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Post code clean-up, before attempt to upgrade controls to FigureWidgets

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lwark
2024-10-21 08:17:43 -05:00
parent 495d1a5a7f
commit 1f83b61c81
29 changed files with 441 additions and 1089 deletions
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2
src/submissions/backend/db/models/__init__.py
View File

@@ -96,7 +96,7 @@ class BaseClass(Base):
output = {} output = {}
for k, v in dicto.items(): for k, v in dicto.items():
if len(args) > 0 and k not in args: if len(args) > 0 and k not in args:
# logger.debug(f"Don't want {k}") # logger.debug(f"{k} not selected as being of interest.")
continue continue
else: else:
output[k] = v output[k] = v

100
src/submissions/backend/db/models/controls.py
View File

@@ -3,14 +3,12 @@ All control related models.
""" """
from __future__ import annotations from __future__ import annotations
from pprint import pformat from pprint import pformat
from PyQt6.QtWidgets import QWidget, QCheckBox, QLabel from PyQt6.QtWidgets import QWidget, QCheckBox, QLabel
from pandas import DataFrame from pandas import DataFrame
from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, case, FLOAT from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, case, FLOAT
from sqlalchemy.orm import relationship, Query, validates from sqlalchemy.orm import relationship, Query, validates
import logging, re import logging, re
from operator import itemgetter from operator import itemgetter
from . import BaseClass from . import BaseClass
from tools import setup_lookup, report_result, Result, Report, Settings, get_unique_values_in_df_column, super_splitter from tools import setup_lookup, report_result, Result, Report, Settings, get_unique_values_in_df_column, super_splitter
from datetime import date, datetime, timedelta from datetime import date, datetime, timedelta
@@ -73,7 +71,6 @@ class ControlType(BaseClass):
if not self.instances: if not self.instances:
return return
jsoner = getattr(self.instances[0], mode) jsoner = getattr(self.instances[0], mode)
# logger.debug(f"JSON retrieved: {jsoner.keys()}")
try: try:
# NOTE: Pick genera (all should have same subtypes) # NOTE: Pick genera (all should have same subtypes)
genera = list(jsoner.keys())[0] genera = list(jsoner.keys())[0]
@@ -81,10 +78,15 @@ class ControlType(BaseClass):
return [] return []
# NOTE: remove items that don't have relevant data # NOTE: remove items that don't have relevant data
subtypes = [item for item in jsoner[genera] if "_hashes" not in item and "_ratio" not in item] subtypes = [item for item in jsoner[genera] if "_hashes" not in item and "_ratio" not in item]
# logger.debug(f"subtypes out: {pformat(subtypes)}")
return subtypes return subtypes
def get_instance_class(self): def get_instance_class(self) -> Control:
"""
Retrieves the Control class associated with this controltype
Returns:
Control: Associated Control class
"""
return Control.find_polymorphic_subclass(polymorphic_identity=self.name) return Control.find_polymorphic_subclass(polymorphic_identity=self.name)
@classmethod @classmethod
@@ -93,7 +95,7 @@ class ControlType(BaseClass):
Gets list of Control types if they have targets Gets list of Control types if they have targets
Returns: Returns:
List[ControlType]: Control types that have targets Generator[str, None, None]: Control types that have targets
""" """
ct = cls.query(name=control_type).targets ct = cls.query(name=control_type).targets
return (item for item in ct.keys() if ct[item]) return (item for item in ct.keys() if ct[item])
@@ -106,7 +108,6 @@ class ControlType(BaseClass):
Returns: Returns:
Pattern: Constructed pattern Pattern: Constructed pattern
""" """
# strings = list(set([item.name.split("-")[0] for item in cls.get_positive_control_types()]))
strings = list(set([super_splitter(item, "-", 0) for item in cls.get_positive_control_types(control_type)])) strings = list(set([super_splitter(item, "-", 0) for item in cls.get_positive_control_types(control_type)]))
return re.compile(rf"(^{'|^'.join(strings)})-.*", flags=re.IGNORECASE) return re.compile(rf"(^{'|^'.join(strings)})-.*", flags=re.IGNORECASE)
@@ -144,7 +145,7 @@ class Control(BaseClass):
@classmethod @classmethod
def find_polymorphic_subclass(cls, polymorphic_identity: str | ControlType | None = None, def find_polymorphic_subclass(cls, polymorphic_identity: str | ControlType | None = None,
attrs: dict | None = None): attrs: dict | None = None) -> Control:
""" """
Find subclass based on polymorphic identity or relevant attributes. Find subclass based on polymorphic identity or relevant attributes.
@@ -153,7 +154,7 @@ class Control(BaseClass):
attrs (str | SubmissionType | None, optional): Attributes of the relevant class. Defaults to None. attrs (str | SubmissionType | None, optional): Attributes of the relevant class. Defaults to None.
Returns: Returns:
_type_: Subclass of interest. Control: Subclass of interest.
""" """
if isinstance(polymorphic_identity, dict): if isinstance(polymorphic_identity, dict):
# logger.debug(f"Controlling for dict value") # logger.debug(f"Controlling for dict value")
@@ -184,6 +185,7 @@ class Control(BaseClass):
@classmethod @classmethod
def make_parent_buttons(cls, parent: QWidget) -> None: def make_parent_buttons(cls, parent: QWidget) -> None:
""" """
Super that will make buttons in a CustomFigure. Made to be overrided.
Args: Args:
parent (QWidget): chart holding widget to add buttons to. parent (QWidget): chart holding widget to add buttons to.
@@ -196,13 +198,11 @@ class Control(BaseClass):
@classmethod @classmethod
def make_chart(cls, parent, chart_settings: dict, ctx): def make_chart(cls, parent, chart_settings: dict, ctx):
""" """
Dummy operation to be overridden by child classes.
Args: Args:
chart_settings (dict): settings passed down from chart widget chart_settings (dict): settings passed down from chart widget
ctx (Settings): settings passed down from gui ctx (Settings): settings passed down from gui
Returns:
""" """
return None return None
@@ -220,7 +220,13 @@ class PCRControl(Control):
polymorphic_load="inline", polymorphic_load="inline",
inherit_condition=(id == Control.id)) inherit_condition=(id == Control.id))
def to_sub_dict(self): def to_sub_dict(self) -> dict:
"""
Creates dictionary of fields for this object
Returns:
dict: Output dict of name, ct, subtype, target, reagent_lot and submitted_date
"""
return dict(name=self.name, ct=self.ct, subtype=self.subtype, target=self.target, reagent_lot=self.reagent_lot, return dict(name=self.name, ct=self.ct, subtype=self.subtype, target=self.target, reagent_lot=self.reagent_lot,
submitted_date=self.submitted_date.date()) submitted_date=self.submitted_date.date())
@@ -237,15 +243,16 @@ class PCRControl(Control):
Lookup control objects in the database based on a number of parameters. Lookup control objects in the database based on a number of parameters.
Args: Args:
sub_type (models.ControlType | str | None, optional): Control archetype. Defaults to None. sub_type (str | None, optional): Control archetype. Defaults to None.
start_date (date | str | int | None, optional): Beginning date to search by. Defaults to 2023-01-01 if end_date not None. start_date (date | str | int | None, optional): Beginning date to search by. Defaults to 2023-01-01 if end_date not None.
end_date (date | str | int | None, optional): End date to search by. Defaults to today if start_date not None. end_date (date | str | int | None, optional): End date to search by. Defaults to today if start_date not None.
control_name (str | None, optional): Name of control. Defaults to None. control_name (str | None, optional): Name of control. Defaults to None.
limit (int, optional): Maximum number of results to return (0 = all). Defaults to 0. limit (int, optional): Maximum number of results to return (0 = all). Defaults to 0.
Returns: Returns:
models.Control|List[models.Control]: Control object of interest. PCRControl|List[PCRControl]: Control object of interest.
""" """
from backend.db import SubmissionType
query: Query = cls.__database_session__.query(cls) query: Query = cls.__database_session__.query(cls)
# NOTE: by date range # NOTE: by date range
if start_date is not None and end_date is None: if start_date is not None and end_date is None:
@@ -282,7 +289,12 @@ class PCRControl(Control):
match sub_type: match sub_type:
case str(): case str():
from backend import BasicSubmission, SubmissionType from backend import BasicSubmission, SubmissionType
# logger.debug(f"Lookup controls by SubmissionType str: {sub_type}")
query = query.join(BasicSubmission).join(SubmissionType).filter(SubmissionType.name == sub_type) query = query.join(BasicSubmission).join(SubmissionType).filter(SubmissionType.name == sub_type)
case SubmissionType():
from backend import BasicSubmission
# logger.debug(f"Lookup controls by SubmissionType: {sub_type}")
query = query.join(BasicSubmission).filter(BasicSubmission.submission_type_name==sub_type.name)
case _: case _:
pass pass
match control_name: match control_name:
@@ -295,7 +307,18 @@ class PCRControl(Control):
return cls.execute_query(query=query, limit=limit) return cls.execute_query(query=query, limit=limit)
@classmethod @classmethod
def make_chart(cls, parent, chart_settings: dict, ctx): def make_chart(cls, parent, chart_settings: dict, ctx: Settings) -> Tuple[Report, "PCRFigure"]:
"""
Creates a PCRFigure. Overrides parent
Args:
parent (__type__): Widget to contain the chart.
chart_settings (dict): settings passed down from chart widget
ctx (Settings): settings passed down from gui. Not used here.
Returns:
Tuple[Report, "PCRFigure"]: Report of status and resulting figure.
"""
from frontend.visualizations.pcr_charts import PCRFigure from frontend.visualizations.pcr_charts import PCRFigure
parent.mode_typer.clear() parent.mode_typer.clear()
parent.mode_typer.setEnabled(False) parent.mode_typer.setEnabled(False)
@@ -308,7 +331,7 @@ class PCRControl(Control):
df = df[df.ct > 0.0] df = df[df.ct > 0.0]
except AttributeError: except AttributeError:
df = df df = df
fig = PCRFigure(df=df, modes=None) fig = PCRFigure(df=df, modes=[])
return report, fig return report, fig
@@ -324,16 +347,26 @@ class IridaControl(Control):
sample = relationship("BacterialCultureSample", back_populates="control") #: This control's submission sample sample = relationship("BacterialCultureSample", back_populates="control") #: This control's submission sample
sample_id = Column(INTEGER, sample_id = Column(INTEGER,
ForeignKey("_basicsample.id", ondelete="SET NULL", name="cont_BCS_id")) #: sample id key ForeignKey("_basicsample.id", ondelete="SET NULL", name="cont_BCS_id")) #: sample id key
# submission_id = Column(INTEGER, ForeignKey("_basicsubmission.id")) #: parent submission id
# submission = relationship("BacterialCulture", back_populates="controls",
# foreign_keys=[submission_id]) #: parent submission
__mapper_args__ = dict(polymorphic_identity="Irida Control", __mapper_args__ = dict(polymorphic_identity="Irida Control",
polymorphic_load="inline", polymorphic_load="inline",
inherit_condition=(id == Control.id)) inherit_condition=(id == Control.id))
@validates("sub_type") @validates("sub_type")
def enforce_subtype_literals(self, key: str, value: str): def enforce_subtype_literals(self, key: str, value: str) -> str:
"""
Validates sub_type field with acceptable values
Args:
key (str): Field name
value (str): Field Value
Raises:
KeyError: Raised if value is not in the acceptable list.
Returns:
str: Validated string.
"""
acceptables = ['ATCC49226', 'ATCC49619', 'EN-NOS', "EN-SSTI", "MCS-NOS", "MCS-SSTI", "SN-NOS", "SN-SSTI"] acceptables = ['ATCC49226', 'ATCC49619', 'EN-NOS', "EN-SSTI", "MCS-NOS", "MCS-SSTI", "SN-NOS", "SN-SSTI"]
if value.upper() not in acceptables: if value.upper() not in acceptables:
raise KeyError(f"Sub-type must be in {acceptables}") raise KeyError(f"Sub-type must be in {acceptables}")
@@ -346,7 +379,6 @@ class IridaControl(Control):
Returns: Returns:
dict: output dictionary containing: Name, Type, Targets, Top Kraken results dict: output dictionary containing: Name, Type, Targets, Top Kraken results
""" """
# logger.debug("loading json string into dict")
try: try:
kraken = self.kraken kraken = self.kraken
except TypeError: except TypeError:
@@ -405,8 +437,6 @@ class IridaControl(Control):
k.strip("*") not in self.controltype.targets[control_sub_type]) k.strip("*") not in self.controltype.targets[control_sub_type])
on_tar['Off-target'] = {f"{mode}_ratio": off_tar} on_tar['Off-target'] = {f"{mode}_ratio": off_tar}
data = on_tar data = on_tar
# logger.debug(pformat(data))
# logger.debug(f"Length of data: {len(data)}")
# logger.debug("dict keys are genera of bacteria, e.g. 'Streptococcus'") # logger.debug("dict keys are genera of bacteria, e.g. 'Streptococcus'")
for genus in data: for genus in data:
_dict = dict( _dict = dict(
@@ -416,7 +446,6 @@ class IridaControl(Control):
target='Target' if genus.strip("*") in self.controltype.targets[control_sub_type] else "Off-target" target='Target' if genus.strip("*") in self.controltype.targets[control_sub_type] else "Off-target"
) )
# logger.debug("get Target or Off-target of genus") # logger.debug("get Target or Off-target of genus")
# logger.debug("set 'contains_hashes', etc for genus")
for key in data[genus]: for key in data[genus]:
_dict[key] = data[genus][key] _dict[key] = data[genus][key]
yield _dict yield _dict
@@ -462,12 +491,7 @@ class IridaControl(Control):
query: Query = cls.__database_session__.query(cls) query: Query = cls.__database_session__.query(cls)
# NOTE: by control type # NOTE: by control type
match sub_type: match sub_type:
# case ControlType():
# # logger.debug(f"Looking up control by control type: {sub_type}")
# query = query.filter(cls.controltype == sub_type)
case str(): case str():
# logger.debug(f"Looking up control by control type: {sub_type}")
# query = query.join(ControlType).filter(ControlType.name == sub_type)
query = query.filter(cls.sub_type == sub_type) query = query.filter(cls.sub_type == sub_type)
case _: case _:
pass pass
@@ -519,8 +543,6 @@ class IridaControl(Control):
Args: Args:
parent (QWidget): chart holding widget to add buttons to. parent (QWidget): chart holding widget to add buttons to.
Returns:
""" """
super().make_parent_buttons(parent=parent) super().make_parent_buttons(parent=parent)
rows = parent.layout.rowCount() rows = parent.layout.rowCount()
@@ -536,6 +558,17 @@ class IridaControl(Control):
@classmethod @classmethod
@report_result @report_result
def make_chart(cls, chart_settings: dict, parent, ctx) -> Tuple[Report, "IridaFigure" | None]: def make_chart(cls, chart_settings: dict, parent, ctx) -> Tuple[Report, "IridaFigure" | None]:
"""
Creates a IridaFigure. Overrides parent
Args:
parent (__type__): Widget to contain the chart.
chart_settings (dict): settings passed down from chart widget
ctx (Settings): settings passed down from gui.
Returns:
Tuple[Report, "IridaFigure"]: Report of status and resulting figure.
"""
from frontend.visualizations import IridaFigure from frontend.visualizations import IridaFigure
try: try:
checker = parent.findChild(QCheckBox, name="irida_check") checker = parent.findChild(QCheckBox, name="irida_check")
@@ -574,8 +607,6 @@ class IridaControl(Control):
# NOTE: send dataframe to chart maker # NOTE: send dataframe to chart maker
df, modes = cls.prep_df(ctx=ctx, df=df) df, modes = cls.prep_df(ctx=ctx, df=df)
# logger.debug(f"prepped df: \n {df}") # logger.debug(f"prepped df: \n {df}")
# assert modes
# logger.debug(f"modes: {modes}")
fig = IridaFigure(df=df, ytitle=title, modes=modes, parent=parent, fig = IridaFigure(df=df, ytitle=title, modes=modes, parent=parent,
months=chart_settings['months']) months=chart_settings['months'])
return report, fig return report, fig
@@ -604,7 +635,6 @@ class IridaControl(Control):
else: else:
safe.append(column) safe.append(column)
if "percent" in column: if "percent" in column:
# count_col = [item for item in df.columns if "count" in item][0]
try: try:
count_col = next(item for item in df.columns if "count" in item) count_col = next(item for item in df.columns if "count" in item)
except StopIteration: except StopIteration:

214
src/submissions/backend/db/models/kits.py
View File

@@ -2,7 +2,6 @@
All kit and reagent related models All kit and reagent related models
""" """
from __future__ import annotations from __future__ import annotations
import datetime import datetime
import json import json
from pprint import pformat from pprint import pformat
@@ -152,7 +151,7 @@ class KitType(BaseClass):
submission_type (str | Submissiontype | None, optional): Submission type to narrow results. Defaults to None. submission_type (str | Submissiontype | None, optional): Submission type to narrow results. Defaults to None.
Returns: Returns:
List[ReagentRole]: List of reagents linked to this kit. Generator[ReagentRole, None, None]: List of reagents linked to this kit.
""" """
match submission_type: match submission_type:
case SubmissionType(): case SubmissionType():
@@ -173,7 +172,7 @@ class KitType(BaseClass):
return (item.reagent_role for item in relevant_associations) return (item.reagent_role for item in relevant_associations)
# TODO: Move to BasicSubmission? # TODO: Move to BasicSubmission?
def construct_xl_map_for_use(self, submission_type: str | SubmissionType) -> Generator[(str, str)]: def construct_xl_map_for_use(self, submission_type: str | SubmissionType) -> Generator[(str, str), None, None]:
""" """
Creates map of locations in Excel workbook for a SubmissionType Creates map of locations in Excel workbook for a SubmissionType
@@ -181,9 +180,8 @@ class KitType(BaseClass):
submission_type (str | SubmissionType): Submissiontype.name submission_type (str | SubmissionType): Submissiontype.name
Returns: Returns:
dict: Dictionary containing information locations. Generator[(str, str), None, None]: Tuple containing information locations.
""" """
# info_map = {}
# NOTE: Account for submission_type variable type. # NOTE: Account for submission_type variable type.
match submission_type: match submission_type:
case str(): case str():
@@ -221,7 +219,7 @@ class KitType(BaseClass):
limit (int, optional): Maximum number of results to return (0 = all). Defaults to 0. limit (int, optional): Maximum number of results to return (0 = all). Defaults to 0.
Returns: Returns:
models.KitType|List[models.KitType]: KitType(s) of interest. KitType|List[KitType]: KitType(s) of interest.
""" """
query: Query = cls.__database_session__.query(cls) query: Query = cls.__database_session__.query(cls)
match used_for: match used_for:
@@ -257,7 +255,16 @@ class KitType(BaseClass):
def save(self): def save(self):
super().save() super().save()
def to_export_dict(self, submission_type: SubmissionType): def to_export_dict(self, submission_type: SubmissionType) -> dict:
"""
Creates dictionary for exporting to yml used in new SubmissionType Construction
Args:
submission_type (SubmissionType): SubmissionType of interest.
Returns:
dict: Dictionary containing relevant info for SubmissionType construction
"""
base_dict = dict(name=self.name) base_dict = dict(name=self.name)
base_dict['reagent roles'] = [] base_dict['reagent roles'] = []
base_dict['equipment roles'] = [] base_dict['equipment roles'] = []
@@ -382,7 +389,13 @@ class ReagentRole(BaseClass):
from backend.validators.pydant import PydReagent from backend.validators.pydant import PydReagent
return PydReagent(lot=None, role=self.name, name=self.name, expiry=date.today()) return PydReagent(lot=None, role=self.name, name=self.name, expiry=date.today())
def to_export_dict(self): def to_export_dict(self) -> dict:
"""
Creates dictionary for exporting to yml used in new SubmissionType Construction
Returns:
dict: Dictionary containing relevant info for SubmissionType construction
"""
return dict(role=self.name, extension_of_life=self.eol_ext.days) return dict(role=self.name, extension_of_life=self.eol_ext.days)
@check_authorization @check_authorization
@@ -664,7 +677,7 @@ class SubmissionType(BaseClass):
"SubmissionTypeTipRoleAssociation", "SubmissionTypeTipRoleAssociation",
back_populates="submission_type", back_populates="submission_type",
cascade="all, delete-orphan" cascade="all, delete-orphan"
) ) #: Association of tiproles
def __repr__(self) -> str: def __repr__(self) -> str:
""" """
@@ -738,12 +751,12 @@ class SubmissionType(BaseClass):
""" """
return self.sample_map return self.sample_map
def construct_equipment_map(self) -> Generator[str, dict]: def construct_equipment_map(self) -> Generator[(str, dict), None, None]:
""" """
Constructs map of equipment to excel cells. Constructs map of equipment to excel cells.
Returns: Returns:
dict: Map equipment locations in excel sheet Generator[(str, dict), None, None]: Map equipment locations in excel sheet
""" """
# logger.debug("Iterating through equipment roles") # logger.debug("Iterating through equipment roles")
for item in self.submissiontype_equipmentrole_associations: for item in self.submissiontype_equipmentrole_associations:
@@ -752,12 +765,12 @@ class SubmissionType(BaseClass):
emap = {} emap = {}
yield item.equipment_role.name, emap yield item.equipment_role.name, emap
def construct_tips_map(self) -> Generator[str, dict]: def construct_tips_map(self) -> Generator[(str, dict), None, None]:
""" """
Constructs map of tips to excel cells. Constructs map of tips to excel cells.
Returns: Returns:
dict: Tip locations in the excel sheet. Generator[(str, dict), None, None]: Tip locations in the excel sheet.
""" """
for item in self.submissiontype_tiprole_associations: for item in self.submissiontype_tiprole_associations:
tmap = item.uses tmap = item.uses
@@ -770,7 +783,7 @@ class SubmissionType(BaseClass):
Returns PydEquipmentRole of all equipment associated with this SubmissionType Returns PydEquipmentRole of all equipment associated with this SubmissionType
Returns: Returns:
List[PydEquipmentRole]: List of equipment roles Generator['PydEquipmentRole', None, None]: List of equipment roles
""" """
return (item.to_pydantic(submission_type=self, extraction_kit=extraction_kit) for item in self.equipment) return (item.to_pydantic(submission_type=self, extraction_kit=extraction_kit) for item in self.equipment)
@@ -846,6 +859,12 @@ class SubmissionType(BaseClass):
return cls.execute_query(query=query, limit=limit) return cls.execute_query(query=query, limit=limit)
def to_export_dict(self): def to_export_dict(self):
"""
Creates dictionary for exporting to yml used in new SubmissionType Construction
Returns:
dict: Dictionary containing relevant info for SubmissionType construction
"""
base_dict = dict(name=self.name) base_dict = dict(name=self.name)
base_dict['info'] = self.construct_info_map(mode='export') base_dict['info'] = self.construct_info_map(mode='export')
base_dict['defaults'] = self.defaults base_dict['defaults'] = self.defaults
@@ -862,7 +881,20 @@ class SubmissionType(BaseClass):
@classmethod @classmethod
@check_authorization @check_authorization
def import_from_json(cls, filepath: Path | str): def import_from_json(cls, filepath: Path | str) -> SubmissionType:
"""
Creates a new SubmissionType from a yml file
Args:
filepath (Path | str): Input yml file.
Raises:
Exception: Raised if filetype is not a yml or json
Returns:
SubmissionType: Created SubmissionType
"""
full = True
yaml.add_constructor("!regex", yaml_regex_creator) yaml.add_constructor("!regex", yaml_regex_creator)
if isinstance(filepath, str): if isinstance(filepath, str):
filepath = Path(filepath) filepath = Path(filepath)
@@ -874,70 +906,76 @@ class SubmissionType(BaseClass):
else: else:
raise Exception(f"Filetype {filepath.suffix} not supported.") raise Exception(f"Filetype {filepath.suffix} not supported.")
logger.debug(pformat(import_dict)) logger.debug(pformat(import_dict))
submission_type = cls.query(name=import_dict['name']) try:
if submission_type: submission_type = cls.query(name=import_dict['name'])
return submission_type except KeyError:
submission_type = cls() logger.error(f"Submission type has no name")
submission_type.name = import_dict['name'] submission_type = None
submission_type.info_map = import_dict['info'] full = False
submission_type.sample_map = import_dict['samples'] if full:
submission_type.defaults = import_dict['defaults'] if submission_type:
for kit in import_dict['kits']: return submission_type
new_kit = KitType.query(name=kit['kit_type']['name']) submission_type = cls()
if not new_kit: submission_type.name = import_dict['name']
new_kit = KitType(name=kit['kit_type']['name']) submission_type.info_map = import_dict['info']
for role in kit['kit_type']['reagent roles']: submission_type.sample_map = import_dict['samples']
new_role = ReagentRole.query(name=role['role']) submission_type.defaults = import_dict['defaults']
if new_role: for kit in import_dict['kits']:
check = input(f"Found existing role: {new_role.name}. Use this? [Y/n]: ") new_kit = KitType.query(name=kit['kit_type']['name'])
if check.lower() == "n": if not new_kit:
new_role = None new_kit = KitType(name=kit['kit_type']['name'])
else: for role in kit['kit_type']['reagent roles']:
pass new_role = ReagentRole.query(name=role['role'])
if not new_role: if new_role:
eol = datetime.timedelta(role['extension_of_life']) check = input(f"Found existing role: {new_role.name}. Use this? [Y/n]: ")
new_role = ReagentRole(name=role['role'], eol_ext=eol) if check.lower() == "n":
uses = dict(expiry=role['expiry'], lot=role['lot'], name=role['name'], sheet=role['sheet']) new_role = None
ktrr_assoc = KitTypeReagentRoleAssociation(kit_type=new_kit, reagent_role=new_role, uses=uses) else:
ktrr_assoc.submission_type = submission_type pass
ktrr_assoc.required = role['required'] if not new_role:
ktst_assoc = SubmissionTypeKitTypeAssociation( eol = datetime.timedelta(role['extension_of_life'])
kit_type=new_kit, new_role = ReagentRole(name=role['role'], eol_ext=eol)
submission_type=submission_type, uses = dict(expiry=role['expiry'], lot=role['lot'], name=role['name'], sheet=role['sheet'])
mutable_cost_sample=kit['mutable_cost_sample'], ktrr_assoc = KitTypeReagentRoleAssociation(kit_type=new_kit, reagent_role=new_role, uses=uses)
mutable_cost_column=kit['mutable_cost_column'], ktrr_assoc.submission_type = submission_type
constant_cost=kit['constant_cost'] ktrr_assoc.required = role['required']
) ktst_assoc = SubmissionTypeKitTypeAssociation(
for role in kit['kit_type']['equipment roles']: kit_type=new_kit,
new_role = EquipmentRole.query(name=role['role']) submission_type=submission_type,
if new_role: mutable_cost_sample=kit['mutable_cost_sample'],
check = input(f"Found existing role: {new_role.name}. Use this? [Y/n]: ") mutable_cost_column=kit['mutable_cost_column'],
if check.lower() == "n": constant_cost=kit['constant_cost']
new_role = None )
else: for role in kit['kit_type']['equipment roles']:
pass new_role = EquipmentRole.query(name=role['role'])
if not new_role: if new_role:
new_role = EquipmentRole(name=role['role']) check = input(f"Found existing role: {new_role.name}. Use this? [Y/n]: ")
for equipment in Equipment.assign_equipment(equipment_role=new_role): if check.lower() == "n":
new_role.instances.append(equipment) new_role = None
ster_assoc = SubmissionTypeEquipmentRoleAssociation(submission_type=submission_type, else:
equipment_role=new_role) pass
try: if not new_role:
uses = dict(name=role['name'], process=role['process'], sheet=role['sheet'], static=role['static']) new_role = EquipmentRole(name=role['role'])
except KeyError: for equipment in Equipment.assign_equipment(equipment_role=new_role):
uses = None new_role.instances.append(equipment)
ster_assoc.uses = uses ster_assoc = SubmissionTypeEquipmentRoleAssociation(submission_type=submission_type,
for process in role['processes']: equipment_role=new_role)
new_process = Process.query(name=process) try:
if not new_process: uses = dict(name=role['name'], process=role['process'], sheet=role['sheet'], static=role['static'])
new_process = Process(name=process) except KeyError:
new_process.submission_types.append(submission_type) uses = None
new_process.kit_types.append(new_kit) ster_assoc.uses = uses
new_process.equipment_roles.append(new_role) for process in role['processes']:
if 'orgs' in import_dict.keys(): new_process = Process.query(name=process)
logger.info("Found Organizations to be imported.") if not new_process:
Organization.import_from_yml(filepath=filepath) new_process = Process(name=process)
return submission_type new_process.submission_types.append(submission_type)
new_process.kit_types.append(new_kit)
new_process.equipment_roles.append(new_role)
if 'orgs' in import_dict.keys():
logger.info("Found Organizations to be imported.")
Organization.import_from_yml(filepath=filepath)
return submission_type
class SubmissionTypeKitTypeAssociation(BaseClass): class SubmissionTypeKitTypeAssociation(BaseClass):
@@ -1574,9 +1612,6 @@ class EquipmentRole(BaseClass):
""" """
return dict(role=self.name, return dict(role=self.name,
processes=self.get_processes(submission_type=submission_type, extraction_kit=kit_type)) processes=self.get_processes(submission_type=submission_type, extraction_kit=kit_type))
# base_dict['role'] = self.name
# base_dict['processes'] = self.get_processes(submission_type=submission_type, extraction_kit=kit_type)
# return base_dict
class SubmissionEquipmentAssociation(BaseClass): class SubmissionEquipmentAssociation(BaseClass):
@@ -1598,7 +1633,7 @@ class SubmissionEquipmentAssociation(BaseClass):
equipment = relationship(Equipment, back_populates="equipment_submission_associations") #: associated equipment equipment = relationship(Equipment, back_populates="equipment_submission_associations") #: associated equipment
def __repr__(self): def __repr__(self) -> str:
return f"<SubmissionEquipmentAssociation({self.submission.rsl_plate_num} & {self.equipment.name})>" return f"<SubmissionEquipmentAssociation({self.submission.rsl_plate_num} & {self.equipment.name})>"
def __init__(self, submission, equipment, role: str = "None"): def __init__(self, submission, equipment, role: str = "None"):
@@ -1699,9 +1734,18 @@ class SubmissionTypeEquipmentRoleAssociation(BaseClass):
def save(self): def save(self):
super().save() super().save()
def to_export_dict(self, kit_type: KitType): def to_export_dict(self, extraction_kit: KitType) -> dict:
"""
Creates dictionary for exporting to yml used in new SubmissionType Construction
Args:
kit_type (KitType): KitType of interest.
Returns:
dict: Dictionary containing relevant info for SubmissionType construction
"""
base_dict = {k: v for k, v in self.equipment_role.to_export_dict(submission_type=self.submission_type, base_dict = {k: v for k, v in self.equipment_role.to_export_dict(submission_type=self.submission_type,
kit_type=kit_type).items()} kit_type=extraction_kit).items()}
base_dict['static'] = self.static base_dict['static'] = self.static
return base_dict return base_dict

7
src/submissions/backend/db/models/organizations.py
View File

@@ -2,7 +2,6 @@
All client organization related models. All client organization related models.
''' '''
from __future__ import annotations from __future__ import annotations
import json, yaml, logging import json, yaml, logging
from pathlib import Path from pathlib import Path
from pprint import pformat from pprint import pformat
@@ -118,8 +117,6 @@ class Organization(BaseClass):
cont.__setattr__(k, v) cont.__setattr__(k, v)
organ.contacts.append(cont) organ.contacts.append(cont)
organ.save() organ.save()
# logger.debug(pformat(organ.__dict__))
class Contact(BaseClass): class Contact(BaseClass):
@@ -136,10 +133,6 @@ class Contact(BaseClass):
submissions = relationship("BasicSubmission", back_populates="contact") #: submissions this contact has submitted submissions = relationship("BasicSubmission", back_populates="contact") #: submissions this contact has submitted
def __repr__(self) -> str: def __repr__(self) -> str:
"""
Returns:
str: Representation of this Contact
"""
return f"<Contact({self.name})>" return f"<Contact({self.name})>"
@classmethod @classmethod

299
src/submissions/backend/db/models/submissions.py
View File

@@ -2,7 +2,6 @@
Models for the main submission and sample types. Models for the main submission and sample types.
""" """
from __future__ import annotations from __future__ import annotations
import sys import sys
import types import types
from copy import deepcopy from copy import deepcopy
@@ -125,10 +124,6 @@ class BasicSubmission(BaseClass):
} }
def __repr__(self) -> str: def __repr__(self) -> str:
"""
Returns:
str: Representation of this BasicSubmission
"""
submission_type = self.submission_type or "Basic" submission_type = self.submission_type or "Basic"
return f"<{submission_type}Submission({self.rsl_plate_num})>" return f"<{submission_type}Submission({self.rsl_plate_num})>"
@@ -184,10 +179,8 @@ class BasicSubmission(BaseClass):
# NOTE: Fields not placed in ui form to be moved to pydantic # NOTE: Fields not placed in ui form to be moved to pydantic
form_recover=recover form_recover=recover
) )
# logger.debug(dicto['singles'])
# NOTE: Singles tells the query which fields to set limit to 1 # NOTE: Singles tells the query which fields to set limit to 1
dicto['singles'] = parent_defs['singles'] dicto['singles'] = parent_defs['singles']
# logger.debug(dicto['singles'])
# NOTE: Grab mode_sub_type specific info. # NOTE: Grab mode_sub_type specific info.
output = {} output = {}
for k, v in dicto.items(): for k, v in dicto.items():
@@ -233,7 +226,7 @@ class BasicSubmission(BaseClass):
sub_type (str | SubmissionType, Optional): Identity of the submission type to retrieve. Defaults to None. sub_type (str | SubmissionType, Optional): Identity of the submission type to retrieve. Defaults to None.
Returns: Returns:
SubmissionType: SubmissionType with name equal to this polymorphic identity SubmissionType: SubmissionType with name equal sub_type or this polymorphic identity if sub_type is None.
""" """
# logger.debug(f"Running search for {sub_type}") # logger.debug(f"Running search for {sub_type}")
if isinstance(sub_type, dict): if isinstance(sub_type, dict):
@@ -274,20 +267,6 @@ class BasicSubmission(BaseClass):
""" """
return cls.get_submission_type(submission_type).construct_sample_map() return cls.get_submission_type(submission_type).construct_sample_map()
@classmethod
def finalize_details(cls, input_dict: dict) -> dict:
"""
Make final adjustments to the details dictionary before display.
Args:
input_dict (dict): Incoming dictionary.
Returns:
dict: Final details dictionary.
"""
del input_dict['id']
return input_dict
def generate_associations(self, name: str, extra: str | None = None): def generate_associations(self, name: str, extra: str | None = None):
try: try:
field = self.__getattribute__(name) field = self.__getattribute__(name)
@@ -362,25 +341,10 @@ class BasicSubmission(BaseClass):
dict(role=k, name="Not Applicable", lot="NA", expiry=expiry, dict(role=k, name="Not Applicable", lot="NA", expiry=expiry,
missing=True)) missing=True))
# logger.debug(f"Running samples.") # logger.debug(f"Running samples.")
# samples = self.adjust_to_dict_samples(backup=backup)
samples = self.generate_associations(name="submission_sample_associations") samples = self.generate_associations(name="submission_sample_associations")
# logger.debug("Running equipment") # logger.debug("Running equipment")
equipment = self.generate_associations(name="submission_equipment_associations") equipment = self.generate_associations(name="submission_equipment_associations")
# try:
# equipment = [item.to_sub_dict() for item in self.submission_equipment_associations]
# if not equipment:
# equipment = None
# except Exception as e:
# logger.error(f"Error setting equipment: {e}")
# equipment = None
tips = self.generate_associations(name="submission_tips_associations") tips = self.generate_associations(name="submission_tips_associations")
# try:
# tips = [item.to_sub_dict() for item in self.submission_tips_associations]
# if not tips:
# tips = None
# except Exception as e:
# logger.error(f"Error setting tips: {e}")
# tips = None
cost_centre = self.cost_centre cost_centre = self.cost_centre
custom = self.custom custom = self.custom
else: else:
@@ -428,7 +392,6 @@ class BasicSubmission(BaseClass):
Returns: Returns:
int: Number of unique columns. int: Number of unique columns.
""" """
# logger.debug(f"Here's the samples: {self.samples}")
columns = set([assoc.column for assoc in self.submission_sample_associations]) columns = set([assoc.column for assoc in self.submission_sample_associations])
# logger.debug(f"Here are the columns for {self.rsl_plate_num}: {columns}") # logger.debug(f"Here are the columns for {self.rsl_plate_num}: {columns}")
return len(columns) return len(columns)
@@ -513,6 +476,7 @@ class BasicSubmission(BaseClass):
Convert all submissions to dataframe Convert all submissions to dataframe
Args: Args:
page_size (int, optional): Number of items to include in query result. Defaults to 250.
page (int, optional): Limits the number of submissions to a page size. Defaults to 1. page (int, optional): Limits the number of submissions to a page size. Defaults to 1.
chronologic (bool, optional): Sort submissions in chronologic order. Defaults to True. chronologic (bool, optional): Sort submissions in chronologic order. Defaults to True.
submission_type (str | None, optional): Filter by SubmissionType. Defaults to None. submission_type (str | None, optional): Filter by SubmissionType. Defaults to None.
@@ -537,11 +501,6 @@ class BasicSubmission(BaseClass):
'signed_by', 'artic_date', 'gel_barcode', 'gel_date', 'ngs_date', 'contact_phone', 'contact', 'signed_by', 'artic_date', 'gel_barcode', 'gel_date', 'ngs_date', 'contact_phone', 'contact',
'tips', 'gel_image_path', 'custom'] 'tips', 'gel_image_path', 'custom']
df = df.loc[:, ~df.columns.isin(exclude)] df = df.loc[:, ~df.columns.isin(exclude)]
# for item in excluded:
# try:
# df = df.drop(item, axis=1)
# except:
# logger.warning(f"Couldn't drop '{item}' column from submissionsheet df.")
if chronologic: if chronologic:
try: try:
df.sort_values(by="id", axis=0, inplace=True, ascending=False) df.sort_values(by="id", axis=0, inplace=True, ascending=False)
@@ -611,6 +570,7 @@ class BasicSubmission(BaseClass):
if value is not None: if value is not None:
existing.append(value) existing.append(value)
self.__setattr__(key, existing) self.__setattr__(key, existing)
# NOTE: Make sure this gets updated by telling SQLAlchemy it's been modified.
flag_modified(self, key) flag_modified(self, key)
return return
case _: case _:
@@ -645,7 +605,7 @@ class BasicSubmission(BaseClass):
for k, v in input_dict.items(): for k, v in input_dict.items():
try: try:
setattr(assoc, k, v) setattr(assoc, k, v)
# NOTE: for some reason I don't think assoc.__setattr__(k, v) doesn't work here. # NOTE: for some reason I don't think assoc.__setattr__(k, v) works here.
except AttributeError: except AttributeError:
logger.error(f"Can't set {k} to {v}") logger.error(f"Can't set {k} to {v}")
result = assoc.save() result = assoc.save()
@@ -703,7 +663,16 @@ class BasicSubmission(BaseClass):
return super().save() return super().save()
@classmethod @classmethod
def get_regex(cls, submission_type: SubmissionType | str | None = None): def get_regex(cls, submission_type: SubmissionType | str | None = None) -> str:
"""
Gets the regex string for identifying a certain class of submission.
Args:
submission_type (SubmissionType | str | None, optional): submission type of interest. Defaults to None.
Returns:
str: _description_
"""
# logger.debug(f"Attempting to get regex for {cls.__mapper_args__['polymorphic_identity']}") # logger.debug(f"Attempting to get regex for {cls.__mapper_args__['polymorphic_identity']}")
logger.debug(f"Attempting to get regex for {submission_type}") logger.debug(f"Attempting to get regex for {submission_type}")
try: try:
@@ -755,11 +724,8 @@ class BasicSubmission(BaseClass):
f"Could not get polymorph {polymorphic_identity} of {cls} due to {e}, falling back to BasicSubmission") f"Could not get polymorph {polymorphic_identity} of {cls} due to {e}, falling back to BasicSubmission")
case _: case _:
pass pass
# if attrs is None or len(attrs) == 0:
# logger.info(f"Recruiting: {cls}")
# return model
if attrs and any([not hasattr(cls, attr) for attr in attrs.keys()]): if attrs and any([not hasattr(cls, attr) for attr in attrs.keys()]):
# looks for first model that has all included kwargs # NOTE: looks for first model that has all included kwargs
try: try:
model = next(subclass for subclass in cls.__subclasses__() if model = next(subclass for subclass in cls.__subclasses__() if
all([hasattr(subclass, attr) for attr in attrs.keys()])) all([hasattr(subclass, attr) for attr in attrs.keys()]))
@@ -797,7 +763,6 @@ class BasicSubmission(BaseClass):
input_dict['custom'][k] = ws.cell(row=v['read']['row'], column=v['read']['column']).value input_dict['custom'][k] = ws.cell(row=v['read']['row'], column=v['read']['column']).value
case "range": case "range":
ws = xl[v['sheet']] ws = xl[v['sheet']]
# input_dict['custom'][k] = []
if v['start_row'] != v['end_row']: if v['start_row'] != v['end_row']:
v['end_row'] = v['end_row'] + 1 v['end_row'] = v['end_row'] + 1
rows = range(v['start_row'], v['end_row']) rows = range(v['start_row'], v['end_row'])
@@ -806,10 +771,6 @@ class BasicSubmission(BaseClass):
columns = range(v['start_column'], v['end_column']) columns = range(v['start_column'], v['end_column'])
input_dict['custom'][k] = [dict(value=ws.cell(row=row, column=column).value, row=row, column=column) input_dict['custom'][k] = [dict(value=ws.cell(row=row, column=column).value, row=row, column=column)
for row in rows for column in columns] for row in rows for column in columns]
# for ii in range(v['start_row'], v['end_row']):
# for jj in range(v['start_column'], v['end_column'] + 1):
# input_dict['custom'][k].append(
# dict(value=ws.cell(row=ii, column=jj).value, row=ii, column=jj))
return input_dict return input_dict
@classmethod @classmethod
@@ -952,7 +913,7 @@ class BasicSubmission(BaseClass):
rsl_plate_number (str): rsl plate num of interest rsl_plate_number (str): rsl plate num of interest
Returns: Returns:
list: _description_ Generator[dict, None, None]: Updated samples
""" """
# 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']
@@ -968,7 +929,17 @@ class BasicSubmission(BaseClass):
yield sample yield sample
@classmethod @classmethod
def parse_pcr_controls(cls, xl: Workbook, rsl_plate_num: str) -> list: def parse_pcr_controls(cls, xl: Workbook, rsl_plate_num: str) -> Generator[dict, None, None]:
"""
Custom parsing of pcr controls from Design & Analysis Software export.
Args:
xl (Workbook): D&A export file
rsl_plate_num (str): Plate number of the submission to be joined.
Yields:
Generator[dict, None, None]: Dictionaries of row values.
"""
location_map = cls.get_submission_type().sample_map['pcr_controls'] location_map = cls.get_submission_type().sample_map['pcr_controls']
submission = cls.query(rsl_plate_num=rsl_plate_num) submission = cls.query(rsl_plate_num=rsl_plate_num)
name_column = 1 name_column = 1
@@ -981,12 +952,16 @@ class BasicSubmission(BaseClass):
logger.debug(f"Pulling from row {iii}, column {item['ct_column']}") logger.debug(f"Pulling from row {iii}, column {item['ct_column']}")
subtype, target = item['name'].split("-") subtype, target = item['name'].split("-")
ct = worksheet.cell(row=iii, column=item['ct_column']).value ct = worksheet.cell(row=iii, column=item['ct_column']).value
# NOTE: Kind of a stop gap solution to find control reagents.
if subtype == "PC": if subtype == "PC":
ctrl = next((assoc.reagent for assoc in submission.submission_reagent_associations ctrl = next((assoc.reagent for assoc in submission.submission_reagent_associations
if any(["positive control" in item.name.lower() for item in assoc.reagent.role])), None) if
any(["positive control" in item.name.lower() for item in assoc.reagent.role])),
None)
elif subtype == "NC": elif subtype == "NC":
ctrl = next((assoc.reagent for assoc in submission.submission_reagent_associations ctrl = next((assoc.reagent for assoc in submission.submission_reagent_associations
if any(["molecular grade water" in item.name.lower() for item in assoc.reagent.role])), None) if any(["molecular grade water" in item.name.lower() for item in
assoc.reagent.role])), None)
try: try:
ct = float(ct) ct = float(ct)
except ValueError: except ValueError:
@@ -1124,8 +1099,6 @@ class BasicSubmission(BaseClass):
case _: case _:
# 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"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")
@@ -1336,7 +1309,7 @@ class BasicSubmission(BaseClass):
def backup(self, obj=None, fname: Path | None = None, full_backup: bool = False): def backup(self, obj=None, fname: Path | None = None, full_backup: bool = False):
""" """
Exports xlsx and yml info files for this instance. Exports xlsx info files for this instance.
Args: Args:
obj (_type_, optional): _description_. Defaults to None. obj (_type_, optional): _description_. Defaults to None.
@@ -1352,13 +1325,6 @@ class BasicSubmission(BaseClass):
if fname.name == "": if fname.name == "":
# logger.debug(f"export cancelled.") # logger.debug(f"export cancelled.")
return return
# if full_backup:
# backup = self.to_dict(full_data=True)
# try:
# with open(self.__backup_path__.joinpath(fname.with_suffix(".yml")), "w") as f:
# yaml.dump(backup, f)
# except KeyError as e:
# logger.error(f"Problem saving yml backup file: {e}")
writer = pyd.to_writer() writer = pyd.to_writer()
writer.xl.save(filename=fname.with_suffix(".xlsx")) writer.xl.save(filename=fname.with_suffix(".xlsx"))
@@ -1436,6 +1402,17 @@ class BacterialCulture(BasicSubmission):
@classmethod @classmethod
def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None, custom_fields: dict = {}) -> dict: def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None, custom_fields: dict = {}) -> dict:
"""
Performs class specific info parsing before info parsing is finalized.
Args:
input_dict (dict): Generic input info
xl (Workbook | None, optional): Original xl workbook. Defaults to None.
custom_fields (dict, optional): Map of custom fields to be parsed. Defaults to {}.
Returns:
dict: Updated info dictionary.
"""
input_dict = super().custom_info_parser(input_dict=input_dict, xl=xl, custom_fields=custom_fields) input_dict = super().custom_info_parser(input_dict=input_dict, xl=xl, custom_fields=custom_fields)
# logger.debug(f"\n\nInfo dictionary:\n\n{pformat(input_dict)}\n\n") # logger.debug(f"\n\nInfo dictionary:\n\n{pformat(input_dict)}\n\n")
return input_dict return input_dict
@@ -1476,12 +1453,30 @@ class Wastewater(BasicSubmission):
output["pcr_technician"] = self.technician output["pcr_technician"] = self.technician
else: else:
output['pcr_technician'] = self.pcr_technician output['pcr_technician'] = self.pcr_technician
############### Updated from finalize_details - testing 2024-1017 ################
if full_data:
output['samples'] = [sample for sample in output['samples']]
dummy_samples = []
for item in output['samples']:
# logger.debug(f"Sample dict: {item}")
thing = deepcopy(item)
try:
thing['row'] = thing['source_row']
thing['column'] = thing['source_column']
except KeyError:
logger.error(f"No row or column for sample: {item['submitter_id']}")
continue
thing['tooltip'] = f"Sample Name: {thing['name']}\nWell: {thing['sample_location']}"
dummy_samples.append(thing)
output['origin_plate'] = self.__class__.make_plate_map(sample_list=dummy_samples, plate_rows=4,
plate_columns=6)
###############################
return output return output
@classmethod @classmethod
def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None, custom_fields: dict = {}) -> dict: def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None, custom_fields: dict = {}) -> dict:
""" """
Update submission dictionary with type specific information. Extends parent Update submission dictionary with class specific information. Extends parent
Args: Args:
input_dict (dict): Input sample dictionary input_dict (dict): Input sample dictionary
@@ -1489,7 +1484,7 @@ class Wastewater(BasicSubmission):
custom_fields: Dictionary of locations, ranges, etc to be used by this function custom_fields: Dictionary of locations, ranges, etc to be used by this function
Returns: Returns:
dict: Updated sample dictionary dict: Updated info dictionary
""" """
input_dict = super().custom_info_parser(input_dict) input_dict = super().custom_info_parser(input_dict)
# logger.debug(f"Input dict: {pformat(input_dict)}") # logger.debug(f"Input dict: {pformat(input_dict)}")
@@ -1513,10 +1508,18 @@ class Wastewater(BasicSubmission):
@classmethod @classmethod
def parse_pcr(cls, xl: Workbook, rsl_plate_num: str) -> Generator[dict, None, None]: def parse_pcr(cls, xl: Workbook, rsl_plate_num: str) -> Generator[dict, None, None]:
""" """
Parse specific to wastewater samples. Perform parsing of pcr info. Since most of our PC outputs are the same format, this should work for most.
Args:
xl (pd.DataFrame): pcr info form
rsl_plate_number (str): rsl plate num of interest
Returns:
Generator[dict, None, None]: Updated samples
""" """
samples = [item for item in super().parse_pcr(xl=xl, rsl_plate_num=rsl_plate_num)] samples = [item for item in 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)}')
# NOTE: Due to having to run through samples in for loop we need to convert to list.
output = [] output = []
for sample in samples: for sample in samples:
# NOTE: remove '-{target}' from controls # NOTE: remove '-{target}' from controls
@@ -1542,20 +1545,23 @@ class Wastewater(BasicSubmission):
del sample['assessment'] del sample['assessment']
except KeyError: except KeyError:
pass pass
# yield sample
output.append(sample) output.append(sample)
# NOTE: And then convert back to list ot keep fidelity with parent method.
for sample in output: for sample in output:
yield sample yield sample
# @classmethod
# def parse_pcr_controls(cls, xl: Workbook, location_map: list) -> list:
@classmethod @classmethod
def enforce_name(cls, instr: str, data: dict | None = {}) -> str: def enforce_name(cls, instr: str, data: dict | None = {}) -> str:
""" """
Extends parent Custom naming method for this class. Extends parent.
"""
Args:
instr (str): Initial name.
data (dict | None, optional): Additional parameters for name. Defaults to None.
Returns:
str: Updated name.
"""
try: try:
# NOTE: Deal with PCR file. # NOTE: Deal with PCR file.
instr = re.sub(r"PCR(-|_)", "", instr) instr = re.sub(r"PCR(-|_)", "", instr)
@@ -1567,27 +1573,18 @@ class Wastewater(BasicSubmission):
@classmethod @classmethod
def adjust_autofill_samples(cls, samples: List[Any]) -> List[Any]: def adjust_autofill_samples(cls, samples: List[Any]) -> List[Any]:
""" """
Extends parent Makes adjustments to samples before writing to excel. Extends parent.
Args:
samples (List[Any]): List of Samples
Returns:
List[Any]: Updated list of samples
""" """
samples = super().adjust_autofill_samples(samples) samples = super().adjust_autofill_samples(samples)
samples = [item for item in samples if not item.submitter_id.startswith("EN")] samples = [item for item in samples if not item.submitter_id.startswith("EN")]
return samples return samples
# @classmethod
# def custom_sample_autofill_row(cls, sample, worksheet: Worksheet) -> int:
# """
# Extends parent
# """
# # logger.debug(f"Checking {sample.well}")
# # logger.debug(f"here's the worksheet: {worksheet}")
# row = super().custom_sample_autofill_row(sample, worksheet)
# df = pd.DataFrame(list(worksheet.values))
# # logger.debug(f"Here's the dataframe: {df}")
# idx = df[df[1] == sample.sample_location]
# # logger.debug(f"Here is the row: {idx}")
# row = idx.index.to_list()[0]
# return row + 1
@classmethod @classmethod
def get_details_template(cls, base_dict: dict) -> Tuple[dict, Template]: def get_details_template(cls, base_dict: dict) -> Tuple[dict, Template]:
""" """
@@ -1603,35 +1600,6 @@ class Wastewater(BasicSubmission):
base_dict['excluded'] += ['origin_plate'] base_dict['excluded'] += ['origin_plate']
return base_dict, template return base_dict, template
@classmethod
def finalize_details(cls, input_dict: dict) -> dict:
"""
Makes changes to information before display
Args:
input_dict (dict): Input information
Returns:
dict: Updated information
"""
input_dict = super().finalize_details(input_dict)
# NOTE: Currently this is preserving the generator items, can we come up with a better way?
input_dict['samples'] = [sample for sample in input_dict['samples']]
dummy_samples = []
for item in input_dict['samples']:
# logger.debug(f"Sample dict: {item}")
thing = deepcopy(item)
try:
thing['row'] = thing['source_row']
thing['column'] = thing['source_column']
except KeyError:
logger.error(f"No row or column for sample: {item['submitter_id']}")
continue
thing['tooltip'] = f"Sample Name: {thing['name']}\nWell: {thing['sample_location']}"
dummy_samples.append(thing)
input_dict['origin_plate'] = cls.make_plate_map(sample_list=dummy_samples, plate_rows=4, plate_columns=6)
return input_dict
def custom_context_events(self) -> dict: def custom_context_events(self) -> dict:
""" """
Sets context events for main widget Sets context events for main widget
@@ -1646,7 +1614,7 @@ class Wastewater(BasicSubmission):
@report_result @report_result
def link_pcr(self, obj): def link_pcr(self, obj):
""" """
Adds PCR info to this submission PYQT6 function to add PCR info to this submission
Args: Args:
obj (_type_): Parent widget obj (_type_): Parent widget
@@ -1733,7 +1701,7 @@ class WastewaterArtic(BasicSubmission):
@classmethod @classmethod
def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None, custom_fields: dict = {}) -> dict: def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None, custom_fields: dict = {}) -> dict:
""" """
Update submission dictionary with type specific information Update submission dictionary with class specific information
Args: Args:
input_dict (dict): Input sample dictionary input_dict (dict): Input sample dictionary
@@ -1763,10 +1731,8 @@ class WastewaterArtic(BasicSubmission):
return None return None
input_dict = super().custom_info_parser(input_dict) input_dict = super().custom_info_parser(input_dict)
input_dict['submission_type'] = dict(value="Wastewater Artic", missing=False) input_dict['submission_type'] = dict(value="Wastewater Artic", missing=False)
# logger.debug(f"Custom fields: {custom_fields}")
logger.debug(f"Custom fields: {custom_fields}")
egel_section = custom_fields['egel_controls'] egel_section = custom_fields['egel_controls']
ws = xl[egel_section['sheet']] ws = xl[egel_section['sheet']]
# NOTE: Here we should be scraping the control results. # NOTE: Here we should be scraping the control results.
@@ -1788,7 +1754,7 @@ class WastewaterArtic(BasicSubmission):
ii in ii in
range(source_plates_section['start_row'], source_plates_section['end_row'] + 1)] range(source_plates_section['start_row'], source_plates_section['end_row'] + 1)]
for datum in data: for datum in data:
logger.debug(f"Datum: {datum}") # logger.debug(f"Datum: {datum}")
if datum['plate'] in ["None", None, ""]: if datum['plate'] in ["None", None, ""]:
continue continue
else: else:
@@ -1843,7 +1809,14 @@ class WastewaterArtic(BasicSubmission):
@classmethod @classmethod
def enforce_name(cls, instr: str, data: dict = {}) -> str: def enforce_name(cls, instr: str, data: dict = {}) -> str:
""" """
Extends parent Custom naming method for this class. Extends parent.
Args:
instr (str): Initial name.
data (dict | None, optional): Additional parameters for name. Defaults to None.
Returns:
str: Updated name.
""" """
try: try:
# NOTE: Deal with PCR file. # NOTE: Deal with PCR file.
@@ -1873,7 +1846,7 @@ class WastewaterArtic(BasicSubmission):
dict: Updated sample dictionary dict: Updated sample dictionary
""" """
input_dict = super().parse_samples(input_dict) input_dict = super().parse_samples(input_dict)
logger.debug(f"WWA input dict: {pformat(input_dict)}") # logger.debug(f"WWA input dict: {pformat(input_dict)}")
input_dict['sample_type'] = "Wastewater Sample" input_dict['sample_type'] = "Wastewater Sample"
# NOTE: Stop gap solution because WW is sloppy with their naming schemes # NOTE: Stop gap solution because WW is sloppy with their naming schemes
try: try:
@@ -1952,14 +1925,14 @@ class WastewaterArtic(BasicSubmission):
@classmethod @classmethod
def pbs_adapter(cls, input_str): def pbs_adapter(cls, input_str):
""" """
Stopgap solution because WW names their controls different Stopgap solution because WW names their controls different
Args: Args:
input_str (str): input name input_str (str): input name
Returns: Returns:
str: output name str: output name
""" """
# logger.debug(f"input string raw: {input_str}") # logger.debug(f"input string raw: {input_str}")
# NOTE: Remove letters. # NOTE: Remove letters.
processed = input_str.replace("RSL", "") processed = input_str.replace("RSL", "")
@@ -2155,7 +2128,7 @@ class WastewaterArtic(BasicSubmission):
def gel_box(self, obj): def gel_box(self, obj):
""" """
Creates widget to perform gel viewing operations Creates PYQT6 widget to perform gel viewing operations
Args: Args:
obj (_type_): parent widget obj (_type_): parent widget
@@ -2221,7 +2194,7 @@ class BasicSample(BaseClass):
submissions = association_proxy("sample_submission_associations", "submission") #: proxy of associated submissions submissions = association_proxy("sample_submission_associations", "submission") #: proxy of associated submissions
@validates('submitter_id') @validates('submitter_id')
def create_id(self, key: str, value: str): def create_id(self, key: str, value: str) -> str:
""" """
Creates a random string as a submitter id. Creates a random string as a submitter id.
@@ -2330,7 +2303,7 @@ class BasicSample(BaseClass):
@classmethod @classmethod
def parse_sample(cls, input_dict: dict) -> dict: def parse_sample(cls, input_dict: dict) -> dict:
f""" """
Custom sample parser Custom sample parser
Args: Args:
@@ -2413,7 +2386,7 @@ class BasicSample(BaseClass):
ValueError: Raised if unallowed key is given. ValueError: Raised if unallowed key is given.
Returns: Returns:
_type_: _description_ BasicSample: Instance of BasicSample
""" """
disallowed = ["id"] disallowed = ["id"]
if kwargs == {}: if kwargs == {}:
@@ -2434,7 +2407,7 @@ class BasicSample(BaseClass):
**kwargs **kwargs
) -> List[BasicSample]: ) -> List[BasicSample]:
""" """
Allows for fuzzy search of samples. (Experimental) Allows for fuzzy search of samples.
Args: Args:
sample_type (str | BasicSample | None, optional): Type of sample. Defaults to None. sample_type (str | BasicSample | None, optional): Type of sample. Defaults to None.
@@ -2764,9 +2737,13 @@ class SubmissionSampleAssociation(BaseClass):
Returns: Returns:
int: incremented id int: incremented id
""" """
if cls.__name__ == "SubmissionSampleAssociation":
model = cls
else:
model = next((base for base in cls.__bases__ if base.__name__ == "SubmissionSampleAssociation"),
SubmissionSampleAssociation)
try: try:
return max([item.id for item in cls.query()]) + 1 return max([item.id for item in model.query()]) + 1
except ValueError as e: except ValueError as e:
logger.error(f"Problem incrementing id: {e}") logger.error(f"Problem incrementing id: {e}")
return 1 return 1
@@ -2980,26 +2957,6 @@ class WastewaterAssociation(SubmissionSampleAssociation):
logger.error(f"Couldn't set tooltip for {self.sample.rsl_number}. Looks like there isn't PCR data.") logger.error(f"Couldn't set tooltip for {self.sample.rsl_number}. Looks like there isn't PCR data.")
return sample return sample
@classmethod
def autoincrement_id_local(cls) -> int:
"""
Increments the association id automatically. Overrides parent
Returns:
int: incremented id
"""
try:
parent = next((base for base in cls.__bases__ if base.__name__ == "SubmissionSampleAssociation"),
SubmissionSampleAssociation)
return max([item.id for item in parent.query()]) + 1
except StopIteration as e:
logger.error(f"Problem incrementing id: {e}")
return 1
@classmethod
def autoincrement_id(cls) -> int:
return super().autoincrement_id()
class WastewaterArticAssociation(SubmissionSampleAssociation): class WastewaterArticAssociation(SubmissionSampleAssociation):
""" """
@@ -3030,19 +2987,3 @@ class WastewaterArticAssociation(SubmissionSampleAssociation):
sample['source_plate_number'] = self.source_plate_number sample['source_plate_number'] = self.source_plate_number
sample['source_well'] = self.source_well sample['source_well'] = self.source_well
return sample return sample
@classmethod
def autoincrement_id(cls) -> int:
"""
Increments the association id automatically. Overrides parent
Returns:
int: incremented id
"""
try:
parent = next((base for base in cls.__bases__ if base.__name__ == "SubmissionSampleAssociation"),
SubmissionSampleAssociation)
return max([item.id for item in parent.query()]) + 1
except StopIteration as e:
logger.error(f"Problem incrementing id: {e}")
return 1

