Generic info fields input into 'custom'.

CHANGELOG.md

@@ -1,3 +1,7 @@
+## 202409.05
+
+- Added in custom field for BasicSubmission which will allow limited new fields to be added to generic submission types.
+
 ## 202409.04
 
 - Fixed wastewater sample writing bug.

TODO.md

@@ -1,3 +1,4 @@
+- [ ] Allow parsing of custom fields to a json 'custom' field in _basicsubmissions
 - [x] Upgrade to generators when returning lists.
 - [x] Revamp frontend.widgets.controls_chart to include visualizations?
 - [x] Convert Parsers to using openpyxl.

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

@@ -932,6 +932,9 @@ class SubmissionType(BaseClass):
                     new_process.submission_types.append(submission_type)
                     new_process.kit_types.append(new_kit)
                     new_process.equipment_roles.append(new_role)
+            if 'orgs' in import_dict.keys():
+                logger.info("Found Organizations to be imported.")
+                Organization.import_from_json(filepath=filepath)
             return submission_type
 
 

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

@@ -2,12 +2,15 @@
 All client organization related models.
 '''
 from __future__ import annotations
+
+import json, yaml, logging
+from pathlib import Path
+from pprint import pformat
 from sqlalchemy import Column, String, INTEGER, ForeignKey, Table
 from sqlalchemy.orm import relationship, Query
 from . import Base, BaseClass
 from tools import check_authorization, setup_lookup
 from typing import List
-import logging
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -74,6 +77,42 @@ class Organization(BaseClass):
     def save(self):
         super().save()
 
+    @classmethod
+    @check_authorization
+    def import_from_json(cls, filepath: Path|str):
+        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)
+            else:
+                raise Exception(f"Filetype {filepath.suffix} not supported.")
+        data = import_dict['orgs']
+        logger.debug(pformat(import_dict))
+        for org in data:
+            organ = Organization.query(name=org['name'])
+            if organ is None:
+                organ = Organization(name=org['name'])
+                try:
+                    organ.cost_centre = org['cost_centre']
+                except KeyError:
+                    organ.cost_centre = "xxx"
+            for contact in org['contacts']:
+                cont = Contact.query(name=contact['name'])
+                if cont is None:
+                    cont = Contact()
+                for k, v in contact.items():
+                    cont.__setattr__(k, v)
+                organ.contacts.append(cont)
+            organ.save()
+            # logger.debug(pformat(organ.__dict__))
+
+
 
 class Contact(BaseClass):
     """
@@ -119,7 +158,7 @@ class Contact(BaseClass):
         match name:
             case str():
                 # logger.debug(f"Looking up contact with name: {name}")
-                query = query.filter(cls.name == name)
+                query = query.filter(cls.name == name.title())
                 limit = 1
             case _:
                 pass

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

@@ -72,6 +72,7 @@ class BasicSubmission(BaseClass):
     contact = relationship("Contact", back_populates="submissions")  #: client org
     contact_id = Column(INTEGER, ForeignKey("_contact.id", ondelete="SET NULL",
                                             name="fk_BS_contact_id"))  #: client lab id from _organizations
+    custom = Column(JSON)
 
     submission_sample_associations = relationship(
         "SubmissionSampleAssociation",
@@ -563,7 +564,11 @@ class BasicSubmission(BaseClass):
                         existing += value
                     else:
                         if value is not None:
+                            if key == "custom":
+                                existing = value
+                            else:
                                 existing.append(value)
+
                 self.__setattr__(key, existing)
                 flag_modified(self, key)
                 return
@@ -741,6 +746,28 @@ class BasicSubmission(BaseClass):
             dict: Updated sample dictionary
         """
         logger.info(f"Calling {cls.__mapper_args__['polymorphic_identity']} info parser.")
+        # logger.debug(f"Input dict: {input_dict}")
+        # logger.debug(f"Custom fields: {custom_fields}")
+        input_dict['custom'] = {}
+        for k,v in custom_fields.items():
+            logger.debug(f"Attempting custom parse of {k}: {v}")
+
+            match v['type']:
+                case "exempt":
+                    continue
+                case "cell":
+                    ws = xl[v['read']['sheet']]
+                    input_dict['custom'][k] = ws.cell(row=v['read']['row'], column=v['read']['column']).value
+                case "range":
+                    ws = xl[v['sheet']]
+                    input_dict['custom'][k] = []
+                    if v['start_row'] != v['end_row']:
+                        v['end_row'] = v['end_row'] + 1
+                    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):
+                            input_dict['custom'][k].append(dict(value=ws.cell(row=ii, column=jj).value, row=ii, column=jj))
         return input_dict
 
