Addition of procedure parser in import.
This commit is contained in:
lwark
@@ -26,7 +26,7 @@ from sqlite3 import OperationalError as SQLOperationalError, IntegrityError as S
|
||||
from openpyxl import Workbook
|
||||
from openpyxl.drawing.image import Image as OpenpyxlImage
|
||||
from tools import row_map, setup_lookup, jinja_template_loading, rreplace, row_keys, check_key_or_attr, Result, Report, \
|
||||
report_result, create_holidays_for_year, check_dictionary_inclusion_equality
|
||||
report_result, create_holidays_for_year, check_dictionary_inclusion_equality, is_power_user
|
||||
from datetime import datetime, date
|
||||
from typing import List, Any, Tuple, Literal, Generator, Type, TYPE_CHECKING
|
||||
from pathlib import Path
|
||||
@@ -100,7 +100,7 @@ class ClientSubmission(BaseClass, LogMixin):
|
||||
Args:
|
||||
submission_type (str | models.SubmissionType | None, optional): Submission type of interest. Defaults to None.
|
||||
id (int | str | None, optional): Submission id in the database (limits results to 1). Defaults to None.
|
||||
rsl_plate_num (str | None, optional): Submission name in the database (limits results to 1). Defaults to None.
|
||||
rsl_plate_number (str | None, optional): Submission name in the database (limits results to 1). Defaults to None.
|
||||
start_date (date | str | int | None, optional): Beginning date to search by. Defaults to None.
|
||||
end_date (date | str | int | None, optional): Ending date to search by. Defaults to None.
|
||||
reagent (models.Reagent | str | None, optional): A reagent used in the procedure. Defaults to None.
|
||||
@@ -304,7 +304,7 @@ class ClientSubmission(BaseClass, LogMixin):
|
||||
samples = [sample.to_pydantic() for sample in self.clientsubmissionsampleassociation]
|
||||
checker = SampleChecker(parent=None, title="Create Run", samples=samples, clientsubmission=self)
|
||||
if checker.exec():
|
||||
run = Run(clientsubmission=self, rsl_plate_num=checker.rsl_plate_num)
|
||||
run = Run(clientsubmission=self, rsl_plate_number=checker.rsl_plate_number)
|
||||
active_samples = [sample for sample in samples if sample.enabled]
|
||||
logger.debug(active_samples)
|
||||
for sample in active_samples:
|
||||
@@ -323,8 +323,12 @@ class ClientSubmission(BaseClass, LogMixin):
|
||||
def add_comment(self, obj):
|
||||
logger.debug("Add Comment")
|
||||
|
||||
def show_details(self, obj):
|
||||
logger.debug("Show Details")
|
||||
# def show_details(self, obj):
|
||||
# logger.debug("Show Details")
|
||||
# from frontend.widgets.submission_details import SubmissionDetails
|
||||
# dlg = SubmissionDetails(parent=obj, sub=self)
|
||||
# if dlg.exec():
|
||||
# pass
|
||||
|
||||
def details_dict(self, **kwargs):
|
||||
output = super().details_dict(**kwargs)
|
||||
@@ -334,6 +338,11 @@ class ClientSubmission(BaseClass, LogMixin):
|
||||
output['run'] = [run.details_dict() for run in output['run']]
|
||||
output['sample'] = [sample.details_dict() for sample in output['clientsubmissionsampleassociation']]
|
||||
output['name'] = self.name
|
||||
output['client_lab'] = output['clientlab']
|
||||
output['submission_type'] = output['submissiontype']
|
||||
output['excluded'] = ['run', "sample", "clientsubmissionsampleassociation", "excluded",
|
||||
"expanded", 'clientlab', 'submissiontype', 'id']
|
||||
output['expanded'] = ["clientlab", "contact", "submissiontype"]
|
||||
return output
|
||||
|
||||
|
||||
@@ -343,7 +352,7 @@ class Run(BaseClass, LogMixin):
|
||||
"""
|
||||
|
||||
id = Column(INTEGER, primary_key=True) #: primary key
|
||||
rsl_plate_num = Column(String(32), unique=True, nullable=False) #: RSL name (e.g. RSL-22-0012)
|
||||
rsl_plate_number = Column(String(32), unique=True, nullable=False) #: RSL name (e.g. RSL-22-0012)
|
||||
clientsubmission_id = Column(INTEGER, ForeignKey("_clientsubmission.id", ondelete="SET NULL",
