Step1_Setup.py

#!/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)  # Avoid changing the working directory

    # Update JSON with directory settings
    with open('stored_variables.json', 'r') as file:
        data = json.load(file)
    data.update({'base_dir': base_dir, 'set_path': set_path})
    with open('stored_variables.json', 'w') as file:
        json.dump(data, file, indent=4)

    # 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
    # Assuming csv_files should be a DataFrame constructed from ls_samples
    csv_files = pd.DataFrame({'CSV Files': ls_samples})
    md_files = [file for file in os.listdir(metadata_dir) if file.endswith(".tif.csv")]
    print(md_files)
    metadata_files_df = pd.DataFrame({'Selected_Metadata_files' : [file for file in os.listdir(metadata_dir) if file.endswith(".tif.csv")]})
    print(metadata_files_df)
    # 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):
    with open('stored_variables.json', 'r') as file:
        data = json.load(file)
    data['ls_samples'] = ls_samples
    with open('stored_variables.json', 'w') as file:
        json.dump(data, file, indent=4)
    print("ls_samples updated in JSON 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', 'r') as file:
        data = json.load(file)
    data['selected_metadata_files'] = selected_metadata_files
    with open('stored_variables.json', 'w') as file:
        json.dump(data, file, indent=4)
    print("selected_metadata_files updated in JSON file.")

# Define the widgets
file_input = pn.widgets.TextInput(
    name="File Path",
    placeholder="Enter the path to your directory"
)

set_name = pn.widgets.TextInput(
    name="Set Name",
    placeholder="Enter the Set"
)

store_button = pn.widgets.Button(name='Store Values')
store_button.on_click(store_values)

checkbox_group = pn.widgets.CheckBoxGroup(name='Select CSV Files', options=[], value=[])
checkbox_group.param.watch(update_ls_samples, 'value')

metadata_checkbox_group = pn.widgets.CheckBoxGroup(name='Select Metadata Files', options=[], value=[])
metadata_checkbox_group.param.watch(update_metadata_files, 'value')

save_button = pn.widgets.Button(name='Save Files')
save_button.on_click(save_selected_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()