     @classmethod
@@ -790,6 +817,29 @@ class BasicSubmission(BaseClass):
             Workbook: Updated workbook
         """
         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():
+            try:
+                assert v['type'] in ['exempt', 'range', 'cell']
+            except (AssertionError, KeyError):
+                continue
+            match v['type']:
+                case "exempt":
+                    continue
+                case "cell":
+                    v['write'].append(v['read'])
+                    for cell in v['write']:
+                        ws = input_excel[cell['sheet']]
+                        ws.cell(row=cell['row'], column=cell['column'], value=info['custom'][k])
+                case "range":
+                    ws = input_excel[v['sheet']]
+                    if v['start_row'] != v['end_row']:
+                        v['end_row'] = v['end_row'] + 1
+                    if v['start_column'] != v['end_column']:
+                        v['end_column'] = v['end_column'] + 1
+                    for item in info['custom'][k]:
+                        ws.cell(row=item['row'], column=item['column'], value=item['value'])
         return input_excel
 
     @classmethod

src/submissions/backend/excel/parser.py

@@ -65,20 +65,28 @@ class SheetParser(object):
         """
         parser = InfoParser(xl=self.xl, submission_type=self.submission_type, sub_object=self.sub_object)
         info = parser.parse_info()
+        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", "", " "]:
+                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
         for k, v in info.items():
             match k:
                 # NOTE: exclude samples.
                 case "sample":
                     continue
-                case "submission_type":
+                # case "submission_type":
-                    self.sub[k] = v
+                #     self.sub[k] = v
-                    # NOTE: Rescue submission type using scraped values to be used in Sample, Reagents, etc.
+                #     # NOTE: Rescue submission type using scraped values to be used in Sample, Reagents, etc.
-                    if v not in [None, "None", "", " "]:
+                #     if v not in [None, "None", "", " "]:
-                        self.submission_type = SubmissionType.query(name=v)
+                #         self.submission_type = SubmissionType.query(name=v)
-                        logger.debug(f"Updated self.submission_type to {self.submission_type}")
+                #         logger.debug(f"Updated self.submission_type to {self.submission_type}")
                 case _:
                     self.sub[k] = v
+        print(f"\n\n {self.sub} \n\n")
 
 
     def parse_reagents(self, extraction_kit: str | None = None):

src/submissions/backend/excel/writer.py

@@ -175,6 +175,8 @@ class InfoWriter(object):
         """
         final_info = {}
         for k, v in self.info:
+            if k == "custom":
+                continue
             # NOTE: merge all comments to fit in single cell.
             if k == "comment" and isinstance(v['value'], list):
                 json_join = [item['text'] for item in v['value'] if 'text' in item.keys()]

src/submissions/backend/validators/pydant.py

@@ -734,11 +734,19 @@ class PydSubmission(BaseModel, extra='allow'):
         # logger.debug(f"Here's our list of duplicate removed samples: {self.samples}")
         for key, value in dicto.items():
             if isinstance(value, dict):
+                try:
                     value = value['value']
+                except KeyError:
+                    if key == "custom":
+                        pass
+                    else:
+                        continue
             if value is None:
                 continue
             # logger.debug(f"Setting {key} to {value}")
             match key:
+                # case "custom":
+                #     instance.custom = value
                 case "reagents":
                     if report.results[0].code == 1:
                         instance.submission_reagent_associations = []
@@ -782,9 +790,13 @@ class PydSubmission(BaseModel, extra='allow'):
                         ii = value.items()
                     except AttributeError:
                         ii = {}
+                    logger.debug(f"ii is {ii}, value is {value}")
                     for k, v in ii:
+                        logger.debug(f"k is {k}, v is {v}")
                         if isinstance(v, datetime):
                             value[k] = v.strftime("%Y-%m-%d %H:%M:%S")
+                        else:
+                            value[k] = v
                     instance.set_attribute(key=key, value=value)
                 case _:
                     try:

