Remove secrets

.gitignore

@@ -1,4 +1,5 @@
 .amlignore
+.env
 .zip
 .chroma/
 .ipynb_checkpoints/

01-Load-Data-ACogSearch.ipynb

@@ -64,7 +64,7 @@
     "import json\n",
     "import requests\n",
     "from dotenv import load_dotenv\n",
-    "load_dotenv(\"credentials.env\")\n",
+    "load_dotenv(\".env\", verbose=True, override=True)\n",
     "\n",
     "# Name of the container in your Blob Storage Datasource ( in credentials.env)\n",
     "BLOB_CONTAINER_NAME = \"arxivcs\""
@@ -85,7 +85,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -103,7 +103,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
@@ -332,7 +332,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
@@ -477,9 +477,11 @@
     "}\n",
     "\n",
     "r = requests.put(os.environ['AZURE_SEARCH_ENDPOINT'] + \"/skillsets/\" + skillset_name,\n",
-    "                 data=json.dumps(skillset_payload), headers=headers, params=params)\n",
+    "                 json=skillset_payload, headers=headers, params=params)\n",
     "print(r.status_code)\n",
-    "print(r.ok)"
+    "print(r.ok)\n",
+    "if not r.ok:\n",
+    "    print(r.text)"
    ]
   },
   {
@@ -579,7 +581,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 8,
    "metadata": {
     "tags": []
    },
@@ -589,8 +591,8 @@
      "output_type": "stream",
      "text": [
       "200\n",
-      "Status: success\n",
-      "Items Processed: 0\n",
+      "Status: transientFailure\n",
+      "Items Processed: 1169\n",
       "True\n"
      ]
     }
@@ -646,9 +648,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3.10 - SDK v2",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "python310-sdkv2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -660,12 +662,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
-  },
-  "vscode": {
-   "interpreter": {
-    "hash": "9ff083f0c83558f9261023d47a77b9b3eb892c62cdbe066d046abcad1a5edb5c"
-   }
+   "version": "3.12.1"
   }
  },
  "nbformat": 4,

