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Various bug fixes

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This commit is contained in:
Landon Wark
2024-03-07 14:26:29 -06:00
parent b466cb61d2
commit d0418ebc9e
7 changed files with 80 additions and 37 deletions
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1
TODO.md
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@@ -1,3 +1,4 @@
- [x] Fix cropping of gel image.
- [ ] Create Tips ... *sigh*.
- [x] Create platemap image from html for export to pdf.
- [x] Move plate map maker to submission.

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requirements.txt
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33
src/submissions/backend/db/models/submissions.py
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@@ -9,7 +9,7 @@ from tempfile import TemporaryDirectory
from reportlab.graphics.barcode import createBarcodeImageInMemory
from reportlab.graphics.shapes import Drawing
from reportlab.lib.units import mm
from operator import attrgetter
from operator import attrgetter, itemgetter
from pprint import pformat
from . import Reagent, SubmissionType, KitType, Organization
from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case
@@ -1349,11 +1349,13 @@ class WastewaterArtic(BasicSubmission):
Returns:
dict: Updated sample dictionary
"""
from backend.validators import RSLNamer
input_dict = super().parse_info(input_dict)
df = xl.parse("First Strand List", header=None)
plates = []
for row in [8,9,10]:
plates.append(dict(plate=df.iat[row-1, 2], start_sample=df.iat[row-1, 3]))
plate_name = RSLNamer(df.iat[row-1, 2]).parsed_name
plates.append(dict(plate=plate_name, start_sample=df.iat[row-1, 3]))
input_dict['source_plates'] = plates
return input_dict
@@ -1373,6 +1375,16 @@ class WastewaterArtic(BasicSubmission):
# Because generate_sample_object needs the submitter_id and the artic has the "({origin well})"
# at the end, this has to be done here. No moving to sqlalchemy object :(
input_dict['submitter_id'] = re.sub(r"\s\(.+\)\s?$", "", str(input_dict['submitter_id'])).strip()
try:
input_dict['ww_processing_num'] = input_dict['sample_name_(lims)']
del input_dict['sample_name_(lims)']
except KeyError:
logger.error(f"Unable to set ww_processing_num for sample {input_dict['submitter_id']}")
try:
input_dict['ww_full_sample_id'] = input_dict['sample_name_(ww)']
del input_dict['sample_name_(ww)']
except KeyError:
logger.error(f"Unable to set ww_processing_num for sample {input_dict['submitter_id']}")
if "ENC" in input_dict['submitter_id']:
input_dict['submitter_id'] = cls.en_adapter(input_str=input_dict['submitter_id'])
return input_dict
@@ -1642,6 +1654,7 @@ class WastewaterArtic(BasicSubmission):
output.append(dicto)
# else:
# output = super().adjust_to_dict_samples(backup=False)
return output
def custom_context_events(self) -> dict:
@@ -1751,7 +1764,7 @@ class BasicSample(BaseClass):
sample['Submitter ID'] = self.submitter_id
sample['Sample Type'] = self.sample_type
if full_data:
sample['submissions'] = [item.to_sub_dict() for item in self.sample_submission_associations]
sample['submissions'] = sorted([item.to_sub_dict() for item in self.sample_submission_associations], key=itemgetter('submitted_date'))
return sample
def set_attribute(self, name:str, value):
@@ -1857,19 +1870,6 @@ class BasicSample(BaseClass):
template = env.get_template("basicsample_details.html")
return base_dict, template
def show_details(self, obj):
"""
Creates Widget for showing sample details.
Args:
obj (_type_): parent widget
"""
logger.debug("Hello from details")
from frontend.widgets.sample_details import SampleDetails
dlg = SampleDetails(parent=obj, samp=self)
if dlg.exec():
pass
@classmethod
@setup_lookup
def query(cls,
@@ -2126,6 +2126,7 @@ class SubmissionSampleAssociation(BaseClass):
sample['Well'] = None
sample['Plate Name'] = self.submission.rsl_plate_num
sample['Positive'] = False
sample['submitted_date'] = self.submission.submitted_date
return sample
def to_hitpick(self) -> dict|None:

8
src/submissions/frontend/widgets/gel_checker.py
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@@ -44,9 +44,11 @@ class GelBox(QDialog):
pg.setConfigOptions(antialias=True)
# creating image view object
self.imv = pg.ImageView()
img = np.array(Image.open(self.img_path).rotate(-90).transpose(Image.FLIP_LEFT_RIGHT))
self.imv.setImage(img, scale=None)#, xvals=np.linspace(1., 3., data.shape[0]))
# Create image.
# For some reason, ImageView wants to flip the image, so we have to rotate and flip the array first.
# Using the Image.rotate function results in cropped image.
img = np.flip(np.rot90(np.array(Image.open(self.img_path)),1),0)
self.imv.setImage(img)
layout = QGridLayout()
layout.addWidget(QLabel("DNA Core Submission Number"),0,1)
self.core_number = QLineEdit()

