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Refactor: remove tp_paths, tp_pos
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And simplify event handler logic.
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@dweindl
dweindl committed Feb 18, 2025
1 parent a4a5518 commit 6e5ceeb
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Showing 3 changed files with 86 additions and 78 deletions.
6 changes: 0 additions & 6 deletions src/ccompass/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -457,13 +457,9 @@ class SessionModel(BaseModel):

## User input total proteome data

#: Filepaths for total proteome data
tp_paths: list[Filepath] = []
#: Total proteome column assignments
# filepath => [column ID, condition]
tp_tables: dict[Filepath, list[list[str]]] = {}
#: ??
tp_pos: dict[Filepath, list[int]] = {}
#: Total proteome input files: filepath => DataFrame
tp_indata: dict[Filepath, pd.DataFrame] = {}
#: Identifier column for the total proteome: filepath => column id
Expand Down Expand Up @@ -516,9 +512,7 @@ def reset_static_statistics(self):
self.status.lipidome_prediction = False

def reset_input_tp(self):
self.tp_paths = []
self.tp_tables = {}
self.tp_pos = {}
self.tp_data = {}

def reset_input_fract(self):
Expand Down
156 changes: 86 additions & 70 deletions src/ccompass/main_gui.py
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Original file line number Diff line number Diff line change
Expand Up @@ -995,7 +995,8 @@ def create_main_window(model: SessionModel) -> sg.Window:
[sg.Menu(menu_def, tearoff=False)],
[
create_data_import_frame(
fract_paths=list(model.fract_indata), tp_paths=model.tp_paths
fract_paths=list(model.fract_indata),
tp_paths=list(model.tp_indata),
),
create_spatial_prediction_frame(),
],
Expand Down Expand Up @@ -1104,20 +1105,18 @@ def run(self):
elif event == "-tp_add-":
tp_add_dataset(
self.main_window,
self.model.tp_paths,
self.model.tp_tables,
self.model.tp_indata,
self.model.tp_pos,
self.model.tp_identifiers,
)
elif event == "-tp_remove-":
if values["-tp_path-"]:
tp_remove_dataset(
values,
self.main_window,
self.model.tp_paths,
self.model.tp_tables,
)
tp_remove_dataset(
values,
self.main_window,
self.model.tp_tables,
self.model.tp_indata,
self.model.tp_identifiers,
)
elif event == "-tp_path-":
tp_refreshtable(
self.main_window,
Expand All @@ -1143,14 +1142,12 @@ def run(self):
else:
messagebox.showerror("Error", "Select (a) row(s).")
elif event == "-tp_edit_identifier-":
if values["-tp_table-"]:
self.model.tp_identifiers = tp_set_identifier(
values,
self.main_window,
self.model.tp_tables,
self.model.tp_pos,
self.model.tp_identifiers,
)
tp_set_identifier(
values,
self.main_window,
self.model.tp_tables,
self.model.tp_identifiers,
)
elif event == "-tp_parameters-":
from .total_proteome_parameters_dialog import show_dialog

Expand Down Expand Up @@ -1638,7 +1635,7 @@ def _handle_session_save(self):

def _handle_process_total_proteome(self):
"""Button-click "process total proteome data"."""
if not self.model.tp_paths:
if not self.model.tp_indata:
messagebox.showerror("No dataset!", "Please import a TP dataset.")
return

Expand Down Expand Up @@ -2011,7 +2008,10 @@ def convert_to_float(x):


def tp_add_dataset(
window, tp_paths, tp_tables, tp_indata, tp_pos, tp_identifiers
window: sg.Window,
tp_tables: dict[str, list],
tp_indata: dict[str, pd.DataFrame],
tp_identifiers: dict[str, str],
):
"""Add a total proteome dataset."""
filename = sg.popup_get_file(
Expand All @@ -2025,44 +2025,50 @@ def tp_add_dataset(
if not filename:
return

tp_paths.append(filename)
window["-tp_path-"].update(values=tp_paths, value=filename)
data = pd.read_csv(filename, sep="\t", header=0)
data = data.replace("NaN", np.nan)
data = data.replace("Filtered", np.nan)
data = data.map(convert_to_float)

rows_with_float = data.map(is_float).any(axis=1)
data = data[rows_with_float]
# read file
df = pd.read_csv(filename, sep="\t", header=0)
df = df.replace("NaN", np.nan)
df = df.replace("Filtered", np.nan)
df = df.map(convert_to_float)
rows_with_float = df.map(is_float).any(axis=1)
df = df[rows_with_float]