117
src/submissions/backend/excel/parser.py
View File

@@ -9,10 +9,10 @@ from typing import List
from openpyxl import load_workbook, Workbook from openpyxl import load_workbook, Workbook
from pathlib import Path from pathlib import Path
from backend.db.models import * from backend.db.models import *
from backend.validators import PydSubmission, PydReagent, RSLNamer, PydSample, PydEquipment, PydTips from backend.validators import PydSubmission, RSLNamer
import logging, re import logging, re
from collections import OrderedDict from collections import OrderedDict
from tools import check_not_nan, convert_nans_to_nones, is_missing, check_key_or_attr from tools import check_not_nan, is_missing, check_key_or_attr
logger = logging.getLogger(f"submissions.{__name__}") logger = logging.getLogger(f"submissions.{__name__}")
@@ -483,17 +483,21 @@ class SampleParser(object):
lookup_samples[ii] = {} lookup_samples[ii] = {}
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']
except KeyError: # except KeyError:
check = False # check = False
if check: # if check:
new = lsample | psample # new = lsample | psample
lookup_samples[jj] = {} # lookup_samples[jj] = {}
break # break
else: # else:
new = psample # new = psample
jj, new = next(((jj, lsample) for jj, lsample in enumerate(lookup_samples) if lsample[merge_on_id] == psample['id']), (-1, psample))
logger.debug(f"Assigning from index {jj} - {new}")
if jj >= 0:
lookup_samples[jj] = {}
if not check_key_or_attr(key='submitter_id', interest=new, check_none=True): if not check_key_or_attr(key='submitter_id', interest=new, check_none=True):
new['submitter_id'] = psample['id'] new['submitter_id'] = psample['id']
new = self.sub_object.parse_samples(new) new = self.sub_object.parse_samples(new)
@@ -546,7 +550,7 @@ class EquipmentParser(object):
logger.error(f"Error getting asset number for {input}: {e}") logger.error(f"Error getting asset number for {input}: {e}")
return input return input
def parse_equipment(self) -> List[dict]: def parse_equipment(self) -> Generator[dict, None, None]:
""" """
Scrapes equipment from xl sheet Scrapes equipment from xl sheet
@@ -554,7 +558,6 @@ class EquipmentParser(object):
List[dict]: list of equipment List[dict]: list of equipment
""" """
# logger.debug(f"Equipment parser going into parsing: {pformat(self.__dict__)}") # logger.debug(f"Equipment parser going into parsing: {pformat(self.__dict__)}")
output = []
# logger.debug(f"Sheets: {sheets}") # logger.debug(f"Sheets: {sheets}")
for sheet in self.xl.sheetnames: for sheet in self.xl.sheetnames:
ws = self.xl[sheet] ws = self.xl[sheet]
@@ -579,13 +582,10 @@ class EquipmentParser(object):
eq = Equipment.query(name=asset) eq = Equipment.query(name=asset)
process = ws.cell(row=v['process']['row'], column=v['process']['column']).value process = ws.cell(row=v['process']['row'], column=v['process']['column']).value
try: try:
# output.append(
yield dict(name=eq.name, processes=[process], role=k, asset_number=eq.asset_number, yield dict(name=eq.name, processes=[process], role=k, asset_number=eq.asset_number,
nickname=eq.nickname) nickname=eq.nickname)
except AttributeError: except AttributeError:
logger.error(f"Unable to add {eq} to list.") logger.error(f"Unable to add {eq} to list.")
# logger.debug(f"Here is the output so far: {pformat(output)}")
# return output
class TipParser(object): class TipParser(object):
@@ -623,7 +623,6 @@ class TipParser(object):
List[dict]: list of equipment List[dict]: list of equipment
""" """
# logger.debug(f"Equipment parser going into parsing: {pformat(self.__dict__)}") # logger.debug(f"Equipment parser going into parsing: {pformat(self.__dict__)}")
output = []
# logger.debug(f"Sheets: {sheets}") # logger.debug(f"Sheets: {sheets}")
for sheet in self.xl.sheetnames: for sheet in self.xl.sheetnames:
ws = self.xl[sheet] ws = self.xl[sheet]
@@ -647,12 +646,9 @@ class TipParser(object):
# logger.debug(f"asset: {asset}") # logger.debug(f"asset: {asset}")
eq = Tips.query(lot=lot, name=asset, limit=1) eq = Tips.query(lot=lot, name=asset, limit=1)
try: try:
# output.append(
yield dict(name=eq.name, role=k, lot=lot) yield dict(name=eq.name, role=k, lot=lot)
except AttributeError: except AttributeError:
logger.error(f"Unable to add {eq} to PydTips list.") logger.error(f"Unable to add {eq} to PydTips list.")
# logger.debug(f"Here is the output so far: {pformat(output)}")
# return output
class PCRParser(object): class PCRParser(object):
@@ -660,9 +656,10 @@ class PCRParser(object):
def __init__(self, filepath: Path | None = None, submission: BasicSubmission | None = None) -> None: def __init__(self, filepath: Path | None = None, submission: BasicSubmission | None = None) -> None:
""" """
Args: Args:
filepath (Path | None, optional): file to parse. Defaults to None. filepath (Path | None, optional): file to parse. Defaults to None.
""" submission (BasicSubmission | None, optional): Submission parsed data to be added to.
"""
# logger.debug(f'Parsing {filepath.__str__()}') # logger.debug(f'Parsing {filepath.__str__()}')
if filepath is None: if filepath is None:
logger.error('No filepath given.') logger.error('No filepath given.')
@@ -709,73 +706,3 @@ class PCRParser(object):
# logger.debug(f"PCR: {pformat(pcr)}") # logger.debug(f"PCR: {pformat(pcr)}")
return pcr return pcr
class EDSParser(object):
expand_device = {"QS7PRO": "QuantStudio tm 7 Pro System"}
expand_block = {"BLOCK_96W_01ML": "96-Well 0.1-mL Block"}
def __init__(self, filepath: str | Path | None = None):
logger.info(f"\n\nParsing {filepath.__str__()}\n\n")
match filepath:
case Path():
self.filepath = filepath
case str():
self.filepath = Path(filepath)
case _:
logger.error(f"No filepath given.")
raise ValueError("No filepath given.")
self.eds = ZipFile(self.filepath)
self.analysis_settings = json.loads(self.eds.read("primary/analysis_setting.json").decode("utf-8"))
self.analysis_results = json.loads(self.eds.read("primary/analysis_setting.json").decode("utf-8"))
self.presence_absence_results = json.loads(
self.eds.read("extensions/am.pa/presence_absence_result.json").decode("utf-8"))
self.presence_absence_settings = json.loads(
self.eds.read("extensions/am.pa/presence_absence_setting.json").decode("utf-8"))
self.run_summary = json.loads(self.eds.read("run/run_summary.json").decode("utf-8"))
self.run_method = json.loads(self.eds.read("setup/run_method.json").decode("utf-8"))
self.plate_setup = json.loads(self.eds.read("setup/plate_setup.json").decode("utf-8"))
self.eds_summary = json.loads(self.eds.read("summary.json").decode("utf-8"))
def parse_DA_date_format(self, value: int) -> datetime:
value = value / 1000
return datetime.utcfromtimestamp(value)
def get_run_time(self, start: datetime, end: datetime) -> Tuple[str, str, str]:
delta = end - start
minutes, seconds = divmod(delta.seconds, 60)
duration = f"{minutes} minutes {seconds} seconds"
start_time = start.strftime("%Y-%m-%d %I:%M:%S %p %Z")
end_time = end.strftime("%Y-%m-%d %I:%M:%S %p %Z")
return start_time, end_time, duration
def parse_summary(self):
summary = dict()
summary['file_name'] = self.filepath.absolute().__str__()
summary['comment'] = self.eds_summary['description']
summary['operator'] = self.run_summary['operator']
summary['barcode'] = self.plate_setup['plateBarcode']
try:
summary['instrument_type'] = self.__class__.expand_device[self.eds_summary['instrumentType']]
except KeyError:
summary['instrument_type'] = self.eds_summary['instrumentType']
try:
summary['block_type'] = self.__class__.expand_block[self.plate_setup['blockType']]
except KeyError:
summary['block_type'] = self.plate_setup['blockType']
summary['instrument_name'] = self.run_summary['instrumentName']
summary['instrument_serial_number'] = self.run_summary['instrumentSerialNumber']
summary['heated_cover_serial_number'] = self.run_summary['coverSerialNumber']
summary['block_serial_number'] = self.run_summary['blockSerialNumber']
run_start = self.parse_DA_date_format(self.run_summary['startTime'])
run_end = self.parse_DA_date_format(self.run_summary['endTime'])
summary['run_start_date/time'], summary['run_end_date/time'], summary['run_duration'] = \
self.get_run_time(run_start, run_end)
summary['sample_volume'] = self.run_method['sampleVolume']
summary['cover_temperature'] = self.run_method['coverTemperature']
summary['passive_reference'] = self.plate_setup['passiveReference']
summary['pcr_stage/step_number'] = f"Stage {self.analysis_settings['cqAnalysisStageNumber']} Step {self.analysis_settings['cqAnalysisStepNumber']}"
summary['quantification_cycle_method'] = self.analysis_results['cqAlgorithmType']
summary['analysis_date/time'] = self.parse_DA_date_format(self.eds_summary['analysis']['primary']['analysisTime'])
summary['software_name_and_version'] = "Design & Analysis Software v2.8.0"
summary['plugin_name_and_version'] = "Primary Analysis v1.8.1, Presence Absence v2.4.0"
return summary