|
||||
name="fk_BS_clientsub_id")) #: client lab id from _organizations)
|
||||
clientsubmission = relationship("ClientSubmission", back_populates="run")
|
||||
@@ -387,7 +396,7 @@ class Run(BaseClass, LogMixin):
|
||||
|
||||
@hybrid_property
|
||||
def name(self):
|
||||
return self.rsl_plate_num
|
||||
return self.rsl_plate_number
|
||||
|
||||
@classmethod
|
||||
def get_default_info(cls, *args, submissiontype: SubmissionType | None = None) -> dict:
|
||||
@@ -593,8 +602,23 @@ class Run(BaseClass, LogMixin):
|
||||
|
||||
def details_dict(self, **kwargs):
|
||||
output = super().details_dict()
|
||||
output['sample'] = [sample.details_dict() for sample in output['runsampleassociation']]
|
||||
submission_samples = [sample for sample in self.clientsubmission.sample]
|
||||
# logger.debug(f"Submission samples:{pformat(submission_samples)}")
|
||||
active_samples = [sample.details_dict() for sample in output['runsampleassociation']
|
||||
if sample.sample.sample_id in [s.sample_id for s in submission_samples]]
|
||||
# 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]]
|
||||
# logger.debug(f"Inactive samples:{pformat(inactive_samples)}")
|
||||
for sample in inactive_samples:
|
||||
sample['active'] = False
|
||||
# output['sample'] = [sample.details_dict() for sample in output['runsampleassociation']]
|
||||
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']
|
||||
|
||||
return output
|
||||
|
||||
@classmethod
|
||||
@@ -890,10 +914,10 @@ class Run(BaseClass, LogMixin):
|
||||
field_value = dict(value=self.__getattribute__(key).name, missing=missing)
|
||||
case "plate_number":
|
||||
key = 'name'
|
||||
field_value = dict(value=self.rsl_plate_num, missing=missing)
|
||||
field_value = dict(value=self.rsl_plate_number, missing=missing)
|
||||
case "submitter_plate_number":
|
||||
key = "submitter_plate_id"
|
||||
field_value = dict(value=self.submitter_plate_num, missing=missing)
|
||||
field_value = dict(value=self.submitter_plate_number, missing=missing)
|
||||
case "id":
|
||||
continue
|
||||
case _:
|
||||
@@ -1168,8 +1192,8 @@ class Run(BaseClass, LogMixin):
|
||||
e: SQLIntegrityError or SQLOperationalError if problem with commit.
|
||||
"""
|
||||
from frontend.widgets.pop_ups import QuestionAsker
|
||||
fname = self.__backup_path__.joinpath(f"{self.rsl_plate_num}-backup({date.today().strftime('%Y%m%d')})")
|
||||
msg = QuestionAsker(title="Delete?", message=f"Are you sure you want to delete {self.rsl_plate_num}?\n")
|
||||
fname = self.__backup_path__.joinpath(f"{self.rsl_plate_number}-backup({date.today().strftime('%Y%m%d')})")
|
||||
msg = QuestionAsker(title="Delete?", message=f"Are you sure you want to delete {self.rsl_plate_number}?\n")
|
||||
if msg.exec():
|
||||
try:
|
||||
# NOTE: backs up file as xlsx, same as export.
|
||||
@@ -1187,17 +1211,17 @@ class Run(BaseClass, LogMixin):
|
||||
except AttributeError:
|
||||
logger.error("App will not refresh data at this time.")
|
||||
|
||||
def show_details(self, obj):
|
||||
"""
|
||||
Creates Widget for showing procedure details.
|
||||
|
||||
Args:
|
||||
obj (Widget): Parent widget
|
||||
"""
|
||||
from frontend.widgets.submission_details import SubmissionDetails
|
||||
dlg = SubmissionDetails(parent=obj, sub=self)
|
||||
if dlg.exec():
|
||||
pass
|
||||
# def show_details(self, obj):
|
||||
# """
|
||||
# Creates Widget for showing procedure details.
|
||||
#
|
||||
# Args:
|
||||
# obj (Widget): Parent widget
|
||||
# """
|
||||
# from frontend.widgets.submission_details import SubmissionDetails
|
||||
# dlg = SubmissionDetails(parent=obj, sub=self)
|
||||
# if dlg.exec():
|
||||
# pass
|
||||
|
||||
def edit(self, obj):
|
||||
"""
|
||||
@@ -1641,12 +1665,12 @@ class ClientSubmissionSampleAssociation(BaseClass):
|
||||
output = super().details_dict()