02-LoadCSVOneToMany-ACogSearch.ipynb

@@ -26,7 +26,7 @@
     "import json\n",
     "import requests\n",
     "from dotenv import load_dotenv\n",
-    "load_dotenv(\"credentials.env\")\n",
+    "load_dotenv(\".env\", verbose=True, override=True)\n",
     "\n",
     "# Name of the container in your Blob Storage Datasource ( in credentials.env)\n",
     "BLOB_CONTAINER_NAME = \"cord19\""
@@ -143,74 +143,81 @@
       "No. of lines: 90000\n"
      ]
     },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "Matplotlib is building the font cache; this may take a moment.\n"
+     ]
+    },
     {
      "data": {
       "text/html": [
        "<style type=\"text/css\">\n",
        "</style>\n",
-       "<table id=\"T_dea2b\">\n",
+       "<table id=\"T_7d742\">\n",
        "  <thead>\n",
        "    <tr>\n",
        "      <th class=\"blank level0\" >&nbsp;</th>\n",
-       "      <th id=\"T_dea2b_level0_col0\" class=\"col_heading level0 col0\" >cord_uid</th>\n",
-       "      <th id=\"T_dea2b_level0_col1\" class=\"col_heading level0 col1\" >source_x</th>\n",
-       "      <th id=\"T_dea2b_level0_col2\" class=\"col_heading level0 col2\" >title</th>\n",
-       "      <th id=\"T_dea2b_level0_col3\" class=\"col_heading level0 col3\" >abstract</th>\n",
-       "      <th id=\"T_dea2b_level0_col4\" class=\"col_heading level0 col4\" >authors</th>\n",
-       "      <th id=\"T_dea2b_level0_col5\" class=\"col_heading level0 col5\" >url</th>\n",
+       "      <th id=\"T_7d742_level0_col0\" class=\"col_heading level0 col0\" >cord_uid</th>\n",
+       "      <th id=\"T_7d742_level0_col1\" class=\"col_heading level0 col1\" >source_x</th>\n",
+       "      <th id=\"T_7d742_level0_col2\" class=\"col_heading level0 col2\" >title</th>\n",
+       "      <th id=\"T_7d742_level0_col3\" class=\"col_heading level0 col3\" >abstract</th>\n",
+       "      <th id=\"T_7d742_level0_col4\" class=\"col_heading level0 col4\" >authors</th>\n",
+       "      <th id=\"T_7d742_level0_col5\" class=\"col_heading level0 col5\" >url</th>\n",
        "    </tr>\n",
        "  </thead>\n",
        "  <tbody>\n",
        "    <tr>\n",
-       "      <th id=\"T_dea2b_level0_row0\" class=\"row_heading level0 row0\" >0</th>\n",
-       "      <td id=\"T_dea2b_row0_col0\" class=\"data row0 col0\" >ug7v899j</td>\n",
-       "      <td id=\"T_dea2b_row0_col1\" class=\"data row0 col1\" >PMC</td>\n",
-       "      <td id=\"T_dea2b_row0_col2\" class=\"data row0 col2\" >Clinical features of culture-p...</td>\n",
-       "      <td id=\"T_dea2b_row0_col3\" class=\"data row0 col3\" >OBJECTIVE: This retrospective ...</td>\n",
-       "      <td id=\"T_dea2b_row0_col4\" class=\"data row0 col4\" >Madani, Tariq A; Al-Ghamdi, Ai...</td>\n",
-       "      <td id=\"T_dea2b_row0_col5\" class=\"data row0 col5\" ><a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC35282/\">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC35282/</a></td>\n",
+       "      <th id=\"T_7d742_level0_row0\" class=\"row_heading level0 row0\" >0</th>\n",
+       "      <td id=\"T_7d742_row0_col0\" class=\"data row0 col0\" >ug7v899j</td>\n",
+       "      <td id=\"T_7d742_row0_col1\" class=\"data row0 col1\" >PMC</td>\n",
+       "      <td id=\"T_7d742_row0_col2\" class=\"data row0 col2\" >Clinical features of culture-p...</td>\n",
+       "      <td id=\"T_7d742_row0_col3\" class=\"data row0 col3\" >OBJECTIVE: This retrospective ...</td>\n",
+       "      <td id=\"T_7d742_row0_col4\" class=\"data row0 col4\" >Madani, Tariq A; Al-Ghamdi, Ai...</td>\n",
+       "      <td id=\"T_7d742_row0_col5\" class=\"data row0 col5\" ><a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC35282/\">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC35282/</a></td>\n",
        "    </tr>\n",
        "    <tr>\n",
-       "      <th id=\"T_dea2b_level0_row1\" class=\"row_heading level0 row1\" >1</th>\n",
-       "      <td id=\"T_dea2b_row1_col0\" class=\"data row1 col0\" >02tnwd4m</td>\n",
