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Bug fixes for omni gui objects.

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This commit is contained in:
lwark
2025-04-16 13:47:07 -05:00
parent 58f5d361b3
commit 1a1f766890
6 changed files with 263 additions and 70 deletions
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6
src/submissions/backend/db/models/__init__.py
View File

@@ -457,12 +457,12 @@ class BaseClass(Base):
"""
match input_date:
case datetime() | date():
output_date = input_date#.strftime("%Y-%m-%d %H:%M:%S")
output_date = input_date
case int():
output_date = datetime.fromordinal(
datetime(1900, 1, 1).toordinal() + input_date - 2)#.date().strftime("%Y-%m-%d %H:%M:%S")
datetime(1900, 1, 1).toordinal() + input_date - 2)
case _:
output_date = parse(input_date)#.strftime("%Y-%m-%d %H:%M:%S")
output_date = parse(input_date)
if eod:
addition_time = datetime.max.time()
else:

16
src/submissions/backend/db/models/kits.py
View File

@@ -126,7 +126,13 @@ class KitType(BaseClass):
submission_type=ST)) #: Association proxy to SubmissionTypeKitTypeAssociation
@classproperty
def aliases(cls):
def aliases(cls) -> List[str]:
"""
Gets other names the sql object of this class might go by.
Returns:
List[str]: List of names
"""
return super().aliases + [cls.query_alias, "kit_types", "kit_type"]
@hybrid_property
@@ -1077,7 +1083,13 @@ class SubmissionType(BaseClass):
return self.processes
@classproperty
def aliases(cls):
def aliases(cls) -> List[str]:
"""
Gets other names the sql object of this class might go by.
Returns:
List[str]: List of names
"""
return super().aliases + ["submission_types", "submission_type"]
@classproperty

22
src/submissions/backend/db/models/submissions.py
View File

@@ -1540,12 +1540,15 @@ class BacterialCulture(BasicSubmission):
return report
parser = ConcentrationParser(filepath=fname, submission=self)
conc_samples = [sample for sample in parser.samples]
# logger.debug(f"Concentration samples: {pformat(conc_samples)}")
for sample in self.samples:
logger.debug(f"Sample {sample.submitter_id}")
# logger.debug(f"Sample {sample.submitter_id}")
# logger.debug(f"Match {item['submitter_id']}")
try:
# NOTE: Fix for ENs which have no rsl_number...
sample_dict = next(item for item in conc_samples if item['submitter_id'] == sample.submitter_id)
sample_dict = next(item for item in conc_samples if str(item['submitter_id']).upper() == sample.submitter_id)
except StopIteration:
logger.error(f"Couldn't find sample dict for {sample.submitter_id}")
continue
logger.debug(f"Sample {sample.submitter_id} conc. = {sample_dict['concentration']}")
if sample_dict['concentration']:
@@ -1734,12 +1737,10 @@ class Wastewater(BasicSubmission):
sample[f"ct_{sample['target'].lower()}"] = sample['ct'] if isinstance(sample['ct'], float) else 0.0
# NOTE: Set assessment
# logger.debug(f"Sample assessemnt: {sample['assessment']}")
# sample[f"{sample['target'].lower()}_status"] = sample['assessment']
# NOTE: Get sample having other target
other_targets = [s for s in samples if re.sub('-N\\d*$', '', s['sample']) == sample['sample']]
for s in other_targets:
sample[f"ct_{s['target'].lower()}"] = s['ct'] if isinstance(s['ct'], float) else 0.0
# sample[f"{s['target'].lower()}_status"] = s['assessment']
try:
del sample['ct']
except KeyError:
@@ -2177,7 +2178,6 @@ class WastewaterArtic(BasicSubmission):
except AttributeError:
plate_num = "1"
plate_num = plate_num.strip("-")
# repeat_num = re.search(r"R(?P<repeat>\d)?$", "PBS20240426-2R").groups()[0]
try:
repeat_num = re.search(r"R(?P<repeat>\d)?$", processed).groups()[0]
except:
@@ -2663,16 +2663,6 @@ class BasicSample(BaseClass, LogMixin):
def delete(self):
raise AttributeError(f"Delete not implemented for {self.__class__}")
# @classmethod
# def get_searchables(cls) -> List[dict]:
# """
# Delivers a list of fields that can be used in fuzzy search.
#
# Returns:
# List[str]: List of fields.
# """
# return [dict(label="Submitter ID", field="submitter_id")]
@classmethod
def samples_to_df(cls, sample_list: List[BasicSample], **kwargs) -> pd.DataFrame:
"""
@@ -2729,8 +2719,6 @@ class WastewaterSample(BasicSample):
Derivative wastewater sample
"""
# searchables = BasicSample.searchables + ['ww_processing_num', 'ww_full_sample_id', 'rsl_number']
id = Column(INTEGER, ForeignKey('_basicsample.id'), primary_key=True)
ww_processing_num = Column(String(64)) #: wastewater processing number
ww_full_sample_id = Column(String(64)) #: full id given by entrics

