Getting results referencing ProcedureSampleAssociation

src/submissions/backend/excel/parsers/__init__.py

@@ -1,26 +1,25 @@
 """
 
 """
+import logging, re
 from pathlib import Path
+from typing import Generator, Tuple
 from openpyxl import load_workbook
+from pandas import DataFrame
 from backend.validators import pydant
 
+logger = logging.getLogger(f"submissions.{__name__}")
+
 class DefaultParser(object):
 
-
-    default_range_dict = dict(
-        start_row=2,
-        end_row=18,
-        key_column=1,
-        value_column=2,
-        sheet="Sample List"
-    )
-
     def __repr__(self):
         return f"{self.__class__.__name__}<{self.filepath.stem}>"
 
-    def __init__(self, filepath: Path | str, range_dict: dict | None = None):
-        self._pyd_object = getattr(pydant, f"Pyd{self.__class__.__name__.replace('Parser', '')}")
+    def __init__(self, filepath: Path | str, range_dict: dict | None = None, *args, **kwargs):
+        try:
+            self._pyd_object = getattr(pydant, f"Pyd{self.__class__.__name__.replace('Parser', '')}")
+        except AttributeError:
+            self._pyd_object = pydant.PydResults
         if isinstance(filepath, str):
             self.filepath = Path(filepath)
         else:
@@ -30,5 +29,63 @@ class DefaultParser(object):
             self.range_dict = self.__class__.default_range_dict
         else:
             self.range_dict = range_dict
+        for item in self.range_dict:
+            item['worksheet'] = self.workbook[item['sheet']]
 
-from .submission_parser import *
+    def to_pydantic(self):
+        data = {key: value for key, value in self.parsed_info}
+        data['filepath'] = self.filepath
+        return self._pyd_object(**data)
+
+
+class DefaultKEYVALUEParser(DefaultParser):
+
+    default_range_dict = [dict(
+        start_row=2,
+        end_row=18,
+        key_column=1,
+        value_column=2,
+        sheet="Sample List"
+    )]
+
+
+
+    @property
+    def parsed_info(self) -> Generator[Tuple, None, None]:
+        for item in self.range_dict:
+            rows = range(item['start_row'], item['end_row'] + 1)
+            for row in rows:
+                key = item['worksheet'].cell(row, item['key_column']).value
+                if key:
+                    # Note: Remove anything in brackets.
+                    key = re.sub(r"\(.*\)", "", key)
+                    key = key.lower().replace(":", "").strip().replace(" ", "_")
+                    value = item['worksheet'].cell(row, item['value_column']).value
+                    value = dict(value=value, missing=False if value else True)
+                    yield key, value
+
+
+class DefaultTABLEParser(DefaultParser):
+
+    default_range_dict = [dict(
+        header_row=20,
+        end_row=116,
+        sheet="Sample List"
+    )]
+
+    @property
+    def parsed_info(self):
+        for item in self.range_dict:
+            list_worksheet = self.workbook[item['sheet']]
+            list_df = DataFrame([item for item in list_worksheet.values][item['header_row'] - 1:])
+            list_df.columns = list_df.iloc[0]
+            list_df = list_df[1:]
+            list_df = list_df.dropna(axis=1, how='all')
+            for ii, row in enumerate(list_df.iterrows()):
+                output = {key.lower().replace(" ", "_"): value for key, value in row[1].to_dict().items()}
+                yield output
+
+    def to_pydantic(self, **kwargs):
+        return [self._pyd_object(**output) for output in self.parsed_info]
+
+from .submission_parser import *