updated the latestcontent of:

revised the UI of the app to add dropdown for IFU
added features for incorporating IFU data in prompting
updated upload conditions as per latest search_term sheet.

On branch main
Changes to be committed:
modified: __pycache__/supplier.cpython-310.pyc
modified: __pycache__/utility.cpython-310.pyc
modified: backend_update.ipynb
modified: chains.py
modified: features.py
modified: ui_study.py

backend_update.ipynb

@@ -25,7 +25,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -39,7 +39,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -68,7 +68,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -225,6 +225,741 @@
     "instruction_objects_other_summary = get_table(\"other-summary-com\")"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Load the latest search terms and prompts after the merging"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "dict_keys(['Checklist', 'Revision', 'terms', 'prompts', 'prompt_agg', 'prompt_sum', 'Overview', 'Overview Command', 'Overview Summary Com.', 'Clinical', 'Clinical Command', 'Clin Summary Com', 'Radiologic', 'Radiologic Command', 'parser_safety', 'Units', 'Notes', 'Rad Summary Com', 'Safety', 'Safety Command', 'Safety Summary Com', 'Other', 'Other Command', 'Oth Summary Com'])"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "import pandas as pd\n",
+    "\n",
+    "raw = pd.read_excel(\".data/AMRA AI Reader_Search Term_V14m.xlsx\",sheet_name=None)\n",
+    "raw.keys()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 25,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>assessment</th>\n",
+       "      <th>region</th>\n",
+       "      <th>instruction</th>\n",
+       "      <th>indication_terms</th>\n",
+       "      <th>prompting_term</th>\n",
+       "      <th>outcome_term</th>\n",
+       "      <th>outcome_summary_term</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>overview</td>\n",
+       "      <td>extremity</td>\n",
+       "      <td>Study-FIN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>overview</td>\n",
+       "      <td>extremity</td>\n",
+       "      <td>Time Frame-FIN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>overview</td>\n",
+       "      <td>extremity</td>\n",
+       "      <td>Device-Extremity-FIN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3</th>\n",
+       "      <td>overview</td>\n",
+       "      <td>extremity</td>\n",
+       "      <td>Bone Graft-FIN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>4</th>\n",
+       "      <td>overview</td>\n",
+       "      <td>extremity</td>\n",
+       "      <td>Procedure-Extremity-FIN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "  assessment     region              instruction indication_terms  \\\n",
+       "0   overview  extremity                Study-FIN              NaN   \n",
+       "1   overview  extremity           Time Frame-FIN              NaN   \n",
+       "2   overview  extremity     Device-Extremity-FIN              NaN   \n",
+       "3   overview  extremity           Bone Graft-FIN              NaN   \n",
+       "4   overview  extremity  Procedure-Extremity-FIN              NaN   \n",
+       "\n",
+       "  prompting_term outcome_term outcome_summary_term  \n",
+       "0            NaN          NaN                  NaN  \n",
+       "1            NaN          NaN                  NaN  \n",
+       "2            NaN          NaN                  NaN  \n",
+       "3            NaN          NaN                  NaN  \n",
+       "4            NaN          NaN                  NaN  "
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>assessment</th>\n",
+       "      <th>region</th>\n",
+       "      <th>instruction</th>\n",
+       "      <th>indication_terms</th>\n",
+       "      <th>prompting_term</th>\n",
+       "      <th>outcome_term</th>\n",
+       "      <th>outcome_summary_term</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>overview</td>\n",
+       "      <td>extremity</td>\n",
+       "      <td>[Study-FIN]</td>\n",
+       "      <td>overview Study-FIN</td>\n",
+       "      <td></td>\n",
+       "      <td></td>\n",
+       "      <td></td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>overview</td>\n",
+       "      <td>extremity</td>\n",
+       "      <td>[Time Frame-FIN]</td>\n",
+       "      <td>overview Time Frame-FIN</td>\n",
+       "      <td></td>\n",
+       "      <td></td>\n",
+       "      <td></td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>overview</td>\n",
