Bug fixes for omni gui objects.

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

@@ -457,12 +457,12 @@ class BaseClass(Base):
         """
         match input_date:
             case datetime() | date():
-                output_date = input_date#.strftime("%Y-%m-%d %H:%M:%S")
+                output_date = input_date
             case int():
                 output_date = datetime.fromordinal(
-                    datetime(1900, 1, 1).toordinal() + input_date - 2)#.date().strftime("%Y-%m-%d %H:%M:%S")
+                    datetime(1900, 1, 1).toordinal() + input_date - 2)
             case _:
-                output_date = parse(input_date)#.strftime("%Y-%m-%d %H:%M:%S")
+                output_date = parse(input_date)
         if eod:
             addition_time = datetime.max.time()
         else:

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

@@ -126,7 +126,13 @@ class KitType(BaseClass):
                                      submission_type=ST))  #: Association proxy to SubmissionTypeKitTypeAssociation
 
     @classproperty
-    def aliases(cls):
+    def aliases(cls) -> List[str]:
+        """
+        Gets other names the sql object of this class might go by.
+
+        Returns:
+            List[str]: List of names
+        """
         return super().aliases + [cls.query_alias, "kit_types", "kit_type"]
 
     @hybrid_property
@@ -1077,7 +1083,13 @@ class SubmissionType(BaseClass):
         return self.processes
 
     @classproperty
-    def aliases(cls):
+    def aliases(cls) -> List[str]:
+        """
+        Gets other names the sql object of this class might go by.
+
+        Returns:
+            List[str]: List of names
+        """
         return super().aliases + ["submission_types", "submission_type"]
 
     @classproperty

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

@@ -1540,12 +1540,15 @@ class BacterialCulture(BasicSubmission):
             return report
         parser = ConcentrationParser(filepath=fname, submission=self)
         conc_samples = [sample for sample in parser.samples]
+        # logger.debug(f"Concentration samples: {pformat(conc_samples)}")
         for sample in self.samples:
-            logger.debug(f"Sample {sample.submitter_id}")
+            # logger.debug(f"Sample {sample.submitter_id}")
+            # logger.debug(f"Match {item['submitter_id']}")
             try:
                 # NOTE: Fix for ENs which have no rsl_number...
-                sample_dict = next(item for item in conc_samples if item['submitter_id'] == sample.submitter_id)
+                sample_dict = next(item for item in conc_samples if str(item['submitter_id']).upper() == sample.submitter_id)
             except StopIteration:
+                logger.error(f"Couldn't find sample dict for {sample.submitter_id}")
                 continue
             logger.debug(f"Sample {sample.submitter_id} conc. = {sample_dict['concentration']}")
             if sample_dict['concentration']:
@@ -1734,12 +1737,10 @@ class Wastewater(BasicSubmission):
             sample[f"ct_{sample['target'].lower()}"] = sample['ct'] if isinstance(sample['ct'], float) else 0.0
             # NOTE: Set 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*$', '', s['sample']) == sample['sample']]
             for s in other_targets:
                 sample[f"ct_{s['target'].lower()}"] = s['ct'] if isinstance(s['ct'], float) else 0.0
-                # sample[f"{s['target'].lower()}_status"] = s['assessment']
             try:
                 del sample['ct']
             except KeyError:
@@ -2177,7 +2178,6 @@ class WastewaterArtic(BasicSubmission):
         except AttributeError:
             plate_num = "1"
         plate_num = plate_num.strip("-")
-        # repeat_num = re.search(r"R(?P<repeat>\d)?$", "PBS20240426-2R").groups()[0]
         try:
             repeat_num = re.search(r"R(?P<repeat>\d)?$", processed).groups()[0]
         except:
@@ -2663,16 +2663,6 @@ class BasicSample(BaseClass, LogMixin):
     def delete(self):
         raise AttributeError(f"Delete not implemented for {self.__class__}")
 
-    # @classmethod
-    # def get_searchables(cls) -> List[dict]:
-    #     """
-    #     Delivers a list of fields that can be used in fuzzy search.
-    #
-    #     Returns:
-    #         List[str]: List of fields.
-    #     """
-    #     return [dict(label="Submitter ID", field="submitter_id")]
-
     @classmethod
     def samples_to_df(cls, sample_list: List[BasicSample], **kwargs) -> pd.DataFrame:
         """
@@ -2729,8 +2719,6 @@ class WastewaterSample(BasicSample):
     Derivative wastewater sample
     """
 
