Returned to pdf exports from details.

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

@@ -1042,7 +1042,7 @@ class BasicSubmission(BaseClass):
     #     return [item.to_sub_dict() for item in self.submission_sample_associations]
 
     @classmethod
-    def get_details_template(cls, base_dict: dict) -> Tuple[dict, Template]:
+    def get_details_template(cls, base_dict: dict) -> Template:
         """
         Get the details jinja template for the correct class
 
@@ -1357,13 +1357,13 @@ class BasicSubmission(BaseClass):
         if fname.name == "":
             # logger.debug(f"export cancelled.")
             return
-        if full_backup:
-            backup = self.to_dict(full_data=True)
-            try:
-                with open(self.__backup_path__.joinpath(fname.with_suffix(".yml")), "w") as f:
-                    yaml.dump(backup, f)
-            except KeyError as e:
-                logger.error(f"Problem saving yml backup file: {e}")
+        # if full_backup:
+        #     backup = self.to_dict(full_data=True)
+        #     try:
+        #         with open(self.__backup_path__.joinpath(fname.with_suffix(".yml")), "w") as f:
+        #             yaml.dump(backup, f)
+        #     except KeyError as e:
+        #         logger.error(f"Problem saving yml backup file: {e}")
         writer = pyd.to_writer()
         writer.xl.save(filename=fname.with_suffix(".xlsx"))
 
@@ -1632,6 +1632,8 @@ class Wastewater(BasicSubmission):
             dict: Updated information
         """
         input_dict = super().finalize_details(input_dict)
+        # NOTE: Currently this is preserving the generator items, can we come up with a better way?
+        input_dict['samples'] = [sample for sample in input_dict['samples']]
         dummy_samples = []
         for item in input_dict['samples']:
             # logger.debug(f"Sample dict: {item}")
@@ -1681,12 +1683,10 @@ class Wastewater(BasicSubmission):
         for sample in self.samples:
             # logger.debug(f"Running update on: {sample}")
             try:
-                # sample_dict = [item for item in parser.samples if item['sample'] == sample.rsl_number][0]
                 sample_dict = next(item for item in parser.samples if item['sample'] == sample.rsl_number)
             except StopIteration:
                 continue
             self.update_subsampassoc(sample=sample, input_dict=sample_dict)
-        # self.report.add_result(Result(msg=f"We added PCR info to {sub.rsl_plate_num}.", status='Information'))
 
     @classmethod
     def custom_docx_writer(cls, input_dict: dict, tpl_obj=None) -> dict:
@@ -1703,6 +1703,7 @@ class Wastewater(BasicSubmission):
         from backend.excel.writer import DocxWriter
         input_dict = super().custom_docx_writer(input_dict)
         well_24 = []
+        input_dict['samples'] = [item for item in input_dict['samples']]
         samples_copy = deepcopy(input_dict['samples'])
         for sample in sorted(samples_copy, key=itemgetter('column', 'row')):
             try:

src/submissions/backend/excel/writer.py

@@ -519,6 +519,7 @@ class DocxWriter(object):
         Args:
             base_dict (dict): dictionary of info to be written to template.
         """
+        logger.debug(f"Incoming base dict: {pformat(base_dict)}")
         self.sub_obj = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=base_dict['submission_type'])
         env = jinja_template_loading()
         temp_name = f"{base_dict['submission_type'].replace(' ', '').lower()}_subdocument.docx"
@@ -528,8 +529,8 @@ class DocxWriter(object):
         if subdocument.exists():
             main_template = self.create_merged_template(main_template, subdocument)
         self.template = DocxTemplate(main_template)
-        base_dict['platemap'] = self.create_plate_map(base_dict['samples'], rows=8, columns=12)
-        # logger.debug(pformat(base_dict['plate_map']))
+        base_dict['platemap'] = [item for item in self.create_plate_map(base_dict['samples'], rows=8, columns=12)]
+        # logger.debug(pformat(base_dict['platemap']))
         try:
             base_dict['excluded'] += ["platemap"]
         except KeyError:

src/submissions/backend/validators/pydant.py

@@ -739,11 +739,22 @@ class PydSubmission(BaseModel, extra='allow'):
                 pass
         else:
             # logger.debug("Extracting 'value' from attributes")
-            output = {k: (getattr(self, k) if not isinstance(getattr(self, k), dict) else getattr(self, k)['value']) for
-                      k in fields}
-
+            output = {k: self.filter_field(k) for k in fields}
         return output
 
+    def filter_field(self, key:str):
+        item = getattr(self, key)
+        # logger.debug(f"Attempting deconstruction of {key}: {item} with type {type(item)}")
+        match item:
+            case dict():
+                try:
+                    item = item['value']
+                except KeyError:
+                    logger.error(f"Couldn't get dict value: {item}")
+            case _:
+                pass
+        return item
+
     def find_missing(self) -> Tuple[dict, dict]:
         """
         Retrieves info and reagents marked as missing.