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Conversion of some functions to generators.

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This commit is contained in:
lwark
2024-07-31 13:08:56 -05:00
parent eb6cdc63e2
commit 8266275354
15 changed files with 374 additions and 369 deletions
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97
src/submissions/backend/excel/writer.py
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@@ -1,13 +1,13 @@
'''
contains writer objects for pushing values to submission sheet templates.
'''
"""
contains writer objects for pushing values to submission sheet templates.
"""
import logging
from copy import copy
from operator import itemgetter
from pathlib import Path
# from pathlib import Path
from pprint import pformat
from typing import List
from typing import List, Generator
from openpyxl import load_workbook, Workbook
from backend.db.models import SubmissionType, KitType, BasicSubmission
from backend.validators.pydant import PydSubmission
@@ -30,7 +30,7 @@ class SheetWriter(object):
Args:
submission (PydSubmission): Object containing submission information.
missing_only (bool, optional): Whether to only fill in missing values. Defaults to False.
"""
"""
self.sub = OrderedDict(submission.improved_dict())
for k, v in self.sub.items():
match k:
@@ -47,7 +47,6 @@ class SheetWriter(object):
else:
self.sub[k] = v
# logger.debug(f"\n\nWriting to {submission.filepath.__str__()}\n\n")
if self.filepath.stem.startswith("tmp"):
template = self.submission_type.template_file
workbook = load_workbook(BytesIO(template))
@@ -124,7 +123,7 @@ class InfoWriter(object):
submission_type (SubmissionType | str): Type of submission expected (Wastewater, Bacterial Culture, etc.)
info_dict (dict): Dictionary of information to write.
sub_object (BasicSubmission | None, optional): Submission object containing methods. Defaults to None.
"""
"""
logger.debug(f"Info_dict coming into InfoWriter: {pformat(info_dict)}")
if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type)
@@ -148,7 +147,7 @@ class InfoWriter(object):
Returns:
dict: merged dictionary
"""
output = {}
# output = {}
for k, v in info_dict.items():
if v is None:
continue
@@ -162,9 +161,10 @@ class InfoWriter(object):
pass
dicto['value'] = v
if len(dicto) > 0:
output[k] = dicto
# output[k] = dicto
yield k, dicto
# logger.debug(f"Reconciled info: {pformat(output)}")
return output
# return output
def write_info(self) -> Workbook:
"""
@@ -173,7 +173,7 @@ class InfoWriter(object):
Returns:
Workbook: workbook with info written.
"""
for k, v in self.info.items():
for k, v in self.info:
# 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()]
@@ -203,16 +203,17 @@ class ReagentWriter(object):
submission_type (SubmissionType | str): Type of submission expected (Wastewater, Bacterial Culture, etc.)
extraction_kit (KitType | str): Extraction kit used.
reagent_list (list): List of reagent dicts to be written to excel.
"""
"""
self.xl = xl
if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type)
if isinstance(extraction_kit, str):
kit_type = KitType.query(name=extraction_kit)
reagent_map = kit_type.construct_xl_map_for_use(submission_type)
reagent_map = {k: v for k, v in kit_type.construct_xl_map_for_use(submission_type)}
# self.reagents = {k: v for k, v in self.reconcile_map(reagent_list=reagent_list, reagent_map=reagent_map)}
self.reagents = self.reconcile_map(reagent_list=reagent_list, reagent_map=reagent_map)
def reconcile_map(self, reagent_list: List[dict], reagent_map: dict) -> List[dict]:
def reconcile_map(self, reagent_list: List[dict], reagent_map: dict) -> Generator[dict, None, None]:
"""
Merge reagents with their locations
@@ -223,7 +224,7 @@ class ReagentWriter(object):
Returns:
List[dict]: merged dictionary
"""
output = []
# output = []
for reagent in reagent_list:
try:
mp_info = reagent_map[reagent['role']]
@@ -238,8 +239,9 @@ class ReagentWriter(object):
dicto = v
placeholder[k] = dicto
placeholder['sheet'] = mp_info['sheet']
output.append(placeholder)
return output
# output.append(placeholder)
yield placeholder
# return output
def write_reagents(self) -> Workbook:
"""
@@ -263,21 +265,24 @@ class SampleWriter(object):
"""
object to write sample data into excel file
"""
def __init__(self, xl: Workbook, submission_type: SubmissionType | str, sample_list: list):
"""
Args:
xl (Workbook): Openpyxl workbook from submitted excel file.
submission_type (SubmissionType | str): Type of submission expected (Wastewater, Bacterial Culture, etc.)
sample_list (list): List of sample dictionaries to be written to excel file.
"""
"""
if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type)
self.submission_type = submission_type
self.xl = xl
self.sample_map = submission_type.construct_sample_map()['lookup_table']
self.samples = self.reconcile_map(sample_list)
# self.samples = self.reconcile_map(sample_list)
samples = [item for item in self.reconcile_map(sample_list)]
self.samples = sorted(samples, key=lambda k: k['submission_rank'])
def reconcile_map(self, sample_list: list) -> List[dict]:
def reconcile_map(self, sample_list: list) -> Generator[dict, None, None]:
"""
Merge sample info with locations
@@ -287,7 +292,7 @@ class SampleWriter(object):
Returns:
List[dict]: List of merged dictionaries
"""
output = []
# output = []
multiples = ['row', 'column', 'assoc_id', 'submission_rank']
for sample in sample_list:
# logger.debug(f"Writing sample: {sample}")
@@ -297,8 +302,8 @@ class SampleWriter(object):
if k in multiples:
continue
new[k] = v
output.append(new)
return sorted(output, key=lambda k: k['submission_rank'])
yield new
# return sorted(output, key=lambda k: k['submission_rank'])
def write_samples(self) -> Workbook:
"""
@@ -331,15 +336,15 @@ class EquipmentWriter(object):
xl (Workbook): Openpyxl workbook from submitted excel file.
submission_type (SubmissionType | str): Type of submission expected (Wastewater, Bacterial Culture, etc.)
equipment_list (list): List of equipment dictionaries to write to excel file.
"""
"""
if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type)
self.submission_type = submission_type
self.xl = xl
equipment_map = self.submission_type.construct_equipment_map()
equipment_map = {k: v for k, v in self.submission_type.construct_equipment_map()}
self.equipment = self.reconcile_map(equipment_list=equipment_list, equipment_map=equipment_map)
def reconcile_map(self, equipment_list: list, equipment_map: dict) -> List[dict]:
def reconcile_map(self, equipment_list: list, equipment_map: dict) -> Generator[dict, None, None]:
"""
Merges equipment with location data
@@ -350,9 +355,9 @@ class EquipmentWriter(object):
Returns:
List[dict]: List of merged dictionaries
"""
output = []
# output = []
if equipment_list is None:
return output
return
for ii, equipment in enumerate(equipment_list, start=1):
mp_info = equipment_map[equipment['role']]
# logger.debug(f"{equipment['role']} map: {mp_info}")
@@ -376,8 +381,9 @@ class EquipmentWriter(object):
except KeyError:
placeholder['sheet'] = "Equipment"
# logger.debug(f"Final output of {equipment['role']} : {placeholder}")
output.append(placeholder)
return output
yield placeholder
# output.append(placeholder)
# return output
def write_equipment(self) -> Workbook:
"""
@@ -419,15 +425,15 @@ class TipWriter(object):
xl (Workbook): Openpyxl workbook from submitted excel file.
submission_type (SubmissionType | str): Type of submission expected (Wastewater, Bacterial Culture, etc.)
tips_list (list): List of tip dictionaries to write to the excel file.
"""
"""
if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type)
self.submission_type = submission_type
self.xl = xl
tips_map = self.submission_type.construct_tips_map()
tips_map = {k: v for k, v in self.submission_type.construct_tips_map()}
self.tips = self.reconcile_map(tips_list=tips_list, tips_map=tips_map)
def reconcile_map(self, tips_list: List[dict], tips_map: dict) -> List[dict]:
def reconcile_map(self, tips_list: List[dict], tips_map: dict) -> Generator[dict, None, None]:
"""
Merges tips with location data
@@ -438,9 +444,9 @@ class TipWriter(object):
Returns:
List[dict]: List of merged dictionaries
"""
output = []
# output = []
if tips_list is None:
return output
return
for ii, tips in enumerate(tips_list, start=1):
mp_info = tips_map[tips['role']]
# logger.debug(f"{tips['role']} map: {mp_info}")
@@ -462,8 +468,9 @@ class TipWriter(object):
except KeyError:
placeholder['sheet'] = "Tips"
# logger.debug(f"Final output of {tips['role']} : {placeholder}")
output.append(placeholder)
return output
yield placeholder
# output.append(placeholder)
# return output
def write_tips(self) -> Workbook:
"""
@@ -497,13 +504,13 @@ class TipWriter(object):
class DocxWriter(object):
"""
Object to render
"""
"""
def __init__(self, base_dict: dict):
"""
Args:
base_dict (dict): dictionary of info to be written to template.
"""
"""
self.sub_obj = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=base_dict['submission_type'])
env = jinja_template_loading()
temp_name = f"{base_dict['submission_type'].replace(' ', '').lower()}_subdocument.docx"
@@ -530,12 +537,12 @@ class DocxWriter(object):
rows = max([sample['row'] for sample in sample_list])
if columns == 0:
columns = max([sample['column'] for sample in sample_list])
output = []
# output = []
for row in range(0, rows):
contents = [''] * columns
for column in range(0, columns):
try:
ooi = [item for item in sample_list if item['row']==row+1 and item['column']==column+1][0]
ooi = [item for item in sample_list if item['row'] == row + 1 and item['column'] == column + 1][0]
except IndexError:
continue
contents[column] = ooi['submitter_id']
@@ -545,8 +552,9 @@ class DocxWriter(object):
contents += [''] * (columns - len(contents))
if not contents:
contents = [''] * columns
output.append(contents)
return output
yield contents
# output.append(contents)
# return output
def create_merged_template(self, *args) -> BytesIO:
"""
@@ -554,7 +562,7 @@ class DocxWriter(object):
Returns:
BytesIO: Merged docx template
"""
"""
merged_document = Document()
output = BytesIO()
for index, file in enumerate(args):
@@ -567,7 +575,6 @@ class DocxWriter(object):
merged_document.save(output)
return output
def save(self, filename: Path | str):
if isinstance(filename, str):
filename = Path(filename)