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New docx templates

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This commit is contained in:
lwark
2024-06-20 13:31:36 -05:00
parent 337112a27d
commit 384bd567ae
12 changed files with 175 additions and 80 deletions
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30
src/submissions/backend/db/models/submissions.py
View File

@@ -4,6 +4,7 @@ Models for the main submission and sample types.
from __future__ import annotations
import sys
from copy import deepcopy
from getpass import getuser
import logging, uuid, tempfile, re, yaml, base64
from zipfile import ZipFile
@@ -728,6 +729,11 @@ class BasicSubmission(BaseClass):
logger.info(f"Hello from {cls.__mapper_args__['polymorphic_identity']} autofill")
return input_excel
@classmethod
def custom_docx_writer(cls, input_dict):
return input_dict
@classmethod
def enforce_name(cls, instr: str, data: dict | None = {}) -> str:
"""
@@ -1439,7 +1445,7 @@ class Wastewater(BasicSubmission):
dummy_samples = []
for item in input_dict['samples']:
# logger.debug(f"Sample dict: {item}")
thing = item
thing = deepcopy(item)
try:
thing['row'] = thing['source_row']
thing['column'] = thing['source_column']
@@ -1486,6 +1492,28 @@ class Wastewater(BasicSubmission):
self.update_subsampassoc(sample=sample, input_dict=sample_dict)
# self.report.add_result(Result(msg=f"We added PCR info to {sub.rsl_plate_num}.", status='Information'))
@classmethod
def custom_docx_writer(cls, input_dict):
from backend.excel.writer import DocxWriter
input_dict = super().custom_docx_writer(input_dict)
well_24 = []
samples_copy = deepcopy(input_dict['samples'])
for sample in sorted(samples_copy, key=itemgetter('column', 'row')):
# for sample in input_dict['samples']:
try:
row = sample['source_row']
except KeyError:
continue
try:
column = sample['source_column']
except KeyError:
continue
copy = dict(submitter_id=sample['submitter_id'], row=row, column=column)
well_24.append(copy)
input_dict['origin_plate'] = DocxWriter.create_plate_map(sample_list=well_24, rows=4, columns=6)
return input_dict
class WastewaterArtic(BasicSubmission):
"""

73
src/submissions/backend/excel/writer.py
View File

@@ -1,10 +1,11 @@
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 collections import OrderedDict
from jinja2 import TemplateNotFound
from openpyxl import load_workbook, Workbook
from backend.db.models import SubmissionType, KitType, BasicSubmission
@@ -13,6 +14,7 @@ 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__}")
@@ -460,14 +462,65 @@ class TipWriter(object):
class DocxWriter(object):
def __init__(self, base_dict: 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()}_document.docx"
path = Path(env.loader.__getattribute__("searchpath")[0]).joinpath(temp_name)
template = DocxTemplate(path)
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'] = self.create_plate_map(base_dict['samples'], rows=8, columns=12)
# logger.debug(pformat(base_dict['plate_map']))
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")
base_dict['excluded'] += ["platemap"]
except KeyError:
base_dict['excluded'] = ["platemap"]
base_dict = self.sub_obj.custom_docx_writer(base_dict)
# 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'))
if rows == 0:
rows = max([sample['row'] for sample in sample_list])
if columns == 0:
columns = max([sample['column'] for sample in sample_list])
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]
except IndexError:
continue
contents[column] = ooi['submitter_id']
# contents = [sample['submitter_id'] for sample in sample_list if sample['row'] == row + 1]
# contents = [f"{sample['row']},{sample['column']}" for sample in sample_list if sample['row'] == row + 1]
if len(contents) < columns:
contents += [''] * (columns - len(contents))
if not contents:
contents = [''] * columns
output.append(contents)
return output
def create_merged_template(self, *args):
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)