src/submissions/frontend/widgets/app.py

@@ -1,6 +1,7 @@
 """
 Constructs main application.
 """
+import yaml
 from PyQt6.QtWidgets import (
     QTabWidget, QWidget, QVBoxLayout,
     QHBoxLayout, QScrollArea, QMainWindow, 
@@ -10,8 +11,9 @@ from PyQt6.QtGui import QAction
 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 .functions import select_save_file
 from datetime import date
 from .pop_ups import HTMLPop
 from .misc import LogParser
@@ -74,6 +76,7 @@ class App(QMainWindow):
         helpMenu.addAction(self.docsAction)
         helpMenu.addAction(self.githubAction)
         fileMenu.addAction(self.importAction)
+        fileMenu.addAction(self.yamlAction)
         methodsMenu.addAction(self.searchLog)
         methodsMenu.addAction(self.searchSample)
         reportMenu.addAction(self.generateReportAction)
@@ -108,6 +111,7 @@ 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)
 
     def _connectActions(self):
         """
@@ -124,6 +128,7 @@ 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)
 
     def showAbout(self):
         """
@@ -197,6 +202,17 @@ class App(QMainWindow):
                 logger.warning(f"Backup function not yet implemented for psql")
                 current_month_bak = current_month_bak.with_suffix(".psql")
 
+    def export_ST_yaml(self):
+        if check_if_app():
+            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:
+            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:
+            yaml.safe_dump(data=data, stream=f)
+
 
 class AddSubForm(QWidget):
     

src/submissions/frontend/widgets/submission_widget.py

@@ -546,7 +546,10 @@ class SubmissionFormWidget(QWidget):
                     # logger.debug(f"Kits received for {submission_type}: {uses}")
                     if check_not_nan(value):
                         # logger.debug(f"The extraction kit in parser was: {value}")
+                        try:
                             uses.insert(0, uses.pop(uses.index(value)))
+                        except ValueError:
+                            logger.warning(f"Couldn't find kit in list, skipping move to top of list.")
                         obj.ext_kit = value
                     else:
                         logger.error(f"Couldn't find {obj.prsr.sub['extraction_kit']}")

