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Various bugfixes, new template sub-docs

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This commit is contained in:
lwark
2024-06-21 12:43:00 -05:00
parent 384bd567ae
commit be142e0f2f
8 changed files with 38 additions and 17 deletions
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4
src/submissions/backend/db/models/kits.py
View File

@@ -1499,7 +1499,7 @@ class Process(BaseClass):
@setup_lookup
def query(cls,
name: str | None = None,
id: int = 1,
id: int | None = None,
limit: int = 0) -> Process | List[Process]:
"""
Lookup Processes
@@ -1514,7 +1514,7 @@ class Process(BaseClass):
query = cls.__database_session__.query(cls)
match name:
case str():
# logger.debug(f"Lookup Process with name str {name}")
logger.debug(f"Lookup Process with name str {name}")
query = query.filter(cls.name == name)
limit = 1
case _:

28
src/submissions/backend/db/models/submissions.py
View File

@@ -31,6 +31,8 @@ from dateutil.parser import parse
from pathlib import Path
from jinja2.exceptions import TemplateNotFound
from jinja2 import Template
from docxtpl import InlineImage
from io import BytesIO
logger = logging.getLogger(f"submissions.{__name__}")
@@ -730,7 +732,7 @@ class BasicSubmission(BaseClass):
return input_excel
@classmethod
def custom_docx_writer(cls, input_dict):
def custom_docx_writer(cls, input_dict:dict, tpl_obj=None):
return input_dict
@@ -1493,7 +1495,7 @@ class Wastewater(BasicSubmission):
# 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):
def custom_docx_writer(cls, input_dict:dict, tpl_obj=None):
from backend.excel.writer import DocxWriter
input_dict = super().custom_docx_writer(input_dict)
well_24 = []
@@ -1551,7 +1553,7 @@ class WastewaterArtic(BasicSubmission):
if report:
return output
output['gel_info'] = self.gel_info
output['gel_image'] = self.gel_image
output['gel_image_path'] = self.gel_image
output['dna_core_submission_number'] = self.dna_core_submission_number
output['source_plates'] = self.source_plates
output['artic_date'] = self.artic_date or self.submitted_date
@@ -1856,7 +1858,7 @@ class WastewaterArtic(BasicSubmission):
"""
base_dict, template = super().get_details_template(base_dict=base_dict)
base_dict['excluded'] += ['gel_info', 'gel_image', 'headers', "dna_core_submission_number", "source_plates",
"gel_controls"]
"gel_controls, gel_image_path"]
base_dict['DNA Core ID'] = base_dict['dna_core_submission_number']
# check = 'gel_info' in base_dict.keys() and base_dict['gel_info'] is not None
if check_key_or_attr(key='gel_info', interest=base_dict, check_none=True):
@@ -1865,9 +1867,9 @@ class WastewaterArtic(BasicSubmission):
base_dict['headers'] += headers
# logger.debug(f"Gel info: {pformat(base_dict['headers'])}")
# check = 'gel_image' in base_dict.keys() and base_dict['gel_image'] is not None
if check_key_or_attr(key='gel_image', interest=base_dict, check_none=True):
if check_key_or_attr(key='gel_image_path', interest=base_dict, check_none=True):
with ZipFile(cls.__directory_path__.joinpath("submission_imgs.zip")) as zipped:
base_dict['gel_image'] = base64.b64encode(zipped.read(base_dict['gel_image'])).decode('utf-8')
base_dict['gel_image'] = base64.b64encode(zipped.read(base_dict['gel_image_path'])).decode('utf-8')
return base_dict, template
# def adjust_to_dict_samples(self, backup: bool = False) -> List[dict]:
@@ -1935,6 +1937,20 @@ class WastewaterArtic(BasicSubmission):
zipf.write(img_path, self.gel_image)
self.save()
@classmethod
def custom_docx_writer(cls, input_dict:dict, tpl_obj=None):
input_dict = super().custom_docx_writer(input_dict)
if check_key_or_attr(key='gel_image_path', interest=input_dict, check_none=True):
with ZipFile(cls.__directory_path__.joinpath("submission_imgs.zip")) as zipped:
img = zipped.read(input_dict['gel_image_path'])
with tempfile.TemporaryFile(mode="wb", suffix=".jpg", delete=False) as tmp:
tmp.write(img)
logger.debug(f"Tempfile: {tmp.name}")
img = InlineImage(tpl_obj, image_descriptor=tmp.name)#, width=5.5)#, height=400)
input_dict['gel_image'] = img
return input_dict
# Sample Classes

2
src/submissions/backend/excel/writer.py
View File

@@ -477,7 +477,7 @@ class DocxWriter(object):
base_dict['excluded'] += ["platemap"]
except KeyError:
base_dict['excluded'] = ["platemap"]
base_dict = self.sub_obj.custom_docx_writer(base_dict)
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})

5
src/submissions/backend/validators/pydant.py
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@@ -304,7 +304,10 @@ class PydEquipment(BaseModel, extra='ignore'):
value = ['']
if len(value) == 0:
value = ['']
value = [item.strip() for item in value]
try:
value = [item.strip() for item in value]
except AttributeError:
pass
return value
def toSQL(self, submission: BasicSubmission | str = None) -> Tuple[Equipment, SubmissionEquipmentAssociation]:

9
src/submissions/frontend/widgets/equipment_usage.py
View File

@@ -59,7 +59,10 @@ class EquipmentUsage(QDialog):
case _:
pass
logger.debug(f"parsed output of Equsage form: {pformat(output)}")
return [item.strip() for item in output if item is not None]
try:
return [item.strip() for item in output if item is not None]
except AttributeError:
return [item for item in output if item is not None]
class LabelRow(QWidget):
@@ -131,8 +134,8 @@ class RoleComboBox(QWidget):
"""
Changes what tips are available when process is changed
"""
process = self.process.currentText()
logger.debug(f"Checking process: {process}")
process = self.process.currentText().strip()
logger.debug(f"Checking process: {process} for equipment {self.role.name}")
process = Process.query(name=process)
if process.tip_roles:
for iii, tip_role in enumerate(process.tip_roles):

2
src/submissions/frontend/widgets/gel_checker.py
View File

@@ -54,9 +54,11 @@ class GelBox(QDialog):
layout = QGridLayout()
layout.addWidget(QLabel("DNA Core Submission Number"),0,1)
self.core_number = QLineEdit()
self.core_number.setText(self.submission.dna_core_submission_number)
layout.addWidget(self.core_number, 0,2)
layout.addWidget(QLabel("Gel Barcode"),0,3)
self.gel_barcode = QLineEdit()
self.gel_barcode.setText(self.submission.gel_barcode)
layout.addWidget(self.gel_barcode, 0, 4)
# setting this layout to the widget
# plot window goes on right side, spanning 3 rows

5
src/submissions/frontend/widgets/submission_details.py
View File

@@ -10,7 +10,6 @@ from backend.db.models import BasicSubmission, BasicSample
from tools import is_power_user, html_to_pdf
from .functions import select_save_file
from io import BytesIO
from tempfile import TemporaryFile, TemporaryDirectory
from pathlib import Path
import logging, base64
from getpass import getuser
@@ -43,7 +42,7 @@ class SubmissionDetails(QDialog):
self.layout = QVBoxLayout()
self.setFixedSize(900, 500)
# NOTE: button to export a pdf version
btn = QPushButton("Export PDF")
btn = QPushButton("Export DOCX")
btn.setFixedWidth(875)
btn.clicked.connect(self.export)
self.layout.addWidget(btn)
@@ -103,8 +102,6 @@ class SubmissionDetails(QDialog):
logger.debug(f"Submission_details: {pformat(self.base_dict)}")
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)
self.setWindowTitle(f"Submission Details - {submission.rsl_plate_num}")
@pyqtSlot(str)