Attempt to update treeview.
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lwark
@@ -15,7 +15,7 @@ from operator import itemgetter
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from pprint import pformat
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from pandas import DataFrame
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from sqlalchemy.ext.hybrid import hybrid_property
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from . import Base, BaseClass, Reagent, SubmissionType, KitType, ClientLab, Contact, LogMixin
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from . import Base, BaseClass, Reagent, SubmissionType, KitType, ClientLab, Contact, LogMixin, Procedure, kittype_procedure
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from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case, func, Table
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from sqlalchemy.orm import relationship, validates, Query
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from sqlalchemy.orm.attributes import flag_modified
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@@ -34,9 +34,8 @@ from jinja2.exceptions import TemplateNotFound
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from jinja2 import Template
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from PIL import Image
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if TYPE_CHECKING:
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from backend.db.models.kits import ProcedureType
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from backend.db.models.kits import ProcedureType, Procedure
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from . import kittype_procedure
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logger = logging.getLogger(f"procedure.{__name__}")
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@@ -233,7 +232,7 @@ class ClientSubmission(BaseClass, LogMixin):
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# dicto, _ = self.kittype.construct_xl_map_for_use(self.proceduretype)
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# sample = self.generate_associations(name="clientsubmissionsampleassociation")
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samples = None
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runs = [item.to_dict() for item in self.run]
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runs = [item.to_dict(full_data=True) for item in self.run]
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# custom = self.custom
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else:
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samples = None
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@@ -263,6 +262,7 @@ class ClientSubmission(BaseClass, LogMixin):
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output["contact_phone"] = contact_phone
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# output["custom"] = custom
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output["run"] = runs
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output['name'] = self.name
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return output
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def add_sample(self, sample: Sample):
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@@ -539,12 +539,14 @@ class Run(BaseClass, LogMixin):
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samples = self.generate_associations(name="clientsubmissionsampleassociation")
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equipment = self.generate_associations(name="submission_equipment_associations")
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tips = self.generate_associations(name="submission_tips_associations")
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procedures = [item.to_dict(full_data=True) for item in self.procedure]
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custom = self.custom
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else:
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samples = None
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equipment = None
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tips = None
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custom = None
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procedures = None
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try:
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comments = self.comment
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except Exception as e:
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@@ -570,6 +572,8 @@ class Run(BaseClass, LogMixin):
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output["contact"] = contact
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output["contact_phone"] = contact_phone
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output["custom"] = custom
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output['procedures'] = procedures
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output['name'] = self.name
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try:
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output["completed_date"] = self.completed_date.strftime("%Y-%m-%d")
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except AttributeError:
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@@ -1131,7 +1135,10 @@ class Run(BaseClass, LogMixin):
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logger.debug(f"Got ProcedureType: {procedure_type}")
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dlg = ProcedureCreation(parent=obj, run=self, proceduretype=procedure_type)
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if dlg.exec():
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pass
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sql, _ = dlg.return_sql()
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logger.debug(f"Output run samples:\n{pformat(sql.run.sample)}")
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sql.save()
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def delete(self, obj=None):
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@@ -1314,8 +1321,9 @@ class Run(BaseClass, LogMixin):
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background_color="#6ffe1d"))
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padded_list = []
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for iii in range(1, proceduretype.total_wells+1):
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row, column = proceduretype.ranked_plate[iii]
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sample = next((item for item in ranked_samples if item['submission_rank']==iii),
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dict(well_id=f"blank_{iii}", sample_id="", row=0, column=0, submission_rank=iii, background_color="#ffffff")
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dict(well_id=f"blank_{iii}", sample_id="", row=row, column=column, submission_rank=iii, background_color="#ffffff")
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)
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padded_list.append(sample)
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# logger.debug(f"Final padded list:\n{pformat(list(sorted(padded_list, key=itemgetter('submission_rank'))))}")
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@@ -1361,6 +1369,14 @@ class Sample(BaseClass, LogMixin):
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run = association_proxy("samplerunassociation", "run") #: proxy of associated procedure
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sampleprocedureassociation = relationship(
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"ProcedureSampleAssociation",
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back_populates="sample",
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cascade="all, delete-orphan",
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)
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procedure = association_proxy("sampleprocedureassociation", "procedure")
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@hybrid_property
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def name(self):
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return self.sample_id
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@@ -1806,10 +1822,10 @@ class RunSampleAssociation(BaseClass):
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"""
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# id = Column(INTEGER, unique=True, nullable=False) #: id to be used for inheriting purposes
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sample_id = Column(INTEGER, ForeignKey("_sample.id"), nullable=False) #: id of associated sample
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sample_id = Column(INTEGER, ForeignKey("_sample.id"), primary_key=True) #: id of associated sample
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run_id = Column(INTEGER, ForeignKey("_run.id"), primary_key=True) #: id of associated procedure
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row = Column(INTEGER, primary_key=True) #: row on the 96 well plate
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column = Column(INTEGER, primary_key=True) #: column on the 96 well plate
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row = Column(INTEGER) #: row on the 96 well plate
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column = Column(INTEGER) #: column on the 96 well plate
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# misc_info = Column(JSON)
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# NOTE: reference to the Submission object
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@@ -2009,3 +2025,16 @@ class RunSampleAssociation(BaseClass):
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def delete(self):
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raise AttributeError(f"Delete not implemented for {self.__class__}")
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class ProcedureSampleAssociation(BaseClass):
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procedure_id = Column(INTEGER, ForeignKey("_procedure.id"), primary_key=True) #: id of associated procedure
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sample_id = Column(INTEGER, ForeignKey("_sample.id"), primary_key=True) #: id of associated equipment
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row = Column(INTEGER)
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column = Column(INTEGER)
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procedure = relationship(Procedure,
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back_populates="proceduresampleassociation") #: associated procedure
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sample = relationship(Sample, back_populates="sampleprocedureassociation") #: associated equipment
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