Added report tab with HTML and excel export.

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

@@ -13,7 +13,7 @@ from tempfile import TemporaryDirectory, TemporaryFile
 from operator import itemgetter
 from pprint import pformat
 from . import BaseClass, Reagent, SubmissionType, KitType, Organization, Contact
-from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case
+from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case, desc
 from sqlalchemy.orm import relationship, validates, Query
 from sqlalchemy.orm.attributes import flag_modified
 from sqlalchemy.ext.associationproxy import association_proxy
@@ -283,7 +283,7 @@ class BasicSubmission(BaseClass):
         del input_dict['id']
         return input_dict
 
-    def generate_associations(self, name:str, extra:str|None=None):
+    def generate_associations(self, name: str, extra: str | None = None):
         try:
             field = self.__getattribute__(name)
         except AttributeError:
@@ -479,15 +479,6 @@ class BasicSubmission(BaseClass):
         Returns:
             str: html output string.
         """
-        # output_samples = []
-        # logger.debug("Setting locations.")
-        # for column in range(1, plate_columns + 1):
-        #     for row in range(1, plate_rows + 1):
-        #         try:
-        #             well = next((item for item in sample_list if item['row'] == row and item['column'] == column), dict(name="", row=row, column=column, background_color="#ffffff"))
-        #         except StopIteration:
-        #             well = dict(name="", row=row, column=column, background_color="#ffffff")
-        #         output_samples.append(well)
         rows = range(1, plate_rows + 1)
         columns = range(1, plate_columns + 1)
         # NOTE: An overly complicated list comprehension create a list of sample locations
@@ -512,11 +503,12 @@ class BasicSubmission(BaseClass):
 
     @classmethod
     def submissions_to_df(cls, submission_type: str | None = None, limit: int = 0,
-                          chronologic: bool = True) -> pd.DataFrame:
+                          chronologic: bool = True, page: int = 1, page_size: int = 250) -> pd.DataFrame:
         """
         Convert all submissions to dataframe
 
         Args:
+            page (int, optional): Limits the number of submissions to a page size. Defaults to 1.
             chronologic (bool, optional): Sort submissions in chronologic order. Defaults to True.
             submission_type (str | None, optional): Filter by SubmissionType. Defaults to None.
             limit (int, optional): Maximum number of results to return. Defaults to 0.
@@ -528,7 +520,7 @@ class BasicSubmission(BaseClass):
         # logger.debug(f"Using limit: {limit}")
         # NOTE: use lookup function to create list of dicts
         subs = [item.to_dict() for item in
-                cls.query(submission_type=submission_type, limit=limit, chronologic=chronologic)]
+                cls.query(submission_type=submission_type, limit=limit, chronologic=chronologic, page=page, page_size=page_size)]
         # logger.debug(f"Got {len(subs)} submissions.")
         df = pd.DataFrame.from_records(subs)
         # logger.debug(f"Column names: {df.columns}")
@@ -829,7 +821,7 @@ class BasicSubmission(BaseClass):
         return input_dict
 
     @classmethod
-    def custom_validation(cls, pyd:"PydSubmission") -> dict:
+    def custom_validation(cls, pyd: "PydSubmission") -> dict:
         """
         Performs any final custom parsing of the excel file.
 
@@ -886,7 +878,6 @@ class BasicSubmission(BaseClass):
                         ws.cell(row=item['row'], column=item['column'], value=item['value'])
         return input_excel
 
-
     @classmethod
     def enforce_name(cls, instr: str, data: dict | None = {}) -> str:
         """
@@ -1061,6 +1052,8 @@ class BasicSubmission(BaseClass):
               reagent: Reagent | str | None = None,
               chronologic: bool = False,
               limit: int = 0,
+              page: int = 1,
+              page_size: int = 250,
               **kwargs
               ) -> BasicSubmission | List[BasicSubmission]:
         """
@@ -1161,7 +1154,13 @@ class BasicSubmission(BaseClass):
             case _:
                 pass
         if chronologic:
-            query.order_by(cls.submitted_date)
+            logger.debug("Attempting sort by date descending")
+            query = query.order_by(cls.submitted_date.desc())
+        if page_size is not None:
+            query = query.limit(page_size)
+        page = page - 1
+        if page is not None:
+            query = query.offset(page * page_size)
         return cls.execute_query(query=query, model=model, limit=limit, **kwargs)
 
     @classmethod

src/submissions/backend/validators/pydant.py

@@ -611,7 +611,7 @@ class PydSubmission(BaseModel, extra='allow'):
     @classmethod
     def expand_samples(cls, value):
         if isinstance(value, Generator):
-            # logger.debug("We have a generator")
+            # logger.debug("We have a generator")[
             return [PydSample(**sample) for sample in value]
         return value
 

src/submissions/frontend/widgets/app.py

@@ -12,11 +12,11 @@ from pathlib import Path
 
 from markdown import markdown
 from __init__ import project_path
-from tools import check_if_app, Settings, Report, jinja_template_loading, check_authorization
+from tools import check_if_app, Settings, Report, jinja_template_loading, check_authorization, page_size
 from .functions import select_save_file,select_open_file
 from datetime import date
 from .pop_ups import HTMLPop, AlertPop
-from .misc import LogParser
+from .misc import LogParser, Pagifier
 import logging, webbrowser, sys, shutil
 from .submission_table import SubmissionsSheet
 from .submission_widget import SubmissionFormContainer
@@ -49,6 +49,7 @@ class App(QMainWindow):
         self.height = 1000
         self.setWindowTitle(self.title)
         self.setGeometry(self.left, self.top, self.width, self.height)
+        self.page_size = page_size
         # NOTE: insert tabs into main app
         self.table_widget = AddSubForm(self)
         self.setCentralWidget(self.table_widget)
@@ -133,6 +134,7 @@ class App(QMainWindow):
         self.githubAction.triggered.connect(self.openGithub)
         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)
 
     def showAbout(self):
         """
@@ -237,6 +239,8 @@ class App(QMainWindow):
             else:
                 logger.warning("Save of submission type cancelled.")
 
+    def update_data(self):
+        self.table_widget.sub_wid.setData(page=int(self.table_widget.pager.current_page.text()), page_size=page_size)
 
 
 class AddSubForm(QWidget):
@@ -272,7 +276,9 @@ class AddSubForm(QWidget):
         self.sheetlayout = QVBoxLayout(self)
         self.sheetwidget.setLayout(self.sheetlayout)
         self.sub_wid = SubmissionsSheet(parent=parent)
+        self.pager = Pagifier(page_max=self.sub_wid.total_count/page_size)
         self.sheetlayout.addWidget(self.sub_wid)
+        self.sheetlayout.addWidget(self.pager)
         # NOTE: Create layout of first tab to hold form and sheet
         self.tab1.layout = QHBoxLayout(self)
         self.tab1.setLayout(self.tab1.layout)

src/submissions/frontend/widgets/misc.py

@@ -1,21 +1,22 @@
 '''
 Contains miscellaneous widgets for frontend functions
 '''
+import math
 from datetime import date
 
-from PyQt6.QtGui import QPageLayout, QPageSize, QStandardItem, QStandardItemModel
+from PyQt6.QtGui import QPageLayout, QPageSize, QStandardItem, QIcon
 from PyQt6.QtWebEngineWidgets import QWebEngineView
 from PyQt6.QtWidgets import (
     QLabel, QVBoxLayout,
     QLineEdit, QComboBox, QDialog,
     QDialogButtonBox, QDateEdit, QPushButton, QFormLayout, QWidget, QHBoxLayout, QSizePolicy
 )
-from PyQt6.QtCore import Qt, QDate, QSize, QMarginsF, pyqtSlot, pyqtSignal, QEvent
+from PyQt6.QtCore import Qt, QDate, QSize, QMarginsF
 from tools import jinja_template_loading
 from backend.db.models import *
 import logging
 from .pop_ups import AlertPop
-from .functions import select_open_file, select_save_file
+from .functions import select_open_file
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -245,3 +246,42 @@ class CheckableComboBox(QComboBox):
     def changed(self):
         logger.debug("emitting updated")
         self.updated.emit()
+
+
+class Pagifier(QWidget):
+
+    def __init__(self, page_max:int):
+        super().__init__()
+        self.page_max = math.ceil(page_max)
+
+        next = QPushButton(parent=self, icon = QIcon.fromTheme(QIcon.ThemeIcon.GoNext))
+        next.pressed.connect(self.increment_page)
+        previous = QPushButton(parent=self, icon=QIcon.fromTheme(QIcon.ThemeIcon.GoPrevious))
+        previous.pressed.connect(self.decrement_page)
+        label = QLabel(f"/ {self.page_max}")
+        label.setMinimumWidth(200)
+        label.setAlignment(Qt.AlignmentFlag.AlignCenter)
+        self.current_page = QLineEdit(self)
+        self.current_page.setEnabled(False)
+        # onlyInt = QIntValidator()
+        # onlyInt.setRange(1, 4)
+        # self.current_page.setValidator(onlyInt)
+        self.current_page.setText("1")
+        self.current_page.setAlignment(Qt.AlignmentFlag.AlignCenter)
+        self.layout = QHBoxLayout()
+        self.layout.addWidget(previous)
+        self.layout.addWidget(self.current_page)
+        self.layout.addWidget(label)
+        self.layout.addWidget(next)
+        self.setLayout(self.layout)
+
+    def increment_page(self):
+        new = int(self.current_page.text())+1
+        if new <= self.page_max:
+            self.current_page.setText(str(new))
+
+    def decrement_page(self):
+        new = int(self.current_page.text())-1
+        if new >= 1:
+            self.current_page.setText(str(new))
+

