Upload Setup.py

Setup.py

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+#!/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()
+
+if __name__ == "__main__":
+    pn.serve(app, port=5009)