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Bug fixes and speed-ups

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Landon Wark
2023-09-12 12:33:33 -05:00
parent 5a978c9bff
commit 0c843d1561
7 changed files with 99 additions and 72 deletions
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34
src/submissions/backend/db/models/submissions.py
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@@ -74,7 +74,7 @@ class BasicSubmission(Base):
"""
return f"{self.rsl_plate_num} - {self.submitter_plate_num}"
def to_dict(self) -> dict:
def to_dict(self, full_data:bool=False) -> dict:
"""
dictionary used in submissions summary
@@ -82,6 +82,7 @@ class BasicSubmission(Base):
dict: dictionary used in submissions summary
"""
# get lab from nested organization object
logger.debug(f"Converting {self.rsl_plate_num} to dict...")
try:
sub_lab = self.submitting_lab.name
except AttributeError:
@@ -104,16 +105,20 @@ class BasicSubmission(Base):
ext_info = None
logger.debug(f"Json error in {self.rsl_plate_num}: {e}")
# Updated 2023-09 to use the extraction kit to pull reagents.
try:
reagents = [item.to_sub_dict(extraction_kit=self.extraction_kit) for item in self.reagents]
except Exception as e:
logger.error(f"We got an error retrieving reagents: {e}")
if full_data:
try:
reagents = [item.to_sub_dict(extraction_kit=self.extraction_kit) for item in self.reagents]
except Exception as e:
logger.error(f"We got an error retrieving reagents: {e}")
reagents = None
samples = [item.sample.to_sub_dict(submission_rsl=self.rsl_plate_num) for item in self.submission_sample_associations]
else:
reagents = None
samples = []
samples = None
# Updated 2023-09 to get sample association with plate number
for item in self.submission_sample_associations:
sample = item.sample.to_sub_dict(submission_rsl=self.rsl_plate_num)
samples.append(sample)
# for item in self.submission_sample_associations:
# sample = item.sample.to_sub_dict(submission_rsl=self.rsl_plate_num)
# samples.append(sample)
try:
comments = self.comment
except:
@@ -240,15 +245,16 @@ class BacterialCulture(BasicSubmission):
controls = relationship("Control", back_populates="submission", uselist=True) #: A control sample added to submission
__mapper_args__ = {"polymorphic_identity": "Bacterial Culture", "polymorphic_load": "inline"}
def to_dict(self) -> dict:
def to_dict(self, full_data:bool=False) -> dict:
"""
Extends parent class method to add controls to dict
Returns:
dict: dictionary used in submissions summary
"""
output = super().to_dict()
output['controls'] = [item.to_sub_dict() for item in self.controls]
output = super().to_dict(full_data=full_data)
if full_data:
output['controls'] = [item.to_sub_dict() for item in self.controls]
return output
class Wastewater(BasicSubmission):
@@ -260,14 +266,14 @@ class Wastewater(BasicSubmission):
pcr_technician = Column(String(64))
__mapper_args__ = {"polymorphic_identity": "Wastewater", "polymorphic_load": "inline"}
def to_dict(self) -> dict:
def to_dict(self, full_data:bool=False) -> dict:
"""
Extends parent class method to add controls to dict
Returns:
dict: dictionary used in submissions summary
"""
output = super().to_dict()
output = super().to_dict(full_data=full_data)
try:
output['pcr_info'] = json.loads(self.pcr_info)
except TypeError as e: