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UPdates to managers.

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This commit is contained in:
lwark
2025-07-09 12:13:43 -05:00
parent 432854e76f
commit d5961f42a5
10 changed files with 147 additions and 89 deletions
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80
src/submissions/backend/db/models/submissions.py
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@@ -9,15 +9,19 @@ from copy import deepcopy
from getpass import getuser
import logging, uuid, tempfile, re, base64, numpy as np, pandas as pd, types, sys
from inspect import isclass
from io import BytesIO
from zipfile import ZipFile, BadZipfile
from tempfile import TemporaryDirectory, TemporaryFile
from operator import itemgetter
from pprint import pformat
import openpyxl
from pandas import DataFrame
from sqlalchemy.ext.hybrid import hybrid_property
from frontend import select_save_file
from . import Base, BaseClass, Reagent, SubmissionType, KitType, ClientLab, Contact, LogMixin, Procedure, kittype_procedure
from frontend.widgets.functions import select_save_file
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, Sequence
from sqlalchemy.orm import relationship, validates, Query
from sqlalchemy.orm.attributes import flag_modified
@@ -35,10 +39,10 @@ from pathlib import Path
from jinja2.exceptions import TemplateNotFound
from jinja2 import Template
from PIL import Image
if TYPE_CHECKING:
from backend.db.models.kits import ProcedureType, Procedure
logger = logging.getLogger(f"procedure.{__name__}")
@@ -73,7 +77,7 @@ class ClientSubmission(BaseClass, LogMixin):
) #: Relation to ClientSubmissionSampleAssociation
sample = association_proxy("clientsubmissionsampleassociation",
"sample") #, creator=lambda sample: ClientSubmissionSampleAssociation(
"sample") #, creator=lambda sample: ClientSubmissionSampleAssociation(
# sample=sample)) #: Association proxy to ClientSubmissionSampleAssociation.sample
@@ -362,10 +366,12 @@ class ClientSubmission(BaseClass, LogMixin):
output['expanded'] = ["clientlab", "contact", "submissiontype"]
return output
def to_pydantic(self, filepath: Path|str|None=None, **kwargs):
def to_pydantic(self, filepath: Path | str | None = None, **kwargs):
output = super().to_pydantic(filepath=filepath, **kwargs)
output.template_file = self.template_file
return output
class Run(BaseClass, LogMixin):
"""
Object for an entire procedure procedure. Links to client procedure, reagents, equipment, process
@@ -634,7 +640,8 @@ class Run(BaseClass, LogMixin):
# logger.debug(f"Active samples:{pformat(active_samples)}")
for sample in active_samples:
sample['active'] = True
inactive_samples = [sample.details_dict() for sample in submission_samples if sample.name not in [s['sample_id'] for s in active_samples]]
inactive_samples = [sample.details_dict() for sample in submission_samples if
sample.name not in [s['sample_id'] for s in active_samples]]
# logger.debug(f"Inactive samples:{pformat(inactive_samples)}")
for sample in inactive_samples:
sample['active'] = False
@@ -642,7 +649,8 @@ class Run(BaseClass, LogMixin):
output['sample'] = active_samples + inactive_samples
output['procedure'] = [procedure.details_dict() for procedure in output['procedure']]
output['permission'] = is_power_user()
output['excluded'] = ['procedure', "runsampleassociation", 'excluded', 'expanded', 'sample', 'id', 'custom', 'permission']
output['excluded'] = ['procedure', "runsampleassociation", 'excluded', 'expanded', 'sample', 'id', 'custom',
'permission']
return output
@@ -727,7 +735,8 @@ class Run(BaseClass, LogMixin):
@property
def sample_dicts(self) -> List[dict]:
return [dict(sample_id=assoc.sample.sample_id, row=assoc.row, column=assoc.column, background_color="#6ffe1d") for assoc in self.runsampleassociation]
return [dict(sample_id=assoc.sample.sample_id, row=assoc.row, column=assoc.column, background_color="#6ffe1d")
for assoc in self.runsampleassociation]
@classmethod
def make_plate_map(cls, sample_list: list, plate_rows: int = 8, plate_columns=12) -> str:
@@ -1010,7 +1019,6 @@ class Run(BaseClass, LogMixin):
regex = re.compile(rstring, flags=re.IGNORECASE | re.VERBOSE)
return regex
# NOTE: Query functions
@classmethod
@@ -1190,14 +1198,15 @@ class Run(BaseClass, LogMixin):
Returns:
dict: dictionary of functions
"""
names = ["Add Procedure", "Edit", "Add Comment", "Show Details", "Delete"]
names = ["Add Procedure", "Edit", "Export", "Add Comment", "Show Details", "Delete"]
output = {item: self.__getattribute__(item.lower().replace(" ", "_")) for item in names}
logger.debug(output)
return output
def add_procedure(self, obj, proceduretype_name: str):
from frontend.widgets.procedure_creation import ProcedureCreation
procedure_type = next((proceduretype for proceduretype in self.allowed_procedures if proceduretype.name == proceduretype_name))
procedure_type = next(
(proceduretype for proceduretype in self.allowed_procedures if proceduretype.name == proceduretype_name))
logger.debug(f"Got ProcedureType: {procedure_type}")
dlg = ProcedureCreation(parent=obj, procedure=procedure_type.construct_dummy_procedure(run=self))
if dlg.exec():
@@ -1279,14 +1288,19 @@ class Run(BaseClass, LogMixin):
self.set_attribute(key='comment', value=comment)
self.save(original=False)
def export(self, obj, output_filepath: str|Path|None=None):
def export(self, obj, output_filepath: str | Path | None = None):
from backend.excel import writers
clientsubmission_pyd = self.clientsubmission.to_pydantic()
if not output_filepath:
output_filepath = select_save_file(obj=obj, default_name=clientsubmission_pyd.construct_filename(), extension="xlsx")
output_filepath = select_save_file(obj=obj, default_name=self.construct_filename(), extension="xlsx")
Writer = getattr(writers, "ClientSubmissionWriter")
writer = Writer(output_filepath=output_filepath, pydant_obj=pyd, range_dict=self.range_dict)
workbook = writer.
writer = Writer(output_filepath=output_filepath, pydant_obj=clientsubmission_pyd,
range_dict=self.clientsubmission.range_dict)
workbook: openpyxl.Workbook = writer.write_info()
workbook.save(filename=output_filepath)
def construct_filename(self):
return f"{self.rsl_plate_number}-{self.clientsubmission.clientlab.name}-{self.clientsubmission.submitter_plate_id}"
def backup(self, obj=None, fname: Path | None = None, full_backup: bool = False):
"""
@@ -1360,7 +1374,7 @@ class Run(BaseClass, LogMixin):
def allowed_procedures(self):
return self.clientsubmission.submissiontype.proceduretype
def get_submission_rank_of_sample(self, sample: Sample|str):
def get_submission_rank_of_sample(self, sample: Sample | str):
if isinstance(sample, str):
sample = Sample.query(sample_id=sample)
clientsubmissionsampleassoc = next((assoc for assoc in self.clientsubmission.clientsubmissionsampleassociation
@@ -1378,10 +1392,12 @@ class Run(BaseClass, LogMixin):
submission_rank = self.get_submission_rank_of_sample(sample=sample)
if submission_rank != 0:
row, column = plate_dict[submission_rank]
ranked_samples.append(dict(well_id=sample.sample_id, sample_id=sample.sample_id, row=row, column=column, submission_rank=submission_rank, background_color="#6ffe1d"))
ranked_samples.append(dict(well_id=sample.sample_id, sample_id=sample.sample_id, row=row, column=column,
submission_rank=submission_rank, background_color="#6ffe1d"))
else:
unranked_samples.append(sample)
possible_ranks = (item for item in list(plate_dict.keys()) if item not in [sample['submission_rank'] for sample in ranked_samples])
possible_ranks = (item for item in list(plate_dict.keys()) if
item not in [sample['submission_rank'] for sample in ranked_samples])
# logger.debug(possible_ranks)
# possible_ranks = (plate_dict[idx] for idx in possible_ranks)
for sample in unranked_samples:
@@ -1391,13 +1407,15 @@ class Run(BaseClass, LogMixin):
continue
row, column = plate_dict[submission_rank]
ranked_samples.append(
dict(well_id=sample.sample_id, sample_id=sample.sample_id, row=row, column=column, submission_rank=submission_rank,
dict(well_id=sample.sample_id, sample_id=sample.sample_id, row=row, column=column,
submission_rank=submission_rank,
background_color="#6ffe1d", enabled=True))
padded_list = []
for iii in range(1, proceduretype.total_wells+1):
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=row, column=column, submission_rank=iii, background_color="#ffffff", enabled=False)
sample = next((item for item in ranked_samples if item['submission_rank'] == iii),
dict(well_id=f"blank_{iii}", sample_id="", row=row, column=column, submission_rank=iii,
background_color="#ffffff", enabled=False)
)
padded_list.append(sample)
# logger.debug(f"Final padded list:\n{pformat(list(sorted(padded_list, key=itemgetter('submission_rank'))))}")
@@ -1485,7 +1503,7 @@ class Sample(BaseClass, LogMixin):
)
if full_data:
sample['clientsubmission'] = sorted([item.to_sub_dict() for item in self.sampleclientsubmissionassociation],
key=itemgetter('submitted_date'))
key=itemgetter('submitted_date'))
return sample
def to_pydantic(self):
@@ -2126,8 +2144,8 @@ class RunSampleAssociation(BaseClass):
output['misc_info'] = misc
return output
class ProcedureSampleAssociation(BaseClass):
class ProcedureSampleAssociation(BaseClass):
id = Column(INTEGER, unique=True, nullable=False)
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
@@ -2142,13 +2160,14 @@ class ProcedureSampleAssociation(BaseClass):
results = relationship("Results", back_populates="sampleprocedureassociation")
@classmethod
def query(cls, sample: Sample|str|None=None, procedure: Procedure|str|None=None, limit: int=0, **kwargs):
def query(cls, sample: Sample | str | None = None, procedure: Procedure | str | None = None, limit: int = 0,
**kwargs):
query = cls.__database_session__.query(cls)
match sample:
case Sample():
query = query.filter(cls.sample==sample)
query = query.filter(cls.sample == sample)
case str():
query = query.join(Sample).filter(Sample.sample_id==sample)
query = query.join(Sample).filter(Sample.sample_id == sample)
case _:
pass
match procedure:
@@ -2162,15 +2181,13 @@ class ProcedureSampleAssociation(BaseClass):
limit = 1
return cls.execute_query(query=query, limit=limit, **kwargs)
def __init__(self, new_id:int|None=None, **kwarg):
def __init__(self, new_id: int | None = None, **kwarg):
if new_id:
self.id = new_id
else:
self.id = self.__class__.autoincrement_id()
super().__init__(**kwarg)
@classmethod
def autoincrement_id(cls) -> int:
"""
@@ -2195,4 +2212,3 @@ class ProcedureSampleAssociation(BaseClass):
output['misc_info'] = misc
output['results'] = [result.details_dict() for result in output['results']]
return output