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Plate map in procedure details.

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This commit is contained in:
lwark
2025-09-15 09:21:52 -05:00
parent 11abaafcfc
commit 3862604dfa
14 changed files with 756 additions and 781 deletions
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27
src/submissions/backend/db/models/procedures.py
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@@ -87,7 +87,7 @@ class ReagentRole(BaseClass):
new = True
for k, v in sanitized_kwargs.items():
setattr(instance, k, v)
logger.info(f"Instance from query or create: {instance}")
# logger.info(f"Instance from query or create: {instance}")
return instance, new
@classmethod
@@ -785,7 +785,7 @@ class ProcedureType(BaseClass):
)
return PydProcedure(**output)
def construct_plate_map(self, sample_dicts: List["PydSample"]) -> str:
def construct_plate_map(self, sample_dicts: List["PydSample"], creation:bool=True, vw_modifier:float=1.0) -> str:
"""
Constructs an html based plate map for procedure details.
@@ -800,13 +800,13 @@ class ProcedureType(BaseClass):
if self.plate_rows == 0 or self.plate_columns == 0:
return "<br/>"
sample_dicts = self.pad_sample_dicts(sample_dicts=sample_dicts)
vw = round((-0.07 * len(sample_dicts)) + 12.2, 1)
vw = round((-0.07 * len(sample_dicts)) + (12.2 * vw_modifier), 1)
# NOTE: An overly complicated list comprehension create a list of sample locations
# NOTE: next will return a blank cell if no value found for row/column
env = jinja_template_loading()
template = env.get_template("support/plate_map.html")
html = template.render(plate_rows=self.plate_rows, plate_columns=self.plate_columns, samples=sample_dicts,
vw=vw)
vw=vw, creation=creation)
return html + "<br/>"
def pad_sample_dicts(self, sample_dicts: List["PydSample"]):
@@ -985,6 +985,7 @@ class Procedure(BaseClass):
output['sample_count'] = len(active_samples)
output['clientlab'] = self.run.clientsubmission.clientlab.name
output['cost'] = 0.00
output['platemap'] = self.make_procedure_platemap()
return output
def to_pydantic(self, **kwargs):
@@ -1038,6 +1039,12 @@ class Procedure(BaseClass):
output = {k: v for k, v in dicto.items()}
return output
def make_procedure_platemap(self):
dicto = [sample.to_pydantic() for sample in self.proceduresampleassociation]
html = self.proceduretype.construct_plate_map(sample_dicts=dicto, creation=False, vw_modifier=1.15)
return html
class ProcedureTypeReagentRoleAssociation(BaseClass):
"""
@@ -1143,7 +1150,7 @@ class ProcedureTypeReagentRoleAssociation(BaseClass):
case _:
pass
setattr(instance, k, v)
logger.info(f"Instance from query or create: {instance.__dict__}\nis new: {new}")
# logger.info(f"Instance from query or create: {instance.__dict__}\nis new: {new}")
return instance, new
@classmethod
@@ -1423,7 +1430,7 @@ class EquipmentRole(BaseClass):
new = True
for k, v in sanitized_kwargs.items():
setattr(instance, k, v)
logger.info(f"Instance from query or create: {instance}")
# logger.info(f"Instance from query or create: {instance}")
return instance, new
@classmethod
@@ -1816,6 +1823,9 @@ class Process(BaseClass):
class ProcessVersion(BaseClass):
pyd_model_name = "Process"
id = Column(INTEGER, primary_key=True) #: Process id, primary key
version = Column(FLOAT(2), default=1.00) #: Version number
date_verified = Column(TIMESTAMP) #: Date this version was deemed worthy
@@ -1867,7 +1877,7 @@ class ProcessVersion(BaseClass):
version: str | float | None = None,
name: str | None = None,
limit: int = 0,
**kwargs) -> ReagentLot | List[ReagentLot]:
**kwargs) -> ProcessVersion | List[ProcessVersion]:
query: Query = cls.__database_session__.query(cls)
match name:
case str():
@@ -1881,6 +1891,9 @@ class ProcessVersion(BaseClass):
pass
return cls.execute_query(query=query, limit=limit)
# def to_pydantic(self, pyd_model_name: str | None = None, **kwargs):
# output = super().to_pydantic(pyd_model_name=pyd_model_name, **kwargs)
class Tips(BaseClass):
"""