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Creation of new scripts.

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This commit is contained in:
lwark
2024-12-16 09:31:34 -06:00
parent 67520cb784
commit b1544da730
15 changed files with 214 additions and 148 deletions
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65
src/submissions/backend/db/models/submissions.py
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@@ -2,6 +2,8 @@
Models for the main submission and sample types.
"""
from __future__ import annotations
from collections import OrderedDict
from copy import deepcopy
from getpass import getuser
import logging, uuid, tempfile, re, base64, numpy as np, pandas as pd, types, sys
@@ -559,7 +561,7 @@ class BasicSubmission(BaseClass, LogMixin):
except AttributeError as e:
logger.error(f"Could not set {self} attribute {key} to {value} due to \n{e}")
def update_subsampassoc(self, sample: BasicSample, input_dict: dict):
def update_subsampassoc(self, sample: BasicSample, input_dict: dict) -> SubmissionSampleAssociation:
"""
Update a joined submission sample association.
@@ -568,7 +570,7 @@ class BasicSubmission(BaseClass, LogMixin):
input_dict (dict): values to be updated
Returns:
Result: _description_
SubmissionSampleAssociation: Updated association
"""
try:
assoc = next(item for item in self.submission_sample_associations if item.sample == sample)
@@ -583,14 +585,14 @@ class BasicSubmission(BaseClass, LogMixin):
# NOTE: for some reason I don't think assoc.__setattr__(k, v) works here.
except AttributeError:
logger.error(f"Can't set {k} to {v}")
result = assoc.save()
return result
return assoc
def update_reagentassoc(self, reagent: Reagent, role: str):
from backend.db import SubmissionReagentAssociation
# NOTE: get the first reagent assoc that fills the given role.
try:
assoc = next(item for item in self.submission_reagent_associations if item.reagent and role in [role.name for role in item.reagent.role])
assoc = next(item for item in self.submission_reagent_associations if
item.reagent and role in [role.name for role in item.reagent.role])
assoc.reagent = reagent
except StopIteration as e:
logger.error(f"Association for {role} not found, creating new association.")
@@ -611,7 +613,8 @@ class BasicSubmission(BaseClass, LogMixin):
missing = value in ['', 'None', None]
match key:
case "reagents":
field_value = [item.to_pydantic(extraction_kit=self.extraction_kit) for item in self.submission_reagent_associations]
field_value = [item.to_pydantic(extraction_kit=self.extraction_kit) for item in
self.submission_reagent_associations]
case "samples":
field_value = [item.to_pydantic() for item in self.submission_sample_associations]
case "equipment":
@@ -643,7 +646,8 @@ class BasicSubmission(BaseClass, LogMixin):
continue
new_dict[key] = field_value
new_dict['filepath'] = Path(tempfile.TemporaryFile().name)
return PydSubmission(**new_dict)
dicto.update(new_dict)
return PydSubmission(**dicto)
def save(self, original: bool = True):
"""
@@ -1006,7 +1010,7 @@ class BasicSubmission(BaseClass, LogMixin):
@setup_lookup
def query(cls,
submission_type: str | SubmissionType | None = None,
submission_type_name: str|None = None,
submission_type_name: str | None = None,
id: int | str | None = None,
rsl_plate_num: str | None = None,
start_date: date | str | int | None = None,
@@ -1287,7 +1291,7 @@ class BasicSubmission(BaseClass, LogMixin):
writer = pyd.to_writer()
writer.xl.save(filename=fname.with_suffix(".xlsx"))
def get_turnaround_time(self) -> Tuple[int|None, bool|None]:
def get_turnaround_time(self) -> Tuple[int | None, bool | None]:
try:
completed = self.completed_date.date()
except AttributeError:
@@ -1295,7 +1299,8 @@ class BasicSubmission(BaseClass, LogMixin):
return self.calculate_turnaround(start_date=self.submitted_date.date(), end_date=completed)
@classmethod
def calculate_turnaround(cls, start_date:date|None=None, end_date:date|None=None) -> Tuple[int|None, bool|None]:
def calculate_turnaround(cls, start_date: date | None = None, end_date: date | None = None) -> Tuple[
int | None, bool | None]:
if 'pytest' not in sys.modules:
from tools import ctx
else:
@@ -1499,7 +1504,7 @@ class Wastewater(BasicSubmission):
output = []
for sample in samples:
# NOTE: remove '-{target}' from controls
sample['sample'] = re.sub('-N\\d$', '', sample['sample'])
sample['sample'] = re.sub('-N\\d*$', '', sample['sample'])
# NOTE: if sample is already in output skip
if sample['sample'] in [item['sample'] for item in output]:
logger.warning(f"Already have {sample['sample']}")
@@ -1509,7 +1514,7 @@ class Wastewater(BasicSubmission):
# NOTE: Set 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$', '', s['sample']) == sample['sample']]
other_targets = [s for s in samples if re.sub('-N\\d*$', '', 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']
@@ -1613,7 +1618,9 @@ class Wastewater(BasicSubmission):
sample_dict = next(item for item in pcr_samples if item['sample'] == sample.rsl_number)
except StopIteration:
continue
self.update_subsampassoc(sample=sample, input_dict=sample_dict)
assoc = self.update_subsampassoc(sample=sample, input_dict=sample_dict)
result = assoc.save()
report.add_result(result)
controltype = ControlType.query(name="PCR Control")
submitted_date = datetime.strptime(" ".join(parser.pcr['run_start_date/time'].split(" ")[:-1]),
"%Y-%m-%d %I:%M:%S %p")
@@ -1623,6 +1630,27 @@ class Wastewater(BasicSubmission):
new_control.controltype = controltype
new_control.submission = self
new_control.save()
return report
def update_subsampassoc(self, sample: BasicSample, input_dict: dict):
"""
Updates a joined submission sample association by assigning ct values to n1 or n2 based on alphabetical sorting.
Args:
sample (BasicSample): Associated sample.
input_dict (dict): values to be updated
Returns:
SubmissionSampleAssociation: Updated association
"""
assoc = super().update_subsampassoc(sample=sample, input_dict=input_dict)
targets = {k: input_dict[k] for k in sorted(input_dict.keys()) if k.startswith("ct_")}
assert 0 < len(targets) <= 2
for i, v in enumerate(targets.values(), start=1):
update_key = f"ct_n{i}"
if getattr(assoc, update_key) is None:
setattr(assoc, update_key, v)
return assoc
class WastewaterArtic(BasicSubmission):
@@ -1661,7 +1689,7 @@ class WastewaterArtic(BasicSubmission):
else:
output['artic_technician'] = self.artic_technician
output['gel_info'] = self.gel_info
output['gel_image_path'] = self.gel_image
output['gel_image'] = self.gel_image
output['dna_core_submission_number'] = self.dna_core_submission_number
output['source_plates'] = self.source_plates
output['artic_date'] = self.artic_date or self.submitted_date
@@ -1988,7 +2016,6 @@ class WastewaterArtic(BasicSubmission):
egel_section = custom_fields['egel_info']
# NOTE: print json field gel results to Egel results
worksheet = input_excel[egel_section['sheet']]
# TODO: Move all this into a seperate function?
start_row = egel_section['start_row'] - 1
start_column = egel_section['start_column'] - 3
for row, ki in enumerate(info['gel_info']['value'], start=1):
@@ -2003,10 +2030,10 @@ class WastewaterArtic(BasicSubmission):
logger.error(f"Failed {kj['name']} with value {kj['value']} to row {row}, column {column}")
else:
logger.warning("No gel info found.")
if check_key_or_attr(key='gel_image_path', interest=info, check_none=True):
if check_key_or_attr(key='gel_image', interest=info, check_none=True):
worksheet = input_excel[egel_section['sheet']]
with ZipFile(cls.__directory_path__.joinpath("submission_imgs.zip")) as zipped:
z = zipped.extract(info['gel_image_path']['value'], Path(TemporaryDirectory().name))
z = zipped.extract(info['gel_image']['value'], Path(TemporaryDirectory().name))
img = OpenpyxlImage(z)
img.height = 400 # insert image height in pixels as float or int (e.g. 305.5)
img.width = 600
@@ -2041,9 +2068,9 @@ class WastewaterArtic(BasicSubmission):
headers = [item['name'] for item in base_dict['gel_info'][0]['values']]
base_dict['headers'] = [''] * (4 - len(headers))
base_dict['headers'] += headers
if check_key_or_attr(key='gel_image_path', interest=base_dict, check_none=True):
if check_key_or_attr(key='gel_image', interest=base_dict, check_none=True):
with ZipFile(cls.__directory_path__.joinpath("submission_imgs.zip")) as zipped:
base_dict['gel_image'] = base64.b64encode(zipped.read(base_dict['gel_image_path'])).decode('utf-8')
base_dict['gel_image_actual'] = base64.b64encode(zipped.read(base_dict['gel_image'])).decode('utf-8')
return base_dict, template
def custom_context_events(self) -> dict: