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Getting results referencing ProcedureSampleAssociation

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This commit is contained in:
lwark
2025-06-09 11:05:10 -05:00
parent db0b65b07b
commit 10d4c9f155
17 changed files with 476 additions and 208 deletions
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26
src/submissions/frontend/widgets/results/PCR.py Normal file
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@@ -0,0 +1,26 @@
"""
"""
from pathlib import Path
from backend.validators import PydResults
from backend.db.models import Procedure, Results
from backend.excel.parsers.pcr_parser import PCRSampleParser, PCRInfoParser
from frontend.widgets.functions import select_open_file
from . import DefaultResults
class PCR(DefaultResults):
def __init__(self, procedure: Procedure, fname:Path|str|None=None):
self.procedure = procedure
if not fname:
self.fname = select_open_file(file_extension="xlsx")
elif isinstance(fname, str):
self.fname = Path(fname)
self.info_parser = PCRInfoParser(filepath=fname)
self.sample_parser = PCRSampleParser(filepath=fname)
def build_procedure(self):
results = PydResults(parent=self.procedure)
results.results =

7
src/submissions/frontend/widgets/results/__init__.py Normal file
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@@ -0,0 +1,7 @@
class DefaultResults(object):
pass
from .PCR import pcr

223
src/submissions/frontend/widgets/submission_table.py
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@@ -231,27 +231,27 @@ class SubmissionsSheet(QTableView):
return report
class ClientSubmissionDelegate(QStyledItemDelegate):
def __init__(self, parent=None):
super(ClientSubmissionDelegate, self).__init__(parent)
pixmapi = QStyle.StandardPixmap.SP_ToolBarHorizontalExtensionButton
icon1 = QWidget().style().standardIcon(pixmapi)
pixmapi = QStyle.StandardPixmap.SP_ToolBarVerticalExtensionButton
icon2 = QWidget().style().standardIcon(pixmapi)
self._plus_icon = icon1
self._minus_icon = icon2
def initStyleOption(self, option, index):
super(ClientSubmissionDelegate, self).initStyleOption(option, index)
if not index.parent().isValid():
is_open = bool(option.state & QStyle.StateFlag.State_Open)
option.features |= QStyleOptionViewItem.ViewItemFeature.HasDecoration
option.icon = self._minus_icon if is_open else self._plus_icon
# class ClientSubmissionDelegate(QStyledItemDelegate):
#
# def __init__(self, parent=None):
# super(ClientSubmissionDelegate, self).__init__(parent)
# pixmapi = QStyle.StandardPixmap.SP_ToolBarHorizontalExtensionButton
# icon1 = QWidget().style().standardIcon(pixmapi)
# pixmapi = QStyle.StandardPixmap.SP_ToolBarVerticalExtensionButton
# icon2 = QWidget().style().standardIcon(pixmapi)
# self._plus_icon = icon1
# self._minus_icon = icon2
#
# def initStyleOption(self, option, index):
# super(ClientSubmissionDelegate, self).initStyleOption(option, index)
# if not index.parent().isValid():
# is_open = bool(option.state & QStyle.StateFlag.State_Open)
# option.features |= QStyleOptionViewItem.ViewItemFeature.HasDecoration
# option.icon = self._minus_icon if is_open else self._plus_icon
class RunDelegate(ClientSubmissionDelegate):
pass
# class RunDelegate(ClientSubmissionDelegate):
# pass
class SubmissionsTree(QTreeView):
@@ -262,11 +262,11 @@ class SubmissionsTree(QTreeView):
def __init__(self, model, parent=None):
super(SubmissionsTree, self).__init__(parent)
self.total_count = ClientSubmission.__database_session__.query(ClientSubmission).count()
self.setIndentation(0)
# self.setIndentation(0)
self.setExpandsOnDoubleClick(False)
self.clicked.connect(self.on_clicked)
delegate1 = ClientSubmissionDelegate(self)
self.setItemDelegateForColumn(0, delegate1)
# self.clicked.connect(self.on_clicked)
# delegate1 = ClientSubmissionDelegate(self)
# self.setItemDelegateForColumn(0, delegate1)
self.model = model
self.setModel(self.model)
# self.header().setSectionResizeMode(0, QHeaderView.sectionResizeMode(self,0).ResizeToContents)
@@ -276,14 +276,42 @@ class SubmissionsTree(QTreeView):
