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lwark
2025-05-09 14:35:53 -05:00
parent 20952f2edd
commit 8a16738e93
6 changed files with 225 additions and 34 deletions
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17
src/submissions/backend/db/models/__init__.py
View File

@@ -389,13 +389,13 @@ class BaseClass(Base):
except AttributeError:
return super().__setattr__(key, value)
if isinstance(field_type, InstrumentedAttribute):
# logger.debug(f"{key} is an InstrumentedAttribute.")
logger.debug(f"{key} is an InstrumentedAttribute.")
match field_type.property:
case ColumnProperty():
# logger.debug(f"Setting ColumnProperty to {value}")
logger.debug(f"Setting ColumnProperty to {value}")
return super().__setattr__(key, value)
case _RelationshipDeclared():
# logger.debug(f"{self.__class__.__name__} Setting _RelationshipDeclared for {key} to {value}")
logger.debug(f"{self.__class__.__name__} Setting _RelationshipDeclared for {key} to {value}")
if field_type.property.uselist:
logger.debug(f"Setting with uselist")
existing = self.__getattribute__(key)
@@ -409,7 +409,8 @@ class BaseClass(Base):
value = existing + [value]
else:
if isinstance(value, list):
value = value
# value = value
pass
else:
value = [value]
value = list(set(value))
@@ -421,7 +422,13 @@ class BaseClass(Base):
value = value[0]
else:
raise ValueError("Object is too long to parse a single value.")
return super().__setattr__(key, value)
try:
return super().__setattr__(key, value)
except AttributeError:
logger.debug(f"Possible attempt to set relationship to simple var type.")
relationship_class = field_type.property.entity.entity
value = relationship_class.query(name=value)
return super().__setattr__(key, value)
case _:
return super().__setattr__(key, value)
else:

27
src/submissions/backend/db/models/submissions.py
View File

@@ -46,7 +46,7 @@ class ClientSubmission(BaseClass, LogMixin):
"""
id = Column(INTEGER, primary_key=True) #: primary key
submitter_plate_num = Column(String(127), unique=True) #: The number given to the submission by the submitting lab
submitter_plate_id = Column(String(127), unique=True) #: The number given to the submission by the submitting lab
submitted_date = Column(TIMESTAMP) #: Date submission received
submitting_lab = relationship("Organization", back_populates="submissions") #: client org
submitting_lab_id = Column(INTEGER, ForeignKey("_organization.id", ondelete="SET NULL",
@@ -56,7 +56,7 @@ class ClientSubmission(BaseClass, LogMixin):
sample_count = Column(INTEGER) #: Number of samples in the submission
comment = Column(JSON)
runs = relationship("BasicSubmission", back_populates="client_submission") #: many-to-one relationship
misc_info = Column(JSON)
contact = relationship("Contact", back_populates="submissions") #: client org
contact_id = Column(INTEGER, ForeignKey("_contact.id", ondelete="SET NULL",
name="fk_BS_contact_id")) #: client lab id from _organizations
@@ -92,6 +92,16 @@ class ClientSubmission(BaseClass, LogMixin):
except AttributeError:
self._submission_category = "NA"
def __init__(self):
super().__init__()
self.misc_info = {}
def set_attribute(self, key, value):
if hasattr(self, key):
super().__setattr__(key, value)
else:
self.misc_info[key] = value
@classmethod
def recruit_parser(cls):
pass
@@ -237,7 +247,7 @@ class ClientSubmission(BaseClass, LogMixin):
output = {
"id": self.id,
"submission_type": self.submission_type_name,
"submitter_plate_number": self.submitter_plate_num,
"submitter_plate_number": self.submitter_plate_id,
"submitted_date": self.submitted_date.strftime("%Y-%m-%d"),
"submitting_lab": sub_lab,
"sample_count": self.sample_count,
@@ -279,11 +289,14 @@ class ClientSubmission(BaseClass, LogMixin):
output["runs"] = runs
return output
class BasicSubmission(BaseClass, LogMixin):
"""
Object for an entire submission run. Links to client submissions, reagents, equipment, processes
"""
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)
client_submission_id = Column(INTEGER, ForeignKey("_clientsubmission.id", ondelete="SET NULL",
@@ -384,6 +397,10 @@ class BasicSubmission(BaseClass, LogMixin):
def organization(self):
return self.submitting_lab
@hybrid_property
def name(self):
return self.rsl_plate_num
@classproperty
def jsons(cls) -> List[str]:
"""
@@ -567,8 +584,8 @@ class BasicSubmission(BaseClass, LogMixin):
"id": self.id,
"plate_number": self.rsl_plate_num,
"submission_type": self.client_submission.submission_type_name,
"submitter_plate_number": self.client_submission.submitter_plate_num,
"submitted_date": self.client_submission.submitted_date.strftime("%Y-%m-%d"),
"submitter_plate_number": self.client_submission.submitter_plate_id,
"started_date": self.client_submission.submitted_date.strftime("%Y-%m-%d"),
"submitting_lab": sub_lab,
"sample_count": self.client_submission.sample_count,
"extraction_kit": "Change submissions.py line 388",

