landon/Submissions-App
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

placeholder

Browse Source
This commit is contained in:
lwark
2025-05-09 14:35:53 -05:00
parent 20952f2edd
commit 8a16738e93
6 changed files with 225 additions and 34 deletions
Download Patch File Download Diff File Expand all files Collapse all files

15
src/submissions/backend/db/models/__init__.py
View File

@@ -389,13 +389,13 @@ class BaseClass(Base):
except AttributeError:
return super().__setattr__(key, value)
if isinstance(field_type, InstrumentedAttribute):
# logger.debug(f"{key} is an InstrumentedAttribute.")
logger.debug(f"{key} is an InstrumentedAttribute.")
match field_type.property:
case ColumnProperty():
# logger.debug(f"Setting ColumnProperty to {value}")
logger.debug(f"Setting ColumnProperty to {value}")
return super().__setattr__(key, value)
case _RelationshipDeclared():
# logger.debug(f"{self.__class__.__name__} Setting _RelationshipDeclared for {key} to {value}")
logger.debug(f"{self.__class__.__name__} Setting _RelationshipDeclared for {key} to {value}")
if field_type.property.uselist:
logger.debug(f"Setting with uselist")
existing = self.__getattribute__(key)
@@ -409,7 +409,8 @@ class BaseClass(Base):
value = existing + [value]
else:
if isinstance(value, list):
value = value
# value = value
pass
else:
value = [value]
value = list(set(value))
@@ -421,6 +422,12 @@ class BaseClass(Base):
value = value[0]
else:
raise ValueError("Object is too long to parse a single value.")
try:
return super().__setattr__(key, value)
except AttributeError:
logger.debug(f"Possible attempt to set relationship to simple var type.")
relationship_class = field_type.property.entity.entity
value = relationship_class.query(name=value)
return super().__setattr__(key, value)
case _:
return super().__setattr__(key, value)

27
src/submissions/backend/db/models/submissions.py
View File

@@ -46,7 +46,7 @@ class ClientSubmission(BaseClass, LogMixin):
"""
id = Column(INTEGER, primary_key=True) #: primary key
submitter_plate_num = Column(String(127), unique=True) #: The number given to the submission by the submitting lab
submitter_plate_id = Column(String(127), unique=True) #: The number given to the submission by the submitting lab
submitted_date = Column(TIMESTAMP) #: Date submission received
submitting_lab = relationship("Organization", back_populates="submissions") #: client org
submitting_lab_id = Column(INTEGER, ForeignKey("_organization.id", ondelete="SET NULL",
@@ -56,7 +56,7 @@ class ClientSubmission(BaseClass, LogMixin):
sample_count = Column(INTEGER) #: Number of samples in the submission
comment = Column(JSON)
runs = relationship("BasicSubmission", back_populates="client_submission") #: many-to-one relationship
misc_info = Column(JSON)
contact = relationship("Contact", back_populates="submissions") #: client org
contact_id = Column(INTEGER, ForeignKey("_contact.id", ondelete="SET NULL",
name="fk_BS_contact_id")) #: client lab id from _organizations
@@ -92,6 +92,16 @@ class ClientSubmission(BaseClass, LogMixin):
except AttributeError:
self._submission_category = "NA"
def __init__(self):
super().__init__()
self.misc_info = {}
def set_attribute(self, key, value):
if hasattr(self, key):
super().__setattr__(key, value)
else:
self.misc_info[key] = value
@classmethod
def recruit_parser(cls):
pass
@@ -237,7 +247,7 @@ class ClientSubmission(BaseClass, LogMixin):
output = {
"id": self.id,
"submission_type": self.submission_type_name,
"submitter_plate_number": self.submitter_plate_num,
"submitter_plate_number": self.submitter_plate_id,
"submitted_date": self.submitted_date.strftime("%Y-%m-%d"),
"submitting_lab": sub_lab,
"sample_count": self.sample_count,
@@ -279,11 +289,14 @@ class ClientSubmission(BaseClass, LogMixin):
output["runs"] = runs
return output
class BasicSubmission(BaseClass, LogMixin):
"""
Object for an entire submission run. Links to client submissions, reagents, equipment, processes
"""
id = Column(INTEGER, primary_key=True) #: primary key
rsl_plate_num = Column(String(32), unique=True, nullable=False) #: RSL name (e.g. RSL-22-0012)
client_submission_id = Column(INTEGER, ForeignKey("_clientsubmission.id", ondelete="SET NULL",
@@ -384,6 +397,10 @@ class BasicSubmission(BaseClass, LogMixin):
def organization(self):
return self.submitting_lab
@hybrid_property
def name(self):
return self.rsl_plate_num
@classproperty
def jsons(cls) -> List[str]:
"""
@@ -567,8 +584,8 @@ class BasicSubmission(BaseClass, LogMixin):
"id": self.id,
"plate_number": self.rsl_plate_num,
"submission_type": self.client_submission.submission_type_name,
"submitter_plate_number": self.client_submission.submitter_plate_num,
"submitted_date": self.client_submission.submitted_date.strftime("%Y-%m-%d"),
"submitter_plate_number": self.client_submission.submitter_plate_id,
"started_date": self.client_submission.submitted_date.strftime("%Y-%m-%d"),
"submitting_lab": sub_lab,
"sample_count": self.client_submission.sample_count,
"extraction_kit": "Change submissions.py line 388",

