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Various bug fixes and streamlining.

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This commit is contained in:
lwark
2024-10-03 15:09:41 -05:00
parent acab9d0f4c
commit c5470b9062
22 changed files with 222 additions and 380 deletions
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106
src/submissions/backend/excel/writer.py
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@@ -3,9 +3,6 @@ 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, Generator
from openpyxl import load_workbook, Workbook
@@ -13,9 +10,6 @@ from backend.db.models import SubmissionType, KitType, BasicSubmission
from backend.validators.pydant import PydSubmission
from io import BytesIO
from collections import OrderedDict
from tools import jinja_template_loading
from docxtpl import DocxTemplate
from docx import Document
logger = logging.getLogger(f"submissions.{__name__}")
@@ -147,7 +141,6 @@ class InfoWriter(object):
Returns:
dict: merged dictionary
"""
# output = {}
for k, v in info_dict.items():
if v is None:
continue
@@ -163,8 +156,6 @@ class InfoWriter(object):
if len(dicto) > 0:
# output[k] = dicto
yield k, dicto
# logger.debug(f"Reconciled info: {pformat(output)}")
# return output
def write_info(self) -> Workbook:
"""
@@ -217,7 +208,6 @@ class ReagentWriter(object):
if isinstance(extraction_kit, str):
kit_type = KitType.query(name=extraction_kit)
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) -> Generator[dict, None, None]:
@@ -231,7 +221,6 @@ class ReagentWriter(object):
Returns:
List[dict]: merged dictionary
"""
# output = []
for reagent in reagent_list:
try:
mp_info = reagent_map[reagent['role']]
@@ -246,9 +235,7 @@ class ReagentWriter(object):
dicto = v
placeholder[k] = dicto
placeholder['sheet'] = mp_info['sheet']
# output.append(placeholder)
yield placeholder
# return output
def write_reagents(self) -> Workbook:
"""
@@ -285,7 +272,6 @@ class SampleWriter(object):
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)
# NOTE: exclude any samples without a submission rank.
samples = [item for item in self.reconcile_map(sample_list) if item['submission_rank'] > 0]
self.samples = sorted(samples, key=lambda k: k['submission_rank'])
@@ -300,7 +286,6 @@ class SampleWriter(object):
Returns:
List[dict]: List of merged dictionaries
"""
# output = []
multiples = ['row', 'column', 'assoc_id', 'submission_rank']
for sample in sample_list:
# logger.debug(f"Writing sample: {sample}")
@@ -311,7 +296,6 @@ class SampleWriter(object):
continue
new[k] = v
yield new
# return sorted(output, key=lambda k: k['submission_rank'])
def write_samples(self) -> Workbook:
"""
@@ -325,6 +309,11 @@ class SampleWriter(object):
for sample in self.samples:
row = self.sample_map['start_row'] + (sample['submission_rank'] - 1)
for k, v in sample.items():
if isinstance(v, dict):
try:
v = v['value']
except KeyError:
logger.error(f"Cant convert {v} to single string.")
try:
column = columns[k]
except KeyError:
@@ -363,7 +352,6 @@ class EquipmentWriter(object):
Returns:
List[dict]: List of merged dictionaries
"""
# output = []
if equipment_list is None:
return
for ii, equipment in enumerate(equipment_list, start=1):
@@ -388,10 +376,7 @@ class EquipmentWriter(object):
placeholder['sheet'] = mp_info['sheet']
except KeyError:
placeholder['sheet'] = "Equipment"
# logger.debug(f"Final output of {equipment['role']} : {placeholder}")
yield placeholder
# output.append(placeholder)
# return output
def write_equipment(self) -> Workbook:
"""
@@ -452,19 +437,19 @@ class TipWriter(object):
Returns:
List[dict]: List of merged dictionaries
"""
# output = []
if tips_list is None:
return
for ii, tips in enumerate(tips_list, start=1):
mp_info = tips_map[tips['role']]
# mp_info = tips_map[tips['role']]
mp_info = tips_map[tips.role]
# logger.debug(f"{tips['role']} map: {mp_info}")
placeholder = copy(tips)
placeholder = {}
if mp_info == {}:
for jj, (k, v) in enumerate(tips.items(), start=1):
for jj, (k, v) in enumerate(tips.__dict__.items(), start=1):
dicto = dict(value=v, row=ii, column=jj)
placeholder[k] = dicto
else:
for jj, (k, v) in enumerate(tips.items(), start=1):
for jj, (k, v) in enumerate(tips.__dict__.items(), start=1):
try:
dicto = dict(value=v, row=mp_info[k]['row'], column=mp_info[k]['column'])
except KeyError as e:
@@ -477,8 +462,6 @@ class TipWriter(object):
placeholder['sheet'] = "Tips"
# logger.debug(f"Final output of {tips['role']} : {placeholder}")
yield placeholder
# output.append(placeholder)
# return output
def write_tips(self) -> Workbook:
"""
@@ -507,72 +490,3 @@ class TipWriter(object):
logger.error(f"Couldn't write to {tips['sheet']}, row: {v['row']}, column: {v['column']}")
logger.error(e)
return self.xl
class DocxWriter(object):
"""
Object to render
"""
def __init__(self, base_dict: dict):
"""
Args:
base_dict (dict): dictionary of info to be written to template.
"""
logger.debug(f"Incoming base dict: {pformat(base_dict)}")
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"
path = Path(env.loader.__getattribute__("searchpath")[0])
main_template = path.joinpath("basicsubmission_document.docx")
subdocument = path.joinpath(temp_name)
if subdocument.exists():
main_template = self.create_merged_template(main_template, subdocument)
self.template = DocxTemplate(main_template)
base_dict['platemap'] = [item for item in self.create_plate_map(base_dict['samples'], rows=8, columns=12)]
# logger.debug(pformat(base_dict['platemap']))
try:
base_dict['excluded'] += ["platemap"]
except KeyError:
base_dict['excluded'] = ["platemap"]
base_dict = self.sub_obj.custom_docx_writer(base_dict, tpl_obj=self.template)
# logger.debug(f"Base dict: {pformat(base_dict)}")
self.template.render({"sub": base_dict})
@classmethod
def create_plate_map(self, sample_list: List[dict], rows: int = 0, columns: int = 0) -> List[list]:
sample_list = sorted(sample_list, key=itemgetter('column', 'row'))
# NOTE if rows or samples is default, set to maximum value in sample list
if rows == 0:
rows = max([sample['row'] for sample in sample_list])
if columns == 0:
columns = max([sample['column'] for sample in sample_list])
for row in range(0, rows):
# NOTE: Create a list with length equal to columns length, padding with '' where necessary
contents = [next((item['submitter_id'] for item in sample_list if item['row'] == row + 1 and
item['column'] == column + 1), '') for column in range(0, columns)]
yield contents
def create_merged_template(self, *args) -> BytesIO:
"""
Appends submission specific information
Returns:
BytesIO: Merged docx template
"""
merged_document = Document()
output = BytesIO()
for index, file in enumerate(args):
sub_doc = Document(file)
# Don't add a page break if you've reached the last file.
# if index < len(args) - 1:
# sub_doc.add_page_break()
for element in sub_doc.element.body:
merged_document.element.body.append(element)
merged_document.save(output)
return output
def save(self, filename: Path | str):
if isinstance(filename, str):
filename = Path(filename)
self.template.save(filename)