2
src/submissions/backend/excel/reports.py
View File

@@ -68,7 +68,7 @@ class ReportMaker(object):
{'extraction_kit': 'count', 'cost': 'sum', 'sample_count': 'sum'})
df2 = df2.rename(columns={"extraction_kit": 'run_count'})
df = df.drop('id', axis=1)
df = df.sort_values(['submitting_lab', "submitted_date"])
df = df.sort_values(['submitting_lab', "started_date"])
return df, df2
def make_report_html(self, df: DataFrame) -> str:

95
src/submissions/backend/validators/pydant.py
View File

@@ -384,7 +384,6 @@ class PydSubmission(BaseModel, extra='allow'):
filepath: Path
submission_type: dict | None
submitter_plate_num: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
submitted_date: dict | None
rsl_plate_num: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
submitted_date: dict | None = Field(default=dict(value=date.today(), missing=True), validate_default=True)
submitting_lab: dict | None
@@ -1331,21 +1330,93 @@ class PydElastic(BaseModel, extra="allow", arbitrary_types_allowed=True):
# NOTE: Generified objects below:
class PydClientSubmission(BaseModel, extra="allow"):
class PydClientSubmission(BaseModel, extra="allow", validate_assignment=True):
sql_object: ClassVar = ClientSubmission
filepath: Path
submission_type: dict | None
submitter_plate_num: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
submitted_date: dict | None
submitted_date: dict | None = Field(default=dict(value=date.today(), missing=True), validate_default=True)
submitting_lab: dict | None
sample_count: dict | None
kittype: dict | None
submission_category: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
comment: dict | None = Field(default=dict(value="", missing=True), validate_default=True)
cost_centre: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
contact: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
submitter_plate_num: dict | None = Field(default=dict(value=None, missing=True), validate_default=True)
@field_validator("sample_count")
@classmethod
def enforce_integer(cls, value):
try:
value['value'] = int(value['value'])
except ValueError:
raise f"sample count value must be an integer"
return value
@field_validator("submitter_plate_num")
@classmethod
def create_submitter_plate_num(cls, value, values):
if value['value'] in [None, "None"]:
val = f"{values.data['submission_type']['value']}-{values.data['submission_category']['value']}-{values.data['submitted_date']['value']}"
return dict(value=val, missing=True)
else:
value['value'] = value['value'].strip()
return value
@field_validator("submitted_date")
@classmethod
def rescue_date(cls, value):
try:
check = value['value'] is None
except TypeError:
check = True
if check:
return dict(value=date.today(), missing=True)
return value
def filter_field(self, key: str) -> Any:
"""
Attempts to get value from field dictionary
Args:
key (str): name of the field of interest
Returns:
Any (): Value found.
"""
item = getattr(self, key)
match item:
case dict():
try:
item = item['value']
except KeyError:
logger.error(f"Couldn't get dict value: {item}")
case _:
pass
return item
def improved_dict(self, dictionaries: bool = True) -> dict:
"""
Adds model_extra to fields.
Args:
dictionaries (bool, optional): Are dictionaries expected as input? i.e. Should key['value'] be retrieved. Defaults to True.
Returns:
dict: This instance as a dictionary
"""
fields = list(self.model_fields.keys()) + list(self.model_extra.keys())
if dictionaries:
output = {k: getattr(self, k) for k in fields}
else:
output = {k: self.filter_field(k) for k in fields}
try:
del output['filepath']
except KeyError:
pass
logger.debug(f"Output; {pformat(output)}")
return output
def to_form(self, parent: QWidget, disable: list | None = None):
"""
@@ -1360,3 +1431,17 @@ class PydClientSubmission(BaseModel, extra="allow"):
"""
from frontend.widgets.submission_widget import ClientSubmissionFormWidget
return ClientSubmissionFormWidget(parent=parent, submission=self, disable=disable)
def to_sql(self):
sql = self.sql_object()
for key, value in self.improved_dict().items():
if isinstance(value, dict):
value = value['value']
# if hasattr(sql, key):
# try:
sql.set_attribute(key, value)
# except AttributeError:
# continue
# else:
# sql.misc_info[key] = value
print(sql.__dict__)