Pre code cleanup

alembic/versions/25b86f5ac2d9_add_custom_info_column_to__.py

@@ -0,0 +1,56 @@
+"""Add custom info column to _basicsubmission
+
+Revision ID: 25b86f5ac2d9
+Revises: 0746f7e2c10e
+Create Date: 2024-09-24 09:09:15.223556
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '25b86f5ac2d9'
+down_revision = '0746f7e2c10e'
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table('_basicsubmission', schema=None) as batch_op:
+        batch_op.add_column(sa.Column('custom', sa.JSON(), nullable=True))
+
+    # with op.batch_alter_table('_process', schema=None) as batch_op:
+    #     batch_op.create_unique_constraint(None, ['name'])
+    #
+    # with op.batch_alter_table('_submissionsampleassociation', schema=None) as batch_op:
+    #     batch_op.create_unique_constraint(None, ['id'])
+
+    with op.batch_alter_table('_wastewaterarticassociation', schema=None) as batch_op:
+        batch_op.alter_column('source_plate',
+               existing_type=sa.VARCHAR(length=16),
+               type_=sa.String(length=32),
+               existing_nullable=True)
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table('_wastewaterarticassociation', schema=None) as batch_op:
+        batch_op.alter_column('source_plate',
+               existing_type=sa.String(length=32),
+               type_=sa.VARCHAR(length=16),
+               existing_nullable=True)
+
+    # with op.batch_alter_table('_submissionsampleassociation', schema=None) as batch_op:
+    #     batch_op.drop_constraint(None, type_='unique')
+    #
+    # with op.batch_alter_table('_process', schema=None) as batch_op:
+    #     batch_op.drop_constraint(None, type_='unique')
+
+    with op.batch_alter_table('_basicsubmission', schema=None) as batch_op:
+        batch_op.drop_column('custom')
+
+    # ### end Alembic commands ###

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

@@ -14,7 +14,8 @@ from sqlalchemy.orm import relationship, validates, Query
 from sqlalchemy.ext.associationproxy import association_proxy
 from datetime import date
 import logging, re
-from tools import check_authorization, setup_lookup, Report, Result, jinja_template_loading, check_regex_match
+from tools import check_authorization, setup_lookup, Report, Result, jinja_template_loading, check_regex_match, \
+    yaml_regex_creator
 from typing import List, Literal, Generator, Any
 from pandas import ExcelFile
 from pathlib import Path
@@ -422,7 +423,7 @@ class Reagent(BaseClass):
         else:
             return f"<Reagent({self.role.name}-{self.lot})>"
 
-    def to_sub_dict(self, extraction_kit: KitType = None, full_data:bool=False) -> dict:
+    def to_sub_dict(self, extraction_kit: KitType = None, full_data: bool = False) -> dict:
         """
         dictionary containing values necessary for gui
 
@@ -873,17 +874,16 @@ class SubmissionType(BaseClass):
 
