placeholder

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

@@ -389,13 +389,13 @@ class BaseClass(Base):
         except AttributeError:
             return super().__setattr__(key, value)
         if isinstance(field_type, InstrumentedAttribute):
-            # logger.debug(f"{key} is an InstrumentedAttribute.")
+            logger.debug(f"{key} is an InstrumentedAttribute.")
             match field_type.property:
                 case ColumnProperty():
-                    # logger.debug(f"Setting ColumnProperty to {value}")
+                    logger.debug(f"Setting ColumnProperty to {value}")
                     return super().__setattr__(key, value)
                 case _RelationshipDeclared():
-                    # logger.debug(f"{self.__class__.__name__} Setting _RelationshipDeclared for {key} to {value}")
+                    logger.debug(f"{self.__class__.__name__} Setting _RelationshipDeclared for {key} to {value}")
                     if field_type.property.uselist:
                         logger.debug(f"Setting with uselist")
                         existing = self.__getattribute__(key)
@@ -409,7 +409,8 @@ class BaseClass(Base):
                                 value = existing + [value]
                         else:
                             if isinstance(value, list):
-                                value = value
+                                # value = value
+                                pass
                             else:
                                 value = [value]
                         value = list(set(value))
@@ -421,7 +422,13 @@ class BaseClass(Base):
                                 value = value[0]
                             else:
                                 raise ValueError("Object is too long to parse a single value.")
-                        return super().__setattr__(key, value)
+                        try:
+                            return super().__setattr__(key, value)
+                        except AttributeError:
+                            logger.debug(f"Possible attempt to set relationship to simple var type.")
+                            relationship_class = field_type.property.entity.entity
+                            value = relationship_class.query(name=value)
+                            return super().__setattr__(key, value)
                 case _:
                     return super().__setattr__(key, value)
         else:

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

@@ -46,7 +46,7 @@ class ClientSubmission(BaseClass, LogMixin):
     """
 
     id = Column(INTEGER, primary_key=True)  #: primary key
-    submitter_plate_num = Column(String(127), unique=True)  #: The number given to the submission by the submitting lab
+    submitter_plate_id = Column(String(127), unique=True)  #: The number given to the submission by the submitting lab
     submitted_date = Column(TIMESTAMP)  #: Date submission received
     submitting_lab = relationship("Organization", back_populates="submissions")  #: client org
     submitting_lab_id = Column(INTEGER, ForeignKey("_organization.id", ondelete="SET NULL",
@@ -56,7 +56,7 @@ class ClientSubmission(BaseClass, LogMixin):
     sample_count = Column(INTEGER)  #: Number of samples in the submission
     comment = Column(JSON)
     runs = relationship("BasicSubmission", back_populates="client_submission")  #: many-to-one relationship
-
+    misc_info = Column(JSON)
     contact = relationship("Contact", back_populates="submissions")  #: client org
     contact_id = Column(INTEGER, ForeignKey("_contact.id", ondelete="SET NULL",
                                             name="fk_BS_contact_id"))  #: client lab id from _organizations
@@ -92,6 +92,16 @@ class ClientSubmission(BaseClass, LogMixin):
             except AttributeError:
                 self._submission_category = "NA"
 
+    def __init__(self):
+        super().__init__()
+        self.misc_info = {}
+
+    def set_attribute(self, key, value):
+        if hasattr(self, key):
+            super().__setattr__(key, value)
+        else:
+            self.misc_info[key] = value
+
     @classmethod
     def recruit_parser(cls):
         pass
@@ -237,7 +247,7 @@ class ClientSubmission(BaseClass, LogMixin):
         output = {
             "id": self.id,
             "submission_type": self.submission_type_name,
-            "submitter_plate_number": self.submitter_plate_num,
+            "submitter_plate_number": self.submitter_plate_id,
             "submitted_date": self.submitted_date.strftime("%Y-%m-%d"),
             "submitting_lab": sub_lab,
             "sample_count": self.sample_count,
@@ -279,11 +289,14 @@ class ClientSubmission(BaseClass, LogMixin):
         output["runs"] = runs
         return output
 
+
 class BasicSubmission(BaseClass, LogMixin):
     """
     Object for an entire submission run. Links to client submissions, reagents, equipment, processes
     """
 