src/submissions/resources/viral_culture.json

@@ -0,0 +1,429 @@
+{
+    "name": "Viral Culture",
+    "defaults": {
+            "abbreviation": "VE",
+            "details_ignore": [
+            ],
+            "form_ignore": [
+                "cost_centre"
+            ],
+            "regex": "(?P<Viral_Culture>RSL(?:-|_)?VE(?:-|_)?20\\d{2}-?\\d{2}-?\\d{2}(?:(_|-)?\\d?([^_0123456789\\sA-QS-Z]|$)?R?\\d?)?)",
+            "sample_type": "Basic Sample"
+        },
+    "info": {
+        "comment": {
+            "read": [
+                {
+                    "column": 2,
+                    "row": 34,
+                    "sheet": "Sample List"
+                }
+            ],
+            "write": []
+        },
+        "contact": {
+            "read": [
+                {
+                    "column": 2,
+                    "row": 4,
+                    "sheet": "Sample List"
+                }
+            ],
+            "write": []
+        },
+        "contact_phone": {
+            "read": [],
+            "write": [
+                {
+                    "column": 2,
+                    "row": 5,
+                    "sheet": "Sample List"
+                }
+            ]
+        },
+        "cost_centre": {
+            "read": [
+                {
+                    "column": 2,
+                    "row": 6,
+                    "sheet": "Sample List"
+                }
+            ],
+            "write": []
+        },
+        "custom": {},
+        "extraction_kit": {
+            "read": [
+                {
+                    "column": 4,
+                    "row": 5,
+                    "sheet": "Sample List"
+                }
+            ],
+            "write": []
+        },
+        "rsl_plate_num": {
+            "read": [
+                {
+                    "column": 2,
+                    "row": 13,
+                    "sheet": "Sample List"
+                }
+            ],
+            "write": []
+        },
+        "sample_count": {
+            "read": [
+                {
+                    "column": 4,
+                    "row": 4,
+                    "sheet": "Sample List"
+                }
+            ],
+            "write": []
+        },
+        "signed_by": {
+            "read": [],
+            "write": [
+                {
+                    "column": 2,
+                    "row": 15,
+                    "sheet": "Sample List"
+                }
+            ]
+        },
+        "submission_category": {
+            "read": [
+                {
+                    "column": 4,
+                    "row": 6,
+                    "sheet": "Sample List"
+                }
+            ],
+            "write": []
+        },
+        "submission_type": {
+            "read": [
+                {
+                    "column": 4,
+                    "row": 3,
+                    "sheet": "Sample List"
+                }
+            ],
+            "write": []
+        },
+        "submitted_date": {
+            "read": [
+                {
+                    "column": 2,
+                    "row": 3,
+                    "sheet": "Sample List"
+                }
+            ],
+            "write": []
+        },
+        "submitter_plate_num": {
+            "read": [
+                {
+                    "column": 2,
+                    "row": 2,
+                    "sheet": "Sample List"
+                }
+            ],
+            "write": []
+        },
+        "submitting_lab": {
+            "read": [
+                {
+                    "column": 4,
+                    "row": 2,
+                    "sheet": "Sample List"
+                }
+            ],
+            "write": []
+        },
+        "technician": {
+            "read": [
+                {
+                    "column": 2,
+                    "row": 14,
+                    "sheet": "Sample List"
+                }
+            ],
+            "write": []
+        }
+    },
+    "samples": {
+        "lookup_table": {
+            "end_row": 132,
+            "merge_on_id": "submitter_id",
+            "sample_columns": {
+                "column": 6,
+                "concentration": 4,
+                "organism": 3,
+                "row": 5,
+                "submitter_id": 2
+            },
+            "sheet": "Sample List",
+            "start_row": 37
+        },
+        "plate_map": {
+            "end_column": 13,
+            "end_row": 14,
+            "sheet": "Plate Map",
+            "start_column": 2,
+            "start_row": 7
+        }
+    },
+    "kits": [
+        {
+            "constant_cost": 0.00,
+            "mutable_cost_column": 0.00,
+            "mutable_cost_sample": 0.00,
+            "kit_type": {
+                "name": "MagMAX-96 Viral RNA Isolation Kit",
+                "reagent roles": [
+                    {
+                        "expiry": {
+                            "column": 4,
+                            "row": 19
+                        },
+                        "lot": {
+                            "column": 3,
+                            "row": 19
+                        },
+                        "name": {
+                            "column": 2,
+                            "row": 19
+                        },
+                        "sheet": "Sample List",
+                        "required": 1,
+                        "role": "Wash Solution 1 (MagMAX-96 Viral)",
+                        "extension_of_life": 0
+                    },
+                    {
+                        "expiry": {
+                            "column": 4,
+                            "row": 20
+                        },
+                        "lot": {
+                            "column": 3,
+                            "row": 20
+                        },
+                        "name": {
+                            "column": 2,
+                            "row": 20
+                        },
+                        "sheet": "Sample List",
+                        "required": 1,
+                        "role": "Wash Solution 2 (MagMAX-96 Viral)",
+                        "extension_of_life": 0
+                    },
+                    {
+                        "expiry": {
+                            "column": 4,
+                            "row": 21
+                        },
+                        "lot": {
+                            "column": 3,
+                            "row": 21
+                        },
+                        "name": {
+                            "column": 2,
+                            "row": 21
+                        },
+                        "sheet": "Sample List",
+                        "required": 1,
+                        "role": "Lysis/Binding Solution (MagMAX-96 Viral)",
+                        "extension_of_life": 0
+                    },