     @classmethod
     @check_authorization
-    def import_from_json(cls, filepath:Path|str):
+    def import_from_json(cls, filepath: Path | str):
+        yaml.add_constructor("!regex", yaml_regex_creator)
         if isinstance(filepath, str):
             filepath = Path(filepath)
-        if not filepath.exists():
+
-            logging.critical(f"Given file could not be found.")
-            return None
         with open(filepath, "r") as f:
             if filepath.suffix == ".json":
                 import_dict = json.load(fp=f)
             elif filepath.suffix == ".yml":
-                import_dict = yaml.safe_load(stream=f)
+                import_dict = yaml.load(stream=f, Loader=yaml.Loader)
             else:
                 raise Exception(f"Filetype {filepath.suffix} not supported.")
         logger.debug(pformat(import_dict))
@@ -901,8 +901,14 @@ class SubmissionType(BaseClass):
                 new_kit = KitType(name=kit['kit_type']['name'])
             for role in kit['kit_type']['reagent roles']:
                 new_role = ReagentRole.query(name=role['role'])
-                eol = datetime.timedelta(role['extension_of_life'])
+                if new_role:
+                    check = input(f"Found existing role: {new_role.name}. Use this? [Y/n]: ")
+                    if check.lower() == "n":
+                        new_role = None
+                    else:
+                        pass
                 if not new_role:
+                    eol = datetime.timedelta(role['extension_of_life'])
                     new_role = ReagentRole(name=role['role'], eol_ext=eol)
                 uses = dict(expiry=role['expiry'], lot=role['lot'], name=role['name'], sheet=role['sheet'])
                 ktrr_assoc = KitTypeReagentRoleAssociation(kit_type=new_kit, reagent_role=new_role, uses=uses)
@@ -917,9 +923,18 @@ class SubmissionType(BaseClass):
             )
             for role in kit['kit_type']['equipment roles']:
                 new_role = EquipmentRole.query(name=role['role'])
+                if new_role:
+                    check = input(f"Found existing role: {new_role.name}. Use this? [Y/n]: ")
+                    if check.lower() == "n":
+                        new_role = None
+                    else:
+                        pass
                 if not new_role:
                     new_role = EquipmentRole(name=role['role'])
-                ster_assoc = SubmissionTypeEquipmentRoleAssociation(submission_type=submission_type, equipment_role=new_role)
+                    for equipment in Equipment.assign_equipment(equipment_role=new_role):
+                        new_role.instances.append(equipment)
+                ster_assoc = SubmissionTypeEquipmentRoleAssociation(submission_type=submission_type,
+                                                                    equipment_role=new_role)
                 try:
                     uses = dict(name=role['name'], process=role['process'], sheet=role['sheet'], static=role['static'])
                 except KeyError:
@@ -1160,6 +1175,7 @@ class KitTypeReagentRoleAssociation(BaseClass):
         for rel_reagent in relevant_reagents:
             yield rel_reagent
 
+
 class SubmissionReagentAssociation(BaseClass):
     """
     table containing submission/reagent associations
@@ -1400,6 +1416,22 @@ class Equipment(BaseClass):
                           (?P<Labcon>\d{4}-\d{3}-\d{3}-\d$)""",
                           re.VERBOSE)
 
+    @classmethod
+    def assign_equipment(cls, equipment_role: EquipmentRole|str) -> List[Equipment]:
+        if isinstance(equipment_role, str):
+            equipment_role = EquipmentRole.query(name=equipment_role)
+        equipment = cls.query()
+        options = "\n".join([f"{ii}. {item.name}" for ii, item in enumerate(equipment)])
+        choices = input(f"Enter equipment numbers to add to {equipment_role.name} (space seperated):\n{options}\n\n")
+        output = []
+        for choice in choices.split(" "):
+            try:
+                choice = int(choice)
+            except (AttributeError, ValueError):
+                continue
+            output.append(equipment[choice])
+        return output
+
 
 class EquipmentRole(BaseClass):
     """

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

@@ -167,10 +167,10 @@ class BasicSubmission(BaseClass):
         dicto = dict(
             details_ignore=['excluded', 'reagents', 'samples',
                             'extraction_info', 'comment', 'barcode',
-                            'platemap', 'export_map', 'equipment', 'tips'],
+                            'platemap', 'export_map', 'equipment', 'tips', 'custom'],
             # NOTE: Fields not placed in ui form
             form_ignore=['reagents', 'ctx', 'id', 'cost', 'extraction_info', 'signed_by', 'comment', 'namer',
-                         'submission_object', "tips", 'contact_phone'] + recover,
+                         'submission_object', "tips", 'contact_phone', 'custom'] + recover,
             # NOTE: Fields not placed in ui form to be moved to pydantic
             form_recover=recover
         )
@@ -347,12 +347,14 @@ class BasicSubmission(BaseClass):
                 logger.error(f"Error setting tips: {e}")
                 tips = None
             cost_centre = self.cost_centre
+            custom = self.custom
         else:
             reagents = None
             samples = None
             equipment = None
             tips = None
             cost_centre = None
+            custom = None
         # logger.debug("Getting comments")
         try:
             comments = self.comment
@@ -381,6 +383,7 @@ class BasicSubmission(BaseClass):
         # logger.debug(f"Setting contact to: {contact} of type: {type(contact)}")
         output["contact"] = contact
         output["contact_phone"] = contact_phone
+        output["custom"] = custom
         return output
 
