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During code cleanup

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This commit is contained in:
lwark
2024-05-23 15:06:22 -05:00
parent d1bf12e8d1
commit 2814be8980
10 changed files with 297 additions and 356 deletions
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7
CHANGELOG.md
View File

@@ -1,3 +1,10 @@
## 202405.04
## 202405.04
- Fixed Reagents not being updated on edit.
- Fixed data resorting after submitting new run.
## 202405.03 ## 202405.03
- Settings can now pull values from the db. - Settings can now pull values from the db.

39
src/submissions/backend/db/models/__init__.py
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@@ -3,7 +3,6 @@ Contains all models for sqlalchemy
''' '''
from __future__ import annotations from __future__ import annotations
import sys, logging import sys, logging
from sqlalchemy import Column, INTEGER, String, JSON from sqlalchemy import Column, INTEGER, String, JSON
from sqlalchemy.orm import DeclarativeMeta, declarative_base, Query, Session from sqlalchemy.orm import DeclarativeMeta, declarative_base, Query, Session
from sqlalchemy.ext.declarative import declared_attr from sqlalchemy.ext.declarative import declared_attr
@@ -81,7 +80,13 @@ class BaseClass(Base):
return ctx.backup_path return ctx.backup_path
@classmethod @classmethod
def get_default_info(cls, *args) -> dict | List[str]: def get_default_info(cls, *args) -> dict | list | str:
"""
Returns default info for a model
Returns:
dict | list | str: Output of key:value dict or single (list, str) desired variable
"""
dicto = dict(singles=['id']) dicto = dict(singles=['id'])
output = {} output = {}
for k, v in dicto.items(): for k, v in dicto.items():
@@ -95,7 +100,13 @@ class BaseClass(Base):
return output return output
@classmethod @classmethod
def query(cls, **kwargs): def query(cls, **kwargs) -> Any | List[Any]:
"""
Default query function for models
Returns:
Any | List[Any]: Result of query execution.
"""
return cls.execute_query(**kwargs) return cls.execute_query(**kwargs)
@classmethod @classmethod
@@ -119,13 +130,12 @@ class BaseClass(Base):
singles = model.get_default_info('singles') singles = model.get_default_info('singles')
logger.debug(f"Querying: {model}, with kwargs: {kwargs}") logger.debug(f"Querying: {model}, with kwargs: {kwargs}")
for k, v in kwargs.items(): for k, v in kwargs.items():
logger.debug(f"Using key: {k} with value: {v}") # logger.debug(f"Using key: {k} with value: {v}")
# logger.debug(f"That key found attribute: {attr} with type: {attr}")
try: try:
attr = getattr(model, k) attr = getattr(model, k)
query = query.filter(attr == v) query = query.filter(attr == v)
except (ArgumentError, AttributeError) as e: except (ArgumentError, AttributeError) as e:
logger.error(f"Attribute {k} available due to:\n\t{e}\nSkipping.") logger.error(f"Attribute {k} unavailable due to:\n\t{e}\nSkipping.")
if k in singles: if k in singles:
limit = 1 limit = 1
with query.session.no_autoflush: with query.session.no_autoflush:
@@ -155,6 +165,9 @@ class BaseClass(Base):
class ConfigItem(BaseClass): class ConfigItem(BaseClass):
"""
Key:JSON objects to store config settings in database.
"""
id = Column(INTEGER, primary_key=True) id = Column(INTEGER, primary_key=True)
key = Column(String(32)) key = Column(String(32))
value = Column(JSON) value = Column(JSON)
@@ -163,8 +176,18 @@ class ConfigItem(BaseClass):
return f"ConfigItem({self.key} : {self.value})" return f"ConfigItem({self.key} : {self.value})"
@classmethod @classmethod
def get_config_items(cls): def get_config_items(cls, *args) -> ConfigItem|List[ConfigItem]:
return cls.__database_session__.query(cls).all() """
Get desired config items from database
Returns:
ConfigItem|List[ConfigItem]: Config item(s)
"""
config_items = cls.__database_session__.query(cls).all()
config_items = [item for item in config_items if item.key in args]
if len(args) == 1:
config_items = config_items[0]
return config_items
from .controls import * from .controls import *

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

@@ -13,6 +13,8 @@ from typing import List, Literal
from pandas import ExcelFile from pandas import ExcelFile
from pathlib import Path from pathlib import Path
from . import Base, BaseClass, Organization from . import Base, BaseClass, Organization
from io import BytesIO
logger = logging.getLogger(f'submissions.{__name__}') logger = logging.getLogger(f'submissions.{__name__}')
@@ -300,7 +302,7 @@ class ReagentType(BaseClass):
# logger.debug(f"Looking up reagent type for {type(kit_type)} {kit_type} and {type(reagent)} {reagent}") # logger.debug(f"Looking up reagent type for {type(kit_type)} {kit_type} and {type(reagent)} {reagent}")
# logger.debug(f"Kit reagent types: {kit_type.reagent_types}") # logger.debug(f"Kit reagent types: {kit_type.reagent_types}")
result = list(set(kit_type.reagent_types).intersection(reagent.type)) result = list(set(kit_type.reagent_types).intersection(reagent.type))
logger.debug(f"Result: {result}") # logger.debug(f"Result: {result}")
try: try:
return result[0] return result[0]
except IndexError: except IndexError:
@@ -386,7 +388,7 @@ class Reagent(BaseClass):
place_holder = self.expiry + reagent_role.eol_ext place_holder = self.expiry + reagent_role.eol_ext
except (TypeError, AttributeError) as e: except (TypeError, AttributeError) as e:
place_holder = date.today() place_holder = date.today()
logger.debug(f"We got a type error setting {self.lot} expiry: {e}. setting to today for testing") logger.error(f"We got a type error setting {self.lot} expiry: {e}. setting to today for testing")
if self.expiry.year == 1970: if self.expiry.year == 1970:
place_holder = "NA" place_holder = "NA"
else: else:
@@ -410,14 +412,14 @@ class Reagent(BaseClass):
Report: Result of operation Report: Result of operation
""" """
report = Report() report = Report()
logger.debug(f"Attempting update of reagent type at intersection of ({self}), ({kit})") # logger.debug(f"Attempting update of last used reagent type at intersection of ({self}), ({kit})")
rt = ReagentType.query(kit_type=kit, reagent=self, limit=1) rt = ReagentType.query(kit_type=kit, reagent=self, limit=1)
if rt is not None: if rt is not None:
logger.debug(f"got reagenttype {rt}") # logger.debug(f"got reagenttype {rt}")
assoc = KitTypeReagentTypeAssociation.query(kit_type=kit, reagent_type=rt) assoc = KitTypeReagentTypeAssociation.query(kit_type=kit, reagent_type=rt)
if assoc is not None: if assoc is not None:
if assoc.last_used != self.lot: if assoc.last_used != self.lot:
logger.debug(f"Updating {assoc} last used to {self.lot}") # logger.debug(f"Updating {assoc} last used to {self.lot}")
assoc.last_used = self.lot assoc.last_used = self.lot
result = assoc.save() result = assoc.save()
report.add_result(result) report.add_result(result)
@@ -607,7 +609,7 @@ class SubmissionType(BaseClass):
Returns: Returns:
List[str]: List of sheet names List[str]: List of sheet names
""" """
return ExcelFile(self.template_file).sheet_names return ExcelFile(BytesIO(self.template_file)).sheet_names
def set_template_file(self, filepath: Path | str): def set_template_file(self, filepath: Path | str):
""" """
@@ -633,7 +635,7 @@ class SubmissionType(BaseClass):
def construct_info_map(self, mode: Literal['read', 'write']) -> dict: def construct_info_map(self, mode: Literal['read', 'write']) -> dict:
info = self.info_map info = self.info_map
logger.debug(f"Info map: {info}") # logger.debug(f"Info map: {info}")
output = {} output = {}
# for k,v in info.items(): # for k,v in info.items():
# info[k]['write'] += info[k]['read'] # info[k]['write'] += info[k]['read']

