Attempt to update treeview.

2025-06-04 07:18:21 -05:00
parent 26292e275c
commit db0b65b07b
11 changed files with 302 additions and 275 deletions
--- a/src/submissions/backend/db/models/kits.py
+++ b/src/submissions/backend/db/models/kits.py
@@ -22,7 +22,7 @@ from . import Base, BaseClass, ClientLab, LogMixin
 from io import BytesIO

 if TYPE_CHECKING:
-    from backend.db.models.submissions import Run
+    from backend.db.models.submissions import Run, ProcedureSampleAssociation

 logger = logging.getLogger(f'procedure.{__name__}')

@@ -1175,8 +1175,9 @@ class ProcedureType(BaseClass):
            proceduretype=self,
            #name=dict(value=self.name, missing=True),
            #possible_kits=[kittype.name for kittype in self.kittype],
-            repeat=False
+            repeat=False,
            # plate_map=plate_map
+            run=run
        )
        return PydProcedure(**output)

@@ -1222,7 +1223,7 @@ class ProcedureType(BaseClass):

 class Procedure(BaseClass):
    id = Column(INTEGER, primary_key=True)
-    name = Column(String, unique=True)
+    _name = Column(String, unique=True)
    repeat = Column(INTEGER, nullable=False)
    technician = Column(JSON)  #: name of processing tech(s)
    proceduretype_id = Column(INTEGER, ForeignKey("_proceduretype.id", ondelete="SET NULL",
@@ -1236,13 +1237,23 @@ class Procedure(BaseClass):
    kittype = relationship("KitType", back_populates="procedure")
    control = relationship("Control", back_populates="procedure", uselist=True)  #: A control sample added to procedure

+    proceduresampleassociation = relationship(
+        "ProcedureSampleAssociation",
+        back_populates="procedure",
+        cascade="all, delete-orphan",
+    )
+
+    sample = association_proxy("proceduresampleassociation",
+                               "sample", creator=lambda sample: ProcedureSampleAssociation(sample=sample)
+                               )
+
    procedurereagentassociation = relationship(
        "ProcedureReagentAssociation",
        back_populates="procedure",
        cascade="all, delete-orphan",
    )  #: Relation to ProcedureReagentAssociation

-    reagents = association_proxy("procedurereagentassociation",
+    reagent = association_proxy("procedurereagentassociation",
                                 "reagent", creator=lambda reg: ProcedureReagentAssociation(
            reagent=reg))  #: Association proxy to RunReagentAssociation.reagent

@@ -1263,6 +1274,14 @@ class Procedure(BaseClass):
    tips = association_proxy("proceduretipsassociation",
                             "tips")

+    @hybrid_property
+    def name(self):
+        return f"{self.proceduretype.name}-{self.run.rsl_plate_num}"
+
+    @name.setter
+    def name(self, value):
+        self._name = value
+
    @validates('repeat')
    def validate_repeat(self, key, value):
        if value > 1:
@@ -1290,6 +1309,12 @@ class Procedure(BaseClass):
                pass
        return cls.execute_query(query=query, limit=limit)

+    def to_dict(self, full_data: bool=False):
+        output = dict()
+        output['name'] = self.name
+        return output
+
+

 class ProcedureTypeKitTypeAssociation(BaseClass):
    """
@@ -2608,171 +2633,4 @@ class ProcedureTipsAssociation(BaseClass):
        from backend.validators import PydTips
        return PydTips(name=self.tips.name, lot=self.tips.lot, role=self.role_name)

