Abstracted button styles. Changed layout of loading section

notebooks/notebook.ipynb

@@ -11,269 +11,7 @@
     }
    },
    "outputs": [],
-   "source": [
-    "import subprocess\n",
-    "from datetime import date\n",
-    "from dateutil.relativedelta import relativedelta\n",
-    "import os\n",
-    "import ipywidgets as widgets\n",
-    "from IPython.display import HTML, clear_output\n",
-    "import warnings\n",
-    "warnings.filterwarnings(\"ignore\")\n",
-    "\n",
-    "from src.handlers.model_wrapper import available_models\n",
-    "\n",
-    "# --- UI Elements ---\n",
-    "\n",
-    "model_dropdown = widgets.Dropdown(\n",
-    "    options=[m.name for m in available_models],\n",
-    "    value=available_models[0].name,\n",
-    "    description='',\n",
-    "    disabled=True,\n",
-    "    layout=widgets.Layout(width='300px')\n",
-    ")\n",
-    "\n",
-    "selected_model = available_models[0]\n",
-    "\n",
-    "query_method = widgets.RadioButtons(\n",
-    "    options=['default', 'custom'],\n",
-    "    value='default',\n",
-    "    layout=widgets.Layout(width='180px')\n",
-    ")\n",
-    "\n",
-    "custom_query_file = widgets.Text(\n",
-    "    placeholder='Enter query filename',\n",
-    "    description='',\n",
-    "    disabled=True,\n",
-    "    layout=widgets.Layout(width='300px')\n",
-    ")\n",
-    "\n",
-    "def toggle_custom_query(change):\n",
-    "    custom_query_file.disabled = (change.new != 'custom')\n",
-    "\n",
-    "query_method.observe(toggle_custom_query, names='value')\n",
-    "\n",
-    "start_date_value = date.today() - relativedelta(months=1)\n",
-    "end_date_value = date.today()\n",
-    "\n",
-    "start_date = widgets.DatePicker(\n",
-    "    description='Start date:   ',\n",
-    "    value=start_date_value\n",
-    ")\n",
-    "\n",
-    "end_date = widgets.DatePicker(\n",
-    "    description='End Date:   ',\n",
-    "    value=end_date_value\n",
-    ")\n",
-    "\n",
-    "recall_target = widgets.Dropdown(\n",
-    "    options=[('95%', 95), ('90%', 90), ('80%', 80), ('70%', 70), ('60%', 60)],\n",
-    "    value=95,\n",
-    "    description='',\n",
-    "    layout=widgets.Layout(width='120px')\n",
-    ")\n",
-    "\n",
-    "# Button style\n",
-    "display(HTML(\"\"\"\n",
-    "<style>\n",
-    ".widget-button {\n",
-    "    justify-content: flex-start !important;\n",
-    "    text-align: left !important;\n",
-    "    font-weight: bold !important;\n",
-    "    font-size: 15px !important;\n",
-    "    padding-left: 12px !important;\n",
-    "}\n",
-    "</style>\n",
-    "\"\"\"))\n",
-    "\n",
-    "load_btn = widgets.Button(\n",
-    "    description='Load',\n",
-    "    layout=widgets.Layout(width='100px'),\n",
-    "    style=widgets.ButtonStyle(font_weight='bold')\n",
-    ")\n",
-    "\n",
-    "download_btn = widgets.Button(\n",
-    "    description='Download abstracts from PubMed',\n",
-    "    layout=widgets.Layout(width='300px'),\n",
-    "    style=widgets.ButtonStyle(font_weight='bold')\n",
-    ")\n",
-    "\n",
-    "predict_btn = widgets.Button(\n",
-    "    description='Run the model and screen articles',\n",
-    "    layout=widgets.Layout(width='300px'),\n",
-    "    style=widgets.ButtonStyle(font_weight='bold')\n",
-    ")\n",
-    "\n",
-    "# Output areas\n",
-    "download_output = widgets.Output()\n",
-    "load_model_output = widgets.Output()\n",
-    "predict_output = widgets.Output()\n",
-    "\n",
-    "\n",
-    "# --- Helper ---\n",
-    "def mark_done(output_placeholder, header_widget):\n",
-    "    output_placeholder.clear_output()\n",
-    "    with output_placeholder:\n",
-    "        display(header_widget)\n",
-    "        display(widgets.HTML(\n",
-    "            \"<span style='color: green; font-weight: bold; font-size:15px; margin-left:12px;'>&#10004; Done</span>\"\n",
-    "        ))\n",
-    "\n",
-    "\n",
-    "# --- Event Handlers ---\n",