261
src/submissions/backend/db/models/submissions.py
View File

@@ -226,7 +226,7 @@ class BasicSubmission(BaseClass):
if report: if report:
return output return output
if full_data: if full_data:
logger.debug(f"Attempting reagents.") # logger.debug(f"Attempting reagents.")
try: try:
reagents = [item.to_sub_dict(extraction_kit=self.extraction_kit) for item in reagents = [item.to_sub_dict(extraction_kit=self.extraction_kit) for item in
self.submission_reagent_associations] self.submission_reagent_associations]
@@ -240,9 +240,9 @@ class BasicSubmission(BaseClass):
except Exception as e: except Exception as e:
logger.error(f"We got an error retrieving reagents: {e}") logger.error(f"We got an error retrieving reagents: {e}")
reagents = None reagents = None
logger.debug(f"Running samples.") # logger.debug(f"Running samples.")
samples = self.adjust_to_dict_samples(backup=backup) samples = self.adjust_to_dict_samples(backup=backup)
logger.debug("Running equipment") # logger.debug("Running equipment")
try: try:
equipment = [item.to_sub_dict() for item in self.submission_equipment_associations] equipment = [item.to_sub_dict() for item in self.submission_equipment_associations]
if len(equipment) == 0: if len(equipment) == 0:
@@ -297,7 +297,7 @@ class BasicSubmission(BaseClass):
# Get kit associated with this submission # Get kit associated with this submission
assoc = [item for item in self.extraction_kit.kit_submissiontype_associations if assoc = [item for item in self.extraction_kit.kit_submissiontype_associations if
item.submission_type == self.submission_type][0] item.submission_type == self.submission_type][0]
logger.debug(f"Came up with association: {assoc}") # logger.debug(f"Came up with association: {assoc}")
# If every individual cost is 0 this is probably an old plate. # If every individual cost is 0 this is probably an old plate.
if all(item == 0.0 for item in [assoc.constant_cost, assoc.mutable_cost_column, assoc.mutable_cost_sample]): if all(item == 0.0 for item in [assoc.constant_cost, assoc.mutable_cost_column, assoc.mutable_cost_sample]):
try: try:
@@ -369,7 +369,7 @@ class BasicSubmission(BaseClass):
return [item.role for item in self.submission_equipment_associations] return [item.role for item in self.submission_equipment_associations]
@classmethod @classmethod
def submissions_to_df(cls, submission_type: str | None = None, limit: int = 0) -> pd.DataFrame: def submissions_to_df(cls, submission_type: str | None = None, limit: int = 0, chronologic:bool=True) -> pd.DataFrame:
""" """
Convert all submissions to dataframe Convert all submissions to dataframe
@@ -380,11 +380,11 @@ class BasicSubmission(BaseClass):
Returns: Returns:
pd.DataFrame: Pandas Dataframe of all relevant submissions pd.DataFrame: Pandas Dataframe of all relevant submissions
""" """
logger.debug(f"Querying Type: {submission_type}") # logger.debug(f"Querying Type: {submission_type}")
logger.debug(f"Using limit: {limit}") # logger.debug(f"Using limit: {limit}")
# use lookup function to create list of dicts # use lookup function to create list of dicts
subs = [item.to_dict() for item in cls.query(submission_type=submission_type, limit=limit)] subs = [item.to_dict() for item in cls.query(submission_type=submission_type, limit=limit, chronologic=chronologic)]
logger.debug(f"Got {len(subs)} submissions.") # logger.debug(f"Got {len(subs)} submissions.")
df = pd.DataFrame.from_records(subs) df = pd.DataFrame.from_records(subs)
# Exclude sub information # Exclude sub information
for item in ['controls', 'extraction_info', 'pcr_info', 'comment', 'comments', 'samples', 'reagents', for item in ['controls', 'extraction_info', 'pcr_info', 'comment', 'comments', 'samples', 'reagents',
@@ -393,6 +393,8 @@ class BasicSubmission(BaseClass):
df = df.drop(item, axis=1) df = df.drop(item, axis=1)
except: except:
logger.warning(f"Couldn't drop '{item}' column from submissionsheet df.") logger.warning(f"Couldn't drop '{item}' column from submissionsheet df.")
if chronologic:
df.sort_values(by="Submitted Date", axis=0, inplace=True, ascending=False)
return df return df
def set_attribute(self, key: str, value): def set_attribute(self, key: str, value):
@@ -466,6 +468,9 @@ class BasicSubmission(BaseClass):
flag_modified(self, key) flag_modified(self, key)
return return
case _: case _:
try:
field_value = value.strip()
except AttributeError:
field_value = value field_value = value
# insert into field # insert into field
try: try:
@@ -502,7 +507,7 @@ class BasicSubmission(BaseClass):
""" """
from backend.validators import PydSubmission, PydSample, PydReagent, PydEquipment from backend.validators import PydSubmission, PydSample, PydReagent, PydEquipment
dicto = self.to_dict(full_data=True, backup=backup) dicto = self.to_dict(full_data=True, backup=backup)
logger.debug("To dict complete") # logger.debug("To dict complete")
new_dict = {} new_dict = {}
for key, value in dicto.items(): for key, value in dicto.items():
# start = time() # start = time()
@@ -526,11 +531,11 @@ class BasicSubmission(BaseClass):
case "id": case "id":
pass pass
case _: case _:
logger.debug(f"Setting dict {key} to {value}") # logger.debug(f"Setting dict {key} to {value}")
new_dict[key.lower().replace(" ", "_")] = dict(value=value, missing=missing) new_dict[key.lower().replace(" ", "_")] = dict(value=value, missing=missing)
# logger.debug(f"{key} complete after {time()-start}") # logger.debug(f"{key} complete after {time()-start}")
new_dict['filepath'] = Path(tempfile.TemporaryFile().name) new_dict['filepath'] = Path(tempfile.TemporaryFile().name)
logger.debug("Done converting fields.") # logger.debug("Done converting fields.")
return PydSubmission(**new_dict) return PydSubmission(**new_dict)
def save(self, original: bool = True): def save(self, original: bool = True):
@@ -604,20 +609,20 @@ class BasicSubmission(BaseClass):
# Child class custom functions # Child class custom functions
@classmethod # @classmethod
def custom_platemap(cls, xl: pd.ExcelFile, plate_map: pd.DataFrame) -> pd.DataFrame: # def custom_platemap(cls, xl: pd.ExcelFile, plate_map: pd.DataFrame) -> pd.DataFrame:
""" # """
Stupid stopgap solution to there being an issue with the Bacterial Culture plate map # Stupid stopgap solution to there being an issue with the Bacterial Culture plate map
#
Args: # Args:
xl (pd.ExcelFile): original xl workbook, used for child classes mostly # xl (pd.ExcelFile): original xl workbook, used for child classes mostly
plate_map (pd.DataFrame): original plate map # plate_map (pd.DataFrame): original plate map
#
Returns: # Returns:
pd.DataFrame: updated plate map. # pd.DataFrame: updated plate map.
""" # """
logger.info(f"Calling {cls.__mapper_args__['polymorphic_identity']} plate mapper.") # logger.info(f"Calling {cls.__mapper_args__['polymorphic_identity']} plate mapper.")
return plate_map # return plate_map
@classmethod @classmethod
def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None) -> dict: def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None) -> dict:
@@ -696,15 +701,15 @@ class BasicSubmission(BaseClass):
# logger.info(f"Hello from {cls.__mapper_args__['polymorphic_identity']} Enforcer!") # logger.info(f"Hello from {cls.__mapper_args__['polymorphic_identity']} Enforcer!")
# return instr # return instr
from backend.validators import RSLNamer from backend.validators import RSLNamer
logger.debug(f"instr coming into {cls}: {instr}") # logger.debug(f"instr coming into {cls}: {instr}")
logger.debug(f"data coming into {cls}: {data}") # logger.debug(f"data coming into {cls}: {data}")
defaults = cls.get_default_info("abbreviation", "submission_type") defaults = cls.get_default_info("abbreviation", "submission_type")
data['abbreviation'] = defaults['abbreviation'] data['abbreviation'] = defaults['abbreviation']
if 'submission_type' not in data.keys() or data['submission_type'] in [None, ""]: if 'submission_type' not in data.keys() or data['submission_type'] in [None, ""]:
data['submission_type'] = defaults['submission_type'] data['submission_type'] = defaults['submission_type']
# outstr = super().enforce_name(instr=instr, data=data) # outstr = super().enforce_name(instr=instr, data=data)
if instr in [None, ""]: if instr in [None, ""]:
logger.debug("Sending to RSLNamer to make new plate name.") # logger.debug("Sending to RSLNamer to make new plate name.")
outstr = RSLNamer.construct_new_plate_name(data=data) outstr = RSLNamer.construct_new_plate_name(data=data)
else: else:
outstr = instr outstr = instr
@@ -761,9 +766,9 @@ class BasicSubmission(BaseClass):
Returns: Returns:
list: _description_ list: _description_
""" """
logger.debug(f"Hello from {cls.__mapper_args__['polymorphic_identity']} PCR parser!") # logger.debug(f"Hello from {cls.__mapper_args__['polymorphic_identity']} PCR parser!")
pcr_sample_map = cls.get_submission_type().sample_map['pcr_samples'] pcr_sample_map = cls.get_submission_type().sample_map['pcr_samples']
logger.debug(f'sample map: {pcr_sample_map}') # logger.debug(f'sample map: {pcr_sample_map}')
main_sheet = xl[pcr_sample_map['main_sheet']] main_sheet = xl[pcr_sample_map['main_sheet']]
samples = [] samples = []
fields = {k: v for k, v in pcr_sample_map.items() if k not in ['main_sheet', 'start_row']} fields = {k: v for k, v in pcr_sample_map.items() if k not in ['main_sheet', 'start_row']}
@@ -816,7 +821,7 @@ class BasicSubmission(BaseClass):
Returns: Returns:
List[dict]: Updated dictionaries List[dict]: Updated dictionaries
""" """
logger.debug(f"Hello from {self.__class__.__name__} dictionary sample adjuster.") # logger.debug(f"Hello from {self.__class__.__name__} dictionary sample adjuster.")
return [item.to_sub_dict() for item in self.submission_sample_associations] return [item.to_sub_dict() for item in self.submission_sample_associations]
@classmethod @classmethod
@@ -833,7 +838,7 @@ class BasicSubmission(BaseClass):
base_dict['excluded'] = cls.get_default_info('details_ignore') base_dict['excluded'] = cls.get_default_info('details_ignore')
env = jinja_template_loading() env = jinja_template_loading()
temp_name = f"{cls.__name__.lower()}_details.html" temp_name = f"{cls.__name__.lower()}_details.html"
logger.debug(f"Returning template: {temp_name}") # logger.debug(f"Returning template: {temp_name}")
try: try:
template = env.get_template(temp_name) template = env.get_template(temp_name)
except TemplateNotFound as e: except TemplateNotFound as e:
@@ -872,7 +877,7 @@ class BasicSubmission(BaseClass):
Returns: Returns:
models.BasicSubmission | List[models.BasicSubmission]: Submission(s) of interest models.BasicSubmission | List[models.BasicSubmission]: Submission(s) of interest
""" """
logger.debug(f"Incoming kwargs: {kwargs}") # logger.debug(f"Incoming kwargs: {kwargs}")
# NOTE: if you go back to using 'model' change the appropriate cls to model in the query filters # NOTE: if you go back to using 'model' change the appropriate cls to model in the query filters
if submission_type is not None: if submission_type is not None:
# if isinstance(submission_type, SubmissionType): # if isinstance(submission_type, SubmissionType):
@@ -882,7 +887,7 @@ class BasicSubmission(BaseClass):