-#
-# class ProcedureType(BaseClass):
-#     id = Column(INTEGER, primary_key=True)
-#     name = Column(String(64))
-#     reagent_map = Column(JSON)
-#
-#     procedure = relationship("Procedure",
-#                              back_populates="proceduretype")  #: Concrete control of this type.
-#
-#     process = relationship("Process", back_populates="proceduretype",
-#                            secondary=proceduretype_process)  #: Relation to equipment process used for this type.
-#
-#     proceduretypekittypeassociation = relationship(
-#         "ProcedureTypeKitTypeAssociation",
-#         back_populates="proceduretype",
-#         cascade="all, delete-orphan",
-#     )  #: Association of kittypes
-#
-#     kittype = association_proxy("proceduretypekittypeassociation", "kittype",
-#                                 creator=lambda kit: ProcedureTypeKitTypeAssociation(
-#                                     kittype=kit))  #: Proxy of kittype association
-#
-#     proceduretypeequipmentroleassociation = relationship(
-#         "ProcedureTypeEquipmentRoleAssociation",
-#         back_populates="proceduretype",
-#         cascade="all, delete-orphan"
-#     )  #: Association of equipmentroles
-#
-#     equipment = association_proxy("proceduretypeequipmentroleassociation", "equipmentrole",
-#                                   creator=lambda eq: ProcedureTypeEquipmentRoleAssociation(
-#                                       equipment_role=eq))  #: Proxy of equipmentrole associations
-#
-#     kittypereagentroleassociation = relationship(
-#         "KitTypeReagentRoleAssociation",
-#         back_populates="proceduretype",
-#         cascade="all, delete-orphan"
-#     )  #: triple association of KitTypes, ReagentTypes, SubmissionTypes
-#
-#     proceduretypetiproleassociation = relationship(
-#         "ProcedureTypeTipRoleAssociation",
-#         back_populates="proceduretype",
-#         cascade="all, delete-orphan"
-#     )  #: Association of tiproles
-#
-#     def construct_field_map(self, field: Literal['equipment', 'tip']) -> Generator[(str, dict), None, None]:
-#         """
-#         Make a map of all locations for tips or equipment.
-#
-#         Args:
-#             field (Literal['equipment', 'tip']): the field to construct a map for
-#
-#         Returns:
-#             Generator[(str, dict), None, None]: Generator composing key, locations for each item in the map
-#         """
-#         for item in self.__getattribute__(f"proceduretype{field}role_associations"):
-#             fmap = item.uses
-#             if fmap is None:
-#                 fmap = {}
-#             yield getattr(item, f"{field}_role").name, fmap
-#
-#     @property
-#     def default_kit(self) -> KitType | None:
-#         """
-#         If only one kits exists for this Submission Type, return it.
-#
-#         Returns:
-#             KitType | None:
-#         """
-#         if len(self.kittype) == 1:
-#             return self.kittype[0]
-#         else:
-#             return None
-#
-#     def get_equipment(self, kittype: str | KitType | None = None) -> Generator['PydEquipmentRole', None, None]:
-#         """
-#         Returns PydEquipmentRole of all equipment associated with this SubmissionType
-#
-#         Returns:
-#             Generator['PydEquipmentRole', None, None]: List of equipment roles
-#         """
-#         return (item.to_pydantic(proceduretype=self, kittype=kittype) for item in self.equipment)
-#
-#     def get_processes_for_role(self, equipmentrole: str | EquipmentRole, kittype: str | KitType | None = None) -> list:
-#         """
-#         Get process associated with this SubmissionType for an EquipmentRole
-#
-#         Args:
-#             equipmentrole (str | EquipmentRole): EquipmentRole of interest
-#             kittype (str | KitType | None, optional): Kit of interest. Defaults to None.
-#
-#         Raises:
-#             TypeError: Raised if wrong type given for equipmentrole
-#
-#         Returns:
-#             list: list of associated process
-#         """
-#         match equipmentrole:
-#             case str():
-#                 relevant = [item.get_all_processes(kittype) for item in self.proceduretypeequipmentroleassociation if
-#                             item.equipmentrole.name == equipmentrole]
-#             case EquipmentRole():
-#                 relevant = [item.get_all_processes(kittype) for item in self.proceduretypeequipmentroleassociation if
-#                             item.equipmentrole == equipmentrole]
-#             case _:
-#                 raise TypeError(f"Type {type(equipmentrole)} is not allowed")
-#         return list(set([item for items in relevant for item in items if item is not None]))
-#
-#
-# class Procedure(BaseClass):
-#     id = Column(INTEGER, primary_key=True)
-#     name = Column(String, unique=True)
-#     technician = Column(JSON)  #: name of processing tech(s)
-#     proceduretype_id = Column(INTEGER, ForeignKey("_proceduretype.id", ondelete="SET NULL",
-#                                                   name="fk_PRO_proceduretype_id"))  #: client lab id from _organizations))
-#     proceduretype = relationship("ProcedureType", back_populates="procedure")
-#     run_id = Column(INTEGER, ForeignKey("_run.id", ondelete="SET NULL",
-#                                         name="fk_PRO_basicrun_id"))  #: client lab id from _organizations))
-#     run = relationship("Run", back_populates="procedure")
-#     kittype_id = Column(INTEGER, ForeignKey("_kittype.id", ondelete="SET NULL",
-#                                             name="fk_PRO_kittype_id"))  #: client lab id from _organizations))
-#     kittype = relationship("KitType", back_populates="procedure")
-#
-#     control = relationship("Control", back_populates="procedure",
-#                             uselist=True)  #: A control sample added to procedure
-#
-#     procedurereagentassociations = relationship(
-#         "ProcedureReagentAssociation",
-#         back_populates="procedure",
-#         cascade="all, delete-orphan",
-#     )  #: Relation to ProcedureReagentAssociation
-#
-#     reagents = association_proxy("procedurereagentassociations",
-#                                  "reagent")  #: Association proxy to RunReagentAssociation.reagent
-#
-#     procedureequipmentassociations = relationship(
-#         "ProcedureEquipmentAssociation",
-#         back_populates="procedure",
-#         cascade="all, delete-orphan"
-#     )  #: Relation to Equipment
-#
-#     equipment = association_proxy("procedureequipmentassociations",
-#                                   "equipment")  #: Association proxy to RunEquipmentAssociation.equipment
-#
-#     proceduretipsassociations = relationship(
-#         "ProcedureTipsAssociation",
-#         back_populates="procedure",
-#         cascade="all, delete-orphan")
-#
-#     tips = association_proxy("proceduretipsassociations",
-#                              "tips")
-#
-#     @classmethod
-#     @setup_lookup
-#     def query(cls, id: int|None = None, name: str | None = None, limit: int = 0, **kwargs) -> Procedure | List[Procedure]:
-#         query: Query = cls.__database_session__.query(cls)
-#         match id:
-#             case int():
-#                 query = query.filter(cls.id == id)
-#                 limit = 1
-#             case _:
-#                 pass
-#         match name:
-#             case str():
-#                 query = query.filter(cls.name == name)
-#                 limit = 1
-#             case _:
-#                 pass
-#         return cls.execute_query(query=query, limit=limit)
+
--- a/src/submissions/backend/db/models/submissions.py
+++ b/src/submissions/backend/db/models/submissions.py
@@ -15,7 +15,7 @@ from operator import itemgetter
 from pprint import pformat
 from pandas import DataFrame
 from sqlalchemy.ext.hybrid import hybrid_property
-from . import Base, BaseClass, Reagent, SubmissionType, KitType, ClientLab, Contact, LogMixin
+from . import Base, BaseClass, Reagent, SubmissionType, KitType, ClientLab, Contact, LogMixin, Procedure, kittype_procedure
 from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case, func, Table
 from sqlalchemy.orm import relationship, validates, Query
 from sqlalchemy.orm.attributes import flag_modified
@@ -34,9 +34,8 @@ from jinja2.exceptions import TemplateNotFound
 from jinja2 import Template
 from PIL import Image
 if TYPE_CHECKING:
-    from backend.db.models.kits import ProcedureType
+    from backend.db.models.kits import ProcedureType, Procedure