7
src/submissions/backend/excel/reports.py
View File

@@ -7,8 +7,7 @@ from pathlib import Path
from datetime import date from datetime import date
from typing import Tuple from typing import Tuple
from backend.db.models import BasicSubmission from backend.db.models import BasicSubmission
from tools import jinja_template_loading, get_first_blank_df_row, \ from tools import jinja_template_loading, get_first_blank_df_row, row_map
row_map
from PyQt6.QtWidgets import QWidget from PyQt6.QtWidgets import QWidget
from openpyxl.worksheet.worksheet import Worksheet from openpyxl.worksheet.worksheet import Worksheet
@@ -65,7 +64,7 @@ class ReportMaker(object):
old_lab = "" old_lab = ""
output = [] output = []
# logger.debug(f"Report DataFrame: {df}") # logger.debug(f"Report DataFrame: {df}")
for ii, row in enumerate(df.iterrows()): for row in df.iterrows():
# logger.debug(f"Row {ii}: {row}") # logger.debug(f"Row {ii}: {row}")
lab = row[0][0] lab = row[0][0]
# logger.debug(type(row)) # logger.debug(type(row))
@@ -111,7 +110,7 @@ class ReportMaker(object):
def fix_up_xl(self): def fix_up_xl(self):
""" """
Handles formatting of xl file. Handles formatting of xl file, mediocrely.
""" """
# logger.debug(f"Updating worksheet") # logger.debug(f"Updating worksheet")
worksheet: Worksheet = self.writer.sheets['Report'] worksheet: Worksheet = self.writer.sheets['Report']

33
src/submissions/backend/excel/writer.py
View File

@@ -4,7 +4,7 @@ contains writer objects for pushing values to submission sheet templates.
import logging import logging
from copy import copy from copy import copy
from pprint import pformat from pprint import pformat
from typing import List, Generator from typing import List, Generator, Tuple
from openpyxl import load_workbook, Workbook from openpyxl import load_workbook, Workbook
from backend.db.models import SubmissionType, KitType, BasicSubmission from backend.db.models import SubmissionType, KitType, BasicSubmission
from backend.validators.pydant import PydSubmission from backend.validators.pydant import PydSubmission
@@ -19,13 +19,13 @@ class SheetWriter(object):
object to manage data placement into excel file object to manage data placement into excel file
""" """
def __init__(self, submission: PydSubmission, missing_only: bool = False): def __init__(self, submission: PydSubmission):
""" """
Args: Args:
submission (PydSubmission): Object containing submission information. submission (PydSubmission): Object containing submission information.
missing_only (bool, optional): Whether to only fill in missing values. Defaults to False.
""" """
self.sub = OrderedDict(submission.improved_dict()) self.sub = OrderedDict(submission.improved_dict())
# NOTE: Set values from pydantic object.
for k, v in self.sub.items(): for k, v in self.sub.items():
match k: match k:
case 'filepath': case 'filepath':
@@ -41,18 +41,16 @@ class SheetWriter(object):
else: else:
self.sub[k] = v self.sub[k] = v
# logger.debug(f"\n\nWriting to {submission.filepath.__str__()}\n\n") # logger.debug(f"\n\nWriting to {submission.filepath.__str__()}\n\n")
if self.filepath.stem.startswith("tmp"): # if self.filepath.stem.startswith("tmp"):
template = self.submission_type.template_file # template = self.submission_type.template_file
workbook = load_workbook(BytesIO(template)) # workbook = load_workbook(BytesIO(template))
missing_only = False # else:
else: # try:
try: # workbook = load_workbook(self.filepath)
workbook = load_workbook(self.filepath) # except Exception as e:
except Exception as e: # logger.error(f"Couldn't open workbook due to {e}")
logger.error(f"Couldn't open workbook due to {e}") template = self.submission_type.template_file
template = self.submission_type.template_file workbook = load_workbook(BytesIO(template))
workbook = load_workbook(BytesIO(template))
missing_only = False
# self.workbook = workbook # self.workbook = workbook
self.xl = workbook self.xl = workbook
self.write_info() self.write_info()
@@ -130,7 +128,7 @@ class InfoWriter(object):
self.info = self.reconcile_map(info_dict, self.info_map) self.info = self.reconcile_map(info_dict, self.info_map)
# logger.debug(pformat(self.info)) # logger.debug(pformat(self.info))
def reconcile_map(self, info_dict: dict, info_map: dict) -> dict: def reconcile_map(self, info_dict: dict, info_map: dict) -> Generator[(Tuple[str, dict]), None, None]:
""" """
Merge info with its locations Merge info with its locations
@@ -246,7 +244,7 @@ class ReagentWriter(object):
""" """
for reagent in self.reagents: for reagent in self.reagents:
sheet = self.xl[reagent['sheet']] sheet = self.xl[reagent['sheet']]
for k, v in reagent.items(): for v in reagent.values():
if not isinstance(v, dict): if not isinstance(v, dict):
continue continue
# logger.debug( # logger.debug(
@@ -440,7 +438,6 @@ class TipWriter(object):
if tips_list is None: if tips_list is None:
return return
for ii, tips in enumerate(tips_list, start=1): for ii, tips in enumerate(tips_list, start=1):
# mp_info = tips_map[tips['role']]
mp_info = tips_map[tips.role] mp_info = tips_map[tips.role]
# logger.debug(f"{tips['role']} map: {mp_info}") # logger.debug(f"{tips['role']} map: {mp_info}")
placeholder = {} placeholder = {}

10
src/submissions/backend/validators/__init__.py
View File

@@ -23,15 +23,15 @@ class RSLNamer(object):
# NOTE: Preferred method is path retrieval, but might also need validation for just string. # NOTE: Preferred method is path retrieval, but might also need validation for just string.
filename = Path(filename) if Path(filename).exists() else filename filename = Path(filename) if Path(filename).exists() else filename
self.submission_type = sub_type self.submission_type = sub_type
if self.submission_type is None: if not self.submission_type:
# logger.debug("Creating submission type because none exists") # logger.debug("Creating submission type because none exists")
self.submission_type = self.retrieve_submission_type(filename=filename) self.submission_type = self.retrieve_submission_type(filename=filename)
logger.info(f"got submission type: {self.submission_type}") logger.info(f"got submission type: {self.submission_type}")
if self.submission_type is not None: if self.submission_type:
# logger.debug("Retrieving BasicSubmission subclass") # logger.debug("Retrieving BasicSubmission subclass")
self.sub_object = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type) self.sub_object = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
self.parsed_name = self.retrieve_rsl_number(filename=filename, regex=self.sub_object.get_regex(submission_type=sub_type)) self.parsed_name = self.retrieve_rsl_number(filename=filename, regex=self.sub_object.get_regex(submission_type=sub_type))
if data is None: if not data:
data = dict(submission_type=self.submission_type) data = dict(submission_type=self.submission_type)
if "submission_type" not in data.keys(): if "submission_type" not in data.keys():
data['submission_type'] = self.submission_type data['submission_type'] = self.submission_type
@@ -45,6 +45,9 @@ class RSLNamer(object):
Args: Args:
filename (str | Path): filename filename (str | Path): filename
Raises:
TypeError: Raised if unsupported variable type for filename given.
Returns: Returns:
str: parsed submission type str: parsed submission type
""" """
@@ -84,6 +87,7 @@ class RSLNamer(object):
case str(): case str():
submission_type = st_from_str(filename=filename) submission_type = st_from_str(filename=filename)
case _: case _:
raise TypeError(f"Unsupported filename type: {type(filename)}.")
submission_type = None submission_type = None
try: try:
check = submission_type is None check = submission_type is None

12
src/submissions/backend/validators/pydant.py
View File

@@ -157,7 +157,6 @@ class PydReagent(BaseModel):
if submission is not None and reagent not in submission.reagents: if submission is not None and reagent not in submission.reagents:
assoc = SubmissionReagentAssociation(reagent=reagent, submission=submission) assoc = SubmissionReagentAssociation(reagent=reagent, submission=submission)
assoc.comments = self.comment assoc.comments = self.comment
# reagent.reagent_submission_associations.append(assoc)
else: else:
assoc = None assoc = None
report.add_result(Result(owner=__name__, code=0, msg="New reagent created.", status="Information")) report.add_result(Result(owner=__name__, code=0, msg="New reagent created.", status="Information"))
@@ -165,7 +164,6 @@ class PydReagent(BaseModel):
if submission is not None and reagent not in submission.reagents: if submission is not None and reagent not in submission.reagents:
assoc = SubmissionReagentAssociation(reagent=reagent, submission=submission) assoc = SubmissionReagentAssociation(reagent=reagent, submission=submission)
assoc.comments = self.comment assoc.comments = self.comment
# reagent.reagent_submission_associations.append(assoc)
else: else:
assoc = None assoc = None
# add end-of-life extension from reagent type to expiry date # add end-of-life extension from reagent type to expiry date
@@ -187,12 +185,10 @@ class PydSample(BaseModel, extra='allow'):
# logger.debug(f"Data for pydsample: {data}") # logger.debug(f"Data for pydsample: {data}")
model = BasicSample.find_polymorphic_subclass(polymorphic_identity=data.sample_type) model = BasicSample.find_polymorphic_subclass(polymorphic_identity=data.sample_type)
for k, v in data.model_extra.items(): for k, v in data.model_extra.items():
# print(k, v)
if k in model.timestamps(): if k in model.timestamps():
if isinstance(v, str): if isinstance(v, str):
v = datetime.strptime(v, "%Y-%m-%d") v = datetime.strptime(v, "%Y-%m-%d")
data.__setattr__(k, v) data.__setattr__(k, v)
# print(dir(data))
# logger.debug(f"Data coming out of validation: {pformat(data)}") # logger.debug(f"Data coming out of validation: {pformat(data)}")
return data return data
@@ -329,8 +325,6 @@ class PydEquipment(BaseModel, extra='ignore'):
value = convert_nans_to_nones(value) value = convert_nans_to_nones(value)
if not value: if not value:
value = [''] value = ['']
# if len(value) == 0:
# value = ['']
try: try:
value = [item.strip() for item in value] value = [item.strip() for item in value]
except AttributeError: except AttributeError:
@@ -416,7 +410,6 @@ class PydSubmission(BaseModel, extra='allow'):
@field_validator("tips", mode="before") @field_validator("tips", mode="before")
@classmethod @classmethod
def expand_tips(cls, value): def expand_tips(cls, value):
# print(f"\n{type(value)}\n")
if isinstance(value, dict): if isinstance(value, dict):
value = value['value'] value = value['value']
if isinstance(value, Generator): if isinstance(value, Generator):
@@ -594,7 +587,6 @@ class PydSubmission(BaseModel, extra='allow'):
value = value['value'].title() value = value['value'].title()
return dict(value=value, missing=False) return dict(value=value, missing=False)
else: else:
# return dict(value=RSLNamer(instr=values.data['filepath'].__str__()).submission_type.title(), missing=True)
return dict(value=RSLNamer.retrieve_submission_type(filename=values.data['filepath']).title(), missing=True) return dict(value=RSLNamer.retrieve_submission_type(filename=values.data['filepath']).title(), missing=True)
@field_validator("submission_category", mode="before") @field_validator("submission_category", mode="before")
@@ -688,7 +680,6 @@ class PydSubmission(BaseModel, extra='allow'):
def __init__(self, run_custom: bool = False, **data): def __init__(self, run_custom: bool = False, **data):
super().__init__(**data) super().__init__(**data)
# NOTE: this could also be done with default_factory # NOTE: this could also be done with default_factory
logger.debug(data)
self.submission_object = BasicSubmission.find_polymorphic_subclass( self.submission_object = BasicSubmission.find_polymorphic_subclass(
polymorphic_identity=self.submission_type['value']) polymorphic_identity=self.submission_type['value'])
self.namer = RSLNamer(self.rsl_plate_num['value'], sub_type=self.submission_type['value']) self.namer = RSLNamer(self.rsl_plate_num['value'], sub_type=self.submission_type['value'])
@@ -729,7 +720,6 @@ class PydSubmission(BaseModel, extra='allow'):
output.append(dummy) output.append(dummy)
self.samples = output self.samples = output
# TODO: Return samples, reagents, etc to dictionaries as well.
def improved_dict(self, dictionaries: bool = True) -> dict: def improved_dict(self, dictionaries: bool = True) -> dict:
""" """
Adds model_extra to fields. Adds model_extra to fields.
@@ -786,7 +776,6 @@ class PydSubmission(BaseModel, extra='allow'):
Returns: Returns:
Tuple[BasicSubmission, Result]: BasicSubmission instance, result object Tuple[BasicSubmission, Result]: BasicSubmission instance, result object
""" """
# self.__dict__.update(self.model_extra)
report = Report() report = Report()
dicto = self.improved_dict() dicto = self.improved_dict()
instance, result = BasicSubmission.query_or_create(submission_type=self.submission_type['value'], instance, result = BasicSubmission.query_or_create(submission_type=self.submission_type['value'],
@@ -817,7 +806,6 @@ class PydSubmission(BaseModel, extra='allow'):
# logger.debug(f"Association: {assoc}") # logger.debug(f"Association: {assoc}")
if assoc is not None: # and assoc not in instance.submission_reagent_associations: 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)
case "samples": case "samples":
for sample in self.samples: for sample in self.samples:
sample, associations, _ = sample.toSQL(submission=instance) sample, associations, _ = sample.toSQL(submission=instance)

2
src/submissions/frontend/visualizations/__init__.py
View File

@@ -4,6 +4,7 @@ Contains all operations for creating charts, graphs and visual effects.
from PyQt6.QtWidgets import QWidget from PyQt6.QtWidgets import QWidget
import plotly import plotly
from plotly.graph_objects import Figure from plotly.graph_objects import Figure
from plotly.graph_objs import FigureWidget
import pandas as pd import pandas as pd
from frontend.widgets.functions import select_save_file from frontend.widgets.functions import select_save_file
@@ -35,7 +36,6 @@ class CustomFigure(Figure):
output = select_save_file(obj=parent, default_name=group_name, extension="xlsx") output = select_save_file(obj=parent, default_name=group_name, extension="xlsx")
self.df.to_excel(output.absolute().__str__(), engine="openpyxl", index=False) self.df.to_excel(output.absolute().__str__(), engine="openpyxl", index=False)
def to_html(self) -> str: def to_html(self) -> str:
""" """
Creates final html code from plotly Creates final html code from plotly

22
src/submissions/frontend/visualizations/irida_charts.py
View File

@@ -3,14 +3,13 @@ Functions for constructing irida controls graphs using plotly.
""" """
from datetime import date from datetime import date
from pprint import pformat from pprint import pformat
import plotly from typing import Generator
import plotly.express as px import plotly.express as px
import pandas as pd import pandas as pd
from PyQt6.QtWidgets import QWidget from PyQt6.QtWidgets import QWidget
from . import CustomFigure from . import CustomFigure
import logging import logging
from tools import get_unique_values_in_df_column, divide_chunks from tools import get_unique_values_in_df_column, divide_chunks
from frontend.widgets.functions import select_save_file
logger = logging.getLogger(f"submissions.{__name__}") logger = logging.getLogger(f"submissions.{__name__}")
@@ -67,7 +66,6 @@ class IridaFigure(CustomFigure):
) )
bar.update_traces(visible=ii == 0) bar.update_traces(visible=ii == 0)
self.add_traces(bar.data) self.add_traces(bar.data)
# return generic_figure_markers(modes=modes, ytitle=ytitle)
def generic_figure_markers(self, modes: list = [], ytitle: str | None = None, months: int = 6): def generic_figure_markers(self, modes: list = [], ytitle: str | None = None, months: int = 6):
""" """
@@ -83,7 +81,7 @@ class IridaFigure(CustomFigure):
""" """
if modes: if modes:
ytitle = modes[0] ytitle = modes[0]
# Creating visibles list for each mode. # logger.debug("Creating visibles list for each mode.")
self.update_layout( self.update_layout(
xaxis_title="Submitted Date (* - Date parsed from fastq file creation date)", xaxis_title="Submitted Date (* - Date parsed from fastq file creation date)",
yaxis_title=ytitle, yaxis_title=ytitle,
@@ -100,7 +98,6 @@ class IridaFigure(CustomFigure):
) )
] ]
) )
self.update_xaxes( self.update_xaxes(
rangeslider_visible=True, rangeslider_visible=True,
rangeselector=dict( rangeselector=dict(
@@ -109,7 +106,16 @@ class IridaFigure(CustomFigure):
) )
assert isinstance(self, CustomFigure) assert isinstance(self, CustomFigure)
def make_plotly_buttons(self, months: int = 6): def make_plotly_buttons(self, months: int = 6) -> Generator[dict, None, None]:
"""
Creates html buttons to zoom in on date areas
Args:
months (int, optional): Number of months of data given. Defaults to 6.
Yields:
Generator[dict, None, None]: Button details.
"""
rng = [1] rng = [1]
if months > 2: if months > 2:
rng += [iii for iii in range(3, months, 3)] rng += [iii for iii in range(3, months, 3)]
@@ -121,7 +127,7 @@ class IridaFigure(CustomFigure):
for button in buttons: for button in buttons:
yield button yield button
def make_pyqt_buttons(self, modes: list) -> list: def make_pyqt_buttons(self, modes: list) -> Generator[dict, None, None]:
""" """
Creates list of buttons with one for each mode to be used in showing/hiding mode traces. Creates list of buttons with one for each mode to be used in showing/hiding mode traces.
@@ -130,7 +136,7 @@ class IridaFigure(CustomFigure):
fig_len (int): number of traces in the figure fig_len (int): number of traces in the figure
Returns: Returns:
list: list of buttons. Generator[dict, None, None]: list of buttons.
""" """
fig_len = len(self.data) fig_len = len(self.data)
if len(modes) > 1: if len(modes) > 1:

