import json import os import numpy as np import pandas as pd from dataclasses import dataclass, field from typing import List, Optional, Dict from PIL import Image import streamlit as st import streamlit.components.v1 as components from streamlit.components.v1 import html as st_html from markdown import markdown st.set_page_config(layout="wide", page_title="Annotation of Simulated Patients", initial_sidebar_state="collapsed") import re, textwrap, html as py_html from pathlib import Path from fsspec.implementations.local import LocalFileSystem from huggingface_hub import HfFileSystem from annotation_questions import ( Field, STEPS, INPUT_FIELD_DEFAULT_VALUES, COLS_TO_SAVE, consent_text, SHOW_HELP_ICON, SHOW_VALIDATION_ERROR_MESSAGE, yes_no_labels, # if you still use these in y_n_radio default_labels # if you still use this fallback # plus any others you rely on in app.py ) ######################################################################################## # Function to get user ID from URL def get_param_from_url(param: str, default: str = ""): return st.query_params.get(param, default) #def get_param_from_url(param): # user_id = st.query_params.get(param, "") # return user_id # 'local' or 'hf'. hf is for Hugging Face file system but has limits on the number of access per hour filesystem = 'hf' input_repo_path = 'datasets/emvecchi/therapy_annotation' output_repo_path = 'datasets/emvecchi/therapy_annotation/pilot' to_annotate_file_name = 'to_annotate.csv' # CSV file to annotate INPUT_FIELD_DEFAULT_VALUES = {'slider': 0, 'text': '', 'textarea': '', 'checkbox': False, 'radio': None, 'select_slider': 0, 'multiselect': [], 'likert_radio': None, 'y_n_radio': None} SHOW_HELP_ICON = False SHOW_VALIDATION_ERROR_MESSAGE = True ######################################################################################## if filesystem == 'hf': HF_TOKEN = os.environ.get("HF_TOKEN_WRITE") print("is none?", HF_TOKEN is None) hf_fs = HfFileSystem(token=HF_TOKEN) else: hf_fs = LocalFileSystem() def get_start_index(): base_dir = f"{output_repo_path}/{get_base_path()}" try: files = hf_fs.ls(base_dir) except Exception as e: return -3 return len(files) def read_data(): with hf_fs.open(input_repo_path + '/' + to_annotate_file_name) as f: return pd.read_csv(f) def read_saved_data(): _path = get_path() if hf_fs.exists(output_repo_path + '/' + _path): with hf_fs.open(output_repo_path + '/' + _path) as f: try: return json.load(f) except json.JSONDecodeError as e: print(e) return None # Write a remote file def save_data(data): if not hf_fs.exists(f"{output_repo_path}/{get_base_path()}"): hf_fs.mkdir(f"{output_repo_path}/{get_base_path()}") with hf_fs.open(f"{output_repo_path}/{get_path()}", "w") as f: f.write(json.dumps(data)) def get_base_path(): return f"{st.session_state.user_id}" def get_path(): return f"{get_base_path()}/{st.session_state.current_index}.json" def display_dialogue(hf_path: str): with hf_fs.open(hf_path, "rb") as f: txt = f.read().decode("utf-8") txt = load_text(hf_path) st.markdown(txt, unsafe_allow_html=True) def _ensure_key(key: str, default): if key not in st.session_state: st.session_state[key] = default return st.session_state[key] SPEAKER_RE = re.compile(r'^\s*\*\*(T|P):\*\*\s*(.*)$') def read_md(path: str) -> str: """Read .md file from HF dataset or local disk.""" if filesystem == 'hf': with hf_fs.open(path, "rb") as f: return f.read().decode("utf-8") else: # local path return Path(path).read_text(encoding="utf-8") def wrap_para(text: str, width: int) -> list[str]: if not text.strip(): return [""] return textwrap.wrap( text.strip().replace("\u00A0", " "), width=width, break_long_words=False, break_on_hyphens=False, drop_whitespace=True, replace_whitespace=True, ) or [""] def md_dialogue_to_visual_lines(md_text: str, width: int) -> list[str]: """Return a list of wrapped visual lines with T:/P: on first line.""" md_text = md_text.replace("\r\n", "\n").replace("\r", "\n").strip("\n") paragraphs = re.split(r"\n\s*\n", md_text) out = [] for p in paragraphs: p = p.strip() if not p: out.append("") continue m = SPEAKER_RE.match(p) if m: speaker, content = m.group(1), m.group(2) wrapped = wrap_para(content, width) out.append(f"{speaker}: {py_html.escape(wrapped[0])}".rstrip()) for w in wrapped[1:]: out.append(py_html.escape(w)) else: for w in wrap_para(p, width): out.append(py_html.escape(w)) out.append("") # blank between paragraphs if out and out[-1] == "": out.pop() return out def render_markdown_simple(md_path, height_px=520): md = read_md(md_path) st.markdown( f"
{markdown(md, extensions=['extra','codehilite'])}
", unsafe_allow_html=True ) def render_dialogue(md_path: str, width_chars: int = 100, height_px: int = 520, font_family: str = "system-ui, -apple-system, 'Segoe UI', Roboto, Helvetica, Arial, 'Noto Sans', sans-serif", font_size: str = "1.05rem", show_border: bool = False): """Render the .md dialogue with line numbers inside an iframe to avoid Streamlit CSS quirks.""" text = read_md(md_path) lines = md_dialogue_to_visual_lines(text, width_chars) border_css = "1px solid #e6e6e6" if show_border else "none" radius_css = ".6rem" if show_border else "0" padding_css = ".8rem 1rem" if show_border else "0" # Build stable HTML (table keeps gutter aligned) rows = "\n".join( f"{i}{ln or ' '}" for i, ln in enumerate(lines, 1) ) html_doc = f"""
{rows}
""" # iframe height = inner height; no external scrollbars flashing st_html(html_doc, height=height_px + (16 if show_border else 0), scrolling=False) def _get_value_for_field(f: Field, index: int): """Return the session value for input fields or None.""" if f.type in INPUT_FIELD_DEFAULT_VALUES: key = f.name + str(index) return st.session_state.get(key, INPUT_FIELD_DEFAULT_VALUES[f.type]) return None def _is_default_value(f: Field, val): """Check if current value equals the default for this widget type.""" return val == INPUT_FIELD_DEFAULT_VALUES.get(f.type) def validate_current_page(fields: List[Field], index: int) -> bool: """ Walk the field tree and verify mandatory inputs are filled. Honors `following_mandatory_values`: if a field's value is in that list, subsequent siblings become mandatory. """ ok = True def walk(nodes: List[Field], following_required: bool = False): nonlocal ok # local flag that can be turned on by a node for its following siblings req_for_following = following_required for f in nodes: if f.children: # containers/expanders: recurse; pass the current rule downward walk(f.children, req_for_following) continue if f.type in INPUT_FIELD_DEFAULT_VALUES: val = _get_value_for_field(f, index) # decide if THIS field is required required = bool(f.mandatory or req_for_following) # if required and default → error if required and _is_default_value(f, val): ok = False # update the "following required" rule for siblings if f.following_mandatory_values: try: if val in f.following_mandatory_values: req_for_following = True except Exception: pass # structural types (markdown/input_col/etc.) don’t affect validation walk(fields, False) if not ok: st.error("Please fill in all mandatory fields.") return ok #################################### Streamlit App #################################### # Function to navigate rows def navigate(index_change): st.session_state.step = 0 st.session_state.current_index += index_change # only works consistently if done before rerun js = ''' ''' st.components.v1.html(js, height=0) # https://discuss.streamlit.io/t/click-twice-on-button-for-changing-state/45633/2 # disable text input enter to submit # https://discuss.streamlit.io/t/text-input-how-to-disable-press-enter-to-apply/14457/6 components.html( """ """, height=0 ) st.rerun() def show_field(f: Field, index: int, data_collected): if f.type not in INPUT_FIELD_DEFAULT_VALUES.keys(): st.session_state.following_mandatory = False match f.type: case 'input_col': value = ( st.session_state.data.iloc[index][f.name] if f.name and f.name in st.session_state.data.columns else None ) #elif f.name == 'dialogue_name' and value: # render_dialogue( # os.path.join(input_repo_path, 'dialogues', value), # width_chars=115, height_px=520, show_border=False # ) if f.name == 'dialogue_name' and value: render_markdown_simple(os.path.join(input_repo_path, 'dialogues', st.session_state.batch, value), height_px=720) elif f.name == 'role_name' and value: render_markdown_simple(os.path.join(input_repo_path, 'role_descriptions', value), height_px=520) elif f.name == 'patient' and value: st.markdown(f"#### Patient:  {value}") elif value not in (None, np.nan, ""): if f.title: st.write(f.title) st.write(value) case 'markdown': if f.other_params and f.other_params.get("use_dialogue_name"): row = st.session_state.data.iloc[index] dialogue_name = row["dialogue_name"] md_path = os.path.join(input_repo_path, "dialogues", st.session_state.batch, dialogue_name) content = load_text(md_path) st.markdown(content, unsafe_allow_html=True) elif f.other_params and f.other_params.get("use_roledesc_name"): row = st.session_state.data.iloc[index] role_name = row["role_name"] md_path = os.path.join(input_repo_path, "role_descriptions", role_name) content = load_text(md_path) st.markdown(content, unsafe_allow_html=True) elif f.other_params and f.other_params.get("use_guidelines"): md_path = os.path.join(input_repo_path, "guidelines.md") content = load_text(md_path) st.markdown(content, unsafe_allow_html=True) elif f.other_params and f.other_params.get("instruction_content"): content = f.other_params.get("content", "") if content: st.markdown(content, unsafe_allow_html=True) else: path = f.other_params.get("path") if f.other_params else None if path: content = load_text(os.path.join(input_repo_path, path)) st.markdown(content, unsafe_allow_html=True) else: st.markdown(f.title) case 'expander': with (st.expander(f.title) if f.type == 'expander' else st.container(border=True)): for child in f.children: show_field(child, index, data_collected) case 'container': with st.container(border=True): st.markdown(f.title) for child in (f.children or []): show_field(child, index, data_collected) case 'skip_checkbox': st.checkbox(f.title, key=f.name, value=False) return else: key = f.name + str(index) # track the logical field name once per page; prep_and_save_data relies on this st.session_state.data_inputs_keys.append(f.name) if data_collected and f.name in data_collected: st.session_state[key] = data_collected[f.name] elif key not in st.session_state: st.session_state[key] = INPUT_FIELD_DEFAULT_VALUES[f.type] value = st.session_state[key] label = f.title if not SHOW_HELP_ICON: label = f'**{label}**\n\n{f.help}' if f.help else label validation_error = False if st.session_state.form_displayed == st.session_state.current_index: if st.session_state.following_mandatory and f.skip_mandatory: st.session_state.following_mandatory = False if f.following_mandatory_values and st.session_state[key] in f.following_mandatory_values: st.session_state.following_mandatory = True if f.mandatory or st.session_state.following_mandatory: if value == INPUT_FIELD_DEFAULT_VALUES[f.type]: #if st.session_state[key] == INPUT_FIELD_DEFAULT_VALUES[f.type]: st.session_state.valid = False validation_error = True elif f.following_mandatory_values and st.session_state[key] in f.following_mandatory_values: st.session_state.following_mandatory = True if f.mandatory or st.session_state.following_mandatory: label += (" :red[* required!]" if (validation_error and not SHOW_VALIDATION_ERROR_MESSAGE) else " :red[*]") #f.title += " :red[* required!]" if (validation_error and not SHOW_VALIDATION_ERROR_MESSAGE) else' :red[*]' help_text = None if not SHOW_HELP_ICON else f.help #f.help = None value = st.session_state[key] match f.type: case 'checkbox': st.checkbox(label, key=key, value=value, help=help_text) case 