     def calculate_column_count(self) -> int:
@@ -549,26 +552,29 @@ class BasicSubmission(BaseClass):
             case "ctx" | "csv" | "filepath" | "equipment":
                 return
             case item if item in self.jsons():
-                # logger.debug(f"Setting JSON attribute.")
+                match value:
-                existing = self.__getattribute__(key)
+                    case list():
-                if value is None or value in ['', 'null']:
+                        # logger.debug(f"Setting JSON attribute.")
-                    logger.error(f"No value given, not setting.")
+                        existing = self.__getattribute__(key)
-                    return
+                        if value is None or value in ['', 'null']:
-                if existing is None:
+                            logger.error(f"No value given, not setting.")
-                    existing = []
+                            return
-                if value in existing:
+                        if existing is None:
-                    logger.warning("Value already exists. Preventing duplicate addition.")
+                            existing = []
-                    return
+                        if value in existing:
-                else:
+                            logger.warning("Value already exists. Preventing duplicate addition.")
-                    if isinstance(value, list):
+                            return
-                        existing += value
+                        else:
-                    else:
+                            if isinstance(value, list):
-                        if value is not None:
+                                existing += value
-                            if key == "custom":
-                                existing = value
                             else:
-                                existing.append(value)
+                                if value is not None:
-
+                                    if key == "custom":
+                                        existing = value
+                                    else:
+                                        existing.append(value)
+                    case _:
+                        existing = value
                 self.__setattr__(key, existing)
                 flag_modified(self, key)
                 return
@@ -749,9 +755,8 @@ class BasicSubmission(BaseClass):
         # logger.debug(f"Input dict: {input_dict}")
         # logger.debug(f"Custom fields: {custom_fields}")
         input_dict['custom'] = {}
-        for k,v in custom_fields.items():
+        for k, v in custom_fields.items():
-            logger.debug(f"Attempting custom parse of {k}: {v}")
+            # logger.debug(f"Attempting custom parse of {k}: {v}")
-
             match v['type']:
                 case "exempt":
                     continue
@@ -766,8 +771,9 @@ class BasicSubmission(BaseClass):
                     if v['start_column'] != v['end_column']:
                         v['end_column'] = v['end_column'] + 1
                     for ii in range(v['start_row'], v['end_row']):
-                        for jj in range(v['start_column'], v['end_column']+1):
+                        for jj in range(v['start_column'], v['end_column'] + 1):
-                            input_dict['custom'][k].append(dict(value=ws.cell(row=ii, column=jj).value, row=ii, column=jj))
+                            input_dict['custom'][k].append(
+                                dict(value=ws.cell(row=ii, column=jj).value, row=ii, column=jj))
         return input_dict
 
     @classmethod
@@ -819,7 +825,7 @@ class BasicSubmission(BaseClass):
         logger.info(f"Hello from {cls.__mapper_args__['polymorphic_identity']} autofill")
         logger.debug(f"Input dict: {info}")
         logger.debug(f"Custom fields: {custom_fields}")
-        for k,v in custom_fields.items():
+        for k, v in custom_fields.items():
             try:
                 assert v['type'] in ['exempt', 'range', 'cell']
             except (AssertionError, KeyError):
@@ -1170,6 +1176,7 @@ class BasicSubmission(BaseClass):
             if "submitted_date" not in kwargs.keys():
                 instance.submitted_date = date.today()
         else:
+            logger.warning(f"Found existing instance: {instance}, asking to overwrite.")
             code = 1
             msg = "This submission already exists.\nWould you like to overwrite?"
         report.add_result(Result(msg=msg, code=code))
@@ -1659,7 +1666,8 @@ class Wastewater(BasicSubmission):
                 continue
             copy = dict(submitter_id=sample['submitter_id'], row=row, column=column)
             well_24.append(copy)
-        input_dict['origin_plate'] = [item for item in DocxWriter.create_plate_map(sample_list=well_24, rows=4, columns=6)]
+        input_dict['origin_plate'] = [item for item in
+                                      DocxWriter.create_plate_map(sample_list=well_24, rows=4, columns=6)]
         return input_dict
 