-    # searchables = BasicSample.searchables + ['ww_processing_num', 'ww_full_sample_id', 'rsl_number']
-
     id = Column(INTEGER, ForeignKey('_basicsample.id'), primary_key=True)
     ww_processing_num = Column(String(64))  #: wastewater processing number
     ww_full_sample_id = Column(String(64))  #: full id given by entrics

src/submissions/backend/validators/omni_gui_objects.py

@@ -24,10 +24,25 @@ class BaseOmni(BaseModel):
             return f"<{self.__class__.__name__}({self.__repr_name__})>"
 
     @classproperty
-    def aliases(cls):
+    def aliases(cls) -> List[str]:
+        """
+        Gets other names the sql object of this class might go by.
+
+        Returns:
+            List[str]: List of names
+        """
         return cls.class_object.aliases
 
     def check_all_attributes(self, attributes: dict) -> bool:
+        """
+        Compares this pobject to dictionary of attributes to determine equality.
+
+        Args:
+            attributes (dict):
+
+        Returns:
+            bool: result
+        """
         # logger.debug(f"Incoming attributes: {attributes}")
         attributes = {k : v for k, v in attributes.items() if k in self.list_searchables.keys()}
         for key, value in attributes.items():
@@ -47,7 +62,14 @@ class BaseOmni(BaseModel):
         # logger.debug("Everything checks out, these are the same object.")
         return True
 
-    def __setattr__(self, key, value):
+    def __setattr__(self, key: str, value: Any):
+        """
+        Overrides built in dunder method
+
+        Args:
+            key (str):
+            value (Any):
+        """
         try:
             class_value = getattr(self.class_object, key)
         except AttributeError:
@@ -151,12 +173,22 @@ class OmniSubmissionType(BaseOmni):
         super().__init__(**data)
         self.instance_object = instance_object
 
-    def to_dataframe_dict(self):
+    @property
+    def dataframe_dict(self) -> dict:
+        """
+        Dictionary of gui relevant values.
+
+        Returns:
+            dict: result
+        """
         return dict(
             name=self.name
         )
 
     def to_sql(self):
+        """
+        Convert this object to an instance of its class object.
+        """
         instance, new = self.class_object.query_or_create(name=self.name)
         instance.info_map = self.info_map
         instance.defaults = self.defaults
@@ -191,12 +223,23 @@ class OmniReagentRole(BaseOmni):
         super().__init__(**data)
         self.instance_object = instance_object
 
-    def to_dataframe_dict(self):
+    @property
+    def dataframe_dict(self) -> dict:
+        """
+        Dictionary of gui relevant values.
+
+        Returns:
+            dict: result
+        """
         return dict(
             name=self.name
         )
 
     def to_sql(self):
+        """
+        Convert this object to an instance of its class object.
+        """
+
         instance, new = self.class_object.query_or_create(name=self.name)
         if new:
             instance.eol_ext = self.eol_ext
@@ -252,7 +295,14 @@ class OmniSubmissionTypeKitTypeAssociation(BaseOmni):
         super().__init__(**data)
         self.instance_object = instance_object
 
-    def to_dataframe_dict(self):
+    @property
+    def dataframe_dict(self) -> dict:
+        """
+        Dictionary of gui relevant values.
+
+        Returns:
+            dict: result
+        """
         if isinstance(self.submissiontype, OmniSubmissionType):
             submissiontype = self.submissiontype.name
         else:
@@ -270,6 +320,10 @@ class OmniSubmissionTypeKitTypeAssociation(BaseOmni):
         )
 
     def to_sql(self):
+        """
+        Convert this object to an instance of its class object.
+        """
+
         # logger.debug(f"Self kittype: {self.submissiontype}")
         if issubclass(self.submissiontype.__class__, BaseOmni):
             submissiontype = SubmissionType.query(name=self.submissiontype.name)
@@ -288,7 +342,13 @@ class OmniSubmissionTypeKitTypeAssociation(BaseOmni):
         return instance
 
     @property
-    def list_searchables(self):
+    def list_searchables(self) -> dict:
+        """
+        Provides attributes for checking this object against a dictionary.
+
+        Returns:
+            dict: result
+        """
         if isinstance(self.kittype, OmniKitType):
             kit = self.kittype.name
         else:
@@ -334,7 +394,14 @@ class OmniKitTypeReagentRoleAssociation(BaseOmni):
         super().__init__(**data)
         self.instance_object = instance_object
 