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

@@ -68,7 +68,7 @@ class ReportMaker(object):
{'extraction_kit': 'count', 'cost': 'sum', 'sample_count': 'sum'})
df2 = df2.rename(columns={"extraction_kit": 'run_count'})
df = df.drop('id', axis=1)
df = df.sort_values(['submitting_lab', "submitted_date"])
df = df.sort_values(['submitting_lab', "started_date"])
return df, df2
def make_report_html(self, df: DataFrame) -> str:

95
src/submissions/backend/validators/pydant.py
View File

@@ -384,7 +384,6 @@ class PydSubmission(BaseModel, extra='allow'):
filepath: Path
submission_type: dict | None
submitter_plate_num: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
submitted_date: dict | None
rsl_plate_num: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
submitted_date: dict | None = Field(default=dict(value=date.today(), missing=True), validate_default=True)
submitting_lab: dict | None
@@ -1331,21 +1330,93 @@ class PydElastic(BaseModel, extra="allow", arbitrary_types_allowed=True):
# NOTE: Generified objects below:
class PydClientSubmission(BaseModel, extra="allow"):
class PydClientSubmission(BaseModel, extra="allow", validate_assignment=True):
sql_object: ClassVar = ClientSubmission
filepath: Path
submission_type: dict | None
submitter_plate_num: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
submitted_date: dict | None
submitted_date: dict | None = Field(default=dict(value=date.today(), missing=True), validate_default=True)
submitting_lab: dict | None
sample_count: dict | None
kittype: dict | None
submission_category: dict | None = Field(default=dict(value=None, missing=True), validate_default=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)
@field_validator("sample_count")
@classmethod
def enforce_integer(cls, value):
try:
value['value'] = int(value['value'])
except ValueError:
raise f"sample count value must be an integer"
return value
@field_validator("submitter_plate_num")
@classmethod
def create_submitter_plate_num(cls, value, values):
if value['value'] in [None, "None"]:
val = f"{values.data['submission_type']['value']}-{values.data['submission_category']['value']}-{values.data['submitted_date']['value']}"
return dict(value=val, missing=True)
else:
value['value'] = value['value'].strip()
return value
@field_validator("submitted_date")
@classmethod
def rescue_date(cls, value):
try:
check = value['value'] is None
except TypeError:
check = True
if check:
return dict(value=date.today(), missing=True)
return value
def filter_field(self, key: str) -> Any:
"""
Attempts to get value from field dictionary
Args:
key (str): name of the field of interest
Returns:
Any (): Value found.
"""
item = getattr(self, key)
match item:
case dict():
try:
item = item['value']
except KeyError:
logger.error(f"Couldn't get dict value: {item}")
case _:
pass
return item
def improved_dict(self, dictionaries: bool = True) -> dict:
"""
Adds model_extra to fields.
Args:
dictionaries (bool, optional): Are dictionaries expected as input? i.e. Should key['value'] be retrieved. Defaults to True.
Returns:
dict: This instance as a dictionary
"""
fields = list(self.model_fields.keys()) + list(self.model_extra.keys())
if dictionaries:
output = {k: getattr(self, k) for k in fields}
else:
output = {k: self.filter_field(k) for k in fields}
try:
del output['filepath']
except KeyError:
pass
logger.debug(f"Output; {pformat(output)}")
return output
def to_form(self, parent: QWidget, disable: list | None = None):
"""
@@ -1360,3 +1431,17 @@ class PydClientSubmission(BaseModel, extra="allow"):
"""
from frontend.widgets.submission_widget import ClientSubmissionFormWidget
return ClientSubmissionFormWidget(parent=parent, submission=self, disable=disable)
def to_sql(self):
sql = self.sql_object()
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__)

