Various bug fixes.

src/submissions/backend/excel/parser.py

@@ -35,7 +35,7 @@ class SheetParser(object):
         Args:
             filepath (Path | None, optional): file path to excel sheet. Defaults to None.
         """
-        logger.debug(f"\n\nParsing {filepath.__str__()}\n\n")
+        logger.info(f"\n\nParsing {filepath.__str__()}\n\n")
         match filepath:
             case Path():
                 self.filepath = filepath
@@ -651,6 +651,15 @@ class PCRParser(object):
         info_map = self.submission_obj.get_submission_type().sample_map['pcr_general_info']
         sheet = self.xl[info_map['sheet']]
         iter_rows = sheet.iter_rows(min_row=info_map['start_row'], max_row=info_map['end_row'])
-        pcr = {row[0].value.lower().replace(' ', '_'): row[1].value for row in iter_rows}
+        pcr = {}
+        for row in iter_rows:
+            try:
+                key = row[0].value.lower().replace(' ', '_')
+            except AttributeError as e:
+                logger.error(f"No key: {row[0].value} due to {e}")
+                continue
+            value = row[1].value or ""
+            pcr[key] = value
         pcr['imported_by'] = getuser()
+        # logger.debug(f"PCR: {pformat(pcr)}")
         return pcr

src/submissions/backend/excel/reports.py

@@ -23,13 +23,13 @@ def make_report_xlsx(records:list[dict]) -> Tuple[DataFrame, DataFrame]:
     """    
     df = DataFrame.from_records(records)
     # put submissions with the same lab together
-    df = df.sort_values("Submitting Lab")
+    df = df.sort_values("submitting_lab")
     # aggregate cost and sample count columns
-    df2 = df.groupby(["Submitting Lab", "Extraction Kit"]).agg({'Extraction Kit':'count', 'Cost': 'sum', 'Sample Count':'sum'})
-    df2 = df2.rename(columns={"Extraction Kit": 'Run Count'})
+    df2 = df.groupby(["submitting_lab", "extraction_kit"]).agg({'extraction_kit':'count', 'cost': 'sum', 'sample_count':'sum'})
+    df2 = df2.rename(columns={"extraction_kit": 'run_count'})
     # logger.debug(f"Output daftaframe for xlsx: {df2.columns}")
     df = df.drop('id', axis=1)
-    df = df.sort_values(['Submitting Lab', "Submitted Date"])
+    df = df.sort_values(['submitting_lab', "submitted_date"])
     return df, df2
 
 def make_report_html(df:DataFrame, start_date:date, end_date:date) -> str:

src/submissions/backend/excel/writer.py

@@ -85,6 +85,7 @@ class SheetWriter(object):
 class InfoWriter(object):
 
     def __init__(self, xl: Workbook, submission_type: SubmissionType | str, info_dict: dict, sub_object:BasicSubmission|None=None):
+        logger.debug(f"Info_dict coming into InfoWriter: {pformat(info_dict)}")
         if isinstance(submission_type, str):
             submission_type = SubmissionType.query(name=submission_type)
         if sub_object is None:
@@ -110,10 +111,15 @@ class InfoWriter(object):
             dicto['value'] = v
             if len(dicto) > 0:
                 output[k] = dicto
+        # logger.debug(f"Reconciled info: {pformat(output)}")
         return output
 
     def write_info(self):
         for k, v in self.info.items():
+            # 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()]
+                v['value'] = "\n".join(json_join)
             try:
                 locations = v['locations']
             except KeyError:
@@ -183,6 +189,7 @@ class SampleWriter(object):
         output = []
         multiples = ['row', 'column', 'assoc_id', 'submission_rank']
         for sample in sample_list:
+            # logger.debug(f"Writing sample: {sample}")
             for assoc in zip(sample['row'], sample['column'], sample['submission_rank']):
                 new = dict(row=assoc[0], column=assoc[1], submission_rank=assoc[2])
                 for k, v in sample.items():