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Adding sample associations to basicsubmission

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This commit is contained in:
lwark
2025-05-12 13:31:26 -05:00
parent 8a16738e93
commit 0dbb4ae77a
4 changed files with 50 additions and 38 deletions
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42
src/submissions/backend/db/models/submissions.py
View File

@@ -336,15 +336,15 @@ class BasicSubmission(BaseClass, LogMixin):
kittypes = relationship("KitType", back_populates="submissions",
secondary=kittypes_submissions) #: submissions this kit was used for
# submission_sample_associations = relationship(
# "SubmissionSampleAssociation",
# back_populates="submission",
# cascade="all, delete-orphan",
# ) #: Relation to SubmissionSampleAssociation
#
# samples = association_proxy("submission_sample_associations",
# "sample", creator=lambda sample: SubmissionSampleAssociation(
# sample=sample)) #: Association proxy to SubmissionSampleAssociation.samples
submission_sample_associations = relationship(
"SubmissionSampleAssociation",
back_populates="submission",
cascade="all, delete-orphan",
) #: Relation to SubmissionSampleAssociation
samples = association_proxy("submission_sample_associations",
"sample", creator=lambda sample: SubmissionSampleAssociation(
sample=sample)) #: Association proxy to SubmissionSampleAssociation.samples
submission_reagent_associations = relationship(
"SubmissionReagentAssociation",
@@ -600,20 +600,20 @@ class BasicSubmission(BaseClass, LogMixin):
except Exception as e:
logger.error(f"We got an error retrieving reagents: {e}")
reagents = []
finally:
dicto, _ = self.extraction_kit.construct_xl_map_for_use(self.submission_type)
for k, v in dicto.items():
if k == 'info':
continue
if not any([item['role'] == k for item in reagents]):
expiry = "NA"
reagents.append(
dict(role=k, name="Not Applicable", lot="NA", expiry=expiry,
missing=True))
# finally:
# dicto, _ = self.extraction_kit.construct_xl_map_for_use(self.submission_type)
# for k, v in dicto.items():
# if k == 'info':
# continue
# if not any([item['role'] == k for item in reagents]):
# expiry = "NA"
# reagents.append(
# dict(role=k, name="Not Applicable", lot="NA", expiry=expiry,
# missing=True))
samples = self.generate_associations(name="submission_sample_associations")
equipment = self.generate_associations(name="submission_equipment_associations")
tips = self.generate_associations(name="submission_tips_associations")
cost_centre = self.cost_centre
# cost_centre = self.cost_centre
custom = self.custom
controls = [item.to_sub_dict() for item in self.controls]
else:
@@ -648,7 +648,7 @@ class BasicSubmission(BaseClass, LogMixin):
output["comment"] = comments
output["equipment"] = equipment
output["tips"] = tips
output["cost_centre"] = cost_centre
# output["cost_centre"] = cost_centre
output["signed_by"] = self.signed_by
output["contact"] = contact
output["contact_phone"] = contact_phone

19
src/submissions/backend/validators/pydant.py
View File

@@ -1343,7 +1343,7 @@ class PydClientSubmission(BaseModel, extra="allow", validate_assignment=True):
comment: dict | None = Field(default=dict(value="", missing=True), validate_default=True)
cost_centre: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
contact: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
submitter_plate_num: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
submitter_plate_id: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
@field_validator("sample_count")
@classmethod
@@ -1354,7 +1354,7 @@ class PydClientSubmission(BaseModel, extra="allow", validate_assignment=True):
raise f"sample count value must be an integer"
return value
@field_validator("submitter_plate_num")
@field_validator("submitter_plate_id")
@classmethod
def create_submitter_plate_num(cls, value, values):
if value['value'] in [None, "None"]:
@@ -1373,6 +1373,13 @@ class PydClientSubmission(BaseModel, extra="allow", validate_assignment=True):
check = True
if check:
return dict(value=date.today(), missing=True)
else:
match value['value']:
case str():
value['value'] = datetime.strptime(value['value'], "%Y-%m-%d")
value['value'] = datetime.combine(value['value'], datetime.now().time())
case _:
pass
return value
def filter_field(self, key: str) -> Any:
@@ -1437,11 +1444,5 @@ class PydClientSubmission(BaseModel, extra="allow", validate_assignment=True):
for key, value in self.improved_dict().items():
if isinstance(value, dict):
value = value['value']
# if hasattr(sql, key):
# try:
sql.set_attribute(key, value)
# except AttributeError:
# continue
# else:
# sql.misc_info[key] = value
print(sql.__dict__)
return sql

