diff --git a/CHANGELOG.md b/CHANGELOG.md
index 98eafad..530b6d2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,7 @@
+# 202412.06
+
+- Switched startup/teardown scripts to importlib/getattr addition to ctx.
+
# 202412.05
- Switched startup/teardown scripts to decorator registration.
diff --git a/src/submissions/tools/scripts/backup_database.py b/src/scripts/backup_database.py
similarity index 97%
rename from src/submissions/tools/scripts/backup_database.py
rename to src/scripts/backup_database.py
index daa3cd5..7ba17d5 100644
--- a/src/submissions/tools/scripts/backup_database.py
+++ b/src/scripts/backup_database.py
@@ -5,11 +5,9 @@ import logging, shutil, pyodbc
from datetime import date
from pathlib import Path
from tools import Settings
-# from .. import register_script
logger = logging.getLogger(f"submissions.{__name__}")
-# @register_script
def backup_database(ctx: Settings):
"""
Copies the database into the backup directory the first time it is opened every month.
diff --git a/src/scripts/goodbye.py b/src/scripts/goodbye.py
new file mode 100644
index 0000000..dbc80c3
--- /dev/null
+++ b/src/scripts/goodbye.py
@@ -0,0 +1,22 @@
+"""
+Test script for teardown_scripts
+"""
+
+
+def goodbye(ctx):
+ """
+ Args:
+ ctx (Settings): All scripts must take ctx as an argument to maintain interoperability.
+
+ Returns:
+ None: Scripts are currently unable to return results to the program.
+ """
+ print("\n\nGoodbye. Thank you for using Robotics Submission Tracker.\n\n")
+
+
+"""
+For scripts to be run, they must be added to the _configitem.startup_scripts or _configitem.teardown_scripts
+rows as a key: value (name: null) entry in the JSON.
+ex: {"goodbye": null, "backup_database": null}
+The program will overwrite null with the actual function upon startup.
+"""
diff --git a/src/scripts/hello.py b/src/scripts/hello.py
new file mode 100644
index 0000000..efb7cb7
--- /dev/null
+++ b/src/scripts/hello.py
@@ -0,0 +1,22 @@
+"""
+Test script for startup_scripts
+"""
+
+
+def hello(ctx) -> None:
+ """
+ Args:
+ ctx (Settings): All scripts must take ctx as an argument to maintain interoperability.
+
+ Returns:
+ None: Scripts are currently unable to return results to the program.
+ """
+ print("\n\nHello! Welcome to Robotics Submission Tracker.\n\n")
+
+
+"""
+For scripts to be run, they must be added to the _configitem.startup_scripts or _configitem.teardown_scripts
+rows as a key: value (name: null) entry in the JSON.
+ex: {"hello": null, "import_irida": null}
+The program will overwrite null with the actual function upon startup.
+"""
diff --git a/src/submissions/tools/scripts/import_irida.py b/src/scripts/import_irida.py
similarity index 86%
rename from src/submissions/tools/scripts/import_irida.py
rename to src/scripts/import_irida.py
index f3e8349..3ea84dd 100644
--- a/src/submissions/tools/scripts/import_irida.py
+++ b/src/scripts/import_irida.py
@@ -4,11 +4,9 @@ from datetime import datetime
from tools import Settings
from sqlalchemy.orm import Session
-# from .. import register_script
logger = logging.getLogger(f"submissions.{__name__}")
-# @register_script
def import_irida(ctx: Settings):
"""
Grabs Irida controls from secondary database.
@@ -38,7 +36,6 @@ def import_irida(ctx: Settings):
subtype=row[6], refseq_version=row[7], kraken2_version=row[8], kraken2_db_version=row[9],
sample_id=row[10]) for row in cursor]
for record in records:
- # instance = IridaControl.query(name=record['name'])
instance = new_session.query(IridaControl).filter(IridaControl.name == record['name']).first()
if instance:
logger.warning(f"Irida Control {instance.name} already exists, skipping.")