-    def to_dataframe_dict(self):
+    @property
+    def dataframe_dict(self) -> dict:
+        """
+        Dictionary of gui relevant values.
+
+        Returns:
+            dict: result
+        """
         if isinstance(self.submission_type, OmniSubmissionType):
             submission_type = self.submission_type.name
         else:
@@ -349,12 +416,16 @@ class OmniKitTypeReagentRoleAssociation(BaseOmni):
         else:
             reagent_role = self.reagent_role
         return dict(
-            reagent_role=reagent_role,
+            reagentrole=reagent_role,
-            submission_type=submission_type,
+            submissiontype=submission_type,
-            kit_type=kit_type
+            kittype=kit_type
         )
 
     def to_sql(self):
+        """
+        Convert this object to an instance of its class object.
+        """
+
         if isinstance(self.reagent_role, OmniReagentRole):
             reagent_role = self.reagent_role.name
         else:
@@ -387,7 +458,13 @@ class OmniKitTypeReagentRoleAssociation(BaseOmni):
         return instance
 
     @property
-    def list_searchables(self):
+    def list_searchables(self) -> dict:
+        """
+        Provides attributes for checking this object against a dictionary.
+
+        Returns:
+            dict: result
+        """
         if isinstance(self.kit_type, OmniKitType):
             kit = self.kit_type.name
         else:
@@ -420,12 +497,23 @@ class OmniEquipmentRole(BaseOmni):
         super().__init__(**data)
         self.instance_object = instance_object
 
-    def to_dataframe_dict(self):
+    @property
+    def dataframe_dict(self) -> dict:
+        """
+        Dictionary of gui relevant values.
+
+        Returns:
+            dict: result
+        """
         return dict(
             name=self.name
         )
 
     def to_sql(self):
+        """
+        Convert this object to an instance of its class object.
+        """
+
         instance, new = self.class_object.query_or_create(name=self.name)
         return instance
 
@@ -447,12 +535,23 @@ class OmniTips(BaseOmni):
         super().__init__(**data)
         self.instance_object = instance_object
 
-    def to_dataframe_dict(self):
+    @property
+    def dataframe_dict(self) -> dict:
+        """
+        Dictionary of gui relevant values.
+
+        Returns:
+            dict: result
+        """
         return dict(
             name=self.name
         )
 
     def to_sql(self):
+        """
+        Convert this object to an instance of its class object.
+        """
+
         instance, new = self.class_object.query_or_create(name=self.name)
         return instance
 
@@ -475,13 +574,24 @@ class OmniTipRole(BaseOmni):
         super().__init__(**data)
         self.instance_object = instance_object
 
-    def to_dataframe_dict(self):
+    @property
+    def dataframe_dict(self) -> dict:
+        """
+        Dictionary of gui relevant values.
+
+        Returns:
+            dict: result
+        """
         return dict(
             name=self.name,
             tips=[item.name for item in self.tips]
         )
 
     def to_sql(self):
+        """
+        Convert this object to an instance of its class object.
+        """
+
         instance, new = self.class_object.query_or_create(name=self.name)
         for tips in self.tips:
             tips.to_sql()
@@ -504,10 +614,17 @@ class OmniProcess(BaseOmni):
         super().__init__(**data)
         self.instance_object = instance_object
 
-    def to_dataframe_dict(self):
+    @property
-        submissiontypes = [item.name for item in self.submission_types]
+    def dataframe_dict(self) -> dict:
+        """
+        Dictionary of gui relevant values.
+
+        Returns:
+            dict: result
+        """
+        submissiontypes = [item if isinstance(item, str) else item.name for item in self.submission_types]
         logger.debug(f"Submission Types: {submissiontypes}")
-        equipmentroles = [item.name for item in self.equipment_roles]
+        equipmentroles = [item if isinstance(item, str) else item.name for item in self.equipment_roles]
         logger.debug(f"Equipment Roles: {equipmentroles}")
         return dict(
             name=self.name,
@@ -523,6 +640,10 @@ class OmniProcess(BaseOmni):
         return value
 
     def to_sql(self):
+        """
+        Convert this object to an instance of its class object.
+        """
+
         instance, new = self.class_object.query_or_create(name=self.name)
         for st in self.submission_types:
             try:
@@ -548,7 +669,13 @@ class OmniProcess(BaseOmni):
         return instance
 
     @property
-    def list_searchables(self):
+    def list_searchables(self) -> dict:
+        """
+        Provides attributes for checking this object against a dictionary.
+
+        Returns:
+            dict: result
+        """
         return dict(name=self.name)
 
 
@@ -572,17 +699,24 @@ class OmniKitType(BaseOmni):
         super().__init__(**data)
         self.instance_object = instance_object
 
