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Added Postgres support.

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This commit is contained in:
lwark
2024-07-25 08:41:44 -05:00
parent 54e1e55804
commit 4bc5e08ac6
32 changed files with 579 additions and 1030 deletions
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92
src/submissions/backend/validators/pydant.py
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@@ -108,7 +108,7 @@ class PydReagent(BaseModel):
Returns:
dict: Information dictionary
"""
"""
try:
extras = list(self.model_extra.keys())
except AttributeError:
@@ -161,7 +161,7 @@ class PydReagent(BaseModel):
# reagent.reagent_submission_associations.append(assoc)
else:
assoc = None
report.add_result(Result(owner = __name__, code=0, msg="New reagent created.", status="Information"))
report.add_result(Result(owner=__name__, code=0, msg="New reagent created.", status="Information"))
else:
if submission is not None and reagent not in submission.reagents:
assoc = SubmissionReagentAssociation(reagent=reagent, submission=submission)
@@ -217,7 +217,7 @@ class PydSample(BaseModel, extra='allow'):
Returns:
dict: Information dictionary
"""
"""
fields = list(self.model_fields.keys()) + list(self.model_extra.keys())
return {k: getattr(self, k) for k in fields}
@@ -254,7 +254,8 @@ class PydSample(BaseModel, extra='allow'):
submission=submission,
sample=instance,
row=row, column=column, id=aid,
submission_rank=submission_rank, **self.model_extra)
submission_rank=submission_rank,
**self.model_extra)
# logger.debug(f"Using submission_sample_association: {association}")
try:
# instance.sample_submission_associations.append(association)
@@ -270,7 +271,7 @@ class PydSample(BaseModel, extra='allow'):
Returns:
dict: Information dictionary
"""
"""
try:
extras = list(self.model_extra.keys())
except AttributeError:
@@ -281,10 +282,10 @@ class PydSample(BaseModel, extra='allow'):
class PydTips(BaseModel):
name: str
lot: str|None = Field(default=None)
lot: str | None = Field(default=None)
role: str
def to_sql(self, submission:BasicSubmission) -> SubmissionTipsAssociation:
def to_sql(self, submission: BasicSubmission) -> SubmissionTipsAssociation:
"""
Con
@@ -293,7 +294,7 @@ class PydTips(BaseModel):
Returns:
SubmissionTipsAssociation: Association between queried tips and submission
"""
"""
tips = Tips.query(name=self.name, lot=self.lot, limit=1)
assoc = SubmissionTipsAssociation(submission=submission, tips=tips, role_name=self.role)
return assoc
@@ -305,7 +306,7 @@ class PydEquipment(BaseModel, extra='ignore'):
nickname: str | None
processes: List[str] | None
role: str | None
tips: List[PydTips]|None = Field(default=None)
tips: List[PydTips] | None = Field(default=None)
@field_validator('processes', mode='before')
@classmethod
@@ -338,23 +339,19 @@ class PydEquipment(BaseModel, extra='ignore'):
if equipment is None:
return
if submission is not None:
assoc = SubmissionEquipmentAssociation(submission=submission, equipment=equipment)
process = Process.query(name=self.processes[0])
if process is None:
logger.error(f"Found unknown process: {process}.")
# from frontend.widgets.pop_ups import QuestionAsker
# dlg = QuestionAsker(title="Add Process?",
# message=f"Unable to find {self.processes[0]} in the database.\nWould you like to add it?")
# if dlg.exec():
# kit = submission.extraction_kit
# submission_type = submission.submission_type
# process = Process(name=self.processes[0])
# process.kit_types.append(kit)
# process.submission_types.append(submission_type)
# process.equipment.append(equipment)
# process.save()
assoc.process = process
assoc.role = self.role
# NOTE: Need to make sure the same association is not added to the submission
assoc = SubmissionEquipmentAssociation.query(equipment_id=equipment.id, submission_id=submission.id,
role=self.role, limit=1)
if assoc is None:
assoc = SubmissionEquipmentAssociation(submission=submission, equipment=equipment)
process = Process.query(name=self.processes[0])
if process is None:
logger.error(f"Found unknown process: {process}.")
assoc.process = process
assoc.role = self.role
else:
assoc = None
else:
assoc = None
return equipment, assoc
@@ -365,7 +362,7 @@ class PydEquipment(BaseModel, extra='ignore'):
Returns:
dict: Information dictionary
"""
"""
try:
extras = list(self.model_extra.keys())
except AttributeError:
@@ -441,7 +438,7 @@ class PydSubmission(BaseModel, extra='allow'):
return value.date()
case int():
return dict(value=datetime.fromordinal(datetime(1900, 1, 1).toordinal() + value['value'] - 2).date(),
missing=True)
missing=True)
case str():
string = re.sub(r"(_|-)\d$", "", value['value'])
try:
@@ -508,7 +505,7 @@ class PydSubmission(BaseModel, extra='allow'):
output = "RSL-BS-Test001"
else:
output = RSLNamer(filename=values.data['filepath'].__str__(), sub_type=sub_type,
data=values.data).parsed_name
data=values.data).parsed_name
return dict(value=output, missing=True)
@field_validator("technician", mode="before")
@@ -637,14 +634,14 @@ class PydSubmission(BaseModel, extra='allow'):
self.submission_object = BasicSubmission.find_polymorphic_subclass(
polymorphic_identity=self.submission_type['value'])
def set_attribute(self, key:str, value):
def set_attribute(self, key: str, value):
"""
Better handling of attribute setting.
