Adding sample associations to basicsubmission

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

@@ -336,15 +336,15 @@ class BasicSubmission(BaseClass, LogMixin):
     kittypes = relationship("KitType", back_populates="submissions",
                                secondary=kittypes_submissions)  #: submissions this kit was used for
 
-    # submission_sample_associations = relationship(
+    submission_sample_associations = relationship(
-    #     "SubmissionSampleAssociation",
+        "SubmissionSampleAssociation",
-    #     back_populates="submission",
+        back_populates="submission",
-    #     cascade="all, delete-orphan",
+        cascade="all, delete-orphan",
-    # )  #: Relation to SubmissionSampleAssociation
+    )  #: Relation to SubmissionSampleAssociation
-    #
+
-    # samples = association_proxy("submission_sample_associations",
+    samples = association_proxy("submission_sample_associations",
-    #                             "sample", creator=lambda sample: SubmissionSampleAssociation(
+                                "sample", creator=lambda sample: SubmissionSampleAssociation(
-    #         sample=sample))  #: Association proxy to SubmissionSampleAssociation.samples
+            sample=sample))  #: Association proxy to SubmissionSampleAssociation.samples
 
     submission_reagent_associations = relationship(
         "SubmissionReagentAssociation",
@@ -600,20 +600,20 @@ class BasicSubmission(BaseClass, LogMixin):
             except Exception as e:
                 logger.error(f"We got an error retrieving reagents: {e}")
                 reagents = []
-            finally:
+            # finally:
-                dicto, _ = self.extraction_kit.construct_xl_map_for_use(self.submission_type)
+            #     dicto, _ = self.extraction_kit.construct_xl_map_for_use(self.submission_type)
-                for k, v in dicto.items():
+            #     for k, v in dicto.items():
-                    if k == 'info':
+            #         if k == 'info':
-                        continue
+            #             continue
-                    if not any([item['role'] == k for item in reagents]):
+            #         if not any([item['role'] == k for item in reagents]):
-                        expiry = "NA"
+            #             expiry = "NA"
-                        reagents.append(
+            #             reagents.append(
-                            dict(role=k, name="Not Applicable", lot="NA", expiry=expiry,
+            #                 dict(role=k, name="Not Applicable", lot="NA", expiry=expiry,
-                                 missing=True))
+            #                      missing=True))
             samples = self.generate_associations(name="submission_sample_associations")
             equipment = self.generate_associations(name="submission_equipment_associations")
             tips = self.generate_associations(name="submission_tips_associations")
-            cost_centre = self.cost_centre
+            # cost_centre = self.cost_centre
             custom = self.custom
             controls = [item.to_sub_dict() for item in self.controls]
         else:
@@ -648,7 +648,7 @@ class BasicSubmission(BaseClass, LogMixin):
         output["comment"] = comments
         output["equipment"] = equipment
         output["tips"] = tips
-        output["cost_centre"] = cost_centre
+        # output["cost_centre"] = cost_centre
         output["signed_by"] = self.signed_by
         output["contact"] = contact
         output["contact_phone"] = contact_phone

src/submissions/backend/validators/pydant.py

@@ -1343,7 +1343,7 @@ class PydClientSubmission(BaseModel, extra="allow", validate_assignment=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)
+    submitter_plate_id: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
 
     @field_validator("sample_count")
     @classmethod
@@ -1354,7 +1354,7 @@ class PydClientSubmission(BaseModel, extra="allow", validate_assignment=True):
             raise f"sample count value must be an integer"
         return value
 
-    @field_validator("submitter_plate_num")
+    @field_validator("submitter_plate_id")
     @classmethod
     def create_submitter_plate_num(cls, value, values):
         if value['value'] in [None, "None"]:
@@ -1373,6 +1373,13 @@ class PydClientSubmission(BaseModel, extra="allow", validate_assignment=True):
             check = True
         if check:
             return dict(value=date.today(), missing=True)
+        else:
+            match value['value']:
+                case str():
+                    value['value'] = datetime.strptime(value['value'], "%Y-%m-%d")
+                    value['value'] = datetime.combine(value['value'], datetime.now().time())
+                case _:
+                    pass
         return value
 
     def filter_field(self, key: str) -> Any:
@@ -1437,11 +1444,5 @@ class PydClientSubmission(BaseModel, extra="allow", validate_assignment=True):
         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:
+        return sql
-            #         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, QWidget
+    QHeaderView, QAbstractItemView, QWidget, QTreeWidgetItemIterator
 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
@@ -250,7 +250,7 @@ class SubmissionsTree(QTreeView):
     """
     def __init__(self, model, parent=None):
         super(SubmissionsTree, self).__init__(parent)
-        self.total_count = 1
+        self.total_count = ClientSubmission.__database_session__.query(ClientSubmission).count()
         self.setIndentation(0)
         self.setExpandsOnDoubleClick(False)
         self.clicked.connect(self.on_clicked)
@@ -277,6 +277,7 @@ class SubmissionsTree(QTreeView):
         """
         sets data in model
         """
+        self.clear()
         # self.data = ClientSubmission.submissions_to_df(page=page, page_size=page_size)
         self.data = [item.to_dict(full_data=True) for item in ClientSubmission.query(chronologic=True, page=page, page_size=page_size)]
         logger.debug(pformat(self.data))
@@ -287,6 +288,12 @@ class SubmissionsTree(QTreeView):
             for run in submission['runs']:
                 self.model.append_element_to_group(group_item=group_item, element=run)
 
+
+    def clear(self):
+        if self.model != None:
+            # self.model.clear()       # works
+            self.model.setRowCount(0)  # works
+
     def show_details(self, sel: QModelIndex):
         id = self.selectionModel().currentIndex()
         # NOTE: Convert to data in id column (i.e. column 0)
@@ -356,9 +363,7 @@ class ClientRunModel(QStandardItemModel):
                 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)

src/submissions/frontend/widgets/submission_widget.py

@@ -785,12 +785,13 @@ 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")
+        self.disabler.setHidden(True)
-        start_run_btn = QPushButton("Save && Add Run")
+        # save_btn = QPushButton("Save")
-        self.layout.addWidget(save_btn)
+        start_run_btn = QPushButton("Save")
+        # 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:
         """
@@ -834,5 +835,10 @@ class ClientSubmissionFormWidget(SubmissionFormWidget):
     def create_new_submission(self, *args) -> Report:
         self.parse_form()
         sql = self.pyd.to_sql()
+        logger.debug(sql.__dict__)
+        sql.save()
+        self.app.table_widget.sub_wid.set_data()
+        self.setParent(None)
+