+                    {
+                        "expiry": {
+                            "column": 4,
+                            "row": 22
+                        },
+                        "lot": {
+                            "column": 3,
+                            "row": 22
+                        },
+                        "name": {
+                            "column": 2,
+                            "row": 22
+                        },
+                        "sheet": "Sample List",
+                        "required": 1,
+                        "role": "RNA Binding Beads (MagMAX-96 Viral)",
+                        "extension_of_life": 0
+                    },
+                    {
+                        "expiry": {
+                            "column": 4,
+                            "row": 23
+                        },
+                        "lot": {
+                            "column": 3,
+                            "row": 23
+                        },
+                        "name": {
+                            "column": 2,
+                            "row": 23
+                        },
+                        "sheet": "Sample List",
+                        "required": 1,
+                        "role": "Lysis/Binding Enhancer (MagMAX-96 Viral)",
+                        "extension_of_life": 0
+                    },
+                    {
+                        "expiry": {
+                            "column": 4,
+                            "row": 24
+                        },
+                        "lot": {
+                            "column": 3,
+                            "row": 24
+                        },
+                        "name": {
+                            "column": 2,
+                            "row": 24
+                        },
+                        "sheet": "Sample List",
+                        "required": 0,
+                        "role": "Bacterial-Lysis Buffer",
+                        "extension_of_life": 0
+                    },
+                    {
+                        "expiry": {
+                            "column": 4,
+                            "row": 25
+                        },
+                        "lot": {
+                            "column": 3,
+                            "row": 25
+                        },
+                        "name": {
+                            "column": 2,
+                            "row": 25
+                        },
+                        "sheet": "Sample List",
+                        "required": 1,
+                        "role": "Elution Buffer (MagMAX-96 Viral)",
+                        "extension_of_life": 0
+                    },
+                    {
+                        "expiry": {
+                            "column": 4,
+                            "row": 30
+                        },
+                        "lot": {
+                            "column": 3,
+                            "row": 30
+                        },
+                        "name": {
+                            "column": 2,
+                            "row": 30
+                        },
+                        "sheet": "Sample List",
+                        "required": 0,
+                        "role": "Bacterial-Positive Control",
+                        "extension_of_life": 0
+                    },
+                    {
+                        "expiry": {
+                            "column": 4,
+                            "row": 31
+                        },
+                        "lot": {
+                            "column": 3,
+                            "row": 31
+                        },
+                        "name": {
+                            "column": 2,
+                            "row": 31
+                        },
+                        "sheet": "Sample List",
+                        "required": 1,
+                        "role": "Bead Plate",
+                        "extension_of_life": 0
+                    },
+                    {
+                        "expiry": {
+                            "column": 4,
+                            "row": 28
+                        },
+                        "lot": {
+                            "column": 3,
+                            "row": 28
+                        },
+                        "name": {
+                            "column": 2,
+                            "row": 28
+                        },
+                        "sheet": "Sample List",
+                        "required": 1,
+                        "role": "Isopropanol",
+                        "extension_of_life": 0
+                    },
+                    {
+                        "expiry": {
+                            "column": 4,
+                            "row": 29
+                        },
+                        "lot": {
+                            "column": 3,
+                            "row": 29
+                        },
+                        "name": {
+                            "column": 2,
+                            "row": 29
+                        },
+                        "sheet": "Sample List",
+                        "required": 1,
+                        "role": "Ethanol",
+                        "extension_of_life": 0
+                    },
+                    {
+                        "expiry": {
+                            "column": 4,
+                            "row": 32
+                        },
+                        "lot": {
+                            "column": 3,
+                            "row": 32
+                        },
+                        "name": {
+                            "column": 2,
+                            "row": 32
+                        },
+                        "sheet": "Sample List",
+                        "required": 1,
+                        "role": "Carrier RNA",
+                        "extension_of_life": 0
+                    }
+                ],
+                "equipment roles": [
+                    {
+                        "static": 0,
+                        "role": "Extractor",
+                        "processes": [
+                            "OBT_M4029_KFF_v1.0"
+                        ]
+                    },
+                    {
+                        "static": 1,
+                        "role": "Momentum - Extraction",
+                        "processes": [
+                            "Omega_MagBind_Universal_VarCol"
+                        ]
+                    },
+                    {
+                        "static": 1,
+                        "role": "Liquid Handler",
+                        "processes": [
+                            "Bacterial_Core_Submission"
+                        ]
+                    }
+                ]
+            }
+        }       
+    ]
+}