colnames = data.columns.values.tolist()
table = []
for name in colnames:
namelist = [name, ""]
table.append(namelist)
table = [[name, ""] for name in df.columns]
tp_tables[filename] = table
tp_indata[filename] = data
tp_pos[filename] = []
tp_identifiers[filename] = []
tp_indata[filename] = df
tp_identifiers[filename] = ""

tp_refreshtable(window, table)
window["-tp_path-"].update(values=list(tp_indata), value=filename)


def tp_remove_dataset(values, window, tp_paths, tp_tables):
def tp_remove_dataset(
values,
window: sg.Window,
tp_tables: dict[str, list],
tp_indata: dict[str, pd.DataFrame],
tp_identifiers: dict[str, str],
):
"""Remove a total proteome dataset."""
if not (selected_file := values["-tp_path-"]):
return

sure = sg.popup_yes_no("Remove data from list?")
if sure != "Yes":
return

tp_paths.remove(values["-tp_path-"])
del tp_tables[values["-tp_path-"]]
# del tp_data[values['-tp_path-']]
if tp_paths:
curr = tp_paths[0]
tp_refreshtable(window, tp_tables[curr])
else:
curr = []
tp_refreshtable(window, curr)
window["-tp_path-"].update(values=tp_paths, value=curr)
del tp_tables[selected_file]
del tp_indata[selected_file]
del tp_identifiers[selected_file]

files = list(tp_tables)
selected_file_new = files[0] if files else []
window["-tp_path-"].update(
values=files, value=selected_file_new, size=window["-tp_path-"].Size
)

cur_table = tp_tables[selected_file_new] if selected_file_new else []
tp_refreshtable(window, cur_table)


def tp_remove_row(values, window, tp_tables):
Expand All @@ -2072,8 +2078,7 @@ def tp_remove_row(values, window, tp_tables):
table = tp_tables[path]
for index in sorted(selected, reverse=True):
del table[index]
tp_tables[path] = table
window["-tp_table-"].update(values=tp_tables[path])
window["-tp_table-"].update(values=table)


def tp_set_keep(values, window, tp_tables):
Expand All @@ -2082,8 +2087,7 @@ def tp_set_keep(values, window, tp_tables):
table = tp_tables[path]
for pos in values["-tp_table-"]:
table[pos][1] = KEEP
tp_tables[path] = table
window["-tp_table-"].update(values=tp_tables[path])
window["-tp_table-"].update(values=table)


def tp_set_condition(values, window, tp_tables):
Expand All @@ -2098,28 +2102,40 @@ def tp_set_condition(values, window, tp_tables):
tp_tables[path] = table
else:
messagebox.showerror("Error", "Select (a) sample(s).")

window["-tp_table-"].update(values=tp_tables[values["-tp_path-"]])


def tp_set_identifier(values, window, tp_tables, tp_pos, tp_identifiers):
def tp_set_identifier(
values,
window: sg.Window,
tp_tables: dict[str, list],
tp_identifiers: dict[str, str],
) -> None:
"""Set the identifier of the selected total proteome row."""
pos = values["-tp_table-"]
if pos:
if len(pos) > 1:
messagebox.showerror("Error", "Please set only one Identifier!")
elif len(pos) == 1:
path = values["-tp_path-"]
table = tp_tables[path]
if tp_pos[path]:
table[tp_pos[path][0]][1] = ""
tp_identifiers[path] = table[pos[0]][0]
tp_pos[path] = pos
table[pos[0]][1] = IDENTIFIER
tp_tables[path] = table
window["-tp_table-"].update(values=tp_tables[values["-tp_path-"]])
else:
messagebox.showerror("Error", "No sample selected.")
return tp_identifiers
if not (pos := values["-tp_table-"]):
messagebox.showerror("Error", "No sample selected.")
return

if len(pos) > 1:
messagebox.showerror("Error", "Please set only one Identifier!")
return

path = values["-tp_path-"]
table = tp_tables[path]

# unset condition for previous identifier row
prev_id_row = [i for i, row in enumerate(table) if row[1] == IDENTIFIER]
if prev_id_row:
assert len(prev_id_row) == 1
prev_id_row = prev_id_row[0]
table[prev_id_row][1] = ""

new_row_idx = pos[0]
tp_identifiers[path] = table[new_row_idx][0]
table[new_row_idx][1] = IDENTIFIER

window["-tp_table-"].update(values=table)


def tp_export(export_folder: str | Path, experiment: str, tp_data, tp_info):
Expand Down
2 changes: 0 additions & 2 deletions tests/test_full_analysis.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -140,8 +140,6 @@ def test_full():
logger.info("Full profiles created")

# process total proteome data
# TODO: we can get rid of tp_paths
sess.tp_paths = [total_prot_filepath]
sess.tp_tables = {
total_prot_filepath: [
tp_col_id_to_row(col_id)
Expand Down

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