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Prior to creation of omni-search

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This commit is contained in:
lwark
2024-11-15 09:34:28 -06:00
parent 514781fd29
commit 3d6a42b36f
5 changed files with 157 additions and 3 deletions
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18
src/submissions/backend/db/models/submissions.py
View File

@@ -844,6 +844,9 @@ class BasicSubmission(BaseClass):
ws.cell(row=item['row'], column=item['column'], value=item['value'])
return input_excel
def custom_sample_writer(self, sample:dict) -> dict:
return sample
@classmethod
def enforce_name(cls, instr: str, data: dict | None = {}) -> str:
"""
@@ -1692,6 +1695,8 @@ class WastewaterArtic(BasicSubmission):
output['artic_technician'] = self.technician
else:
output['artic_technician'] = self.artic_technician
# logger.debug(full_data)
# logger.debug(output.keys())
output['gel_info'] = self.gel_info
output['gel_image_path'] = self.gel_image
output['dna_core_submission_number'] = self.dna_core_submission_number
@@ -1850,13 +1855,17 @@ class WastewaterArtic(BasicSubmission):
dict: Updated sample dictionary
"""
input_dict = super().parse_samples(input_dict)
# logger.debug(f"WWA input dict: {pformat(input_dict)}")
logger.debug(f"WWA input dict: {pformat(input_dict)}")
input_dict['sample_type'] = "Wastewater Sample"
# NOTE: Stop gap solution because WW is sloppy with their naming schemes
try:
input_dict['source_plate'] = input_dict['source_plate'].replace("WW20", "WW-20")
except KeyError:
pass
try:
input_dict['source_plate_number'] = int(input_dict['source_plate_number'])
except ValueError:
input_dict['source_plate_number'] = 0
# NOTE: Because generate_sample_object needs the submitter_id and the artic has the "({origin well})"
# at the end, this has to be done here. No moving to sqlalchemy object :(
input_dict['submitter_id'] = re.sub(r"\s\(.+\)\s?$", "", str(input_dict['submitter_id'])).strip()
@@ -2081,6 +2090,13 @@ class WastewaterArtic(BasicSubmission):
logger.warning("No gel image found.")
return input_excel
@classmethod
def custom_sample_writer(self, sample:dict) -> dict:
logger.debug("Wastewater Artic custom sample writer")
if sample['source_plate_number'] in [0, "0"]:
sample['source_plate_number'] = "control"
return sample
@classmethod
def get_details_template(cls, base_dict: dict) -> Tuple[dict, Template]:
"""

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

@@ -48,7 +48,7 @@ class ReportMaker(object):
# logger.debug(f"Output daftaframe for xlsx: {df2.columns}")
df = df.drop('id', axis=1)
df = df.sort_values(['submitting_lab', "submitted_date"])
logger.debug(f"Details dataframe:\n{df2}")
# logger.debug(f"Details dataframe:\n{df2}")
return df, df2
def make_report_html(self, df: DataFrame) -> str:

3
src/submissions/backend/excel/writer.py
View File

@@ -291,7 +291,8 @@ class SampleWriter(object):
"""
multiples = ['row', 'column', 'assoc_id', 'submission_rank']
for sample in sample_list:
# logger.debug(f"Writing sample: {sample}")
sample = self.submission_type.get_submission_class().custom_sample_writer(sample)
logger.debug(f"Writing sample: {sample}")
for assoc in zip(sample['row'], sample['column'], sample['submission_rank']):
new = dict(row=assoc[0], column=assoc[1], submission_rank=assoc[2])
for k, v in sample.items():

9
src/submissions/frontend/widgets/app.py
View File

@@ -71,6 +71,7 @@ class App(QMainWindow):
# logger.debug(f"Creating menu bar...")
menuBar = self.menuBar()
fileMenu = menuBar.addMenu("&File")
editMenu = menuBar.addMenu("&Edit")
# NOTE: Creating menus using a title
methodsMenu = menuBar.addMenu("&Methods")
maintenanceMenu = menuBar.addMenu("&Monthly")
@@ -85,6 +86,7 @@ class App(QMainWindow):
methodsMenu.addAction(self.searchSample)
maintenanceMenu.addAction(self.joinExtractionAction)
maintenanceMenu.addAction(self.joinPCRAction)
editMenu.addAction(self.editReagentAction)
def _createToolBar(self):
"""
@@ -115,6 +117,7 @@ class App(QMainWindow):
self.githubAction = QAction("Github", self)
self.yamlExportAction = QAction("Export Type Example", self)
self.yamlImportAction = QAction("Import Type Template", self)
self.editReagentAction = QAction("Edit Reagent", self)
def _connectActions(self):
"""
@@ -133,6 +136,7 @@ class App(QMainWindow):
self.yamlExportAction.triggered.connect(self.export_ST_yaml)
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)
def showAbout(self):
"""
@@ -220,6 +224,11 @@ class App(QMainWindow):
fname = select_save_file(obj=self, default_name="Submission Type Template.yml", extension="yml")
shutil.copyfile(yaml_path, fname)
@check_authorization
def edit_reagent(self, *args, **kwargs):
dlg = EditReagent()
dlg.exec()
@check_authorization
def import_ST_yaml(self, *args, **kwargs):
fname = select_open_file(obj=self, file_extension="yml")

