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Moments before disaster.

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This commit is contained in:
lwark
2024-05-01 08:08:34 -05:00
parent 5378c79933
commit 61c1a613e2
9 changed files with 605 additions and 480 deletions
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65
src/submissions/backend/db/models/__init__.py
View File

@@ -1,26 +1,32 @@
'''
Contains all models for sqlalchemy
'''
import sys
from __future__ import annotations
import sys, logging
from sqlalchemy.orm import DeclarativeMeta, declarative_base, Query, Session
from sqlalchemy.ext.declarative import declared_attr
from sqlalchemy.exc import ArgumentError
from typing import Any, List
from pathlib import Path
# Load testing environment
if 'pytest' in sys.modules:
from pathlib import Path
sys.path.append(Path(__file__).parents[4].absolute().joinpath("tests").__str__())
Base: DeclarativeMeta = declarative_base()
logger = logging.getLogger(f"submissions.{__name__}")
class BaseClass(Base):
"""
Abstract class to pass ctx values to all SQLAlchemy objects.
"""
__abstract__ = True #: Will not be added to DB
__table_args__ = {'extend_existing': True} #: Will only add new columns
__table_args__ = {'extend_existing': True} #: Will only add new columns
@declared_attr
def __tablename__(cls) -> str:
@@ -29,7 +35,7 @@ class BaseClass(Base):
Returns:
str: lower case class name
"""
"""
return f"_{cls.__name__.lower()}"
@declared_attr
@@ -39,7 +45,7 @@ class BaseClass(Base):
Returns:
Session: DB session from ctx settings.
"""
"""
if not 'pytest' in sys.modules:
from tools import ctx
else:
@@ -53,13 +59,13 @@ class BaseClass(Base):
Returns:
Path: Location of the Submissions directory in Settings object
"""
"""
if not 'pytest' in sys.modules:
from tools import ctx
else:
from test_settings import ctx
return ctx.directory_path
@declared_attr
def __backup_path__(cls) -> Path:
"""
@@ -67,7 +73,7 @@ class BaseClass(Base):
Returns:
Path: Location of the Submissions backup directory in Settings object
"""
"""
if not 'pytest' in sys.modules:
from tools import ctx
else:
@@ -75,7 +81,25 @@ class BaseClass(Base):
return ctx.backup_path
@classmethod
def execute_query(cls, query: Query, limit: int = 0) -> Any | List[Any]:
def get_default_info(cls, *args) -> dict | List[str]:
dicto = dict(singles=['id'])
output = {}
for k, v in dicto.items():
if len(args) > 0 and k not in args:
# logger.debug(f"Don't want {k}")
continue
else:
output[k] = v
if len(args) == 1:
return output[args[0]]
return output
@classmethod
def query(cls, **kwargs):
return cls.execute_query(**kwargs)
@classmethod
def execute_query(cls, query: Query = None, model=None, limit: int = 0, **kwargs) -> Any | List[Any]:
"""
Execute sqlalchemy query.
@@ -85,7 +109,24 @@ class BaseClass(Base):
Returns:
Any | List[Any]: Single result if limit = 1 or List if other.
"""
"""
if model is None:
model = cls
if query is None:
query: Query = cls.__database_session__.query(model)
# logger.debug(f"Grabbing singles using {model.get_default_info}")
singles = model.get_default_info('singles')
logger.debug(f"Querying: {model}, singles: {singles}")
for k, v in kwargs.items():
logger.debug(f"Using key: {k} with value: {v}")
# logger.debug(f"That key found attribute: {attr} with type: {attr}")
try:
attr = getattr(model, k)
query = query.filter(attr == v)
except (ArgumentError, AttributeError) as e:
logger.error(f"Attribute {k} available due to:\n\t{e}\nSkipping.")
if k in singles:
limit = 1
with query.session.no_autoflush:
match limit:
case 0:
@@ -95,6 +136,10 @@ class BaseClass(Base):
case _:
return query.limit(limit).all()
@classmethod
def default_info_return(cls, info, *args):
return info
def save(self):
"""
Add the object to the database and commit

3
src/submissions/backend/db/models/kits.py
View File

@@ -947,7 +947,8 @@ class SubmissionReagentAssociation(BaseClass):
match submission:
case BasicSubmission() | str():
if isinstance(submission, str):
submission = BasicSubmission.query(rsl_number=submission)
# submission = BasicSubmission.query(rsl_number=submission)
submission = BasicSubmission.query(rsl_plate_num=submission)
# logger.debug(f"Lookup SubmissionReagentAssociation by submission BasicSubmission {submission}")
query = query.filter(cls.submission==submission)
case int():