+       "      <td>extremity</td>\n",
+       "      <td>[Device-Extremity-FIN]</td>\n",
+       "      <td>overview Device-Extremity-FIN</td>\n",
+       "      <td></td>\n",
+       "      <td></td>\n",
+       "      <td></td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3</th>\n",
+       "      <td>overview</td>\n",
+       "      <td>extremity</td>\n",
+       "      <td>[Bone Graft-FIN]</td>\n",
+       "      <td>overview Bone Graft-FIN</td>\n",
+       "      <td></td>\n",
+       "      <td></td>\n",
+       "      <td></td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>4</th>\n",
+       "      <td>overview</td>\n",
+       "      <td>extremity</td>\n",
+       "      <td>[Procedure-Extremity-FIN]</td>\n",
+       "      <td>overview Procedure-Extremity-FIN</td>\n",
+       "      <td></td>\n",
+       "      <td></td>\n",
+       "      <td></td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>...</th>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3488</th>\n",
+       "      <td>other</td>\n",
+       "      <td>all</td>\n",
+       "      <td>[Length of Hospital Stay]</td>\n",
+       "      <td>LOS, hospital stay</td>\n",
+       "      <td>Length of Hospital Stay</td>\n",
+       "      <td>Length of Hospital Stay</td>\n",
+       "      <td></td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3489</th>\n",
+       "      <td>other</td>\n",
+       "      <td>all</td>\n",
+       "      <td>[Length of Hospital Stay]</td>\n",
+       "      <td>ICU, LOS, hospital stay</td>\n",
+       "      <td>Length of Hospital Stay</td>\n",
+       "      <td>Length of Hospital Stay</td>\n",
+       "      <td></td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3490</th>\n",
+       "      <td>other</td>\n",
+       "      <td>all</td>\n",
+       "      <td>[Operation Time]</td>\n",
+       "      <td>Operation time, hrs</td>\n",
+       "      <td>Operation Time</td>\n",
+       "      <td>Operation Time</td>\n",
+       "      <td></td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3491</th>\n",
+       "      <td>other</td>\n",
+       "      <td>all</td>\n",
+       "      <td>[Operation Time]</td>\n",
+       "      <td>Operative time, hrs</td>\n",
+       "      <td>Operation Time</td>\n",
+       "      <td>Operation Time</td>\n",
+       "      <td></td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3492</th>\n",
+       "      <td>other</td>\n",
+       "      <td>all</td>\n",
+       "      <td>[Length of Hospital Stay]</td>\n",
+       "      <td>ICU stay</td>\n",
+       "      <td>Length of Hospital Stay</td>\n",
+       "      <td>Length of Hospital Stay</td>\n",
+       "      <td></td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "<p>3493 rows × 7 columns</p>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "     assessment     region                instruction  \\\n",
+       "0      overview  extremity                [Study-FIN]   \n",
+       "1      overview  extremity           [Time Frame-FIN]   \n",
+       "2      overview  extremity     [Device-Extremity-FIN]   \n",
+       "3      overview  extremity           [Bone Graft-FIN]   \n",
+       "4      overview  extremity  [Procedure-Extremity-FIN]   \n",
+       "...         ...        ...                        ...   \n",
+       "3488      other        all  [Length of Hospital Stay]   \n",
+       "3489      other        all  [Length of Hospital Stay]   \n",
+       "3490      other        all           [Operation Time]   \n",
+       "3491      other        all           [Operation Time]   \n",
+       "3492      other        all  [Length of Hospital Stay]   \n",
+       "\n",
+       "                      indication_terms           prompting_term  \\\n",
+       "0                   overview Study-FIN                            \n",
+       "1              overview Time Frame-FIN                            \n",
+       "2        overview Device-Extremity-FIN                            \n",
+       "3              overview Bone Graft-FIN                            \n",
+       "4     overview Procedure-Extremity-FIN                            \n",
+       "...                                ...                      ...   \n",
+       "3488                LOS, hospital stay  Length of Hospital Stay   \n",
+       "3489           ICU, LOS, hospital stay  Length of Hospital Stay   \n",
+       "3490               Operation time, hrs           Operation Time   \n",
+       "3491               Operative time, hrs           Operation Time   \n",