128
src/submissions/frontend/widgets/omni_search.py Normal file
View File

@@ -0,0 +1,128 @@
'''
Search box that performs fuzzy search for samples
'''
from pprint import pformat
from typing import Tuple
from pandas import DataFrame
from PyQt6.QtCore import QSortFilterProxyModel
from PyQt6.QtWidgets import (
QLabel, QVBoxLayout, QDialog,
QComboBox, QTableView, QWidget, QLineEdit, QGridLayout
)
from backend.db.models import BasicSample
from .submission_table import pandasModel
import logging
logger = logging.getLogger(f"submissions.{__name__}")
class SearchBox(QDialog):
def __init__(self, parent):
super().__init__(parent)
self.layout = QGridLayout(self)
self.sample_type = QComboBox(self)
self.sample_type.setObjectName("sample_type")
self.sample_type.currentTextChanged.connect(self.update_widgets)
options = ["Any"] + [cls.__mapper_args__['polymorphic_identity'] for cls in BasicSample.__subclasses__()]
self.sample_type.addItems(options)
self.sample_type.setEditable(False)
self.setMinimumSize(600, 600)
self.sample_type.setMinimumWidth(self.minimumWidth())
self.layout.addWidget(self.sample_type, 0, 0)
self.results = SearchResults()
self.layout.addWidget(self.results, 5, 0)
self.setLayout(self.layout)
self.update_widgets()
self.update_data()
def update_widgets(self):
"""
Changes form inputs based on sample type
"""
deletes = [item for item in self.findChildren(FieldSearch)]
# logger.debug(deletes)
for item in deletes:
item.setParent(None)
if self.sample_type.currentText() == "Any":
self.type = BasicSample
else:
self.type = BasicSample.find_polymorphic_subclass(self.sample_type.currentText())
# logger.debug(f"Sample type: {self.type}")
searchables = self.type.get_searchables()
start_row = 1
for iii, item in enumerate(searchables):
widget = FieldSearch(parent=self, label=item['label'], field_name=item['field'])
self.layout.addWidget(widget, start_row + iii, 0)
widget.search_widget.textChanged.connect(self.update_data)
self.update_data()
def parse_form(self) -> dict:
"""
Converts form into dictionary.
Returns:
dict: Fields dictionary
"""
fields = [item.parse_form() for item in self.findChildren(FieldSearch)]
return {item[0]: item[1] for item in fields if item[1] is not None}
def update_data(self):
"""
Shows dataframe of relevant samples.
"""
# logger.debug(f"Running update_data with sample type: {self.type}")
fields = self.parse_form()
# logger.debug(f"Got fields: {fields}")
sample_list_creator = self.type.fuzzy_search(**fields)
data = self.type.samples_to_df(sample_list=sample_list_creator)
# logger.debug(f"Data: {data}")
self.results.setData(df=data)
class FieldSearch(QWidget):
def __init__(self, parent, label, field_name):
super().__init__(parent)
self.layout = QVBoxLayout(self)
label_widget = QLabel(label)
self.layout.addWidget(label_widget)
self.search_widget = QLineEdit()
self.search_widget.setObjectName(field_name)
self.layout.addWidget(self.search_widget)
self.setLayout(self.layout)
self.search_widget.returnPressed.connect(self.enter_pressed)
def enter_pressed(self):
"""
Triggered when enter is pressed on this input field.
"""
self.parent().update_data()
def parse_form(self) -> Tuple:
field_value = self.search_widget.text()
if field_value == "":
field_value = None
return self.search_widget.objectName(), field_value
class SearchResults(QTableView):
def __init__(self):
super().__init__()
self.doubleClicked.connect(
lambda x: BasicSample.query(submitter_id=x.sibling(x.row(), 0).data()).show_details(self))
def setData(self, df: DataFrame) -> None:
"""
sets data in model
"""
self.data = df
try:
self.data['id'] = self.data['id'].apply(str)
self.data['id'] = self.data['id'].str.zfill(3)
except (TypeError, KeyError):
logger.error("Couldn't format id string.")
proxy_model = QSortFilterProxyModel()
proxy_model.setSourceModel(pandasModel(self.data))
self.setModel(proxy_model)