Start of custom context menu for procedure creation
This commit is contained in:
lwark
@@ -1297,7 +1297,7 @@ class Run(BaseClass, LogMixin):
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submission_rank = self.get_submission_rank_of_sample(sample=sample)
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if submission_rank != 0:
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row, column = plate_dict[submission_rank]
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ranked_samples.append(dict(sample_id=sample.sample_id, row=row, column=column, submission_rank=submission_rank, background_color="#6ffe1d"))
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ranked_samples.append(dict(well_id=sample.sample_id, sample_id=sample.sample_id, row=row, column=column, submission_rank=submission_rank, background_color="#6ffe1d"))
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else:
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unranked_samples.append(sample)
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possible_ranks = (item for item in list(plate_dict.keys()) if item not in [sample['submission_rank'] for sample in ranked_samples])
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@@ -1310,21 +1310,18 @@ class Run(BaseClass, LogMixin):
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continue
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row, column = plate_dict[submission_rank]
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ranked_samples.append(
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dict(sample_id=sample.sample_id, row=row, column=column, submission_rank=submission_rank,
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dict(well_id=sample.sample_id, sample_id=sample.sample_id, row=row, column=column, submission_rank=submission_rank,
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background_color="#6ffe1d"))
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padded_list = []
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for iii in range(1, proceduretype.total_wells+1):
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sample = next((item for item in ranked_samples if item['submission_rank']==iii),
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dict(sample_id="", row=0, column=0, submission_rank=iii)
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dict(well_id=f"blank_{iii}", sample_id="", row=0, column=0, submission_rank=iii, background_color="#ffffff")
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)
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padded_list.append(sample)
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logger.debug(f"Final padded list:\n{pformat(list(sorted(padded_list, key=itemgetter('submission_rank'))))}")
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# logger.debug(f"Final padded list:\n{pformat(list(sorted(padded_list, key=itemgetter('submission_rank'))))}")
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return list(sorted(padded_list, key=itemgetter('submission_rank')))
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class SampleType(BaseClass):
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id = Column(INTEGER, primary_key=True) #: primary key
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name = Column(String(64), nullable=False, unique=True) #: identification from submitter
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@@ -1397,53 +1397,17 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
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self.reagentrole = {}
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self.possible_kits.insert(0, self.possible_kits.pop(self.possible_kits.index(kittype)))
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def shuffle_samples(self, source_row: int, source_column: int, destination_row: int, destination_column=int):
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logger.debug(f"Attempting sample shuffle.")
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try:
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source_sample = next(
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(sample for sample in self.samples if sample.row == source_row and sample.column == source_column))
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except StopIteration:
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raise StopIteration("Couldn't find proper sample.")
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logger.debug(f"Source Well: {source_row}, {source_column}")
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logger.debug(f"Destination Well: {destination_row}, {destination_column}")
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updateable_samples = []
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if source_row > destination_row and source_column >= destination_column:
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logger.debug(f"Sample was moved ahead.")
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movement = "pos"
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for sample in self.samples:
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if sample.row >= destination_row and sample.column >= destination_column:
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if sample.row <= source_row and sample.column <= source_column:
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updateable_samples.append(sample)
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elif source_row < destination_row and source_column <= destination_column:
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logger.debug(f"Sample was moved back.")
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movement = "neg"
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for sample in self.samples:
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if sample.row <= destination_row and sample.column <= destination_column:
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if sample.row >= source_row and sample.column >= source_column:
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updateable_samples.append(sample)
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else:
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logger.debug(f"Don't know what happened.")