-from . import kittype_procedure

 logger = logging.getLogger(f"procedure.{__name__}")

@@ -233,7 +232,7 @@ class ClientSubmission(BaseClass, LogMixin):
            # dicto, _ = self.kittype.construct_xl_map_for_use(self.proceduretype)
            # sample = self.generate_associations(name="clientsubmissionsampleassociation")
            samples = None
-            runs = [item.to_dict() for item in self.run]
+            runs = [item.to_dict(full_data=True) for item in self.run]
            # custom = self.custom
        else:
            samples = None
@@ -263,6 +262,7 @@ class ClientSubmission(BaseClass, LogMixin):
        output["contact_phone"] = contact_phone
        # output["custom"] = custom
        output["run"] = runs
+        output['name'] = self.name
        return output

    def add_sample(self, sample: Sample):
@@ -539,12 +539,14 @@ class Run(BaseClass, LogMixin):
            samples = self.generate_associations(name="clientsubmissionsampleassociation")
            equipment = self.generate_associations(name="submission_equipment_associations")
            tips = self.generate_associations(name="submission_tips_associations")
+            procedures = [item.to_dict(full_data=True) for item in self.procedure]
            custom = self.custom
        else:
            samples = None
            equipment = None
            tips = None
            custom = None
+            procedures = None
        try:
            comments = self.comment
        except Exception as e:
@@ -570,6 +572,8 @@ class Run(BaseClass, LogMixin):
        output["contact"] = contact
        output["contact_phone"] = contact_phone
        output["custom"] = custom
+        output['procedures'] = procedures
+        output['name'] = self.name
        try:
            output["completed_date"] = self.completed_date.strftime("%Y-%m-%d")
        except AttributeError:
@@ -1131,7 +1135,10 @@ class Run(BaseClass, LogMixin):
        logger.debug(f"Got ProcedureType: {procedure_type}")
        dlg = ProcedureCreation(parent=obj, run=self, proceduretype=procedure_type)
        if dlg.exec():
-            pass
+            sql, _ = dlg.return_sql()
+            logger.debug(f"Output run samples:\n{pformat(sql.run.sample)}")
+            sql.save()
+


    def delete(self, obj=None):
@@ -1314,8 +1321,9 @@ class Run(BaseClass, LogMixin):
                     background_color="#6ffe1d"))
        padded_list = []
        for iii in range(1, proceduretype.total_wells+1):
+            row, column = proceduretype.ranked_plate[iii]
            sample = next((item for item in ranked_samples if item['submission_rank']==iii),
-                          dict(well_id=f"blank_{iii}", sample_id="", row=0, column=0, submission_rank=iii, background_color="#ffffff")
+                          dict(well_id=f"blank_{iii}", sample_id="", row=row, column=column, submission_rank=iii, background_color="#ffffff")
                          )
            padded_list.append(sample)
        # logger.debug(f"Final padded list:\n{pformat(list(sorted(padded_list, key=itemgetter('submission_rank'))))}")
@@ -1361,6 +1369,14 @@ class Sample(BaseClass, LogMixin):

    run = association_proxy("samplerunassociation", "run")  #: proxy of associated procedure