 
@@ -1728,14 +1736,22 @@ class WastewaterArtic(BasicSubmission):
             ws = wb[info_dict['sheet']]
             img_loader = SheetImageLoader(ws)
             for ii in range(info_dict['start_row'], info_dict['end_row'] + 1):
-                logger.debug(f"Checking row: {ii}")
+                # logger.debug(f"Checking row: {ii}")
                 for jj in range(info_dict['start_column'], info_dict['end_column'] + 1):
+                    # logger.debug(f"Checking column: {jj}")
                     cell_str = f"{row_map[jj]}{ii}"
                     if img_loader.image_in(cell_str):
-                        return img_loader.get(cell_str)
+                        try:
+                            return img_loader.get(cell_str)
+                        except ValueError as e:
+                            logger.error(f"Could not open image from cell: {cell_str} due to {e}")
+                            return None
             return None
 
         input_dict = super().custom_info_parser(input_dict)
+
+        input_dict['submission_type'] = dict(value="Wastewater Artic", missing=False)
+
         logger.debug(f"Custom fields: {custom_fields}")
         egel_section = custom_fields['egel_controls']
         ws = xl[egel_section['sheet']]

src/submissions/backend/excel/parser.py

@@ -65,14 +65,24 @@ class SheetParser(object):
         """
         parser = InfoParser(xl=self.xl, submission_type=self.submission_type, sub_object=self.sub_object)
         info = parser.parse_info()
+        self.info_map = parser.map
+        try:
+            check = info['submission_type']['value'] not in [None, "None", "", " "]
+        except KeyError:
+            return
         logger.debug(f"Checking old submission type: {self.submission_type.name} against new: {info['submission_type']['value']}")
         if self.submission_type.name != info['submission_type']['value']:
-            if info['submission_type']['value'] not in [None, "None", "", " "]:
+            # logger.debug(f"info submission type: {info}")
+            if check:
                 self.submission_type = SubmissionType.query(name=info['submission_type']['value'])
                 logger.debug(f"Updated self.submission_type to {self.submission_type}. Rerunning parse.")
                 self.parse_info()
-                return
+
-        self.info_map = parser.map
+            else:
+                self.submission_type = RSLNamer.retrieve_submission_type(filename=self.filepath)
+                self.parse_info()
+
+
         for k, v in info.items():
             match k:
                 # NOTE: exclude samples.
@@ -86,7 +96,7 @@ class SheetParser(object):
                 #         logger.debug(f"Updated self.submission_type to {self.submission_type}")
                 case _:
                     self.sub[k] = v
-        print(f"\n\n {self.sub} \n\n")
+        # print(f"\n\n {self.sub} \n\n")
 
 
     def parse_reagents(self, extraction_kit: str | None = None):

src/submissions/backend/validators/pydant.py

@@ -729,6 +729,7 @@ class PydSubmission(BaseModel, extra='allow'):
         dicto = self.improved_dict()
         instance, result = BasicSubmission.query_or_create(submission_type=self.submission_type['value'],
                                                            rsl_plate_num=self.rsl_plate_num['value'])
+        logger.debug(f"Result of query or create: {type(result)}")
         report.add_result(result)
         self.handle_duplicate_samples()
         # logger.debug(f"Here's our list of duplicate removed samples: {self.samples}")

src/submissions/frontend/widgets/app.py

@@ -1,7 +1,7 @@
 """
 Constructs main application.
 """
-import yaml
+from pprint import pformat
 from PyQt6.QtWidgets import (
     QTabWidget, QWidget, QVBoxLayout,
     QHBoxLayout, QScrollArea, QMainWindow, 
@@ -12,17 +12,17 @@ from pathlib import Path
 
 from markdown import markdown
 from __init__ import project_path
-from tools import check_if_app, Settings, Report, jinja_template_loading
+from tools import check_if_app, Settings, Report, jinja_template_loading, check_authorization
-from .functions import select_save_file
+from .functions import select_save_file,select_open_file
 from datetime import date
-from .pop_ups import HTMLPop
+from .pop_ups import HTMLPop, AlertPop
 from .misc import LogParser
 import logging, webbrowser, sys, shutil
 from .submission_table import SubmissionsSheet
 from .submission_widget import SubmissionFormContainer
 from .controls_chart import ControlsViewer
 from .kit_creator import KitAdder
-from .submission_type_creator import SubmissionTypeAdder
+from .submission_type_creator import SubmissionTypeAdder, SubmissionType
 from .sample_search import SearchBox
 