13
src/submissions/frontend/widgets/submission_table.py
View File

@@ -5,7 +5,7 @@ import logging
import sys
from pprint import pformat
from PyQt6.QtWidgets import QTableView, QMenu, QTreeView, QStyledItemDelegate, QStyle, QStyleOptionViewItem, \
QHeaderView, QAbstractItemView, QWidget
QHeaderView, QAbstractItemView, QWidget, QTreeWidgetItemIterator
from PyQt6.QtCore import Qt, QAbstractTableModel, QSortFilterProxyModel, pyqtSlot, QModelIndex
from PyQt6.QtGui import QAction, QCursor, QStandardItemModel, QStandardItem, QIcon, QColor
from backend.db.models import BasicSubmission, ClientSubmission
@@ -250,7 +250,7 @@ class SubmissionsTree(QTreeView):
"""
def __init__(self, model, parent=None):
super(SubmissionsTree, self).__init__(parent)
self.total_count = 1
self.total_count = ClientSubmission.__database_session__.query(ClientSubmission).count()
self.setIndentation(0)
self.setExpandsOnDoubleClick(False)
self.clicked.connect(self.on_clicked)
@@ -277,6 +277,7 @@ class SubmissionsTree(QTreeView):
"""
sets data in model
"""
self.clear()
# self.data = ClientSubmission.submissions_to_df(page=page, page_size=page_size)
self.data = [item.to_dict(full_data=True) for item in ClientSubmission.query(chronologic=True, page=page, page_size=page_size)]
logger.debug(pformat(self.data))
@@ -287,6 +288,12 @@ class SubmissionsTree(QTreeView):
for run in submission['runs']:
self.model.append_element_to_group(group_item=group_item, element=run)
def clear(self):
if self.model != None:
# self.model.clear() # works
self.model.setRowCount(0) # works
def show_details(self, sel: QModelIndex):
id = self.selectionModel().currentIndex()
# NOTE: Convert to data in id column (i.e. column 0)
@@ -356,9 +363,7 @@ class ClientRunModel(QStandardItemModel):
continue
if not key:
continue
logger.debug(f"Looking for {key} in column {i}")
value = str(element[key])
logger.debug(f"Got value: {value}")
item = QStandardItem(value)
item.setBackground(QColor("#CFE2F3"))
item.setEditable(False)

14
src/submissions/frontend/widgets/submission_widget.py
View File

@@ -785,12 +785,13 @@ class ClientSubmissionFormWidget(SubmissionFormWidget):
def __init__(self, parent: QWidget, submission: PydSubmission, disable: list | None = None) -> None:
super().__init__(parent, submission=submission, disable=disable)
save_btn = QPushButton("Save")
start_run_btn = QPushButton("Save && Add Run")
self.layout.addWidget(save_btn)
self.disabler.setHidden(True)
# save_btn = QPushButton("Save")
start_run_btn = QPushButton("Save")
# self.layout.addWidget(save_btn)
self.layout.addWidget(start_run_btn)
start_run_btn.clicked.connect(self.create_new_submission)
del self.disabler
def parse_form(self) -> Report:
"""
@@ -834,5 +835,10 @@ class ClientSubmissionFormWidget(SubmissionFormWidget):
def create_new_submission(self, *args) -> Report:
self.parse_form()
sql = self.pyd.to_sql()
logger.debug(sql.__dict__)
sql.save()
self.app.table_widget.sub_wid.set_data()
self.setParent(None)