217
src/submissions/backend/validators/omni_gui_objects.py
View File

@@ -24,10 +24,25 @@ class BaseOmni(BaseModel):
return f"<{self.__class__.__name__}({self.__repr_name__})>"
@classproperty
def aliases(cls):
def aliases(cls) -> List[str]:
"""
Gets other names the sql object of this class might go by.
Returns:
List[str]: List of names
"""
return cls.class_object.aliases
def check_all_attributes(self, attributes: dict) -> bool:
"""
Compares this pobject to dictionary of attributes to determine equality.
Args:
attributes (dict):
Returns:
bool: result
"""
# logger.debug(f"Incoming attributes: {attributes}")
attributes = {k : v for k, v in attributes.items() if k in self.list_searchables.keys()}
for key, value in attributes.items():
@@ -47,7 +62,14 @@ class BaseOmni(BaseModel):
# logger.debug("Everything checks out, these are the same object.")
return True
def __setattr__(self, key, value):
def __setattr__(self, key: str, value: Any):
"""
Overrides built in dunder method
Args:
key (str):
value (Any):
"""
try:
class_value = getattr(self.class_object, key)
except AttributeError:
@@ -151,12 +173,22 @@ class OmniSubmissionType(BaseOmni):
super().__init__(**data)
self.instance_object = instance_object
def to_dataframe_dict(self):
@property
def dataframe_dict(self) -> dict:
"""
Dictionary of gui relevant values.
Returns:
dict: result
"""
return dict(
name=self.name
)
def to_sql(self):
"""
Convert this object to an instance of its class object.
"""
instance, new = self.class_object.query_or_create(name=self.name)
instance.info_map = self.info_map
instance.defaults = self.defaults
@@ -191,12 +223,23 @@ class OmniReagentRole(BaseOmni):
super().__init__(**data)
self.instance_object = instance_object
def to_dataframe_dict(self):
@property
def dataframe_dict(self) -> dict:
"""
Dictionary of gui relevant values.
Returns:
dict: result
"""
return dict(
name=self.name
)
def to_sql(self):
"""
Convert this object to an instance of its class object.
"""
instance, new = self.class_object.query_or_create(name=self.name)
if new:
instance.eol_ext = self.eol_ext
@@ -252,7 +295,14 @@ class OmniSubmissionTypeKitTypeAssociation(BaseOmni):
super().__init__(**data)
self.instance_object = instance_object
def to_dataframe_dict(self):
@property
def dataframe_dict(self) -> dict:
"""
Dictionary of gui relevant values.
Returns:
dict: result
"""
if isinstance(self.submissiontype, OmniSubmissionType):
submissiontype = self.submissiontype.name
else:
@@ -270,6 +320,10 @@ class OmniSubmissionTypeKitTypeAssociation(BaseOmni):
)
def to_sql(self):
"""
Convert this object to an instance of its class object.
"""
# logger.debug(f"Self kittype: {self.submissiontype}")
if issubclass(self.submissiontype.__class__, BaseOmni):
submissiontype = SubmissionType.query(name=self.submissiontype.name)
@@ -288,7 +342,13 @@ class OmniSubmissionTypeKitTypeAssociation(BaseOmni):
return instance
@property
def list_searchables(self):
def list_searchables(self) -> dict:
"""
Provides attributes for checking this object against a dictionary.
Returns:
dict: result
"""
if isinstance(self.kittype, OmniKitType):
kit = self.kittype.name
else:
@@ -334,7 +394,14 @@ class OmniKitTypeReagentRoleAssociation(BaseOmni):
super().__init__(**data)
self.instance_object = instance_object
def to_dataframe_dict(self):
@property
def dataframe_dict(self) -> dict:
"""
Dictionary of gui relevant values.
Returns:
dict: result
"""
if isinstance(self.submission_type, OmniSubmissionType):
submission_type = self.submission_type.name
else:
@@ -349,12 +416,16 @@ class OmniKitTypeReagentRoleAssociation(BaseOmni):
else:
reagent_role = self.reagent_role
return dict(
reagent_role=reagent_role,
submission_type=submission_type,
kit_type=kit_type
reagentrole=reagent_role,
submissiontype=submission_type,
kittype=kit_type
)
def to_sql(self):
"""
Convert this object to an instance of its class object.
"""
if isinstance(self.reagent_role, OmniReagentRole):
reagent_role = self.reagent_role.name
else:
@@ -387,7 +458,13 @@ class OmniKitTypeReagentRoleAssociation(BaseOmni):
return instance
@property
def list_searchables(self):
def list_searchables(self) -> dict:
"""
Provides attributes for checking this object against a dictionary.
Returns:
dict: result
"""
if isinstance(self.kit_type, OmniKitType):
kit = self.kit_type.name
else:
@@ -420,12 +497,23 @@ class OmniEquipmentRole(BaseOmni):
super().__init__(**data)
self.instance_object = instance_object
def to_dataframe_dict(self):
@property
def dataframe_dict(self) -> dict:
"""
Dictionary of gui relevant values.
Returns:
dict: result
"""
return dict(