60
src/submissions/frontend/widgets/submission_details.py
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@@ -37,21 +37,21 @@ class SubmissionDetails(QDialog):
# create scrollable interior
interior = QScrollArea()
interior.setParent(self)
self.base_dict = sub.to_dict(full_data=True)
logger.debug(f"Submission details data:\n{pformat({k:v for k,v in self.base_dict.items() if k != 'samples'})}")
# don't want id
del self.base_dict['id']
logger.debug(f"Creating barcode.")
if not check_if_app():
self.base_dict['barcode'] = base64.b64encode(sub.make_plate_barcode(width=120, height=30)).decode('utf-8')
logger.debug(f"Making platemap...")
self.base_dict['platemap'] = sub.make_plate_map()
self.base_dict, self.template = sub.get_details_template(base_dict=self.base_dict)
self.html = self.template.render(sub=self.base_dict)
# self.base_dict = sub.to_dict(full_data=True)
# logger.debug(f"Submission details data:\n{pformat({k:v for k,v in self.base_dict.items() if k != 'samples'})}")
# # don't want id
# del self.base_dict['id']
# logger.debug(f"Creating barcode.")
# if not check_if_app():
# self.base_dict['barcode'] = base64.b64encode(sub.make_plate_barcode(width=120, height=30)).decode('utf-8')
# logger.debug(f"Making platemap...")
# self.base_dict['platemap'] = sub.make_plate_map()
# self.base_dict, self.template = sub.get_details_template(base_dict=self.base_dict)
# self.html = self.template.render(sub=self.base_dict)
self.webview = QWebEngineView(parent=self)
self.webview.setMinimumSize(900, 500)
self.webview.setMaximumSize(900, 500)
self.webview.setHtml(self.html)
# self.webview.setHtml(self.html)
self.layout = QVBoxLayout()
interior.resize(900, 500)
interior.setWidget(self.webview)
@@ -64,18 +64,46 @@ class SubmissionDetails(QDialog):
# setup channel
self.channel = QWebChannel()
self.channel.registerObject('backend', self)
self.submission_details(submission=sub)
self.webview.page().setWebChannel(self.channel)
@pyqtSlot(str)
def sample_details(self, sample):
# print(f"{string} is in row {row}, column {column}")
# self.webview.setHtml(f"<html><body><br><br>{sample}</body></html>")
def sample_details(self, sample:str):
"""
Changes details view to summary of Sample
Args:
sample (str): Submitter Id of the sample.
"""
sample = BasicSample.query(submitter_id=sample)
base_dict = sample.to_sub_dict(full_data=True)
base_dict, template = sample.get_details_template(base_dict=base_dict)
html = template.render(sample=base_dict)
self.webview.setHtml(html)
# sample.show_details(obj=self)
@pyqtSlot(str)
def submission_details(self, submission:str|BasicSubmission):
"""
Sets details view to summary of Submission.
Args:
submission (str | BasicSubmission): Submission of interest.
"""
logger.debug(f"Details for: {submission}")
if isinstance(submission, str):
submission = BasicSubmission.query(rsl_number=submission)
self.base_dict = submission.to_dict(full_data=True)
logger.debug(f"Submission details data:\n{pformat({k:v for k,v in self.base_dict.items() if k != 'samples'})}")
# don't want id
del self.base_dict['id']
logger.debug(f"Creating barcode.")
if not check_if_app():
self.base_dict['barcode'] = base64.b64encode(submission.make_plate_barcode(width=120, height=30)).decode('utf-8')
logger.debug(f"Making platemap...")
self.base_dict['platemap'] = submission.make_plate_map()
self.base_dict, self.template = submission.get_details_template(base_dict=self.base_dict)
self.html = self.template.render(sub=self.base_dict)
self.webview.setHtml(self.html)
def export(self):
"""

2
src/submissions/frontend/widgets/submission_widget.py
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@@ -395,7 +395,7 @@ class SubmissionFormWidget(QWidget):
def __init__(self, parent: QWidget, **kwargs) -> None:
super().__init__(parent)
self.ignore = ['filepath', 'samples', 'reagents', 'csv', 'ctx', 'comment', 'equipment']
self.ignore = ['filepath', 'samples', 'reagents', 'csv', 'ctx', 'comment', 'equipment', 'source_plates']
self.recover = ['filepath', 'samples', 'csv', 'comment', 'equipment']
layout = QVBoxLayout()
for k, v in kwargs.items():

13
src/submissions/templates/basicsample_details.html
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@@ -46,9 +46,20 @@
{% endfor %}</p>
{% if sample['submissions'] %}<h2>Submissions:</h2>
{% for submission in sample['submissions'] %}
<p>{{ submission['Plate Name'] }}: {{ submission['Well'] }}</p>
<p id="{{ submission['Plate Name'] }}"><b>{{ submission['Plate Name'] }}:</b> {{ submission['Well'] }}</p>
{% endfor %}
{% endif %}
{% endblock %}
</body>
<script>
var backend;
new QWebChannel(qt.webChannelTransport, function (channel) {
backend = channel.objects.backend;
});
{% for submission in sample['submissions'] %}
document.getElementById("{{ submission['Plate Name'] }}").addEventListener("dblclick", function(){
backend.submission_details("{{ submission['Plate Name'] }}");
});
{% endfor %}
</script>
</html>