Addition of procedure parser in import.

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

@@ -0,0 +1,138 @@
+"""
+
+"""
+from __future__ import annotations
+import logging
+from pathlib import Path
+from string import ascii_lowercase
+from typing import Generator
+
+from openpyxl.reader.excel import load_workbook
+
+from tools import row_keys
+# from backend.db.models import SubmissionType
+from . import DefaultKEYVALUEParser, DefaultTABLEParser
+from backend.managers import procedures as procedure_managers
+
+logger = logging.getLogger(f"submissions.{__name__}")
+
+
+class SubmissionTyperMixin(object):
+
+    @classmethod
+    def retrieve_submissiontype(cls, filepath: Path):
+        # NOTE: Attempt 1, get from form properties:
+        sub_type = cls.get_subtype_from_properties(filepath=filepath)
+        if not sub_type:
+            # NOTE: Attempt 2, get by opening file and using default parser
+            logger.warning(
+                f"Getting submissiontype from file properties failed, falling back on preparse.\nDepending on excel structure this might yield an incorrect submissiontype")
+            sub_type = cls.get_subtype_from_preparse(filepath=filepath)
+        if not sub_type:
+            logger.warning(
+                f"Getting submissiontype from preparse failed, falling back on filename regex.\nDepending on excel structure this might yield an incorrect submissiontype")
+            sub_type = cls.get_subtype_from_regex(filepath=filepath)
+        return sub_type
+
+    @classmethod
+    def get_subtype_from_regex(cls, filepath: Path):
+        from backend.db.models import SubmissionType
+        regex = SubmissionType.regex
+        m = regex.search(filepath.__str__())
+        try:
+            sub_type = m.lastgroup
+        except AttributeError as e:
+            sub_type = None
+            logger.critical(f"No procedure type found or procedure type found!: {e}")
+        return sub_type
+
+    @classmethod
+    def get_subtype_from_preparse(cls, filepath: Path):
+        from backend.db.models import SubmissionType
+        parser = ClientSubmissionInfoParser(filepath)
+        sub_type = next((value for k, value in parser.parsed_info if k == "submissiontype"), None)
+        sub_type = SubmissionType.query(name=sub_type)
+        if isinstance(sub_type, list):
+            sub_type = None
+        return sub_type
+
+    @classmethod
+    def get_subtype_from_properties(cls, filepath: Path):
+        from backend.db.models import SubmissionType
+        wb = load_workbook(filepath)
+        # NOTE: Gets first category in the metadata.
+        categories = wb.properties.category.split(";")
+        sub_type = next((item.strip().title() for item in categories), None)
+        sub_type = SubmissionType.query(name=sub_type)
+        if isinstance(sub_type, list):
+            sub_type = None
+        return sub_type
+
+
+class ClientSubmissionInfoParser(DefaultKEYVALUEParser, SubmissionTyperMixin):
+    """
+    Object for retrieving submitter info from "sample list" sheet
+    """
+
+    default_range_dict = [dict(
+        start_row=2,
+        end_row=18,
+        key_column=1,
+        value_column=2,
+        sheet="Sample List"
+    )]
+
+    def __init__(self, filepath: Path | str, *args, **kwargs):
+        from frontend.widgets.pop_ups import QuestionAsker
+        self.submissiontype = self.retrieve_submissiontype(filepath=filepath)
+        if "range_dict" not in kwargs:
+            kwargs['range_dict'] = self.submissiontype.info_map
+        super().__init__(filepath=filepath, **kwargs)
+        allowed_procedure_types = [item.name for item in self.submissiontype.proceduretype]
+        for name in allowed_procedure_types:
+            if name in self.workbook.sheetnames:
+                # TODO: check if run with name already exists
+                add_run = QuestionAsker(title="Add Run?", message="We've detected a sheet corresponding to an associated procedure type.\nWould you like to add a new run?")
+                if add_run.accepted:
+
+
+                # NOTE: recruit parser.
+                    try:
+                        manager = getattr(procedure_managers, name)
+                    except AttributeError:
+                        manager = procedure_managers.DefaultManager
+                    self.manager = manager(proceduretype=name)
+                pass
+
+
+class ClientSubmissionSampleParser(DefaultTABLEParser, SubmissionTyperMixin):
+    """
+    Object for retrieving submitter samples from "sample list" sheet
+    """
+
+    default_range_dict = [dict(
+        header_row=20,
+        end_row=116,
+        sheet="Sample List"
+    )]
+
+    def __init__(self, filepath: Path | str, *args, **kwargs):
+        self.submissiontype = self.retrieve_submissiontype(filepath=filepath)
+        if "range_dict" not in kwargs:
+            kwargs['range_dict'] = self.submissiontype.sample_map
+        super().__init__(filepath=filepath, **kwargs)
+
+    @property
+    def parsed_info(self) -> Generator[dict, None, None]:
+        output = super().parsed_info
+        for ii, sample in enumerate(output):
+            if isinstance(sample["row"], str) and sample["row"].lower() in ascii_lowercase[0:8]:
+                try:
+                    sample["row"] = row_keys[sample["row"]]
+                except KeyError:
+                    pass
+            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']]