+
+
     id = Column(INTEGER, primary_key=True)  #: primary key
     rsl_plate_num = Column(String(32), unique=True, nullable=False)  #: RSL name (e.g. RSL-22-0012)
     client_submission_id = Column(INTEGER, ForeignKey("_clientsubmission.id", ondelete="SET NULL",
@@ -384,6 +397,10 @@ class BasicSubmission(BaseClass, LogMixin):
     def organization(self):
         return self.submitting_lab
 
+    @hybrid_property
+    def name(self):
+        return self.rsl_plate_num
+
     @classproperty
     def jsons(cls) -> List[str]:
         """
@@ -567,8 +584,8 @@ class BasicSubmission(BaseClass, LogMixin):
             "id": self.id,
             "plate_number": self.rsl_plate_num,
             "submission_type": self.client_submission.submission_type_name,
-            "submitter_plate_number": self.client_submission.submitter_plate_num,
+            "submitter_plate_number": self.client_submission.submitter_plate_id,
-            "submitted_date": self.client_submission.submitted_date.strftime("%Y-%m-%d"),
+            "started_date": self.client_submission.submitted_date.strftime("%Y-%m-%d"),
             "submitting_lab": sub_lab,
             "sample_count": self.client_submission.sample_count,
             "extraction_kit": "Change submissions.py line 388",

src/submissions/backend/excel/reports.py

@@ -68,7 +68,7 @@ class ReportMaker(object):
             {'extraction_kit': 'count', 'cost': 'sum', 'sample_count': 'sum'})
         df2 = df2.rename(columns={"extraction_kit": 'run_count'})
         df = df.drop('id', axis=1)
-        df = df.sort_values(['submitting_lab', "submitted_date"])
+        df = df.sort_values(['submitting_lab', "started_date"])
         return df, df2
 
     def make_report_html(self, df: DataFrame) -> str:

src/submissions/backend/validators/pydant.py

@@ -384,7 +384,6 @@ class PydSubmission(BaseModel, extra='allow'):
     filepath: Path
     submission_type: dict | None
     submitter_plate_num: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
-    submitted_date: dict | None
     rsl_plate_num: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
     submitted_date: dict | None = Field(default=dict(value=date.today(), missing=True), validate_default=True)
     submitting_lab: dict | None
@@ -1331,21 +1330,93 @@ class PydElastic(BaseModel, extra="allow", arbitrary_types_allowed=True):
 
 # NOTE: Generified objects below:
 
-class PydClientSubmission(BaseModel, extra="allow"):
+class PydClientSubmission(BaseModel, extra="allow", validate_assignment=True):
+
+    sql_object: ClassVar = ClientSubmission
 
     filepath: Path
     submission_type: dict | None
-    submitter_plate_num: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
-    submitted_date: dict | None
     submitted_date: dict | None = Field(default=dict(value=date.today(), missing=True), validate_default=True)
     submitting_lab: dict | None
     sample_count: dict | None
-    kittype: dict | None
     submission_category: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
     comment: dict | None = Field(default=dict(value="", missing=True), validate_default=True)
     cost_centre: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
     contact: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
+    submitter_plate_num: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
 
+    @field_validator("sample_count")
+    @classmethod
+    def enforce_integer(cls, value):
+        try:
+            value['value'] = int(value['value'])
+        except ValueError:
+            raise f"sample count value must be an integer"
+        return value
+
+    @field_validator("submitter_plate_num")
+    @classmethod
+    def create_submitter_plate_num(cls, value, values):
+        if value['value'] in [None, "None"]:
+            val = f"{values.data['submission_type']['value']}-{values.data['submission_category']['value']}-{values.data['submitted_date']['value']}"
+            return dict(value=val, missing=True)
+        else:
+            value['value'] = value['value'].strip()
+            return value
+
+    @field_validator("submitted_date")
+    @classmethod
+    def rescue_date(cls, value):
+        try:
+            check = value['value'] is None
+        except TypeError:
+            check = True
+        if check:
+            return dict(value=date.today(), missing=True)
+        return value
+
+    def filter_field(self, key: str) -> Any:
+        """
+        Attempts to get value from field dictionary
+
+        Args:
+            key (str): name of the field of interest
+
+        Returns:
+            Any (): Value found.
+        """
+        item = getattr(self, key)
+        match item:
+            case dict():
+                try:
+                    item = item['value']
+                except KeyError:
+                    logger.error(f"Couldn't get dict value: {item}")
+            case _:
+                pass
+        return item
+
+    def improved_dict(self, dictionaries: bool = True) -> dict:
+        """
+        Adds model_extra to fields.
+
+        Args:
+            dictionaries (bool, optional): Are dictionaries expected as input? i.e. Should key['value'] be retrieved. Defaults to True.
+
+        Returns:
+            dict: This instance as a dictionary
+        """
+        fields = list(self.model_fields.keys()) + list(self.model_extra.keys())
+        if dictionaries:
+            output = {k: getattr(self, k) for k in fields}
+        else:
+            output = {k: self.filter_field(k) for k in fields}
+        try:
+            del output['filepath']
+        except KeyError:
+            pass
+        logger.debug(f"Output; {pformat(output)}")
+        return output
 
