedure_item = self.model.add_child(parent=run_item, child=dict(
                         name=procedure['name'],
                         query_str=procedure['name'],
                         item_type=Procedure
                     ))
-                    logger.debug(f"Added {procedure_item}")
+                    # logger.debug(f"Added {procedure_item}")
 
     def _populateTree(self, children, parent):
         for child in children:
@@ -415,7 +415,6 @@ class SubmissionsTree(QTreeView):
         # id = id.sibling(id.row(), 1)
         indexes = self.selectedIndexes()
         dicto = next((item.data(1) for item in indexes if item.data(1)))
-        logger.debug(dicto)
         # try:
         #     id = int(id.data())
         # except ValueError:
@@ -423,6 +422,7 @@ class SubmissionsTree(QTreeView):
         # Run.query(id=id).show_details(self)
         obj = dicto['item_type'].query(name=dicto['query_str'], limit=1)
         logger.debug(obj)
+        obj.show_details(obj)
 
     def link_extractions(self):
         pass

src/submissions/frontend/widgets/submission_widget.py

@@ -10,7 +10,7 @@ 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, get_application_from_parent
-from backend.excel import ClientSubmissionParser, ClientSampleParser
+from backend.excel.parsers.clientsubmission_parser import ClientSubmissionInfoParser, ClientSubmissionSampleParser
 from backend.validators import PydSubmission, PydReagent, PydClientSubmission, PydSample
 from backend.db import (
     ClientLab, SubmissionType, Reagent,
@@ -121,20 +121,20 @@ class SubmissionFormContainer(QWidget):
             return report
         # NOTE: create sheetparser using excel sheet and context from gui
         try:
-            self.clientsubmissionparser = ClientSubmissionParser(filepath=fname)
+            self.clientsubmissionparser = ClientSubmissionInfoParser(filepath=fname)
         except PermissionError:
             logger.error(f"Couldn't get permission to access file: {fname}")
             return
         except AttributeError:
-            self.clientsubmissionparser = ClientSubmissionParser(filepath=fname)
+            self.clientsubmissionparser = ClientSubmissionInfoParser(filepath=fname)
         try:
             # self.prsr = SheetParser(filepath=fname)
-            self.sampleparser = ClientSampleParser(filepath=fname)
+            self.sampleparser = ClientSubmissionSampleParser(filepath=fname)
         except PermissionError:
             logger.error(f"Couldn't get permission to access file: {fname}")
             return
         except AttributeError:
-            self.sampleparser = ClientSampleParser(filepath=fname)
+            self.sampleparser = ClientSubmissionSampleParser(filepath=fname)
         self.pydclientsubmission = self.clientsubmissionparser.to_pydantic()
         self.pydsamples = self.sampleparser.to_pydantic()
         # logger.debug(f"Samples: {pformat(self.pydclientsubmission.sample)}")
@@ -368,7 +368,7 @@ class SubmissionFormWidget(QWidget):
                 pass
             # NOTE: code 1: ask for overwrite
             case 1:
-                dlg = QuestionAsker(title=f"Review {base_submission.rsl_plate_num}?", message=trigger.msg)
+                dlg = QuestionAsker(title=f"Review {base_submission.rsl_plate_number}?", message=trigger.msg)
                 if dlg.exec():
                     # NOTE: Do not add duplicate reagents.
                     pass

src/submissions/templates/clientsubmission_details.html

@@ -0,0 +1,37 @@
+{% extends "details.html"%}
+
+<head>
+    {% block head %}
+    {{ super() }}
+    <title>ClientSubmission Details for {{ clientsubmission['name'] }}</title>
+    {% endblock %}
+</head>
+<body>
+    {% block body %}
+    <h2><u>Submission Details for {{ clientsubmission['name'] }}</u></h2>
+    {{ super() }}
+    <p>{% for key, value in clientsubmission.items() if key not in clientsubmission['excluded'] %}
+        &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key | replace("_", " ") | title | replace("Id", "ID") }}: </b>{% if key=='cost' %}{% if clientsubmission['cost'] %} {{ "${:,.2f}".format(value) }}{% endif %}{% else %}{{ value }}{% endif %}<br>
+    {% endfor %}
+    </p>
+
+    {% if clientsubmission['sample'] %}
+    <button type="button" class="collapsible"><h3><u>Client Submitted Samples:</u></h3></button>
+    <div class="nested">
+    <p>{% for sample in clientsubmission['sample'] %}
+        &nbsp;&nbsp;&nbsp;&nbsp;<a class="data-link sample" id="{{ sample['sample_id'] }}">{{ sample['sample_id']}}</a><br>
+    {% endfor %}</p>
+    </div>
+    {% endif %}
+    {% if clientsubmission['run'] %}
+    <button type="button" class="collapsible"><h3><u>Runs:</u></h3></button>
+    <div class="nested">
+    {% for run in clientsubmission['run'] %}
+        {% with run=run, child=True %}
+            {% include "run_details.html" %}
+        {% endwith %}
+    {% endfor %}
+    </div>
+    {% endif %}
+    {% endblock %}
+</body>