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logger.debug(f"Samples to be updated: {pformat(updateable_samples)}")
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for sample in updateable_samples:
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if sample.row == source_row and sample.column == source_column:
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sample.row = destination_row
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sample.column = destination_column
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else:
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match movement:
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case "pos":
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if sample.row + 1 > 8:
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sample.column += 1
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sample.row = 1
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else:
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sample.row += 1
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case "neg":
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if sample.row - 1 <= 0:
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sample.column -= 1
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sample.row = 8
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else:
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sample.row -= 1
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def update_samples(self, sample_list: List[dict]):
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logger.debug(f"Incoming sample_list:\n{pformat(sample_list)}")
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for sample_dict in sample_list:
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try:
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sample = next((item for item in self.samples if item.sample_id.upper()==sample_dict['sample_id'].upper()))
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except StopIteration:
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continue
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row, column = self.proceduretype.ranked_plate[sample_dict['index']]
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sample.row = row
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sample.column = column
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logger.debug(f"Updated samples:\n{pformat(self.samples)}")
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class PydClientSubmission(PydBaseClass):
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117
src/submissions/frontend/widgets/procedure_creation.py
Normal file
117
src/submissions/frontend/widgets/procedure_creation.py
Normal file
@@ -0,0 +1,117 @@
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"""
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"""
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from __future__ import annotations
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import sys, logging
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from pathlib import Path
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from pprint import pformat
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from PyQt6.QtCore import pyqtSlot, Qt
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from PyQt6.QtGui import QContextMenuEvent, QAction
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from PyQt6.QtWebChannel import QWebChannel
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from PyQt6.QtWebEngineWidgets import QWebEngineView
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from PyQt6.QtWidgets import QDialog, QGridLayout, QMenu
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from typing import TYPE_CHECKING, Any
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if TYPE_CHECKING:
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from backend.db.models import Run, ProcedureType
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from tools import jinja_template_loading, get_application_from_parent
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from backend.validators import PydProcedure
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logger = logging.getLogger(f"submissions.{__name__}")
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class ProcedureCreation(QDialog):
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def __init__(self, parent, run: Run, proceduretype: ProcedureType):
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super().__init__(parent)
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self.run = run
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self.proceduretype = proceduretype
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self.setWindowTitle(f"New {proceduretype.name} for { run.rsl_plate_num }")
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self.created_procedure = self.proceduretype.construct_dummy_procedure(run=self.run)
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self.created_procedure.update_kittype_reagentroles(kittype=self.created_procedure.possible_kits[0])
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self.created_procedure.samples = self.run.constuct_sample_dicts_for_proceduretype(proceduretype=self.proceduretype)
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# logger.debug(f"Samples to map\n{pformat(self.created_procedure.samples)}")
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self.plate_map = self.proceduretype.construct_plate_map(sample_dicts=self.created_procedure.samples)
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# logger.debug(f"Plate map: {self.plate_map}")
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# logger.debug(f"Created dummy: {self.created_procedure}")
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self.app = get_application_from_parent(parent)
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self.webview = QWebEngineView(parent=self)
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self.webview.setContextMenuPolicy(Qt.ContextMenuPolicy.NoContextMenu)
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self.webview.setMinimumSize(1200, 800)
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self.webview.setMaximumWidth(1200)
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# NOTE: Decide if exporting should be allowed.
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# self.webview.loadFinished.connect(self.activate_export)
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self.layout = QGridLayout()
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# NOTE: button to export a pdf version
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self.layout.addWidget(self.webview, 1, 0, 10, 10)
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self.setLayout(self.layout)
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self.setFixedWidth(self.webview.width() + 20)
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# NOTE: setup channel
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self.channel = QWebChannel()
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self.channel.registerObject('backend', self)
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self.set_html()
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self.webview.page().setWebChannel(self.channel)
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def set_html(self):
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env = jinja_template_loading()
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template = env.get_template("procedure_creation.html")
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template_path = Path(template.environment.loader.__getattribute__("searchpath")[0])
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with open(template_path.joinpath("css", "styles.css"), "r") as f:
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css = f.read()
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html = template.render(proceduretype=self.proceduretype.as_dict, run=self.run.to_dict(),
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procedure=self.created_procedure.__dict__, plate_map=self.plate_map, css=css)
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with open("procedure.html", "w") as f:
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f.write(html)
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self.webview.setHtml(html)
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@pyqtSlot(str, str)
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def text_changed(self, key: str, new_value: str):
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# logger.debug(f"New value for {key}: {new_value}")
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attribute = getattr(self.created_procedure, key)
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attribute['value'] = new_value
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@pyqtSlot(str, bool)
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def check_toggle(self, key: str, ischecked: bool):
