Delete Setup.py

Setup.py

@@ -1,196 +0,0 @@
-#!/usr/bin/env python
-# coding: utf-8
-import panel as pn
-import os
-import pandas as pd
-import json
-pn.extension()
-
-# Global variables to store the input values
-input_path = ""
-set_path = ""
-ls_samples = []
-metadata_files = []
-selected_metadata_files = []
-
-# Define a callback to store values when the button is clicked
-def store_values(event):
-    global input_path, set_path, ls_samples, metadata_files
-    input_path = file_input.value
-    set_path = set_name.value
-
-    # Update the global variables
-    global base_dir, input_data_dir, output_data_dir, output_images_dir, metadata_dir, metadata_images_dir
-    present_dir = os.path.dirname(os.path.realpath(__file__))
-    input_path = os.path.join(present_dir, input_path)
-    base_dir = input_path
-    project_name = set_path
-    step_suffix = 'qc_eda'
-    previous_step_suffix_long = ""
-
-    input_data_dir = os.path.join(base_dir, project_name + "_data")
-    output_data_dir = os.path.join(base_dir, project_name + "_" + step_suffix)
-    output_images_dir = os.path.join(output_data_dir, "images")
-    metadata_dir = os.path.join(base_dir, project_name + "_metadata")
-    metadata_images_dir = os.path.join(metadata_dir, "images")
-
-    # Create directories if they don't already exist
-    for d in [base_dir, input_data_dir, output_data_dir, output_images_dir, metadata_dir, metadata_images_dir]:
-        if not os.path.exists(d):
-            print(f"Creation of the {d} directory...")
-            os.makedirs(d)
-        else:
-            print(f"The {d} directory already exists!")
-
-    os.chdir(input_data_dir)
-
-    # Create a DataFrame with the directory paths
-    data = {
-        'Directory': ['Base Directory', 'Input Data Directory', 'Output Data Directory', 'Output Images Directory', 'Metadata Directory', 'Metadata Images Directory'],
-        'Path': [base_dir, input_data_dir, output_data_dir, output_images_dir, metadata_dir, metadata_images_dir]
-    }
-    df = pd.DataFrame(data)
-
-    # List CSV files in the input_data_dir
-    ls_samples = [sample for sample in os.listdir(input_data_dir) if sample.endswith(".csv")]
-    print(f"The following CSV files were detected:\n\n{ls_samples}\n\nin {input_data_dir} directory.")
-
-    # List CSV files in the metadata_dir
-    metadata_files = [file for file in os.listdir(metadata_dir) if file.endswith(".tif.csv")]
-    print(f"The following metadata CSV files were detected:\n\n{metadata_files}\n\nin {metadata_dir} directory.")
-
-    # Update the CheckBoxGroup options
-    checkbox_group.options = ls_samples
-    metadata_checkbox_group.options = metadata_files
-
-    # Create a DataFrame with the CSV files
-    csv_files = pd.DataFrame({'CSV Files': ls_samples})
-    metadata_files_df = pd.DataFrame({'Metadata Files': metadata_files})
-
-    # Update the output panes
-    output_pane_1.object = f"**File Path:** {input_path}\n\n**Set Name:** {set_path}"
-    output_pane_2.object = df.to_html(index=False)
-    output_pane_3.object = csv_files.to_html(index=False)
-    output_pane_4.object = metadata_files_df.to_html(index=False)
-
-# Define a callback to save the selected CSV files when the button is clicked
-def save_selected_files(event):
-    # Store the variables in a JSON file
-    with open('stored_variables.json', 'w') as file:
-        json.dump({'base_dir': base_dir, 'set_path': set_path}, file)
-
-# Define a callback to update the ls_samples list based on the selected options
-def update_ls_samples(event):
-    global ls_samples
-    ls_samples = event.new
-
-# Define a callback to update the metadata_files list based on the selected options
-def update_metadata_files(event):
-    global metadata_files, selected_metadata_files
-    metadata_files = event.new
-    selected_metadata_files = event.new
-
-# Define a callback to save the selected metadata files when the button is clicked
-def save_selected_metadata_files(event):
-    with open('stored_variables.json', 'w') as file:
-        json.dump({'selected_metadata_files': selected_metadata_files}, file)
-
-# Define the widgets
-file_input = pn.widgets.TextInput(
-    name="File Path",
-    placeholder="Enter the path to your directory"
-)
-
-# Define the set name
-set_name = pn.widgets.TextInput(
-    name="Set Name",
-    placeholder="Enter the Set"
-)
-
-# Button to trigger storing values
-store_button = pn.widgets.Button(name='Store Values')
-store_button.on_click(store_values)
-
-# CheckBoxGroup to select CSV files
-checkbox_group = pn.widgets.CheckBoxGroup(name='Select CSV Files', options=[], value=[])
-checkbox_group.param.watch(update_ls_samples, 'value')
-
-# CheckBoxGroup to select metadata files
-metadata_checkbox_group = pn.widgets.CheckBoxGroup(name='Select Metadata Files', options=[], value=[])
-metadata_checkbox_group.param.watch(update_metadata_files, 'value')
-
-# Button to save selected CSV files
-save_button = pn.widgets.Button(name='Save Files')
-save_button.on_click(save_selected_files)
-
-# Button to save selected metadata files
-save_metadata_button = pn.widgets.Button(name='Save Metadata Files')
-save_metadata_button.on_click(save_selected_metadata_files)
-
-output_pane_1 = pn.pane.Markdown("")
-output_pane_2 = pn.pane.HTML("")
-output_pane_3 = pn.pane.HTML("")
-output_pane_4 = pn.pane.HTML("")
-
-# Create the cards
-card_1 = pn.Card(
-    pn.Column(
-        pn.pane.Markdown("### Input Form"),
-        file_input,
-        set_name,
-        store_button,
-        output_pane_1,
-        sizing_mode="stretch_width"
-    ),
-    title="Input Form",
-    sizing_mode="stretch_width"
-)
-
-card_2 = pn.Card(
-    pn.Column(
-        pn.pane.Markdown("### Directory Paths"),
-        output_pane_2,
-        sizing_mode="stretch_width"
-    ),
-    title="Directory Paths",
-    sizing_mode="stretch_width"
-)
-
-card_3 = pn.Card(
-    pn.Column(
-        pn.pane.Markdown("### CSV Files"),
-        output_pane_3,
-        pn.pane.Markdown("### Selection of CSV files for the further analysis"),
-        checkbox_group,
-        save_button,
-        sizing_mode="stretch_width"
-    ),
-    title="CSV Files",
-    sizing_mode="stretch_width"
-)
-
-card_4 = pn.Card(
-    pn.Column(
-        pn.pane.Markdown("### Metadata Files"),
-        output_pane_4,
-        pn.pane.Markdown("### Selection of Metadata Files"),
-        metadata_checkbox_group,
-        save_metadata_button,
-        sizing_mode="stretch_width"
-    ),
-    title="Metadata Files",
-    sizing_mode="stretch_width"
-)
-
-# Create the main column with the cards
-main_column = pn.Column(card_1, card_2, card_3, card_4)
-
-# Create the GoldenTemplate with the main column
-app = pn.template.GoldenTemplate(
-    site="Cyc-IF",
-    title="Setup",
-    main=[main_column],
-    header_color="black",
-)
-
-app.servable()