src/submissions/templates/css/styles.css

@@ -146,3 +146,36 @@ ul.no-bullets {
   background-color: pink;
 }
 
+/*  */
+.nested {
+  margin-left: 50px;
+  padding: 0 18px;
+  display: none;
+  overflow: hidden;
+  background-color: #f1f1f1;
+}
+
+/* Style the button that is used to open and close the collapsible content */
+.collapsible {
+  background-color: #eee;
+  color: #444;
+  cursor: pointer;
+  padding: 18px;
+  width: 100%;
+  border: none;
+  text-align: left;
+  outline: none;
+  font-size: 15px;
+}
+
+/* Add a background color to the button if it is clicked on (add the .active class with JS), and when you move the mouse over it (hover) */
+.active, .collapsible:hover {
+  background-color: #ccc;
+}
+
+.unused {
+  color: red;
+  text-decoration-line: line-through;
+  text-decoration-color: red;
+}
+

src/submissions/templates/details.html

@@ -1,4 +1,4 @@
-<!DOCTYPE html>
+{% if not child %}
 <html lang="en">
 <head>
     {% block head %}
@@ -14,17 +14,41 @@
     {% endblock %}
 </head>
 <body>
+{% endif %}
 {% block body %}
-<!--<button type="button" id="back_btn">Back</button>-->
 {% endblock %}
 {% block signing_button %}{% endblock %}
+{% if not child %}
 </body>
+{% endif %}
 
 {% block script %}
+{% if not child %}
+<script>
+var coll = document.getElementsByClassName("collapsible");
+var i;
+
+for (i = 0; i < coll.length; i++) {
+  coll[i].addEventListener("click", function() {
+    this.classList.toggle("active");
+    var content = this.nextElementSibling;
+    if (content.style.display === "block") {
+      content.style.display = "none";
+    } else {
+      content.style.display = "block";
+    }
+  });
+}
+</script>
+{% endif %}
 {% for j in js%}
+
 <script>
     {{ j }}
 </script>
+
 {% endfor %}
 {% endblock %}
+{% if not child %}
 </html>
+{% endif %}

src/submissions/templates/procedure_creation.html

@@ -28,10 +28,21 @@
                     <br><hr><br>
                     {% for key, value in procedure['reagentrole'].items() %}
                     <label for="{{ key }}">{{ key }}:</label><br>
-                    <select class="reagentrole dropdown" id="{{ key }}" name="{{ reagentrole }}"><br>
+                    <datalist class="reagentrole dropdown" id="{{ key }}" name="{{ reagentrole }}"><br>
                         {% for reagent in value %}
                         <option value="{{ reagent }}">{{ reagent }}</option>
                         {% endfor %}
+                    </datalist>
+                    {% endfor %}
+                  {% endif %}
+                  {% if proceduretype['equipment'] %}
+                    <br><hr><br>
+                    {% for equipmentrole in proceduretype['equipment'] %}
+                    <label for="{{ equipmentrole['name'] }}">{{ equipmentrole['name'] }}:</label><br>
+                    <select class="equipmentrole dropdown" id="{{ equipmentrole['name'] }}" name="{{ equipmentrole['name'] }}"><br>
+                        {% for equipment in equipmentrole['equipment'] %}
+                        <option value="{{ equipment['name'] }}">{{ equipment['name'] }}</option>
+                        {% endfor %}
                     </select>
                     {% endfor %}
                   {% endif%}