+    sampleprocedureassociation = relationship(
+        "ProcedureSampleAssociation",
+        back_populates="sample",
+        cascade="all, delete-orphan",
+    )
+
+    procedure = association_proxy("sampleprocedureassociation", "procedure")
+
    @hybrid_property
    def name(self):
        return self.sample_id
@@ -1806,10 +1822,10 @@ class RunSampleAssociation(BaseClass):
    """

    # id = Column(INTEGER, unique=True, nullable=False)  #: id to be used for inheriting purposes
-    sample_id = Column(INTEGER, ForeignKey("_sample.id"), nullable=False)  #: id of associated sample
+    sample_id = Column(INTEGER, ForeignKey("_sample.id"), primary_key=True)  #: id of associated sample
    run_id = Column(INTEGER, ForeignKey("_run.id"), primary_key=True)  #: id of associated procedure
-    row = Column(INTEGER, primary_key=True)  #: row on the 96 well plate
-    column = Column(INTEGER, primary_key=True)  #: column on the 96 well plate
+    row = Column(INTEGER)  #: row on the 96 well plate
+    column = Column(INTEGER)  #: column on the 96 well plate
    # misc_info = Column(JSON)

    # NOTE: reference to the Submission object
@@ -2009,3 +2025,16 @@ class RunSampleAssociation(BaseClass):

    def delete(self):
        raise AttributeError(f"Delete not implemented for {self.__class__}")
+
+
+class ProcedureSampleAssociation(BaseClass):
+    procedure_id = Column(INTEGER, ForeignKey("_procedure.id"), primary_key=True)  #: id of associated procedure
+    sample_id = Column(INTEGER, ForeignKey("_sample.id"), primary_key=True)  #: id of associated equipment
+    row = Column(INTEGER)
+    column = Column(INTEGER)
+
+    procedure = relationship(Procedure,
+                             back_populates="proceduresampleassociation")  #: associated procedure
+
+    sample = relationship(Sample, back_populates="sampleprocedureassociation")  #: associated equipment
+
--- a/src/submissions/backend/validators/pydant.py
+++ b/src/submissions/backend/validators/pydant.py
@@ -105,7 +105,6 @@ class PydBaseClass(BaseModel, extra='allow', validate_assignment=True):
        dicto = self.improved_dict(dictionaries=False)
        logger.debug(f"Dicto: {dicto}")
        sql, _ = self._sql_object().query_or_create(**dicto)
-
        return sql


@@ -1383,8 +1382,6 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
                value = {item.name: item.reagents for item in kittype.reagentrole}
        return value

-
-
    def update_kittype_reagentroles(self, kittype: str | KitType):
        if kittype == self.__class__.model_fields['kittype'].default['value']:
            return
@@ -1395,20 +1392,60 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
                                kittype_obj.get_reagents(proceduretype=self.proceduretype)}
        except AttributeError:
            self.reagentrole = {}
+        self.kittype['value'] = kittype
        self.possible_kits.insert(0, self.possible_kits.pop(self.possible_kits.index(kittype)))

    def update_samples(self, sample_list: List[dict]):
        logger.debug(f"Incoming sample_list:\n{pformat(sample_list)}")
        for sample_dict in sample_list:
-            try:
-                sample = next((item for item in self.samples if item.sample_id.upper()==sample_dict['sample_id'].upper()))
-            except StopIteration:
+            if sample_dict['sample_id'].startswith("blank_"):
                continue
            row, column = self.proceduretype.ranked_plate[sample_dict['index']]
+            logger.debug(f"Row: {row}, Column: {column}")
+            try:
+                sample = next(
+                    (item for item in self.samples if item.sample_id.upper() == sample_dict['sample_id'].upper()))
+            except StopIteration:
+                # NOTE: Code to check for added controls.
+                logger.debug(f"Sample not found by name: {sample_dict['sample_id']}, checking row {row} column {column}")
+                try:
+                    sample = next(
+                        (item for item in self.samples if item.row == row and item.column == column))
+                except StopIteration:
+                    logger.error(f"Couldn't find sample: {pformat(sample_dict)}")
+                    continue
+            logger.debug(f"Sample of interest: {sample.improved_dict()}")
+            sample.sample_id = sample_dict['sample_id']
+            sample.well_id = sample_dict['sample_id']
            sample.row = row
            sample.column = column
        logger.debug(f"Updated samples:\n{pformat(self.samples)}")