-       "      <td id=\"T_dea2b_row1_col1\" class=\"data row1 col1\" >PMC</td>\n",
-       "      <td id=\"T_dea2b_row1_col2\" class=\"data row1 col2\" >Nitric oxide: a pro-inflammato...</td>\n",
-       "      <td id=\"T_dea2b_row1_col3\" class=\"data row1 col3\" >Inflammatory diseases of the r...</td>\n",
-       "      <td id=\"T_dea2b_row1_col4\" class=\"data row1 col4\" >Vliet, Albert van der; Eiseric...</td>\n",
-       "      <td id=\"T_dea2b_row1_col5\" class=\"data row1 col5\" ><a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59543/\">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59543/</a></td>\n",
+       "      <th id=\"T_7d742_level0_row1\" class=\"row_heading level0 row1\" >1</th>\n",
+       "      <td id=\"T_7d742_row1_col0\" class=\"data row1 col0\" >02tnwd4m</td>\n",
+       "      <td id=\"T_7d742_row1_col1\" class=\"data row1 col1\" >PMC</td>\n",
+       "      <td id=\"T_7d742_row1_col2\" class=\"data row1 col2\" >Nitric oxide: a pro-inflammato...</td>\n",
+       "      <td id=\"T_7d742_row1_col3\" class=\"data row1 col3\" >Inflammatory diseases of the r...</td>\n",
+       "      <td id=\"T_7d742_row1_col4\" class=\"data row1 col4\" >Vliet, Albert van der; Eiseric...</td>\n",
+       "      <td id=\"T_7d742_row1_col5\" class=\"data row1 col5\" ><a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59543/\">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59543/</a></td>\n",
        "    </tr>\n",
        "    <tr>\n",
-       "      <th id=\"T_dea2b_level0_row2\" class=\"row_heading level0 row2\" >2</th>\n",
-       "      <td id=\"T_dea2b_row2_col0\" class=\"data row2 col0\" >ejv2xln0</td>\n",
-       "      <td id=\"T_dea2b_row2_col1\" class=\"data row2 col1\" >PMC</td>\n",
-       "      <td id=\"T_dea2b_row2_col2\" class=\"data row2 col2\" >Surfactant protein-D and pulmo...</td>\n",
-       "      <td id=\"T_dea2b_row2_col3\" class=\"data row2 col3\" >Surfactant protein-D (SP-D) pa...</td>\n",
-       "      <td id=\"T_dea2b_row2_col4\" class=\"data row2 col4\" >Crouch, Erika C...</td>\n",
-       "      <td id=\"T_dea2b_row2_col5\" class=\"data row2 col5\" ><a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59549/\">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59549/</a></td>\n",
+       "      <th id=\"T_7d742_level0_row2\" class=\"row_heading level0 row2\" >2</th>\n",
+       "      <td id=\"T_7d742_row2_col0\" class=\"data row2 col0\" >ejv2xln0</td>\n",
+       "      <td id=\"T_7d742_row2_col1\" class=\"data row2 col1\" >PMC</td>\n",
+       "      <td id=\"T_7d742_row2_col2\" class=\"data row2 col2\" >Surfactant protein-D and pulmo...</td>\n",
+       "      <td id=\"T_7d742_row2_col3\" class=\"data row2 col3\" >Surfactant protein-D (SP-D) pa...</td>\n",
+       "      <td id=\"T_7d742_row2_col4\" class=\"data row2 col4\" >Crouch, Erika C...</td>\n",
+       "      <td id=\"T_7d742_row2_col5\" class=\"data row2 col5\" ><a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59549/\">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59549/</a></td>\n",
        "    </tr>\n",
        "    <tr>\n",
-       "      <th id=\"T_dea2b_level0_row3\" class=\"row_heading level0 row3\" >3</th>\n",
-       "      <td id=\"T_dea2b_row3_col0\" class=\"data row3 col0\" >2b73a28n</td>\n",
-       "      <td id=\"T_dea2b_row3_col1\" class=\"data row3 col1\" >PMC</td>\n",
-       "      <td id=\"T_dea2b_row3_col2\" class=\"data row3 col2\" >Role of endothelin-1 in lung d...</td>\n",
-       "      <td id=\"T_dea2b_row3_col3\" class=\"data row3 col3\" >Endothelin-1 (ET-1) is a 21 am...</td>\n",
-       "      <td id=\"T_dea2b_row3_col4\" class=\"data row3 col4\" >Fagan, Karen A; McMurtry, Ivan...</td>\n",
-       "      <td id=\"T_dea2b_row3_col5\" class=\"data row3 col5\" ><a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59574/\">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59574/</a></td>\n",