src/submissions/templates/procedure_details.html

@@ -1,4 +1,5 @@
 {% extends "details.html" %}
+{% if not child %}
 
 <head>
     {% block head %}
@@ -7,9 +8,31 @@
     {% endblock %}
 </head>
 <body>
+{% endif %}
     {% block body %}
-
+    <h2><u>Procedure Details for {{ procedure['name'] }}</u></h2>
-
+    {{ super() }}
+    <p>{% for key, value in procedure.items() if key not in procedure['excluded'] %}
+        &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key | replace("_", " ") | title | replace("Pcr", "PCR") }}: {{ value }}</b><br>
+    {% endfor %}</p>
+    {% if procedure['results'] %}
+    <button type="button" class="collapsible"><h3><u>Results:</u></h3></button>
+    <div class="nested">
+    {% for result in procedure['results'] %}
+    <p>{% for k, v in result['result'].items() %}
+        <b>{{ key | replace("_", " ") | title | replace("Rsl", "RSL") }}:</b> {{ value }}<br>
+    {% endfor %}</p>
+    {% endfor %}
+    </div>
+    {% endif %}
+    {% if procedure['sample'] %}
+    <button type="button" class="collapsible"><h3><u>Procedure Samples:</u></h3></button>
+    <div class="nested">
+    <p>{% for sample in procedure['sample'] %}
+        &nbsp;&nbsp;&nbsp;&nbsp;<a class="{% if sample['active'] %}data-link {% else %}unused {% endif %}sample" id="{{ sample['sample_id'] }}">{{ sample['sample_id']}}</a><br>
+    {% endfor %}</p>
+    </div>
+    {% endif %}
 
     {% endblock %}
 </body>

src/submissions/templates/run_details.html

@@ -1,81 +1,41 @@
 {% extends "details.html" %}
 
-<html>
 <head>
     {% block head %}
     {{ super() }}
-        <title>Submission Details for {{ sub['plate_number'] }}</title>
+    <title>Run Details for {{ run['rsl_plate_number'] }}</title>
     {% endblock %}
 </head>
 <body>
+
     {% block body %}
-        <h2><u>Submission Details for {{ sub['plate_number'] }}</u></h2>&nbsp;&nbsp;&nbsp;{% if sub['barcode'] %}<img align='right' height="30px" width="120px" src="data:image/jpeg;base64,{{ sub['barcode'] | safe }}">{% endif %}
+    <h2><u>Run Details for {{ run['rsl_plate_number'] }}</u></h2>
     {{ super() }}
-        <p>{% for key, value in sub.items() if key not in sub['excluded'] %}
+    <p>{% for key, value in run.items() if key not in run['excluded'] %}
-            &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key | replace("_", " ") | title | replace("Pcr", "PCR") }}: </b>{% if key=='cost' %}{% if sub['cost'] %} {{ "${:,.2f}".format(value) }}{% endif %}{% else %}{{ value }}{% endif %}<br>
+        &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key | replace("_", " ") | title | replace("Rsl", "RSL") }}:</b> {{ value }}<br>
+    {% endfor %}</p>
+    {% if run['sample'] %}
+    <button type="button" class="collapsible"><h3><u>Run Samples:</u></h3></button>
+    <p>{% for sample in run['sample'] %}
+        &nbsp;&nbsp;&nbsp;&nbsp;<a class="{% if sample['active'] %}data-link {% else %}unused {% endif %}sample" id="{{ sample['sample_id'] }}">{{ sample['sample_id']}}</a><br>
+    {% endfor %}</p>
+    {% endif %}
+    {% if run['procedure'] %}
+    <button type="button" class="collapsible"><h3><u>Procedures:</u></h3></button>
+    <div class="nested">
+    {% for procedure in run['procedure'] %}
+    {% with procedure=procedure, child=True %}
+        {% include "procedure_details.html" %}
+    {% endwith %}
     {% endfor %}
-        {% if sub['custom'] %}{% for key, value in sub['custom'].items() %}
+    </div>
-            &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key | replace("_", " ") | title }}: </b>{{ value }}<br>
-        {% endfor %}{% endif %}</p>
-        {% if sub['reagents'] %}
-        <h3><u>Reagents:</u></h3>
-        <p>{% for item in sub['reagents'] %}
-            &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ item['role'] }}:</b> <a class="data-link reagent" id="{{ item['lot'] }}">{{ item['lot'] }} (EXP: {{ item['expiry'] }})</a><br>
-        {% endfor %}</p>
-        {% endif %}
-        {% if sub['equipment'] %}
-        <h3><u>Equipment:</u></h3>
-        <p>{% for item in sub['equipment'] %}
-            &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ item['role'] }}:</b> <a class="data-link equipment" id="{{ item['name'] }}"> {{ item['name'] }} ({{ item['asset_number'] }})</a>: <a class="data-link process" id="{{ item['processes'][0]|replace('\n\t', '') }}">{{ item['processes'][0]|replace('\n\t', '<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;') }}</a><br>
-        {% endfor %}</p>
-        {% endif %}
-        {% if sub['tips'] %}
-        <h3><u>Tips:</u></h3>
-        <p>{% for item in sub['tips'] %}
-            &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ item['role'] }}:</b> <a class="data-link tips" id="{{ item['lot'] }}">{{ item['name'] }} ({{ item['lot'] }})</a><br>
-        {% endfor %}</p>
-        {% endif %}
-        {% if sub['samples'] %}
-        <h3><u>Samples:</u></h3>
-        <p>{% for item in sub['samples'] %}
-            &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ item['well'] }}:</b><a class="data-link sample" id="{{ item['submitter_id'] }}">{% if item['organism'] %} {{ item['name'] }} - ({{ item['organism']|replace('\n\t', '<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;') }}){% else %} {{ item['name']|replace('\n\t', '<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;') }}{% endif %}</a><br>
-        {% endfor %}</p>
-        {% endif %}
-
-        {% if sub['ext_info'] %}
-        {% for entry in sub['ext_info'] %}
-        <h3><u>Extraction Status:</u></h3>
-        <p>{% for key, value in entry.items() %}
-            {% if "column" in key %}
-                &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key|replace('_', ' ')|title() }}:</b> {{ value }}uL<br>
-            {% else %}
-                &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key|replace('_', ' ')|title() }}:</b> {{ value }}<br>
-            {% endif %}
-        {% endfor %}</p>
-        {% endfor %}
-        {% endif %}
-
-        {% if sub['comment'] %}
-        <h3><u>Comments:</u></h3>
-        <p>{% for entry in sub['comment'] %}
-            &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<b>{{ entry['name'] }}:</b><br> {{ entry['text'] }}<br>- {{ entry['time'] }}<br>
-        {% endfor %}</p>
-        {% endif %}
-        {% if sub['platemap'] %}
-        <h3><u>Plate map:</u></h3>
-        {{ sub['platemap'] }}
-        {% endif %}
-        {% if sub['export_map'] %}
-        <h3><u>Plate map:</u></h3>
-        <img height="600px" width="1300px" src="data:image/jpeg;base64,{{ sub['export_map'] | safe }}">
     {% endif %}
     {% endblock %}
     {% block signing_button %}
-        <button type="button" id="sign_btn" {% if permission and not sub['signed_by'] %}{% else %}hidden{% endif %}>Sign Off</button>
+    <button type="button" id="sign_btn" {% if run['permission'] and not run['signed_by'] %}{% else %}hidden{% endif %}>Sign Off</button>
     {% endblock %}
     <br>
-        <br>
+
-        <br>
 </body>
 