+       "3492                          ICU stay  Length of Hospital Stay   \n",
+       "\n",
+       "                 outcome_term outcome_summary_term  \n",
+       "0                                                   \n",
+       "1                                                   \n",
+       "2                                                   \n",
+       "3                                                   \n",
+       "4                                                   \n",
+       "...                       ...                  ...  \n",
+       "3488  Length of Hospital Stay                       \n",
+       "3489  Length of Hospital Stay                       \n",
+       "3490           Operation Time                       \n",
+       "3491           Operation Time                       \n",
+       "3492  Length of Hospital Stay                       \n",
+       "\n",
+       "[3493 rows x 7 columns]"
+      ]
+     },
+     "execution_count": 25,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "df_terms = raw[\"terms\"].copy()\n",
+    "display(df_terms.head())\n",
+    "\n",
+    "df_terms.loc[df_terms[\"assessment\"] == \"overview\", \"indication_terms\"] = df_terms.loc[df_terms[\"assessment\"] == \"overview\", \"assessment\"] + \" \" + df_terms.loc[df_terms[\"assessment\"] == \"overview\", \"instruction\"]\n",
+    "df_terms.fillna(\"\",inplace=True)\n",
+    "df_terms[\"instruction\"] = df_terms[\"instruction\"].apply(lambda x: [i.strip() for i in x.split(\",\") if i.strip()])\n",
+    "df_terms"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 26,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "3493/3493\n",
+      "upload erros count: 0\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "[]"
+      ]
+     },
+     "execution_count": 26,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "df_local_to_aws_dynamodb(\"terms\",df_terms)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "23-12-10 00:36:53 - executing function: get_table\n",
+      "23-12-10 00:36:53 - completed function: get_table, runtime: 0:00:00.667078 seconds\n"
+     ]
+    }
+   ],
+   "source": [
+    "# get the current prompts to update new df_prompts' section_sequence\n",
+    "current = get_table(\"prompts\")\n",
+    "current_prompts = {p[\"name\"]:p for p in current}"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>name</th>\n",
+       "      <th>assessment</th>\n",
+       "      <th>inputs</th>\n",
+       "      <th>section_sequence</th>\n",
+       "      <th>chain</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>Article ID</td>\n",
+       "      <td>overview</td>\n",
+       "      <td>[Authors, Acceptance Month, Acceptance Year]</td>\n",
+       "      <td>1</td>\n",
+       "      <td>[From the System, Perform the following tasks:...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>Study-FIN</td>\n",
+       "      <td>overview</td>\n",
+       "      <td>[Material and Methods]</td>\n",
+       "      <td>2</td>\n",
+       "      <td>[From the System, Extract the following inform...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>Time Frame-FIN</td>\n",
+       "      <td>overview</td>\n",
+       "      <td>[Material and Methods]</td>\n",
+       "      <td>3</td>\n",
+       "      <td>[From the System, Extract the following inform...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3</th>\n",
+       "      <td>Device-Spine-FIN</td>\n",
+       "      <td>overview</td>\n",
+       "      <td>[Introduction, Material and Methods]</td>\n",
+       "      <td>4</td>\n",
+       "      <td>[From the System, Extract the following inform...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>4</th>\n",
+       "      <td>SupFix-Spine-FIN</td>\n",
+       "      <td>overview</td>\n",
+       "      <td>[Introduction, Material and Methods]</td>\n",
+       "      <td>5</td>\n",
+       "      <td>[From the System, Extract the following inform...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>...</th>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>84</th>\n",
+       "      <td>Length of Hospital Stay</td>\n",
+       "      <td>other</td>\n",
+       "      <td>[Abstract, Material and Methods, Results, Mark...</td>\n",
+       "      <td></td>\n",
+       "      <td>[From the System and/or previous Assistant res...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>85</th>\n",
+       "      <td>Need for ICU</td>\n",
+       "      <td>other</td>\n",
+       "      <td>[Abstract, Material and Methods, Results, Mark...</td>\n",
+       "      <td></td>\n",
+       "      <td>[From the System and/or previous Assistant res...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>86</th>\n",
+       "      <td>Operation Time</td>\n",
+       "      <td>other</td>\n",
+       "      <td>[Abstract, Material and Methods, Results, Mark...</td>\n",
+       "      <td></td>\n",
+       "      <td>[From the System and/or previous Assistant res...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>87</th>\n",
+       "      <td>Transfusion Rate</td>\n",
+       "      <td>other</td>\n",
+       "      <td>[Abstract, Material and Methods, Results, Mark...</td>\n",
+       "      <td></td>\n",
+       "      <td>[From the System and/or previous Assistant res...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>88</th>\n",
+       "      <td>Time to Readmission</td>\n",
+       "      <td>other</td>\n",
+       "      <td>[Abstract, Material and Methods, Results, Mark...</td>\n",
+       "      <td></td>\n",
+       "      <td>[From the System and/or previous Assistant res...</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "<p>89 rows × 5 columns</p>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "                       name assessment  \\\n",
+       "0                Article ID   overview   \n",
+       "1                 Study-FIN   overview   \n",
+       "2            Time Frame-FIN   overview   \n",
+       "3          Device-Spine-FIN   overview   \n",
+       "4          SupFix-Spine-FIN   overview   \n",
+       "..                      ...        ...   \n",
+       "84  Length of Hospital Stay      other   \n",
+       "85             Need for ICU      other   \n",
+       "86           Operation Time      other   \n",
+       "87         Transfusion Rate      other   \n",
+       "88      Time to Readmission      other   \n",
+       "\n",
+       "                                               inputs section_sequence  \\\n",
+       "0        [Authors, Acceptance Month, Acceptance Year]                1   \n",
+       "1                              [Material and Methods]                2   \n",
+       "2                              [Material and Methods]                3   \n",
+       "3                [Introduction, Material and Methods]                4   \n",
+       "4                [Introduction, Material and Methods]                5   \n",
+       "..                                                ...              ...   \n",
+       "84  [Abstract, Material and Methods, Results, Mark...                    \n",
+       "85  [Abstract, Material and Methods, Results, Mark...                    \n",
+       "86  [Abstract, Material and Methods, Results, Mark...                    \n",
+       "87  [Abstract, Material and Methods, Results, Mark...                    \n",
+       "88  [Abstract, Material and Methods, Results, Mark...                    \n",
+       "\n",
+       "                                                chain  \n",
+       "0   [From the System, Perform the following tasks:...  \n",
+       "1   [From the System, Extract the following inform...  \n",
+       "2   [From the System, Extract the following inform...  \n",
+       "3   [From the System, Extract the following inform...  \n",
+       "4   [From the System, Extract the following inform...  \n",
+       "..                                                ...  \n",
+       "84  [From the System and/or previous Assistant res...  \n",
+       "85  [From the System and/or previous Assistant res...  \n",
+       "86  [From the System and/or previous Assistant res...  \n",
+       "87  [From the System and/or previous Assistant res...  \n",
+       "88  [From the System and/or previous Assistant res...  \n",
+       "\n",
+       "[89 rows x 5 columns]"
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# preprocess df_prompts before upload\n",
+    "df_prompts = raw[\"prompts\"].copy()\n",
+    "df_prompts[\"section_sequence\"] = df_prompts.apply(lambda x: current_prompts[x[\"name\"].strip()][\"section_sequence\"] if x[\"name\"] in current_prompts else \"\", axis=1)\n",
+    "df_prompts.fillna(\"\",inplace=True)\n",
+    "df_prompts.inputs = df_prompts.inputs.apply(lambda x: [i.strip() for i in x.split(\",\") if i.strip()])\n",
+    "df_prompts[\"chain\"] = df_prompts.apply(lambda x: [x[\"root\"],x[\"group\"],x[\"outcome\"],x[\"preoperative\"],x[\"postoperative\"],x[\"study_n\"]],axis=1)\n",