+    def to_sql(self):
+        from backend.db.models import RunSampleAssociation, ProcedureSampleAssociation
+        sql = super().to_sql()
+        if self.run:
+            sql.run = self.run
+        if self.proceduretype:
+            sql.proceduretype = self.proceduretype
+        for sample in self.samples:
+            if sample.sample_id.startswith("blank_") or sample.sample_id == "":
+                continue
+            sample_sql = sample.to_sql()
+            if sql.run:
+                if sample_sql not in sql.run.sample:
+                    logger.debug(f"sample {sample_sql} not found in {sql.run.sample}")
+                    run_assoc = RunSampleAssociation(sample=sample_sql, run=self.run, row=sample.row, column=sample.column)
+                else:
+                    logger.debug(f"sample {sample_sql} found in {sql.run.sample}")
+            proc_assoc = ProcedureSampleAssociation(procedure=sql, sample=sample_sql, row=sample.row, column=sample.column)
+        if self.kittype['value'] not in ["NA", None, ""]:
+            kittype = KitType.query(name=self.kittype['value'], limit=1)
+            if kittype:
+                sql.kittype = kittype
+        return sql, None
+
+

 class PydClientSubmission(PydBaseClass):
    # sql_object: ClassVar = ClientSubmission
--- a/src/submissions/frontend/widgets/procedure_creation.py
+++ b/src/submissions/frontend/widgets/procedure_creation.py
@@ -12,7 +12,7 @@ from PyQt6.QtCore import pyqtSlot, Qt
 from PyQt6.QtGui import QContextMenuEvent, QAction
 from PyQt6.QtWebChannel import QWebChannel
 from PyQt6.QtWebEngineWidgets import QWebEngineView
-from PyQt6.QtWidgets import QDialog, QGridLayout, QMenu
+from PyQt6.QtWidgets import QDialog, QGridLayout, QMenu, QDialogButtonBox
 from typing import TYPE_CHECKING, Any

 if TYPE_CHECKING:
@@ -54,6 +54,11 @@ class ProcedureCreation(QDialog):
        self.channel.registerObject('backend', self)
        self.set_html()
        self.webview.page().setWebChannel(self.channel)
+        QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
+        self.buttonBox = QDialogButtonBox(QBtn)
+        self.buttonBox.accepted.connect(self.accept)
+        self.buttonBox.rejected.connect(self.reject)
+        self.layout.addWidget(self.buttonBox, 11, 1, 1, 1)

    def set_html(self):
        html = render_details_template(
@@ -71,9 +76,9 @@ class ProcedureCreation(QDialog):

    @pyqtSlot(str, str)
    def text_changed(self, key: str, new_value: str):
-        # logger.debug(f"New value for {key}: {new_value}")
+        logger.debug(f"New value for {key}: {new_value}")
        attribute = getattr(self.created_procedure, key)
-        attribute['value'] = new_value
+        attribute['value'] = new_value.strip('\"')

    @pyqtSlot(str, bool)
    def check_toggle(self, key: str, ischecked: bool):
@@ -94,6 +99,9 @@ class ProcedureCreation(QDialog):
    def log(self, logtext: str):
        logger.debug(logtext)

+    def return_sql(self):
+        return self.created_procedure.to_sql()
+

 # class ProcedureWebViewer(QWebEngineView):
 #
--- a/src/submissions/frontend/widgets/submission_table.py
+++ b/src/submissions/frontend/widgets/submission_table.py
@@ -9,7 +9,9 @@ from PyQt6.QtWidgets import QTableView, QMenu, QTreeView, QStyledItemDelegate, Q
    QHeaderView, QAbstractItemView, QWidget, QTreeWidgetItemIterator
 from PyQt6.QtCore import Qt, QAbstractTableModel, QSortFilterProxyModel, pyqtSlot, QModelIndex
 from PyQt6.QtGui import QAction, QCursor, QStandardItemModel, QStandardItem, QIcon, QColor, QContextMenuEvent
+from typing import Dict, List