# model = cls.find_subclasses(submission_type=submission_type) # model = cls.find_subclasses(submission_type=submission_type)
elif len(kwargs) > 0: elif len(kwargs) > 0:
# find the subclass containing the relevant attributes # find the subclass containing the relevant attributes
logger.debug(f"Attributes for search: {kwargs}") # logger.debug(f"Attributes for search: {kwargs}")
# model = cls.find_subclasses(attrs=kwargs) # model = cls.find_subclasses(attrs=kwargs)
model = cls.find_polymorphic_subclass(attrs=kwargs) model = cls.find_polymorphic_subclass(attrs=kwargs)
else: else:
@@ -895,7 +900,7 @@ class BasicSubmission(BaseClass):
logger.warning(f"End date with no start date, using Jan 1, 2023") logger.warning(f"End date with no start date, using Jan 1, 2023")
start_date = date(2023, 1, 1) start_date = date(2023, 1, 1)
if start_date is not None: if start_date is not None:
logger.debug(f"Querying with start date: {start_date} and end date: {end_date}") # logger.debug(f"Querying with start date: {start_date} and end date: {end_date}")
match start_date: match start_date:
case date(): case date():
# logger.debug(f"Lookup BasicSubmission by start_date({start_date})") # logger.debug(f"Lookup BasicSubmission by start_date({start_date})")
@@ -919,7 +924,7 @@ class BasicSubmission(BaseClass):
# logger.debug(f"Lookup BasicSubmission by parsed str end_date {end_date}") # logger.debug(f"Lookup BasicSubmission by parsed str end_date {end_date}")
end_date = parse(end_date).strftime("%Y-%m-%d") end_date = parse(end_date).strftime("%Y-%m-%d")
# logger.debug(f"Looking up BasicSubmissions from start date: {start_date} and end date: {end_date}") # logger.debug(f"Looking up BasicSubmissions from start date: {start_date} and end date: {end_date}")
logger.debug(f"Start date {start_date} == End date {end_date}: {start_date == end_date}") # logger.debug(f"Start date {start_date} == End date {end_date}: {start_date == end_date}")
# logger.debug(f"Compensating for same date by using time") # logger.debug(f"Compensating for same date by using time")
if start_date == end_date: if start_date == end_date:
start_date = datetime.strptime(start_date, "%Y-%m-%d").strftime("%Y-%m-%d %H:%M:%S.%f") start_date = datetime.strptime(start_date, "%Y-%m-%d").strftime("%Y-%m-%d %H:%M:%S.%f")
@@ -999,7 +1004,7 @@ class BasicSubmission(BaseClass):
f"{key} is not allowed as a query argument as it could lead to creation of duplicate objects. Use .query() instead.") f"{key} is not allowed as a query argument as it could lead to creation of duplicate objects. Use .query() instead.")
instance = cls.query(submission_type=submission_type, limit=1, **kwargs) instance = cls.query(submission_type=submission_type, limit=1, **kwargs)
# logger.debug(f"Retrieved instance: {instance}") # logger.debug(f"Retrieved instance: {instance}")
if instance == None: if instance is None:
used_class = cls.find_polymorphic_subclass(attrs=kwargs, polymorphic_identity=submission_type) used_class = cls.find_polymorphic_subclass(attrs=kwargs, polymorphic_identity=submission_type)
instance = used_class(**kwargs) instance = used_class(**kwargs)
match submission_type: match submission_type:
@@ -1041,11 +1046,11 @@ class BasicSubmission(BaseClass):
e: _description_ e: _description_
""" """
from frontend.widgets.pop_ups import QuestionAsker from frontend.widgets.pop_ups import QuestionAsker
logger.debug("Hello from delete") # logger.debug("Hello from delete")
fname = self.__backup_path__.joinpath(f"{self.rsl_plate_num}-backup({date.today().strftime('%Y%m%d')})") fname = self.__backup_path__.joinpath(f"{self.rsl_plate_num}-backup({date.today().strftime('%Y%m%d')})")
msg = QuestionAsker(title="Delete?", message=f"Are you sure you want to delete {self.rsl_plate_num}?\n") msg = QuestionAsker(title="Delete?", message=f"Are you sure you want to delete {self.rsl_plate_num}?\n")
if msg.exec(): if msg.exec():
# self.backup(fname=fname, full_backup=True) self.backup(fname=fname, full_backup=True)
self.__database_session__.delete(self) self.__database_session__.delete(self)
try: try:
self.__database_session__.commit() self.__database_session__.commit()
@@ -1061,7 +1066,7 @@ class BasicSubmission(BaseClass):
Args: Args:
obj (_type_): parent widget obj (_type_): parent widget
""" """
logger.debug("Hello from details") # logger.debug("Hello from details")
from frontend.widgets.submission_details import SubmissionDetails from frontend.widgets.submission_details import SubmissionDetails
dlg = SubmissionDetails(parent=obj, sub=self) dlg = SubmissionDetails(parent=obj, sub=self)
if dlg.exec(): if dlg.exec():
@@ -1070,7 +1075,7 @@ class BasicSubmission(BaseClass):
def edit(self, obj): def edit(self, obj):
from frontend.widgets.submission_widget import SubmissionFormWidget from frontend.widgets.submission_widget import SubmissionFormWidget
for widg in obj.app.table_widget.formwidget.findChildren(SubmissionFormWidget): for widg in obj.app.table_widget.formwidget.findChildren(SubmissionFormWidget):
logger.debug(widg) # logger.debug(widg)
widg.setParent(None) widg.setParent(None)
pyd = self.to_pydantic(backup=True) pyd = self.to_pydantic(backup=True)
form = pyd.to_form(parent=obj) form = pyd.to_form(parent=obj)
@@ -1088,7 +1093,7 @@ class BasicSubmission(BaseClass):
if dlg.exec(): if dlg.exec():
comment = dlg.parse_form() comment = dlg.parse_form()
self.set_attribute(key='comment', value=comment) self.set_attribute(key='comment', value=comment)
logger.debug(self.comment) # logger.debug(self.comment)
self.save(original=False) self.save(original=False)
def add_equipment(self, obj): def add_equipment(self, obj):
@@ -1102,11 +1107,11 @@ class BasicSubmission(BaseClass):
dlg = EquipmentUsage(parent=obj, submission=self) dlg = EquipmentUsage(parent=obj, submission=self)
if dlg.exec(): if dlg.exec():
equipment = dlg.parse_form() equipment = dlg.parse_form()
logger.debug(f"We've got equipment: {equipment}") # logger.debug(f"We've got equipment: {equipment}")
for equip in equipment: for equip in equipment:
logger.debug(f"Processing: {equip}") # logger.debug(f"Processing: {equip}")
_, assoc = equip.toSQL(submission=self) _, assoc = equip.toSQL(submission=self)
logger.debug(f"Appending SubmissionEquipmentAssociation: {assoc}") # logger.debug(f"Appending SubmissionEquipmentAssociation: {assoc}")
assoc.save() assoc.save()
else: else:
pass pass
@@ -1120,14 +1125,14 @@ class BasicSubmission(BaseClass):
fname (Path | None, optional): Filename of xlsx file. Defaults to None. fname (Path | None, optional): Filename of xlsx file. Defaults to None.
full_backup (bool, optional): Whether or not to make yaml file. Defaults to False. full_backup (bool, optional): Whether or not to make yaml file. Defaults to False.
""" """
logger.debug("Hello from backup.") # logger.debug("Hello from backup.")
pyd = self.to_pydantic(backup=True) pyd = self.to_pydantic(backup=True)
if fname == None: if fname is None:
from frontend.widgets.functions import select_save_file from frontend.widgets.functions import select_save_file
fname = select_save_file(default_name=pyd.construct_filename(), extension="xlsx", obj=obj) fname = select_save_file(default_name=pyd.construct_filename(), extension="xlsx", obj=obj)
logger.debug(fname.name) # logger.debug(fname.name)
if fname.name == "": if fname.name == "":
logger.debug(f"export cancelled.") # logger.debug(f"export cancelled.")
return return
# pyd.filepath = fname # pyd.filepath = fname
if full_backup: if full_backup:
@@ -1171,28 +1176,28 @@ class BacterialCulture(BasicSubmission):
output['controls'] = [item.to_sub_dict() for item in self.controls] output['controls'] = [item.to_sub_dict() for item in self.controls]
return output return output
@classmethod # @classmethod
def custom_platemap(cls, xl: pd.ExcelFile, plate_map: pd.DataFrame) -> pd.DataFrame: # def custom_platemap(cls, xl: pd.ExcelFile, plate_map: pd.DataFrame) -> pd.DataFrame:
""" # """
Stupid stopgap solution to there being an issue with the Bacterial Culture plate map. Extends parent. # Stupid stopgap solution to there being an issue with the Bacterial Culture plate map. Extends parent.
#
Args: # Args:
xl (pd.ExcelFile): original xl workbook # xl (pd.ExcelFile): original xl workbook
plate_map (pd.DataFrame): original plate map # plate_map (pd.DataFrame): original plate map
#
Returns: # Returns:
pd.DataFrame: updated plate map. # pd.DataFrame: updated plate map.
""" # """
plate_map = super().custom_platemap(xl, plate_map) # plate_map = super().custom_platemap(xl, plate_map)
num1 = xl.parse("Sample List").iloc[40, 1] # num1 = xl.parse("Sample List").iloc[40, 1]
num2 = xl.parse("Sample List").iloc[41, 1] # num2 = xl.parse("Sample List").iloc[41, 1]
logger.debug(f"Broken: {plate_map.iloc[5, 0]}, {plate_map.iloc[6, 0]}") # # logger.debug(f"Broken: {plate_map.iloc[5, 0]}, {plate_map.iloc[6, 0]}")
logger.debug(f"Replace: {num1}, {num2}") # # logger.debug(f"Replace: {num1}, {num2}")
if not check_not_nan(plate_map.iloc[5, 0]): # if not check_not_nan(plate_map.iloc[5, 0]):
plate_map.iloc[5, 0] = num1 # plate_map.iloc[5, 0] = num1
if not check_not_nan(plate_map.iloc[6, 0]): # if not check_not_nan(plate_map.iloc[6, 0]):
plate_map.iloc[6, 0] = num2 # plate_map.iloc[6, 0] = num2
return plate_map # return plate_map
# @classmethod # @classmethod
# def custom_writer(cls, input_excel: Workbook, info: dict | None = None, backup: bool = False) -> Workbook: # def custom_writer(cls, input_excel: Workbook, info: dict | None = None, backup: bool = False) -> Workbook:
@@ -1255,7 +1260,7 @@ class BacterialCulture(BasicSubmission):
for sample in input_dict['samples']: for sample in input_dict['samples']:
matched = regex.match(sample['submitter_id']) matched = regex.match(sample['submitter_id'])
if bool(matched): if bool(matched):
logger.debug(f"Control match found: {sample['submitter_id']}") # logger.debug(f"Control match found: {sample['submitter_id']}")
new_lot = matched.group() new_lot = matched.group()
try: try:
pos_control_reg = \ pos_control_reg = \
@@ -1272,8 +1277,8 @@ class BacterialCulture(BasicSubmission):
""" """
Extends parent Extends parent
""" """
logger.debug(f"Checking {sample.well}") # logger.debug(f"Checking {sample.well}")
logger.debug(f"here's the worksheet: {worksheet}") # logger.debug(f"here's the worksheet: {worksheet}")
row = super().custom_sample_autofill_row(sample, worksheet) row = super().custom_sample_autofill_row(sample, worksheet)
df = pd.DataFrame(list(worksheet.values)) df = pd.DataFrame(list(worksheet.values))
# logger.debug(f"Here's the dataframe: {df}") # logger.debug(f"Here's the dataframe: {df}")
@@ -1282,7 +1287,7 @@ class BacterialCulture(BasicSubmission):
new = f"{sample.well[0]}{sample.well[1:].zfill(2)}" new = f"{sample.well[0]}{sample.well[1:].zfill(2)}"
logger.debug(f"Checking: {new}") logger.debug(f"Checking: {new}")
idx = df[df[0] == new] idx = df[df[0] == new]
logger.debug(f"Here is the row: {idx}") # logger.debug(f"Here is the row: {idx}")
row = idx.index.to_list()[0] row = idx.index.to_list()[0]
return row + 1 return row + 1
@@ -1386,14 +1391,19 @@ class Wastewater(BasicSubmission):