+    "df_prompts.drop(columns=[\"root\",\"group\",\"outcome\",\"preoperative\",\"postoperative\",\"study_n\"],inplace=True)\n",
+    "df_prompts"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "89/89\n",
+      "upload erros count: 0\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "[]"
+      ]
+     },
+     "execution_count": 10,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "df_local_to_aws_dynamodb(\"prompts\",df_prompts)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 87,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>name</th>\n",
+       "      <th>assessment</th>\n",
+       "      <th>inputs</th>\n",
+       "      <th>chain</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>clin-perfFUtable-FIN</td>\n",
+       "      <td>clinical</td>\n",
+       "      <td>Change in Probing Depth\\nFFI\\nGlobal Rating of...</td>\n",
+       "      <td>[Report ALL of the CLINICAL OUTCOME informatio...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>rad-perfFUtable-FIN</td>\n",
+       "      <td>radiologic</td>\n",
+       "      <td>Adjacent Segment ROM\\nCarpal Height Ratio\\nCer...</td>\n",
+       "      <td>[Report ALL of the RADIOLOGIC OUTCOME informat...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>saf-Futable-FIN</td>\n",
+       "      <td>safety</td>\n",
+       "      <td>abb Nonunion-NG\\nGeneric Combo-NG\\nMerged Revi...</td>\n",
+       "      <td>[Report ALL of the SAFETY OUTCOME information ...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3</th>\n",
+       "      <td>oth-perfFUtable-FIN</td>\n",
+       "      <td>other</td>\n",
+       "      <td>Blood Loss\\nHospital Charge\\nLength of Hospita...</td>\n",
+       "      <td>[Report ALL of the OTHER OUTCOME information f...</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "                   name  assessment  \\\n",
+       "0  clin-perfFUtable-FIN    clinical   \n",
+       "1   rad-perfFUtable-FIN  radiologic   \n",
+       "2       saf-Futable-FIN      safety   \n",
+       "3   oth-perfFUtable-FIN       other   \n",
+       "\n",
+       "                                              inputs  \\\n",
+       "0  Change in Probing Depth\\nFFI\\nGlobal Rating of...   \n",
+       "1  Adjacent Segment ROM\\nCarpal Height Ratio\\nCer...   \n",
+       "2  abb Nonunion-NG\\nGeneric Combo-NG\\nMerged Revi...   \n",
+       "3  Blood Loss\\nHospital Charge\\nLength of Hospita...   \n",
+       "\n",
+       "                                               chain  \n",
+       "0  [Report ALL of the CLINICAL OUTCOME informatio...  \n",
+       "1  [Report ALL of the RADIOLOGIC OUTCOME informat...  \n",
+       "2  [Report ALL of the SAFETY OUTCOME information ...  \n",
+       "3  [Report ALL of the OTHER OUTCOME information f...  "
+      ]
+     },
+     "execution_count": 87,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# update the aggregate prompts\n",
+    "df_prompts_agg = raw[\"prompt_agg\"].copy()\n",
+    "df_prompts_agg.dropna(subset=[\"name\"],inplace=True)\n",
+    "df_prompts_agg[\"chain\"] = df_prompts_agg.apply(lambda x: [x[\"root\"]],axis=1)\n",
+    "columns_to_drop = [c for c in df_prompts_agg.columns if \"Unnamed\" in c]\n",
+    "columns_to_drop.append(\"root\")\n",
+    "df_prompts_agg.drop(columns=columns_to_drop,inplace=True)\n",
+    "\n",
+    "df_prompts_agg"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 88,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "4/4\n",
+      "upload erros count: 0\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "[]"
+      ]
+     },
+     "execution_count": 88,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "df_local_to_aws_dynamodb(\"prompts_agg\",df_prompts_agg)"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -234,7 +969,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 28,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
@@ -243,7 +978,7 @@
        "dict_keys(['Checklist', 'Revision', 'terms', 'prompts', 'prompt_agg', 'prompt_sum', 'Overview', 'Overview Command', 'Overview Summary Com.', 'Clinical', 'Clinical Command', 'Clin Summary Com', 'Radiologic', 'Radiologic Command', 'parser_safety', 'Units', 'Notes', 'Rad Summary Com', 'Safety', 'Safety Command', 'Safety Summary Com', 'Other', 'Other Command', 'Oth Summary Com'])"
       ]
      },
-     "execution_count": 28,
+     "execution_count": 4,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -255,6 +990,13 @@
     "raw.keys()"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

