landon/Submissions-App
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Bug fixes

Browse Source
This commit is contained in:
lwark
2025-04-02 13:08:32 -05:00
parent d3807dac57
commit 3a318fff38
4 changed files with 82 additions and 76 deletions
Download Patch File Download Diff File Expand all files Collapse all files

56
src/submissions/backend/db/models/submissions.py
View File

@@ -1880,34 +1880,34 @@ class Wastewater(BasicSubmission):
new_control.save() new_control.save()
return report return report
def update_subsampassoc(self, assoc: SubmissionSampleAssociation, input_dict: dict) -> SubmissionSampleAssociation: # def update_subsampassoc(self, assoc: SubmissionSampleAssociation, input_dict: dict) -> SubmissionSampleAssociation:
""" # """
Updates a joined submission sample association by assigning ct values to n1 or n2 based on alphabetical sorting. # Updates a joined submission sample association by assigning ct values to n1 or n2 based on alphabetical sorting.
#
Args: # Args:
sample (BasicSample): Associated sample. # sample (BasicSample): Associated sample.
input_dict (dict): values to be updated # input_dict (dict): values to be updated
#
Returns: # Returns:
SubmissionSampleAssociation: Updated association # SubmissionSampleAssociation: Updated association
""" # """
# logger.debug(f"Input dict: {pformat(input_dict)}") # # logger.debug(f"Input dict: {pformat(input_dict)}")
# # #
assoc = super().update_subsampassoc(assoc=assoc, input_dict=input_dict) # assoc = super().update_subsampassoc(assoc=assoc, input_dict=input_dict)
# targets = {k: input_dict[k] for k in sorted(input_dict.keys()) if k.startswith("ct_")} # # targets = {k: input_dict[k] for k in sorted(input_dict.keys()) if k.startswith("ct_")}
# assert 0 < len(targets) <= 2 # # assert 0 < len(targets) <= 2
# for k, v in targets.items(): # # for k, v in targets.items():
# # logger.debug(f"Setting sample {sample} with key {k} to value {v}") # # # logger.debug(f"Setting sample {sample} with key {k} to value {v}")
# # update_key = f"ct_n{i}" # # # update_key = f"ct_n{i}"
# current_value = getattr(assoc, k) # # current_value = getattr(assoc, k)
# logger.debug(f"Current value came back as: {current_value}") # # logger.debug(f"Current value came back as: {current_value}")
# if current_value is None: # # if current_value is None:
# setattr(assoc, k, v) # # setattr(assoc, k, v)
# else: # # else:
# logger.debug(f"Have a value already, {current_value}... skipping.") # # logger.debug(f"Have a value already, {current_value}... skipping.")
if assoc.column == 3: # if assoc.column == 3:
logger.debug(f"Final association for association {assoc}:\n{pformat(assoc.__dict__)}") # logger.debug(f"Final association for association {assoc}:\n{pformat(assoc.__dict__)}")
return assoc # return assoc
class WastewaterArtic(BasicSubmission): class WastewaterArtic(BasicSubmission):

10
src/submissions/backend/excel/reports.py
View File

@@ -2,6 +2,7 @@
Contains functions for generating summary reports Contains functions for generating summary reports
""" """
import itertools import itertools
import re
import sys import sys
from pprint import pformat from pprint import pformat
from pandas import DataFrame, ExcelWriter from pandas import DataFrame, ExcelWriter
@@ -211,8 +212,13 @@ class ConcentrationMaker(ReportArchetype):
@classmethod @classmethod
def build_record(cls, control) -> dict: def build_record(cls, control) -> dict:
regex = re.compile(r"^(ATCC)|(MCS)", flags=re.IGNORECASE)
positive = not control.submitter_id.lower().startswith("en") if bool(regex.match(control.submitter_id)):
positive = "positive"
elif control.submitter_id.lower().startswith("en"):
positive = "negative"
else:
positive = "sample"
try: try:
concentration = float(control.concentration) concentration = float(control.concentration)
except (TypeError, ValueError): except (TypeError, ValueError):

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

@@ -34,7 +34,7 @@ class ConcentrationsChart(CustomFigure):
# logger.debug(f"DF after changes:\n{self.df}") # logger.debug(f"DF after changes:\n{self.df}")
scatter = px.scatter(data_frame=self.df, x='submission', y="concentration", scatter = px.scatter(data_frame=self.df, x='submission', y="concentration",
hover_data=["name", "submission", "submitted_date", "concentration"], hover_data=["name", "submission", "submitted_date", "concentration"],
color="positive", color_discrete_map={True: "red", False: "green"} color="positive", color_discrete_map={"positive": "red", "negative": "green", "sample":"orange"}
) )
except (ValueError, AttributeError) as e: except (ValueError, AttributeError) as e:
logger.error(f"Error constructing chart: {e}") logger.error(f"Error constructing chart: {e}")