Parse specific to wastewater samples. Parse specific to wastewater samples.
""" """
samples = super().parse_pcr(xl=xl, rsl_plate_num=rsl_plate_num) samples = super().parse_pcr(xl=xl, rsl_plate_num=rsl_plate_num)
logger.debug(f'Samples from parent pcr parser: {pformat(samples)}') # logger.debug(f'Samples from parent pcr parser: {pformat(samples)}')
output = [] output = []
for sample in samples: 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]: if sample['sample'] in [item['sample'] for item in output]:
continue continue
# NOTE: Set ct values
sample[f"ct_{sample['target'].lower()}"] = sample['ct'] if isinstance(sample['ct'], float) else 0.0 sample[f"ct_{sample['target'].lower()}"] = sample['ct'] if isinstance(sample['ct'], float) else 0.0
# NOTE: Set assessment
sample[f"{sample['target'].lower()}_status"] = 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$', '', s['sample']) == sample['sample']] other_targets = [s for s in samples if re.sub('-N\\d$', '', s['sample']) == sample['sample']]
for s in other_targets: for s in other_targets:
sample[f"ct_{s['target'].lower()}"] = s['ct'] if isinstance(s['ct'], float) else 0.0 sample[f"ct_{s['target'].lower()}"] = s['ct'] if isinstance(s['ct'], float) else 0.0
@@ -1446,13 +1456,13 @@ class Wastewater(BasicSubmission):
""" """
Extends parent Extends parent
""" """
logger.debug(f"Checking {sample.well}") # logger.debug(f"Checking {sample.well}")
logger.debug(f"here's the worksheet: {worksheet}") # logger.debug(f"here's the worksheet: {worksheet}")
row = super().custom_sample_autofill_row(sample, worksheet) row = super().custom_sample_autofill_row(sample, worksheet)
df = pd.DataFrame(list(worksheet.values)) df = pd.DataFrame(list(worksheet.values))
logger.debug(f"Here's the dataframe: {df}") # logger.debug(f"Here's the dataframe: {df}")
idx = df[df[1] == sample.sample_location] idx = df[df[1] == sample.sample_location]
logger.debug(f"Here is the row: {idx}") # logger.debug(f"Here is the row: {idx}")
row = idx.index.to_list()[0] row = idx.index.to_list()[0]
return row + 1 return row + 1
@@ -1468,10 +1478,10 @@ class Wastewater(BasicSubmission):
parser = PCRParser(filepath=fname) parser = PCRParser(filepath=fname)
self.set_attribute("pcr_info", parser.pcr) self.set_attribute("pcr_info", parser.pcr)
self.save(original=False) self.save(original=False)
logger.debug(f"Got {len(parser.samples)} samples to update!") # logger.debug(f"Got {len(parser.samples)} samples to update!")
logger.debug(f"Parser samples: {parser.samples}") # logger.debug(f"Parser samples: {parser.samples}")
for sample in self.samples: for sample in self.samples:
logger.debug(f"Running update on: {sample}") # logger.debug(f"Running update on: {sample}")
try: try:
sample_dict = [item for item in parser.samples if item['sample'] == sample.rsl_number][0] sample_dict = [item for item in parser.samples if item['sample'] == sample.rsl_number][0]
except IndexError: except IndexError:
@@ -1551,19 +1561,18 @@ class WastewaterArtic(BasicSubmission):
Extends parent Extends parent
""" """
try: try:
# Deal with PCR file. # NOTE: Deal with PCR file.
instr = re.sub(r"Artic", "", instr, flags=re.IGNORECASE) instr = re.sub(r"Artic", "", instr, flags=re.IGNORECASE)
except (AttributeError, TypeError) as e: except (AttributeError, TypeError) as e:
logger.error(f"Problem using regex: {e}") logger.error(f"Problem using regex: {e}")
logger.debug(f"Before RSL addition: {instr}") # logger.debug(f"Before RSL addition: {instr}")
try: try:
instr = instr.replace("-", "") instr = instr.replace("-", "")
except AttributeError: except AttributeError:
instr = date.today().strftime("%Y%m%d") instr = date.today().strftime("%Y%m%d")
instr = re.sub(r"^(\d{6})", f"RSL-AR-\\1", instr) instr = re.sub(r"^(\d{6})", f"RSL-AR-\\1", instr)
logger.debug(f"name coming out of Artic namer: {instr}") # logger.debug(f"name coming out of Artic namer: {instr}")
outstr = super().enforce_name(instr=instr, data=data) outstr = super().enforce_name(instr=instr, data=data)
return outstr return outstr
@classmethod @classmethod
@@ -1611,39 +1620,39 @@ class WastewaterArtic(BasicSubmission):
Returns: Returns:
str: output name str: output name
""" """
logger.debug(f"input string raw: {input_str}") # logger.debug(f"input string raw: {input_str}")
# Remove letters. # Remove letters.
processed = input_str.replace("RSL", "") processed = input_str.replace("RSL", "")
processed = re.sub(r"\(.*\)$", "", processed).strip() processed = re.sub(r"\(.*\)$", "", processed).strip()
processed = re.sub(r"[A-QS-Z]+\d*", "", processed) processed = re.sub(r"[A-QS-Z]+\d*", "", processed)
# Remove trailing '-' if any # Remove trailing '-' if any
processed = processed.strip("-") processed = processed.strip("-")
logger.debug(f"Processed after stripping letters: {processed}") # logger.debug(f"Processed after stripping letters: {processed}")
try: try:
en_num = re.search(r"\-\d{1}$", processed).group() en_num = re.search(r"\-\d{1}$", processed).group()
processed = rreplace(processed, en_num, "") processed = rreplace(processed, en_num, "")
except AttributeError: except AttributeError:
en_num = "1" en_num = "1"
en_num = en_num.strip("-") en_num = en_num.strip("-")
logger.debug(f"Processed after en_num: {processed}") # logger.debug(f"Processed after en_num: {processed}")
try: try:
plate_num = re.search(r"\-\d{1}R?\d?$", processed).group() plate_num = re.search(r"\-\d{1}R?\d?$", processed).group()
processed = rreplace(processed, plate_num, "") processed = rreplace(processed, plate_num, "")
except AttributeError: except AttributeError:
plate_num = "1" plate_num = "1"
plate_num = plate_num.strip("-") plate_num = plate_num.strip("-")
logger.debug(f"Processed after plate-num: {processed}") # logger.debug(f"Processed after plate-num: {processed}")
day = re.search(r"\d{2}$", processed).group() day = re.search(r"\d{2}$", processed).group()
processed = rreplace(processed, day, "") processed = rreplace(processed, day, "")
logger.debug(f"Processed after day: {processed}") # logger.debug(f"Processed after day: {processed}")
month = re.search(r"\d{2}$", processed).group() month = re.search(r"\d{2}$", processed).group()
processed = rreplace(processed, month, "") processed = rreplace(processed, month, "")
processed = processed.replace("--", "") processed = processed.replace("--", "")
logger.debug(f"Processed after month: {processed}") # logger.debug(f"Processed after month: {processed}")
year = re.search(r'^(?:\d{2})?\d{2}', processed).group() year = re.search(r'^(?:\d{2})?\d{2}', processed).group()
year = f"20{year}" year = f"20{year}"
final_en_name = f"EN{en_num}-{year}{month}{day}" final_en_name = f"EN{en_num}-{year}{month}{day}"
logger.debug(f"Final EN name: {final_en_name}") # logger.debug(f"Final EN name: {final_en_name}")
return final_en_name return final_en_name
@classmethod @classmethod
@@ -1657,14 +1666,14 @@ class WastewaterArtic(BasicSubmission):
Returns: Returns:
str: output name str: output name
""" """
logger.debug(f"input string raw: {input_str}") # logger.debug(f"input string raw: {input_str}")
# Remove letters. # Remove letters.
processed = input_str.replace("RSL", "") processed = input_str.replace("RSL", "")
processed = re.sub(r"\(.*\)$", "", processed).strip() processed = re.sub(r"\(.*\)$", "", processed).strip()
processed = re.sub(r"[A-QS-Z]+\d*", "", processed) processed = re.sub(r"[A-QS-Z]+\d*", "", processed)
# Remove trailing '-' if any # Remove trailing '-' if any
processed = processed.strip("-") processed = processed.strip("-")
logger.debug(f"Processed after stripping letters: {processed}") # logger.debug(f"Processed after stripping letters: {processed}")
# try: # try:
# en_num = re.search(r"\-\d{1}$", processed).group() # en_num = re.search(r"\-\d{1}$", processed).group()
# processed = rreplace(processed, en_num, "") # processed = rreplace(processed, en_num, "")
@@ -1678,23 +1687,23 @@ class WastewaterArtic(BasicSubmission):
except AttributeError: except AttributeError:
plate_num = "1" plate_num = "1"
plate_num = plate_num.strip("-") plate_num = plate_num.strip("-")
logger.debug(f"Plate num: {plate_num}") # logger.debug(f"Plate num: {plate_num}")
repeat_num = re.search(r"R(?P<repeat>\d)?$", "PBS20240426-2R").groups()[0] repeat_num = re.search(r"R(?P<repeat>\d)?$", "PBS20240426-2R").groups()[0]
if repeat_num is None and "R" in plate_num: if repeat_num is None and "R" in plate_num:
repeat_num = "1" repeat_num = "1"
plate_num = re.sub(r"R", rf"R{repeat_num}", plate_num) plate_num = re.sub(r"R", rf"R{repeat_num}", plate_num)
logger.debug(f"Processed after plate-num: {processed}") # logger.debug(f"Processed after plate-num: {processed}")
day = re.search(r"\d{2}$", processed).group() day = re.search(r"\d{2}$", processed).group()
processed = rreplace(processed, day, "") processed = rreplace(processed, day, "")
logger.debug(f"Processed after day: {processed}") # logger.debug(f"Processed after day: {processed}")
month = re.search(r"\d{2}$", processed).group() month = re.search(r"\d{2}$", processed).group()
processed = rreplace(processed, month, "") processed = rreplace(processed, month, "")
processed = processed.replace("--", "") processed = processed.replace("--", "")
logger.debug(f"Processed after month: {processed}") # logger.debug(f"Processed after month: {processed}")
year = re.search(r'^(?:\d{2})?\d{2}', processed).group() year = re.search(r'^(?:\d{2})?\d{2}', processed).group()
year = f"20{year}" year = f"20{year}"
final_en_name = f"PBS{year}{month}{day}-{plate_num}" final_en_name = f"PBS{year}{month}{day}-{plate_num}"
logger.debug(f"Final EN name: {final_en_name}") # logger.debug(f"Final EN name: {final_en_name}")
return final_en_name return final_en_name
@classmethod @classmethod
@@ -1722,12 +1731,12 @@ class WastewaterArtic(BasicSubmission):
dict: Updated parser product. dict: Updated parser product.
""" """
input_dict = super().finalize_parse(input_dict, xl, info_map) input_dict = super().finalize_parse(input_dict, xl, info_map)
logger.debug(f"Incoming input_dict: {pformat(input_dict)}") # logger.debug(f"Incoming input_dict: {pformat(input_dict)}")
# TODO: Move to validator? # TODO: Move to validator?
for sample in input_dict['samples']: for sample in input_dict['samples']:
logger.debug(f"Sample: {sample}") # logger.debug(f"Sample: {sample}")
if re.search(r"^NTC", sample['submitter_id']): if re.search(r"^NTC", sample['submitter_id']):
sample['submitter_id'] = sample['submitter_id'] + "-WWG-" + input_dict['rsl_plate_num']['value'] sample['submitter_id'] = f"{sample['submitter_id']}-WWG-{input_dict['rsl_plate_num']['value']}"
input_dict['csv'] = xl["hitpicks_csv_to_export"] input_dict['csv'] = xl["hitpicks_csv_to_export"]
return input_dict return input_dict
@@ -1748,13 +1757,13 @@ class WastewaterArtic(BasicSubmission):
# worksheet = input_excel["First Strand List"] # worksheet = input_excel["First Strand List"]
# samples = cls.query(rsl_number=info['rsl_plate_num']['value']).submission_sample_associations # samples = cls.query(rsl_number=info['rsl_plate_num']['value']).submission_sample_associations
# samples = sorted(samples, key=attrgetter('column', 'row')) # samples = sorted(samples, key=attrgetter('column', 'row'))
logger.debug(f"Info:\n{pformat(info)}") # logger.debug(f"Info:\n{pformat(info)}")
check = 'source_plates' in info.keys() and info['source_plates'] is not None check = 'source_plates' in info.keys() and info['source_plates'] is not None
if check: if check:
worksheet = input_excel['First Strand List'] worksheet = input_excel['First Strand List']
start_row = 8 start_row = 8
for iii, plate in enumerate(info['source_plates']['value']): for iii, plate in enumerate(info['source_plates']['value']):
logger.debug(f"Plate: {plate}") # logger.debug(f"Plate: {plate}")
row = start_row + iii row = start_row + iii
try: try:
worksheet.cell(row=row, column=3, value=plate['plate']) worksheet.cell(row=row, column=3, value=plate['plate'])
@@ -1782,12 +1791,16 @@ class WastewaterArtic(BasicSubmission):
# logger.debug(f"vj: {vj}") # logger.debug(f"vj: {vj}")
column = start_column + 2 + jjj column = start_column + 2 + jjj
worksheet.cell(row=start_row, column=column, value=kj['name']) worksheet.cell(row=start_row, column=column, value=kj['name'])
# logger.debug(f"Writing {kj['name']} with value {kj['value']} to row {row}, column {column}")
try:
worksheet.cell(row=row, column=column, value=kj['value']) worksheet.cell(row=row, column=column, value=kj['value'])
except AttributeError:
logger.error(f"Failed {kj['name']} with value {kj['value']} to row {row}, column {column}")
check = 'gel_image' in info.keys() and info['gel_image']['value'] is not None check = 'gel_image' in info.keys() and info['gel_image']['value'] is not None
if check: if check:
if info['gel_image'] != None: if info['gel_image'] != None:
worksheet = input_excel['Egel results'] worksheet = input_excel['Egel results']
logger.debug(f"We got an image: {info['gel_image']}") # logger.debug(f"We got an image: {info['gel_image']}")
with ZipFile(cls.__directory_path__.joinpath("submission_imgs.zip")) as zipped: with ZipFile(cls.__directory_path__.joinpath("submission_imgs.zip")) as zipped:
z = zipped.extract(info['gel_image']['value'], Path(TemporaryDirectory().name)) z = zipped.extract(info['gel_image']['value'], Path(TemporaryDirectory().name))
img = OpenpyxlImage(z) img = OpenpyxlImage(z)
@@ -1817,7 +1830,7 @@ class WastewaterArtic(BasicSubmission):
headers = [item['name'] for item in base_dict['gel_info'][0]['values']] headers = [item['name'] for item in base_dict['gel_info'][0]['values']]
base_dict['headers'] = [''] * (4 - len(headers)) base_dict['headers'] = [''] * (4 - len(headers))
base_dict['headers'] += headers base_dict['headers'] += headers
logger.debug(f"Gel info: {pformat(base_dict['headers'])}") # logger.debug(f"Gel info: {pformat(base_dict['headers'])}")
check = 'gel_image' in base_dict.keys() and base_dict['gel_image'] != None check = 'gel_image' in base_dict.keys() and base_dict['gel_image'] != None
if check: if check:
with ZipFile(cls.__directory_path__.joinpath("submission_imgs.zip")) as zipped: with ZipFile(cls.__directory_path__.joinpath("submission_imgs.zip")) as zipped:
@@ -1834,7 +1847,7 @@ class WastewaterArtic(BasicSubmission):
Returns: Returns:
List[dict]: Updated dictionaries List[dict]: Updated dictionaries
""" """
logger.debug(f"Hello from {self.__class__.__name__} dictionary sample adjuster.") # logger.debug(f"Hello from {self.__class__.__name__} dictionary sample adjuster.")
output = [] output = []
set_plate = None set_plate = None
for assoc in self.submission_sample_associations: for assoc in self.submission_sample_associations:
@@ -1888,7 +1901,7 @@ class WastewaterArtic(BasicSubmission):
self.comment.append(com) self.comment.append(com)
else: else:
self.comment = [com] self.comment = [com]
logger.debug(pformat(self.gel_info)) # logger.debug(pformat(self.gel_info))
with ZipFile(self.__directory_path__.joinpath("submission_imgs.zip"), 'a') as zipf: with ZipFile(self.__directory_path__.joinpath("submission_imgs.zip"), 'a') as zipf:
# Add a file located at the source_path to the destination within the zip # Add a file located at the source_path to the destination within the zip
# file. It will overwrite existing files if the names collide, but it # file. It will overwrite existing files if the names collide, but it
@@ -1966,7 +1979,7 @@ class BasicSample(BaseClass):
Returns: Returns:
dict: well location and name (sample id, organism) NOTE: keys must sync with WWSample to_sub_dict above dict: well location and name (sample id, organism) NOTE: keys must sync with WWSample to_sub_dict above
""" """
logger.debug(f"Converting {self} to dict.") # logger.debug(f"Converting {self} to dict.")
# start = time() # start = time()
sample = {} sample = {}
sample['Submitter ID'] = self.submitter_id sample['Submitter ID'] = self.submitter_id
@@ -2042,7 +2055,7 @@ class BasicSample(BaseClass):
Returns: Returns:
dict: Updated parser results. dict: Updated parser results.
""" """
logger.debug(f"Hello from {cls.__name__} sample parser!") # logger.debug(f"Hello from {cls.__name__} sample parser!")
return input_dict return input_dict
@classmethod @classmethod
@@ -2059,7 +2072,7 @@ class BasicSample(BaseClass):
base_dict['excluded'] = ['submissions', 'excluded', 'colour', 'tooltip'] base_dict['excluded'] = ['submissions', 'excluded', 'colour', 'tooltip']
env = jinja_template_loading() env = jinja_template_loading()
temp_name = f"{cls.__name__.lower()}_details.html" temp_name = f"{cls.__name__.lower()}_details.html"
logger.debug(f"Returning template: {temp_name}") # logger.debug(f"Returning template: {temp_name}")
try: try:
template = env.get_template(temp_name) template = env.get_template(temp_name)
except TemplateNotFound as e: except TemplateNotFound as e:
@@ -2091,7 +2104,7 @@ class BasicSample(BaseClass):
model = cls.find_polymorphic_subclass(attrs=kwargs) model = cls.find_polymorphic_subclass(attrs=kwargs)
else: else:
model = cls.find_polymorphic_subclass(polymorphic_identity=sample_type) model = cls.find_polymorphic_subclass(polymorphic_identity=sample_type)
logger.debug(f"Length of kwargs: {len(kwargs)}") # logger.debug(f"Length of kwargs: {len(kwargs)}")
# model = models.BasicSample.find_subclasses(ctx=ctx, attrs=kwargs) # model = models.BasicSample.find_subclasses(ctx=ctx, attrs=kwargs)
# query: Query = setup_lookup(ctx=ctx, locals=locals()).query(model) # query: Query = setup_lookup(ctx=ctx, locals=locals()).query(model)
query: Query = cls.__database_session__.query(model) query: Query = cls.__database_session__.query(model)
@@ -2141,7 +2154,7 @@ class BasicSample(BaseClass):
# f"{key} is not allowed as a query argument as it could lead to creation of duplicate objects.") # f"{key} is not allowed as a query argument as it could lead to creation of duplicate objects.")
sanitized_kwargs = {k:v for k,v in kwargs.items() if k not in disallowed} sanitized_kwargs = {k:v for k,v in kwargs.items() if k not in disallowed}
instance = cls.query(sample_type=sample_type, limit=1, **kwargs) instance = cls.query(sample_type=sample_type, limit=1, **kwargs)
logger.debug(f"Retrieved instance: {instance}") # logger.debug(f"Retrieved instance: {instance}")
if instance is None: if instance is None:
used_class = cls.find_polymorphic_subclass(attrs=sanitized_kwargs, polymorphic_identity=sample_type) used_class = cls.find_polymorphic_subclass(attrs=sanitized_kwargs, polymorphic_identity=sample_type)
instance = used_class(**sanitized_kwargs) instance = used_class(**sanitized_kwargs)
@@ -2219,7 +2232,7 @@ class WastewaterSample(BasicSample):
dict: Updated parser results. dict: Updated parser results.
""" """
output_dict = super().parse_sample(input_dict) output_dict = super().parse_sample(input_dict)
logger.debug(f"Initial sample dict: {pformat(output_dict)}") # logger.debug(f"Initial sample dict: {pformat(output_dict)}")
disallowed = ["", None, "None"] disallowed = ["", None, "None"]
try: try:
check = output_dict['rsl_number'] in [None, "None"] check = output_dict['rsl_number'] in [None, "None"]
@@ -2258,7 +2271,7 @@ class WastewaterSample(BasicSample):
plates = [item.rsl_plate_num for item in plates = [item.rsl_plate_num for item in
self.submissions[:self.submissions.index(current_artic_submission)]] self.submissions[:self.submissions.index(current_artic_submission)]]
subs = [sub for sub in self.submissions if sub.rsl_plate_num in plates] subs = [sub for sub in self.submissions if sub.rsl_plate_num in plates]
logger.debug(f"Submissions: {subs}") # logger.debug(f"Submissions: {subs}")
try: try:
return subs[-1] return subs[-1]
except IndexError: except IndexError:
@@ -2339,7 +2352,7 @@ class SubmissionSampleAssociation(BaseClass):
self.id = id self.id = id
else: else:
self.id = self.__class__.autoincrement_id() self.id = self.__class__.autoincrement_id()
logger.debug(f"Using id: {self.id}") # logger.debug(f"Using submission sample association id: {self.id}")
def __repr__(self) -> str: def __repr__(self) -> str:
try: try:
@@ -2356,9 +2369,9 @@ class SubmissionSampleAssociation(BaseClass):
dict: Updated dictionary with row, column and well updated dict: Updated dictionary with row, column and well updated
""" """
# Get sample info # Get sample info
logger.debug(f"Running {self.__repr__()}") # logger.debug(f"Running {self.__repr__()}")
sample = self.sample.to_sub_dict() sample = self.sample.to_sub_dict()
logger.debug("Sample conversion complete.") # logger.debug("Sample conversion complete.")
sample['Name'] = self.sample.submitter_id sample['Name'] = self.sample.submitter_id
sample['Row'] = self.row sample['Row'] = self.row
sample['Column'] = self.column sample['Column'] = self.column
@@ -2382,7 +2395,7 @@ class SubmissionSampleAssociation(BaseClass):
""" """
# Since there is no PCR, negliable result is necessary. # Since there is no PCR, negliable result is necessary.
sample = self.to_sub_dict() sample = self.to_sub_dict()
logger.debug(f"Sample dict to hitpick: {sample}") # logger.debug(f"Sample dict to hitpick: {sample}")
env = jinja_template_loading() env = jinja_template_loading()
template = env.get_template("tooltip.html") template = env.get_template("tooltip.html")
tooltip_text = template.render(fields=sample) tooltip_text = template.render(fields=sample)
@@ -2430,7 +2443,7 @@ class SubmissionSampleAssociation(BaseClass):
except Exception as e: except Exception as e:
logger.error(f"Could not get polymorph {polymorphic_identity} of {cls} due to {e}") logger.error(f"Could not get polymorph {polymorphic_identity} of {cls} due to {e}")
output = cls output = cls
logger.debug(f"Using SubmissionSampleAssociation subclass: {output}") # logger.debug(f"Using SubmissionSampleAssociation subclass: {output}")
return output return output
@classmethod @classmethod
@@ -2519,7 +2532,7 @@ class SubmissionSampleAssociation(BaseClass):
Returns: Returns:
SubmissionSampleAssociation: Queried or new association. SubmissionSampleAssociation: Queried or new association.
""" """
logger.debug(f"Attempting create or query with {kwargs}") # logger.debug(f"Attempting create or query with {kwargs}")
match submission: match submission:
case BasicSubmission(): case BasicSubmission():
pass pass

189
src/submissions/backend/excel/parser.py
View File

@@ -19,6 +19,7 @@ from datetime import date
from dateutil.parser import parse, ParserError from dateutil.parser import parse, ParserError
from tools import check_not_nan, convert_nans_to_nones, row_map, row_keys, is_missing, remove_key_from_list_of_dicts from tools import check_not_nan, convert_nans_to_nones, row_map, row_keys, is_missing, remove_key_from_list_of_dicts
logger = logging.getLogger(f"submissions.{__name__}") logger = logging.getLogger(f"submissions.{__name__}")
@@ -44,26 +45,24 @@ class SheetParser(object):
logger.error(f"No filepath given.") logger.error(f"No filepath given.")
raise ValueError("No filepath given.") raise ValueError("No filepath given.")
try: try:
# self.xl = pd.ExcelFile(filepath)
self.xl = load_workbook(filepath, data_only=True) self.xl = load_workbook(filepath, data_only=True)
except ValueError as e: except ValueError as e:
logger.error(f"Incorrect value: {e}") logger.error(f"Incorrect value: {e}")
raise FileNotFoundError(f"Couldn't parse file {self.filepath}") raise FileNotFoundError(f"Couldn't parse file {self.filepath}")
self.sub = OrderedDict() self.sub = OrderedDict()
# make decision about type of sample we have # NOTE: make decision about type of sample we have
self.sub['submission_type'] = dict(value=RSLNamer.retrieve_submission_type(filename=self.filepath), self.sub['submission_type'] = dict(value=RSLNamer.retrieve_submission_type(filename=self.filepath),
missing=True) missing=True)
self.submission_type = SubmissionType.query(name=self.sub['submission_type']) self.submission_type = SubmissionType.query(name=self.sub['submission_type'])
self.sub_object = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type) self.sub_object = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
# grab the info map from the submission type in database # NOTE: grab the info map from the submission type in database
self.parse_info() self.parse_info()
self.import_kit_validation_check() self.import_kit_validation_check()
self.parse_reagents() self.parse_reagents()
# self.import_reagent_validation_check()
self.parse_samples() self.parse_samples()
self.parse_equipment() self.parse_equipment()
self.finalize_parse() self.finalize_parse()
logger.debug(f"Parser.sub after info scrape: {pformat(self.sub)}") # logger.debug(f"Parser.sub after info scrape: {pformat(self.sub)}")
def parse_info(self): def parse_info(self):
""" """
@@ -141,7 +140,7 @@ class SheetParser(object):
pyd_dict = copy(self.sub) pyd_dict = copy(self.sub)
pyd_dict['samples'] = [PydSample(**sample) for sample in self.sub['samples']] pyd_dict['samples'] = [PydSample(**sample) for sample in self.sub['samples']]
pyd_dict['reagents'] = [PydReagent(**reagent) for reagent in self.sub['reagents']] pyd_dict['reagents'] = [PydReagent(**reagent) for reagent in self.sub['reagents']]
logger.debug(f"Equipment: {self.sub['equipment']}") # logger.debug(f"Equipment: {self.sub['equipment']}")
try: try:
check = len(self.sub['equipment']) == 0 check = len(self.sub['equipment']) == 0
except TypeError: except TypeError:
@@ -157,7 +156,7 @@ class SheetParser(object):
class InfoParser(object): class InfoParser(object):
def __init__(self, xl: Workbook, submission_type: str|SubmissionType, sub_object: BasicSubmission|None=None): def __init__(self, xl: Workbook, submission_type: str|SubmissionType, sub_object: BasicSubmission|None=None):
logger.info(f"\n\Hello from InfoParser!\n\n") logger.info(f"\n\nHello from InfoParser!\n\n")
if isinstance(submission_type, str): if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type) submission_type = SubmissionType.query(name=submission_type)
if sub_object is None: if sub_object is None:
@@ -166,7 +165,7 @@ class InfoParser(object):
self.sub_object = sub_object self.sub_object = sub_object
self.map = self.fetch_submission_info_map() self.map = self.fetch_submission_info_map()
self.xl = xl self.xl = xl
logger.debug(f"Info map for InfoParser: {pformat(self.map)}") # logger.debug(f"Info map for InfoParser: {pformat(self.map)}")
def fetch_submission_info_map(self) -> dict: def fetch_submission_info_map(self) -> dict:
""" """
@@ -179,13 +178,9 @@ class InfoParser(object):
dict: Location map of all info for this submission type dict: Location map of all info for this submission type
""" """
self.submission_type = dict(value=self.submission_type_obj.name, missing=True) self.submission_type = dict(value=self.submission_type_obj.name, missing=True)
logger.debug(f"Looking up submission type: {self.submission_type['value']}") # logger.debug(f"Looking up submission type: {self.submission_type['value']}")
# submission_type = SubmissionType.query(name=self.submission_type['value'])
# info_map = submission_type.info_map
# self.sub_object: BasicSubmission = \
# BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type['value'])
info_map = self.sub_object.construct_info_map("read") info_map = self.sub_object.construct_info_map("read")
# Get the parse_info method from the submission type specified # NOTE: Get the parse_info method from the submission type specified
return info_map return info_map
def parse_info(self) -> dict: def parse_info(self) -> dict:
@@ -195,30 +190,19 @@ class InfoParser(object):
Returns: Returns:
dict: key:value of basic info dict: key:value of basic info
""" """
# if isinstance(self.submission_type, str):
# self.submission_type = dict(value=self.submission_type, missing=True)
dicto = {} dicto = {}
# exclude_from_generic = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type['value']).get_default_info("parser_ignore") # NOTE: This loop parses generic info
# This loop parses generic info # logger.debug(f"Map: {self.map}")
logger.debug(f"Map: {self.map}")
# for sheet in self.xl.sheet_names:
for sheet in self.xl.sheetnames: for sheet in self.xl.sheetnames:
# df = self.xl.parse(sheet, header=None)
ws = self.xl[sheet] ws = self.xl[sheet]
relevant = [] relevant = []
for k, v in self.map.items(): for k, v in self.map.items():
# If the value is hardcoded put it in the dictionary directly. # NOTE: If the value is hardcoded put it in the dictionary directly.
if isinstance(v, str): if isinstance(v, str):
dicto[k] = dict(value=v, missing=False) dicto[k] = dict(value=v, missing=False)
continue continue
logger.debug(f"Looking for {k} in self.map") # logger.debug(f"Looking for {k} in self.map")
logger.debug(f"Locations: {v}") # logger.debug(f"Locations: {v}")
# try:
# check = sheet in self.map[k]['sheets']
# except TypeError:
# continue
# if check:
# relevant[k] = v
for location in v: for location in v:
try: try:
check = location['sheet'] == sheet check = location['sheet'] == sheet
@@ -235,7 +219,6 @@ class InfoParser(object):
continue continue
for item in relevant: for item in relevant:
# NOTE: Get cell contents at this location # NOTE: Get cell contents at this location
# value = df.iat[item['row']-1, item['column']-1]
value = ws.cell(row=item['row'], column=item['column']).value value = ws.cell(row=item['row'], column=item['column']).value
logger.debug(f"Value for {item['name']} = {value}") logger.debug(f"Value for {item['name']} = {value}")
match item['name']: match item['name']:
@@ -250,10 +233,10 @@ class InfoParser(object):
dicto[item['name']]['value'] += value dicto[item['name']]['value'] += value
continue continue
except KeyError: except KeyError:
logger.debug(f"New value for {item['name']}") logger.error(f"New value for {item['name']}")
case _: case _:
value, missing = is_missing(value) value, missing = is_missing(value)
logger.debug(f"Setting {item} on {sheet} to {value}") # logger.debug(f"Setting {item} on {sheet} to {value}")
if item['name'] not in dicto.keys(): if item['name'] not in dicto.keys():
try: try:
dicto[item['name']] = dict(value=value, missing=missing) dicto[item['name']] = dict(value=value, missing=missing)
@@ -265,14 +248,14 @@ class InfoParser(object):
class ReagentParser(object): class ReagentParser(object):
def __init__(self, xl: Workbook, submission_type: str, extraction_kit: str, sub_object:BasicSubmission|None=None): def __init__(self, xl: Workbook, submission_type: str, extraction_kit: str, sub_object:BasicSubmission|None=None):
logger.debug("\n\nHello from ReagentParser!\n\n") # logger.debug("\n\nHello from ReagentParser!\n\n")
self.submission_type_obj = submission_type self.submission_type_obj = submission_type
self.sub_object = sub_object self.sub_object = sub_object
if isinstance(extraction_kit, dict): if isinstance(extraction_kit, dict):
extraction_kit = extraction_kit['value'] extraction_kit = extraction_kit['value']
self.kit_object = KitType.query(name=extraction_kit) self.kit_object = KitType.query(name=extraction_kit)
self.map = self.fetch_kit_info_map(extraction_kit=extraction_kit, submission_type=submission_type) self.map = self.fetch_kit_info_map(extraction_kit=extraction_kit, submission_type=submission_type)
logger.debug(f"Reagent Parser map: {self.map}") # logger.debug(f"Reagent Parser map: {self.map}")
self.xl = xl self.xl = xl
def fetch_kit_info_map(self, extraction_kit: dict, submission_type: str) -> dict: def fetch_kit_info_map(self, extraction_kit: dict, submission_type: str) -> dict:
@@ -305,45 +288,40 @@ class ReagentParser(object):
""" """
listo = [] listo = []
for sheet in self.xl.sheetnames: for sheet in self.xl.sheetnames:
# df = self.xl.parse(sheet, header=None, dtype=object)
ws = self.xl[sheet] ws = self.xl[sheet]
# df.replace({np.nan: None}, inplace = True)
relevant = {k.strip(): v for k, v in self.map.items() if sheet in self.map[k]['sheet']} relevant = {k.strip(): v for k, v in self.map.items() if sheet in self.map[k]['sheet']}
logger.debug(f"relevant map for {sheet}: {pformat(relevant)}") # logger.debug(f"relevant map for {sheet}: {pformat(relevant)}")
if relevant == {}: if relevant == {}:
continue continue
for item in relevant: for item in relevant:
logger.debug(f"Attempting to scrape: {item}") # logger.debug(f"Attempting to scrape: {item}")
try: try:
reagent = relevant[item] reagent = relevant[item]
# name = df.iat[relevant[item]['name']['row']-1, relevant[item]['name']['column']-1]
# lot = df.iat[relevant[item]['lot']['row']-1, relevant[item]['lot']['column']-1]
# expiry = df.iat[relevant[item]['expiry']['row']-1, relevant[item]['expiry']['column']-1]
name = ws.cell(row=reagent['name']['row'], column=reagent['name']['column']).value name = ws.cell(row=reagent['name']['row'], column=reagent['name']['column']).value
lot = ws.cell(row=reagent['lot']['row'], column=reagent['lot']['column']).value lot = ws.cell(row=reagent['lot']['row'], column=reagent['lot']['column']).value
expiry = ws.cell(row=reagent['expiry']['row'], column=reagent['expiry']['column']).value expiry = ws.cell(row=reagent['expiry']['row'], column=reagent['expiry']['column']).value
if 'comment' in relevant[item].keys(): if 'comment' in relevant[item].keys():
logger.debug(f"looking for {relevant[item]} comment.") # logger.debug(f"looking for {relevant[item]} comment.")
# comment = df.iat[relevant[item]['comment']['row']-1, relevant[item]['comment']['column']-1] comment = ws.cell(row=reagent['comment']['row'], column=reagent['comment']['column']).value
expiry = ws.cell(row=reagent['comment']['row'], column=reagent['comment']['column']).value
else: else:
comment = "" comment = ""
except (KeyError, IndexError): except (KeyError, IndexError):
listo.append( listo.append(
PydReagent(type=item.strip(), lot=None, expiry=None, name=None, comment="", missing=True)) PydReagent(type=item.strip(), lot=None, expiry=None, name=None, comment="", missing=True))
continue continue
# If the cell is blank tell the PydReagent # NOTE: If the cell is blank tell the PydReagent
if check_not_nan(lot): if check_not_nan(lot):
missing = False missing = False
else: else:
missing = True missing = True
# logger.debug(f"Got lot for {item}-{name}: {lot} as {type(lot)}") # logger.debug(f"Got lot for {item}-{name}: {lot} as {type(lot)}")
lot = str(lot) lot = str(lot)
logger.debug( # logger.debug(
f"Going into pydantic: name: {name}, lot: {lot}, expiry: {expiry}, type: {item.strip()}, comment: {comment}") # f"Going into pydantic: name: {name}, lot: {lot}, expiry: {expiry}, type: {item.strip()}, comment: {comment}")
try: try:
check = name.lower() != "not applicable" check = name.lower() != "not applicable"
except AttributeError: except AttributeError:
logger.warning(f"name is not a string.")
check = True check = True
if check: if check:
listo.append(dict(type=item.strip(), lot=lot, expiry=expiry, name=name, comment=comment, listo.append(dict(type=item.strip(), lot=lot, expiry=expiry, name=name, comment=comment,
@@ -364,26 +342,20 @@ class SampleParser(object):
df (pd.DataFrame): input sample dataframe df (pd.DataFrame): input sample dataframe
elution_map (pd.DataFrame | None, optional): optional map of elution plate. Defaults to None. elution_map (pd.DataFrame | None, optional): optional map of elution plate. Defaults to None.
""" """
logger.debug("\n\nHello from SampleParser!\n\n") # logger.debug("\n\nHello from SampleParser!\n\n")
self.samples = [] self.samples = []
self.xl = xl self.xl = xl
if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type)
self.submission_type = submission_type.name self.submission_type = submission_type.name
self.submission_type_obj = submission_type self.submission_type_obj = submission_type
if sub_object is None: if sub_object is None:
sub_object = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type_obj.name) sub_object = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type_obj.name)
self.sub_object = sub_object self.sub_object = sub_object
self.sample_info_map = self.fetch_sample_info_map(submission_type=submission_type, sample_map=sample_map) self.sample_info_map = self.fetch_sample_info_map(submission_type=submission_type, sample_map=sample_map)
logger.debug(f"sample_info_map: {self.sample_info_map}") # logger.debug(f"sample_info_map: {self.sample_info_map}")
# self.plate_map = self.construct_plate_map(plate_map_location=sample_info_map['plate_map'])
# logger.debug(f"plate_map: {self.plate_map}")
# self.lookup_table = self.construct_lookup_table(lookup_table_location=sample_info_map['lookup_table'])
# if "plates" in sample_info_map:
# self.plates = sample_info_map['plates']
# self.excel_to_db_map = sample_info_map['xl_db_translation']
self.plate_map_samples = self.parse_plate_map() self.plate_map_samples = self.parse_plate_map()
self.lookup_samples = self.parse_lookup_table() self.lookup_samples = self.parse_lookup_table()
# if isinstance(self.lookup_table, pd.DataFrame):
# self.parse_lookup_table()
def fetch_sample_info_map(self, submission_type: str, sample_map: dict | None = None) -> dict: def fetch_sample_info_map(self, submission_type: str, sample_map: dict | None = None) -> dict:
""" """
@@ -395,17 +367,12 @@ class SampleParser(object):
Returns: Returns:
dict: Info locations. dict: Info locations.
""" """
logger.debug(f"Looking up submission type: {submission_type}") # logger.debug(f"Looking up submission type: {submission_type}")
# submission_type = SubmissionType.query(name=submission_type)
# self.sub_object = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=submission_type)
# self.custom_sub_parser = .parse_samples
self.sample_type = self.sub_object.get_default_info("sample_type") self.sample_type = self.sub_object.get_default_info("sample_type")
self.samp_object = BasicSample.find_polymorphic_subclass(polymorphic_identity=self.sample_type) self.samp_object = BasicSample.find_polymorphic_subclass(polymorphic_identity=self.sample_type)
logger.debug(f"Got sample class: {self.samp_object.__name__}") # logger.debug(f"Got sample class: {self.samp_object.__name__}")
# self.custom_sample_parser = .parse_sample
# logger.debug(f"info_map: {pformat(se)}") # logger.debug(f"info_map: {pformat(se)}")
if sample_map is None: if sample_map is None:
# sample_info_map = submission_type.info_map['samples']
sample_info_map = self.sub_object.construct_sample_map() sample_info_map = self.sub_object.construct_sample_map()
else: else:
sample_info_map = sample_map sample_info_map = sample_map
@@ -459,22 +426,6 @@ class SampleParser(object):
invalids = [0, "0", "EMPTY"] invalids = [0, "0", "EMPTY"]
smap = self.sample_info_map['plate_map'] smap = self.sample_info_map['plate_map']
ws = self.xl[smap['sheet']] ws = self.xl[smap['sheet']]
# ws.protection = SheetProtection()
# new_df = self.plate_map.dropna(axis=1, how='all')
# columns = new_df.columns.tolist()
# for _, iii in new_df.iterrows():
# for c in columns:
# if check_not_nan(iii[c]):
# if iii[c] in invalids:
# logger.debug(f"Invalid sample name: {iii[c]}, skipping.")
# continue
# id = iii[c]
# logger.debug(f"Adding sample {iii[c]}")
# try:
# c = self.plate_map.columns.get_loc(c) + 1
# except Exception as e:
# logger.error(f"Unable to get column index of {c} due to {e}")
# self.samples.append(dict(submitter_id=id, row=row_keys[iii._name], column=c))
plate_map_samples = [] plate_map_samples = []
for ii, row in enumerate(range(smap['start_row'], smap['end_row'] + 1), start=1): for ii, row in enumerate(range(smap['start_row'], smap['end_row'] + 1), start=1):
# logger.debug(f"Parsing row: {row}") # logger.debug(f"Parsing row: {row}")
@@ -494,42 +445,12 @@ class SampleParser(object):
pass pass
return plate_map_samples return plate_map_samples
def parse_lookup_table(self) -> dict: def parse_lookup_table(self) -> List[dict]:
""" """
Parse misc info from lookup table. Parse misc info from lookup table.
""" """
lmap = self.sample_info_map['lookup_table'] lmap = self.sample_info_map['lookup_table']
ws = self.xl[lmap['sheet']] ws = self.xl[lmap['sheet']]
# for sample in self.samples:
# addition = self.lookup_table[self.lookup_table.isin([sample['submitter_id']]).any(axis=1)].squeeze()
# # logger.debug(addition)
# if isinstance(addition, pd.DataFrame) and not addition.empty:
# addition = addition.iloc[0]
# # logger.debug(f"Lookuptable info: {addition.to_dict()}")
# for k,v in addition.to_dict().items():
# # logger.debug(f"Checking {k} in lookup table.")
# if check_not_nan(k) and isinstance(k, str):
# if k.lower() not in sample:
# k = k.replace(" ", "_").replace("#","num").lower()
# # logger.debug(f"Adding {type(v)} - {k}, {v} to the lookuptable output dict")
# match v:
# case pd.Timestamp():
# sample[k] = v.date()
# case str():
# sample[k] = determine_if_date(v)
# case _:
# sample[k] = v
# # Set row in lookup table to blank values to prevent multipe lookups.
# try:
# self.lookup_table.loc[self.lookup_table['Sample #']==addition['Sample #']] = np.nan
# except (ValueError, KeyError):
# pass
# try:
# self.lookup_table.loc[self.lookup_table['Well']==addition['Well']] = np.nan
# except (ValueError, KeyError):
# pass
# # logger.debug(f"Output sample dict: {sample}")
# logger.debug(f"Final lookup_table: \n\n {self.lookup_table}")
lookup_samples = [] lookup_samples = []
for ii, row in enumerate(range(lmap['start_row'], lmap['end_row']+1), start=1): for ii, row in enumerate(range(lmap['start_row'], lmap['end_row']+1), start=1):
row_dict = {k:ws.cell(row=row, column=v).value for k, v in lmap['sample_columns'].items()} row_dict = {k:ws.cell(row=row, column=v).value for k, v in lmap['sample_columns'].items()}
@@ -549,7 +470,7 @@ class SampleParser(object):
def parse_samples(self) -> Tuple[Report | None, List[dict] | List[PydSample]]: def parse_samples(self) -> Tuple[Report | None, List[dict] | List[PydSample]]:
""" """
Parse merged platemap\lookup info into dicts/samples Parse merged platemap/lookup info into dicts/samples
Returns: Returns:
List[dict]|List[models.BasicSample]: List of samples List[dict]|List[models.BasicSample]: List of samples
@@ -567,36 +488,14 @@ class SampleParser(object):
v = convert_nans_to_nones(v) v = convert_nans_to_nones(v)
case _: case _:
v = v v = v
# try:
# translated_dict[self.excel_to_db_map[k]] = convert_nans_to_nones(v)
# except KeyError:
translated_dict[k] = convert_nans_to_nones(v) translated_dict[k] = convert_nans_to_nones(v)
translated_dict['sample_type'] = f"{self.submission_type} Sample" translated_dict['sample_type'] = f"{self.submission_type} Sample"
# translated_dict = self.custom_sub_parser(translated_dict)
translated_dict = self.sub_object.parse_samples(translated_dict) translated_dict = self.sub_object.parse_samples(translated_dict)
# translated_dict = self.custom_sample_parser(translated_dict)
translated_dict = self.samp_object.parse_sample(translated_dict) translated_dict = self.samp_object.parse_sample(translated_dict)
# logger.debug(f"Here is the output of the custom parser:\n{translated_dict}") # logger.debug(f"Here is the output of the custom parser:\n{translated_dict}")
new_samples.append(PydSample(**translated_dict)) new_samples.append(PydSample(**translated_dict))
return result, new_samples return result, new_samples
# def grab_plates(self) -> List[str]:
# """
# Parse plate names from
#
# Returns:
# List[str]: list of plate names.
# """
# plates = []
# for plate in self.plates:
# df = self.xl.parse(plate['sheet'], header=None)
# if isinstance(df.iat[plate['row'] - 1, plate['column'] - 1], str):
# output = RSLNamer.retrieve_rsl_number(filename=df.iat[plate['row'] - 1, plate['column'] - 1])
# else:
# continue
# plates.append(output)
# return plates
def reconcile_samples(self): def reconcile_samples(self):
# TODO: Move to pydantic validator? # TODO: Move to pydantic validator?
if self.plate_map_samples is None or self.lookup_samples is None: if self.plate_map_samples is None or self.lookup_samples is None:
@@ -606,29 +505,17 @@ class SampleParser(object):
merge_on_id = self.sample_info_map['lookup_table']['merge_on_id'] merge_on_id = self.sample_info_map['lookup_table']['merge_on_id']
plate_map_samples = sorted(copy(self.plate_map_samples), key=lambda d: d['id']) plate_map_samples = sorted(copy(self.plate_map_samples), key=lambda d: d['id'])
lookup_samples = sorted(copy(self.lookup_samples), key=lambda d: d[merge_on_id]) lookup_samples = sorted(copy(self.lookup_samples), key=lambda d: d[merge_on_id])
# try:
# assert len(plate_map_samples) == len(lookup_samples)
# except AssertionError:
# if len(plate_map_samples) > len(lookup_samples):
# logger.error(
# f"Plate samples ({len(plate_map_samples)}) is longer than Lookup samples: ({len(lookup_samples)})")
# return plate_map_samples
# else:
# logger.error(
# f"Lookup samples ({len(lookup_samples)}) is longer than Plate samples: ({len(plate_map_samples)})")
# return lookup_samples
for ii, psample in enumerate(plate_map_samples): for ii, psample in enumerate(plate_map_samples):
try: try:
check = psample['id'] == lookup_samples[ii][merge_on_id] check = psample['id'] == lookup_samples[ii][merge_on_id]
except (KeyError, IndexError): except (KeyError, IndexError):
check = False check = False
if check: if check:
logger.debug(f"Direct match found for {psample['id']}") # logger.debug(f"Direct match found for {psample['id']}")
new = lookup_samples[ii] | psample new = lookup_samples[ii] | psample
lookup_samples[ii] = {} lookup_samples[ii] = {}
# samples.append(new)
else: else:
logger.warning(f"Match for {psample['id']} not direct, running search.") # logger.warning(f"Match for {psample['id']} not direct, running search.")
for jj, lsample in enumerate(lookup_samples): for jj, lsample in enumerate(lookup_samples):
try: try:
check = lsample[merge_on_id] == psample['id'] check = lsample[merge_on_id] == psample['id']
@@ -637,13 +524,9 @@ class SampleParser(object):
if check: if check:
new = lsample | psample new = lsample | psample
lookup_samples[jj] = {} lookup_samples[jj] = {}
# self.samples.append(new)
# samples.append(new)
break break
else: else:
new = psample new = psample
# samples.append(psample)
# new['sample_type'] = f"{self.submission_type} Sample"
try: try:
check = new['submitter_id'] is None check = new['submitter_id'] is None
except KeyError: except KeyError:

1
src/submissions/backend/excel/writer.py
View File

@@ -11,6 +11,7 @@ from backend.validators.pydant import PydSubmission
from io import BytesIO from io import BytesIO
from collections import OrderedDict from collections import OrderedDict
logger = logging.getLogger(f"submissions.{__name__}") logger = logging.getLogger(f"submissions.{__name__}")

3
src/submissions/backend/validators/__init__.py
View File

@@ -1,4 +1,5 @@
import logging, re import logging, re
import sys
from pathlib import Path from pathlib import Path
from openpyxl import load_workbook from openpyxl import load_workbook
from backend.db.models import BasicSubmission, SubmissionType from backend.db.models import BasicSubmission, SubmissionType
@@ -79,6 +80,8 @@ class RSLNamer(object):
except UnboundLocalError: except UnboundLocalError:
check = True check = True
if check: if check:
if "pytest" in sys.modules:
return "Bacterial Culture"
# logger.debug("Final option, ask the user for submission type") # logger.debug("Final option, ask the user for submission type")
from frontend.widgets import ObjectSelector from frontend.widgets import ObjectSelector
dlg = ObjectSelector(title="Couldn't parse submission type.", dlg = ObjectSelector(title="Couldn't parse submission type.",

18
src/submissions/backend/validators/pydant.py
View File

@@ -2,6 +2,8 @@
Contains pydantic models and accompanying validators Contains pydantic models and accompanying validators
''' '''
from __future__ import annotations from __future__ import annotations
import sys
from operator import attrgetter from operator import attrgetter
import uuid, re, logging import uuid, re, logging
from pydantic import BaseModel, field_validator, Field, model_validator, PrivateAttr from pydantic import BaseModel, field_validator, Field, model_validator, PrivateAttr
@@ -431,10 +433,14 @@ class PydSubmission(BaseModel, extra='allow'):
value['value'] = None value['value'] = None
if value['value'] is None: if value['value'] is None:
value['missing'] = True value['missing'] = True
if "pytest" in sys.modules:
value['value'] = "Nosocomial"
return value
from frontend.widgets.pop_ups import ObjectSelector from frontend.widgets.pop_ups import ObjectSelector
dlg = ObjectSelector(title="Missing Submitting Lab", dlg = ObjectSelector(title="Missing Submitting Lab",
message="We need a submitting lab. Please select from the list.", message="We need a submitting lab. Please select from the list.",
obj_type=Organization) obj_type=Organization)
if dlg.exec(): if dlg.exec():
value['value'] = dlg.parse_form() value['value'] = dlg.parse_form()
else: else:
@@ -651,9 +657,13 @@ class PydSubmission(BaseModel, extra='allow'):
logger.debug(f"Setting {key} to {value}") logger.debug(f"Setting {key} to {value}")
match key: match key:
case "reagents": case "reagents":
if code == 1:
instance.submission_reagent_associations = []
logger.debug(f"Looking through {self.reagents}")
for reagent in self.reagents: for reagent in self.reagents:
reagent, assoc = reagent.toSQL(submission=instance) reagent, assoc = reagent.toSQL(submission=instance)
if assoc is not None and assoc not in instance.submission_reagent_associations: logger.debug(f"Association: {assoc}")
if assoc is not None:# and assoc not in instance.submission_reagent_associations:
instance.submission_reagent_associations.append(assoc) instance.submission_reagent_associations.append(assoc)
# instance.reagents.append(reagent) # instance.reagents.append(reagent)
case "samples": case "samples":
@@ -666,13 +676,13 @@ class PydSubmission(BaseModel, extra='allow'):
case "equipment": case "equipment":
logger.debug(f"Equipment: {pformat(self.equipment)}") logger.debug(f"Equipment: {pformat(self.equipment)}")
try: try:
if equip == None: if equip is None:
continue continue
except UnboundLocalError: except UnboundLocalError:
continue continue
for equip in self.equipment: for equip in self.equipment:
equip, association = equip.toSQL(submission=instance) equip, association = equip.toSQL(submission=instance)
if association != None: if association is not None:
association.save() association.save()
logger.debug( logger.debug(
f"Equipment association SQL object to be added to submission: {association.__dict__}") f"Equipment association SQL object to be added to submission: {association.__dict__}")
@@ -719,7 +729,7 @@ class PydSubmission(BaseModel, extra='allow'):
# We need to make sure there's a proper rsl plate number # We need to make sure there's a proper rsl plate number
logger.debug(f"We've got a total cost of {instance.run_cost}") logger.debug(f"We've got a total cost of {instance.run_cost}")
try: try:
logger.debug(f"Constructed instance: {instance.to_string()}") logger.debug(f"Constructed instance: {instance}")
except AttributeError as e: except AttributeError as e:
logger.debug(f"Something went wrong constructing instance {self.rsl_plate_num}: {e}") logger.debug(f"Something went wrong constructing instance {self.rsl_plate_num}: {e}")
logger.debug(f"Constructed submissions message: {msg}") logger.debug(f"Constructed submissions message: {msg}")

100
src/submissions/frontend/widgets/submission_widget.py
View File

@@ -263,45 +263,45 @@ class SubmissionFormWidget(QWidget):
self.app.report.add_result(report) self.app.report.add_result(report)
self.app.result_reporter() self.app.result_reporter()
def kit_integrity_completion_function(self, extraction_kit:str|None=None): # def kit_integrity_completion_function(self, extraction_kit:str|None=None):
""" # """
Compare kit contents to parsed contents and creates widgets. # Compare kit contents to parsed contents and creates widgets.
#
Args: # Args:
obj (QMainWindow): The original app window # obj (QMainWindow): The original app window
#
Returns: # Returns:
Tuple[QMainWindow, dict]: Collection of new main app window and result dict # Tuple[QMainWindow, dict]: Collection of new main app window and result dict
""" # """
report = Report() # report = Report()
missing_reagents = [] # missing_reagents = []
# logger.debug(inspect.currentframe().f_back.f_code.co_name) # # logger.debug(inspect.currentframe().f_back.f_code.co_name)
# find the widget that contains kit info # # find the widget that contains kit info
if extraction_kit is None: # if extraction_kit is None:
kit_widget = self.find_widgets(object_name="extraction_kit")[0].input # kit_widget = self.find_widgets(object_name="extraction_kit")[0].input
logger.debug(f"Kit selector: {kit_widget}") # logger.debug(f"Kit selector: {kit_widget}")
# get current kit being used # # get current kit being used
self.ext_kit = kit_widget.currentText() # self.ext_kit = kit_widget.currentText()
else: # else:
self.ext_kit = extraction_kit # self.ext_kit = extraction_kit
for reagent in self.reagents: # for reagent in self.reagents:
logger.debug(f"Creating widget for {reagent}") # logger.debug(f"Creating widget for {reagent}")
add_widget = self.ReagentFormWidget(parent=self, reagent=reagent, extraction_kit=self.ext_kit) # add_widget = self.ReagentFormWidget(parent=self, reagent=reagent, extraction_kit=self.ext_kit)
# self.form.layout().addWidget(add_widget) # # self.form.layout().addWidget(add_widget)
self.layout.addWidget(add_widget) # self.layout.addWidget(add_widget)
if reagent.missing: # if reagent.missing:
missing_reagents.append(reagent) # missing_reagents.append(reagent)
logger.debug(f"Checking integrity of {self.ext_kit}") # logger.debug(f"Checking integrity of {self.ext_kit}")
# TODO: put check_kit_integrity here instead of what's here? # # TODO: put check_kit_integrity here instead of what's here?
# see if there are any missing reagents # # see if there are any missing reagents
if len(missing_reagents) > 0: # if len(missing_reagents) > 0:
result = Result(msg=f"""The submission you are importing is missing some reagents expected by the kit.\n\n # result = Result(msg=f"""The submission you are importing is missing some reagents expected by the kit.\n\n
It looks like you are missing: {[item.type.upper() for item in missing_reagents]}\n\n # It looks like you are missing: {[item.type.upper() for item in missing_reagents]}\n\n
Alternatively, you may have set the wrong extraction kit.\n\nThe program will populate lists using existing reagents. # Alternatively, you may have set the wrong extraction kit.\n\nThe program will populate lists using existing reagents.
\n\nPlease make sure you check the lots carefully!""".replace(" ", ""), status="Warning") # \n\nPlease make sure you check the lots carefully!""".replace(" ", ""), status="Warning")
report.add_result(result) # report.add_result(result)
self.report.add_result(report) # self.report.add_result(report)
logger.debug(f"Outgoing report: {self.report.results}") # logger.debug(f"Outgoing report: {self.report.results}")
def clear_form(self): def clear_form(self):
""" """
@@ -374,17 +374,12 @@ class SubmissionFormWidget(QWidget):
return return
case _: case _:
pass pass
# assert base_submission.reagents != [] # NOTE: add reagents to submission object
# add reagents to submission object
for reagent in base_submission.reagents: for reagent in base_submission.reagents:
# logger.debug(f"Updating: {reagent} with {reagent.lot}") # logger.debug(f"Updating: {reagent} with {reagent.lot}")
reagent.update_last_used(kit=base_submission.extraction_kit) reagent.update_last_used(kit=base_submission.extraction_kit)
# logger.debug(f"Here is the final submission: {pformat(base_submission.__dict__)}") # logger.debug(f"Final reagents: {pformat(base_submission.reagents)}")
# logger.debug(f"Parsed reagents: {pformat(base_submission.reagents)}") # sys.exit("Programmed stop submission_widget.py, line 381")
# logger.debug(f"Sending submission: {base_submission.rsl_plate_num} to database.")
# logger.debug(f"Samples from pyd: {pformat(self.pyd.samples)}")
# logger.debug(f"Samples SQL: {pformat([item.__dict__ for item in base_submission.samples])}")
# logger.debug(f"")
base_submission.save() base_submission.save()
# update summary sheet # update summary sheet
self.app.table_widget.sub_wid.setData() self.app.table_widget.sub_wid.setData()
@@ -414,12 +409,12 @@ class SubmissionFormWidget(QWidget):
except AttributeError: except AttributeError:
logger.error(f"No csv file found in the submission at this point.") logger.error(f"No csv file found in the submission at this point.")
def parse_form(self) -> PydSubmission: def parse_form(self) -> Report:
""" """
Transforms form info into PydSubmission Transforms form info into PydSubmission
Returns: Returns:
PydSubmission: Pydantic submission object Report: Report on status of parse.
""" """
report = Report() report = Report()
logger.debug(f"Hello from form parser!") logger.debug(f"Hello from form parser!")
@@ -430,15 +425,16 @@ class SubmissionFormWidget(QWidget):
match widget: match widget:
case self.ReagentFormWidget(): case self.ReagentFormWidget():
reagent, _ = widget.parse_form() reagent, _ = widget.parse_form()
if reagent != None: if reagent is not None:
reagents.append(reagent) reagents.append(reagent)
case self.InfoItem(): case self.InfoItem():
field, value = widget.parse_form() field, value = widget.parse_form()
if field != None: if field is not None:
info[field] = value info[field] = value
logger.debug(f"Info: {pformat(info)}") logger.debug(f"Info: {pformat(info)}")
logger.debug(f"Reagents: {pformat(reagents)}") logger.debug(f"Reagents going into pyd: {pformat(reagents)}")
self.pyd.reagents = reagents self.pyd.reagents = reagents
# logger.debug(f"Attrs not in info: {[k for k, v in self.__dict__.items() if k not in info.keys()]}") # logger.debug(f"Attrs not in info: {[k for k, v in self.__dict__.items() if k not in info.keys()]}")
for item in self.recover: for item in self.recover:
logger.debug(f"Attempting to recover: {item}") logger.debug(f"Attempting to recover: {item}")

5
src/submissions/tools.py
View File

@@ -238,9 +238,12 @@ class Settings(BaseSettings, extra="allow"):
def __init__(self, *args, **kwargs): def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs) super().__init__(*args, **kwargs)
# self.set_from_db(db_path=kwargs['database_path']) self.set_from_db(db_path=kwargs['database_path'])
def set_from_db(self, db_path:Path): def set_from_db(self, db_path:Path):
if 'pytest' in sys.modules:
config_items = dict(power_users=['lwark', 'styson', 'ruwang'])
else:
session = Session(create_engine(f"sqlite:///{db_path}")) session = Session(create_engine(f"sqlite:///{db_path}"))
config_items = session.execute(text("SELECT * FROM _configitem")).all() config_items = session.execute(text("SELECT * FROM _configitem")).all()
session.close() session.close()