 logger = logging.getLogger(f'submissions.{__name__}')
@@ -76,7 +76,8 @@ class App(QMainWindow):
         helpMenu.addAction(self.docsAction)
         helpMenu.addAction(self.githubAction)
         fileMenu.addAction(self.importAction)
-        fileMenu.addAction(self.yamlAction)
+        fileMenu.addAction(self.yamlExportAction)
+        fileMenu.addAction(self.yamlImportAction)
         methodsMenu.addAction(self.searchLog)
         methodsMenu.addAction(self.searchSample)
         reportMenu.addAction(self.generateReportAction)
@@ -111,7 +112,8 @@ class App(QMainWindow):
         self.searchLog = QAction("Search Log", self)
         self.searchSample = QAction("Search Sample", self)
         self.githubAction = QAction("Github", self)
-        self.yamlAction = QAction("Export Type Template", self)
+        self.yamlExportAction = QAction("Export Type Example", self)
+        self.yamlImportAction = QAction("Import Type Template", self)
 
     def _connectActions(self):
         """
@@ -128,7 +130,8 @@ class App(QMainWindow):
         self.searchLog.triggered.connect(self.runSearch)
         self.searchSample.triggered.connect(self.runSampleSearch)
         self.githubAction.triggered.connect(self.openGithub)
-        self.yamlAction.triggered.connect(self.export_ST_yaml)
+        self.yamlExportAction.triggered.connect(self.export_ST_yaml)
+        self.yamlImportAction.triggered.connect(self.import_ST_yaml)
 
     def showAbout(self):
         """
@@ -207,11 +210,31 @@ class App(QMainWindow):
             yaml_path = Path(sys._MEIPASS).joinpath("resources", "viral_culture.yml")
         else:
             yaml_path = project_path.joinpath("src", "submissions", "resources", "viral_culture.yml")
-        with open(yaml_path, "r") as f:
+        # with open(yaml_path, "r") as f:
-            data = yaml.safe_load(f)
+        #     data = yaml.safe_load(f)
         fname = select_save_file(obj=self, default_name="Submission Type Template.yml", extension="yml")
-        with open(fname, "w") as f:
+        # with open(fname, "w") as f:
-            yaml.safe_dump(data=data, stream=f)
+        #     yaml.safe_dump(data=data, stream=f)
+        shutil.copyfile(yaml_path, fname)
+
+    @check_authorization
+    def import_ST_yaml(self, *args, **kwargs):
+        fname = select_open_file(obj=self, file_extension="yml")
+        if not fname:
+            logger.info(f"Import cancelled.")
+            return
+        ap = AlertPop(message="This function will proceed in the debug window.", status="Warning", owner=self)
+        ap.exec()
+        st = SubmissionType.import_from_json(filepath=fname)
+        if st:
+            print(pformat(st.to_export_dict()))
+            choice = input("Save the above submission type? [y/N]: ")
+            if choice.lower() == "y":
+                # st.save()
+                pass
+            else:
+                logger.warning("Save of submission type cancelled.")
+
 
 
 class AddSubForm(QWidget):

src/submissions/frontend/widgets/functions.py

@@ -31,6 +31,11 @@ def select_open_file(obj: QMainWindow, file_extension: str | None = None) -> Pat
     else:
         fname = Path(
             QFileDialog.getOpenFileName(obj, 'Open file', home_dir, filter=f"{file_extension}(*.{file_extension})")[0])
+        if not fname.exists():
+            raise FileNotFoundError(f"File {fname.__str__()} could not be found.")
+        if fname.__str__() == ".":
+            logger.warning(f"No file selected, cancelling.")
+            return
     obj.last_dir = fname.parent
     return fname
 

src/submissions/frontend/widgets/submission_widget.py

@@ -1,6 +1,8 @@
 '''
 Contains all submission related frontend functions
 '''
+import sys
+
 from PyQt6.QtWidgets import (
     QWidget, QPushButton, QVBoxLayout,
     QComboBox, QDateEdit, QLineEdit, QLabel
@@ -96,6 +98,7 @@ class SubmissionFormContainer(QWidget):
         self.import_submission_function(fname)
         return self.report
 