@@ -49,19 +46,13 @@ def import_irida(ctx: Settings):
assert isinstance(record[thing], dict)
else:
record[thing] = {}
- # record['matches'] = json.loads(record['matches'])
- # assert isinstance(record['matches'], dict)
- # record['kraken'] = json.loads(record['kraken'])
- # assert isinstance(record['kraken'], dict)
record['submitted_date'] = datetime.strptime(record['submitted_date'], "%Y-%m-%d %H:%M:%S.%f")
assert isinstance(record['submitted_date'], datetime)
instance = IridaControl(controltype=ct, **record)
- # sample = BasicSample.query(submitter_id=instance.name)
sample = new_session.query(BasicSample).filter(BasicSample.submitter_id == instance.name).first()
if sample:
instance.sample = sample
instance.submission = sample.submissions[0]
- # instance.save()
new_session.add(instance)
new_session.commit()
new_session.close()
diff --git a/src/submissions/__main__.py b/src/submissions/__main__.py
index 9f7fd7c..d8e2a82 100644
--- a/src/submissions/__main__.py
+++ b/src/submissions/__main__.py
@@ -1,14 +1,13 @@
import sys, os
from tools import ctx, setup_logger, check_if_app
-# environment variable must be set to enable qtwebengine in network path
+# NOTE: environment variable must be set to enable qtwebengine in network path
if check_if_app():
os.environ['QTWEBENGINE_DISABLE_SANDBOX'] = "1"
-# setup custom logger
+# NOTE: setup custom logger
logger = setup_logger(verbosity=3)
-# from backend import scripts
from PyQt6.QtWidgets import QApplication
from frontend.widgets.app import App
diff --git a/src/submissions/backend/db/models/__init__.py b/src/submissions/backend/db/models/__init__.py
index e1a284c..fd3b0be 100644
--- a/src/submissions/backend/db/models/__init__.py
+++ b/src/submissions/backend/db/models/__init__.py
@@ -12,6 +12,7 @@ from typing import Any, List
from pathlib import Path
from tools import report_result
+
# NOTE: Load testing environment
if 'pytest' in sys.modules:
sys.path.append(Path(__file__).parents[4].absolute().joinpath("tests").__str__())
@@ -167,7 +168,10 @@ class BaseClass(Base):
Returns:
Dataframe
"""
- records = [obj.to_sub_dict(**kwargs) for obj in objects]
+ try:
+ records = [obj.to_sub_dict(**kwargs) for obj in objects]
+ except AttributeError:
+ records = [obj.to_dict() for obj in objects]
return DataFrame.from_records(records)
@classmethod
@@ -233,6 +237,15 @@ class BaseClass(Base):
report.add_result(Result(msg=e, status="Critical"))
return report
+ def to_dict(self):
+ return {k: v for k, v in self.__dict__.items() if k not in ["_sa_instance_state", "id"]}
+
+ @classmethod
+ def get_pydantic_model(cls):
+ from backend.validators import pydant
+ model = getattr(pydant, f"Pyd{cls.__name__}")
+ return model
+
class ConfigItem(BaseClass):
"""
diff --git a/src/submissions/backend/db/models/organizations.py b/src/submissions/backend/db/models/organizations.py
index 4f3f191..5424c11 100644
--- a/src/submissions/backend/db/models/organizations.py
+++ b/src/submissions/backend/db/models/organizations.py
@@ -124,6 +124,8 @@ class Contact(BaseClass):
Base of Contact
"""
+ searchables =[]
+
id = Column(INTEGER, primary_key=True) #: primary key
name = Column(String(64)) #: contact name
email = Column(String(64)) #: contact email
diff --git a/src/submissions/backend/db/models/submissions.py b/src/submissions/backend/db/models/submissions.py
index 2538797..50e8001 100644
--- a/src/submissions/backend/db/models/submissions.py
+++ b/src/submissions/backend/db/models/submissions.py
@@ -7,6 +7,7 @@ from collections import OrderedDict
from copy import deepcopy
from getpass import getuser
import logging, uuid, tempfile, re, base64, numpy as np, pandas as pd, types, sys
+from inspect import isclass
from zipfile import ZipFile, BadZipfile
from tempfile import TemporaryDirectory, TemporaryFile
from operator import itemgetter
@@ -175,7 +176,7 @@ class BasicSubmission(BaseClass, LogMixin):
# NOTE: Fields not placed in ui form
form_ignore=['reagents', 'ctx', 'id', 'cost', 'extraction_info', 'signed_by', 'comment', 'namer',
'submission_object', "tips", 'contact_phone', 'custom', 'cost_centre', 'completed_date',
- 'controls'] + recover,
+ 'controls', "origin_plate"] + recover,
# NOTE: Fields not placed in ui form to be moved to pydantic
form_recover=recover
))
@@ -352,7 +353,10 @@ class BasicSubmission(BaseClass, LogMixin):
try:
contact = self.contact.name
except AttributeError as e:
- contact = "NA"
+ try:
+ contact = f"Defaulted to: {self.submitting_lab.contacts[0].name}"
+ except (AttributeError, IndexError):
+ contact = "NA"
try:
contact_phone = self.contact.phone
except AttributeError:
@@ -627,8 +631,14 @@ class BasicSubmission(BaseClass, LogMixin):
continue
case "tips":
field_value = [item.to_pydantic() for item in self.submission_tips_associations]
- case "submission_type" | "contact":
+ case "submission_type":
field_value = dict(value=self.__getattribute__(key).name, missing=missing)
+ # case "contact":
+ # try:
+ # field_value = dict(value=self.__getattribute__(key).name, missing=missing)
+ # except AttributeError:
+ # contact = self.submitting_lab.contacts[0]
+ # field_value = dict(value=contact.name, missing=True)
case "plate_number":
key = 'rsl_plate_num'
field_value = dict(value=self.rsl_plate_num, missing=missing)
@@ -640,10 +650,13 @@ class BasicSubmission(BaseClass, LogMixin):
case _:
try:
key = key.lower().replace(" ", "_")
- field_value = dict(value=self.__getattribute__(key), missing=missing)
+ if isclass(value):
+ field_value = dict(value=self.__getattribute__(key).name, missing=missing)
+ else:
+ field_value = dict(value=self.__getattribute__(key), missing=missing)
except AttributeError:
logger.error(f"{key} is not available in {self}")
- continue
+ field_value = dict(value="NA", missing=True)
new_dict[key] = field_value
new_dict['filepath'] = Path(tempfile.TemporaryFile().name)
dicto.update(new_dict)
@@ -1505,6 +1518,7 @@ class Wastewater(BasicSubmission):
