Increasing generator usage.

CHANGELOG.md

@@ -1,3 +1,8 @@
+## 202410.02
+
+- Trimmed down html timeline buttons for controls window.
+- Improved paginator for submissions table.
+
 ## 202410.01
 
 - Reverted details exports from docx back to pdf.

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

@@ -142,8 +142,8 @@ class KitType(BaseClass):
         """
         return f"<KitType({self.name})>"
 
-    def get_reagents(self, required: bool = False, submission_type: str | SubmissionType | None = None) -> List[
+    def get_reagents(self, required: bool = False, submission_type: str | SubmissionType | None = None) -> Generator[
-        ReagentRole]:
+        ReagentRole, None, None]:
         """
         Return ReagentTypes linked to kit through KitTypeReagentTypeAssociation.
 
@@ -168,9 +168,9 @@ class KitType(BaseClass):
                 relevant_associations = [item for item in self.kit_reagentrole_associations]
         if required:
             # logger.debug(f"Filtering by required.")
-            return [item.reagent_role for item in relevant_associations if item.required == 1]
+            return (item.reagent_role for item in relevant_associations if item.required == 1)
         else:
-            return [item.reagent_role for item in relevant_associations]
+            return (item.reagent_role for item in relevant_associations)
 
     # TODO: Move to BasicSubmission?
     def construct_xl_map_for_use(self, submission_type: str | SubmissionType) -> Generator[(str, str)]:
@@ -198,6 +198,7 @@ class KitType(BaseClass):
         # logger.debug("Get all KitTypeReagentTypeAssociation for SubmissionType")
         for assoc in assocs:
             try:
+                logger.debug(f"Yielding: {assoc.reagent_role.name}, {assoc.uses}")
                 yield assoc.reagent_role.name, assoc.uses
             except TypeError:
                 continue
@@ -764,14 +765,14 @@ class SubmissionType(BaseClass):
                 tmap = {}
             yield item.tip_role.name, tmap
 
-    def get_equipment(self, extraction_kit: str | KitType | None = None) -> List['PydEquipmentRole']:
+    def get_equipment(self, extraction_kit: str | KitType | None = None) -> Generator['PydEquipmentRole', None, None]:
         """
         Returns PydEquipmentRole of all equipment associated with this SubmissionType
 
         Returns:
             List[PydEquipmentRole]: List of equipment roles
         """
-        return [item.to_pydantic(submission_type=self, extraction_kit=extraction_kit) for item in self.equipment]
+        return (item.to_pydantic(submission_type=self, extraction_kit=extraction_kit) for item in self.equipment)
 
     def get_processes_for_role(self, equipment_role: str | EquipmentRole, kit: str | KitType | None = None) -> list:
         """

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

@@ -219,11 +219,11 @@ class BasicSubmission(BaseClass):
         if len(args) == 1:
             try:
                 return output[args[0]]
-            except KeyError:
+            except KeyError as e:
                 if "pytest" in sys.modules and args[0] == "abbreviation":
                     return "BS"
                 else:
-                    raise KeyError("args[0]")
+                    raise KeyError(f"{args[0]} not found in {output}")
         return output
 
     @classmethod
@@ -237,6 +237,13 @@ class BasicSubmission(BaseClass):
         Returns:
             SubmissionType: SubmissionType with name equal to this polymorphic identity
         """
+        logger.debug(f"Running search for {sub_type}")
+        if isinstance(sub_type, dict):
+            try:
+                sub_type = sub_type['value']
+            except KeyError as e:
+                logger.error(f"Couldn't extract value from {sub_type}")
+                raise e
         match sub_type:
             case str():
                 return SubmissionType.query(name=sub_type)

src/submissions/backend/excel/parser.py

@@ -80,14 +80,6 @@ class SheetParser(object):
                 self.submission_type = RSLNamer.retrieve_submission_type(filename=self.filepath)
                 self.parse_info()
         [self.sub.__setitem__(k, v) for k, v in info.items()]
-        # for k, v in info.items():
-        #     match k:
-        #         # NOTE: exclude samples.
-        #         case "sample":
-        #             logger.debug(f"Sample found: {k}: {v}")
-        #             continue
-        #         case _:
-        #             self.sub[k] = v
 