986
src/submissions/backend/db/models/submissions.py
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File diff suppressed because it is too large Load Diff

11
src/submissions/backend/excel/parser.py
View File

@@ -100,7 +100,7 @@ class SheetParser(object):
Enforce that the parser has an extraction kit
"""
from frontend.widgets.pop_ups import ObjectSelector
if not check_not_nan(self.sub['extraction_kit']['value']):
if 'extraction_kit' not in self.sub.keys() or not check_not_nan(self.sub['extraction_kit']['value']):
dlg = ObjectSelector(title="Kit Needed", message="At minimum a kit is needed. Please select one.", obj_type=KitType)
if dlg.exec():
self.sub['extraction_kit'] = dict(value=dlg.parse_form(), missing=True)
@@ -192,13 +192,18 @@ class InfoParser(object):
for k, v in self.map.items():
# exclude from generic parsing
if k in exclude_from_generic:
logger.warning(f"Key {k} is excluded due to parser_ignore")
continue
# If the value is hardcoded put it in the dictionary directly.
if isinstance(v, str):
dicto[k] = dict(value=v, missing=False)
continue
logger.debug(f"Looking for {k} in self.map")
if sheet in self.map[k]['sheets']:
try:
check = sheet in self.map[k]['sheets']
except TypeError:
continue
if check:
relevant[k] = v
logger.debug(f"relevant map for {sheet}: {pformat(relevant)}")
if relevant == {}:
@@ -592,7 +597,7 @@ class PCRParser(object):
self.plate_num = namer.parsed_name
self.submission_type = namer.submission_type
logger.debug(f"Set plate number to {self.plate_num} and type to {self.submission_type}")
parser = BasicSubmission.find_polymorphic_subclass(self.submission_type)
parser = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
self.samples = parser.parse_pcr(xl=self.xl, rsl_number=self.plate_num)
def parse_general(self, sheet_name:str):

1
src/submissions/backend/validators/pydant.py
View File

@@ -576,6 +576,7 @@ class PydSubmission(BaseModel, extra='allow'):
association.save()
logger.debug(f"Equipment association SQL object to be added to submission: {association.__dict__}")
instance.submission_equipment_associations.append(association)
# TODO: case item if item in instance.jsons()
case _:
try:
instance.set_attribute(key=key, value=value)

6
src/submissions/frontend/widgets/submission_details.py
View File

@@ -82,7 +82,8 @@ class SubmissionDetails(QDialog):
"""
logger.debug(f"Details for: {submission}")
if isinstance(submission, str):
submission = BasicSubmission.query(rsl_number=submission)
# submission = BasicSubmission.query(rsl_number=submission)
submission = BasicSubmission.query(rsl_plate_num=submission)
self.base_dict = submission.to_dict(full_data=True)
logger.debug(f"Submission details data:\n{pformat({k:v for k,v in self.base_dict.items() if k != 'samples'})}")
# don't want id
@@ -103,7 +104,8 @@ class SubmissionDetails(QDialog):
def sign_off(self, submission:str|BasicSubmission):
logger.debug(f"Signing off on {submission} - ({getuser()})")
if isinstance(submission, str):
submission = BasicSubmission.query(rsl_number=submission)
# submission = BasicSubmission.query(rsl_number=submission)
submission = BasicSubmission.query(rsl_plate_number=submission)
submission.signed_by = getuser()
submission.save()
self.submission_details(submission=self.rsl_plate_num)

5
src/submissions/frontend/widgets/submission_table.py
View File

@@ -166,9 +166,8 @@ class SubmissionsSheet(QTableView):
for ii in range(6, len(run)):
new_run[f"column{str(ii-5)}_vol"] = run[ii]
# Lookup imported submissions
# sub = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=new_run['rsl_plate_num'])
# sub = lookup_submissions(ctx=obj.ctx, rsl_number=new_run['rsl_plate_num'])
sub = BasicSubmission.query(rsl_number=new_run['rsl_plate_num'])
# sub = BasicSubmission.query(rsl_number=new_run['rsl_plate_num'])
sub = BasicSubmission.query(rsl_plate_num=new_run['rsl_plate_num'])
# If no such submission exists, move onto the next run
if sub == None:
continue