Prior to creation of omni-search

src/submissions/backend/db/models/submissions.py

@@ -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]:
         """

src/submissions/backend/excel/reports.py

@@ -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:

src/submissions/backend/excel/writer.py

@@ -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():

src/submissions/frontend/widgets/app.py

@@ -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")

src/submissions/frontend/widgets/omni_search.py

@@ -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)