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Bug fixes and speed-ups

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This commit is contained in:
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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11
src/submissions/backend/db/functions.py
View File

@@ -369,7 +369,7 @@ def lookup_regent_by_type_name_and_kit_name(ctx:Settings, type_name:str, kit_nam
output = rt_types.instances
return output
def lookup_all_submissions_by_type(ctx:Settings, sub_type:str|None=None, chronologic:bool=False) -> list[models.BasicSubmission]:
def lookup_all_submissions_by_type(ctx:Settings, sub_type:str|None=None, chronologic:bool=False, limit:int=None) -> list[models.BasicSubmission]:
"""
Get all submissions, filtering by type if given
@@ -386,6 +386,8 @@ def lookup_all_submissions_by_type(ctx:Settings, sub_type:str|None=None, chronol
else:
# subs = ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.submission_type==sub_type.lower().replace(" ", "_")).all()
subs = ctx.database_session.query(models.BasicSubmission).filter(models.BasicSubmission.submission_type_name==sub_type)
if limit != None:
subs.limit(limit)
if chronologic:
subs.order_by(models.BasicSubmission.submitted_date)
return subs.all()
@@ -418,7 +420,7 @@ def lookup_org_by_name(ctx:Settings, name:str|None) -> models.Organization:
# return ctx['database_session'].query(models.Organization).filter(models.Organization.name.startswith(name)).first()
return ctx.database_session.query(models.Organization).filter(models.Organization.name.startswith(name)).first()
def submissions_to_df(ctx:Settings, sub_type:str|None=None) -> pd.DataFrame:
def submissions_to_df(ctx:Settings, sub_type:str|None=None, limit:int=None) -> pd.DataFrame:
"""
Convert submissions looked up by type to dataframe
@@ -429,9 +431,10 @@ def submissions_to_df(ctx:Settings, sub_type:str|None=None) -> pd.DataFrame:
Returns:
pd.DataFrame: dataframe constructed from retrieved submissions
"""
logger.debug(f"Type: {sub_type}")
logger.debug(f"Querying Type: {sub_type}")
# use lookup function to create list of dicts
subs = [item.to_dict() for item in lookup_all_submissions_by_type(ctx=ctx, sub_type=sub_type, chronologic=True)]
subs = [item.to_dict() for item in lookup_all_submissions_by_type(ctx=ctx, sub_type=sub_type, chronologic=True, limit=100)]
logger.debug(f"Got {len(subs)} results.")
# make df from dicts (records) in list
df = pd.DataFrame.from_records(subs)
# Exclude sub information

10
src/submissions/backend/db/models/controls.py
View File

@@ -55,7 +55,10 @@ class Control(Base):
dict: output dictionary containing: Name, Type, Targets, Top Kraken results
"""
# load json string into dict
kraken = json.loads(self.kraken)
try:
kraken = json.loads(self.kraken)
except TypeError:
kraken = {}
# calculate kraken count total to use in percentage
kraken_cnt_total = sum([kraken[item]['kraken_count'] for item in kraken])
new_kraken = []
@@ -91,7 +94,10 @@ class Control(Base):
"""
output = []
# load json string for mode (i.e. contains, matches, kraken2)
data = json.loads(getattr(self, mode))
try:
data = json.loads(getattr(self, mode))
except TypeError:
data = {}
logger.debug(f"Length of data: {len(data)}")
# dict keys are genera of bacteria, e.g. 'Streptococcus'
for genus in data:

34
src/submissions/backend/db/models/submissions.py
View File

@@ -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:

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

@@ -335,7 +335,7 @@ class SampleParser(object):
return df
def create_basic_dictionaries_from_plate_map(self):
invalids = [0, "0"]
invalids = [0, "0", "EMPTY"]
new_df = self.plate_map.dropna(axis=1, how='all')
columns = new_df.columns.tolist()
for _, iii in new_df.iterrows():