# NOTE: Due to having to run through samples in for loop we need to convert to list.
output = []
for sample in samples:
+ logger.debug(sample)
# NOTE: remove '-{target}' from controls
sample['sample'] = re.sub('-N\\d*$', '', sample['sample'])
# NOTE: if sample is already in output skip
@@ -1512,14 +1526,16 @@ class Wastewater(BasicSubmission):
logger.warning(f"Already have {sample['sample']}")
continue
# NOTE: Set ct values
+ logger.debug(f"Sample ct: {sample['ct']}")
sample[f"ct_{sample['target'].lower()}"] = sample['ct'] if isinstance(sample['ct'], float) else 0.0
# NOTE: Set assessment
- sample[f"{sample['target'].lower()}_status"] = sample['assessment']
+ logger.debug(f"Sample assessemnt: {sample['assessment']}")
+ # sample[f"{sample['target'].lower()}_status"] = sample['assessment']
# NOTE: Get sample having other target
other_targets = [s for s in samples if re.sub('-N\\d*$', '', s['sample']) == sample['sample']]
for s in other_targets:
sample[f"ct_{s['target'].lower()}"] = s['ct'] if isinstance(s['ct'], float) else 0.0
- sample[f"{s['target'].lower()}_status"] = s['assessment']
+ # sample[f"{s['target'].lower()}_status"] = s['assessment']
try:
del sample['ct']
except KeyError:
@@ -2915,7 +2931,8 @@ class WastewaterAssociation(SubmissionSampleAssociation):
sample['background_color'] = f"rgb({red}, {grn}, {blu})"
try:
sample[
- 'tooltip'] += f"
- ct N1: {'{:.2f}'.format(self.ct_n1)} ({self.n1_status})
- ct N2: {'{:.2f}'.format(self.ct_n2)} ({self.n2_status})"
+ # 'tooltip'] += f"
- ct N1: {'{:.2f}'.format(self.ct_n1)} ({self.n1_status})
- ct N2: {'{:.2f}'.format(self.ct_n2)} ({self.n2_status})"
+ 'tooltip'] += f"
- ct N1: {'{:.2f}'.format(self.ct_n1)}
- ct N2: {'{:.2f}'.format(self.ct_n2)}"
except (TypeError, AttributeError) as e:
logger.error(f"Couldn't set tooltip for {self.sample.rsl_number}. Looks like there isn't PCR data.")
return sample
diff --git a/src/submissions/backend/excel/writer.py b/src/submissions/backend/excel/writer.py
index 17ac7e6..cac6fb8 100644
--- a/src/submissions/backend/excel/writer.py
+++ b/src/submissions/backend/excel/writer.py
@@ -171,9 +171,9 @@ class InfoWriter(object):
try:
sheet.cell(row=loc['row'], column=loc['column'], value=v['value'])
except AttributeError as e:
- logger.error(f"Can't write {k} to that cell due to {e}")
+ logger.error(f"Can't write {k} to that cell due to AttributeError: {e}")
except ValueError as e:
- logger.error(f"Can't write {v} to that cell due to {e}")
+ logger.error(f"Can't write {v} to that cell due to ValueError: {e}")
sheet.cell(row=loc['row'], column=loc['column'], value=v['value'].name)
return self.sub_object.custom_info_writer(self.xl, info=final_info, custom_fields=self.info_map['custom'])
diff --git a/src/submissions/backend/validators/pydant.py b/src/submissions/backend/validators/pydant.py
index 6dc6383..c0701b3 100644
--- a/src/submissions/backend/validators/pydant.py
+++ b/src/submissions/backend/validators/pydant.py
@@ -645,6 +645,7 @@ class PydSubmission(BaseModel, extra='allow'):
@field_validator("contact")
@classmethod
def get_contact_from_org(cls, value, values):
+ logger.debug(f"Value coming in: {value}")
match value:
case dict():
if isinstance(value['value'], tuple):
@@ -653,14 +654,26 @@ class PydSubmission(BaseModel, extra='allow'):
value = dict(value=value[0], missing=False)
case _:
value = dict(value=value, missing=False)
+ logger.debug(f"Value after match: {value}")
check = Contact.query(name=value['value'])
- if check is None:
- org = Organization.query(name=values.data['submitting_lab']['value'])
- contact = org.contacts[0].name
+ logger.debug(f"Check came back with {check}")
+ if not isinstance(check, Contact):
+ org = values.data['submitting_lab']['value']
+ logger.debug(f"Checking organization: {org}")
+ if isinstance(org, str):
+ org = Organization.query(name=values.data['submitting_lab']['value'], limit=1)
+ if isinstance(org, Organization):
+ contact = org.contacts[0].name
+ else:
+ logger.warning(f"All attempts at defaulting Contact failed, returning: {value}")
+ return value
if isinstance(contact, tuple):
contact = contact[0]
- return dict(value=contact, missing=True)
+ value = dict(value=f"Defaulted to: {contact}", missing=True)
+ logger.debug(f"Value after query: {value}")
+ return
else:
+ logger.debug(f"Value after bypass check: {value}")
return value
def __init__(self, run_custom: bool = False, **data):
@@ -983,6 +996,17 @@ class PydContact(BaseModel):
phone: str | None
email: str | None
+ @field_validator("phone")
+ @classmethod
+ def enforce_phone_number(cls, value):
+ area_regex = re.compile(r"^\(?(\d{3})\)?(-| )?")
+ if len(value) > 8:
+ match = area_regex.match(value)
+ logger.debug(f"Match: {match.group(1)}")
+ value = area_regex.sub(f"({match.group(1).strip()}) ", value)
+ logger.debug(f"Output phone: {value}")
+ return value
+
def toSQL(self) -> Contact:
"""
Converts this instance into a backend.db.models.organization.Contact instance
diff --git a/src/submissions/frontend/widgets/app.py b/src/submissions/frontend/widgets/app.py
index 21bdee8..5373c24 100644
--- a/src/submissions/frontend/widgets/app.py
+++ b/src/submissions/frontend/widgets/app.py
@@ -12,8 +12,8 @@ from PyQt6.QtGui import QAction
from pathlib import Path
from markdown import markdown
from __init__ import project_path
-from backend import SubmissionType, Reagent, BasicSample
-from tools import check_if_app, Settings, Report, jinja_template_loading, check_authorization, page_size
+from backend import SubmissionType, Reagent, BasicSample, Organization
+from tools import check_if_app, Settings, Report, jinja_template_loading, check_authorization, page_size, is_power_user
from .functions import select_save_file, select_open_file
# from datetime import date
from .pop_ups import HTMLPop, AlertPop
@@ -25,6 +25,7 @@ from .controls_chart import ControlsViewer
from .summary import Summary
from .turnaround import TurnaroundTime
from .omni_search import SearchBox
+from .omni_manager import ManagerWindow
logger = logging.getLogger(f'submissions.{__name__}')
@@ -69,7 +70,7 @@ class App(QMainWindow):
fileMenu = menuBar.addMenu("&File")
editMenu = menuBar.addMenu("&Edit")
# NOTE: Creating menus using a title
- methodsMenu = menuBar.addMenu("&Methods")
+ methodsMenu = menuBar.addMenu("&Search")
maintenanceMenu = menuBar.addMenu("&Monthly")
helpMenu = menuBar.addMenu("&Help")
helpMenu.addAction(self.helpAction)
@@ -82,6 +83,9 @@ class App(QMainWindow):
maintenanceMenu.addAction(self.joinExtractionAction)
maintenanceMenu.addAction(self.joinPCRAction)
editMenu.addAction(self.editReagentAction)
+ editMenu.addAction(self.manageOrgsAction)
+ if not is_power_user():
+ editMenu.setEnabled(False)
def _createToolBar(self):
"""
@@ -106,6 +110,7 @@ class App(QMainWindow):
self.yamlExportAction = QAction("Export Type Example", self)
self.yamlImportAction = QAction("Import Type Template", self)
self.editReagentAction = QAction("Edit Reagent", self)
+ self.manageOrgsAction = QAction("Manage Clients", self)
def _connectActions(self):
"""
@@ -123,6 +128,7 @@ class App(QMainWindow):
self.yamlImportAction.triggered.connect(self.import_ST_yaml)
self.table_widget.pager.current_page.textChanged.connect(self.update_data)
self.editReagentAction.triggered.connect(self.edit_reagent)
+ self.manageOrgsAction.triggered.connect(self.manage_orgs)
def showAbout(self):
"""
@@ -207,6 +213,11 @@ class App(QMainWindow):
def update_data(self):
self.table_widget.sub_wid.setData(page=self.table_widget.pager.page_anchor, page_size=page_size)
+ def manage_orgs(self):
+ dlg = ManagerWindow(parent=self, object_type=Organization, extras=[])
+ if dlg.exec():
+ new_org = dlg.parse_form()
+ logger.debug(new_org.__dict__)
class AddSubForm(QWidget):
diff --git a/src/submissions/frontend/widgets/omni_add_edit.py b/src/submissions/frontend/widgets/omni_add_edit.py
new file mode 100644
index 0000000..cb7eb05
--- /dev/null
+++ b/src/submissions/frontend/widgets/omni_add_edit.py
@@ -0,0 +1,88 @@
+from typing import Any
+
+from PyQt6.QtWidgets import (
+ QLabel, QDialog, QTableView, QWidget, QLineEdit, QGridLayout, QComboBox, QPushButton, QDialogButtonBox, QDateEdit
+)
+from sqlalchemy import String, TIMESTAMP