-    "\n",
-    "def run_load_model(b):\n",
-    "    b.close()\n",
-    "    with load_model_output:\n",
-    "        clear_output(wait=True)\n",
-    "        header = widgets.HTML(\n",
-    "            \"<div style='font-size:15px; font-weight:bold; margin-left:12px;'>Load the model</div>\"\n",
-    "        )\n",
-    "        display(header)\n",
-    "        try:\n",
-    "            print(' Loading the model...')\n",
-    "            with open(os.path.abspath(os.path.join(os.getcwd(), 'src/load_model.py'))) as f:\n",
-    "                exec(f.read(), globals())\n",
-    "            mark_done(load_model_output, header)\n",
-    "        except Exception:\n",
-    "            import traceback\n",
-    "            traceback.print_exc()\n",
-    "\n",
-    "\n",
-    "def run_download_citations(b):\n",
-    "    b.close()\n",
-    "    with download_output:\n",
-    "        clear_output(wait=True)\n",
-    "        header = widgets.HTML(\n",
-    "            \"<div style='font-size:15px; font-weight:bold; margin-left:12px;'>Download abstracts from PubMed</div>\"\n",
-    "        )\n",
-    "        display(header)\n",
-    "        try:\n",
-    "            print(f' Downloading articles published between {start_date.value} and {end_date.value}...')\n",
-    "            with open(os.path.abspath(os.path.join(os.getcwd(), 'src/download_citations.py'))) as f:\n",
-    "                exec(f.read(), globals())\n",
-    "            mark_done(download_output, header)\n",
-    "            path_to_articles = os.path.join(globals().get('directory'), 'downloaded_articles.csv')\n",
-    "            display(widgets.HTML(\n",
-    "                f\"<p style='font-size:12px; color:gray; margin-top:6px; margin-left:12px; margin-bottom:0px;'>\"\n",
-    "                f\"Article abstracts downloaded to: {path_to_articles}</p>\"\n",
-    "            ))\n",
-    "        except Exception:\n",
-    "            import traceback\n",
-    "            traceback.print_exc()\n",
-    "\n",
-    "\n",
-    "def open_ris_file(b):\n",
-    "    path = os.path.join(globals().get('directory'), 'articles_to_review.ris')\n",
-    "    try:\n",
-    "        if os.name == 'posix':\n",
-    "            subprocess.Popen(['open', path])\n",
-    "        elif os.name == 'nt':\n",
-    "            subprocess.Popen(['start', '', path], shell=True)\n",
-    "    except Exception:\n",
-    "        import traceback\n",
-    "        traceback.print_exc()\n",
-    "\n",
-    "\n",
-    "def run_prediction(b):\n",
-    "    b.close()\n",
-    "    with predict_output:\n",
-    "        clear_output(wait=True)\n",
-    "        header = widgets.HTML(\n",
-    "            \"<div style='font-size:15px; font-weight:bold; margin-left:12px;'>Run the model and screen articles</div>\"\n",
-    "        )\n",
-    "        display(header)\n",
-    "        try:\n",
-    "            print(' Running the model...')\n",
-    "            with open(os.path.abspath(os.path.join(os.getcwd(), 'src/predict.py'))) as f:\n",
-    "                exec(f.read(), globals())\n",
-    "            mark_done(predict_output, header)\n",
-    "        except Exception:\n",
-    "            import traceback\n",
-    "            traceback.print_exc()\n",
-    "\n",
-    "    path_to_ris = os.path.join(globals().get('directory'), 'articles_to_review.ris')\n",
-    "    open_file_btn = widgets.Button(description='📄 Open in EndNote', layout=widgets.Layout(width='350px'))\n",
-    "    open_file_btn.on_click(open_ris_file)\n",
-    "    path_display = widgets.HTML(\n",
-    "        f\"<p style='font-size:12px; color:gray; margin-top:6px; margin-left:12px;'>\"\n",
-    "        f\"Path to the EndNote file: {path_to_ris}</p>\"\n",
-    "    )\n",
-    "    final_message_1 = widgets.HTML(\n",
-    "        \"<p style='font-size:14px; color:black; margin-top:10px; margin-left:12px;'>\"\n",