|
||||
# NOTE: Figure out how to merge the misc_info if doing .update instead.
|
||||
relevant = {k: v for k, v in output.items() if k not in ['sample']}
|
||||
logger.debug(f"Relevant info from assoc output: {pformat(relevant)}")
|
||||
# logger.debug(f"Relevant info from assoc output: {pformat(relevant)}")
|
||||
output = output['sample'].details_dict()
|
||||
misc = output['_misc_info']
|
||||
logger.debug(f"Output from sample: {pformat(output)}")
|
||||
misc = output['misc_info']
|
||||
# logger.debug(f"Output from sample: {pformat(output)}")
|
||||
output.update(relevant)
|
||||
output['_misc_info'] = misc
|
||||
output['misc_info'] = misc
|
||||
# output['sample'] = temp
|
||||
# output.update(output['sample'].details_dict())
|
||||
return output
|
||||
@@ -1815,7 +1839,7 @@ class ClientSubmissionSampleAssociation(BaseClass):
|
||||
case ClientSubmission():
|
||||
pass
|
||||
case str():
|
||||
clientsubmission = ClientSubmission.query(rsl_plate_num=clientsubmission)
|
||||
clientsubmission = ClientSubmission.query(rsl_plate_number=clientsubmission)
|
||||
case _:
|
||||
raise ValueError()
|
||||
match sample:
|
||||
@@ -1879,7 +1903,7 @@ class RunSampleAssociation(BaseClass):
|
||||
|
||||
def __repr__(self) -> str:
|
||||
try:
|
||||
return f"<{self.__class__.__name__}({self.run.rsl_plate_num} & {self.sample.sample_id})"
|
||||
return f"<{self.__class__.__name__}({self.run.rsl_plate_number} & {self.sample.sample_id})"
|
||||
except AttributeError as e:
|
||||
logger.error(f"Unable to construct __repr__ due to: {e}")
|
||||
return super().__repr__()
|
||||
@@ -1901,7 +1925,7 @@ class RunSampleAssociation(BaseClass):
|
||||
except KeyError as e:
|
||||
logger.error(f"Unable to find row {self.row} in row_map.")
|
||||
sample['Well'] = None
|
||||
sample['plate_name'] = self.run.rsl_plate_num
|
||||
sample['plate_name'] = self.run.rsl_plate_number
|
||||
sample['positive'] = False
|
||||
return sample
|
||||
|
||||
@@ -1975,7 +1999,7 @@ class RunSampleAssociation(BaseClass):
|
||||
case Run():
|
||||
query = query.filter(cls.run == run)
|
||||
case str():
|
||||
query = query.join(Run).filter(Run.rsl_plate_num == run)
|
||||
query = query.join(Run).filter(Run.rsl_plate_number == run)
|
||||
case _:
|
||||
pass
|
||||
match sample:
|
||||
@@ -2060,12 +2084,12 @@ class RunSampleAssociation(BaseClass):
|
||||
output = super().details_dict()
|
||||
# NOTE: Figure out how to merge the misc_info if doing .update instead.
|
||||
relevant = {k: v for k, v in output.items() if k not in ['sample']}
|
||||
logger.debug(f"Relevant info from assoc output: {pformat(relevant)}")
|
||||
# logger.debug(f"Relevant info from assoc output: {pformat(relevant)}")
|
||||
output = output['sample'].details_dict()
|
||||
misc = output['_misc_info']
|
||||
logger.debug(f"Output from sample: {pformat(output)}")
|
||||
misc = output['misc_info']
|
||||
# logger.debug(f"Output from sample: {pformat(output)}")
|
||||
output.update(relevant)
|
||||
output['_misc_info'] = misc
|
||||
output['misc_info'] = misc
|
||||
return output
|
||||
|
||||
class ProcedureSampleAssociation(BaseClass):
|
||||
@@ -2132,9 +2156,9 @@ class ProcedureSampleAssociation(BaseClass):
|
||||
# NOTE: Figure out how to merge the misc_info if doing .update instead.
|
||||
relevant = {k: v for k, v in output.items() if k not in ['sample']}
|
||||
output = output['sample'].details_dict()
|
||||
misc = output['_misc_info']
|
||||
misc = output['misc_info']
|
||||
output.update(relevant)
|
||||
output['_misc_info'] = misc
|
||||
output['misc_info'] = misc
|
||||
output['results'] = [result.details_dict() for result in output['results']]
|
||||
return output
|
||||
|
||||
|
||||
Reference in New Issue
Block a user