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basic procedure creation working

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This commit is contained in:
lwark
2025-05-28 14:26:12 -05:00
parent 4e1e06bb5e
commit fef964fba0
7 changed files with 319 additions and 36 deletions
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56
src/submissions/backend/validators/pydant.py
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@@ -243,6 +243,8 @@ class PydSample(PydBaseClass):
sampletype: str | None = Field(default=None)
submission_rank: int | List[int] | None = Field(default=0, validate_default=True)
enabled: bool = Field(default=True)
row: int = Field(default=0)
column: int = Field(default=0)
@field_validator("sample_id", mode="before")
@classmethod
@@ -1336,6 +1338,7 @@ class PydElastic(BaseModel, extra="allow", arbitrary_types_allowed=True):
class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
proceduretype: ProcedureType | None = Field(default=None)
run: Run | None = Field(default=None)
name: dict = Field(default=dict(value="NA", missing=True), validate_default=True)
technician: dict = Field(default=dict(value="NA", missing=True))
repeat: bool = Field(default=False)
@@ -1344,6 +1347,7 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
plate_map: str | None = Field(default=None)
reagent: list | None = Field(default=[])
reagentrole: dict | None = Field(default={}, validate_default=True)
samples: List[PydSample] = Field(default=[])
@field_validator("name")
@classmethod
@@ -1379,18 +1383,68 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
value = {item.name: item.reagents for item in kittype.reagentrole}
return value
def update_kittype_reagentroles(self, kittype: str | KitType):
if kittype == self.__class__.model_fields['kittype'].default['value']:
return
if isinstance(kittype, str):
kittype_obj = KitType.query(name=kittype)
try:
self.reagentrole = {item.name: item.reagents for item in
self.reagentrole = {item.name: item.get_reagents(kittype=kittype_obj) for item in
kittype_obj.get_reagents(proceduretype=self.proceduretype)}
except AttributeError:
self.reagentrole = {}
self.possible_kits.insert(0, self.possible_kits.pop(self.possible_kits.index(kittype)))
def shuffle_samples(self, source_row: int, source_column: int, destination_row: int, destination_column=int):
logger.debug(f"Attempting sample shuffle.")
try:
source_sample = next(
(sample for sample in self.samples if sample.row == source_row and sample.column == source_column))
except StopIteration:
raise StopIteration("Couldn't find proper sample.")
logger.debug(f"Source Well: {source_row}, {source_column}")
logger.debug(f"Destination Well: {destination_row}, {destination_column}")
updateable_samples = []
if source_row > destination_row and source_column >= destination_column:
logger.debug(f"Sample was moved ahead.")
movement = "pos"
for sample in self.samples:
if sample.row >= destination_row and sample.column >= destination_column:
if sample.row <= source_row and sample.column <= source_column:
updateable_samples.append(sample)
elif source_row < destination_row and source_column <= destination_column:
logger.debug(f"Sample was moved back.")
movement = "neg"
for sample in self.samples:
if sample.row <= destination_row and sample.column <= destination_column:
if sample.row >= source_row and sample.column >= source_column:
updateable_samples.append(sample)
else:
logger.debug(f"Don't know what happened.")
logger.debug(f"Samples to be updated: {pformat(updateable_samples)}")
for sample in updateable_samples:
if sample.row == source_row and sample.column == source_column:
sample.row = destination_row
sample.column = destination_column
else:
match movement:
case "pos":
if sample.row + 1 > 8:
sample.column += 1
sample.row = 1
else:
sample.row += 1
case "neg":
if sample.row - 1 <= 0:
sample.column -= 1
sample.row = 8
else:
sample.row -= 1
class PydClientSubmission(PydBaseClass):
# sql_object: ClassVar = ClientSubmission