-    "        \"Open the .ris file in EndNote by clicking on the button above or navigating to the file</p>\"\n",
-    "    )\n",
-    "    final_message_2 = widgets.HTML(\n",
-    "        \"<p style='font-size:14px; color:black; margin-top:10px; margin-left:12px;'>\"\n",
-    "        \"Select RefMan - RIS as the input file format</p>\"\n",
-    "    )\n",
-    "    with predict_output:\n",
-    "        display(widgets.VBox([open_file_btn, path_display, final_message_1, final_message_2]))\n",
-    "\n",
-    "\n",
-    "load_btn.on_click(run_load_model)\n",
-    "download_btn.on_click(run_download_citations)\n",
-    "predict_btn.on_click(run_prediction)\n",
-    "\n",
-    "# --- Layout ---\n",
-    "\n",
-    "title_style = 'font-size: 22px; font-weight: bold; margin-bottom: 40px;'\n",
-    "\n",
-    "header = widgets.HTML(\n",
-    "    f\"<h2 style='margin-left:12px; {title_style}'>Automated screening of the literature</h2>\"\n",
-    ")\n",
-    "\n",
-    "# 1 - Choose model\n",
-    "choose_model_content = widgets.VBox([\n",
-    "    widgets.HTML(\"<b style='font-size:16px;'>Choose a model</b>\"),\n",
-    "    model_dropdown,\n",
-    "    load_model_output,\n",
-    "], layout=widgets.Layout(margin='0 0 0 12px'))\n",
-    "\n",
-    "choose_model = widgets.HBox([\n",
-    "    choose_model_content,\n",
-    "    load_btn,\n",
-    "], layout=widgets.Layout(justify_content='space-between', align_items='flex-end'))\n",
-    "\n",
-    "sep1 = widgets.HTML(\"<hr style='margin: 20px 12px; border: none; border-top: 1px solid #ccc;'>\")\n",
-    "\n",
-    "# 2 - Search PubMed\n",
-    "search_pubmed = widgets.VBox([\n",
-    "    widgets.HTML(\"<b style='font-size:16px;'>Define the PubMed search</b>\"),\n",
-    "    widgets.HBox([\n",
-    "        widgets.VBox([\n",
-    "            start_date,\n",
-    "            end_date\n",
-    "        ], layout=widgets.Layout(margin='0 20px 0 0')),\n",
-    "        widgets.VBox([\n",
-    "            widgets.HBox([\n",
-    "                widgets.Label('Query:   ', layout=widgets.Layout(width='60px')),\n",
-    "                query_method\n",
-    "            ]),\n",
-    "            custom_query_file\n",
-    "        ], layout=widgets.Layout(margin='0 0 0 20px'))\n",
-    "    ], layout=widgets.Layout(justify_content='flex-start', gap='20px', margin='10px 0')),\n",
-    "    widgets.HTML(\"<div style='height:15px;'></div>\"),\n",
-    "    download_btn,\n",
-    "    download_output,\n",
-    "], layout=widgets.Layout(margin='0 0 0 12px'))\n",
-    "\n",
-    "sep2 = widgets.HTML(\"<hr style='margin: 20px 12px; border: none; border-top: 1px solid #ccc;'>\")\n",
-    "\n",
-    "# 3 - Screen articles\n",
-    "screen_articles = widgets.VBox([\n",
-    "    widgets.HTML(\"<b style='font-size:16px;'>Define how inclusive the model should be</b>\"),\n",
-    "    widgets.HTML(\"<span style='font-size:13px; color:gray; margin-top:2px; display:block;'>Based on the recall achieved in previous testing; the higher the recall, the more inclusive the model</span>\"),\n",
-    "    widgets.HTML(\"<div style='height:8px;'></div>\"),\n",
-    "    recall_target,\n",
-    "    widgets.HTML(\"<div style='height:15px;'></div>\"),\n",
-    "    predict_btn,\n",
-    "    predict_output\n",
-    "], layout=widgets.Layout(margin='0 0 0 12px'))\n",
-    "\n",
-    "\n",
-    "display(header, choose_model, sep1, search_pubmed, sep2, screen_articles)"
-   ]