src/submissions/frontend/widgets/submission_table.py

@@ -7,9 +7,9 @@ from PyQt6.QtWidgets import QTableView, QMenu
 from PyQt6.QtCore import Qt, QAbstractTableModel, QSortFilterProxyModel
 from PyQt6.QtGui import QAction, QCursor
 from backend.db.models import BasicSubmission
-from backend.excel import ReportMaker
 from tools import Report, Result, report_result
-from .functions import select_save_file, select_open_file
+from .functions import select_open_file
+
 # from .misc import ReportDatePicker
 
 logger = logging.getLogger(f"submissions.{__name__}")
@@ -20,6 +20,7 @@ class pandasModel(QAbstractTableModel):
     pandas model for inserting summary sheet into gui
     NOTE: Copied from Stack Overflow. I have no idea how it actually works.
     """
+
     def __init__(self, data) -> None:
         QAbstractTableModel.__init__(self)
         self._data = data
@@ -48,7 +49,7 @@ class pandasModel(QAbstractTableModel):
         """
         return self._data.shape[1]
 
-    def data(self, index, role=Qt.ItemDataRole.DisplayRole) -> str|None:
+    def data(self, index, role=Qt.ItemDataRole.DisplayRole) -> str | None:
         if index.isValid():
             if role == Qt.ItemDataRole.DisplayRole:
                 return str(self._data.iloc[index.row(), index.column()])
@@ -64,6 +65,7 @@ class SubmissionsSheet(QTableView):
     """
     presents submission summary to user in tab1
     """
+
     def __init__(self, parent) -> None:
         """
         initialize
@@ -74,17 +76,18 @@ class SubmissionsSheet(QTableView):
         super().__init__(parent)
         self.app = self.parent()
         self.report = Report()
-        self.setData()
+        self.setData(page=1, page_size=self.app.page_size)
         self.resizeColumnsToContents()
         self.resizeRowsToContents()
         self.setSortingEnabled(True)
         self.doubleClicked.connect(lambda x: BasicSubmission.query(id=x.sibling(x.row(), 0).data()).show_details(self))
+        self.total_count = BasicSubmission.__database_session__.query(BasicSubmission).count()
 
-    def setData(self) -> None: 
+    def setData(self, page: int = 1, page_size: int = 250) -> None:
         """
         sets data in model
         """
-        self.data = BasicSubmission.submissions_to_df()
+        self.data = BasicSubmission.submissions_to_df(page=page)
         try:
             self.data['Id'] = self.data['Id'].apply(str)
             self.data['Id'] = self.data['Id'].str.zfill(4)
@@ -103,7 +106,7 @@ class SubmissionsSheet(QTableView):
         """
         # logger.debug(event().__dict__)
         id = self.selectionModel().currentIndex()
-        id = id.sibling(id.row(),0).data()
+        id = id.sibling(id.row(), 0).data()
         submission = BasicSubmission.query(id=id)
         self.menu = QMenu(self)
         self.con_actions = submission.custom_context_events()
@@ -115,7 +118,7 @@ class SubmissionsSheet(QTableView):
         # add other required actions
         self.menu.popup(QCursor.pos())
 
-    def triggered_action(self, action_name:str):
+    def triggered_action(self, action_name: str):
         """
         Calls the triggered action from the context menu
 
@@ -164,7 +167,7 @@ class SubmissionsSheet(QTableView):
             )
             # NOTE: elution columns are item 6 in the comma split list to the end
             for ii in range(6, len(run)):
-                new_run[f"column{str(ii-5)}_vol"] = run[ii]
+                new_run[f"column{str(ii - 5)}_vol"] = run[ii]
             # NOTE: Lookup imported submissions
             sub = BasicSubmission.query(rsl_plate_num=new_run['rsl_plate_num'])
             # NOTE: If no such submission exists, move onto the next run
@@ -225,33 +228,3 @@ class SubmissionsSheet(QTableView):
             sub.save()
         report.add_result(Result(msg=f"We added {count} logs to the database.", status='Information'))
         return report
-
-    # @report_result
-    # def generate_report(self, *args):
-    #     """
-    #     Make a report
-    #     """
-    #     report = Report()
-    #     result = self.generate_report_function()
-    #     report.add_result(result)
-    #     return report
-    #
-    # def generate_report_function(self):
-    #     """
-    #     Generate a summary of activities for a time period
-    #
-    #     Args:
-    #         obj (QMainWindow): original app window
-    #
-    #     Returns:
-    #         Tuple[QMainWindow, dict]: Collection of new main app window and result dict
-    #     """
-    #     report = Report()
-    #     # NOTE: ask for date ranges
-    #     dlg = ReportDatePicker()
-    #     if dlg.exec():
-    #         info = dlg.parse_form()
-    #         fname = select_save_file(obj=self, default_name=f"Submissions_Report_{info['start_date']}-{info['end_date']}.xlsx", extension="xlsx")
-    #         rp = ReportMaker(start_date=info['start_date'], end_date=info['end_date'])
-    #         rp.write_report(filename=fname, obj=self)
-    #     return report