def save_log(self):
"""Save the log"""
options = QFileDialog.Options()
options |= QFileDialog.DontUseNativeDialog
filename, _ = QFileDialog.getSaveFileName(
self,
"QFileDialog.getSaveFileName()",
"",
self.filetype,
options=options)
# Return without doing anything if a valid file wasn't selected
if not filename:
return
# Define a no-parameter function to save the data using a thread
log = self.messages
def save_func():
with open(filename, "w") as o:
o.writelines(log)
RunProgress.run_with_progress(progress_str="Saving Log...",
function=save_func,
slot=None,
parent=self)
def submit(self):
print(f"categorize with {self.cat_min}, {self.cat_max}, {self.cont_min}")
if self.cat_min > self.cat_max:
warnings.show_warning(
"Parameter Error",
f"'Categorical Minimum' must be <= 'Categorical Maximum'",
)
elif self.cat_min > self.cont_min:
warnings.show_warning(
"Parameter Error",
f"'Categorical Minimum' must be < 'Continuous Minimum'",
)
elif self.cat_max >= self.cont_min:
warnings.show_warning(
"Parameter Error",
f"'Categorical Maximum' must be < 'Continuous Minimum'",
)
else:
# Run with a progress dialog
RunProgress.run_with_progress(
progress_str="Categorizing variables...",
function=self.get_func(),
slot=self.appctx.update_data,
parent=self,
)
self.log_command()
self.accept()
def submit(self):
if self.data_name is None:
self.data_name = self.le_data_name.placeholderText()
if self.data_name is not None and self.data_name in [
d.name for d in self.appctx.datasets
]:
warnings.show_warning(
"Dataset already exists",
f"A dataset named '{self.data_name}' already exists.\n"
f"Use a different name.",
)
elif (
self.top_idx is None
or self.bottom_idx is None
or self.top_idx == self.bottom_idx
):
warnings.show_warning(
"Select Two Datasets", "Two different datasets must be selected."
)
else:
RunProgress.run_with_progress(
progress_str="Merging Data...",
function=self.get_func(),
slot=self.appctx.add_dataset,
parent=self,
)
self.log_command()
self.accept()
def submit(self):
type_errors = (
self.update_types()
) # Convert the types of 'from' and 'to', returning None if successful
if self.data_name is not None and self.data_name in [
d.name for d in self.appctx.datasets
]:
warnings.show_warning(
"Dataset already exists",
f"A dataset named '{self.data_name}' already exists.\n"
f"Use a different name or clear the dataset name field.",
)
elif type_errors is not None:
warnings.show_critical("Error", type_errors)
else:
# Run with a progress dialog
if self.data_name is None:
slot = self.appctx.update_data
else:
slot = self.appctx.add_dataset
RunProgress.run_with_progress(
progress_str="Recoding variables...",
function=self.get_func(),
slot=slot,
parent=self,
)
self.log_command()
self.accept()
def submit(self):
if self.data_name is not None and self.data_name in [
d.name for d in self.appctx.datasets
]:
show_warning(
"Dataset already exists",
f"A dataset named '{self.data_name}' already exists.\n"
f"Use a different name or clear the dataset name field.",
)
elif "converged" not in list(self.dataset.df):
show_warning("Incorrect Data Input",
"A 'converged' column must be present")
elif "pvalue" not in list(self.dataset.df):
show_warning("Incorrect Data Input",
"A 'pvalue' column must be present")
else:
print(f"Adding corrected P-values...")
# Run with a progress dialog
if self.data_name is None:
slot = self.appctx.update_data
else:
slot = self.appctx.add_dataset
RunProgress.run_with_progress(
progress_str="Adding corrected P-values...",
function=self.get_func(),
slot=slot,
parent=self,
)
self.log_command()
self.accept()
def submit(self):
if len(self.filename) == 0:
self.reject()
return
datafile = Path(self.filename)
if not datafile.exists():
warnings.show_warning(
title="File Not Found",
text=f"The file could not be found:\n'{str(datafile)}''",
)
elif not datafile.is_file():
warnings.show_warning(
title="Not a File",
text=
f"A folder was given instead of a file:\n'{str(datafile)}''",
)
elif self.data_name in [d.name for d in self.appctx.datasets]:
warnings.show_warning(
title="Dataset already exists",
text=
f"A dataset named '{self.data_name}' already exists. Use a different name.",
)
else:
RunProgress.run_with_progress(
progress_str=f"Loading {self.kind} file...",
function=self.get_func(),
slot=self.appctx.add_dataset,
parent=self,
)
self.log_command()
self.accept()
def save_dataset(self):
"""
Save the currently selected dataset
:return:
"""
options = QFileDialog.Options()
options |= QFileDialog.DontUseNativeDialog
filename, _ = QFileDialog.getSaveFileName(
self,
"QFileDialog.getSaveFileName()",
"",
"All Files (*);;Text Files (*.txt)",
options=options,
)
# Return without doing anything if a valid file wasn't selected
if not filename:
return
# Define a no-parameter function to save the data using a thread
dataset = self.appctx.datasets[self.appctx.current_dataset_idx]
def save_func():
# Save Data
dataset.df.to_csv(filename, sep="\t")
# Save Dtypes
dtypes = {
variable_name: {
"type": str(dtype)
} if str(dtype) != "category" else {
"type": str(dtype),
"categories": list(dtype.categories.values.tolist()),
"ordered": dtype.ordered,
}
for variable_name, dtype in dataset.df.dtypes.iteritems()
}
dtypes_filename = filename + ".dtypes"
dtypes_file = Path(dtypes_filename)
with dtypes_file.open("w") as f:
json.dump(dtypes, f)
RunProgress.run_with_progress(progress_str="Saving Data...",
function=save_func,
slot=None,
parent=self)
# Log Info
save_str = (
f"\nSaved {len(dataset.df):,} observations of {len(list(dataset.df)):,} variables"
f" in '{dataset.get_selector_name()}' to '{filename}'\n")
self.appctx.log_info("\n" + "=" * 80 + save_str + "=" * 80)
# Log Python
self.appctx.log_python(
f"# Save data and it's associated datatypes\n"
f"{dataset.get_python_name()}.to_csv({filename}, sep='\t')\n")
def submit(self):
# Run with a progress dialog
RunProgress.run_with_progress(
progress_str="Converting variable types...",
function=self.get_func(),
slot=self.appctx.update_data,
parent=self,
)
self.log_command()
self.accept()
def submit(self):
# Run with a progress dialog
RunProgress.run_with_progress(
progress_str="Dropping extra categories...",
function=self.get_func(),
slot=self.appctx.update_data,
parent=self,
)
self.log_command()
self.accept()
def save(self):
fileName = QFileDialog.getSaveFileName(
self, self.tr("Save file"), "", self.tr("PDF files (*.pdf)")
)[0]
if fileName:
self.saved_filename = fileName
# Generate and save the PDF
RunProgress.run_with_progress(
progress_str="Saving PDF...",
function=self.get_func(),
slot=lambda: print("Saving PDF"),
parent=self,
)
self.accept()
def submit(self):
if self.data_name is not None and self.data_name in [
d.name for d in self.appctx.datasets
]:
show_warning(
"Dataset already exists",
f"A dataset named '{self.data_name}' already exists.\n"
f"Use a different name or clear the dataset name field.",
)
else:
print(f"Calculating Percent NA")
# Run with a progress dialog
RunProgress.run_with_progress(
progress_str="Calculating Percent NA...",
function=self.get_func(),
slot=self.appctx.add_dataset,
parent=self,
)
self.log_command()
self.accept()
def submit(self):
if self.data_name is not None and self.data_name in [
d.name for d in self.appctx.datasets
]:
show_warning(
"Dataset already exists",
f"A dataset named '{self.data_name}' already exists.\n"
f"Use a different name or clear the dataset name field.",
)
elif self.outcome is None:
show_warning("Missing Parameter", "A phenotype must be selected")
else:
print(f"Running EWAS...")
# Run with a progress dialog
RunProgress.run_with_progress(
progress_str="Running EWAS...",
function=self.get_func(),
slot=self.appctx.add_dataset,
parent=self,
)
self.log_command()
self.accept()
def submit(self):
if self.data_name is not None and self.data_name in [
d.name for d in self.appctx.datasets
]:
warnings.show_warning(
"Dataset already exists",
f"A dataset named '{self.data_name}' already exists.\n"
f"Use a different name or clear the dataset name field.",
)
else:
# Run with a progress dialog
if self.data_name is None:
slot = self.appctx.update_data
else:
slot = self.appctx.add_dataset
RunProgress.run_with_progress(
progress_str="Filtering variables...",
function=self.get_func(),
slot=slot,
parent=self,
)
self.accept()