chains.py

@@ -91,7 +91,7 @@ def gen_chat_prompt(prompt,article):
             messages.append(("human",prompt["chain"][i]))
     else:
         messages.append(("human",prompt["chain"][0]))
-    messages.append(("system",reformat_inst))
+    # messages.append(("system",reformat_inst))
     
     return ChatPromptTemplate.from_messages(messages=messages)
 

features.py

@@ -35,10 +35,18 @@ def init_app_data():
     app_data["terms"] = get_table("terms")
     app_data["articles"] = list_dict_to_dict(get_table("articles"),key="name")
     app_data["summary"] = list_dict_to_dict(get_table("summary"),key="term")
-    with open(".data/instruction_agg_performance.json","r") as f:
-        prompts_agg_json = json.load(f)
-    app_data["prompts_agg"] = list_dict_to_dict(prompts_agg_json,key="assessment")
+    app_data["devices"] = list_dict_to_dict(get_table("devices"),key="device_name")
+    # with open(".data/instruction_agg_performance.json","r") as f:
+    #     prompts_agg_json = json.load(f)
+    app_data["prompts_agg"] = list_dict_to_dict(get_table("prompts_agg"),key="assessment")
     
+def get_ifu(device_name="TranscendTM NanoTec™ Interbody System"):
+    '''
+    This function get the IFU from the cloud S3'''
+    ifu = app_data["devices"][device_name]
+    text = f"{ifu['contraindications']}\n{ifu['indications']}\n{ifu['intended_use']}"
+    return text
+
 @terminal_print
 def get_existing_article(
         article_name,
@@ -64,6 +72,7 @@ def get_existing_article(
 @terminal_print
 def process_study( # need revision
         domain,
+        device_ifu,
         study_file_obj,
         study_content,
         ):
@@ -76,7 +85,7 @@ def process_study( # need revision
         return "No file or content provided","No file or content provided","No file or content provided"
     
     # update the common article segment from its existing attributes.
-    update_article_segment(article)
+    update_article_segment(article,device_ifu)
 
     # perform pathway logic and content extraction
     process_prompts(article=article)
@@ -125,7 +134,7 @@ def create_md_tables(articles):
     return md_text
 
 @terminal_print
-def update_article_segment(article):
+def update_article_segment(article,device_ifu):
     # get the key content between article objective and discussion
     raw_content = article["raw"]
     index_discussion = raw_content.lower().index("discussion") if "discussion" in raw_content.lower() else len(raw_content)
@@ -137,7 +146,6 @@ def update_article_segment(article):
     materials_and_methods,  next_content = get_key_content(next_content,"methods","results")
     results,                _ = get_key_content(next_content,"results","discussion")
 
-
     # update the article object
     article.update({
         "Abstract":             abstract,
@@ -145,6 +153,7 @@ def update_article_segment(article):
         "Material and Methods": materials_and_methods,
         "Results":              results,
         "Meta Content":         meta_content,
+        "IFU":                  get_ifu(device_ifu),
         "tables":               ""
     })
 

ui_study.py

@@ -23,16 +23,21 @@ def init_study_page():
         # user control panel
         with gr.Row(equal_height=False):
             with gr.Column():
-                gr.Markdown("## Studies")
+                gr.Markdown("## Settings")
                 gr.HTML("<hr>")
                 domain = gr.Radio(label="Anatomical Region",choices=anatomic_domains,value=default_region)
+                select_ifu = gr.Dropdown(label="Select an IFU",choices=app_data["devices"].keys(),value=list(app_data["devices"].keys())[0])
+                
+            with gr.Column():
+                gr.Markdown("## Upload")
+                gr.HTML("<hr>")
                 upload_study = gr.File(label="Upload a clinical study report",type="file",file_count="single")
+                input_study = gr.TextArea(label="Or paste a clinical study report content",placeholder="Paste content here...",lines=5)
+
                 with gr.Row():
                     btn_reset = gr.Button(value="Reset",variant="stop")
                     btn_add_study = gr.Button(value="Add",variant="primary")
                 
-            with gr.Column():
-                input_study = gr.TextArea(label="Or paste a clinical study report content",placeholder="Paste content here...",lines=5)
                 
 
         gr.HTML("<hr>")
@@ -84,6 +89,7 @@ def init_study_page():
             process_study,
             inputs=[
                 domain,
+                select_ifu,
                 upload_study,
                 input_study,
             ],