Args:
key (str): Name of field to set
value (_type_): Value to set field to.
"""
"""
self.__setattr__(name=key, value=value)
def handle_duplicate_samples(self):
@@ -710,7 +707,7 @@ class PydSubmission(BaseModel, extra='allow'):
missing_reagents = [reagent for reagent in self.reagents if reagent.missing]
return missing_info, missing_reagents
def to_sql(self) -> Tuple[BasicSubmission, Result]:
def to_sql(self) -> Tuple[BasicSubmission, Report]:
"""
Converts this instance into a backend.db.models.submissions.BasicSubmission instance
@@ -718,13 +715,13 @@ class PydSubmission(BaseModel, extra='allow'):
Tuple[BasicSubmission, Result]: BasicSubmission instance, result object
"""
# self.__dict__.update(self.model_extra)
report = Report()
dicto = self.improved_dict()
instance, code, msg = BasicSubmission.query_or_create(submission_type=self.submission_type['value'],
rsl_plate_num=self.rsl_plate_num['value'])
result = Result(msg=msg, code=code)
instance, result = BasicSubmission.query_or_create(submission_type=self.submission_type['value'],
rsl_plate_num=self.rsl_plate_num['value'])
report.add_result(result)
self.handle_duplicate_samples()
# logger.debug(f"Here's our list of duplicate removed samples: {self.samples}")
# for key, value in self.__dict__.items():
for key, value in dicto.items():
if isinstance(value, dict):
value = value['value']
@@ -733,13 +730,13 @@ class PydSubmission(BaseModel, extra='allow'):
# logger.debug(f"Setting {key} to {value}")
match key:
case "reagents":
if code == 1:
if report.results[0].code == 1:
instance.submission_reagent_associations = []
# logger.debug(f"Looking through {self.reagents}")
for reagent in self.reagents:
reagent, assoc, _ = reagent.toSQL(submission=instance)
# logger.debug(f"Association: {assoc}")
if assoc is not None:# and assoc not in instance.submission_reagent_associations:
if assoc is not None: # and assoc not in instance.submission_reagent_associations:
instance.submission_reagent_associations.append(assoc)
# instance.reagents.append(reagent)
case "samples":
@@ -755,10 +752,7 @@ class PydSubmission(BaseModel, extra='allow'):
if equip is None:
continue
equip, association = equip.toSQL(submission=instance)
if association is not None and association not in instance.submission_equipment_associations:
# association.save()
# logger.debug(
# f"Equipment association SQL object to be added to submission: {association.__dict__}")
if association is not None:
instance.submission_equipment_associations.append(association)
case "tips":
for tips in self.tips:
@@ -817,9 +811,9 @@ class PydSubmission(BaseModel, extra='allow'):
# except AttributeError as e:
# logger.debug(f"Something went wrong constructing instance {self.rsl_plate_num}: {e}")
# logger.debug(f"Constructed submissions message: {msg}")
return instance, result
return instance, report
def to_form(self, parent: QWidget):
def to_form(self, parent: QWidget, disable:list|None=None):
"""
Converts this instance into a frontend.widgets.submission_widget.SubmissionFormWidget
@@ -830,7 +824,8 @@ class PydSubmission(BaseModel, extra='allow'):
SubmissionFormWidget: Submission form widget
"""
from frontend.widgets.submission_widget import SubmissionFormWidget
return SubmissionFormWidget(parent=parent, submission=self)
logger.debug(f"Disbable: {disable}")
return SubmissionFormWidget(parent=parent, submission=self, disable=disable)
def to_writer(self) -> "SheetWriter":
"""
@@ -838,7 +833,7 @@ class PydSubmission(BaseModel, extra='allow'):
Returns:
SheetWriter: Sheetwriter object that will perform writing.
"""
"""
from backend.excel.writer import SheetWriter
return SheetWriter(self)
@@ -896,8 +891,8 @@ class PydSubmission(BaseModel, extra='allow'):
status="Warning")
report.add_result(result)
return output_reagents, report
def export_csv(self, filename:Path|str):
def export_csv(self, filename: Path | str):
try:
worksheet = self.csv
except AttributeError:
@@ -1024,4 +1019,3 @@ class PydEquipmentRole(BaseModel):
"""
from frontend.widgets.equipment_usage import RoleComboBox
return RoleComboBox(parent=parent, role=self, used=used)