26
src/submissions/backend/validators/pydant.py
View File

@@ -327,17 +327,17 @@ class PydEquipment(BaseModel, extra='ignore'):
process = Process.query(name=self.processes[0])
if process is None:
logger.error(f"Found unknown process: {process}.")
from frontend.widgets.pop_ups import QuestionAsker
dlg = QuestionAsker(title="Add Process?",
message=f"Unable to find {self.processes[0]} in the database.\nWould you like to add it?")
if dlg.exec():
kit = submission.extraction_kit
submission_type = submission.submission_type
process = Process(name=self.processes[0])
process.kit_types.append(kit)
process.submission_types.append(submission_type)
process.equipment.append(equipment)
process.save()
# from frontend.widgets.pop_ups import QuestionAsker
# dlg = QuestionAsker(title="Add Process?",
# message=f"Unable to find {self.processes[0]} in the database.\nWould you like to add it?")
# if dlg.exec():
# kit = submission.extraction_kit
# submission_type = submission.submission_type
# process = Process(name=self.processes[0])
# process.kit_types.append(kit)
# process.submission_types.append(submission_type)
# process.equipment.append(equipment)
# process.save()
assoc.process = process
assoc.role = self.role
else:
@@ -727,7 +727,7 @@ class PydSubmission(BaseModel, extra='allow'):
if equip is None:
continue
equip, association = equip.toSQL(submission=instance)
if association is not None:
if association is not None and association not in instance.submission_equipment_associations:
# association.save()
# logger.debug(
# f"Equipment association SQL object to be added to submission: {association.__dict__}")
@@ -738,7 +738,7 @@ class PydSubmission(BaseModel, extra='allow'):
continue
logger.debug(f"Converting tips: {tips} to sql.")
association = tips.to_sql(submission=instance)
if association is not None:
if association is not None and association not in instance.submission_tips_associations:
# association.save()
instance.submission_tips_associations.append(association)
case item if item in instance.jsons():

4
src/submissions/frontend/widgets/equipment_usage.py
View File

@@ -59,7 +59,7 @@ class EquipmentUsage(QDialog):
case _:
pass
logger.debug(f"parsed output of Equsage form: {pformat(output)}")
return [item for item in output if item is not None]
return [item.strip() for item in output if item is not None]
class LabelRow(QWidget):
@@ -165,7 +165,7 @@ class RoleComboBox(QWidget):
try:
return PydEquipment(
name=eq.name,
processes=[self.process.currentText()],
processes=[self.process.currentText().strip()],
role=self.role.name,
asset_number=eq.asset_number,
nickname=eq.nickname,

57
src/submissions/frontend/widgets/submission_details.py
View File

@@ -1,3 +1,5 @@
from PyQt6.QtGui import QPageSize
from PyQt6.QtPrintSupport import QPrinter
from PyQt6.QtWidgets import (QDialog, QPushButton, QVBoxLayout, QMessageBox,
QDialogButtonBox, QTextEdit)
from PyQt6.QtWebEngineWidgets import QWebEngineView
@@ -17,6 +19,8 @@ from pprint import pformat
from html2image import Html2Image
from PIL import Image
from typing import List
from backend.excel.writer import DocxWriter
logger = logging.getLogger(f"submissions.{__name__}")
@@ -90,13 +94,17 @@ class SubmissionDetails(QDialog):
# del self.base_dict['id']
# logger.debug(f"Creating barcode.")
# logger.debug(f"Making platemap...")
self.base_dict['platemap'] = BasicSubmission.make_plate_map(sample_list=submission.hitpick_plate())
self.base_dict, self.template = submission.get_details_template(base_dict=self.base_dict)
template_path = Path(self.template.environment.loader.__getattribute__("searchpath")[0])
with open(template_path.joinpath("css", "styles.css"), "r") as f:
css = f.read()
logger.debug(f"Submission_details: {pformat(self.base_dict)}")
self.html = self.template.render(sub=self.base_dict, signing_permission=is_power_user())
self.html = self.template.render(sub=self.base_dict, signing_permission=is_power_user(), css=css)
self.webview.setHtml(self.html)
# with open("test.html", "w") as f:
# f.write(self.html)
with open("test.html", "w") as f:
f.write(self.html)
self.setWindowTitle(f"Submission Details - {submission.rsl_plate_num}")
@pyqtSlot(str)
@@ -112,31 +120,32 @@ class SubmissionDetails(QDialog):
"""
Renders submission to html, then creates and saves .pdf file to user selected file.
"""
logger.debug(f"Base dict: {pformat(self.base_dict)}")
writer = DocxWriter(base_dict=self.base_dict)
fname = select_save_file(obj=self, default_name=self.base_dict['plate_number'], extension="docx")
image_io = BytesIO()
temp_dir = Path(TemporaryDirectory().name)
hti = Html2Image(output_path=temp_dir, size=(2400, 1500))
temp_file = Path(TemporaryFile(dir=temp_dir, suffix=".png").name)
screenshot = hti.screenshot(self.base_dict['platemap'], save_as=temp_file.name)
export_map = Image.open(screenshot[0])
export_map = export_map.convert('RGB')
writer.save(fname)
# image_io = BytesIO()
# temp_dir = Path(TemporaryDirectory().name)
# hti = Html2Image(output_path=temp_dir, size=(2400, 1500))
# temp_file = Path(TemporaryFile(dir=temp_dir, suffix=".png").name)
# screenshot = hti.screenshot(self.base_dict['platemap'], save_as=temp_file.name)
# export_map = Image.open(screenshot[0])
# export_map = export_map.convert('RGB')
# try:
# export_map.save(image_io, 'JPEG')
# except AttributeError:
# logger.error(f"No plate map found")
# self.base_dict['export_map'] = base64.b64encode(image_io.getvalue()).decode('utf-8')
# del self.base_dict['platemap']
# self.html2 = self.template.render(sub=self.base_dict)
try:
export_map.save(image_io, 'JPEG')
except AttributeError:
logger.error(f"No plate map found")
self.base_dict['export_map'] = base64.b64encode(image_io.getvalue()).decode('utf-8')
del self.base_dict['platemap']
self.html2 = self.template.render(sub=self.base_dict)
try:
html_to_pdf(html=self.html2, output_file=fname)
html_to_pdf(html=self.html, output_file=fname)
except PermissionError as e:
logger.error(f"Error saving pdf: {e}")
msg = QMessageBox()
msg.setText("Permission Error")
msg.setInformativeText(f"Looks like {fname.__str__()} is open.\nPlease close it and try again.")
msg.setWindowTitle("Permission Error")
msg.exec()
# msg = QMessageBox()
# msg.setText("Permission Error")
# msg.setInformativeText(f"Looks like {fname.__str__()} is open.\nPlease close it and try again.")
# msg.setWindowTitle("Permission Error")
# msg.exec()
class SubmissionComment(QDialog):

