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import yaml
import gradio as gr
import pandas as pd
from functools import partial
from nist_cda_dashboard.component import ComponentHelper
from nist_cda_dashboard.utils import DownloadHelper
with open("./config.yml", 'r') as file:
config = yaml.safe_load(file)
component_helper = ComponentHelper(file_qc_results=pd.read_csv(config["file_path"]["file_qc_results"]),
dataset_qc_results=pd.read_csv(
config["file_path"]["dataset_qc_results"]),
analyzed_gating_results=pd.read_csv(
config["file_path"]["analyzed_gating_results"]),
analyzed_gating_results_wCDAResults=pd.read_csv(
config["file_path"]["analyzed_gating_results_wCDAResults"]),
config=config)
custom_css = """
#plot_wScrollBar {
overflow-x: auto !important;
text-align: center !important;
}
#plot_wScrollBar > .js-plotly-plot,
#plot_wScrollBar > .plotly,
#plot_wScrollBar > div:first-child {
display: inline-block !important;
text-align: left !important;
}
"""
with gr.Blocks(css=custom_css) as demo:
with gr.Sidebar(position="left", width=700):
gr.Markdown("# STEP 1: Filter Dataset")
clear_all_models_button, select_all_models_button, model_filter, \
clear_all_datasets_button, select_all_datasets_button, dataset_filter, \
main_apply_filters_button = component_helper.creator.main_filter_components()
clear_all_models_button.click(fn=partial(component_helper.updater.clean_all_choices),
outputs=model_filter)
select_all_models_button.click(fn=partial(component_helper.updater.select_all_choices, "model_filter"),
outputs=model_filter)
clear_all_datasets_button.click(fn=partial(component_helper.updater.clean_all_choices),
outputs=dataset_filter)
select_all_datasets_button.click(fn=partial(component_helper.updater.select_all_choices, "dataset_filter"),
outputs=dataset_filter)
model_filter.change(fn=component_helper.updater.update_dataset_filter,
inputs=[model_filter,
dataset_filter],
outputs=dataset_filter)
gr.Markdown("# STEP 2: Choose QC or Analysis Tab")
with gr.Tab(label="Quality Check"):
gr.Markdown("# STEP 3: Filter File")
clear_all_sop_exps_qc_tab_button, select_all_sop_exps_qc_tab_button, sop_exp_qc_tab_filter, \
clear_all_materials_button, select_all_materials_button, material_filter, \
clear_all_issues_button, select_all_issues_button, issue_filter, \
qc_tab_apply_filters_button = component_helper.creator.qc_tab_filter_components()
clear_all_sop_exps_qc_tab_button.click(fn=partial(component_helper.updater.clean_all_choices),
outputs=sop_exp_qc_tab_filter)
select_all_sop_exps_qc_tab_button.click(fn=partial(component_helper.updater.select_all_choices, "sop_exp_qc_tab_filter"),
outputs=sop_exp_qc_tab_filter)
clear_all_materials_button.click(fn=partial(component_helper.updater.clean_all_choices),
outputs=material_filter)
select_all_materials_button.click(fn=partial(component_helper.updater.select_all_choices, "material_filter"),
outputs=material_filter)
clear_all_issues_button.click(fn=partial(component_helper.updater.clean_all_choices),
outputs=issue_filter)
select_all_issues_button.click(fn=partial(component_helper.updater.select_all_choices, "issue_filter"),
outputs=issue_filter)
sop_exp_qc_tab_filter.change(fn=component_helper.updater.update_material_filter,
inputs=[sop_exp_qc_tab_filter,
material_filter],
outputs=material_filter)
gr.Markdown("<br><br>")
gr.Markdown("# STEP 4: Results")
qc_tab_dataset_qc_status_filter = component_helper.creator.qc_tab_dataset_qc_status_filter_component()
with gr.Row():
gr.Markdown("## File QC Results Table")
download_file_qc_button = gr.Button(
"Download File QC Results")
file_qc_status_filter, file_qc_table, file_qc_table_no_file_msg = component_helper.creator.file_qc_result_components()
download_file_qc_button_hidden = gr.DownloadButton(
visible=False, elem_id="download_file_qc_button_hidden")
download_file_qc_button.click(fn=(lambda df: DownloadHelper.df2csv(df, "file_qc_table")),
inputs=[file_qc_table],
outputs=[download_file_qc_button_hidden]). \
then(fn=None,
inputs=None,
outputs=None,
js="() => document.querySelector('#download_file_qc_button_hidden').click()")
gr.Markdown("<br><br>")
with gr.Row():
gr.Markdown("## Dataset QC Results Table")
download_dataset_qc_button = gr.Button(
"Download Dataset QC Results")
dataset_qc_table, dataset_qc_table_no_dataset_msg = component_helper.creator.dataset_qc_result_components()
download_dataset_qc_button_hidden = gr.DownloadButton(
visible=False, elem_id="download_dataset_qc_button_hidden")
download_dataset_qc_button.click(fn=(lambda df: DownloadHelper.df2csv(df, "dataset_qc_table")),
inputs=[dataset_qc_table],
outputs=[download_dataset_qc_button_hidden]). \
then(fn=None,
inputs=None,
outputs=None,
js="() => document.querySelector('#download_dataset_qc_button_hidden').click()")
gr.Markdown("<br><br>")
with gr.Row():
gr.Markdown("## QC Results Visualization")
download_qc_fig_button = gr.Button(
"Download QC Visualization Figure")
qc_fig, qc_fig_no_file_msg = component_helper.creator.qc_result_visual_components()
download_qc_fig_button_hidden = gr.DownloadButton(
