Changed main app title

Dockerfile

@@ -17,4 +17,4 @@ RUN mamba env create --prefix $HOME/env  -f ./environment.yml
 EXPOSE 7860
 WORKDIR $HOME/app
 
-CMD mamba run -p $HOME/env --no-capture-output voila --no-browser notebooks/PopulationHealthScreener-Anthro.ipynb
+CMD mamba run -p $HOME/env --no-capture-output voila --no-browser notebooks/PopulationHealthScreener.ipynb

notebooks/PopulationHealthScreener-Anthro.ipynb

@@ -1,47 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "35bcc7331ef5d1dc",
-   "metadata": {
-    "ExecuteTime": {
-     "end_time": "2025-04-10T15:52:17.264471Z",
-     "start_time": "2025-04-10T15:52:17.156072Z"
-    }
-   },
-   "outputs": [],
-   "source": "import subprocess\nimport logging\nimport os\nimport base64\nimport uuid\nimport warnings\nfrom datetime import date\nfrom dateutil.relativedelta import relativedelta\n\nimport ipywidgets as widgets\nfrom IPython.display import clear_output, HTML, Javascript\nfrom IPython.utils.capture import capture_output\n\nfrom src.utils.prediction_table import PredictionTable\n\nwarnings.filterwarnings(\"ignore\")\nos.environ['TRANSFORMERS_VERBOSITY'] = 'error'\nos.environ['TQDM_DISABLE'] = '1'\nlogging.getLogger(\"transformers\").setLevel(logging.ERROR)\nlogging.getLogger(\"torch\").setLevel(logging.ERROR)\n\nwith capture_output():\n    from src.handlers.model_wrapper import available_models\n\nfrom src.utils.ui_elements import (\n    inject_styles, BOX_WIDTH, BUTTON_WIDTH, QUERY_WIDTH,\n    make_button, make_separator, make_spacer, make_section_header,\n    RunButton, error_html\n)\n\ninject_styles()\n\n# --- Globals ---\n\narticles_table = None\nmodel_loaded = False\noutput_dir = os.path.join(os.getcwd(), 'outputs')\nos.makedirs(output_dir, exist_ok=True)\ndirectory = output_dir\n\n# --- UI Elements ---\n\nmodel_dropdown = widgets.Dropdown(\n    options=[m.name for m in available_models],\n    value=available_models[0].name,\n    description='',\n    disabled=False,\n    layout=widgets.Layout(width=BOX_WIDTH)\n)\n\n# Hidden Python-state widget for query source; visual display handled by _query_selector_ui below\nquery_selector = widgets.Dropdown(\n    options=['paper', 'custom'],\n    value='paper',\n    layout=widgets.Layout(display='none')\n)\n\n_qid   = query_selector.model_id\n_rname = f\"qs_{uuid.uuid4().hex[:8]}\"\n\ndef _js_sync(val):\n    return (\n        f\"(function(){{\"\n        f\"try{{requirejs(['@jupyter-widgets/base'],function(b){{\"\n        f\"var ms=b.ManagerBase._managers;\"\n        f\"var mgr=ms?Object.values(ms)[0]:null;\"\n        f\"mgr&&mgr.get_model('{_qid}').then(function(m){{m.set('value','{val}');m.save_changes();}});\"\n        f\"}})}}catch(e){{}}\"\n        f\"}})();\"\n    )\n\ndef _render_query_html(disabled=False):\n    dis     = 'disabled' if disabled else ''\n    opacity = 'opacity:0.6;' if disabled else ''\n    cursor  = 'default' if disabled else 'pointer'\n    p_chk   = 'checked' if query_selector.value == 'paper' else ''\n    c_chk   = 'checked' if query_selector.value == 'custom' else ''\n    url     = 'https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(16)30054-X/abstract'\n    return (\n        f\"<div style='font-size:13px;line-height:2.2;{opacity}'>\"\n        f\"<label style='cursor:{cursor};display:block;'>\"\n        f\"<input type='radio' name='{_rname}' value='paper' {p_chk} {dis} onchange=\\\"{_js_sync('paper')}\\\">\"\n        f\"&nbsp;Use the query from the \"\n        f\"<a href='{url}' target='_blank' style='color:inherit;text-decoration:underline;'>\"\n        f\"2016 paper by the NCD-RisC</a>\"\n        f\"</label>\"\n        f\"<label style='cursor:{cursor};display:block;'>\"\n        f\"<input type='radio' name='{_rname}' value='custom' {c_chk} {dis} onchange=\\\"{_js_sync('custom')}\\\">\"\n        f\"&nbsp;Use a custom query\"\n        f\"</label>\"\n        f\"</div>\"\n    )\n\n_query_selector_ui = widgets.HTML(value=_render_query_html())\n\nquery_input = widgets.Textarea(\n    placeholder='Enter PubMed query...',\n    disabled=True,\n    layout=widgets.Layout(width=QUERY_WIDTH, height='60px')\n)\n\ndef on_query_source_change(change):\n    query_input.disabled = (change.new == 'paper')\n\nquery_selector.observe(on_query_source_change, names='value')\n\nstart_date_value = date.today() - relativedelta(months=1)\nend_date_value = date.today()\n\n_label_style = \"text-align:right; display:inline-block; width:75px; font-size:13px; line-height:28px; padding-right:6px;\"\n\nstart_date = widgets.DatePicker(value=start_date_value, description='')\nend_date   = widgets.DatePicker(value=end_date_value,   description='')\n\nstart_date_row = widgets.HBox([\n    widgets.HTML(f\"<span style='{_label_style}'>Start date:</span>\"),\n    start_date\n])\nend_date_row = widgets.HBox([\n    widgets.HTML(f\"<span style='{_label_style}'>End date:</span>\"),\n    end_date\n])\n\nrecall_target = widgets.Dropdown(\n    options=[('95%', 95), ('90%', 90), ('80%', 80), ('70%', 70), ('60%', 60)],\n    value=95,\n    description='',\n    disabled=True,\n    layout=widgets.Layout(width='120px')\n)\n\n# RunButtons\nload_run    = RunButton('Load',            executing_msg='Loading...',   error_label='Model')\nsearch_run  = RunButton('Search',          executing_msg='Searching...',  error_label='Search')\npredict_run = RunButton('Screen articles', executing_msg='Screening...',  error_label='Screening')\npredict_run.btn.disabled = True\n\n_predict_reset_btn = widgets.Button(\n    description='\\u21ba',\n    layout=widgets.Layout(width='32px', height='28px', display='none'),\n    style=widgets.ButtonStyle()\n)\n\nunload_btn = make_button('Unload', width='100px')\nunload_btn.layout.display = 'none'\n\nfile_uploader = widgets.FileUpload(\n    accept='.csv',\n    multiple=False,\n    description='Upload',\n    layout=widgets.Layout(width=BUTTON_WIDTH, height='28px')\n)\n\n# Status widget — blank until articles are loaded\narticles_status = widgets.HTML(value='')\n\n# Error outputs\nload_file_error_out = widgets.Output()\n\n# Progress kept in memory for screen_articles.py callbacks (not displayed)\n_screen_progress = widgets.IntProgress(value=0, min=0, max=1)\n\ndef _on_screen_progress(change):\n    if predict_run.btn.disabled:\n        predict_run.btn.description = f'Screening... {change.new}/{_screen_progress.max}'\n\n_screen_progress.observe(_on_screen_progress, names='value')\n\n\n# --- Download link helpers ---\n# Each renders as:  Download [editable box] .ext\n# \"Download\" is the underlined clickable word; the box sets the filename.\n\n_DL_SPAN = \"display:inline-flex;align-items:center;margin-left:12px;line-height:28px;\"\n_DL_LINK = \"font-size:12px;color:black;text-decoration:underline;line-height:28px;margin-right:3px;\"\n_DL_BOX  = \"font-size:12px;border:1px solid #ccc;border-radius:3px;padding:1px 5px;height:20px;line-height:18px;width:130px;margin:0 2px;\"\n_DL_EXT  = \"font-size:12px;line-height:28px;\"\n\n\ndef _download_link(df, default_stem):\n    \"\"\"Download [box].csv\"\"\"\n    b64 = base64.b64encode(df.to_csv(index=False).encode()).decode()\n    uid = uuid.uuid4().hex[:8]\n    return (\n        f\"<span style='{_DL_SPAN}'>\"\n        f\"<a id='anc-{uid}' href='data:text/csv;base64,{b64}' style='display:none'></a>\"\n        f\"<a href='#' style='{_DL_LINK}'\"\n        f\" onclick=\\\"var s=document.getElementById('inp-{uid}').value||'{default_stem}';\"\n        f\"document.getElementById('anc-{uid}').download=s+'.csv';\"\n        f\"document.getElementById('anc-{uid}').click();return false;\\\">Download</a>\"\n        f\"<input id='inp-{uid}' type='text' value='{default_stem}' style='{_DL_BOX}'>\"\n        f\"<span style='{_DL_EXT}'>.csv</span>\"\n        f\"</span>\"\n    )\n\n\ndef _ris_content(df):\n    lines = []\n    for _, row in df.iterrows():\n        lines.append(\"TI  - \" + str(row.get('Title') or ''))\n        lines.append(\"AB  - \" + str(row.get('Abstract') or ''))\n        for author in str(row.get('Authors') or '').split(','):\n            lines.append(\"AU  - \" + author.strip())\n        lines.append(\"DO  - \" + str(row.get('DOI') or ''))\n        lines.append(\"PM  - \" + str(row.get('PMID') or ''))\n        lines.append(\"PY  - \" + str(row.get('Year') or ''))\n        lines.append(\"JO  - \" + str(row.get('Journal') or ''))\n        lines.append(\"ER  - \")\n        lines.append(\"\")\n    return \"\\n\".join(lines)\n\n\ndef _download_link_combined(df, default_stem):\n    \"\"\"Download [box].csv — also triggers .ris download on same click.\"\"\"\n    csv_b64 = base64.b64encode(df.to_csv(index=False).encode()).decode()\n    ris_b64 = base64.b64encode(_ris_content(df).encode('utf-8')).decode()\n    uid = uuid.uuid4().hex[:8]\n    return (\n        f\"<span style='{_DL_SPAN}'>\"\n        f\"<a id='csv-{uid}' href='data:text/csv;base64,{csv_b64}' style='display:none'></a>\"\n        f\"<a id='ris-{uid}' href='data:application/x-research-info-systems;base64,{ris_b64}' style='display:none'></a>\"\n        f\"<a href='#' style='{_DL_LINK}'\"\n        f\" onclick=\\\"var s=document.getElementById('inp-{uid}').value||'{default_stem}';\"\n        f\"document.getElementById('csv-{uid}').download=s+'.csv';\"\n        f\"document.getElementById('csv-{uid}').click();\"\n        f\"setTimeout(function(){{document.getElementById('ris-{uid}').download=s+'.ris';\"\n        f\"document.getElementById('ris-{uid}').click();}},150);\"\n        f\"return false;\\\">Download</a>\"\n        f\"<input id='inp-{uid}' type='text' value='{default_stem}' style='{_DL_BOX}'>\"\n        f\"<span style='{_DL_EXT}'>.csv</span>\"\n        f\"</span>\"\n    )\n\n\ndef _download_link_predictions(df, default_stem):\n    \"\"\"Download [box] predictions.csv\"\"\"\n    b64 = base64.b64encode(df.to_csv(index=False).encode()).decode()\n    uid = uuid.uuid4().hex[:8]\n    return (\n        f\"<span style='{_DL_SPAN}'>\"\n        f\"<a id='anc-{uid}' href='data:text/csv;base64,{b64}' style='display:none'></a>\"\n        f\"<a href='#' style='{_DL_LINK}'\"\n        f\" onclick=\\\"var s=document.getElementById('inp-{uid}').value||'{default_stem}';\"\n        f\"document.getElementById('anc-{uid}').download=s+' predictions.csv';\"\n        f\"document.getElementById('anc-{uid}').click();return false;\\\">Download</a>\"\n        f\"<input id='inp-{uid}' type='text' value='{default_stem}' style='{_DL_BOX}'>\"\n        f\"<span style='{_DL_EXT}'>&nbsp;predictions.csv</span>\"\n        f\"</span>\"\n    )\n\n\ndef _set_search_side_disabled(disabled):\n    query_selector.disabled = disabled\n    _query_selector_ui.value = _render_query_html(disabled)\n    query_input.disabled = disabled or (query_selector.value == 'paper')\n    start_date.disabled = disabled\n    end_date.disabled = disabled\n    search_run.btn.disabled = disabled\n\n\ndef _set_load_side_disabled(disabled):\n    file_uploader.disabled = disabled\n\n\ndef _update_predict_state():\n    ready = model_loaded and articles_table is not None\n    recall_target.disabled = not ready\n    predict_run.btn.disabled = not ready\n\n\ndef _set_articles(table, display_name):\n    global articles_table\n    articles_table = table\n    articles_status.value = (\n        f\"<span style='color:#28a745; font-size:13px; line-height:28px; margin-right:10px;'>\"\n        f\"Loaded {display_name}</span>\"\n    )\n    unload_btn.layout.display = ''\n    _update_predict_state()\n\n\ndef _unset_articles():\n    global articles_table\n    articles_table = None\n    articles_status.value = ''\n    unload_btn.layout.display = 'none'\n    _update_predict_state()\n\n\n# --- Event Handlers ---\n\ndef run_load_model(b):\n    global model_loaded\n    load_run.start()\n    try:\n        with capture_output():\n            with open(os.path.abspath(os.path.join(os.getcwd(), 'src/choose_model.py'))) as f:\n                exec(f.read(), globals())\n        model_loaded = True\n        load_run.done('\\u2713 Model loaded')\n        _update_predict_state()\n    except Exception as e:\n        model_loaded = False\n        load_run.fail(e)\n\n\ndef run_search(b):\n    global articles_table\n    search_run.start()\n    _saved_start = start_date.value\n    _saved_end   = end_date.value\n    _set_search_side_disabled(True)\n    start_date.value = _saved_start\n    end_date.value   = _saved_end\n    try:\n        with capture_output():\n            with open(os.path.abspath(os.path.join(os.getcwd(), 'src/search_pubmed.py'))) as f:\n                exec(f.read(), globals())\n        search_run.done('\\u2713 Search completed')\n        _set_load_side_disabled(True)\n        _set_articles(articles_table, 'Articles.csv')\n        search_run.out.value = _download_link(articles_table.df, 'Articles')\n    except Exception as e:\n        _set_search_side_disabled(False)\n        search_run.fail(e)\n\n\ndef on_file_uploaded(change):\n    if not change.new:\n        return\n    with load_file_error_out:\n        clear_output(wait=True)\n    try:\n        file_info = change.new[0]\n        name = file_info['name']\n        content = bytes(file_info['content'])\n        table = PredictionTable.from_bytes(content)\n        file_uploader.description = '\\u2713 Upload completed'\n        file_uploader.add_class('done-button')\n        _set_articles(table, name)\n        _set_search_side_disabled(True)\n    except Exception as e:\n        from IPython.display import display\n        with load_file_error_out:\n            clear_output(wait=True)\n            display(widgets.HTML(\n                f\"<span style='color:#dc3545; font-size:12px; margin-left:12px; line-height:28px;'>\"\n                f\"<b>{type(e).__name__}</b>: {e}</span>\"\n            ))\n\nfile_uploader.observe(on_file_uploaded, names='value')\n\n\ndef on_unload(b):\n    _unset_articles()\n    _set_search_side_disabled(False)\n    _set_load_side_disabled(False)\n    file_uploader.description = 'Upload'\n    file_uploader.remove_class('done-button')\n    search_run.reset()\n    _predict_reset_btn.layout.display = 'none'\n    with load_file_error_out:\n        clear_output(wait=True)\n\n\ndef run_screen_articles(b):\n    predict_run.start()\n    _predict_reset_btn.layout.display = 'none'\n    _screen_progress.value = 0\n    try:\n        