+from sqlalchemy.orm import InstrumentedAttribute
+import logging
+
+logger = logging.getLogger(f"submissions.{__name__}")
+
+
+class AddEdit(QDialog):
+
+ def __init__(self, parent, instance: Any):
+ super().__init__(parent)
+ self.instance = instance
+ self.object_type = instance.__class__
+ self.layout = QGridLayout(self)
+
+ QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
+ self.buttonBox = QDialogButtonBox(QBtn)
+ self.buttonBox.accepted.connect(self.accept)
+ self.buttonBox.rejected.connect(self.reject)
+ fields = {k: v for k, v in self.object_type.__dict__.items() if
+ isinstance(v, InstrumentedAttribute) and k != "id"}
+ for key, field in fields.items():
+ try:
+ widget = EditProperty(self, key=key, column_type=field.property.expression.type,
+ value=getattr(self.instance, key))
+ except AttributeError:
+ continue
+ self.layout.addWidget(widget, self.layout.rowCount(), 0)
+ self.layout.addWidget(self.buttonBox)
+ self.setWindowTitle(f"Add/Edit {self.object_type.__name__}")
+ self.setMinimumSize(600, 50 * len(fields))
+ self.setLayout(self.layout)
+
+ def parse_form(self):
+ results = {result[0]:result[1] for result in [item.parse_form() for item in self.findChildren(EditProperty)]}
+ # logger.debug(results)
+ model = self.object_type.get_pydantic_model()
+ model = model(**results)
+ try:
+ extras = list(model.model_extra.keys())
+ except AttributeError:
+ extras = []
+ fields = list(model.model_fields.keys()) + extras
+ for field in fields:
+ # logger.debug(result)
+ self.instance.__setattr__(field, model.__getattribute__(field))
+ return self.instance
+
+
+class EditProperty(QWidget):
+
+ def __init__(self, parent: AddEdit, key: str, column_type: Any, value):
+ super().__init__(parent)
+ self.label = QLabel(key.title().replace("_", " "))
+ self.layout = QGridLayout()
+ self.layout.addWidget(self.label, 0, 0, 1, 1)
+ self.setObjectName(key)
+ match column_type:
+ case String():
+ self.widget = QLineEdit(self)
+ self.widget.setText(value)
+ case TIMESTAMP():
+ self.widget = QDateEdit(self)
+ self.widget.setDate(value)
+ case _:
+ logger.error(f"{column_type} not a supported type.")
+ self.widget = None
+ self.layout.addWidget(self.widget, 0, 1, 1, 3)
+ self.setLayout(self.layout)
+
+ def parse_form(self):
+ match self.widget:
+ case QLineEdit():
+ value = self.widget.text()
+ case QDateEdit():
+ value = self.widget.date()
+ case _:
+ value = None
+ return self.objectName(), value
+
+
+
+
diff --git a/src/submissions/frontend/widgets/omni_manager.py b/src/submissions/frontend/widgets/omni_manager.py
new file mode 100644
index 0000000..5e79099
--- /dev/null
+++ b/src/submissions/frontend/widgets/omni_manager.py
@@ -0,0 +1,227 @@
+from typing import Any, List
+from PyQt6.QtCore import QSortFilterProxyModel, Qt
+from PyQt6.QtWidgets import (
+ QLabel, QDialog,
+ QTableView, QWidget, QLineEdit, QGridLayout, QComboBox, QPushButton, QDialogButtonBox, QDateEdit
+)
+from sqlalchemy import String, TIMESTAMP
+from sqlalchemy.orm import InstrumentedAttribute
+from sqlalchemy.orm.collections import InstrumentedList
+from sqlalchemy.orm.properties import ColumnProperty
+from sqlalchemy.orm.relationships import _RelationshipDeclared
+from pandas import DataFrame
+from backend import db
+import logging
+from .omni_add_edit import AddEdit
+from .omni_search import SearchBox
+
+from frontend.widgets.submission_table import pandasModel
+
+logger = logging.getLogger(f"submissions.{__name__}")
+
+
+class ManagerWindow(QDialog):
+ """
+ Initially this is a window to manage Organization Contacts, but hope to abstract it more later.