     def to_form(self, parent: QWidget, disable: list | None = None):
         """
@@ -1360,3 +1431,17 @@ class PydClientSubmission(BaseModel, extra="allow"):
         """
         from frontend.widgets.submission_widget import ClientSubmissionFormWidget
         return ClientSubmissionFormWidget(parent=parent, submission=self, disable=disable)
+
+    def to_sql(self):
+        sql = self.sql_object()
+        for key, value in self.improved_dict().items():
+            if isinstance(value, dict):
+                value = value['value']
+            # if hasattr(sql, key):
+            #     try:
+            sql.set_attribute(key, value)
+            #     except AttributeError:
+            #         continue
+            # else:
+            #     sql.misc_info[key] = value
+        print(sql.__dict__)

src/submissions/frontend/widgets/submission_table.py

@@ -5,7 +5,7 @@ import logging
 import sys
 from pprint import pformat
 from PyQt6.QtWidgets import QTableView, QMenu, QTreeView, QStyledItemDelegate, QStyle, QStyleOptionViewItem, \
-    QHeaderView, QAbstractItemView
+    QHeaderView, QAbstractItemView, QWidget
 from PyQt6.QtCore import Qt, QAbstractTableModel, QSortFilterProxyModel, pyqtSlot, QModelIndex
 from PyQt6.QtGui import QAction, QCursor, QStandardItemModel, QStandardItem, QIcon, QColor
 from backend.db.models import BasicSubmission, ClientSubmission
@@ -230,8 +230,12 @@ class SubmissionsSheet(QTableView):
 class RunDelegate(QStyledItemDelegate):
     def __init__(self, parent=None):
         super(RunDelegate, self).__init__(parent)
-        self._plus_icon = QIcon("plus.png")
+        pixmapi = QStyle.StandardPixmap.SP_ToolBarHorizontalExtensionButton
-        self._minus_icon = QIcon("minus.png")
+        icon1 = QWidget().style().standardIcon(pixmapi)
+        pixmapi = QStyle.StandardPixmap.SP_ToolBarVerticalExtensionButton
+        icon2 = QWidget().style().standardIcon(pixmapi)
+        self._plus_icon = icon1
+        self._minus_icon = icon2
 
     def initStyleOption(self, option, index):
         super(RunDelegate, self).initStyleOption(option, index)
@@ -258,6 +262,11 @@ class SubmissionsTree(QTreeView):
         self.setSelectionBehavior(QAbstractItemView.selectionBehavior(self).SelectRows)
         # self.setStyleSheet("background-color: #0D1225;")
         self.set_data()
+        self.doubleClicked.connect(self.show_details)
+
+        for ii in range(2):
+            self.resizeColumnToContents(ii)
+
 
     @pyqtSlot(QModelIndex)
     def on_clicked(self, index):
@@ -273,9 +282,20 @@ class SubmissionsTree(QTreeView):
         logger.debug(pformat(self.data))
         # sys.exit()
         for submission in self.data:
-            group_item = self.model.add_group(submission['submitter_plate_number'])
+            group_str = f"{submission['submission_type']}-{submission['submitter_plate_number']}-{submission['submitted_date']}"
+            group_item = self.model.add_group(group_str)
             for run in submission['runs']:
-                self.model.append_element_to_group(group_item=group_item, texts=run['plate_number'])
+                self.model.append_element_to_group(group_item=group_item, element=run)
+
+    def show_details(self, sel: QModelIndex):
+        id = self.selectionModel().currentIndex()
+        # NOTE: Convert to data in id column (i.e. column 0)
+        id = id.sibling(id.row(), 1)
+        try:
+            id = int(id.data())
+        except ValueError:
+            return
+        BasicSubmission.query(id=id).show_details(self)
 
 
     def link_extractions(self):
@@ -286,12 +306,19 @@ class SubmissionsTree(QTreeView):
 