+       "      <th id=\"T_7d742_level0_row3\" class=\"row_heading level0 row3\" >3</th>\n",
+       "      <td id=\"T_7d742_row3_col0\" class=\"data row3 col0\" >2b73a28n</td>\n",
+       "      <td id=\"T_7d742_row3_col1\" class=\"data row3 col1\" >PMC</td>\n",
+       "      <td id=\"T_7d742_row3_col2\" class=\"data row3 col2\" >Role of endothelin-1 in lung d...</td>\n",
+       "      <td id=\"T_7d742_row3_col3\" class=\"data row3 col3\" >Endothelin-1 (ET-1) is a 21 am...</td>\n",
+       "      <td id=\"T_7d742_row3_col4\" class=\"data row3 col4\" >Fagan, Karen A; McMurtry, Ivan...</td>\n",
+       "      <td id=\"T_7d742_row3_col5\" class=\"data row3 col5\" ><a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59574/\">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59574/</a></td>\n",
        "    </tr>\n",
        "    <tr>\n",
-       "      <th id=\"T_dea2b_level0_row4\" class=\"row_heading level0 row4\" >4</th>\n",
-       "      <td id=\"T_dea2b_row4_col0\" class=\"data row4 col0\" >9785vg6d</td>\n",
-       "      <td id=\"T_dea2b_row4_col1\" class=\"data row4 col1\" >PMC</td>\n",
-       "      <td id=\"T_dea2b_row4_col2\" class=\"data row4 col2\" >Gene expression in epithelial ...</td>\n",
-       "      <td id=\"T_dea2b_row4_col3\" class=\"data row4 col3\" >Respiratory syncytial virus (R...</td>\n",
-       "      <td id=\"T_dea2b_row4_col4\" class=\"data row4 col4\" >Domachowske, Joseph B; Bonvill...</td>\n",
-       "      <td id=\"T_dea2b_row4_col5\" class=\"data row4 col5\" ><a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59580/\">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59580/</a></td>\n",
+       "      <th id=\"T_7d742_level0_row4\" class=\"row_heading level0 row4\" >4</th>\n",
+       "      <td id=\"T_7d742_row4_col0\" class=\"data row4 col0\" >9785vg6d</td>\n",
+       "      <td id=\"T_7d742_row4_col1\" class=\"data row4 col1\" >PMC</td>\n",
+       "      <td id=\"T_7d742_row4_col2\" class=\"data row4 col2\" >Gene expression in epithelial ...</td>\n",
+       "      <td id=\"T_7d742_row4_col3\" class=\"data row4 col3\" >Respiratory syncytial virus (R...</td>\n",
+       "      <td id=\"T_7d742_row4_col4\" class=\"data row4 col4\" >Domachowske, Joseph B; Bonvill...</td>\n",
+       "      <td id=\"T_7d742_row4_col5\" class=\"data row4 col5\" ><a href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59580/\">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59580/</a></td>\n",
        "    </tr>\n",
        "  </tbody>\n",
        "</table>\n"
       ],
       "text/plain": [
-       "<pandas.io.formats.style.Styler at 0x7f0ca0a41ff0>"
+       "<pandas.io.formats.style.Styler at 0x21b55823020>"
       ]
      },
      "execution_count": 6,
@@ -253,7 +260,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 7,
    "id": "74913764-9dfb-4646-aac8-d389cd4533e6",
    "metadata": {},
    "outputs": [
@@ -354,7 +361,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 8,
    "id": "b46cfa90-28b4-4602-b6ff-743a3407fd72",
    "metadata": {},
    "outputs": [
@@ -472,7 +479,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 9,
    "id": "b87b8ebd-8091-43b6-9124-cc17021cfb78",
    "metadata": {},
    "outputs": [
@@ -521,7 +528,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 10,
    "id": "6132c041-7213-410e-a206-1a8c7385128e",
    "metadata": {},
    "outputs": [
@@ -530,8 +537,8 @@
      "output_type": "stream",
      "text": [
       "200\n",
-      "Status: inProgress\n",
-      "Items Processed: 209\n",
+      "Status: success\n",
+      "Items Processed: 0\n",
       "True\n"
      ]
     }
@@ -590,9 +597,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3.10 - SDK v2",
+   "display_name": "Python 3",
    "language": "python",
-   "name": "python310-sdkv2"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -604,7 +611,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "version": "3.12.1"
   }
  },
  "nbformat": 4,