+from backend import Procedure
 from backend.db.models import Run, ClientSubmission
 from tools import Report, Result, report_result
 from .functions import select_open_file
@@ -263,8 +265,8 @@ class SubmissionsTree(QTreeView):
        self.setIndentation(0)
        self.setExpandsOnDoubleClick(False)
        self.clicked.connect(self.on_clicked)
-        delegate = ClientSubmissionDelegate(self)
-        self.setItemDelegateForColumn(0, delegate)
+        delegate1 = ClientSubmissionDelegate(self)
+        self.setItemDelegateForColumn(0, delegate1)
        self.model = model
        self.setModel(self.model)
        # self.header().setSectionResizeMode(0, QHeaderView.sectionResizeMode(self,0).ResizeToContents)
@@ -329,11 +331,49 @@ class SubmissionsTree(QTreeView):
                     ClientSubmission.query(chronologic=True, page=page, page_size=page_size)]
        logger.debug(f"setting data:\n {pformat(self.data)}")
        # sys.exit()
+        root = self.model.invisibleRootItem()
        for submission in self.data:
            group_str = f"{submission['submissiontype']}-{submission['submitter_plate_id']}-{submission['submitted_date']}"
-            group_item = self.model.add_group(group_str, query_str=submission['submitter_plate_id'])
+            submission_item = self.model.add_group(parent=root, item_data=dict(
+                name=group_str,
+                query_str=submission['submitter_plate_id'],
+                item_type=ClientSubmission
+            ))
            for run in submission['run']:
-                self.model.append_element_to_group(group_item=group_item, element=run)
+                # self.model.append_element_to_group(group_item=group_item, element=run)
+                run_item = self.model.add_group(parent=submission_item, item_data=dict(
+                    name=run['plate_number'],
+                    query_str=run['plate_number'],
+                    item_type=Run
+                ))
+
+                for procedure in run['procedures']:
+                    self.model.add_group(parent=run_item, item_data=dict(
+                        name=procedure['name'],
+                        query_str=procedure['name'],
+                        item_type=Procedure
+                    ))
+        # root = self.model.invisibleRootItem()
+        # for submission in self.data:
+        #     submission_item = QStandardItem(submission['name'])
+        #     root.appendRow(submission_item)
+        #     for run in submission['run']:
+        #         run_item = QStandardItem(run['name'])
+        #         submission_item.appendRow(run_item)
+        #         for procedure in run['procedures']:
+        #             procedure_item = QStandardItem(procedure['name'])
+        #             run_item.appendRow(procedure_item)
+        # self._populateTree(self.data, self.model.invisibleRootItem())
+
+    def _populateTree(self, children, parent):
+        for child in children:
+            logger.debug(child)
+            child_item = QStandardItem(child['name'])
+            parent.appendRow(child_item)
+            if isinstance(children, List):
+                self._populateTree(child, child_item)
+
+

    def clear(self):
        if self.model != None:
@@ -366,27 +406,26 @@ class ClientSubmissionRunModel(QStandardItemModel):
        self.setColumnCount(len(headers))
        self.setHorizontalHeaderLabels(headers)

-    def add_group(self, item_name, query_str: str):
+    def add_group(self, parent, item_data):
        item_root = QStandardItem()
        item_root.setEditable(False)
-        item = QStandardItem(item_name)
+        item = QStandardItem(item_data['name'])
        item.setEditable(False)
-        ii = self.invisibleRootItem()
-        i = ii.rowCount()
+        i = parent.rowCount()
        for j, it in enumerate((item_root, item)):
            # NOTE: Adding item to invisible root row i, column j (wherever j comes from)
-            ii.setChild(i, j, it)
-            ii.setEditable(False)
+            parent.setChild(i, j, it)
+            parent.setEditable(False)
        for j in range(self.columnCount()):
-            it = ii.child(i, j)
+            it = parent.child(i, j)
            if it is None:
                # NOTE: Set invisible root child to empty if it is None.
                it = QStandardItem()
-                ii.setChild(i, j, it)
-        item_root.setData(dict(item_type=ClientSubmission, query_str=query_str), 1)
+                parent.setChild(i, j, it)
+        item_root.setData(dict(item_type=item_data['item_type'], query_str=item_data['query_str']), 1)
        return item_root

-    def append_element_to_group(self, group_item, element: dict):
+    def append_element_to_group(self, group_item, item_data: dict):
        # logger.debug(f"Element: {pformat(element)}")
        j = group_item.rowCount()
        item_icon = QStandardItem()
@@ -402,14 +441,15 @@ class ClientSubmissionRunModel(QStandardItemModel):
                key = None
            if not key:
                continue
-            value = str(element[key])
+            value = str(item_data[key])
            item = QStandardItem(value)
            item.setBackground(QColor("#CFE2F3"))
            item.setEditable(False)
            # item_icon.setChild(j, i, item)
-            item.setData(dict(item_type=Run, query_str=element['plate_number']),1)
+            item.setData(dict(item_type=item_data['item_type'], query_str=item_data['query_str']),1)
            group_item.setChild(j, i, item)
        # group_item.setChild(j, 1, QStandardItem("B"))
+        return item

    def get_value(self, idx: int, column: int = 1):
        return self.item(idx, column)
--- a/src/submissions/templates/css/styles.css
+++ b/src/submissions/templates/css/styles.css
@@ -85,6 +85,27 @@ div.gallery {
  object-fit: contain;
 }