'radio': labels = (f.other_params.get('labels') if f.other_params and f.other_params.get('labels') else default_labels) st.radio( label, options=range(len(labels)), format_func=lambda x: labels[x], key=key, index=value, help=help_text, horizontal=False ) case 'slider': st.slider(label, min_value=0, max_value=6, step=1, key=key, value=value, help=help_text) case 'select_slider': labels = (f.other_params.get('labels') if f.other_params and f.other_params.get('labels') else default_labels) st.select_slider( label, options=[0, 20, 40, 60, 80, 100], format_func=lambda x: labels[x // 20], key=key, value=value, help=help_text ) case 'multiselect': choices = (f.other_params.get('choices') if f.other_params and f.other_params.get('choices') else default_choices) st.multiselect( label, options=choices, format_func=lambda x: x, key=key, default=value, max_selections=3, help=help_text ) case 'likert_radio': labels = (f.other_params.get('labels') if f.other_params and f.other_params.get('labels') else default_labels) st.radio( label, options=[0, 1, 2, 3, 4], format_func=lambda x: labels[x], key=key, index=value, help=help_text, horizontal=True ) case 'y_n_radio': labels = (f.other_params.get('labels') if f.other_params and f.other_params.get('labels') else yes_no_labels) st.radio( label, options=[0, 1], format_func=lambda x: labels[x], key=key, index=value, help=help_text, horizontal=True ) case 'text': st.text_input(label, key=key, value=(value if value is not None else ""), max_chars=None, help=help_text) case 'textarea': st.text_area(label, key=key, value=(value if value is not None else ""), max_chars=None, help=help_text) def show_fields(fields: List[Field]): index = st.session_state.current_index data_collected = read_saved_data() st.session_state.data_inputs_keys = [] # rebuilt each render st.session_state.following_mandatory = False for field in fields: show_field(field, index, data_collected) # mark that the page has been rendered at least once (if you still use this elsewhere) st.session_state.form_displayed = st.session_state.current_index def iter_all_input_fields(): """Yield all Field objects which are real input widgets, across all steps.""" def walk(nodes): for f in nodes: if f.children: walk(f.children) elif f.type in INPUT_FIELD_DEFAULT_VALUES: yield f for step_fields in STEPS: yield from walk(step_fields) def prep_and_save_data(index, skip_sample, completed: bool): existing = read_saved_data() or {} base = {} if 0 <= index < len(st.session_state.data): base = st.session_state.data.iloc[index][COLS_TO_SAVE].to_dict() payload = { **existing, **base, 'user_id': st.session_state.user_id, 'batch': st.session_state.batch, 'index': st.session_state.current_index, 'skip': skip_sample, 'completed': int(completed), } for k in st.session_state.data_inputs_keys: key = k + str(index) if key in st.session_state: payload[k] = st.session_state[key] for f in iter_all_input_fields(): key = f.name + str(index) val = st.session_state.get(key, INPUT_FIELD_DEFAULT_VALUES[f.type]) payload[f.name] = val save_data(payload) #st.set_page_config(layout='wide') # Title of the app st.title("Annotation of Simulated Patients") st.markdown( """ """, unsafe_allow_html=True) def add_annotation_guidelines(): guidelines_text = load_text("guidelines.md") st.markdown( f"
Annotation Guidelines
{guidelines_text}

", unsafe_allow_html=True) if 'unacceptable_response' in st.session_state and st.session_state.unacceptable_response: #error_message = "You are not eligible for this study.

" error_message = "
" if st.session_state.current_index >= -5: error_message += ( "Thank you for your time! You will receive a small compensation for your contribution up to now.

" f'Please return to the study and copy/paste this code: {failed_sanity_check_code}, or ' f'Click Here' ) # Display the error message using custom HTML st.markdown( f"""

Error: You are not eligible for this study.

