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
+