+.context-menu {
+  display: none;
+  flex-direction: column;
+  align-items: flex-start;
+  width: 150px;
+  margin: 32px;
+  position: absolute;
+
+}
+
+
+.context-menu--active {
+  display: block;
+  z-index: 10;
+  background-color: white;
+  border: 2px solid black;
+  padding: 5px;
+}
+
+
+
 .plate {
    display: inline-grid;
    grid-auto-flow: column;
@@ -111,15 +132,17 @@ div.gallery {
  border-radius: 8px;
 }

-.context-menu {
-    display: none;
-    position: absolute;
-    z-index: 10;
-    background-color: rgba(229, 231, 228, 0.7);
-    border-radius: 2px;
-    border-color: black;
+ul.no-bullets {
+  list-style-type: none; /* Remove bullets */
+  padding: 0; /* Remove padding */
+  margin: 0; /* Remove margins */
 }

-.context-menu--active {
-    display: block;
+.negativecontrol {
+  background-color: cyan;
 }
+
+.positivecontrol {
+  background-color: pink;
+}
+
--- a/src/submissions/templates/js/context_menu.js
+++ b/src/submissions/templates/js/context_menu.js
@@ -12,7 +12,7 @@
 //  menuIndex = eval(event.target.parentNode.id.slice(-1));
 //  document.querySelectorAll(".multiSelect")[menuIndex].style.transform =
 //    "translateX(-100%)";
-//  // document.querySelectorAll(".multiSelect")[menuIndex].style.clipPath = "polygon(0 0, 0 0, 0 100%, 0% 100%)";
+//  document.querySelectorAll(".multiSelect")[menuIndex].style.clipPath = "polygon(0 0, 0 0, 0 100%, 0% 100%)";
 //  document.querySelectorAll(".multiSelect")[menuIndex].style.clipPath =
 //    "polygon(100% 0, 100% 0, 100% 100%, 100% 100%)";
 //  document.querySelectorAll(".multiSelect")[menuIndex + 1].style.transform =
@@ -116,7 +116,7 @@ function menuItemListener( link ) {
            insertSample(contextIndex, task_id);
        break;
        case "InsertControl":
-            insertControl(contextIndex);
+            insertControl(taskItemInContext);
        break;
        case "RemoveSample":
            removeSample(contextIndex);
@@ -125,6 +125,7 @@ function menuItemListener( link ) {
            backend.log("default");
        break;
    }
+    rearrange_plate();
    toggleMenuOff();
 }

@@ -149,7 +150,7 @@ var clickCoordsX;
 var clickCoordsY;
 var menu = document.getElementById(contextMenuClassName);
 var menuItems = menu.getElementsByClassName(contextMenuItemClassName);
-var menuHeader = document.getElementById("menu-header");
+const menuHeader = document.getElementById("menu-header");
 var menuState = 0;
 var menuWidth;
 var menuHeight;
@@ -158,6 +159,7 @@ var menuPositionX;
 var menuPositionY;
 var windowWidth;
 var windowHeight;
+
 /**
 * Initialise our application's code.
 */
@@ -192,6 +194,7 @@ function contextListener() {
 function clickListener() {
    document.addEventListener( "click", function(e) {
        var clickeElIsLink = clickInsideElement( e, contextMenuLinkClassName );
+        backend.log(e.target.id)
        if ( clickeElIsLink ) {
            e.preventDefault();
            menuItemListener( clickeElIsLink );
@@ -241,17 +244,39 @@ function insertSample( index ) {
    backend.log( "Index - " + index + ", InsertSample");
 }

-function insertControl( index ) {
-    backend.log( "Index - " + index + ", InsertEN");
+function insertControl( targetItem ) {
+
+    const gridC = document.getElementById("plate-container");
    var existing_ens = document.getElementsByClassName("EN");
-    backend.log(existing_ens.length);
+    var en_num = existing_ens.length + 1;
+    const en_name = "EN" + en_num + "-" + rsl_plate_num;
+    var elem = document.createElement("div");
+    elem.setAttribute("id", en_name);
+    elem.setAttribute("class", "well negativecontrol EN");
+    elem.setAttribute("draggable", "true");
+    elem.innerHTML = '<p style="font-size: 0.7em; text-align: center; word-wrap: break-word;">' + en_name + '</p>'
+    gridC.insertBefore(elem, targetItem.nextSibling);
+    targetItem.remove();
 }

