Generic info fields input into 'custom'.

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:
-                            existing.append(value)
+                            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