     def parse_reagents(self, extraction_kit: str | None = None):
         """
@@ -147,30 +139,8 @@ class SheetParser(object):
         Returns:
             PydSubmission: output pydantic model
         """
-        # logger.debug(f"Submission dictionary coming into 'to_pydantic':\n{pformat(self.sub)}")
-        # pyd_dict = copy(self.sub)
-        # self.sub['samples'] = [PydSample(**sample) for sample in self.sub['samples']]
-        # logger.debug(f"Reagents: {pformat(self.sub['reagents'])}")
-        # self.sub['reagents'] = [PydReagent(**reagent) for reagent in self.sub['reagents']]
-        # logger.debug(f"Equipment: {self.sub['equipment']}")
-        # try:
-        #     check = bool(self.sub['equipment'])
-        # except TypeError:
-        #     check = False
-        # if check:
-        #     self.sub['equipment'] = [PydEquipment(**equipment) for equipment in self.sub['equipment']]
-        # else:
-        #     self.sub['equipment'] = None
-        # try:
-        #     check = bool(self.sub['tips'])
-        # except TypeError:
-        #     check = False
-        # if check:
-        #     self.sub['tips'] = [PydTips(**tips) for tips in self.sub['tips']]
-        # else:
-        #     self.sub['tips'] = None
         return PydSubmission(filepath=self.filepath, run_custom=True, **self.sub)
-        # return psm
+
 
 
 class InfoParser(object):
@@ -298,6 +268,7 @@ class ReagentParser(object):
         if isinstance(extraction_kit, dict):
             extraction_kit = extraction_kit['value']
         self.kit_object = KitType.query(name=extraction_kit)
+        # logger.debug(f"Got extraction kit object: {self.kit_object}")
         self.map = self.fetch_kit_info_map(submission_type=submission_type)
         # logger.debug(f"Reagent Parser map: {self.map}")
         self.xl = xl
@@ -329,15 +300,14 @@ class ReagentParser(object):
         Returns:
             List[PydReagent]: List of parsed reagents.
         """
-        # listo = []
         for sheet in self.xl.sheetnames:
             ws = self.xl[sheet]
             relevant = {k.strip(): v for k, v in self.map.items() if sheet in self.map[k]['sheet']}
-            # logger.debug(f"relevant map for {sheet}: {pformat(relevant)}")
+            logger.debug(f"relevant map for {sheet}: {pformat(relevant)}")
             if relevant == {}:
                 continue
             for item in relevant:
-                # logger.debug(f"Attempting to scrape: {item}")
+                logger.debug(f"Attempting to scrape: {item}")
                 try:
                     reagent = relevant[item]
                     name = ws.cell(row=reagent['name']['row'], column=reagent['name']['column']).value
@@ -350,16 +320,15 @@ class ReagentParser(object):
                         comment = ""
                 except (KeyError, IndexError):
                     yield dict(role=item.strip(), lot=None, expiry=None, name=None, comment="", missing=True)
-                    # continue
                 # NOTE: If the cell is blank tell the PydReagent
                 if check_not_nan(lot):
                     missing = False
                 else:
                     missing = True
-                # logger.debug(f"Got lot for {item}-{name}: {lot} as {type(lot)}")
+                logger.debug(f"Got lot for {item}-{name}: {lot} as {type(lot)}")
                 lot = str(lot)
-                # logger.debug(
+                logger.debug(
-                #     f"Going into pydantic: name: {name}, lot: {lot}, expiry: {expiry}, type: {item.strip()}, comment: {comment}")
+                    f"Going into pydantic: name: {name}, lot: {lot}, expiry: {expiry}, type: {item.strip()}, comment: {comment}")
                 try:
                     check = name.lower() != "not applicable"
                 except AttributeError:
@@ -368,7 +337,6 @@ class ReagentParser(object):
                 if check:
                     yield dict(role=item.strip(), lot=lot, expiry=expiry, name=name, comment=comment,
                                missing=missing)
-        # return listo
 
 
 class SampleParser(object):
@@ -480,34 +448,6 @@ class SampleParser(object):
                 lookup_samples.append(self.samp_object.parse_sample(row_dict))
         return lookup_samples
 
-    # def parse_samples(self) -> Tuple[Report | None, List[dict] | List[PydSample]]:
-    #     """
-    #     Parse merged platemap/lookup info into dicts/samples
-    #
-    #     Returns:
-    #         List[dict]|List[models.BasicSample]: List of samples
-    #     """
-    #     result = None
-    #     new_samples = []
-    #     # logger.debug(f"Starting samples: {pformat(self.samples)}")
-    #     for sample in self.samples:
-    #         translated_dict = {}
-    #         for k, v in sample.items():
-    #             match v:
-    #                 case dict():
-    #                     v = None
-    #                 case float():
-    #                     v = convert_nans_to_nones(v)
-    #                 case _:
-    #                     v = v
-    #             translated_dict[k] = convert_nans_to_nones(v)
-    #         translated_dict['sample_type'] = f"{self.submission_type} Sample"
-    #         translated_dict = self.sub_object.parse_samples(translated_dict)
-    #         translated_dict = self.samp_object.parse_sample(translated_dict)
-    #         # logger.debug(f"Here is the output of the custom parser:\n{translated_dict}")
-    #         new_samples.append(PydSample(**translated_dict))
-    #     return result, new_samples
-
     def parse_samples(self) -> Generator[dict, None, None]:
         """
         Merges sample info from lookup table and plate map.
@@ -522,9 +462,8 @@ class SampleParser(object):
         merge_on_id = self.sample_info_map['lookup_table']['merge_on_id']
         plate_map_samples = sorted(copy(self.plate_map_samples), key=lambda d: d['id'])
         lookup_samples = sorted(copy(self.lookup_samples), key=lambda d: d[merge_on_id])
-        # print(pformat(plate_map_samples))
-        # print(pformat(lookup_samples))
         for ii, psample in enumerate(plate_map_samples):
+            # NOTE: See if we can do this the easy way and just use the same list index.
             try:
                 check = psample['id'] == lookup_samples[ii][merge_on_id]
             except (KeyError, IndexError):
@@ -534,7 +473,7 @@ class SampleParser(object):
                 new = lookup_samples[ii] | psample
                 lookup_samples[ii] = {}
             else:
-                # logger.warning(f"Match for {psample['id']} not direct, running search.")
+                logger.warning(f"Match for {psample['id']} not direct, running search.")
                 for jj, lsample in enumerate(lookup_samples):
                     try:
                         check = lsample[merge_on_id] == psample['id']
@@ -551,9 +490,6 @@ class SampleParser(object):
             new = self.sub_object.parse_samples(new)
             del new['id']
             yield new
-            # samples.append(new)
-        # samples = remove_key_from_list_of_dicts(samples, "id")
-        # return sorted(samples, key=lambda k: (k['row'], k['column']))
 
 
 class EquipmentParser(object):

src/submissions/frontend/visualizations/control_charts.py

@@ -2,6 +2,7 @@
 Functions for constructing controls graphs using plotly.
 """
 from copy import deepcopy
+from datetime import date
 from pprint import pformat
 
 import plotly
@@ -18,10 +19,12 @@ logger = logging.getLogger(f"submissions.{__name__}")
 
 class CustomFigure(Figure):
 
-    def __init__(self, df: pd.DataFrame, modes: list, ytitle: str | None = None, parent: QWidget | None = None):
+    def __init__(self, df: pd.DataFrame, modes: list, ytitle: str | None = None, parent: QWidget | None = None,
+                 months: int = 6):
         super().__init__()
+
         self.construct_chart(df=df, modes=modes)
-        self.generic_figure_markers(modes=modes, ytitle=ytitle)
+        self.generic_figure_markers(modes=modes, ytitle=ytitle, months=months)
 
     def construct_chart(self, df: pd.DataFrame, modes: list):
         """
@@ -67,7 +70,7 @@ class CustomFigure(Figure):
             self.add_traces(bar.data)
         # return generic_figure_markers(modes=modes, ytitle=ytitle)
 
-    def generic_figure_markers(self, modes: list = [], ytitle: str | None = None):
+    def generic_figure_markers(self, modes: list = [], ytitle: str | None = None, months: int = 6):
         """
         Adds standard layout to figure.
 
