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Context menu for runs working.

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This commit is contained in:
lwark
2025-05-22 10:00:25 -05:00
parent 75c665ea05
commit d850166e08
40 changed files with 2852 additions and 3329 deletions
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46
src/submissions/backend/excel/writer.py
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@@ -1,5 +1,5 @@
"""
contains writer objects for pushing values to run sheet templates.
contains writer objects for pushing values to procedure sheet templates.
"""
import logging
from copy import copy
@@ -8,7 +8,7 @@ from operator import itemgetter
from pprint import pformat
from typing import List, Generator, Tuple
from openpyxl import load_workbook, Workbook
from backend.db.models import SubmissionType, KitType, BasicRun
from backend.db.models import SubmissionType, KitType, Run
from backend.validators.pydant import PydSubmission
from io import BytesIO
from collections import OrderedDict
@@ -24,7 +24,7 @@ class SheetWriter(object):
def __init__(self, submission: PydSubmission):
"""
Args:
submission (PydSubmission): Object containing run information.
submission (PydSubmission): Object containing procedure information.
"""
self.sub = OrderedDict(submission.improved_dict())
# NOTE: Set values from pydantic object.
@@ -32,7 +32,7 @@ class SheetWriter(object):
match k:
case 'filepath':
self.__setattr__(k, v)
case 'submission_type':
case 'proceduretype':
self.sub[k] = v['value']
self.submission_type = SubmissionType.query(name=v['value'])
self.run_object = BasicRun.find_polymorphic_subclass(
@@ -58,7 +58,7 @@ class SheetWriter(object):
"""
Calls info writer
"""
disallowed = ['filepath', 'reagents', 'samples', 'equipment', 'controls']
disallowed = ['filepath', 'reagents', 'sample', 'equipment', 'control']
info_dict = {k: v for k, v in self.sub.items() if k not in disallowed}
writer = InfoWriter(xl=self.xl, submission_type=self.submission_type, info_dict=info_dict)
self.xl = writer.write_info()
@@ -69,14 +69,14 @@ class SheetWriter(object):
"""
reagent_list = self.sub['reagents']
writer = ReagentWriter(xl=self.xl, submission_type=self.submission_type,
extraction_kit=self.sub['extraction_kit'], reagent_list=reagent_list)
extraction_kit=self.sub['kittype'], reagent_list=reagent_list)
self.xl = writer.write_reagents()
def write_samples(self):
"""
Calls sample writer
"""
sample_list = self.sub['samples']
sample_list = self.sub['sample']
writer = SampleWriter(xl=self.xl, submission_type=self.submission_type, sample_list=sample_list)
self.xl = writer.write_samples()
@@ -99,22 +99,22 @@ class SheetWriter(object):
class InfoWriter(object):
"""
object to write general run info into excel file
object to write general procedure info into excel file
"""
def __init__(self, xl: Workbook, submission_type: SubmissionType | str, info_dict: dict,
sub_object: BasicRun | None = None):
sub_object: Run | None = None):
"""
Args:
xl (Workbook): Openpyxl workbook from submitted excel file.
submission_type (SubmissionType | str): Type of run expected (Wastewater, Bacterial Culture, etc.)
submission_type (SubmissionType | str): Type of procedure expected (Wastewater, Bacterial Culture, etc.)
info_dict (dict): Dictionary of information to write.
sub_object (BasicRun | None, optional): Submission object containing methods. Defaults to None.
"""
if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type)
if sub_object is None:
sub_object = BasicRun.find_polymorphic_subclass(polymorphic_identity=submission_type.name)
sub_object = Run.find_polymorphic_subclass(polymorphic_identity=submission_type.name)
self.submission_type = submission_type
self.sub_object = sub_object
self.xl = xl
@@ -196,8 +196,8 @@ class ReagentWriter(object):
"""
Args:
xl (Workbook): Openpyxl workbook from submitted excel file.
submission_type (SubmissionType | str): Type of run expected (Wastewater, Bacterial Culture, etc.)
extraction_kit (KitType | str): Extraction kit used.
submission_type (SubmissionType | str): Type of procedure expected (Wastewater, Bacterial Culture, etc.)
extraction_kit (KitType | str): Extraction kittype used.
reagent_list (list): List of reagent dicts to be written to excel.