visible=False, elem_id="download_qc_fig_button_hidden")
download_qc_fig_button.click(fn=(lambda fig: DownloadHelper.fig2png(fig, "qc_visual_fig")),
inputs=[qc_fig],
outputs=[download_qc_fig_button_hidden]). \
then(fn=None,
inputs=None,
outputs=None,
js="() => document.querySelector('#download_qc_fig_button_hidden').click()")
gr.on(fn=component_helper.updater.update_file_qc_table,
triggers=[main_apply_filters_button.click, qc_tab_apply_filters_button.click,
qc_tab_dataset_qc_status_filter.change, file_qc_status_filter.change],
inputs=[dataset_filter, sop_exp_qc_tab_filter, material_filter,
issue_filter, qc_tab_dataset_qc_status_filter, file_qc_status_filter],
outputs=[file_qc_table, file_qc_table_no_file_msg,
dataset_qc_table, dataset_qc_table_no_dataset_msg])
gr.on(fn=component_helper.updater.update_qc_fig,
triggers=[main_apply_filters_button.click, qc_tab_apply_filters_button.click,
qc_tab_dataset_qc_status_filter.change],
inputs=[dataset_filter, sop_exp_qc_tab_filter, material_filter,
issue_filter, qc_tab_dataset_qc_status_filter],
outputs=[qc_fig, qc_fig_no_file_msg])
with gr.Tab(label="Gating Result Analysis"):
gr.Markdown("# STEP 3: Filter File")
sample_filter, sop_exp_analysis_tab_filter, compensation_control_filter, \
gating_control_filter, pop_pheno_parent_filter, clear_gating_tab_filters_button, analysis_tab_apply_filters_button = component_helper.creator.analysis_tab_filter_components()
gr.Markdown("<br><br>")
gr.Markdown("# STEP 4: Results")
gr.Markdown("## Analysis Visualization")
analysis_tab_dataset_qc_status_filter, analyzed_result_filter = component_helper.creator.analyzed_result_filter_component()
with gr.Tab(label="Single Result Barplot"):
download_barplot_fig_button = gr.Button("Download Barplot Figure")
analysis_barplot_fig, barplot_not_reportable_msg = component_helper.creator.analysis_barplot_components()
download_barplot_fig_button_hidden = gr.DownloadButton(
visible=False, elem_id="download_barplot_fig_button_hidden")
download_barplot_fig_button.click(fn=(lambda fig: DownloadHelper.fig2png(fig, "analysis_barplot_fig")),
inputs=[analysis_barplot_fig],
outputs=[download_barplot_fig_button_hidden]). \
then(fn=None,
inputs=None,
outputs=None,
js="() => document.querySelector('#download_barplot_fig_button_hidden').click()")
with gr.Tab(label="Multiple Results Heatmap"):
download_heatmap_fig_button = gr.Button(
"Download Heatmap Figure")
compared_protocol_filter, include_CDA_results_checkbox, analysis_heatmap_exp_info_table, analysis_heatmap_exp_comparison_table, \
analysis_heatmap_fig, heatmap_not_reportable_msg = component_helper.creator.analysis_heatmap_components()
download_heatmap_fig_button_hidden = gr.DownloadButton(
visible=False, elem_id="download_heatmap_fig_button_hidden")
download_heatmap_fig_button.click(fn=(lambda fig: DownloadHelper.fig2png(fig, "analysis_heatmap_fig")),
inputs=[analysis_heatmap_fig],
outputs=[download_heatmap_fig_button_hidden]). \
then(fn=None,
inputs=None,
outputs=None,
js="() => document.querySelector('#download_heatmap_fig_button_hidden').click()")
gr.on(fn=component_helper.updater.update_barplot_fig,
triggers=[main_apply_filters_button.click, analysis_tab_apply_filters_button.click,
analysis_tab_dataset_qc_status_filter.change, analyzed_result_filter.change],
inputs=[dataset_filter, analysis_tab_dataset_qc_status_filter,
sample_filter, sop_exp_analysis_tab_filter, compensation_control_filter,
gating_control_filter, pop_pheno_parent_filter, analyzed_result_filter],
outputs=[analysis_barplot_fig, barplot_not_reportable_msg])
gr.on(fn=component_helper.updater.update_heatmap_fig,
triggers=[main_apply_filters_button.click, analysis_tab_apply_filters_button.click,
analysis_tab_dataset_qc_status_filter.change, analyzed_result_filter.change,
compared_protocol_filter.change, include_CDA_results_checkbox.change],
inputs=[dataset_filter, analysis_tab_dataset_qc_status_filter,
sample_filter, sop_exp_analysis_tab_filter, compensation_control_filter,
gating_control_filter, pop_pheno_parent_filter,
analyzed_result_filter, compared_protocol_filter, include_CDA_results_checkbox],
outputs=[analysis_heatmap_exp_info_table, analysis_heatmap_exp_comparison_table,
analysis_heatmap_fig, heatmap_not_reportable_msg])
gr.on(fn=component_helper.updater.update_analysis_tab_filters,
triggers=[sample_filter.change,
sop_exp_analysis_tab_filter.change, compensation_control_filter.change,
gating_control_filter.change, pop_pheno_parent_filter.change],
inputs=[sample_filter,
sop_exp_analysis_tab_filter, compensation_control_filter,
gating_control_filter, pop_pheno_parent_filter],
outputs=[sample_filter,
sop_exp_analysis_tab_filter, compensation_control_filter,
gating_control_filter, pop_pheno_parent_filter])
clear_gating_tab_filters_button.click(fn=component_helper.updater.clear_analysis_tab_filters,
outputs=[sample_filter,
sop_exp_analysis_tab_filter, compensation_control_filter,
gating_control_filter, pop_pheno_parent_filter])
demo.launch(inbrowser=True)
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