-    def to_dataframe_dict(self):
+    @property
+    def dataframe_dict(self) -> dict:
+        """
+        Dictionary of gui relevant values.
+
+        Returns:
+            dict: result
+        """
         return dict(
             name=self.name
         )
 
     def to_sql(self) -> KitType:
+        """
+        Convert this object to an instance of its class object.
+        """
+
         kit, is_new = KitType.query_or_create(name=self.name)
-        # if is_new:
-        #     logger.debug(f"New kit made: {kit}")
-        # else:
-        #     logger.debug(f"Kit retrieved: {kit}")
         new_rr = []
         for rr_assoc in self.kit_reagentrole_associations:
             new_assoc = rr_assoc.to_sql()
@@ -603,9 +737,6 @@ class OmniKitType(BaseOmni):
             if new_process not in new_processes:
                 new_processes.append(new_process)
         kit.processes = new_processes
-        # logger.debug(f"Kit: {pformat(kit.__dict__)}")
-        # for item in kit.kit_reagentrole_associations:
-        #     logger.debug(f"KTRRassoc: {item.__dict__}")
         return kit
 
 
@@ -622,7 +753,14 @@ class OmniOrganization(BaseOmni):
         super().__init__(**data)
         self.instance_object = instance_object
 
-    def to_dataframe_dict(self):
+    @property
+    def dataframe_dict(self) -> dict:
+        """
+        Dictionary of gui relevant values.
+
+        Returns:
+            dict: result
+        """
         return dict(
             name=self.name,
             cost_centre=self.cost_centre,
@@ -639,14 +777,27 @@ class OmniContact(BaseOmni):
     phone: str = Field(default="", description="property")
 
     @property
-    def list_searchables(self):
+    def list_searchables(self) -> dict:
+        """
+        Provides attributes for checking this object against a dictionary.
+
+        Returns:
+            dict: result
+        """
         return dict(name=self.name, email=self.email)
 
     def __init__(self, instance_object: Any, **data):
         super().__init__(**data)
         self.instance_object = instance_object
 
-    def to_dataframe_dict(self):
+    @property
+    def dataframe_dict(self) -> dict:
+        """
+        Dictionary of gui relevant values.
+
+        Returns:
+            dict: result
+        """
         return dict(
             name=self.name,
             email=self.email,
@@ -654,9 +805,9 @@ class OmniContact(BaseOmni):
         )
 
     def to_sql(self):
+        """
+        Convert this object to an instance of its class object.
+        """
+
         contact, is_new = Contact.query_or_create(name=self.name, email=self.email, phone=self.phone)
-        # if is_new:
-        #     logger.debug(f"New contact made: {contact}")
-        # else:
-        #     logger.debug(f"Contact retrieved: {contact}")
         return contact

src/submissions/frontend/visualizations/__init__.py

@@ -4,6 +4,8 @@ Contains all operations for creating charts, graphs and visual effects.
 from datetime import timedelta, date
 from pathlib import Path
 from typing import Generator
+
+import plotly
 from PyQt6.QtWidgets import QWidget
 import pandas as pd, logging
 from plotly.graph_objects import Figure
@@ -126,8 +128,8 @@ class CustomFigure(Figure):
         html = f'<html><body>'
         if self is not None:
             # NOTE: Just cannot get this load from string to freaking work.
-            html += self.to_html(include_plotlyjs='cdn', full_html=False)
+            # html += self.to_html(include_plotlyjs='cdn', full_html=False)
-            # html += plotly.offline.plot(self, output_type='div', include_plotlyjs=True)
+            html += plotly.offline.plot(self, output_type='div', include_plotlyjs="cdn")
         else:
             html += "<h1>No data was retrieved for the given parameters.</h1>"
         html += '</body></html>'

src/submissions/frontend/widgets/omni_manager_pydant.py

@@ -6,7 +6,7 @@ from json.decoder import JSONDecodeError
 from datetime import datetime, timedelta
 from pprint import pformat
 from typing import Any, List, Literal
-from PyQt6.QtCore import QSortFilterProxyModel, Qt
+from PyQt6.QtCore import QSortFilterProxyModel, Qt, QModelIndex
 from PyQt6.QtGui import QAction, QCursor
 from PyQt6.QtWidgets import (
     QLabel, QDialog,
@@ -114,7 +114,16 @@ class ManagerWindow(QDialog):
         # logger.debug(f"Instance: {self.instance}")
         self.update_data()
 