1
src/submissions/frontend/widgets/submission_widget.py
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@@ -312,6 +312,7 @@ class SubmissionFormWidget(QWidget):
if dlg.exec():
# NOTE: Do not add duplicate reagents.
result = None
else:
self.app.ctx.database_session.rollback()
report.add_result(Result(msg="Overwrite cancelled", status="Information"))

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src/submissions/templates/bacterialculture_subdocument.docx Normal file
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33
src/submissions/templates/basicsubmission_details.html
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@@ -2,38 +2,11 @@
<html>
<head>
{% block head %}
{% if css %}
<style>
/* Tooltip container */
.tooltip {
position: relative;
display: inline-block;
border-bottom: 1px dotted black; /* If you want dots under the hoverable text */
}
/* Tooltip text */
.tooltip .tooltiptext {
visibility: hidden;
width: 120px;
background-color: black;
color: #fff;
text-align: center;
padding: 5px 0;
border-radius: 6px;
/* Position the tooltip text - see examples below! */
position: absolute;
z-index: 1;
bottom: 100%;
left: 50%;
margin-left: -60px;
}
/* Show the tooltip text when you mouse over the tooltip container */
.tooltip:hover .tooltiptext {
visibility: visible;
font-size: large;
}
{{ css }}
</style>
{% endif %}
<title>Submission Details for {{ sub['Plate Number'] }}</title>
<script src="qrc:///qtwebchannel/qwebchannel.js"></script>
{% endblock %}

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src/submissions/templates/basicsubmission_document.docx Normal file
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29
src/submissions/templates/css/styles.css Normal file
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@@ -0,0 +1,29 @@
/* Tooltip container */
.tooltip {
position: relative;
display: inline-block;
border-bottom: 1px dotted black; /* If you want dots under the hoverable text */
}
/* Tooltip text */
.tooltip .tooltiptext {
visibility: hidden;
width: 120px;
background-color: black;
color: #fff;
text-align: center;
padding: 5px 0;
border-radius: 6px;
/* Position the tooltip text - see examples below! */
position: absolute;
z-index: 1;
bottom: 100%;
left: 50%;
margin-left: -60px;
}
/* Show the tooltip text when you mouse over the tooltip container */
.tooltip:hover .tooltiptext {
visibility: visible;
font-size: large;
}

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src/submissions/templates/wastewater_subdocument.docx Normal file
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2
src/submissions/tools.py
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@@ -658,11 +658,13 @@ def html_to_pdf(html, output_file: Path | str):
logger.debug(f"Printing PDF to {output_file}")
document = QWebEngineView()
document.setHtml(html)
# document.show()
printer = QPrinter(QPrinter.PrinterMode.HighResolution)
printer.setOutputFormat(QPrinter.OutputFormat.PdfFormat)
printer.setOutputFileName(output_file.absolute().__str__())
printer.setPageSize(QPageSize(QPageSize.PageSizeId.A4))
document.print(printer)
# document.close()
# HTML(string=html).write_pdf(output_file)
# new_parser = HtmlToDocx()
# docx = new_parser.parse_html_string(html)