03-Quering-AOpenAI.ipynb

@@ -71,7 +71,7 @@
     "from common.utils import get_search_results\n",
     "\n",
     "from dotenv import load_dotenv\n",
-    "load_dotenv(\"credentials.env\")"
+    "load_dotenv(\".env\", verbose=True, override=True)"
    ]
   },
   {

04-Complex-Docs.ipynb

@@ -58,7 +58,7 @@
     "from IPython.display import Markdown, HTML, display  \n",
     "\n",
     "from dotenv import load_dotenv\n",
-    "load_dotenv(\"credentials.env\")\n",
+    "load_dotenv(\".env\", verbose=True, override=True)\n",
     "\n",
     "def printmd(string):\n",
     "    display(Markdown(string))\n",

05-Adding_Memory.ipynb

@@ -52,7 +52,7 @@
     "from common.prompts import DOCSEARCH_PROMPT\n",
     "\n",
     "from dotenv import load_dotenv\n",
-    "load_dotenv(\"credentials.env\")\n",
+    "load_dotenv(\".env\", verbose=True, override=True)\n",
     "\n",
     "import logging\n",
     "\n",

06-First-RAG.ipynb

@@ -70,7 +70,7 @@
     "    display(Markdown(string))\n",
     "\n",
     "from dotenv import load_dotenv\n",
-    "load_dotenv(\"credentials.env\")\n"
+    "load_dotenv(\".env\", verbose=True, override=True)\n"
    ]
   },
   {

07-TabularDataQA.ipynb

@@ -40,7 +40,7 @@
     "from IPython.display import Markdown, HTML, display  \n",
     "\n",
     "from dotenv import load_dotenv\n",
-    "load_dotenv(\"credentials.env\")\n",
+    "load_dotenv(\".env\", verbose=True, override=True)\n",
     "\n",
     "def printmd(string):\n",
     "    display(Markdown(string))"

08-SQLDB_QA.ipynb

@@ -45,7 +45,7 @@
     "from IPython.display import Markdown, HTML, display  \n",
     "\n",
     "from dotenv import load_dotenv\n",
-    "load_dotenv(\"credentials.env\")\n",
+    "load_dotenv(\".env\", verbose=True, override=True)\n",
     "\n",
     "def printmd(string):\n",
     "    display(Markdown(string))"

09-BingChatClone.ipynb

@@ -67,7 +67,7 @@
     "    display(Markdown(string.replace(\"$\",\"USD \")))\n",
     "\n",
     "from dotenv import load_dotenv\n",
-    "load_dotenv(\"credentials.env\")\n"
+    "load_dotenv(\".env\", verbose=True, override=True)\n"
    ]
   },
   {

10-API-Search.ipynb

@@ -56,7 +56,7 @@
     "from IPython.display import Markdown, HTML, display  \n",
     "\n",
     "from dotenv import load_dotenv\n",
-    "load_dotenv(\"credentials.env\")\n",
+    "load_dotenv(\".env\", verbose=True, override=True)\n",
     "\n",
     "def printmd(string):\n",
     "    display(Markdown(string.replace(\"$\",\"USD \")))\n"

11-Smart_Agent.ipynb

@@ -91,7 +91,7 @@
     "from common.prompts import CUSTOM_CHATBOT_PROMPT \n",
     "\n",
     "from dotenv import load_dotenv\n",
-    "load_dotenv(\"credentials.env\")\n",
+    "load_dotenv(\".env\", verbose=True, override=True)\n",
     "\n",
     "from IPython.display import Markdown, HTML, display \n",
     "\n",

11.5-Smart_Agent-LangGraph.ipynb

@@ -61,7 +61,7 @@
     "from common.prompts import CUSTOM_CHATBOT_PROMPT, CUSTOM_CHATBOT_PREFIX\n",
     "\n",
     "from dotenv import load_dotenv\n",
-    "load_dotenv(\"credentials.env\")\n",
+    "load_dotenv(\".env\", verbose=True, override=True)\n",
     "\n",
     "from IPython.display import Markdown, HTML, display \n",
     "\n",