"""Streamlit-based web interface for ProteoBench."""
import copy
import logging
import subprocess
import uuid
from pathlib import Path
from typing import Any, Dict
import pages.texts.proteobench_builder as pbb
import streamlit as st
from pages.pages_variables.Quant.lfq_DDA_ion_QExactive_variables import (
VariablesDDAQuant,
)
from proteobench.exceptions import DatasetAlreadyExistsOnServerError
from proteobench.io.params import ProteoBenchParameters
from proteobench.io.parsing.parse_settings import ParseSettingsBuilder
from proteobench.modules.quant.quant_lfq_ion_DDA_QExactive import (
DDAQuantIonModuleQExactive as IonModule,
)
from proteobench.utils.server_io import dataset_folder_exists
from . import (
tab1_results,
tab2_form_upload_data,
tab3_1_pmultiqc_report,
tab3_indepth_plots,
tab4_display_results_submitted,
tab5_public_submission,
)
logger: logging.Logger = logging.getLogger(__name__)
[docs]
class QuantUIObjects:
"""Main class for the Streamlit interface of ProteoBench quantification.
This class handles the creation of the Streamlit UI elements, including the main page layout,
input forms, results display, and data submission elements.
Parameters
----------
variables : VariablesDDAQuant
The variables for the quantification module.
ionmodule : IonModule
The quantification module.
parsesettingsbuilder : ParseSettingsBuilder
The parse settings builder.
"""
def __init__(
self,
variables: VariablesDDAQuant,
ionmodule: IonModule,
parsesettingsbuilder: ParseSettingsBuilder,
page_name: str = "/",
) -> None:
"""
Initialize the Streamlit UI objects for the quantification modules.
Parameters
----------
variables : VariablesDDAQuant
The variables for the quantification module.
ionmodule : IonModule
The quantification module.
parsesettingsbuilder : ParseSettingsBuilder
The parse settings builder.
"""
self.variables: VariablesDDAQuant = variables
self.ionmodule: IonModule = ionmodule
self.parsesettingsbuilder: ParseSettingsBuilder = parsesettingsbuilder
self.user_input: Dict[str, Any] = {}
self.page_name = page_name
self.submission_ready = False
self.params_file_dict_copy: Dict[str, Any] = {}
# Create page config and sidebar
pbb.proteobench_page_config()
pbb.proteobench_sidebar(current_page=self.page_name)
self.first_point_plotted = False
st.session_state[self.variables.submit] = False
self.stop_duplicating = False
if self.variables.params_file_dict not in st.session_state.keys():
st.session_state[self.variables.params_file_dict] = {}
if self.variables.slider_id_submitted_uuid not in st.session_state.keys():
st.session_state[self.variables.slider_id_submitted_uuid] = str()
[docs]
def display_indepth_plots(self) -> None:
"""
Display the dataset selection dropdown and plot the selected dataset (Tab 3).
"""
# the key is a string and links to a pandas.DataFrame
key_in_state = self.variables.all_datapoints
if key_in_state not in st.session_state.keys():
st.error("No data available for plotting.", icon="🚨")
return
df = st.session_state[key_in_state]
if df.empty:
st.error("No data available for plotting.", icon="🚨")
return
downloads_df = df[["id", "intermediate_hash"]]
downloads_df.set_index("intermediate_hash", drop=False, inplace=True)
key_in_state = self.variables.placeholder_dataset_selection_container
if key_in_state not in st.session_state.keys():
st.session_state[key_in_state] = st.empty()
key_in_state = self.variables.dataset_selector_id_uuid
st.session_state[key_in_state] = uuid.uuid4()
st.subheader("Select dataset to plot")
dataset_options = [("Uploaded dataset", None)] + list(
zip(downloads_df["id"], downloads_df["intermediate_hash"])
)
dataset_selection = st.selectbox(
"Select dataset",
dataset_options,
index=0,
key=st.session_state[self.variables.dataset_selector_id_uuid],
format_func=lambda x: x[0],
)
public_id, selected_hash = dataset_selection
tab3_indepth_plots.generate_indepth_plots(
module=self.ionmodule,
variables=self.variables,
parsesettingsbuilder=self.parsesettingsbuilder,
user_input=self.user_input,
public_id=public_id,
public_hash=selected_hash,
)
[docs]
@st.fragment
def display_pmultiqc_report(self):
"""Display the pMultiQC report download option of the page in Tab 3.1.
Build pmultiqc based on intermediate data and save self-contained html file.