@@ -94,27 +97,41 @@ class CustomFigure(Figure):
                     x=0.7,
                     y=1.2,
                     showactive=True,
-                    buttons=[button for button in self.make_buttons(modes=modes)],
+                    buttons=[button for button in self.make_pyqt_buttons(modes=modes)],
                 )
             ]
         )
+
         self.update_xaxes(
             rangeslider_visible=True,
             rangeselector=dict(
-                buttons=list([
+                # buttons=list([
-                    dict(count=1, label="1m", step="month", stepmode="backward"),
+                #     dict(count=1, label="1m", step="month", stepmode="backward"),
-                    dict(count=3, label="3m", step="month", stepmode="backward"),
+                #     dict(count=3, label="3m", step="month", stepmode="backward"),
-                    dict(count=6, label="6m", step="month", stepmode="backward"),
+                #     dict(count=6, label="6m", step="month", stepmode="backward"),
-                    dict(count=1, label="YTD", step="year", stepmode="todate"),
+                #     dict(count=1, label="YTD", step="year", stepmode="todate"),
-                    dict(count=1, label="1y", step="year", stepmode="backward"),
+                #     dict(count=12, label="1y", step="month", stepmode="backward"),
-                    dict(step="all")
+                #     dict(step="all")
-                ])
+                # ])
+                buttons=[button for button in self.make_plotly_buttons(months=months)]
             )
         )
         assert isinstance(self, Figure)
         # return fig
 
-    def make_buttons(self, modes: list) -> list:
+    def make_plotly_buttons(self, months:int=6):
+        rng = [1]
+        if months > 2:
+            rng += [iii for iii in range(3, months, 3)]
+        logger.debug(f"Making buttons for months: {rng}")
+        buttons = [dict(count=iii, label=f"{iii}m", step="month", stepmode="backward") for iii in rng]
+        if months > date.today().month:
+            buttons += [dict(count=1, label="YTD", step="year", stepmode="todate")]
+        buttons += [dict(step="all")]
+        for button in buttons:
+            yield button
+
+    def make_pyqt_buttons(self, modes: list) -> list:
         """
         Creates list of buttons with one for each mode to be used in showing/hiding mode traces.
 
@@ -158,7 +175,6 @@ class CustomFigure(Figure):
         output = select_save_file(obj=parent, default_name=group_name, extension="png")
         self.write_image(output.absolute().__str__(), engine="kaleido")
 
-
     def to_html(self) -> str:
         """
         Creates final html code from plotly

src/submissions/frontend/widgets/app.py

@@ -240,7 +240,7 @@ class App(QMainWindow):
                 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)
+        self.table_widget.sub_wid.setData(page=self.table_widget.pager.page_anchor, page_size=page_size)
 
 
 class AddSubForm(QWidget):

src/submissions/frontend/widgets/controls_chart.py

@@ -3,7 +3,7 @@ Handles display of control charts
 """
 import re
 import sys
-from datetime import timedelta
+from datetime import timedelta, date
 from typing import Tuple
 from PyQt6.QtWebEngineWidgets import QWebEngineView
 from PyQt6.QtWidgets import (
@@ -113,6 +113,9 @@ class ControlsViewer(QWidget):
         self.chart_maker()
         return report
 