 
 class ClientRunModel(QStandardItemModel):
+
     def __init__(self, parent=None):
         super(ClientRunModel, self).__init__(parent)
-        self.setColumnCount(8)
+        headers = ["", "id", "Plate Number", "Started Date", "Completed Date", "Technician", "Signed By"]
-        self.setHorizontalHeaderLabels(["id", "Name", "Library", "Release Date", "Genre(s)", "Last Played", "Time Played", ""])
+        self.setColumnCount(len(headers))
+        self.setHorizontalHeaderLabels(headers)
+
         for i in range(self.columnCount()):
             it = self.horizontalHeaderItem(i)
+            try:
+                logger.debug(it.text())
+            except AttributeError:
+                pass
             # it.setForeground(QColor("#F2F2F2"))
 
     def add_group(self, group_name):
@@ -313,18 +340,29 @@ class ClientRunModel(QStandardItemModel):
             # it.setForeground(QColor("#F2F2F2"))
         return item_root
 
-    def append_element_to_group(self, group_item, texts):
+    def append_element_to_group(self, group_item, element:dict):
+        logger.debug(f"Element: {pformat(element)}")
         j = group_item.rowCount()
         item_icon = QStandardItem()
         item_icon.setEditable(False)
-        item_icon.setIcon(QIcon("game.png"))
+
         # item_icon.setBackground(QColor("#0D1225"))
-        group_item.setChild(j, 0, item_icon)
+        # group_item.setChild(j, 0, item_icon)
-        for i, text in enumerate(texts):
+        for i in range(self.columnCount()):
-            item = QStandardItem(text)
+            it = self.horizontalHeaderItem(i)
+            try:
+                key = it.text().lower().replace(" ", "_")
+            except AttributeError:
+                continue
+            if not key:
+                continue
+            logger.debug(f"Looking for {key} in column {i}")
+            value = str(element[key])
+            logger.debug(f"Got value: {value}")
+            item = QStandardItem(value)
+            item.setBackground(QColor("#CFE2F3"))
             item.setEditable(False)
-            # item.setBackground(QColor("#0D1225"))
+            group_item.setChild(j, i, item)
-            # item.setForeground(QColor("#F2F2F2"))
+        # group_item.setChild(j, 1, QStandardItem("B"))
-            group_item.setChild(j, i+1, item)
 
 

src/submissions/frontend/widgets/submission_widget.py

@@ -438,7 +438,7 @@ class SubmissionFormWidget(QWidget):
                 value = getattr(self, item)
                 info[item] = value
         for k, v in info.items():
-            self.pyd.set_attribute(key=k, value=v)
+            self.pyd.__setattr__(k, v)
         report.add_result(report)
         return report
 
@@ -786,9 +786,53 @@ class ClientSubmissionFormWidget(SubmissionFormWidget):
     def __init__(self, parent: QWidget, submission: PydSubmission, disable: list | None = None) -> None:
         super().__init__(parent, submission=submission, disable=disable)
         save_btn = QPushButton("Save")
-        start_run_btn = QPushButton("Save && Start Run")
+        start_run_btn = QPushButton("Save && Add Run")
         self.layout.addWidget(save_btn)
         self.layout.addWidget(start_run_btn)
-
+        start_run_btn.clicked.connect(self.create_new_submission)
+        del self.disabler
+
+    def parse_form(self) -> Report:
+        """
+        Transforms form info into PydSubmission
+
+        Returns:
+            Report: Report on status of parse.
+        """
+        report = Report()
+        logger.info(f"Hello from client submission form parser!")
+        info = {}
+        reagents = []
+        for widget in self.findChildren(QWidget):
+            match widget:
+                case self.ReagentFormWidget():
+                    reagent = widget.parse_form()
+                    if reagent is not None:
+                        reagents.append(reagent)
+                    else:
+                        report.add_result(Result(msg="Failed integrity check", status="Critical"))
+                        return report
+                case self.InfoItem():
+                    field, value = widget.parse_form()
+                    if field is not None:
+                        info[field] = value
+        # logger.debug(f"Reagents from form: {reagents}")
+        for item in self.recover:
+            if hasattr(self, item):
+                value = getattr(self, item)
+                info[item] = value
+        for k, v in info.items():
+            self.pyd.__setattr__(k, v)
+        report.add_result(report)
+        return report
+
+    @report_result
+    def to_pydantic(self, *args):
+        self.parse_form()
+        return self.pyd
+
+    def create_new_submission(self, *args) -> Report:
+        self.parse_form()
+        sql = self.pyd.to_sql()