90
src/submissions/frontend/widgets/app.py
View File

@@ -80,8 +80,8 @@ class App(QMainWindow):
helpMenu.addAction(self.docsAction) helpMenu.addAction(self.docsAction)
helpMenu.addAction(self.githubAction) helpMenu.addAction(self.githubAction)
fileMenu.addAction(self.importAction) fileMenu.addAction(self.importAction)
fileMenu.addAction(self.yamlExportAction) # fileMenu.addAction(self.yamlExportAction)
fileMenu.addAction(self.yamlImportAction) # fileMenu.addAction(self.yamlImportAction)
methodsMenu.addAction(self.searchSample) methodsMenu.addAction(self.searchSample)
maintenanceMenu.addAction(self.joinExtractionAction) maintenanceMenu.addAction(self.joinExtractionAction)
maintenanceMenu.addAction(self.joinPCRAction) maintenanceMenu.addAction(self.joinPCRAction)
@@ -112,8 +112,8 @@ class App(QMainWindow):
self.docsAction = QAction("&Docs", self) self.docsAction = QAction("&Docs", self)
self.searchSample = QAction("Search Sample", self) self.searchSample = QAction("Search Sample", self)
self.githubAction = QAction("Github", self) self.githubAction = QAction("Github", self)
self.yamlExportAction = QAction("Export Type Example", self) # self.yamlExportAction = QAction("Export Type Example", self)
self.yamlImportAction = QAction("Import Type Template", self) # self.yamlImportAction = QAction("Import Type Template", self)
self.editReagentAction = QAction("Edit Reagent", self) self.editReagentAction = QAction("Edit Reagent", self)
self.manageOrgsAction = QAction("Manage Clients", self) self.manageOrgsAction = QAction("Manage Clients", self)
self.manageKitsAction = QAction("Manage Kits", self) self.manageKitsAction = QAction("Manage Kits", self)
@@ -130,8 +130,8 @@ class App(QMainWindow):
self.docsAction.triggered.connect(self.openDocs) self.docsAction.triggered.connect(self.openDocs)
self.searchSample.triggered.connect(self.runSampleSearch) self.searchSample.triggered.connect(self.runSampleSearch)
self.githubAction.triggered.connect(self.openGithub) self.githubAction.triggered.connect(self.openGithub)
self.yamlExportAction.triggered.connect(self.export_ST_yaml) # self.yamlExportAction.triggered.connect(self.export_ST_yaml)
self.yamlImportAction.triggered.connect(self.import_ST_yaml) # self.yamlImportAction.triggered.connect(self.import_ST_yaml)
self.table_widget.pager.current_page.textChanged.connect(self.update_data) self.table_widget.pager.current_page.textChanged.connect(self.update_data)
self.editReagentAction.triggered.connect(self.edit_reagent) self.editReagentAction.triggered.connect(self.edit_reagent)
self.manageOrgsAction.triggered.connect(self.manage_orgs) self.manageOrgsAction.triggered.connect(self.manage_orgs)
@@ -186,46 +186,46 @@ class App(QMainWindow):
dlg = SearchBox(parent=self, object_type=Reagent, extras=[dict(name='Role', field="role")]) dlg = SearchBox(parent=self, object_type=Reagent, extras=[dict(name='Role', field="role")])
dlg.exec() dlg.exec()
def export_ST_yaml(self): # def export_ST_yaml(self):
""" # """
Copies submission type yaml to file system for editing and remport # Copies submission type yaml to file system for editing and remport
#
# Returns:
# None
# """
# if check_if_app():
# yaml_path = Path(sys._MEIPASS).joinpath("files", "resources", "viral_culture.yml")
# else:
# yaml_path = project_path.joinpath("src", "submissions", "resources", "viral_culture.yml")
# fname = select_save_file(obj=self, default_name="Submission Type Template.yml", extension="yml")
# shutil.copyfile(yaml_path, fname)
Returns: # @check_authorization
None # def import_ST_yaml(self, *args, **kwargs):
""" # """
if check_if_app(): # Imports a yml form into a submission type.
yaml_path = Path(sys._MEIPASS).joinpath("files", "resources", "viral_culture.yml") #
else: # Args:
yaml_path = project_path.joinpath("src", "submissions", "resources", "viral_culture.yml") # *args ():
fname = select_save_file(obj=self, default_name="Submission Type Template.yml", extension="yml") # **kwargs ():
shutil.copyfile(yaml_path, fname) #
# Returns:
@check_authorization #
def import_ST_yaml(self, *args, **kwargs): # """
""" # fname = select_open_file(obj=self, file_extension="yml")
Imports a yml form into a submission type. # if not fname:
# logger.info(f"Import cancelled.")
Args: # return
*args (): # ap = AlertPop(message="This function will proceed in the debug window.", status="Warning", owner=self)
**kwargs (): # ap.exec()
# st = SubmissionType.import_from_json(filepath=fname)
Returns: # if st:
# # NOTE: Do not delete the print statement below.
""" # choice = input("Save the above submission type? [y/N]: ")
fname = select_open_file(obj=self, file_extension="yml") # if choice.lower() == "y":
if not fname: # pass
logger.info(f"Import cancelled.") # else:
return # logger.warning("Save of submission type cancelled.")
ap = AlertPop(message="This function will proceed in the debug window.", status="Warning", owner=self)
ap.exec()
st = SubmissionType.import_from_json(filepath=fname)
if st:
# NOTE: Do not delete the print statement below.
choice = input("Save the above submission type? [y/N]: ")
if choice.lower() == "y":
pass
else:
logger.warning("Save of submission type cancelled.")
def update_data(self): def update_data(self):
self.table_widget.sub_wid.setData(page=self.table_widget.pager.page_anchor, page_size=page_size) self.table_widget.sub_wid.setData(page=self.table_widget.pager.page_anchor, page_size=page_size)