     {% block script %}
@@ -90,46 +50,10 @@
       })
     }
 
-        var reagentSelection = document.getElementsByClassName('reagent');
-
-        for(let i = 0; i < reagentSelection.length; i++) {
-          reagentSelection[i].addEventListener("click", function() {
-            console.log(reagentSelection[i].id);
-            backend.reagent_details(reagentSelection[i].id, "{{ sub['extraction_kit'] }}");
-          })
-        }
-
-        var equipmentSelection = document.getElementsByClassName('equipment');
-
-        for(let i = 0; i < equipmentSelection.length; i++) {
-          equipmentSelection[i].addEventListener("click", function() {
-            console.log(equipmentSelection[i].id);
-            backend.equipment_details(equipmentSelection[i].id);
-          })
-        }
-
-        var processSelection = document.getElementsByClassName('process');
-
-        for(let i = 0; i < processSelection.length; i++) {
-          processSelection[i].addEventListener("click", function() {
-            console.log(processSelection[i].id);
-            backend.process_details(processSelection[i].id);
-          })
-        }
-
-        var tipsSelection = document.getElementsByClassName('tips');
-
-        for(let i = 0; i < tipsSelection.length; i++) {
-          tipsSelection[i].addEventListener("click", function() {
-            console.log(tipsSelection[i].id);
-            backend.tips_details(tipsSelection[i].id);
-          })
-        }
-
     document.getElementById("sign_btn").addEventListener("click", function(){
-            backend.sign_off("{{ sub['plate_number'] }}");
+        backend.sign_off("{{ run['rsl_plate_num'] }}");
     });
     </script>
     {% endblock %}
 
-</html>
+

src/submissions/templates/sample_checker.html

@@ -10,8 +10,8 @@
     <h2><u>Sample Checker</u></h2>
     <br>
     {% if rsl_plate_num %}
-    <label for="rsl_plate_num">RSL Plate Number:</label><br>
+    <label for="rsl_plate_number">RSL Plate Number:</label><br>
-    <input type="text" id="rsl_plate_num" name="sample_id" value="{{ rsl_plate_num }}" size="40">
+    <input type="text" id="rsl_plate_number" name="sample_id" value="{{ rsl_plate_number }}" size="40">
 
     {% endif %}
     <br>