{error_message}
""", unsafe_allow_html=True ) st.stop() # Load the data to annotate if 'data' not in st.session_state: st.session_state.data = read_data() # user id user_id_from_url = get_param_from_url("user_id") if user_id_from_url and not st.session_state.get("user_id"): st.session_state.user_id = user_id_from_url # batch batch_from_url = get_param_from_url("batch") if batch_from_url and not st.session_state.get("batch"): st.session_state.batch = batch_from_url # current index if 'current_index' not in st.session_state: start_index = get_start_index() target_index = start_index if start_index > 0: last_idx = start_index - 1 last_path = f"{output_repo_path}/{get_base_path()}/{last_idx}.json" try: with hf_fs.open(last_path, "rb") as f: last_data = json.load(f) except Exception: last_data = {} completed_val = last_data.get("completed", 1) is_completed = bool(completed_val) if not is_completed: target_index = last_idx if target_index < len(st.session_state.data)-1: st.session_state.current_index = target_index else: st.session_state.current_index = target_index+1 st.session_state.form_displayed = -3 if 'step' not in st.session_state: st.session_state.step = 0 def add_validated_submit(fields, message): st.session_state.form_displayed = st.session_state.current_index if st.form_submit_button("Submit"): if all(not x for x in fields): st.error(message) else: navigate(1) def add_checked_submit(): check = st.checkbox('I agree', key='consent') add_validated_submit([check], "Please agree to give your consent to proceed") def add_guidelines_submit(): check = st.checkbox('I have read the guidelines in detail, and I understand the study', key='consent') add_validated_submit([check], "Please confirm to have carefully read the guidelines.") def load_text(path: str) -> str: if filesystem == 'hf': with hf_fs.open(path, "rb") as f: return f.read().decode("utf-8") else: with open(path, "r", encoding="utf-8") as f: return f.read() if st.session_state.current_index == -3: with st.form("data_form"): st.markdown(consent_text) add_checked_submit() elif st.session_state.current_index == -2: with st.form("data_form"): st.markdown("# Annotation Guidelines") md_path = os.path.join(input_repo_path, "guidelines.md") content = load_text(md_path) st.markdown(content, unsafe_allow_html=True) add_guidelines_submit() elif st.session_state.current_index == -1: if st.session_state.get('user_id') and st.session_state.get("batch"): navigate(1) else: with st.form("user_id_form"): st.session_state.user_id = st.text_input("User ID", value="") add_validated_submit([st.session_state.user_id], "Please enter a valid user ID") elif st.session_state.current_index < len(st.session_state.data): step = st.session_state.step total_steps = len(STEPS) show_fields(STEPS[step]) c1, c2, c3 = st.columns([1,5,2]) with c1: if st.button("<< Previous"): if step > 0: st.session_state.step -= 1 st.rerun() else: st.session_state.current_index -= 1 st.session_state.step = total_steps - 1 st.rerun() with c2: label = " **Submit >>**" if step < total_steps - 1 else "**Submit & next session**" if st.button(label): if validate_current_page(STEPS[step], st.session_state.current_index): is_last_page = (step == total_steps - 1) with st.spinner("saving"): prep_and_save_data(st.session_state.current_index, ('skip' in st.session_state and st.session_state['skip']), completed=is_last_page) if is_last_page: st.success("Saved!") navigate(1) else: st.session_state.step += 1 st.rerun() elif st.session_state.current_index == len(st.session_state.data): st.write(f"**Thank you for taking part in this study!** \n ") c1, c2, c3 = st.columns([1,5,2]) step = st.session_state.step total_steps = len(STEPS) with c1: if st.button("<< Previous"): if step > 0: st.session_state.step -= 1 st.rerun() else: st.session_state.current_index -= 1 st.session_state.step = total_steps - 1 st.rerun() if 0 <= st.session_state.current_index < len(st.session_state.data): st.write(f"Session {st.session_state.current_index + 1} out of {len(st.session_state.data)}") st.markdown( """""", unsafe_allow_html=True )