+    def diff_month(self, d1:date, d2:date):
+        return abs((d1.year - d2.year) * 12 + d1.month - d2.month)
+
     def chart_maker(self):
         """
         Creates plotly charts for webview
@@ -132,7 +135,8 @@ class ControlsViewer(QWidget):
         """
         report = Report()
         # logger.debug(f"Control getter context: \n\tControl type: {self.con_type}\n\tMode: {self.mode}\n\tStart
-        # Date: {self.start_date}\n\tEnd Date: {self.end_date}") NOTE: set the subtype for kraken
+        # Date: {self.start_date}\n\tEnd Date: {self.end_date}")
+        # NOTE: set the subtype for kraken
         if self.sub_typer.currentText() == "":
             self.subtype = None
         else:
@@ -161,7 +165,8 @@ class ControlsViewer(QWidget):
                 title = f"{self.mode} - {self.subtype}"
             # NOTE: send dataframe to chart maker
             df, modes = self.prep_df(ctx=self.app.ctx, df=df)
-            fig = CustomFigure(df=df, ytitle=title, modes=modes, parent=self)
+            months = self.diff_month(self.start_date, self.end_date)
+            fig = CustomFigure(df=df, ytitle=title, modes=modes, parent=self, months=months)
             self.save_button.setEnabled(True)
         # logger.debug(f"Updating figure...")
         self.fig = fig

src/submissions/frontend/widgets/misc.py

@@ -108,43 +108,6 @@ class AddReagentForm(QDialog):
         self.name_input.addItems(list(set([item.name for item in lookup])))
 
 
-# class ReportDatePicker(QDialog):
-#     """
-#     custom dialog to ask for report start/stop dates
-#     """
-#     def __init__(self) -> None:
-#         super().__init__()
-#         self.setWindowTitle("Select Report Date Range")
-#         # NOTE: make confirm/reject buttons
-#         QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
-#         self.buttonBox = QDialogButtonBox(QBtn)
-#         self.buttonBox.accepted.connect(self.accept)
-#         self.buttonBox.rejected.connect(self.reject)
-#         # NOTE: widgets to ask for dates
-#         self.start_date = QDateEdit(calendarPopup=True)
-#         self.start_date.setObjectName("start_date")
-#         self.start_date.setDate(QDate.currentDate())
-#         self.end_date = QDateEdit(calendarPopup=True)
-#         self.end_date.setObjectName("end_date")
-#         self.end_date.setDate(QDate.currentDate())
-#         self.layout = QVBoxLayout()
-#         self.layout.addWidget(QLabel("Start Date"))
-#         self.layout.addWidget(self.start_date)
-#         self.layout.addWidget(QLabel("End Date"))
-#         self.layout.addWidget(self.end_date)
-#         self.layout.addWidget(self.buttonBox)
-#         self.setLayout(self.layout)
-#
-#     def parse_form(self) -> dict:
-#         """
-#         Converts information in this object to a dict
-#
-#         Returns:
-#             dict: output dict.
-#         """
-#         return dict(start_date=self.start_date.date().toPyDate(), end_date = self.end_date.date().toPyDate())
-
-
 class LogParser(QDialog):
 
     def __init__(self, parent):
@@ -253,35 +216,32 @@ class Pagifier(QWidget):
     def __init__(self, page_max:int):
         super().__init__()
         self.page_max = math.ceil(page_max)
-
+        self.page_anchor = 1
         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()
+        self.update_current_page()
-        # 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
+        new = self.page_anchor + 1
         if new <= self.page_max:
-            self.current_page.setText(str(new))
+            self.page_anchor = new
+        self.update_current_page()
 
     def decrement_page(self):
-        new = int(self.current_page.text())-1
+        new = self.page_anchor - 1
         if new >= 1:
-            self.current_page.setText(str(new))
+            self.page_anchor = new
+        self.update_current_page()
 
+    def update_current_page(self):
+        self.current_page.setText(f"{self.page_anchor} of {self.page_max}")

src/submissions/tools/__init__.py

@@ -19,7 +19,7 @@ from pydantic_settings import BaseSettings, SettingsConfigDict
 from typing import Any, Tuple, Literal, List
 from __init__ import project_path
 from configparser import ConfigParser
-from tkinter import Tk  # from tkinter import Tk for Python 3.x
+from tkinter import Tk  # NOTE: This is for choosing database path before app is created.
 from tkinter.filedialog import askdirectory
 from sqlalchemy.exc import IntegrityError as sqlalcIntegrityError