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Mid change in details templates

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This commit is contained in:
lwark
2024-06-20 07:46:46 -05:00
parent 12e552800a
commit 337112a27d
20 changed files with 575 additions and 300 deletions
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67
src/submissions/backend/excel/writer.py
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@@ -1,14 +1,18 @@
import logging
from copy import copy
from pathlib import Path
# from pathlib import Path
from pprint import pformat
from typing import List
from jinja2 import TemplateNotFound
from openpyxl import load_workbook, Workbook
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
logger = logging.getLogger(f"submissions.{__name__}")
@@ -31,7 +35,8 @@ class SheetWriter(object):
case 'submission_type':
self.sub[k] = v['value']
self.submission_type = SubmissionType.query(name=v['value'])
self.sub_object = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
self.sub_object = BasicSubmission.find_polymorphic_subclass(
polymorphic_identity=self.submission_type)
case _:
if isinstance(v, dict):
self.sub[k] = v['value']
@@ -62,7 +67,7 @@ class SheetWriter(object):
def write_info(self):
"""
Calls info writer
"""
"""
disallowed = ['filepath', 'reagents', 'samples', 'equipment', 'controls']
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)
@@ -71,7 +76,7 @@ class SheetWriter(object):
def write_reagents(self):
"""
Calls reagent writer
"""
"""
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)
@@ -80,7 +85,7 @@ class SheetWriter(object):
def write_samples(self):
"""
Calls sample writer
"""
"""
sample_list = self.sub['samples']
writer = SampleWriter(xl=self.xl, submission_type=self.submission_type, sample_list=sample_list)
self.xl = writer.write_samples()
@@ -88,7 +93,7 @@ class SheetWriter(object):
def write_equipment(self):
"""
Calls equipment writer
"""
"""
equipment_list = self.sub['equipment']
writer = EquipmentWriter(xl=self.xl, submission_type=self.submission_type, equipment_list=equipment_list)
self.xl = writer.write_equipment()
@@ -96,7 +101,7 @@ class SheetWriter(object):
def write_tips(self):
"""
Calls tip writer
"""
"""
tips_list = self.sub['tips']
writer = TipWriter(xl=self.xl, submission_type=self.submission_type, tips_list=tips_list)
self.xl = writer.write_tips()
@@ -106,7 +111,9 @@ class InfoWriter(object):
"""
object to write general submission info into excel file
"""
def __init__(self, xl: Workbook, submission_type: SubmissionType | str, info_dict: dict, sub_object:BasicSubmission|None=None):
def __init__(self, xl: Workbook, submission_type: SubmissionType | str, info_dict: dict,
sub_object: BasicSubmission | None = None):
logger.debug(f"Info_dict coming into InfoWriter: {pformat(info_dict)}")
if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type)
@@ -129,7 +136,7 @@ class InfoWriter(object):
Returns:
dict: merged dictionary
"""
"""
output = {}
for k, v in info_dict.items():
if v is None:
@@ -152,7 +159,7 @@ class InfoWriter(object):
Returns:
Workbook: workbook with info written.
"""
"""
for k, v in self.info.items():
# NOTE: merge all comments to fit in single cell.
if k == "comment" and isinstance(v['value'], list):
@@ -174,6 +181,7 @@ class ReagentWriter(object):
"""
object to write reagent data into excel file
"""
def __init__(self, xl: Workbook, submission_type: SubmissionType | str, extraction_kit: KitType | str,
reagent_list: list):
self.xl = xl
@@ -184,7 +192,7 @@ class ReagentWriter(object):
reagent_map = kit_type.construct_xl_map_for_use(submission_type)
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) -> List[dict]:
"""
Merge reagents with their locations
@@ -194,7 +202,7 @@ class ReagentWriter(object):
Returns:
List[dict]: merged dictionary
"""
"""
output = []
for reagent in reagent_list:
try:
@@ -219,14 +227,14 @@ class ReagentWriter(object):
Returns:
Workbook: Workbook with reagents written
"""
"""
for reagent in self.reagents:
sheet = self.xl[reagent['sheet']]
for k, v in reagent.items():
if not isinstance(v, dict):
continue
# logger.debug(
# f"Writing {reagent['type']} {k} to {reagent['sheet']}, row: {v['row']}, column: {v['column']}")
# f"Writing {reagent['type']} {k} to {reagent['sheet']}, row: {v['row']}, column: {v['column']}")
sheet.cell(row=v['row'], column=v['column'], value=v['value'])
return self.xl
@@ -235,6 +243,7 @@ class SampleWriter(object):
"""
object to write sample data into excel file
"""
def __init__(self, xl: Workbook, submission_type: SubmissionType | str, sample_list: list):
if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type)
@@ -252,7 +261,7 @@ class SampleWriter(object):
Returns:
List[dict]: List of merged dictionaries
"""
"""
output = []
multiples = ['row', 'column', 'assoc_id', 'submission_rank']
for sample in sample_list:
@@ -272,7 +281,7 @@ class SampleWriter(object):
Returns:
Workbook: Workbook with samples written
"""
"""
sheet = self.xl[self.sample_map['sheet']]
columns = self.sample_map['sample_columns']
for sample in self.samples:
@@ -290,6 +299,7 @@ class EquipmentWriter(object):
"""
object to write equipment data into excel file
"""
def __init__(self, xl: Workbook, submission_type: SubmissionType | str, equipment_list: list):
if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type)
@@ -308,7 +318,7 @@ class EquipmentWriter(object):
Returns:
List[dict]: List of merged dictionaries
"""
"""
output = []
if equipment_list is None:
return output
@@ -344,7 +354,7 @@ class EquipmentWriter(object):
Returns:
Workbook: Workbook with equipment written
"""
"""
for equipment in self.equipment:
try:
sheet = self.xl[equipment['sheet']]
@@ -371,6 +381,7 @@ class TipWriter(object):
"""
object to write tips data into excel file
"""
def __init__(self, xl: Workbook, submission_type: SubmissionType | str, tips_list: list):
if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type)
@@ -389,7 +400,7 @@ class TipWriter(object):
Returns:
List[dict]: List of merged dictionaries
"""
"""
output = []
if tips_list is None:
return output
@@ -423,7 +434,7 @@ class TipWriter(object):
Returns:
Workbook: Workbook with tips written
"""
"""
for tips in self.tips:
try:
sheet = self.xl[tips['sheet']]
@@ -444,3 +455,19 @@ 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):
def __init__(self, base_dict: dict):
env = jinja_template_loading()
temp_name = f"{base_dict['submission_type'].replace(' ', '').lower()}_document.docx"
path = Path(env.loader.__getattribute__("searchpath")[0]).joinpath(temp_name)
template = DocxTemplate(path)
try:
template.render(base_dict)
except FileNotFoundError:
template = DocxTemplate(
Path(env.loader.__getattribute__("searchpath")[0]).joinpath("basicsubmission_document.docx"))
template.render({"sub": base_dict})
template.save("test.docx")