+    @report_result
     def import_submission_function(self, fname: Path | None = None):
         """
         Import a new submission to the app window
@@ -119,7 +122,7 @@ class SubmissionFormContainer(QWidget):
         if isinstance(fname, bool) or fname is None:
             fname = select_open_file(self, file_extension="xlsx")
         # logger.debug(f"Attempting to parse file: {fname}")
-        if not fname.exists():
+        if not fname:
             report.add_result(Result(msg=f"File {fname.__str__()} not found.", status="critical"))
             return report
         # NOTE: create sheetparser using excel sheet and context from gui
@@ -347,9 +350,14 @@ class SubmissionFormWidget(QWidget):
         # logger.debug(f"SQL object: {pformat(base_submission.__dict__)}")
         # logger.debug(f"Base submission: {base_submission.to_dict()}")
         # NOTE: check output message for issues
+        # logger.debug(f"Result of to_sql: {result}")
         try:
-            code = report.results[-1].code
+            trigger = result.results[-1]
-        except IndexError:
+            code = trigger.code
+            # logger.debug(f"Code from return: {code}")
+        except IndexError as e:
+            logger.error(result.results)
+            logger.error(f"Problem getting error code: {e}")
             code = 0
         match code:
             # NOTE: code 0: everything is fine.
@@ -357,7 +365,7 @@ class SubmissionFormWidget(QWidget):
                 pass
             # NOTE: code 1: ask for overwrite
             case 1:
-                dlg = QuestionAsker(title=f"Review {base_submission.rsl_plate_num}?", message=result.msg)
+                dlg = QuestionAsker(title=f"Review {base_submission.rsl_plate_num}?", message=trigger.msg)
                 if dlg.exec():
                     # NOTE: Do not add duplicate reagents.
                     pass

src/submissions/resources/viral_culture.yml

@@ -46,7 +46,35 @@ info:
             row: 6
             sheet: Sample List
         write: []
-    custom: {}
+#    The 'custom' field is currently under development and will allow parsing, storage and writing of new fields in
+#    generic submission types.
+#    Examples of the types of fields are given below.
+    custom: {
+      #        The 'cell' type will read a single cell from the excel sheet and write it to the same cell as well as
+      #        any specified in the write list.
+      #        "test cell": {
+      #            "read": {
+      #                "column": 3,
+      #                "row": 1,
+      #                "sheet": "Plate Map"
+      #            },
+      #            "type": "cell",
+      #            "write": [{
+      #                      "column": 8,
+      #                      "row": 8,
+      #                      "sheet": "Sample List"
+      #                    }]
+      #        },
+      #        The 'range' type will read a group of cells, store them as a list of values, row and column integers
+      #        and write to that range.
+      #        "test range": {
+      #             "sheet": "First Strand",
+      #             "start_row": 1,
+      #             "end_row":9,
+      #             "start_column": 1,
+      #             "end_column": 5
+      #        }
+    }
     extraction_kit:
         read:
         -   column: 4
@@ -107,9 +135,9 @@ info:
             row: 14
             sheet: Sample List
         write: []
+# The 'kits' field holds reagents, equipment and tips information. It's a list of kit_type objects.
 kits:
--   constant_cost: 0.0
+-   kit_type:
-    kit_type:
         name: MagMAX-96 Viral RNA Isolation Kit
         equipment roles:
         -   role: Extractor
@@ -281,6 +309,7 @@ kits:
             required: 1
             role: Carrier RNA
             sheet: Sample List
+    constant_cost: 0.0
     mutable_cost_column: 0.0
     mutable_cost_sample: 0.0
 samples:

src/submissions/templates/basicsubmission_details.html

@@ -13,7 +13,10 @@
         {{ super() }}
         <p>{% for key, value in sub.items() if key not in sub['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>
-        {% endfor %}</p>
+        {% endfor %}
+        {% if sub['custom'] %}{% for key, value in sub['custom'].items() %}
+            &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key | replace("_", " ") | title }}: </b>{{ value }}<br>
+        {% endfor %}{% endif %}</p>
 
         <h3><u>Reagents:</u></h3>
         <p>{% for item in sub['reagents'] %}

src/submissions/tools/__init__.py

@@ -831,7 +831,10 @@ class Report(BaseModel):
     results: List[Result] = Field(default=[])
 
     def __repr__(self):
-        return f"Report(result_count:{len(self.results)})"
+        return f"<Report(result_count:{len(self.results)})>"
+
+    def __str__(self):
+        return f"<Report(result_count:{len(self.results)})>"
 
     def add_result(self, result: Result | Report | None):
         """
@@ -918,6 +921,7 @@ def yaml_regex_creator(loader, node):
     return f"(?P<{name}>RSL(?:-|_)?{abbr}(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\sA-QS-Z]|$)?R?\d?)?)"
 
 
+
 ctx = get_config(None)
 
 
@@ -1004,3 +1008,5 @@ def report_result(func):
 @check_authorization
 def test_function():
     print("Success!")
+
+