68
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
QHeaderView, QAbstractItemView, QWidget
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
@@ -230,8 +230,12 @@ class SubmissionsSheet(QTableView):
class RunDelegate(QStyledItemDelegate):
def __init__(self, parent=None):
super(RunDelegate, self).__init__(parent)
self._plus_icon = QIcon("plus.png")
self._minus_icon = QIcon("minus.png")
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(RunDelegate, self).initStyleOption(option, index)
@@ -258,6 +262,11 @@ class SubmissionsTree(QTreeView):
self.setSelectionBehavior(QAbstractItemView.selectionBehavior(self).SelectRows)
# self.setStyleSheet("background-color: #0D1225;")
self.set_data()
self.doubleClicked.connect(self.show_details)
for ii in range(2):
self.resizeColumnToContents(ii)
@pyqtSlot(QModelIndex)
def on_clicked(self, index):
@@ -273,9 +282,20 @@ class SubmissionsTree(QTreeView):
logger.debug(pformat(self.data))
# sys.exit()
for submission in self.data:
group_item = self.model.add_group(submission['submitter_plate_number'])
group_str = f"{submission['submission_type']}-{submission['submitter_plate_number']}-{submission['submitted_date']}"
group_item = self.model.add_group(group_str)
for run in submission['runs']:
self.model.append_element_to_group(group_item=group_item, texts=run['plate_number'])
self.model.append_element_to_group(group_item=group_item, element=run)
def show_details(self, sel: QModelIndex):
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
BasicSubmission.query(id=id).show_details(self)
def link_extractions(self):
@@ -286,12 +306,19 @@ class SubmissionsTree(QTreeView):
class ClientRunModel(QStandardItemModel):
def __init__(self, parent=None):
super(ClientRunModel, self).__init__(parent)
self.setColumnCount(8)
self.setHorizontalHeaderLabels(["id", "Name", "Library", "Release Date", "Genre(s)", "Last Played", "Time Played", ""])
headers = ["", "id", "Plate Number", "Started Date", "Completed Date", "Technician", "Signed By"]
self.setColumnCount(len(headers))
self.setHorizontalHeaderLabels(headers)
for i in range(self.columnCount()):
it = self.horizontalHeaderItem(i)
try:
logger.debug(it.text())
except AttributeError:
pass
# it.setForeground(QColor("#F2F2F2"))
def add_group(self, group_name):
@@ -313,18 +340,29 @@ class ClientRunModel(QStandardItemModel):
# it.setForeground(QColor("#F2F2F2"))
return item_root
def append_element_to_group(self, group_item, texts):
def append_element_to_group(self, group_item, element:dict):
logger.debug(f"Element: {pformat(element)}")
j = group_item.rowCount()
item_icon = QStandardItem()
item_icon.setEditable(False)
item_icon.setIcon(QIcon("game.png"))
# item_icon.setBackground(QColor("#0D1225"))
group_item.setChild(j, 0, item_icon)
for i, text in enumerate(texts):
item = QStandardItem(text)
# 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:
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)
# item.setBackground(QColor("#0D1225"))
# item.setForeground(QColor("#F2F2F2"))
group_item.setChild(j, i+1, item)
group_item.setChild(j, i, item)
# group_item.setChild(j, 1, QStandardItem("B"))

50
src/submissions/frontend/widgets/submission_widget.py
View File

@@ -438,7 +438,7 @@ class SubmissionFormWidget(QWidget):
value = getattr(self, item)
info[item] = value
for k, v in info.items():
self.pyd.set_attribute(key=k, value=v)
self.pyd.__setattr__(k, v)
report.add_result(report)
return report
@@ -786,9 +786,53 @@ 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 && Start Run")
start_run_btn = QPushButton("Save && Add Run")
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:
"""
Transforms form info into PydSubmission
Returns:
Report: Report on status of parse.
"""
report = Report()
logger.info(f"Hello from client submission form parser!")
info = {}
reagents = []
for widget in self.findChildren(QWidget):
match widget:
case self.ReagentFormWidget():
reagent = widget.parse_form()
if reagent is not None:
reagents.append(reagent)
else:
report.add_result(Result(msg="Failed integrity check", status="Critical"))
return report
case self.InfoItem():
field, value = widget.parse_form()
if field is not None:
info[field] = value
# logger.debug(f"Reagents from form: {reagents}")
for item in self.recover:
if hasattr(self, item):
value = getattr(self, item)
info[item] = value
for k, v in info.items():
self.pyd.__setattr__(k, v)
report.add_result(report)
return report
@report_result
def to_pydantic(self, *args):
self.parse_form()
return self.pyd
def create_new_submission(self, *args) -> Report:
self.parse_form()
sql = self.pyd.to_sql()