self.doubleClicked.connect(self.show_details)
# self.setContextMenuPolicy(Qt.ContextMenuPolicy.CustomContextMenu)
# self.customContextMenuRequested.connect(self.open_menu)
self.setStyleSheet("""
QTreeView {
background-color: #f5f5f5;
alternate-background-color: "#cfe2f3";
border: 1px solid #d3d3d3;
}
QTreeView::item {
padding: 5px;
border-bottom: 1px solid #d3d3d3;
}
QTreeView::item:selected {
background-color: #0078d7;
color: white;
}
""")
# Enable alternating row colors
self.setAlternatingRowColors(True)
self.setIndentation(20)
self.setItemsExpandable(True)
self.expanded.connect(self.expand_item)
for ii in range(2):
self.resizeColumnToContents(ii)
@pyqtSlot(QModelIndex)
def on_clicked(self, index):
if not index.parent().isValid() and index.column() == 0:
self.setExpanded(index, not self.isExpanded(index))
# @pyqtSlot(QModelIndex)
# def on_clicked(self, index):
# if not index.parent().isValid() and index.column() == 0:
# self.setExpanded(index, not self.isExpanded(index))
def expand_item(self, event: QModelIndex):
logger.debug(f"Data: {event.data()}")
logger.debug(f"Parent {event.parent().data()}")
logger.debug(f"Row: {event.row()}")
logger.debug(f"Sibling: {event.siblingAtRow(event.row()).data()}")
logger.debug(f"Model: {event.model().event()}")
def contextMenuEvent(self, event: QContextMenuEvent):
"""
@@ -306,19 +334,30 @@ class SubmissionsTree(QTreeView):
self.menu = QMenu(self)
self.con_actions = query_obj.custom_context_events
for key in self.con_actions.keys():
if key.lower() == "add procedure":
action = QMenu(self.menu)
action.setTitle("Add Procedure")
for procedure in query_obj.allowed_procedures:
proc_name = procedure.name
proc = QAction(proc_name, action)
proc.triggered.connect(lambda _, procedure_name=proc_name: self.con_actions['Add Procedure'](obj=self, proceduretype_name=procedure_name))
action.addAction(proc)
self.menu.addMenu(action)
else:
action = QAction(key, self)
action.triggered.connect(lambda _, action_name=key: self.con_actions[action_name](obj=self))
self.menu.addAction(action)
logger.debug(key)
match key.lower():
case "add procedure":
action = QMenu(self.menu)
action.setTitle("Add Procedure")
for procedure in query_obj.allowed_procedures:
proc_name = procedure.name
proc = QAction(proc_name, action)
proc.triggered.connect(lambda _, procedure_name=proc_name: self.con_actions['Add Procedure'](obj=self, proceduretype_name=procedure_name))
action.addAction(proc)
self.menu.addMenu(action)
case "add results":
action = QMenu(self.menu)
action.setTitle("Add Results")
for results in query_obj.proceduretype.allowed_result_methods:
res_name = results
res = QAction(res_name, action)
res.triggered.connect(lambda _, procedure_name=res_name: self.con_actions['Add Results'](obj=self, resultstype_name=procedure_name))
action.addAction(res)
self.menu.addMenu(action)
case _:
action = QAction(key, self)
action.triggered.connect(lambda _, action_name=key: self.con_actions[action_name](obj=self))
self.menu.addAction(action)
# # NOTE: add other required actions
self.menu.popup(QCursor.pos())
@@ -334,36 +373,27 @@ class SubmissionsTree(QTreeView):
root = self.model.invisibleRootItem()
for submission in self.data:
group_str = f"{submission['submissiontype']}-{submission['submitter_plate_id']}-{submission['submitted_date']}"
submission_item = self.model.add_group(parent=root, item_data=dict(
submission_item = self.model.add_child(parent=root, child=dict(
name=group_str,
query_str=submission['submitter_plate_id'],
item_type=ClientSubmission
))
logger.debug(f"Added {submission_item}")
for run in submission['run']:
# self.model.append_element_to_group(group_item=group_item, element=run)
run_item = self.model.add_group(parent=submission_item, item_data=dict(
run_item = self.model.add_child(parent=submission_item, child=dict(
name=run['plate_number'],
query_str=run['plate_number'],
item_type=Run
))
logger.debug(f"Added {run_item}")
for procedure in run['procedures']:
self.model.add_group(parent=run_item, item_data=dict(
procedure_item = self.model.add_child(parent=run_item, child=dict(
name=procedure['name'],
query_str=procedure['name'],
item_type=Procedure
))
# root = self.model.invisibleRootItem()
# for submission in self.data:
# submission_item = QStandardItem(submission['name'])
# root.appendRow(submission_item)
# for run in submission['run']:
# run_item = QStandardItem(run['name'])
# submission_item.appendRow(run_item)
# for procedure in run['procedures']:
# procedure_item = QStandardItem(procedure['name'])
# run_item.appendRow(procedure_item)
# self._populateTree(self.data, self.model.invisibleRootItem())
logger.debug(f"Added {procedure_item}")
def _populateTree(self, children, parent):
for child in children:
@@ -381,14 +411,20 @@ class SubmissionsTree(QTreeView):
self.model.setRowCount(0) # works
def show_details(self, sel: QModelIndex):
id = self.selectionModel().currentIndex()
# id = self.selectionModel().currentIndex()
# NOTE: Convert to data in id column (i.e. column 0)
id = id.sibling(id.row(), 1)
try:
id = int(id.data())
except ValueError:
return
Run.query(id=id).show_details(self)
# id = id.sibling(id.row(), 1)
indexes = self.selectedIndexes()
dicto = next((item.data(1) for item in indexes if item.data(1)))
logger.debug(dicto)
# try:
# id = int(id.data())
# except ValueError:
# return
# Run.query(id=id).show_details(self)
obj = dicto['item_type'].query(name=dicto['query_str'], limit=1)
logger.debug(obj)
def link_extractions(self):
pass
@@ -402,59 +438,18 @@ class ClientSubmissionRunModel(QStandardItemModel):
def __init__(self, parent=None):
super(ClientSubmissionRunModel, self).__init__(parent)
headers = ["", "id", "Plate Number", "Started Date", "Completed Date", "Signed By"]
self.setColumnCount(len(headers))
self.setHorizontalHeaderLabels(headers)
# headers = ["", "id", "Plate Number", "Started Date", "Completed Date", "Signed By"]
# self.setColumnCount(len(headers))
# self.setHorizontalHeaderLabels(headers)
def add_group(self, parent, item_data):
item_root = QStandardItem()
item_root.setEditable(False)
item = QStandardItem(item_data['name'])
def add_child(self, parent: QStandardItem, child:dict):
item = QStandardItem(child['name'])
item.setData(dict(item_type=child['item_type'], query_str=child['query_str']), 1)
parent.appendRow(item)
item.setEditable(False)
i = parent.rowCount()
for j, it in enumerate((item_root, item)):
# NOTE: Adding item to invisible root row i, column j (wherever j comes from)
parent.setChild(i, j, it)
parent.setEditable(False)
for j in range(self.columnCount()):
it = parent.child(i, j)
if it is None:
# NOTE: Set invisible root child to empty if it is None.
it = QStandardItem()
parent.setChild(i, j, it)
item_root.setData(dict(item_type=item_data['item_type'], query_str=item_data['query_str']), 1)
return item_root
def append_element_to_group(self, group_item, item_data: dict):
# logger.debug(f"Element: {pformat(element)}")
j = group_item.rowCount()
item_icon = QStandardItem()
item_icon.setEditable(False)
# item_icon.setBackground(QColor("#0D1225"))
# item_icon.setData(dict(item_type="Run", query_str=element['plate_number']), 1)
# group_item.setChild(j, 0, item_icon)
for i in range(self.columnCount()):
it = self.horizontalHeaderItem(i)
try:
key = it.text().lower().replace(" ", "_")
except AttributeError:
key = None
if not key:
continue
value = str(item_data[key])
item = QStandardItem(value)
item.setBackground(QColor("#CFE2F3"))
item.setEditable(False)
# item_icon.setChild(j, i, item)
item.setData(dict(item_type=item_data['item_type'], query_str=item_data['query_str']),1)
group_item.setChild(j, i, item)
# group_item.setChild(j, 1, QStandardItem("B"))
return item
def get_value(self, idx: int, column: int = 1):
return self.item(idx, column)
def query_group_object(self, idx: int):
row_obj = self.get_value(idx)
logger.debug(row_obj.query_str)
return self.sql_object.query(name=row_obj.query_str, limit=1)
def edit_item(self):
pass