-    def update_instance(self, initial: bool = False):
+    def update_instance(self, initial: bool = False) -> None:
+        """
+        Gets the proper instance of this object's class object.
+
+        Args:
+            initial (bool): Whether this is the initial creation of this object.
+
+        Returns:
+            None
+        """
         if self.add_edit == "edit" or initial:
             try:
                 # logger.debug(f"Querying with {self.options.currentText()}")
@@ -146,6 +155,7 @@ class ManagerWindow(QDialog):
                   [item for item in self.findChildren(QDialogButtonBox)]
         for item in deletes:
             item.setParent(None)
+        logger.debug(f"Self.omni_object: {self.omni_object}")
         fields = self.omni_object.__class__.model_fields
         for key, info in fields.items():
             # logger.debug(f"Attempting to set {key}, {info} widget")
@@ -193,14 +203,22 @@ class ManagerWindow(QDialog):
         # logger.debug(f"Instance coming from parsed form: {self.omni_object.__dict__}")
         return self.omni_object
 
-    def add_new(self):
+    def add_new(self) -> None:
+        """
+        Creates a new instance of this object's class object.
+
+        Returns:
+            None
+        """
         new_instance = self.class_object()
         self.instance = new_instance
         self.update_options()
 
 
 class EditProperty(QWidget):
-
+    """
+    Class to manage info items of SQL objects.
+    """
     def __init__(self, parent: ManagerWindow, key: str, column_type: Any, value):
         super().__init__(parent)
         self.label = QLabel(key.title().replace("_", " "))
@@ -245,7 +263,13 @@ class EditProperty(QWidget):
         self.layout.addWidget(self.widget, 0, 1, 1, 3)
         self.setLayout(self.layout)
 
-    def parse_form(self):
+    def parse_form(self) -> dict:
+        """
+        Gets values from this EditProperty form.
+
+        Returns:
+            dict: Dictionary of values.
+        """
         # logger.debug(f"Parsing widget {self.objectName()}: {type(self.widget)}")
         match self.widget:
             case QLineEdit():
@@ -269,7 +293,7 @@ class EditRelationship(QWidget):
         from backend.db import models
         super().__init__(parent)
         self.class_object = getattr(models, class_object)
-        logger.debug(f"Attempt value: {value}")
+        # logger.debug(f"Attempt value: {value}")
         # logger.debug(f"Class object: {self.class_object}")
         self.setParent(parent)
         # logger.debug(f"Edit relationship class_object: {self.class_object}")
@@ -317,7 +341,13 @@ class EditRelationship(QWidget):
         self.setLayout(self.layout)
         self.set_data()
 
-    def update_buttons(self):
+    def update_buttons(self) -> None:
+        """
+        Enables/disables buttons based on whether property is a list and has data.
+
+        Returns:
+            None
+        """
         if not self.relationship.property.uselist and len(self.data) >= 1:
             # logger.debug(f"Property {self.relationship} doesn't use list and data is of length: {len(self.data)}")
             self.add_button.setEnabled(False)
@@ -326,14 +356,23 @@ class EditRelationship(QWidget):
             self.add_button.setEnabled(True)
             self.existing_button.setEnabled(True)
 
-    def parse_row(self, x):
+    def parse_row(self, x: QModelIndex) -> None:
+        """
+
+        Args:
+            x ():
+
+        Returns:
+
+        """
         context = {item: x.sibling(x.row(), self.df.columns.get_loc(item)).data() for item in self.df.columns}
+        # logger.debug(f"Context: {pformat(context)}")
         try:
             object = self.class_object.query(**context)
         except KeyError:
             object = None
         self.widget.doubleClicked.disconnect()
-        self.add_edit(instance=object)
+        self.add_new(instance=object)
 
     def add_new(self, instance: Any = None, add_edit: Literal["add", "edit"] = "add", index: int | None = None):
         if add_edit == "edit":
@@ -388,12 +427,13 @@ class EditRelationship(QWidget):
         """
         sets data in model
         """
-        # logger.debug(f"Self.data: {self.data}")
+        logger.debug(f"Self.data: {self.data}")
         try:
-            records = [item.to_dataframe_dict() for item in self.data]
+            records = [item.dataframe_dict for item in self.data]
-        except AttributeError:
+        except AttributeError as e:
+            logger.error(e)
             records = []
-        # logger.debug(f"Records: {records}")
+        logger.debug(f"Records: {records}")
         self.df = DataFrame.from_records(records)
         try:
             self.columns_of_interest = [dict(name=item, column=self.df.columns.get_loc(item)) for item in self.extras]