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# logger.debug(f"{key} is checked: {ischecked}")
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setattr(self.created_procedure, key, ischecked)
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@pyqtSlot(str)
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def update_kit(self, kittype):
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self.created_procedure.update_kittype_reagentroles(kittype=kittype)
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logger.debug({k: v for k, v in self.created_procedure.__dict__.items() if k != "plate_map"})
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self.set_html()
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@pyqtSlot(list)
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def rearrange_plate(self, sample_list: list):
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self.created_procedure.update_samples(sample_list=sample_list)
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@pyqtSlot(str, str)
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def log_drag(self, source_well: str, destination_well: str):
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logger.debug(f"Source Index: {source_well} Destination Index: {destination_well}")
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# source_well = source_well.split("-")
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# destination_well = destination_well.split("-")
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# source_row = int(source_well[0])
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# source_column = int(source_well[1])
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# destination_row = int(destination_well[0])
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# destination_column = int(destination_well[1])
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# self.created_procedure.shuffle_samples(
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# source_row=source_row,
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# source_column=source_column,
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# destination_row=destination_row,
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# destination_column=destination_column
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# )
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# class ProcedureWebViewer(QWebEngineView):
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#
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# def __init__(self, *args, **kwargs):
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# super().__init__(*args, **kwargs)
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#
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# def contextMenuEvent(self, event: QContextMenuEvent):
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# self.menu = self.page().createStandardContextMenu()
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# self.menu = self.createStandardContextMenu()
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# add_sample = QAction("Add Sample")
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# self.menu = QMenu()
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# self.menu.addAction(add_sample)
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# self.menu.popup(event.globalPos())
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@@ -110,3 +110,13 @@ div.gallery {
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max-width: 100%;
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border-radius: 8px;
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}
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.context-menu {
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display: none;
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position: absolute;
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z-index: 10;
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}
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.context-menu--active {
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display: block;
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}
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@@ -1,6 +1,6 @@
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<div class="plate" id="plate-container" style="grid-template-columns: repeat({{ plate_columns }}, {{ vw }}vw);grid-template-rows: repeat({{ plate_rows }}, {{ vw }}vw);">
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{% for sample in samples %}
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<div class="well" draggable="true" id="sample_{{ sample['submission_rank'] }}" style="background-color: {{ sample['background_color'] }};">
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<div class="well" draggable="true" id="{{ sample['well_id'] }}" style="background-color: {{ sample['background_color'] }};">
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<p style="font-size: 0.7em; text-align: center; word-wrap: break-word;">{{ sample['sample_id'] }}</p>
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<!-- <div class="tooltip" style="font-size: 0.5em; text-align: center; word-wrap: break-word;">{{ sample['sample_id'] }}-->
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<!-- <span class="tooltiptext">{{ sample['tooltip'] }}</span>-->
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@@ -45,6 +45,25 @@
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</div>
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</div>
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{% endblock %}
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<nav class="context-menu">
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<ul class="context-menu__items">
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<li class="context-menu__item">
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<a href="#" class="context-menu__link">
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<i class="fa fa-eye"></i> View Task
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</a>
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</li>
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<li class="context-menu__item">
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<a href="#" class="context-menu__link">
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<i class="fa fa-edit"></i> Edit Task
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</a>
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</li>
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<li class="context-menu__item">
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<a href="#" class="context-menu__link">
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<i class="fa fa-times"></i> Delete Task
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</a>
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</li>
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</ul>
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</nav>
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</body>
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<script>
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{% block script %}
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@@ -114,11 +133,25 @@
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output = [];
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fullGrid = [...gridContainer.children];
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fullGrid.forEach(function(item, index) {
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output.push({item: item, index: index})
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output.push({sample_id: item.id, index: index + 1})
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});
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backend.replow(output);
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backend.rearrange_plate(output);
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}
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});
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// Context Menu Functionality
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var wells = document.querySelectorAll(".well");
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for ( var i = 0, len = wells.length; i < len; i++ ) {
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var welloi = wells[i];
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welloi.addEventListener( "contextmenu", function(e) {
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well = e.target
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backend.log_drag(well.id, "el");
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});
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};
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{% endblock %}
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</script>
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</html>
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