"""
if self.variables.result_perf in st.session_state.keys():
html_content = st.session_state.get("tab31_pmultiqc_html_content", "")
if not html_content:
html_content = tab3_1_pmultiqc_report.create_pmultiqc_report_section(self.variables)
st.session_state["tab31_pmultiqc_html_content"] = html_content
logger.info(
"pMultiQC report generated.",
)
else:
logger.info('using cached pMultiQC report from session_state["tab31_pmultiqc_html_content"].')
download_disactivate = True
if html_content:
download_disactivate = False
tab3_1_pmultiqc_report.show_download_button(html_content, disabled=download_disactivate)
else:
st.warning("No intermediate data available for pMultiQC report. Please first submit data.")
[docs]
def display_public_submission_ui(self) -> None:
"""
Display the public submission section of the page in Tab 5.
"""
try:
resolved_hash = st.session_state[self.variables.all_datapoints][
st.session_state[self.variables.all_datapoints][st.session_state["old_new"] == "new"]
]["intermediate_hash"].values[0]
if resolved_hash and dataset_folder_exists(resolved_hash):
st.error(
f":no_entry: This dataset was already submitted. A folder for hash '{resolved_hash}' exists on the server. Submission disabled.",
icon="🚫",
)
return
except Exception:
# Fail-soft; backend will still enforce protection
pass
# Initialize Unchecked submission box variable
if self.variables.check_submission not in st.session_state:
st.session_state[self.variables.check_submission] = False
if self.variables.first_new_plot:
self.submission_ready = tab5_public_submission.generate_submission_ui_elements(
variables=self.variables,
user_input=self.user_input,
)
if self.user_input[self.variables.meta_data]:
params = tab5_public_submission.load_user_parameters(
variables=self.variables,
ionmodule=self.ionmodule,
user_input=self.user_input,
)
st.session_state[self.variables.params_file_dict] = params.__dict__
self.params_file_dict_copy = copy.deepcopy(params.__dict__)
tab5_public_submission.generate_additional_parameters_fields_submission(
variables=self.variables,
user_input=self.user_input,
)
tab5_public_submission.generate_comments_section(
variables=self.variables,
user_input=self.user_input,
)
# ? stop_duplicating is not used?
self.stop_duplicating = tab5_public_submission.generate_confirmation_checkbox(
check_submission=self.variables.check_submission
)
else:
params = None
pr_url = None
if st.session_state[self.variables.check_submission] and params is not None:
get_form_values = tab5_public_submission.get_form_values(
variables=self.variables,
)
params = ProteoBenchParameters(**get_form_values, filename=self.variables.additional_params_json)
try:
pr_url = tab5_public_submission.submit_to_repository(
variables=self.variables,
ionmodule=self.ionmodule,
user_input=self.user_input,
params_from_file=self.params_file_dict_copy,
params=params,
)
except DatasetAlreadyExistsOnServerError as e:
st.error(str(e), icon="🚫")
return
if not self.submission_ready:
return
if (
st.session_state[self.variables.check_submission]
and params is not None
and self.variables.submit in st.session_state
and pr_url is not None
):
tab5_public_submission.show_submission_success_message(
variables=self.variables,
pr_url=pr_url,
)
[docs]
@st.fragment
def display_all_data_results_main(self) -> None:
"""Display the results for all data in Tab 1."""
st.title("Results (All Data)")
tab1_results.initialize_main_slider(
slider_id_uuid=self.variables.slider_id_uuid,
default_val_slider=self.variables.default_val_slider,
)
tab1_results.generate_main_slider(
slider_id_uuid=self.variables.slider_id_uuid,
description_slider_md=self.variables.description_slider_md,
default_val_slider=self.variables.default_val_slider,
)
tab1_results.generate_main_selectbox(self.variables, selectbox_id_uuid=self.variables.selectbox_id_uuid)
tab1_results.display_existing_results(variables=self.variables, ionmodule=self.ionmodule)
[docs]
def display_all_data_results_submitted(self) -> None:
"""Display the results for all data in Tab 4."""
st.title("Results (All Data)")
tab4_display_results_submitted.initialize_submitted_slider(
self.variables.slider_id_submitted_uuid,
self.variables.default_val_slider,
)
tab4_display_results_submitted.generate_submitted_slider(self.variables)
tab4_display_results_submitted.generate_submitted_selectbox(self.variables)
tab4_display_results_submitted.display_submitted_results(
variables=self.variables,
ionmodule=self.ionmodule,
)