+ """
+
+ def __init__(self, parent, object_type: Any, extras: List[str], **kwargs):
+ super().__init__(parent)
+ self.object_type = self.original_type = object_type
+ self.instance = None
+ self.extras = extras
+ self.context = kwargs
+ self.layout = QGridLayout(self)
+ QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
+ self.buttonBox = QDialogButtonBox(QBtn)
+ self.buttonBox.accepted.connect(self.accept)
+ self.buttonBox.rejected.connect(self.reject)
+ self.setMinimumSize(600, 600)
+ sub_classes = ["Any"] + [cls.__name__ for cls in self.object_type.__subclasses__()]
+ if len(sub_classes) > 1:
+ self.sub_class = QComboBox(self)
+ self.sub_class.setObjectName("sub_class")
+ self.sub_class.addItems(sub_classes)
+ self.sub_class.currentTextChanged.connect(self.update_options)
+ self.sub_class.setEditable(False)
+ self.sub_class.setMinimumWidth(self.minimumWidth())
+ self.layout.addWidget(self.sub_class, 0, 0)
+ else:
+ self.sub_class = None
+ # self.layout.addWidget(self.buttonBox, self.layout.rowCount(), 0)
+ self.options = QComboBox(self)
+ self.options.setObjectName("options")
+ self.update_options()
+ self.setLayout(self.layout)
+ self.setWindowTitle(f"Manage {self.object_type.__name__}")
+
+ def update_options(self):
+ """
+ Changes form inputs based on sample type
+ """
+
+ if self.sub_class:
+ self.object_type = getattr(db, self.sub_class.currentText())
+ options = [item.name for item in self.object_type.query()]
+ self.options.clear()
+ self.options.addItems(options)
+ self.options.setEditable(False)
+ self.options.setMinimumWidth(self.minimumWidth())
+ self.layout.addWidget(self.options, 1, 0, 1, 1)
+ self.add_button = QPushButton("Add New")
+ self.layout.addWidget(self.add_button, 1, 1, 1, 1)
+ self.options.currentTextChanged.connect(self.update_data)
+ self.add_button.clicked.connect(self.add_new)
+ self.update_data()
+
+ def update_data(self):
+ deletes = [item for item in self.findChildren(EditProperty)] + \
+ [item for item in self.findChildren(EditRelationship)] + \
+ [item for item in self.findChildren(QDialogButtonBox)]
+ for item in deletes:
+ item.setParent(None)
+ self.instance = self.object_type.query(name=self.options.currentText())
+ fields = {k: v for k, v in self.object_type.__dict__.items() if
+ isinstance(v, InstrumentedAttribute) and k != "id"}
+ for key, field in fields.items():
+ # logger.debug(f"Key: {key}, Value: {field}")
+ match field.property:
+ case ColumnProperty():
+ widget = EditProperty(self, key=key, column_type=field.property.expression.type,
+ value=getattr(self.instance, key))
+ case _RelationshipDeclared():
+ if key != "submissions":
+ widget = EditRelationship(self, key=key, entity=field.comparator.entity.class_,
+ value=getattr(self.instance, key))
+ else:
+ continue
+ case _:
+ continue
+ if widget:
+ self.layout.addWidget(widget, self.layout.rowCount(), 0, 1, 2)
+ self.layout.addWidget(self.buttonBox, self.layout.rowCount(), 0, 1, 2)
+
+ def parse_form(self):
+ results = [item.parse_form() for item in self.findChildren(EditProperty)]
+ # logger.debug(results)
+ for result in results:
+ # logger.debug(result)
+ self.instance.__setattr__(result[0], result[1])
+ return self.instance
+
+ def add_new(self):
+ dlg = AddEdit(parent=self, instance=self.object_type())
+ if dlg.exec():
+ new_instance = dlg.parse_form()
+ # logger.debug(new_instance.__dict__)
+ new_instance.save()
+ self.update_options()
+
+
+class EditProperty(QWidget):
+
+ def __init__(self, parent: ManagerWindow, key: str, column_type: Any, value):
+ super().__init__(parent)
+ self.label = QLabel(key.title().replace("_", " "))
+ self.layout = QGridLayout()
+ self.layout.addWidget(self.label, 0, 0, 1, 1)
+ match column_type:
+ case String():
+ self.widget = QLineEdit(self)
+ self.widget.setText(value)
+ case TIMESTAMP():
+ self.widget = QDateEdit(self)
+ self.widget.setDate(value)
+ case _:
+ self.widget = None
+ self.layout.addWidget(self.widget, 0, 1, 1, 3)
+ self.setLayout(self.layout)
+
+ def parse_form(self):
+ match self.widget:
+ case QLineEdit():
+ value = self.widget.text()
+ case QDateEdit():
+ value = self.widget.date()
+ case _:
+ value = None
+ return self.objectName(), value
+
+
+class EditRelationship(QWidget):
+
+ def __init__(self, parent, key: str, entity: Any, value):
+ super().__init__(parent)
+ self.entity = entity
+ self.data = value
+ self.label = QLabel(key.title().replace("_", " "))
+ self.setObjectName(key)
+ self.table = QTableView()
+ self.add_button = QPushButton("Add New")
+ self.add_button.clicked.connect(self.add_new)
+ self.existing_button = QPushButton("Add Existing")
+ self.existing_button.clicked.connect(self.add_existing)
+ self.layout = QGridLayout()
