Upgrade of WastewaterArtic parsers/writers for flexibility.

src/submissions/backend/excel/parser.py

@@ -212,12 +212,14 @@ class InfoParser(object):
         """
         dicto = {}
         # NOTE: This loop parses generic info
-        # logger.debug(f"Map: {self.map}")
+        logger.debug(f"Map: {self.map}")
         for sheet in self.xl.sheetnames:
             ws = self.xl[sheet]
             relevant = []
             for k, v in self.map.items():
                 # NOTE: If the value is hardcoded put it in the dictionary directly.
+                if k == "custom":
+                    continue
                 if isinstance(v, str):
                     dicto[k] = dict(value=v, missing=False)
                     continue
@@ -265,7 +267,7 @@ class InfoParser(object):
                     except (KeyError, IndexError):
                         continue
         # Return after running the parser components held in submission object.
-        return self.sub_object.custom_info_parser(input_dict=dicto, xl=self.xl)
+        return self.sub_object.custom_info_parser(input_dict=dicto, xl=self.xl, custom_fields=self.map['custom'])
 
 
 class ReagentParser(object):

src/submissions/backend/excel/writer.py

@@ -8,8 +8,6 @@ from pathlib import Path
 # from pathlib import Path
 from pprint import pformat
 from typing import List
-from collections import OrderedDict
-from jinja2 import TemplateNotFound
 from openpyxl import load_workbook, Workbook
 from backend.db.models import SubmissionType, KitType, BasicSubmission
 from backend.validators.pydant import PydSubmission
@@ -135,8 +133,8 @@ class InfoWriter(object):
         self.submission_type = submission_type
         self.sub_object = sub_object
         self.xl = xl
-        info_map = submission_type.construct_info_map(mode='write')
-        self.info = self.reconcile_map(info_dict, info_map)
+        self.info_map = submission_type.construct_info_map(mode='write')
+        self.info = self.reconcile_map(info_dict, self.info_map)
         # logger.debug(pformat(self.info))
 
     def reconcile_map(self, info_dict: dict, info_map: dict) -> dict:
@@ -154,6 +152,8 @@ class InfoWriter(object):
         for k, v in info_dict.items():
             if v is None:
                 continue
+            if k == "custom":
+                continue
             dicto = {}
             try:
                 dicto['locations'] = info_map[k]
@@ -187,7 +187,7 @@ class InfoWriter(object):
                 logger.debug(f"Writing {k} to {loc['sheet']}, row: {loc['row']}, column: {loc['column']}")
                 sheet = self.xl[loc['sheet']]
                 sheet.cell(row=loc['row'], column=loc['column'], value=v['value'])
-        return self.sub_object.custom_info_writer(self.xl, info=self.info)
+        return self.sub_object.custom_info_writer(self.xl, info=self.info, custom_fields=self.info_map['custom'])
 
 
 class ReagentWriter(object):