-function removeSample( index ) {
-    backend.log( "Index - " + index + ", RemoveSample");
+function removeSample( targetItem ) {
+    const gridC = document.getElementById("plate-container");
+    var existing_wells = document.getElementsByClassName("well");
+    var en_num = existing_wells.length + 1;
+    var well_name = "blank_" + en_num;
+    var elem = document.createElement("div");
+    elem.setAttribute("id", well_name);
+    elem.setAttribute("class", "well");
+    elem.setAttribute("draggable", "true");
+    elem.innerHTML = '<p style="font-size: 0.7em; text-align: center; word-wrap: break-word;"></p>'
+    gridC.insertBefore(elem, targetItem.nextSibling);
+    targetItem.remove();
 }


+
+
+
 /**
 * Run the app.
 */
--- a/src/submissions/templates/js/grid_drag.js
+++ b/src/submissions/templates/js/grid_drag.js
@@ -5,6 +5,7 @@

 //Handle Drag start
 gridContainer.addEventListener("dragstart", (e) => {
+
  draggedItem = e.target;
  draggedItem.style.opacity = "0.5";
 });
@@ -25,27 +26,30 @@
  e.preventDefault();

  const targetItem = e.target;
+
  if (
    targetItem &&
-        targetItem !== draggedItem &&
-        targetItem.classList.contains("well")
+    targetItem !== draggedItem //&&
+    //targetItem.classList.contains("well")
  ) {
+    backend.log(targetItem.id);
    const draggedIndex = [...gridContainer.children].indexOf(draggedItem);
    const targetIndex = [...gridContainer.children].indexOf(targetItem);
    if (draggedIndex < targetIndex) {
-          backend.log_drag(draggedIndex.toString(), targetIndex.toString() + " Lesser");
+      backend.log(draggedIndex.toString() + " " + targetIndex.toString() + " Lesser");
      gridContainer.insertBefore(draggedItem, targetItem.nextSibling);

    } else {
-          backend.log_drag(draggedIndex.toString(), targetIndex.toString() + " Greater");
+      backend.log(draggedIndex.toString() + " " + targetIndex.toString() + " Greater");
      gridContainer.insertBefore(draggedItem, targetItem);

    }
-        output = [];
-        fullGrid = [...gridContainer.children];
-        fullGrid.forEach(function(item, index) {
-            output.push({sample_id: item.id, index: index + 1})
-        });
-        backend.rearrange_plate(output);
+//    output = [];
+//    fullGrid = [...gridContainer.children];
+//    fullGrid.forEach(function(item, index) {
+//        output.push({sample_id: item.id, index: index + 1})
+//    });
+//    backend.rearrange_plate(output);
+    rearrange_plate();
  }
 });
--- a/src/submissions/templates/procedure_creation.html
+++ b/src/submissions/templates/procedure_creation.html
@@ -50,6 +50,17 @@
    </body>

    {% block script %}
+    <script>
+        var rsl_plate_num = "{{ run['plate_number'] }}";
+        function rearrange_plate() {
+            output = [];
+            fullGrid = [...gridContainer.children];
+            fullGrid.forEach(function(item, index) {
+                output.push({sample_id: item.id, index: index + 1})
+            });
+            backend.rearrange_plate(output);
+        }
+    </script>
    {{ super() }}
    {% endblock %}

--- a/src/submissions/templates/support/context_menu.html
+++ b/src/submissions/templates/support/context_menu.html
@@ -1,6 +1,6 @@
-        <nav class="context-menu" id="context-menu">
+        <nav class="flexDiv context-menu" id="context-menu">
            <h4 id="menu-header"></h4>
-            <ul class="context-menu__items">
+            <ul class="context-menu__items no-bullets">
                <li class="context-menu__item">
                    <a href="#" class="context-menu__link" data-action="InsertSample">
                        <i class="fa fa-eye"></i> Insert Sample
--- a/src/submissions/templates/support/plate_map.html
+++ b/src/submissions/templates/support/plate_map.html
@@ -2,14 +2,6 @@
            {% for sample in samples %}
                <div class="well" draggable="true" id="{{ sample['well_id'] }}" style="background-color: {{ sample['background_color'] }};">
                  <p style="font-size: 0.7em; text-align: center; word-wrap: break-word;">{{ sample['sample_id'] }}</p>
-<!--                    <div class="tooltip" style="font-size: 0.5em; text-align: center; word-wrap: break-word;">{{ sample['sample_id'] }}-->
-<!--                        <span class="tooltiptext">{{ sample['tooltip'] }}</span>-->
-<!--                    </div>--
-                    grid-column-start: {{sample['column']}};
-                grid-column-end: {{sample['column']}};
-                grid-row-start: {{sample['row']}};
-                grid-row-end: {{sample['row']}};-->
                </div>
            {% endfor %}
-
        </div>