+ self.layout.addWidget(self.label, 0, 0, 1, 5)
+ self.layout.addWidget(self.table, 1, 0, 1, 8)
+ self.layout.addWidget(self.add_button, 0, 6, 1, 1, alignment=Qt.AlignmentFlag.AlignRight)
+ self.layout.addWidget(self.existing_button, 0, 7, 1, 1, alignment=Qt.AlignmentFlag.AlignRight)
+ self.setLayout(self.layout)
+ self.set_data()
+
+ def parse_row(self, x):
+ context = {item: x.sibling(x.row(), self.data.columns.get_loc(item)).data() for item in self.data.columns}
+ try:
+ object = self.entity.query(**context)
+ except KeyError:
+ object = None
+ # logger.debug(object)
+ self.table.doubleClicked.disconnect()
+ self.add_edit(instance=object)
+
+ def add_new(self, instance: Any = None):
+ if not instance:
+ instance = self.entity()
+ dlg = AddEdit(self, instance=instance)
+ if dlg.exec():
+ new_instance = dlg.parse_form()
+ # logger.debug(new_instance.__dict__)
+ addition = getattr(self.parent().instance, self.objectName())
+ if isinstance(addition, InstrumentedList):
+ addition.append(new_instance)
+ self.parent().instance.save()
+ self.parent().update_data()
+
+ def add_existing(self):
+ dlg = SearchBox(self, object_type=self.entity, returnable=True, extras=[])
+ if dlg.exec():
+ rows = dlg.return_selected_rows()
+ # print(f"Rows selected: {[row for row in rows]}")
+ for row in rows:
+ instance = self.entity.query(**row)
+ # logger.debug(instance)
+ addition = getattr(self.parent().instance, self.objectName())
+ if isinstance(addition, InstrumentedList):
+ addition.append(instance)
+ self.parent().instance.save()
+ self.parent().update_data()
+
+ def set_data(self) -> None:
+ """
+ sets data in model
+ """
+ # logger.debug(self.data)
+ self.data = DataFrame.from_records([item.to_dict() for item in self.data])
+ try:
+ self.columns_of_interest = [dict(name=item, column=self.data.columns.get_loc(item)) for item in self.extras]
+ except (KeyError, AttributeError):
+ self.columns_of_interest = []
+ # try:
+ # self.data['id'] = self.data['id'].apply(str)
+ # self.data['id'] = self.data['id'].str.zfill(3)
+ # except (TypeError, KeyError) as e:
+ # logger.error(f"Couldn't format id string: {e}")
+ proxy_model = QSortFilterProxyModel()
+ proxy_model.setSourceModel(pandasModel(self.data))
+ self.table.setModel(proxy_model)
+ self.table.doubleClicked.connect(self.parse_row)
diff --git a/src/submissions/frontend/widgets/omni_search.py b/src/submissions/frontend/widgets/omni_search.py
index eec6771..b74d57f 100644
--- a/src/submissions/frontend/widgets/omni_search.py
+++ b/src/submissions/frontend/widgets/omni_search.py
@@ -7,7 +7,7 @@ from pandas import DataFrame
from PyQt6.QtCore import QSortFilterProxyModel
from PyQt6.QtWidgets import (
QLabel, QVBoxLayout, QDialog,
- QTableView, QWidget, QLineEdit, QGridLayout, QComboBox
+ QTableView, QWidget, QLineEdit, QGridLayout, QComboBox, QDialogButtonBox
)
from .submission_table import pandasModel
import logging
@@ -20,7 +20,7 @@ class SearchBox(QDialog):
The full search widget.
"""
- def __init__(self, parent, object_type: Any, extras: List[str], **kwargs):
+ def __init__(self, parent, object_type: Any, extras: List[str], returnable: bool = False, **kwargs):
super().__init__(parent)
self.object_type = self.original_type = object_type
self.extras = extras
@@ -44,6 +44,14 @@ class SearchBox(QDialog):
self.setWindowTitle(f"Search {self.object_type.__name__}")
self.update_widgets()
self.update_data()
+ if returnable:
+ QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
+ self.buttonBox = QDialogButtonBox(QBtn)
+ self.buttonBox.accepted.connect(self.accept)
+ self.buttonBox.rejected.connect(self.reject)
+ self.layout.addWidget(self.buttonBox, self.layout.rowCount(), 0, 1, 2)
+ self.results.doubleClicked.disconnect()
+ self.results.doubleClicked.connect(self.accept)
def update_widgets(self):
"""
@@ -63,7 +71,7 @@ class SearchBox(QDialog):
for iii, searchable in enumerate(self.object_type.searchables):
widget = FieldSearch(parent=self, label=searchable, field_name=searchable)
widget.setObjectName(searchable)
- self.layout.addWidget(widget, 1+iii, 0)
+ self.layout.addWidget(widget, 1 + iii, 0)
widget.search_widget.textChanged.connect(self.update_data)
self.update_data()
@@ -87,6 +95,13 @@ class SearchBox(QDialog):
# NOTE: Setting results moved to here from __init__ 202411118
self.results.setData(df=data)
+ def return_selected_rows(self):
+ rows = sorted(set(index.row() for index in
+ self.results.selectedIndexes()))
+ for index in rows:
+ output = {column:self.results.model().data(self.results.model().index(index, ii)) for ii, column in enumerate(self.results.data.columns)}
+ yield output
+
class FieldSearch(QWidget):
"""
diff --git a/src/submissions/tools/__init__.py b/src/submissions/tools/__init__.py
index 4bff1e6..9684887 100644
--- a/src/submissions/tools/__init__.py
+++ b/src/submissions/tools/__init__.py
@@ -7,9 +7,9 @@ import importlib
import time
from datetime import date, datetime, timedelta
from json import JSONDecodeError
-import logging, re, yaml, sys, os, stat, platform, getpass, inspect, json, numpy as np, pandas as pd
+import logging, re, yaml, sys, os, stat, platform, getpass, json, numpy as np, pandas as pd
from threading import Thread
-
+from inspect import getmembers, isfunction, stack
from dateutil.easter import easter
from jinja2 import Environment, FileSystemLoader
from logging import handlers
@@ -478,23 +478,25 @@ class Settings(BaseSettings, extra="allow"):
def set_scripts(self):
"""
- Imports all functions from "scripts" folder which will run their @registers, adding them to ctx scripts
+ Imports all functions from "scripts" folder, adding them to ctx scripts
"""
- p = Path(__file__).parent.joinpath("scripts").absolute()
- subs = [item.stem for item in p.glob("*.py") if "__" not in item.stem]
- for sub in subs:
- mod = importlib.import_module(f"tools.scripts.{sub}")
- try:
- func = mod.__getattribute__(sub)
- except AttributeError:
- try:
- func = mod.__getattribute__("script")
- except AttributeError:
- continue
- if sub in self.startup_scripts.keys():
- self.startup_scripts[sub] = func
- if sub in self.teardown_scripts.keys():
- self.teardown_scripts[sub] = func
+ if check_if_app():
+ p = Path(sys._MEIPASS).joinpath("files", "scripts")
+ else:
+ p = Path(__file__).parents[2].joinpath("scripts").absolute()
+ if p.__str__() not in sys.path:
+ sys.path.append(p.__str__())
+ modules = p.glob("[!__]*.py")
+ for module in modules:
+ mod = importlib.import_module(module.stem)
+ for function in getmembers(mod, isfunction):
+ name = function[0]
+ func = function[1]
+ # NOTE: assign function based on its name being in config: startup/teardown
+ if name in self.startup_scripts.keys():
+ self.startup_scripts[name] = func
+ if name in self.teardown_scripts.keys():
+ self.teardown_scripts[name] = func
@timer
def run_startup(self):
@@ -502,9 +504,12 @@ class Settings(BaseSettings, extra="allow"):
Runs startup scripts.
"""
for script in self.startup_scripts.values():
- logger.info(f"Running startup script: {script.__name__}")
- thread = Thread(target=script, args=(ctx,))
- thread.start()
+ try:
+ logger.info(f"Running startup script: {script.__name__}")
+ thread = Thread(target=script, args=(ctx,))
+ thread.start()
+ except AttributeError:
+ logger.error(f"Couldn't run startup script: {script}")
@timer
def run_teardown(self):
@@ -512,9 +517,12 @@ class Settings(BaseSettings, extra="allow"):
Runs teardown scripts.
"""
for script in self.teardown_scripts.values():
- logger.info(f"Running teardown script: {script.__name__}")
- thread = Thread(target=script, args=(ctx,))
- thread.start()
+ try:
+ logger.info(f"Running teardown script: {script.__name__}")
+ thread = Thread(target=script, args=(ctx,))
+ thread.start()
+ except AttributeError:
+ logger.error(f"Couldn't run teardown script: {script}")
@classmethod
def get_alembic_db_path(cls, alembic_path, mode=Literal['path', 'schema', 'user', 'pass']) -> Path | str:
@@ -874,7 +882,7 @@ class Result(BaseModel, arbitrary_types_allowed=True):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
- self.owner = inspect.stack()[1].function
+ self.owner = stack()[1].function
def report(self):
from frontend.widgets.pop_ups import AlertPop
diff --git a/src/submissions/tools/scripts/goodbye.py b/src/submissions/tools/scripts/goodbye.py
deleted file mode 100644
index c76d69e..0000000
--- a/src/submissions/tools/scripts/goodbye.py
+++ /dev/null
@@ -1,9 +0,0 @@
-"""
-Test script for teardown_scripts
-"""
-
-# from .. import register_script
-
-# @register_script
-def goodbye(ctx):
- print("\n\nGoodbye. Thank you for using Robotics Submission Tracker.\n\n")
diff --git a/src/submissions/tools/scripts/hello.py b/src/submissions/tools/scripts/hello.py
deleted file mode 100644
index 5cbec2d..0000000
--- a/src/submissions/tools/scripts/hello.py
+++ /dev/null
@@ -1,8 +0,0 @@
-"""
-Test script for startup_scripts
-"""
-# from .. import register_script
-
-# @register_script
-def hello(ctx):
- print("\n\nHello! Welcome to Robotics Submission Tracker.\n\n")
diff --git a/submissions.spec b/submissions.spec
index 7f95b62..d3326f5 100644
--- a/submissions.spec
+++ b/submissions.spec
@@ -36,6 +36,7 @@ a = Analysis(
("docs\\build", "files\\docs"),
("src\\submissions\\resources\\*", "files\\resources"),
("alembic.ini", "files"),
+ ("src\\scripts\\*.py", "files\\scripts")
],
hiddenimports=["pyodbc"],
hookspath=[],