+   "source": "import subprocess\nfrom datetime import date\nfrom dateutil.relativedelta import relativedelta\nimport os\nimport ipywidgets as widgets\nfrom IPython.display import clear_output\nimport warnings\nwarnings.filterwarnings(\"ignore\")\n\nfrom src.handlers.model_wrapper import available_models\nfrom src.utils.ui_elements import inject_styles, make_button, set_executing, set_done, set_error\n\ninject_styles()\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='300px')\n)\n\nselected_model = available_models[0]\n\nquery_method = widgets.RadioButtons(\n    options=['default', 'custom'],\n    value='default',\n    layout=widgets.Layout(width='180px')\n)\n\ncustom_query_file = widgets.Text(\n    placeholder='Enter query filename',\n    description='',\n    disabled=True,\n    layout=widgets.Layout(width='300px')\n)\n\ndef toggle_custom_query(change):\n    custom_query_file.disabled = (change.new != 'custom')\n\nquery_method.observe(toggle_custom_query, names='value')\n\nstart_date_value = date.today() - relativedelta(months=1)\nend_date_value = date.today()\n\nstart_date = widgets.DatePicker(\n    description='Start date:   ',\n    value=start_date_value\n)\n\nend_date = widgets.DatePicker(\n    description='End Date:   ',\n    value=end_date_value\n)\n\nrecall_target = widgets.Dropdown(\n    options=[('95%', 95), ('90%', 90), ('80%', 80), ('70%', 70), ('60%', 60)],\n    value=95,\n    description='',\n    layout=widgets.Layout(width='120px')\n)\n\n# Buttons\nload_btn     = make_button('Load', width='300px')\ndownload_btn = make_button('Download abstracts from PubMed')\npredict_btn  = make_button('Run the model and screen articles')\n\n# Output areas\nload_model_output = widgets.Output()\ndownload_output   = widgets.Output()\npredict_output    = widgets.Output()\n\n\n# --- Event Handlers ---\n\ndef run_load_model(b):\n    set_executing(load_btn, 'Loading...')\n    with load_model_output:\n        clear_output(wait=True)\n        try:\n            with open(os.path.abspath(os.path.join(os.getcwd(), 'src/load_model.py'))) as f:\n                exec(f.read(), globals())\n            set_done(load_btn, '\\u2713 Loaded')\n        except Exception:\n            set_error(load_btn, 'Load')\n            import traceback\n            traceback.print_exc()\n\n\ndef run_download_citations(b):\n    set_executing(download_btn, 'Downloading...')\n    with download_output:\n        clear_output(wait=True)\n        try:\n            with open(os.path.abspath(os.path.join(os.getcwd(), 'src/download_citations.py'))) as f:\n                exec(f.read(), globals())\n            set_done(download_btn, '\\u2713 Downloaded')\n            path_to_articles = os.path.join(globals().get('directory'), 'downloaded_articles.csv')\n            with download_output:\n                display(widgets.HTML(\n                    f\"<p style='font-size:12px; color:gray; margin-top:6px; margin-left:12px; margin-bottom:0px;'>\"\n                    f\"Article abstracts downloaded to: {path_to_articles}</p>\"\n                ))\n        except Exception:\n            set_error(download_btn, 'Download abstracts from PubMed')\n            import traceback\n            traceback.print_exc()\n\n\ndef open_ris_file(b):\n    path = os.path.join(globals().get('directory'), 'articles_to_review.ris')\n    try:\n        if os.name == 'posix':\n            subprocess.Popen(['open', path])\n        elif os.name == 'nt':\n            subprocess.Popen(['start', '', path], shell=True)\n    except Exception:\n        import traceback\n        traceback.print_exc()\n\n\ndef run_prediction(b):\n    set_executing(predict_btn, 'Running...')\n    with predict_output:\n        clear_output(wait=True)\n        try:\n            with open(os.path.abspath(os.path.join(os.getcwd(), 'src/predict.py'))) as f:\n                exec(f.read(), globals())\n            set_done(predict_btn, '\\u2713 Done')\n        except Exception:\n            set_error(predict_btn, 'Run the model and screen articles')\n            import traceback\n            traceback.print_exc()\n\n    path_to_ris = os.path.join(globals().get('directory'), 'articles_to_review.ris')\n    open_file_btn = make_button('📄 Open in EndNote', width='350px')\n    open_file_btn.on_click(open_ris_file)\n    path_display = widgets.HTML(\n        f\"<p style='font-size:12px; color:gray; margin-top:6px; margin-left:12px;'>\"\n        f\"Path to the EndNote