Writers and managers
This commit is contained in:
lwark
@@ -22,6 +22,7 @@ from sqlalchemy.ext.hybrid import hybrid_property
|
||||
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
|
||||
@@ -43,7 +44,7 @@ from PIL import Image
|
||||
if TYPE_CHECKING:
|
||||
from backend.db.models.kits import ProcedureType, Procedure
|
||||
|
||||
logger = logging.getLogger(f"procedure.{__name__}")
|
||||
logger = logging.getLogger(f"submissions.{__name__}")
|
||||
|
||||
|
||||
class ClientSubmission(BaseClass, LogMixin):
|
||||
@@ -630,6 +631,10 @@ class Run(BaseClass, LogMixin):
|
||||
output["completed_date"] = self.completed_date
|
||||
return output
|
||||
|
||||
@property
|
||||
def sample_count(self):
|
||||
return len(self.sample)
|
||||
|
||||
def details_dict(self, **kwargs):
|
||||
output = super().details_dict()
|
||||
output['plate_number'] = self.plate_number
|
||||
@@ -651,7 +656,7 @@ class Run(BaseClass, LogMixin):
|
||||
output['permission'] = is_power_user()
|
||||
output['excluded'] = ['procedure', "runsampleassociation", 'excluded', 'expanded', 'sample', 'id', 'custom',
|
||||
'permission']
|
||||
|
||||
output['sample_count'] = self.sample_count
|
||||
return output
|
||||
|
||||
@classmethod
|
||||
@@ -923,37 +928,24 @@ class Run(BaseClass, LogMixin):
|
||||
Returns:
|
||||
PydSubmission: converted object.
|
||||
"""
|
||||
from backend.validators import PydSubmission
|
||||
dicto = self.to_dict(full_data=True, backup=backup)
|
||||
from backend.validators import PydRun
|
||||
dicto = self.details_dict(full_data=True, backup=backup)
|
||||
new_dict = {}
|
||||
for key, value in dicto.items():
|
||||
missing = value in ['', 'None', None]
|
||||
match key:
|
||||
case "reagents":
|
||||
field_value = [item.to_pydantic(kittype=self.extraction_kit) for item in
|
||||
self.submission_reagent_associations]
|
||||
case "sample":
|
||||
field_value = [item.to_pydantic() for item in self.submission_sample_associations]
|
||||
case "equipment":
|
||||
field_value = [item.to_pydantic() for item in self.submission_equipment_associations]
|
||||
case "control":
|
||||
try:
|
||||
field_value = [item.to_pydantic() for item in self.__getattribute__(key)]
|
||||
except TypeError as e:
|
||||
logger.error(f"Error converting {key} to pydantic :{e}")
|
||||
continue
|
||||
case "tips":
|
||||
field_value = [item.to_pydantic() for item in self.submission_tips_associations]
|
||||
case "proceduretype":
|
||||
field_value = dict(value=self.__getattribute__(key).name, missing=missing)
|
||||
field_value = [item.to_pydantic() for item in self.runsampleassociation]
|
||||
case "plate_number":
|
||||
key = 'name'
|
||||
key = 'rsl_plate_number'
|
||||
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_number, missing=missing)
|
||||
new_dict['name'] = field_value
|
||||
case "id":
|
||||
continue
|
||||
case "clientsubmission":
|
||||
field_value = self.clientsubmission.to_pydantic()
|
||||
case "procedure":
|
||||
field_value = [item.to_pydantic() for item in self.procedure]
|
||||
case _:
|
||||
try:
|
||||
key = key.lower().replace(" ", "_")
|
||||
@@ -967,7 +959,7 @@ class Run(BaseClass, LogMixin):
|
||||
new_dict[key] = field_value
|
||||
new_dict['filepath'] = Path(tempfile.TemporaryFile().name)
|
||||
dicto.update(new_dict)
|
||||
return PydSubmission(**dicto)
|
||||
return PydRun(**dicto)
|
||||
|
||||
def save(self, original: bool = True):
|
||||
"""
|
||||
@@ -1289,14 +1281,12 @@ class Run(BaseClass, LogMixin):
|
||||
self.save(original=False)
|
||||
|
||||
def export(self, obj, output_filepath: str | Path | None = None):
|
||||
from backend.excel import writers
|
||||
clientsubmission_pyd = self.clientsubmission.to_pydantic()
|
||||
from backend import managers
|
||||
if not output_filepath:
|
||||
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=clientsubmission_pyd,
|
||||
range_dict=self.clientsubmission.range_dict)
|
||||
workbook: openpyxl.Workbook = writer.write_info()
|
||||
Manager = getattr(managers, f"Default{self.__class__.__name__}Manager")
|
||||
manager = Manager(parent=obj, input_object=self.to_pydantic())
|
||||
workbook = manager.write()
|
||||
workbook.save(filename=output_filepath)
|
||||
|
||||
def construct_filename(self):
|
||||
@@ -1970,13 +1960,13 @@ class RunSampleAssociation(BaseClass):
|
||||
# NOTE: Get associated sample info
|
||||
sample = self.sample.to_sub_dict()
|
||||
sample['name'] = self.sample.sample_id
|
||||
sample['row'] = self.row
|
||||
sample['column'] = self.column
|
||||
try:
|
||||
sample['well'] = f"{row_map[self.row]}{self.column}"
|
||||
except KeyError as e:
|
||||
logger.error(f"Unable to find row {self.row} in row_map.")
|
||||
sample['Well'] = None
|
||||
# sample['row'] = self.row
|
||||
# sample['column'] = self.column
|
||||
# try:
|
||||
# sample['well'] = f"{row_map[self.row]}{self.column}"
|
||||
# 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_number
|
||||
sample['positive'] = False
|
||||
return sample
|
||||
@@ -1989,7 +1979,7 @@ class RunSampleAssociation(BaseClass):
|
||||
PydSample: Pydantic Model
|
||||
"""
|
||||
from backend.validators import PydSample
|
||||
return PydSample(**self.to_sub_dict())
|
||||
return PydSample(**self.details_dict())
|
||||
|
||||
@property
|
||||
def hitpicked(self) -> dict | None:
|
||||
|
||||
Reference in New Issue
Block a user