name=self.name
)
def to_sql(self):
"""
Convert this object to an instance of its class object.
"""
instance, new = self.class_object.query_or_create(name=self.name)
return instance
@@ -447,12 +535,23 @@ class OmniTips(BaseOmni):
super().__init__(**data)
self.instance_object = instance_object
def to_dataframe_dict(self):
@property
def dataframe_dict(self) -> dict:
"""
Dictionary of gui relevant values.
Returns:
dict: result
"""
return dict(
name=self.name
)
def to_sql(self):
"""
Convert this object to an instance of its class object.
"""
instance, new = self.class_object.query_or_create(name=self.name)
return instance
@@ -475,13 +574,24 @@ class OmniTipRole(BaseOmni):
super().__init__(**data)
self.instance_object = instance_object
def to_dataframe_dict(self):
@property
def dataframe_dict(self) -> dict:
"""
Dictionary of gui relevant values.
Returns:
dict: result
"""
return dict(
name=self.name,
tips=[item.name for item in self.tips]
)
def to_sql(self):
"""
Convert this object to an instance of its class object.
"""
instance, new = self.class_object.query_or_create(name=self.name)
for tips in self.tips:
tips.to_sql()
@@ -504,10 +614,17 @@ class OmniProcess(BaseOmni):
super().__init__(**data)
self.instance_object = instance_object
def to_dataframe_dict(self):
submissiontypes = [item.name for item in self.submission_types]
@property
def dataframe_dict(self) -> dict:
"""
Dictionary of gui relevant values.
Returns:
dict: result
"""
submissiontypes = [item if isinstance(item, str) else item.name for item in self.submission_types]
logger.debug(f"Submission Types: {submissiontypes}")
equipmentroles = [item.name for item in self.equipment_roles]
equipmentroles = [item if isinstance(item, str) else item.name for item in self.equipment_roles]
logger.debug(f"Equipment Roles: {equipmentroles}")
return dict(
name=self.name,
@@ -523,6 +640,10 @@ class OmniProcess(BaseOmni):
return value
def to_sql(self):
"""
Convert this object to an instance of its class object.
"""
instance, new = self.class_object.query_or_create(name=self.name)
for st in self.submission_types:
try:
@@ -548,7 +669,13 @@ class OmniProcess(BaseOmni):
return instance
@property
def list_searchables(self):
def list_searchables(self) -> dict:
"""
Provides attributes for checking this object against a dictionary.
Returns:
dict: result
"""
return dict(name=self.name)
@@ -572,17 +699,24 @@ class OmniKitType(BaseOmni):
super().__init__(**data)
self.instance_object = instance_object
def to_dataframe_dict(self):
@property
def dataframe_dict(self) -> dict:
"""
Dictionary of gui relevant values.
Returns:
dict: result
"""
return dict(
name=self.name
)
def to_sql(self) -> KitType:
"""
Convert this object to an instance of its class object.
"""
kit, is_new = KitType.query_or_create(name=self.name)
# if is_new:
# logger.debug(f"New kit made: {kit}")
# else:
# logger.debug(f"Kit retrieved: {kit}")
new_rr = []
for rr_assoc in self.kit_reagentrole_associations:
new_assoc = rr_assoc.to_sql()
@@ -603,9 +737,6 @@ class OmniKitType(BaseOmni):
if new_process not in new_processes:
new_processes.append(new_process)
kit.processes = new_processes
# logger.debug(f"Kit: {pformat(kit.__dict__)}")
# for item in kit.kit_reagentrole_associations:
# logger.debug(f"KTRRassoc: {item.__dict__}")
return kit
@@ -622,7 +753,14 @@ class OmniOrganization(BaseOmni):
super().__init__(**data)
self.instance_object = instance_object
def to_dataframe_dict(self):
@property
def dataframe_dict(self) -> dict:
"""
Dictionary of gui relevant values.
Returns:
dict: result
"""
return dict(
name=self.name,
cost_centre=self.cost_centre,
@@ -639,14 +777,27 @@ class OmniContact(BaseOmni):
phone: str = Field(default="", description="property")
@property
def list_searchables(self):
def list_searchables(self) -> dict:
"""
Provides attributes for checking this object against a dictionary.
Returns:
dict: result
"""
return dict(name=self.name, email=self.email)
def __init__(self, instance_object: Any, **data):
super().__init__(**data)
self.instance_object = instance_object
def to_dataframe_dict(self):
@property
def dataframe_dict(self) -> dict:
"""
Dictionary of gui relevant values.
Returns:
dict: result
"""
return dict(
name=self.name,
email=self.email,
@@ -654,9 +805,9 @@ class OmniContact(BaseOmni):
)
def to_sql(self):
"""
Convert this object to an instance of its class object.
"""
contact, is_new = Contact.query_or_create(name=self.name, email=self.email, phone=self.phone)
# if is_new:
# logger.debug(f"New contact made: {contact}")
# else:
# logger.debug(f"Contact retrieved: {contact}")
return contact