diff --git a/src/submissions/backend/db/models/kits.py b/src/submissions/backend/db/models/kits.py
index 5156f18..e6936c5 100644
--- 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)
+
diff --git a/src/submissions/backend/db/models/submissions.py b/src/submissions/backend/db/models/submissions.py
index c83dc17..cc8fc33 100644
--- 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
+
diff --git a/src/submissions/backend/validators/pydant.py b/src/submissions/backend/validators/pydant.py
index e6801e8..bf2e58f 100644
--- 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
diff --git a/src/submissions/frontend/widgets/procedure_creation.py b/src/submissions/frontend/widgets/procedure_creation.py
index aabf1d2..e1454fb 100644
--- 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):
#
diff --git a/src/submissions/frontend/widgets/submission_table.py b/src/submissions/frontend/widgets/submission_table.py
index 27d6882..f327af1 100644
--- 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)
diff --git a/src/submissions/templates/css/styles.css b/src/submissions/templates/css/styles.css
index 11df3b1..305bf6d 100644
--- 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;
+}
+
diff --git a/src/submissions/templates/js/context_menu.js b/src/submissions/templates/js/context_menu.js
index 65a221c..cb6df05 100644
--- 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 = '' + en_name + '
'
+ 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 = ''
+ gridC.insertBefore(elem, targetItem.nextSibling);
+ targetItem.remove();
}
+
+
+
/**
* Run the app.
*/
diff --git a/src/submissions/templates/js/grid_drag.js b/src/submissions/templates/js/grid_drag.js
index 39f87c7..49a4538 100644
--- a/src/submissions/templates/js/grid_drag.js
+++ b/src/submissions/templates/js/grid_drag.js
@@ -1,51 +1,55 @@
- const gridContainer = document.getElementById("plate-container");
- let draggedItem = null;
+const gridContainer = document.getElementById("plate-container");
+let draggedItem = null;
- //Handle Drag start
- gridContainer.addEventListener("dragstart", (e) => {
- draggedItem = e.target;
- draggedItem.style.opacity = "0.5";
- });
+//Handle Drag start
+gridContainer.addEventListener("dragstart", (e) => {
- //Handle Drag End
- gridContainer.addEventListener("dragend", (e) => {
- e.target.style.opacity = "1";
- draggedItem = null;
- });
+ draggedItem = e.target;
+ draggedItem.style.opacity = "0.5";
+});
- //handle dragging ove grid items
- gridContainer.addEventListener("dragover", (e) => {
- e.preventDefault();
- });
+//Handle Drag End
+gridContainer.addEventListener("dragend", (e) => {
+ e.target.style.opacity = "1";
+ draggedItem = null;
+});
- //Handle Drop
- gridContainer.addEventListener("drop", (e) => {
- e.preventDefault();
+//handle dragging ove grid items
+gridContainer.addEventListener("dragover", (e) => {
+ e.preventDefault();
+});
- const targetItem = e.target;
- if (
- targetItem &&
- targetItem !== draggedItem &&
- targetItem.classList.contains("well")
- ) {
- const draggedIndex = [...gridContainer.children].indexOf(draggedItem);
- const targetIndex = [...gridContainer.children].indexOf(targetItem);
- if (draggedIndex < targetIndex) {
- backend.log_drag(draggedIndex.toString(), targetIndex.toString() + " Lesser");
- gridContainer.insertBefore(draggedItem, targetItem.nextSibling);
+//Handle Drop
+gridContainer.addEventListener("drop", (e) => {
+ e.preventDefault();
- } else {
- backend.log_drag(draggedIndex.toString(), targetIndex.toString() + " Greater");
- gridContainer.insertBefore(draggedItem, targetItem);
+ const targetItem = e.target;
- }
- output = [];
- fullGrid = [...gridContainer.children];
- fullGrid.forEach(function(item, index) {
- output.push({sample_id: item.id, index: index + 1})
- });
- backend.rearrange_plate(output);
- }
- });
\ No newline at end of file
+ if (
+ targetItem &&
+ 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(draggedIndex.toString() + " " + targetIndex.toString() + " Lesser");
+ gridContainer.insertBefore(draggedItem, targetItem.nextSibling);
+
+ } else {
+ 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);
+ rearrange_plate();
+ }
+});
\ No newline at end of file
diff --git a/src/submissions/templates/procedure_creation.html b/src/submissions/templates/procedure_creation.html
index 73370a9..614c8f6 100644
--- a/src/submissions/templates/procedure_creation.html
+++ b/src/submissions/templates/procedure_creation.html
@@ -50,6 +50,17 @@
{% block script %}
+