file: {path_to_ris}</p>\"\n    )\n    final_message_1 = widgets.HTML(\n        \"<p style='font-size:14px; color:black; margin-top:10px; margin-left:12px;'>\"\n        \"Open the .ris file in EndNote by clicking on the button above or navigating to the file</p>\"\n    )\n    final_message_2 = widgets.HTML(\n        \"<p style='font-size:14px; color:black; margin-top:10px; margin-left:12px;'>\"\n        \"Select RefMan - RIS as the input file format</p>\"\n    )\n    with predict_output:\n        display(widgets.VBox([open_file_btn, path_display, final_message_1, final_message_2]))\n\n\nload_btn.on_click(run_load_model)\ndownload_btn.on_click(run_download_citations)\npredict_btn.on_click(run_prediction)\n\n# --- Layout ---\n\ntitle_style = 'font-size: 22px; font-weight: bold; margin-bottom: 40px;'\n\nheader = widgets.HTML(\n    f\"<h2 style='margin-left:12px; {title_style}'>Automated screening of the literature</h2>\"\n)\n\n# 1 - Choose model\nchoose_model = widgets.VBox([\n    widgets.HTML(\"<b style='font-size:16px;'>Choose a model</b>\"),\n    model_dropdown,\n    load_btn,\n    load_model_output,\n], layout=widgets.Layout(margin='0 0 0 12px'))\n\nsep1 = widgets.HTML(\"<hr style='margin: 20px 12px; border: none; border-top: 1px solid #ccc;'>\")\n\n# 2 - Search PubMed\nsearch_pubmed = widgets.VBox([\n    widgets.HTML(\"<b style='font-size:16px;'>Define the PubMed search</b>\"),\n    widgets.HBox([\n        widgets.VBox([\n            start_date,\n            end_date\n        ], layout=widgets.Layout(margin='0 20px 0 0')),\n        widgets.VBox([\n            widgets.HBox([\n                widgets.Label('Query:   ', layout=widgets.Layout(width='60px')),\n                query_method\n            ]),\n            custom_query_file\n        ], layout=widgets.Layout(margin='0 0 0 20px'))\n    ], layout=widgets.Layout(justify_content='flex-start', gap='20px', margin='10px 0')),\n    widgets.HTML(\"<div style='height:15px;'></div>\"),\n    download_btn,\n    download_output,\n], layout=widgets.Layout(margin='0 0 0 12px'))\n\nsep2 = widgets.HTML(\"<hr style='margin: 20px 12px; border: none; border-top: 1px solid #ccc;'>\")\n\n# 3 - Screen articles\nscreen_articles = widgets.VBox([\n    widgets.HTML(\"<b style='font-size:16px;'>Define how inclusive the model should be</b>\"),\n    widgets.HTML(\"<span style='font-size:13px; color:gray; margin-top:2px; display:block;'>Based on the recall achieved in previous testing; the higher the recall, the more inclusive the model</span>\"),\n    widgets.HTML(\"<div style='height:8px;'></div>\"),\n    recall_target,\n    widgets.HTML(\"<div style='height:15px;'></div>\"),\n    predict_btn,\n    predict_output\n], layout=widgets.Layout(margin='0 0 0 12px'))\n\n\ndisplay(header, choose_model, sep1, search_pubmed, sep2, screen_articles)"
   },
   {
    "cell_type": "code",
@@ -306,4 +44,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}

notebooks/src/utils/ui_elements.py

@@ -0,0 +1,43 @@
+import ipywidgets as widgets
+from IPython.display import HTML, display
+
+
+_BUTTON_STYLE_CSS = """
+<style>
+.widget-button {
+    justify-content: flex-start !important;
+    text-align: left !important;
+    font-weight: bold !important;
+    font-size: 15px !important;
+    padding-left: 12px !important;
+}
+</style>
+"""
+
+
+def inject_styles():
+    display(HTML(_BUTTON_STYLE_CSS))
+
+
+def make_button(description, width='300px'):
+    return widgets.Button(
+        description=description,
+        layout=widgets.Layout(width=width),
+        style=widgets.ButtonStyle(font_weight='bold')
+    )
+
+
+def set_executing(btn, message='Running...'):
+    btn.description = message
+    btn.disabled = True
+
+
+def set_done(btn, message):
+    btn.description = message
+    btn.disabled = True
+    btn.style.button_color = '#c3e6cb'
+
+
+def set_error(btn, original_description):
+    btn.description = original_description
+    btn.disabled = False