26
src/submissions/frontend/visualizations/pcr_charts.py
View File

@@ -1,20 +1,21 @@
""" """
Functions for constructing irida controls graphs using plotly. Functions for constructing irida controls graphs using plotly.
""" """
from datetime import date
from pprint import pformat from pprint import pformat
import plotly
from plotly.graph_objs import FigureWidget, Scatter
from . import CustomFigure from . import CustomFigure
import plotly.express as px import plotly.express as px
import pandas as pd import pandas as pd
from PyQt6.QtWidgets import QWidget from PyQt6.QtWidgets import QWidget
from plotly.graph_objects import Figure
import logging import logging
from tools import get_unique_values_in_df_column, divide_chunks
from frontend.widgets.functions import select_save_file
logger = logging.getLogger(f"submissions.{__name__}") logger = logging.getLogger(f"submissions.{__name__}")
# NOTE: For click events try (haven't got working yet) ipywidgets >=7.0.0 required for figurewidgets:
# https://plotly.com/python/click-events/
class PCRFigure(CustomFigure): class PCRFigure(CustomFigure):
@@ -23,13 +24,20 @@ class PCRFigure(CustomFigure):
super().__init__(df=df, modes=modes) super().__init__(df=df, modes=modes)
logger.debug(f"DF: {self.df}") logger.debug(f"DF: {self.df}")
self.construct_chart(df=df) self.construct_chart(df=df)
# self.generic_figure_markers(modes=modes, ytitle=ytitle, months=months)
def hello(self):
print("hello")
def construct_chart(self, df: pd.DataFrame): def construct_chart(self, df: pd.DataFrame):
logger.debug(f"PCR df: {df}") logger.debug(f"PCR df:\n {df}")
try: try:
scatter = px.scatter(data_frame=df, x='submitted_date', y="ct", hover_data=["name", "target", "ct", "reagent_lot"], color='target') express = px.scatter(data_frame=df, x='submitted_date', y="ct",
hover_data=["name", "target", "ct", "reagent_lot"],
color="target")
except ValueError: except ValueError:
scatter = px.scatter() express = px.scatter()
scatter = FigureWidget([datum for datum in express.data])
self.add_traces(scatter.data) self.add_traces(scatter.data)
self.update_traces(marker={'size': 15})

7
src/submissions/frontend/widgets/__init__.py
View File

@@ -1,17 +1,14 @@
''' """
Contains all custom generated PyQT6 derivative widgets. Contains all custom generated PyQT6 derivative widgets.
''' """
# from .app import App
from .functions import * from .functions import *
from .misc import * from .misc import *
from .pop_ups import * from .pop_ups import *
from .submission_table import * from .submission_table import *
from .submission_widget import * from .submission_widget import *
from .controls_chart import * from .controls_chart import *
from .kit_creator import *
from .submission_details import * from .submission_details import *
from .equipment_usage import * from .equipment_usage import *
from .gel_checker import * from .gel_checker import *
from .submission_type_creator import *
from .app import App from .app import App

15
src/submissions/frontend/widgets/app.py
View File

@@ -9,7 +9,6 @@ from PyQt6.QtWidgets import (
) )
from PyQt6.QtGui import QAction from PyQt6.QtGui import QAction
from pathlib import Path from pathlib import Path
from markdown import markdown from markdown import markdown
from __init__ import project_path from __init__ import project_path
from tools import check_if_app, Settings, Report, jinja_template_loading, check_authorization, page_size from tools import check_if_app, Settings, Report, jinja_template_loading, check_authorization, page_size
@@ -21,8 +20,6 @@ import logging, webbrowser, sys, shutil
from .submission_table import SubmissionsSheet from .submission_table import SubmissionsSheet
from .submission_widget import SubmissionFormContainer from .submission_widget import SubmissionFormContainer
from .controls_chart import ControlsViewer from .controls_chart import ControlsViewer
from .kit_creator import KitAdder
from .submission_type_creator import SubmissionTypeAdder, SubmissionType
from .sample_search import SearchBox from .sample_search import SearchBox
from .summary import Summary from .summary import Summary
@@ -72,7 +69,6 @@ class App(QMainWindow):
fileMenu = menuBar.addMenu("&File") fileMenu = menuBar.addMenu("&File")
# NOTE: Creating menus using a title # NOTE: Creating menus using a title
methodsMenu = menuBar.addMenu("&Methods") methodsMenu = menuBar.addMenu("&Methods")
# reportMenu = menuBar.addMenu("&Reports")
maintenanceMenu = menuBar.addMenu("&Monthly") maintenanceMenu = menuBar.addMenu("&Monthly")
helpMenu = menuBar.addMenu("&Help") helpMenu = menuBar.addMenu("&Help")
helpMenu.addAction(self.helpAction) helpMenu.addAction(self.helpAction)
@@ -83,7 +79,6 @@ class App(QMainWindow):
fileMenu.addAction(self.yamlImportAction) fileMenu.addAction(self.yamlImportAction)
methodsMenu.addAction(self.searchLog) methodsMenu.addAction(self.searchLog)
methodsMenu.addAction(self.searchSample) methodsMenu.addAction(self.searchSample)
# reportMenu.addAction(self.generateReportAction)
maintenanceMenu.addAction(self.joinExtractionAction) maintenanceMenu.addAction(self.joinExtractionAction)
maintenanceMenu.addAction(self.joinPCRAction) maintenanceMenu.addAction(self.joinPCRAction)
@@ -105,7 +100,6 @@ class App(QMainWindow):
# logger.debug(f"Creating actions...") # logger.debug(f"Creating actions...")
self.importAction = QAction("&Import Submission", self) self.importAction = QAction("&Import Submission", self)
self.addReagentAction = QAction("Add Reagent", self) self.addReagentAction = QAction("Add Reagent", self)
# self.generateReportAction = QAction("Make Report", self)
self.addKitAction = QAction("Import Kit", self) self.addKitAction = QAction("Import Kit", self)
self.addOrgAction = QAction("Import Org", self) self.addOrgAction = QAction("Import Org", self)
self.joinExtractionAction = QAction("Link Extraction Logs") self.joinExtractionAction = QAction("Link Extraction Logs")
@@ -125,7 +119,6 @@ class App(QMainWindow):
# logger.debug(f"Connecting actions...") # logger.debug(f"Connecting actions...")
self.importAction.triggered.connect(self.table_widget.formwidget.importSubmission) self.importAction.triggered.connect(self.table_widget.formwidget.importSubmission)
self.addReagentAction.triggered.connect(self.table_widget.formwidget.add_reagent) self.addReagentAction.triggered.connect(self.table_widget.formwidget.add_reagent)
# self.generateReportAction.triggered.connect(self.table_widget.sub_wid.generate_report)
self.joinExtractionAction.triggered.connect(self.table_widget.sub_wid.link_extractions) self.joinExtractionAction.triggered.connect(self.table_widget.sub_wid.link_extractions)
self.joinPCRAction.triggered.connect(self.table_widget.sub_wid.link_pcr) self.joinPCRAction.triggered.connect(self.table_widget.sub_wid.link_pcr)
self.helpAction.triggered.connect(self.showAbout) self.helpAction.triggered.connect(self.showAbout)
@@ -233,6 +226,7 @@ class App(QMainWindow):
ap.exec() ap.exec()
st = SubmissionType.import_from_json(filepath=fname) st = SubmissionType.import_from_json(filepath=fname)
if st: if st:
# NOTE: Do not delete the print statement below.
print(pformat(st.to_export_dict())) print(pformat(st.to_export_dict()))
choice = input("Save the above submission type? [y/N]: ") choice = input("Save the above submission type? [y/N]: ")
if choice.lower() == "y": if choice.lower() == "y":
@@ -262,7 +256,6 @@ class AddSubForm(QWidget):
self.tabs.addTab(self.tab2, "Irida Controls") self.tabs.addTab(self.tab2, "Irida Controls")
self.tabs.addTab(self.tab3, "PCR Controls") self.tabs.addTab(self.tab3, "PCR Controls")
self.tabs.addTab(self.tab4, "Cost Report") self.tabs.addTab(self.tab4, "Cost Report")
# self.tabs.addTab(self.tab4, "Add Kit")
# NOTE: Create submission adder form # NOTE: Create submission adder form
self.formwidget = SubmissionFormContainer(self) self.formwidget = SubmissionFormContainer(self)
self.formlayout = QVBoxLayout(self) self.formlayout = QVBoxLayout(self)
@@ -294,16 +287,10 @@ class AddSubForm(QWidget):
self.pcr_viewer = ControlsViewer(self, archetype="PCR Control") self.pcr_viewer = ControlsViewer(self, archetype="PCR Control")
self.tab3.layout.addWidget(self.pcr_viewer) self.tab3.layout.addWidget(self.pcr_viewer)
self.tab3.setLayout(self.tab3.layout) self.tab3.setLayout(self.tab3.layout)
# NOTE: create custom widget to add new tabs
# ST_adder = SubmissionTypeAdder(self)
summary_report = Summary(self) summary_report = Summary(self)
self.tab4.layout = QVBoxLayout(self) self.tab4.layout = QVBoxLayout(self)
self.tab4.layout.addWidget(summary_report) self.tab4.layout.addWidget(summary_report)
self.tab4.setLayout(self.tab4.layout) self.tab4.setLayout(self.tab4.layout)
# kit_adder = KitAdder(self)
# self.tab4.layout = QVBoxLayout(self)
# self.tab4.layout.addWidget(kit_adder)
# self.tab4.setLayout(self.tab4.layout)
# NOTE: add tabs to main widget # NOTE: add tabs to main widget
self.layout.addWidget(self.tabs) self.layout.addWidget(self.tabs)
self.setLayout(self.layout) self.setLayout(self.layout)

195
src/submissions/frontend/widgets/controls_chart.py
View File

@@ -1,23 +1,17 @@
""" """
Handles display of control charts Handles display of control charts
""" """
import re from datetime import date
import sys
from datetime import timedelta, date
from pprint import pformat from pprint import pformat
from typing import Tuple
from PyQt6.QtWebEngineWidgets import QWebEngineView from PyQt6.QtWebEngineWidgets import QWebEngineView
from PyQt6.QtWidgets import ( from PyQt6.QtWidgets import (
QWidget, QVBoxLayout, QComboBox, QHBoxLayout, QWidget, QComboBox, QPushButton, QGridLayout
QDateEdit, QLabel, QSizePolicy, QPushButton, QGridLayout
) )
from PyQt6.QtCore import QSignalBlocker from PyQt6.QtCore import QSignalBlocker
from backend.db import ControlType, IridaControl from backend.db import ControlType, IridaControl
from PyQt6.QtCore import QDate, QSize
import logging import logging
from pandas import DataFrame from tools import Report, report_result
from tools import Report, Result, get_unique_values_in_df_column, Settings, report_result from frontend.visualizations import CustomFigure
from frontend.visualizations import IridaFigure, PCRFigure, CustomFigure
from .misc import StartEndDatePicker from .misc import StartEndDatePicker
logger = logging.getLogger(f"submissions.{__name__}") logger = logging.getLogger(f"submissions.{__name__}")
@@ -70,19 +64,12 @@ class ControlsViewer(QWidget):
self.save_button.pressed.connect(self.save_chart_function) self.save_button.pressed.connect(self.save_chart_function)
self.export_button.pressed.connect(self.save_data_function) self.export_button.pressed.connect(self.save_data_function)
def save_chart_function(self): def save_chart_function(self):
self.fig.save_figure(parent=self) self.fig.save_figure(parent=self)
def save_data_function(self): def save_data_function(self):
self.fig.save_data(parent=self) self.fig.save_data(parent=self)
# def controls_getter(self):
# """
# Lookup controls from database and send to chartmaker
# """
# self.controls_getter_function()
@report_result @report_result
def controls_getter_function(self, *args, **kwargs): def controls_getter_function(self, *args, **kwargs):
""" """
@@ -128,7 +115,18 @@ class ControlsViewer(QWidget):
self.chart_maker_function() self.chart_maker_function()
return report return report
def diff_month(self, d1: date, d2: date): @classmethod
def diff_month(self, d1: date, d2: date) -> float:
"""
Gets the number of months difference between two different dates
Args:
d1 (date): Start date.
d2 (date): End date.
Returns:
float: Number of months difference
"""
return abs((d1.year - d2.year) * 12 + d1.month - d2.month) return abs((d1.year - d2.year) * 12 + d1.month - d2.month)
@report_result @report_result
@@ -169,164 +167,3 @@ class ControlsViewer(QWidget):
# logger.debug("Figure updated... I hope.") # logger.debug("Figure updated... I hope.")
return report return report
# def convert_data_list_to_df(self, input_df: list[dict]) -> DataFrame:
# """
# Convert list of control records to dataframe
#
# Args:
# ctx (dict): settings passed from gui
# input_df (list[dict]): list of dictionaries containing records
# mode_sub_type (str | None, optional): sub_type of submission type. Defaults to None.
#
# Returns:
# DataFrame: dataframe of controls
# """
#
# df = DataFrame.from_records(input_df)
# safe = ['name', 'submitted_date', 'genus', 'target']
# for column in df.columns:
# if column not in safe:
# if self.mode_sub_type is not None and column != self.mode_sub_type:
# continue
# else:
# safe.append(column)
# if "percent" in column:
# # count_col = [item for item in df.columns if "count" in item][0]
# try:
# count_col = next(item for item in df.columns if "count" in item)
# except StopIteration:
# continue
# # NOTE: The actual percentage from kraken was off due to exclusion of NaN, recalculating.
# df[column] = 100 * df[count_col] / df.groupby('name')[count_col].transform('sum')
# df = df[[c for c in df.columns if c in safe]]
# # NOTE: move date of sample submitted on same date as previous ahead one.
# df = self.displace_date(df=df)
# # NOTE: ad hoc method to make data labels more accurate.
# df = self.df_column_renamer(df=df)
# return df
#
# def df_column_renamer(self, df: DataFrame) -> DataFrame:
# """
# Ad hoc function I created to clarify some fields
#
# Args:
# df (DataFrame): input dataframe
#
# Returns:
# DataFrame: dataframe with 'clarified' column names
# """
# df = df[df.columns.drop(list(df.filter(regex='_hashes')))]
# return df.rename(columns={
# "contains_ratio": "contains_shared_hashes_ratio",
# "matches_ratio": "matches_shared_hashes_ratio",
# "kraken_count": "kraken2_read_count_(top_50)",
# "kraken_percent": "kraken2_read_percent_(top_50)"
# })
#
# def displace_date(self, df: DataFrame) -> DataFrame:
# """
# This function serves to split samples that were submitted on the same date by incrementing dates.
# It will shift the date forward by one day if it is the same day as an existing date in a list.
#
# Args:
# df (DataFrame): input dataframe composed of control records
#
# Returns:
# DataFrame: output dataframe with dates incremented.
# """
# # logger.debug(f"Unique items: {df['name'].unique()}")
# # NOTE: get submitted dates for each control
# dict_list = [dict(name=item, date=df[df.name == item].iloc[0]['submitted_date']) for item in
# sorted(df['name'].unique())]
# previous_dates = set()
# # for _, item in enumerate(dict_list):
# for item in dict_list:
# df, previous_dates = self.check_date(df=df, item=item, previous_dates=previous_dates)
# return df
#
# def check_date(self, df: DataFrame, item: dict, previous_dates: set) -> Tuple[DataFrame, list]:
# """
# Checks if an items date is already present in df and adjusts df accordingly
#
# Args:
# df (DataFrame): input dataframe
# item (dict): control for checking
# previous_dates (list): list of dates found in previous controls
#
# Returns:
# Tuple[DataFrame, list]: Output dataframe and appended list of previous dates
# """
# try:
# check = item['date'] in previous_dates
# except IndexError:
# check = False
# previous_dates.add(item['date'])
# if check:
# # logger.debug(f"We found one! Increment date!\n\t{item['date']} to {item['date'] + timedelta(days=1)}")
# # NOTE: get df locations where name == item name
# mask = df['name'] == item['name']
# # NOTE: increment date in dataframe
# df.loc[mask, 'submitted_date'] = df.loc[mask, 'submitted_date'].apply(lambda x: x + timedelta(days=1))
# item['date'] += timedelta(days=1)
# passed = False
# else:
# passed = True
# # logger.debug(f"\n\tCurrent date: {item['date']}\n\tPrevious dates:{previous_dates}")
# # logger.debug(f"DF: {type(df)}, previous_dates: {type(previous_dates)}")
# # NOTE: if run didn't lead to changed date, return values
# if passed:
# # logger.debug(f"Date check passed, returning.")
# return df, previous_dates
# # NOTE: if date was changed, rerun with new date
# else:
# logger.warning(f"Date check failed, running recursion")
# df, previous_dates = self.check_date(df, item, previous_dates)
# return df, previous_dates
#
# def prep_df(self, ctx: Settings, df: DataFrame) -> Tuple[DataFrame, list]:
# """
# Constructs figures based on parsed pandas dataframe.
#
# Args:
# ctx (Settings): settings passed down from gui
# df (pd.DataFrame): input dataframe
# ytitle (str | None, optional): title for the y-axis. Defaults to None.
#
# Returns:
# Figure: Plotly figure
# """
# # NOTE: converts starred genera to normal and splits off list of starred
# if df.empty:
# return None
# df['genus'] = df['genus'].replace({'\*': ''}, regex=True).replace({"NaN": "Unknown"})
# df['genera'] = [item[-1] if item and item[-1] == "*" else "" for item in df['genus'].to_list()]
# # NOTE: remove original runs, using reruns if applicable
# df = self.drop_reruns_from_df(ctx=ctx, df=df)
# # NOTE: sort by and exclude from
# sorts = ['submitted_date', "target", "genus"]
# exclude = ['name', 'genera']
# modes = [item for item in df.columns if item not in sorts and item not in exclude]
# # NOTE: Set descending for any columns that have "{mode}" in the header.
# ascending = [False if item == "target" else True for item in sorts]
# df = df.sort_values(by=sorts, ascending=ascending)
# # logger.debug(df[df.isna().any(axis=1)])
# # NOTE: actual chart construction is done by
# return df, modes
#
# def drop_reruns_from_df(self, ctx: Settings, df: DataFrame) -> DataFrame:
# """
# Removes semi-duplicates from dataframe after finding sequencing repeats.
#
# Args:
# settings (dict): settings passed from gui
# df (DataFrame): initial dataframe
#
# Returns:
# DataFrame: dataframe with originals removed in favour of repeats.
# """
# if 'rerun_regex' in ctx:
# sample_names = get_unique_values_in_df_column(df, column_name="name")
# rerun_regex = re.compile(fr"{ctx.rerun_regex}")
# exclude = [re.sub(rerun_regex, "", sample) for sample in sample_names if rerun_regex.search(sample)]
# df = df[df.name not in exclude]
# return df