src/submissions/resources/viral_culture.yml

@@ -0,0 +1,310 @@
+name: &NAME Viral Culture
+# The defaults section helps us with some parsing and writing functions
+defaults:
+#    The abbreviation gets put in the RSL-{abbreviation}-20XXXXXX-1 plate name
+    abbreviation: &ABBREV VE
+#    Details ignore tells us what to leave out of the details view.
+#    For basic submissions this is typically and empty list or '[]'
+#    To add entries, remove [] and add list entries preceded by dashes (see 'form_ignore' as an example)
+    details_ignore: []
+#    Form ignore tells us what to leave out of the form created when importing the submission.
+#    It is in list format. Each entry is preceded by a dash.
+    form_ignore:
+    - cost_centre
+    sample_type: Basic Sample
+    #    The regex is used to identify a submission type by its file name, example: RSL-WW-20240924-1R1
+    #    By default the regex will be programmatically constructed using the submission type name and abbreviation
+    #    https://stackoverflow.com/a/23212501
+    regex: !regex [*NAME, *ABBREV]
+# The info section holds a map of where submission info can be located  in the submission form.
+# For example, below the 'comment' field is found on the 'Sample List' tab in column 2 of tow 34.
+# 'read' is a list of where the info can be parsed from, write is a list of where it will be written to.
+# By default, items in the 'read' list will be appended to the 'write' list.
+# These fields are common to all submissions. Without programming changes, at present no new fields can be added.
+info:
+    comment:
+        read:
+        -   column: 2
+            row: 34
+            sheet: Sample List
+        write: []
+    contact:
+        read:
+        -   column: 2
+            row: 4
+            sheet: Sample List
+        write: []
+    contact_phone:
+        read: []
+        write:
+        -   column: 2
+            row: 5
+            sheet: Sample List
+    cost_centre:
+        read:
+        -   column: 2
+            row: 6
+            sheet: Sample List
+        write: []
+    custom: {}
+    extraction_kit:
+        read:
+        -   column: 4
+            row: 5
+            sheet: Sample List
+        write: []
+    rsl_plate_num:
+        read:
+        -   column: 2
+            row: 13
+            sheet: Sample List
+        write: []
+    sample_count:
+        read:
+        -   column: 4
+            row: 4
+            sheet: Sample List
+        write: []
+    signed_by:
+        read: []
+        write:
+        -   column: 2
+            row: 15
+            sheet: Sample List
+    submission_category:
+        read:
+        -   column: 4
+            row: 6
+            sheet: Sample List
+        write: []
+    submission_type:
+        read:
+        -   column: 4
+            row: 3
+            sheet: Sample List
+        write: []
+    submitted_date:
+        read:
+        -   column: 2
+            row: 3
+            sheet: Sample List
+        write: []
+    submitter_plate_num:
+        read:
+        -   column: 2
+            row: 2
+            sheet: Sample List
+        write: []
+    submitting_lab:
+        read:
+        -   column: 4
+            row: 2
+            sheet: Sample List
+        write: []
+    technician:
+        read:
+        -   column: 2
+            row: 14
+            sheet: Sample List
+        write: []
+kits:
+-   constant_cost: 0.0
+    kit_type:
+        name: MagMAX-96 Viral RNA Isolation Kit
+        equipment roles:
+        -   role: Extractor
+            processes:
+            - OBT_M4029_KFF_v1.0
+            static: 0
+        -   processes:
+            - Omega_MagBind_Universal_VarCol
+            role: Momentum - Extraction
+            static: 1
+        -   processes:
+            - Bacterial_Core_Submission
+            role: Liquid Handler
+            static: 1
+        reagent roles:
+        -   expiry:
+                column: 4
+                row: 19
+            extension_of_life: 0
+            lot:
+                column: 3
+                row: 19
+            name:
+                column: 2
+                row: 19
+            required: 1
+            role: Wash Solution 1 (MagMAX-96 Viral)
+            sheet: Sample List
+        -   expiry:
+                column: 4
+                row: 20
+            extension_of_life: 0
+            lot:
+                column: 3
+                row: 20
+            name:
+                column: 2
+                row: 20
+            required: 1
+            role: Wash Solution 2 (MagMAX-96 Viral)
+            sheet: Sample List
+        -   expiry:
+                column: 4
+                row: 21
+            extension_of_life: 0
+            lot:
+                column: 3
+                row: 21
+            name:
+                column: 2
+                row: 21
+            required: 1
+            role: Lysis/Binding Solution (MagMAX-96 Viral)
+            sheet: Sample List
+        -   expiry:
+                column: 4
+                row: 22
+            extension_of_life: 0
+            lot:
+                column: 3
+                row: 22
+            name:
+                column: 2
+                row: 22
+            required: 1
+            role: RNA Binding Beads (MagMAX-96 Viral)
+            sheet: Sample List
+        -   expiry:
+                column: 4
+                row: 23
+            extension_of_life: 0
+            lot:
+                column: 3
+                row: 23
+            name:
+                column: 2
+                row: 23
+            required: 1
+            role: Lysis/Binding Enhancer (MagMAX-96 Viral)
+            sheet: Sample List
+        -   expiry:
+                column: 4
+                row: 24
+            extension_of_life: 0
+            lot:
+                column: 3
+                row: 24
+            name:
+                column: 2
+                row: 24
+            required: 0
+            role: Bacterial-Lysis Buffer
+            sheet: Sample List
+        -   expiry:
+                column: 4
+                row: 25
+            extension_of_life: 0
+            lot:
+                column: 3
+                row: 25
+            name:
+                column: 2
+                row: 25
+            required: 1
+            role: Elution Buffer (MagMAX-96 Viral)
+            sheet: Sample List
+        -   expiry:
+                column: 4
+                row: 30
+            extension_of_life: 0
+            lot:
+                column: 3
+                row: 30
+            name:
+                column: 2
+                row: 30
+            required: 0
+            role: Bacterial-Positive Control
+            sheet: Sample List
+        -   expiry:
+                column: 4
+                row: 31
+            extension_of_life: 0
+            lot:
+                column: 3
+                row: 31
+            name:
+                column: 2
+                row: 31
+            required: 0
+            role: Bead Plate
+            sheet: Sample List
+        -   expiry:
+                column: 4
+                row: 28
+            extension_of_life: 0
+            lot:
+                column: 3
+                row: 28
+            name:
+                column: 2
+                row: 28
+            required: 1
+            role: Isopropanol
+            sheet: Sample List
+        -   expiry:
+                column: 4
+                row: 29
+            extension_of_life: 0
+            lot:
+                column: 3
+                row: 29
+            name:
+                column: 2
+                row: 29
+            required: 1
+            role: Ethanol
+            sheet: Sample List
+        -   expiry:
+                column: 4
+                row: 32
+            extension_of_life: 0
+            lot:
+                column: 3
+                row: 32
+            name:
+                column: 2
+                row: 32
+            required: 1
+            role: Carrier RNA
+            sheet: Sample List
+    mutable_cost_column: 0.0
+    mutable_cost_sample: 0.0
+samples:
+    lookup_table:
+        end_row: 132
+        merge_on_id: submitter_id
+        sample_columns:
+            column: 6
+            concentration: 4
+            organism: 3
+            row: 5
+            submitter_id: 2
+        sheet: Sample List
+        start_row: 37
+    plate_map:
+        end_column: 13
+        end_row: 14
+        sheet: Plate Map
+        start_column: 2
+        start_row: 7
+orgs:
+    - name: IRVC-Genomics
+      cost_centre: xxx
+      contacts:
+          - name: Ruimin Gao
+            phone: (204) 789-5078
+            email: Ruimin.Gao@phac-aspc.gc.ca

src/submissions/tools/__init__.py

@@ -909,6 +909,15 @@ def remove_key_from_list_of_dicts(input: list, key: str) -> list:
     return input
 
 
+def yaml_regex_creator(loader, node):
+    # Note: Add to import from json, NOT export yaml in app.
+    # base = node[0].value
+    nodes = loader.construct_sequence(node)
+    name = nodes[0].replace(" ", "_")
+    abbr = nodes[1]
+    return f"(?P<{name}>RSL(?:-|_)?{abbr}(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\sA-QS-Z]|$)?R?\d?)?)"
+
+
 ctx = get_config(None)