"""
self.xl = xl
@@ -208,7 +208,7 @@ class ReagentWriter(object):
extraction_kit = KitType.query(name=extraction_kit)
self.kit_object = extraction_kit
associations, self.kit_object = self.kit_object.construct_xl_map_for_use(
submission_type=self.submission_type_obj)
proceduretype=self.submission_type_obj)
reagent_map = {k: v for k, v in associations.items()}
self.reagents = self.reconcile_map(reagent_list=reagent_list, reagent_map=reagent_map)
@@ -223,13 +223,13 @@ class ReagentWriter(object):
Returns:
List[dict]: merged dictionary
"""
filled_roles = [item['role'] for item in reagent_list]
filled_roles = [item['reagentrole'] for item in reagent_list]
for map_obj in reagent_map.keys():
if map_obj not in filled_roles:
reagent_list.append(dict(name="Not Applicable", role=map_obj, lot="Not Applicable", expiry="Not Applicable"))
for reagent in reagent_list:
try:
mp_info = reagent_map[reagent['role']]
mp_info = reagent_map[reagent['reagentrole']]
except KeyError:
continue
placeholder = copy(reagent)
@@ -273,7 +273,7 @@ class SampleWriter(object):
"""
Args:
xl (Workbook): Openpyxl workbook from submitted excel file.
submission_type (SubmissionType | str): Type of run expected (Wastewater, Bacterial Culture, etc.)
submission_type (SubmissionType | str): Type of procedure expected (Wastewater, Bacterial Culture, etc.)
sample_list (list): List of sample dictionaries to be written to excel file.
"""
if isinstance(submission_type, str):
@@ -281,7 +281,7 @@ class SampleWriter(object):
self.submission_type = submission_type
self.xl = xl
self.sample_map = submission_type.sample_map['lookup_table']
# NOTE: exclude any samples without a run rank.
# NOTE: exclude any sample without a procedure rank.
samples = [item for item in self.reconcile_map(sample_list) if item['submission_rank'] > 0]
self.samples = sorted(samples, key=itemgetter('submission_rank'))
self.blank_lookup_table()
@@ -322,7 +322,7 @@ class SampleWriter(object):
Performs writing operations.
Returns:
Workbook: Workbook with samples written
Workbook: Workbook with sample written
"""
sheet = self.xl[self.sample_map['sheet']]
columns = self.sample_map['sample_columns']
@@ -351,7 +351,7 @@ class EquipmentWriter(object):
"""
Args:
xl (Workbook): Openpyxl workbook from submitted excel file.
submission_type (SubmissionType | str): Type of run expected (Wastewater, Bacterial Culture, etc.)
submission_type (SubmissionType | str): Type of procedure expected (Wastewater, Bacterial Culture, etc.)
equipment_list (list): List of equipment dictionaries to write to excel file.
"""
if isinstance(submission_type, str):
@@ -376,9 +376,9 @@ class EquipmentWriter(object):
return
for ii, equipment in enumerate(equipment_list, start=1):
try:
mp_info = equipment_map[equipment['role']]
mp_info = equipment_map[equipment['reagentrole']]
except KeyError:
logger.error(f"No {equipment['role']} in {pformat(equipment_map)}")
logger.error(f"No {equipment['reagentrole']} in {pformat(equipment_map)}")
mp_info = None
placeholder = copy(equipment)
if not mp_info:
@@ -433,7 +433,7 @@ class TipWriter(object):
"""
Args:
xl (Workbook): Openpyxl workbook from submitted excel file.
submission_type (SubmissionType | str): Type of run expected (Wastewater, Bacterial Culture, etc.)
submission_type (SubmissionType | str): Type of procedure expected (Wastewater, Bacterial Culture, etc.)
tips_list (list): List of tip dictionaries to write to the excel file.
"""
if isinstance(submission_type, str):