4
src/submissions/frontend/widgets/equipment_usage.py
View File

@@ -8,7 +8,7 @@ from PyQt6.QtWidgets import (QDialog, QComboBox, QCheckBox,
from backend.db.models import Equipment, BasicSubmission, Process from backend.db.models import Equipment, BasicSubmission, Process
from backend.validators.pydant import PydEquipment, PydEquipmentRole, PydTips from backend.validators.pydant import PydEquipment, PydEquipmentRole, PydTips
import logging import logging
from typing import List, Generator from typing import Generator
logger = logging.getLogger(f"submissions.{__name__}") logger = logging.getLogger(f"submissions.{__name__}")
@@ -50,7 +50,7 @@ class EquipmentUsage(QDialog):
Pull info from all RoleComboBox widgets Pull info from all RoleComboBox widgets
Returns: Returns:
List[PydEquipment]: All equipment pulled from widgets Generator[PydEquipment, None, None]: All equipment pulled from widgets
""" """
for widget in self.findChildren(QWidget): for widget in self.findChildren(QWidget):
match widget: match widget:

1
src/submissions/frontend/widgets/functions.py
View File

@@ -4,7 +4,6 @@ functions used by all windows in the application's frontend
from pathlib import Path from pathlib import Path
import logging import logging
from PyQt6.QtWidgets import QMainWindow, QFileDialog from PyQt6.QtWidgets import QMainWindow, QFileDialog
from tools import Result
logger = logging.getLogger(f"submissions.{__name__}") logger = logging.getLogger(f"submissions.{__name__}")

232
src/submissions/frontend/widgets/kit_creator.py
View File

@@ -1,232 +0,0 @@
from PyQt6.QtWidgets import (
QWidget, QVBoxLayout, QScrollArea,
QGridLayout, QPushButton, QLabel,
QLineEdit, QComboBox, QDoubleSpinBox,
QSpinBox, QDateEdit
)
from sqlalchemy import FLOAT, INTEGER
from backend.db import SubmissionTypeKitTypeAssociation, SubmissionType, ReagentRole
from backend.validators import PydReagentRole, PydKit
import logging
from pprint import pformat
from tools import Report
from typing import Tuple
logger = logging.getLogger(f"submissions.{__name__}")
class KitAdder(QWidget):
"""
dialog to get information to add kit
"""
def __init__(self, parent) -> None:
super().__init__(parent)
self.report = Report()
self.app = parent.parent
main_box = QVBoxLayout(self)
scroll = QScrollArea(self)
main_box.addWidget(scroll)
scroll.setWidgetResizable(True)
scrollContent = QWidget(scroll)
self.grid = QGridLayout()
scrollContent.setLayout(self.grid)
# NOTE: insert submit button at top
self.submit_btn = QPushButton("Submit")
self.grid.addWidget(self.submit_btn,0,0,1,1)
self.grid.addWidget(QLabel("Kit Name:"),2,0)
# NOTE: widget to get kit name
kit_name = QLineEdit()
kit_name.setObjectName("kit_name")
self.grid.addWidget(kit_name,2,1)
self.grid.addWidget(QLabel("Used For Submission Type:"),3,0)
# NOTE: widget to get uses of kit
used_for = QComboBox()
used_for.setObjectName("used_for")
# NOTE: Insert all existing sample types
used_for.addItems([item.name for item in SubmissionType.query()])
used_for.setEditable(True)
self.grid.addWidget(used_for,3,1)
# NOTE: Get all fields in SubmissionTypeKitTypeAssociation
self.columns = [item for item in SubmissionTypeKitTypeAssociation.__table__.columns if len(item.foreign_keys) == 0]
for iii, column in enumerate(self.columns):
idx = iii + 4
# NOTE: convert field name to human readable.
field_name = column.name.replace("_", " ").title()
self.grid.addWidget(QLabel(field_name),idx,0)
match column.type:
case FLOAT():
add_widget = QDoubleSpinBox()
add_widget.setMinimum(0)
add_widget.setMaximum(9999)
case INTEGER():
add_widget = QSpinBox()
add_widget.setMinimum(0)
add_widget.setMaximum(9999)
case _:
add_widget = QLineEdit()
add_widget.setObjectName(column.name)
self.grid.addWidget(add_widget, idx,1)
self.add_RT_btn = QPushButton("Add Reagent Type")
self.grid.addWidget(self.add_RT_btn)
self.add_RT_btn.clicked.connect(self.add_RT)
self.submit_btn.clicked.connect(self.submit)
scroll.setWidget(scrollContent)
self.ignore = [None, "", "qt_spinbox_lineedit", "qt_scrollarea_viewport", "qt_scrollarea_hcontainer",
"qt_scrollarea_vcontainer", "submit_btn"
]
def add_RT(self) -> None:
"""
insert new reagent type row
"""
# NOTE: get bottommost row
maxrow = self.grid.rowCount()
reg_form = ReagentRoleForm(parent=self)
reg_form.setObjectName(f"ReagentForm_{maxrow}")
self.grid.addWidget(reg_form, maxrow,0,1,4)
def submit(self) -> None:
"""
send kit to database
"""
report = Report()
# NOTE: get form info
info, reagents = self.parse_form()
info = {k:v for k,v in info.items() if k in [column.name for column in self.columns] + ['kit_name', 'used_for']}
# logger.debug(f"kit info: {pformat(info)}")
# logger.debug(f"kit reagents: {pformat(reagents)}")
info['reagent_roles'] = reagents
# logger.debug(pformat(info))
# NOTE: send to kit constructor
kit = PydKit(name=info['kit_name'])
for reagent in info['reagent_roles']:
uses = {
info['used_for']:
{'sheet':reagent['sheet'],
'name':reagent['name'],
'lot':reagent['lot'],
'expiry':reagent['expiry']
}}
kit.reagent_roles.append(PydReagentRole(name=reagent['rtname'], eol_ext=reagent['eol'], uses=uses))
# logger.debug(f"Output pyd object: {kit.__dict__}")
sqlobj, result = kit.toSQL(self.ctx)
report.add_result(result=result)
sqlobj.save()
self.__init__(self.parent())
def parse_form(self) -> Tuple[dict, list]:
"""
Pulls reagent and general info from form
Returns:
Tuple[dict, list]: dict=info, list=reagents
"""
# logger.debug(f"Hello from {self.__class__} parser!")
info = {}
reagents = []
widgets = [widget for widget in self.findChildren(QWidget) if widget.objectName() not in self.ignore and not isinstance(widget.parent(), ReagentRoleForm)]
for widget in widgets:
# logger.debug(f"Parsed widget: {widget.objectName()} of type {type(widget)} with parent {widget.parent()}")
match widget:
case ReagentRoleForm():
reagents.append(widget.parse_form())
case QLineEdit():
info[widget.objectName()] = widget.text()
case QComboBox():
info[widget.objectName()] = widget.currentText()
case QDateEdit():
info[widget.objectName()] = widget.date().toPyDate()
return info, reagents
class ReagentRoleForm(QWidget):
"""
custom widget to add information about a new reagenttype
"""
def __init__(self, parent) -> None:
super().__init__(parent)
grid = QGridLayout()
self.setLayout(grid)
grid.addWidget(QLabel("Reagent Type Name"),0,0)
# Widget to get reagent info
self.reagent_getter = QComboBox()
self.reagent_getter.setObjectName("rtname")
# lookup all reagent type names from db
lookup = ReagentRole.query()
# logger.debug(f"Looked up ReagentType names: {lookup}")
self.reagent_getter.addItems([item.name for item in lookup])
self.reagent_getter.setEditable(True)
grid.addWidget(self.reagent_getter,0,1)
grid.addWidget(QLabel("Extension of Life (months):"),0,2)
# NOTE: widget to get extension of life
self.eol = QSpinBox()
self.eol.setObjectName('eol')
self.eol.setMinimum(0)
grid.addWidget(self.eol, 0,3)
grid.addWidget(QLabel("Excel Location Sheet Name:"),1,0)
self.location_sheet_name = QLineEdit()
self.location_sheet_name.setObjectName("sheet")
self.location_sheet_name.setText("e.g. 'Reagent Info'")
grid.addWidget(self.location_sheet_name, 1,1)
for iii, item in enumerate(["Name", "Lot", "Expiry"]):
idx = iii + 2
grid.addWidget(QLabel(f"{item} Row:"), idx, 0)
row = QSpinBox()
row.setFixedWidth(50)
row.setObjectName(f'{item.lower()}_row')
row.setMinimum(0)
grid.addWidget(row, idx, 1)
grid.addWidget(QLabel(f"{item} Column:"), idx, 2)
col = QSpinBox()
col.setFixedWidth(50)
col.setObjectName(f'{item.lower()}_column')
col.setMinimum(0)
grid.addWidget(col, idx, 3)
self.setFixedHeight(175)
max_row = grid.rowCount()
self.r_button = QPushButton("Remove")
self.r_button.clicked.connect(self.remove)
grid.addWidget(self.r_button,max_row,0,1,1)
self.ignore = [None, "", "qt_spinbox_lineedit", "qt_scrollarea_viewport", "qt_scrollarea_hcontainer",
"qt_scrollarea_vcontainer", "submit_btn", "eol", "sheet", "rtname"
]
def remove(self):
"""
Destroys this row of reagenttype from the form
"""
self.setParent(None)
self.destroy()
def parse_form(self) -> dict:
"""
Pulls ReagentType info from the form.
Returns:
dict: _description_
"""
# logger.debug(f"Hello from {self.__class__} parser!")
info = {}
info['eol'] = self.eol.value()
info['sheet'] = self.location_sheet_name.text()
info['rtname'] = self.reagent_getter.currentText()
widgets = [widget for widget in self.findChildren(QWidget) if widget.objectName() not in self.ignore]
for widget in widgets:
# logger.debug(f"Parsed widget: {widget.objectName()} of type {type(widget)} with parent {widget.parent()}")
match widget:
case QLineEdit():
info[widget.objectName()] = widget.text()
case QComboBox():
info[widget.objectName()] = widget.currentText()
case QDateEdit():
info[widget.objectName()] = widget.date().toPyDate()
case QSpinBox() | QDoubleSpinBox():
if "_" in widget.objectName():
key, sub_key = widget.objectName().split("_")
if key not in info.keys():
info[key] = {}
# logger.debug(f"Adding key {key}, {sub_key} and value {widget.value()} to {info}")
info[key][sub_key] = widget.value()
return info

2
src/submissions/frontend/widgets/misc.py
View File

@@ -3,7 +3,6 @@ Contains miscellaneous widgets for frontend functions
''' '''
import math import math
from datetime import date from datetime import date
from PyQt6.QtGui import QPageLayout, QPageSize, QStandardItem, QIcon from PyQt6.QtGui import QPageLayout, QPageSize, QStandardItem, QIcon
from PyQt6.QtWebEngineWidgets import QWebEngineView from PyQt6.QtWebEngineWidgets import QWebEngineView
from PyQt6.QtWidgets import ( from PyQt6.QtWidgets import (
@@ -51,7 +50,6 @@ class AddReagentForm(QDialog):
self.exp_input.setObjectName('expiry') self.exp_input.setObjectName('expiry')
# NOTE: if expiry is not passed in from gui, use today # NOTE: if expiry is not passed in from gui, use today
if expiry is None: if expiry is None:
# self.exp_input.setDate(QDate.currentDate())
self.exp_input.setDate(QDate(1970, 1, 1)) self.exp_input.setDate(QDate(1970, 1, 1))
else: else:
try: try:

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

@@ -9,7 +9,7 @@ from PyQt6.QtWebEngineWidgets import QWebEngineView
from tools import jinja_template_loading from tools import jinja_template_loading
import logging import logging
from backend.db import models from backend.db import models
from typing import Literal from typing import Any, Literal
logger = logging.getLogger(f"submissions.{__name__}") logger = logging.getLogger(f"submissions.{__name__}")
@@ -54,9 +54,8 @@ class AlertPop(QMessageBox):
class HTMLPop(QDialog): class HTMLPop(QDialog):
def __init__(self, html: str, owner: str | None = None, title: str = "python"): def __init__(self, html: str, title: str = "python"):
super().__init__() super().__init__()
self.webview = QWebEngineView(parent=self) self.webview = QWebEngineView(parent=self)
self.layout = QVBoxLayout() self.layout = QVBoxLayout()
self.setWindowTitle(title) self.setWindowTitle(title)

1
src/submissions/frontend/widgets/sample_search.py
View File

@@ -74,7 +74,6 @@ class SearchBox(QDialog):
# logger.debug(f"Running update_data with sample type: {self.type}") # logger.debug(f"Running update_data with sample type: {self.type}")
fields = self.parse_form() fields = self.parse_form()
# logger.debug(f"Got fields: {fields}") # logger.debug(f"Got fields: {fields}")
# sample_list_creator = self.type.fuzzy_search(sample_type=self.type, **fields)
sample_list_creator = self.type.fuzzy_search(**fields) sample_list_creator = self.type.fuzzy_search(**fields)
data = self.type.samples_to_df(sample_list=sample_list_creator) data = self.type.samples_to_df(sample_list=sample_list_creator)
# logger.debug(f"Data: {data}") # logger.debug(f"Data: {data}")

7
src/submissions/frontend/widgets/submission_details.py
View File

@@ -1,13 +1,11 @@
""" """
Webview to show submission and sample details. Webview to show submission and sample details.
""" """
from PyQt6.QtGui import QColor, QPageSize, QPageLayout
from PyQt6.QtPrintSupport import QPrinter
from PyQt6.QtWidgets import (QDialog, QPushButton, QVBoxLayout, from PyQt6.QtWidgets import (QDialog, QPushButton, QVBoxLayout,
QDialogButtonBox, QTextEdit, QGridLayout) QDialogButtonBox, QTextEdit, QGridLayout)
from PyQt6.QtWebEngineWidgets import QWebEngineView from PyQt6.QtWebEngineWidgets import QWebEngineView
from PyQt6.QtWebChannel import QWebChannel from PyQt6.QtWebChannel import QWebChannel
from PyQt6.QtCore import Qt, pyqtSlot, QMarginsF, QSize from PyQt6.QtCore import Qt, pyqtSlot
from jinja2 import TemplateNotFound from jinja2 import TemplateNotFound
from backend.db.models import BasicSubmission, BasicSample, Reagent, KitType from backend.db.models import BasicSubmission, BasicSample, Reagent, KitType
from tools import is_power_user, jinja_template_loading from tools import is_power_user, jinja_template_loading
@@ -41,7 +39,6 @@ class SubmissionDetails(QDialog):
self.webview.setMaximumWidth(900) self.webview.setMaximumWidth(900)
self.webview.loadFinished.connect(self.activate_export) self.webview.loadFinished.connect(self.activate_export)
self.layout = QGridLayout() self.layout = QGridLayout()
# self.setFixedSize(900, 500)
# NOTE: button to export a pdf version # NOTE: button to export a pdf version
self.btn = QPushButton("Export PDF") self.btn = QPushButton("Export PDF")
self.btn.setFixedWidth(775) self.btn.setFixedWidth(775)
@@ -69,7 +66,6 @@ class SubmissionDetails(QDialog):
def back_function(self): def back_function(self):
self.webview.back() self.webview.back()
# @pyqtSlot(bool)
def activate_export(self): def activate_export(self):
title = self.webview.title() title = self.webview.title()
self.setWindowTitle(title) self.setWindowTitle(title)
@@ -144,7 +140,6 @@ class SubmissionDetails(QDialog):
self.base_dict = submission.to_dict(full_data=True) 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 == 'reagents'})}") # logger.debug(f"Submission details data:\n{pformat({k:v for k,v in self.base_dict.items() if k == 'reagents'})}")
# NOTE: don't want id # NOTE: don't want id
self.base_dict = submission.finalize_details(self.base_dict)
# logger.debug(f"Creating barcode.") # logger.debug(f"Creating barcode.")
# logger.debug(f"Making platemap...") # logger.debug(f"Making platemap...")
self.base_dict['platemap'] = submission.make_plate_map(sample_list=submission.hitpick_plate()) self.base_dict['platemap'] = submission.make_plate_map(sample_list=submission.hitpick_plate())