with capture_output():\n            with open(os.path.abspath(os.path.join(os.getcwd(), 'src/screen_articles.py'))) as f:\n                exec(f.read(), globals())\n        predict_run.done('\\u2713 Screening completed')\n        _predict_reset_btn.layout.display = ''\n        review_df = globals().get('review_data')\n        pred_df   = globals().get('data')\n        predict_run.out.value = (\n            _download_link_combined(review_df, 'Screened articles') +\n            '<br>' +\n            _download_link_predictions(pred_df, 'Screened articles')\n        )\n    except Exception as e:\n        predict_run.fail(e)\n\n\ndef on_predict_reset(b):\n    predict_run.reset()\n    _predict_reset_btn.layout.display = 'none'\n    _update_predict_state()\n\n_predict_reset_btn.on_click(on_predict_reset)\n\nload_run.on_click(run_load_model)\nsearch_run.on_click(run_search)\npredict_run.on_click(run_screen_articles)\nunload_btn.on_click(on_unload)\n\n# --- Layout ---\n\nheader = widgets.HTML(\n    \"<h2 style='margin: 8px 0 12px 12px; font-size:22px; font-weight:bold;'>PopulationHealthScreener</h2>\"\n)\n\n# 1 - Choose a model\nchoose_model = widgets.VBox([\n    make_section_header('Choose a model'),\n    model_dropdown,\n    make_spacer('20px'),\n    load_run.row,\n], layout=widgets.Layout(margin='0 0 0 12px'))\n\n# 2 - Search PubMed (left) | or + Load from file (right) | articles status (bottom)\n_search_left = widgets.VBox([\n    make_section_header('Search PubMed'),\n    make_spacer('8px'),\n    query_selector,\n    _query_selector_ui,\n    make_spacer('2px'),\n    query_input,\n    make_spacer('10px'),\n    start_date_row,\n    end_date_row,\n    make_spacer('12px'),\n    search_run.row,\n])\n\n_load_content = widgets.VBox([\n    make_section_header('Load articles from a file'),\n    make_spacer('8px'),\n    widgets.HBox([file_uploader, load_file_error_out]),\n], layout=widgets.Layout(margin='0 0 0 20px'))\n\n_load_section = widgets.HBox(\n    [widgets.HTML(\"<span style='font-size:16px;'>or</span>\"), _load_content],\n    layout=widgets.Layout(align_items='flex-start', margin='0 0 0 24px')\n)\n\nsearch_pubmed = widgets.VBox([\n    widgets.HBox(\n        [_search_left, _load_section],\n        layout=widgets.Layout(align_items='flex-start')\n    ),\n    make_spacer('12px'),\n    widgets.HBox([articles_status, unload_btn]),\n], layout=widgets.Layout(margin='0 0 0 12px'))\n\n# 3 - Screen articles\n_screen_title_row = widgets.HBox([\n    make_section_header('Screen articles'),\n    _predict_reset_btn,\n], layout=widgets.Layout(align_items='center'))\n\nscreen_articles = widgets.VBox([\n    _screen_title_row,\n    make_spacer('8px'),\n    widgets.HBox([\n        widgets.HTML(\"<span style='font-size:13px; line-height:28px; margin-right:8px;'>Target recall</span>\"),\n        recall_target,\n        widgets.HTML(\"<span style='font-size:13px; color:gray; margin-left:12px; line-height:28px;'>Based on the recall achieved in previous testing; the higher the recall, the more inclusive the model</span>\"),\n    ], layout=widgets.Layout(align_items='center')),\n    make_spacer('12px'),\n    predict_run.row,\n], layout=widgets.Layout(margin='0 0 0 12px'))\n\n\ndisplay(header, choose_model, make_separator(), search_pubmed, make_separator(), screen_articles)\n"
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "eeebfa287ae99109",
-   "metadata": {},
-   "outputs": [],
-   "source": ""
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.12.9"
-  },
-  "trusted": true
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}