Context menu for runs working.

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

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+"""
+
+"""
+from pathlib import Path
+from openpyxl import load_workbook
+from backend.validators import pydant
+
+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', '')}")
+        if isinstance(filepath, str):
+            self.filepath = Path(filepath)
+        else:
+            self.filepath = filepath
+        self.workbook = load_workbook(self.filepath, data_only=True)
+        if not range_dict:
+            self.range_dict = self.__class__.default_range_dict
+        else:
+            self.range_dict = range_dict
+
+from .submission_parser import *

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

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+"""
+
+"""
+import logging, re
+from pathlib import Path
+from typing import Generator, Tuple
+from pandas import DataFrame
+
+from . import DefaultParser
+
+logger = logging.getLogger(f"submissions.{__name__}")
+
+
+class ClientSubmissionParser(DefaultParser):
+    """
+    Object for retrieving submitter info from "sample list" sheet
+    """
+
+    def __init__(self, filepath: Path | str, range_dict: dict | None = None):
+        super().__init__(filepath=filepath, range_dict=range_dict)
+        self.worksheet = self.workbook[self.range_dict['sheet']]
+        self.rows = range(self.range_dict['start_row'], self.range_dict['end_row'] + 1)
+
+    @property
+    def parsed_info(self) -> Generator[Tuple, None, None]:
+        for row in self.rows:
+            key = self.worksheet.cell(row, self.range_dict['key_column']).value
+            if key:
+                key = re.sub(r"\(.*\)", "", key)
+                key = key.lower().replace(":", "").strip().replace(" ", "_")
+                value = self.worksheet.cell(row, self.range_dict['value_column']).value
+                value = dict(value=value, missing=False if value else True)
+                yield key, value
+
+    def to_pydantic(self):
+        data = {key: value for key, value in self.parsed_info}
+        data['filepath'] = self.filepath
+        return self._pyd_object(**data)
+
+
+class SampleParser(DefaultParser):
+    """
+    Object for retrieving submitter info from "sample list" sheet
+    """
+
+    default_range_dict = dict(
+        header_row=20,
+        end_row=116,
+        list_sheet="Sample List"
+    )
+
+    def __init__(self, filepath: Path | str, range_dict: dict | None = None):
+        super().__init__(filepath=filepath, range_dict=range_dict)
+        self.list_worksheet = self.workbook[self.range_dict['list_sheet']]
+        self.list_df = DataFrame([item for item in self.list_worksheet.values][self.range_dict['header_row'] - 1:])
+        self.list_df.columns = self.list_df.iloc[0]
+        self.list_df = self.list_df[1:]
+        self.list_df = self.list_df.dropna(axis=1, how='all')
+
+    @property
+    def parsed_info(self) -> Generator[dict, None, None]:
+        for ii, row in enumerate(self.list_df.iterrows()):
+            sample = {key.lower().replace(" ", "_"): value for key, value in row[1].to_dict().items()}
+            sample['submission_rank'] = ii + 1
+            yield sample
+
+    def to_pydantic(self):
+        return [self._pyd_object(**sample) for sample in self.parsed_info if sample['sample_id']]