8
src/submissions/frontend/widgets/submission_table.py
View File

@@ -10,8 +10,6 @@ from backend.db.models import BasicSubmission
from tools import Report, Result, report_result from tools import Report, Result, report_result
from .functions import select_open_file from .functions import select_open_file
# from .misc import ReportDatePicker
logger = logging.getLogger(f"submissions.{__name__}") logger = logging.getLogger(f"submissions.{__name__}")
@@ -91,7 +89,7 @@ class SubmissionsSheet(QTableView):
""" """
sets data in model sets data in model
""" """
self.data = BasicSubmission.submissions_to_df(page=page) self.data = BasicSubmission.submissions_to_df(page=page, page_size=page_size)
try: try:
self.data['Id'] = self.data['Id'].apply(str) self.data['Id'] = self.data['Id'].apply(str)
self.data['Id'] = self.data['Id'].str.zfill(4) self.data['Id'] = self.data['Id'].str.zfill(4)
@@ -101,7 +99,7 @@ class SubmissionsSheet(QTableView):
proxyModel.setSourceModel(pandasModel(self.data)) proxyModel.setSourceModel(pandasModel(self.data))
self.setModel(proxyModel) self.setModel(proxyModel)
def contextMenuEvent(self, event): def contextMenuEvent(self):
""" """
Creates actions for right click menu events. Creates actions for right click menu events.
@@ -157,7 +155,7 @@ class SubmissionsSheet(QTableView):
report = Report() report = Report()
fname = select_open_file(self, file_extension="csv") fname = select_open_file(self, file_extension="csv")
with open(fname.__str__(), 'r') as f: with open(fname.__str__(), 'r') as f:
# split csv on commas # NOTE: split csv on commas
runs = [col.strip().split(",") for col in f.readlines()] runs = [col.strip().split(",") for col in f.readlines()]
count = 0 count = 0
for run in runs: for run in runs:

124
src/submissions/frontend/widgets/submission_type_creator.py
View File

@@ -1,124 +0,0 @@
from PyQt6.QtCore import Qt
from PyQt6.QtWidgets import (
QWidget, QVBoxLayout, QScrollArea,
QGridLayout, QPushButton, QLabel,
QLineEdit, QSpinBox, QCheckBox
)
from sqlalchemy.orm.attributes import InstrumentedAttribute
from backend.db import SubmissionType, BasicSubmission
import logging
from tools import Report
from .functions import select_open_file
logger = logging.getLogger(f"submissions.{__name__}")
class SubmissionTypeAdder(QWidget):
def __init__(self, parent) -> None:
super().__init__(parent)
self.report = Report()
self.app = parent.parent()
self.template_path = ""
main_box = QVBoxLayout(self)
scroll = QScrollArea(self)
main_box.addWidget(scroll)
scroll.setWidgetResizable(True)
scrollContent = QWidget(scroll)
self.grid = QGridLayout()
scrollContent.setLayout(self.grid)
# NOTE: insert submit button at top
self.submit_btn = QPushButton("Submit")
self.grid.addWidget(self.submit_btn,0,0,1,1)
self.grid.addWidget(QLabel("Submission Type Name:"),2,0)
# NOTE: widget to get kit name
self.st_name = QLineEdit()
self.st_name.setObjectName("submission_type_name")
self.grid.addWidget(self.st_name,2,1,1,2)
self.grid.addWidget(QLabel("Template File"),3,0)
template_selector = QPushButton("Select")
self.grid.addWidget(template_selector,3,1)
self.template_label = QLabel("None")
self.grid.addWidget(self.template_label,3,2)
# NOTE: widget to get uses of kit
exclude = ['id', 'submitting_lab_id', 'extraction_kit_id', 'reagents_id', 'extraction_info', 'pcr_info', 'run_cost']
self.columns = {key:value for key, value in BasicSubmission.__dict__.items() if isinstance(value, InstrumentedAttribute)}
self.columns = {key:value for key, value in self.columns.items() if hasattr(value, "type") and key not in exclude}
for iii, key in enumerate(self.columns):
idx = iii + 4
self.grid.addWidget(InfoWidget(parent=self, key=key), idx,0,1,3)
scroll.setWidget(scrollContent)
self.submit_btn.clicked.connect(self.submit)
template_selector.clicked.connect(self.get_template_path)
def submit(self):
"""
Create SubmissionType and send to db
"""
info = self.parse_form()
ST = SubmissionType(name=self.st_name.text(), info_map=info)
try:
with open(self.template_path, "rb") as f:
ST.template_file = f.read()
except FileNotFoundError:
logger.error(f"Could not find template file: {self.template_path}")
ST.save()
def parse_form(self) -> dict:
"""
Pulls info from form
Returns:
dict: information from form
"""
widgets = [widget for widget in self.findChildren(QWidget) if isinstance(widget, InfoWidget)]
return {widget.objectName():widget.parse_form() for widget in widgets}
def get_template_path(self):
"""
Sets path for loading a submission form template
"""
self.template_path = select_open_file(obj=self, file_extension="xlsx")
self.template_label.setText(self.template_path.__str__())
class InfoWidget(QWidget):
def __init__(self, parent: QWidget, key) -> None:
super().__init__(parent)
grid = QGridLayout()
self.setLayout(grid)
self.active = QCheckBox()
self.active.setChecked(True)
grid.addWidget(self.active, 0,0,1,1)
grid.addWidget(QLabel(key.replace("_", " ").title()),0,1,1,4)
self.setObjectName(key)
grid.addWidget(QLabel("Sheet Names (comma seperated):"),1,0)
self.sheet = QLineEdit()
self.sheet.setObjectName("sheets")
grid.addWidget(self.sheet, 1,1,1,3)
grid.addWidget(QLabel("Row:"),2,0,alignment=Qt.AlignmentFlag.AlignRight)
self.row = QSpinBox()
self.row.setObjectName("row")
grid.addWidget(self.row,2,1)
grid.addWidget(QLabel("Column:"),2,2,alignment=Qt.AlignmentFlag.AlignRight)
self.column = QSpinBox()
self.column.setObjectName("column")
grid.addWidget(self.column,2,3)
def parse_form(self) -> dict|None:
"""
Pulls info from the Info form.
Returns:
dict: sheets, row, column
"""
if self.active.isChecked():
return dict(
sheets = self.sheet.text().split(","),
row = self.row.value(),
column = self.column.value()
)
else:
return None

49
src/submissions/frontend/widgets/submission_widget.py
View File

@@ -1,8 +1,6 @@
''' '''
Contains all submission related frontend functions Contains all submission related frontend functions
''' '''
import sys
from PyQt6.QtWidgets import ( from PyQt6.QtWidgets import (
QWidget, QPushButton, QVBoxLayout, QWidget, QPushButton, QVBoxLayout,
QComboBox, QDateEdit, QLineEdit, QLabel QComboBox, QDateEdit, QLineEdit, QLabel
@@ -11,7 +9,7 @@ from PyQt6.QtCore import pyqtSignal, Qt
from . import select_open_file, select_save_file from . import select_open_file, select_save_file
import logging, difflib import logging, difflib
from pathlib import Path from pathlib import Path
from tools import Report, Result, check_not_nan, main_form_style, report_result, check_regex_match from tools import Report, Result, check_not_nan, main_form_style, report_result
from backend.excel.parser import SheetParser from backend.excel.parser import SheetParser
from backend.validators import PydSubmission, PydReagent from backend.validators import PydSubmission, PydReagent
from backend.db import ( from backend.db import (
@@ -28,6 +26,9 @@ logger = logging.getLogger(f"submissions.{__name__}")
class MyQComboBox(QComboBox): class MyQComboBox(QComboBox):
"""
Custom combobox that disables wheel events until focussed on.
"""
def __init__(self, scrollWidget=None, *args, **kwargs): def __init__(self, scrollWidget=None, *args, **kwargs):
super(MyQComboBox, self).__init__(*args, **kwargs) super(MyQComboBox, self).__init__(*args, **kwargs)
self.scrollWidget = scrollWidget self.scrollWidget = scrollWidget
@@ -42,6 +43,9 @@ class MyQComboBox(QComboBox):
class MyQDateEdit(QDateEdit): class MyQDateEdit(QDateEdit):
"""
Custom date editor that disables wheel events until focussed on.
"""
def __init__(self, scrollWidget=None, *args, **kwargs): def __init__(self, scrollWidget=None, *args, **kwargs):
super(MyQDateEdit, self).__init__(*args, **kwargs) super(MyQDateEdit, self).__init__(*args, **kwargs)
self.scrollWidget = scrollWidget self.scrollWidget = scrollWidget
@@ -340,8 +344,6 @@ class SubmissionFormWidget(QWidget):
_, result = self.pyd.check_kit_integrity() _, result = self.pyd.check_kit_integrity()
report.add_result(result) report.add_result(result)
if len(result.results) > 0: if len(result.results) > 0:
# self.app.report.add_result(report)
# self.app.report_result()
return return
# logger.debug(f"PYD before transformation into SQL:\n\n{self.pyd}\n\n") # logger.debug(f"PYD before transformation into SQL:\n\n{self.pyd}\n\n")
base_submission, result = self.pyd.to_sql() base_submission, result = self.pyd.to_sql()
@@ -370,14 +372,10 @@ class SubmissionFormWidget(QWidget):
else: else:
self.app.ctx.database_session.rollback() self.app.ctx.database_session.rollback()
report.add_result(Result(msg="Overwrite cancelled", status="Information")) report.add_result(Result(msg="Overwrite cancelled", status="Information"))
# self.app.report.add_result(report)
# self.app.report_result()
return report return report
# NOTE: code 2: No RSL plate number given # NOTE: code 2: No RSL plate number given
case 2: case 2:
report.add_result(result) report.add_result(result)
# self.app.report.add_result(report)
# self.app.report_result()
return report return report
case _: case _:
pass pass
@@ -451,7 +449,6 @@ class SubmissionFormWidget(QWidget):
info[item] = value info[item] = value
for k, v in info.items(): for k, v in info.items():
self.pyd.set_attribute(key=k, value=v) self.pyd.set_attribute(key=k, value=v)
# NOTE: return submission
report.add_result(report) report.add_result(report)
return report return report
@@ -527,18 +524,18 @@ class SubmissionFormWidget(QWidget):
match key: match key:
case 'submitting_lab': case 'submitting_lab':
add_widget = MyQComboBox(scrollWidget=parent) add_widget = MyQComboBox(scrollWidget=parent)
# lookup organizations suitable for submitting_lab (ctx: self.InfoItem.SubmissionFormWidget.SubmissionFormContainer.AddSubForm ) # NOTE: lookup organizations suitable for submitting_lab (ctx: self.InfoItem.SubmissionFormWidget.SubmissionFormContainer.AddSubForm )
labs = [item.name for item in Organization.query()] labs = [item.name for item in Organization.query()]
# try to set closest match to top of list # NOTE: try to set closest match to top of list
try: try:
labs = difflib.get_close_matches(value, labs, len(labs), 0) labs = difflib.get_close_matches(value, labs, len(labs), 0)
except (TypeError, ValueError): except (TypeError, ValueError):
pass pass
# set combobox values to lookedup values # NOTE: set combobox values to lookedup values
add_widget.addItems(labs) add_widget.addItems(labs)
add_widget.setToolTip("Select submitting lab.") add_widget.setToolTip("Select submitting lab.")
case 'extraction_kit': case 'extraction_kit':
# if extraction kit not available, all other values fail # NOTE: if extraction kit not available, all other values fail
if not check_not_nan(value): if not check_not_nan(value):
msg = AlertPop(message="Make sure to check your extraction kit in the excel sheet!", msg = AlertPop(message="Make sure to check your extraction kit in the excel sheet!",
status="warning") status="warning")
@@ -573,8 +570,6 @@ class SubmissionFormWidget(QWidget):
add_widget.addItems(cats) add_widget.addItems(cats)
add_widget.setToolTip("Enter submission category or select from list.") add_widget.setToolTip("Enter submission category or select from list.")
case _: case _:
# if key in sub_obj.get_default_info("form_ignore", submission_type=submission_type):
# return None
if key in sub_obj.timestamps(): if key in sub_obj.timestamps():
add_widget = MyQDateEdit(calendarPopup=True, scrollWidget=parent) add_widget = MyQDateEdit(calendarPopup=True, scrollWidget=parent)
# NOTE: sets submitted date based on date found in excel sheet # NOTE: sets submitted date based on date found in excel sheet
@@ -593,7 +588,6 @@ class SubmissionFormWidget(QWidget):
if add_widget is not None: if add_widget is not None:
add_widget.setObjectName(key) add_widget.setObjectName(key)
add_widget.setParent(parent) add_widget.setParent(parent)
# add_widget.setStyleSheet(main_form_style)
return add_widget return add_widget
def update_missing(self): def update_missing(self):
@@ -649,7 +643,6 @@ class SubmissionFormWidget(QWidget):
self.label = self.ReagentParsedLabel(reagent=reagent) self.label = self.ReagentParsedLabel(reagent=reagent)
layout.addWidget(self.label) layout.addWidget(self.label)
self.lot = self.ReagentLot(scrollWidget=parent, reagent=reagent, extraction_kit=extraction_kit) self.lot = self.ReagentLot(scrollWidget=parent, reagent=reagent, extraction_kit=extraction_kit)
# self.lot.setStyleSheet(main_form_style)
layout.addWidget(self.lot) layout.addWidget(self.lot)
# NOTE: Remove spacing between reagents # NOTE: Remove spacing between reagents
layout.setContentsMargins(0, 0, 0, 0) layout.setContentsMargins(0, 0, 0, 0)
@@ -738,8 +731,6 @@ class SubmissionFormWidget(QWidget):
if check_not_nan(reagent.lot): if check_not_nan(reagent.lot):
relevant_reagents.insert(0, str(reagent.lot)) relevant_reagents.insert(0, str(reagent.lot))
else: else:
# looked_up_rt = KitTypeReagentRoleAssociation.query(reagent_role=reagent.role,
# kit_type=extraction_kit)
try: try:
looked_up_reg = Reagent.query(lot_number=looked_up_rt.last_used) looked_up_reg = Reagent.query(lot_number=looked_up_rt.last_used)
except AttributeError: except AttributeError:
@@ -768,22 +759,4 @@ class SubmissionFormWidget(QWidget):
self.setObjectName(f"lot_{reagent.role}") self.setObjectName(f"lot_{reagent.role}")
self.addItems(relevant_reagents) self.addItems(relevant_reagents)
self.setToolTip(f"Enter lot number for the reagent used for {reagent.role}") self.setToolTip(f"Enter lot number for the reagent used for {reagent.role}")
# self.setStyleSheet(main_form_style)
# def relevant_reagents(self, assoc: KitTypeReagentRoleAssociation):
# # logger.debug(f"Attempting lookup of reagents by type: {reagent.type}")
# lookup = Reagent.query(reagent_role=assoc.reagent_role)
# try:
# regex = assoc.uses['exclude_regex']
# except KeyError:
# regex = "^$"
# relevant_reagents = [item for item in lookup if
# not check_regex_match(pattern=regex, check=str(item.lot))]
# for rel_reagent in relevant_reagents:
# # # NOTE: extract strings from any sets.
# # if isinstance(rel_reagent, set):
# # for thing in rel_reagent:
# # yield thing
# # elif isinstance(rel_reagent, str):
# # yield rel_reagent
# yield rel_reagent

3
src/submissions/frontend/widgets/summary.py
View File

@@ -1,6 +1,6 @@
from PyQt6.QtCore import QSignalBlocker from PyQt6.QtCore import QSignalBlocker
from PyQt6.QtWebEngineWidgets import QWebEngineView from PyQt6.QtWebEngineWidgets import QWebEngineView
from PyQt6.QtWidgets import QWidget, QGridLayout, QPushButton, QComboBox, QLabel from PyQt6.QtWidgets import QWidget, QGridLayout, QPushButton, QLabel
from backend.db import Organization from backend.db import Organization
from backend.excel import ReportMaker from backend.excel import ReportMaker
from tools import Report from tools import Report
@@ -34,7 +34,6 @@ class Summary(QWidget):
for org in [org.name for org in Organization.query()]: for org in [org.name for org in Organization.query()]:
self.org_select.addItem(org) self.org_select.addItem(org)
self.org_select.model().itemChanged.connect(self.get_report) self.org_select.model().itemChanged.connect(self.get_report)
# self.org_select.itemChecked.connect(self.get_report)
self.layout.addWidget(self.save_excel_button, 0, 2, 1, 1) self.layout.addWidget(self.save_excel_button, 0, 2, 1, 1)
self.layout.addWidget(self.save_pdf_button, 0, 3, 1, 1) self.layout.addWidget(self.save_pdf_button, 0, 3, 1, 1)
self.layout.addWidget(self.webview, 2, 0, 1, 4) self.layout.addWidget(self.webview, 2, 0, 1, 4)

8
src/submissions/templates/experiment_template.json
View File

@@ -1,8 +0,0 @@
{
"submission_type" : {
},
"kit_type": {
}
}

4
src/submissions/tools/__init__.py
View File

@@ -153,7 +153,6 @@ def check_not_nan(cell_contents) -> bool:
try: try:
if cell_contents.lower() in exclude: if cell_contents.lower() in exclude:
cell_contents = np.nan cell_contents = np.nan
# cell_contents = cell_contents.lower()
except (TypeError, AttributeError): except (TypeError, AttributeError):
pass pass
try: try:
@@ -314,7 +313,7 @@ class Settings(BaseSettings, extra="allow"):
check = value.exists() check = value.exists()
except AttributeError: except AttributeError:
check = False check = False
if not check: # and values.data['database_schema'] == "sqlite": if not check:
# print(f"No directory found, using Documents/submissions") # print(f"No directory found, using Documents/submissions")
value.mkdir(exist_ok=True) value.mkdir(exist_ok=True)
# print(f"Final return of directory_path: {value}") # print(f"Final return of directory_path: {value}")
@@ -922,7 +921,6 @@ def check_authorization(func):
return func(*args, **kwargs) return func(*args, **kwargs)
else: else:
logger.error(f"User {getpass.getuser()} is not authorized for this function.") logger.error(f"User {getpass.getuser()} is not authorized for this function.")
# return dict(code=1, message="This user does not have permission for this function.", status="warning")
report = Report() report = Report()
report.add_result(Result(owner=func.__str__(), code=1, msg="This user does not have permission for this function.", status="warning")) report.add_result(Result(owner=func.__str__(), code=1, msg="This user does not have permission for this function.", status="warning"))
return report return report