Update db example

Author: kks32

examples/db.ipynb

@@ -11,6 +11,87 @@
   {
    "cell_type": "code",
    "execution_count": 1,
+   "id": "5a76c77b-0078-48fc-ade6-e46cbac010dd",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Found existing installation: dapi 1.0.0\n",
+      "Uninstalling dapi-1.0.0:\n",
+      "  Successfully uninstalled dapi-1.0.0\n",
+      "Collecting git+https://github.com/DesignSafe-CI/dapi.git@t3\n",
+      "  Cloning https://github.com/DesignSafe-CI/dapi.git (to revision t3) to /tmp/pip-req-build-f6bbn80i\n",
+      "  Running command git clone --filter=blob:none --quiet https://github.com/DesignSafe-CI/dapi.git /tmp/pip-req-build-f6bbn80i\n",
+      "  Running command git checkout -b t3 --track origin/t3\n",
+      "  Switched to a new branch 't3'\n",
+      "  Branch 't3' set up to track remote branch 't3' from 'origin'.\n",
+      "  Resolved https://github.com/DesignSafe-CI/dapi.git to commit 6e85ea5b2b26fe7a82220db6260ac6c2124caaee\n",
+      "  Installing build dependencies ... \u001b[?25ldone\n",
+      "\u001b[?25h  Getting requirements to build wheel ... \u001b[?25ldone\n",
+      "\u001b[?25h  Preparing metadata (pyproject.toml) ... \u001b[?25ldone\n",
+      "\u001b[?25hRequirement already satisfied: exceptiongroup<2.0.0,>=1.2.0 in /home/jupyter/.local/lib/python3.11/site-packages (from dapi==1.0.0) (1.2.2)\n",
+      "Requirement already satisfied: jsonschema>=4.18.0 in /opt/conda/lib/python3.11/site-packages (from dapi==1.0.0) (4.23.0)\n",
+      "Requirement already satisfied: numpy<3.0.0,>=2.1.1 in /home/jupyter/.local/lib/python3.11/site-packages (from dapi==1.0.0) (2.2.5)\n",
+      "Requirement already satisfied: pandas<3.0.0,>=2.2.3 in /home/jupyter/.local/lib/python3.11/site-packages (from dapi==1.0.0) (2.2.3)\n",
+      "Requirement already satisfied: pymysql<2.0.0,>=1.1.0 in /home/jupyter/.local/lib/python3.11/site-packages (from dapi==1.0.0) (1.1.1)\n",
+      "Requirement already satisfied: python-dotenv<2.0.0,>=1.0.1 in /home/jupyter/.local/lib/python3.11/site-packages (from dapi==1.0.0) (1.1.0)\n",
+      "Requirement already satisfied: sqlalchemy<3.0.0,>=2.0.23 in /home/jupyter/.local/lib/python3.11/site-packages (from dapi==1.0.0) (2.0.40)\n",
+      "Requirement already satisfied: tapipy<2.0.0,>=1.6.3 in /opt/conda/lib/python3.11/site-packages (from dapi==1.0.0) (1.7.0)\n",
+      "Requirement already satisfied: tqdm<5.0.0,>=4.66.1 in /opt/conda/lib/python3.11/site-packages (from dapi==1.0.0) (4.66.1)\n",
+      "Requirement already satisfied: attrs>=22.2.0 in /opt/conda/lib/python3.11/site-packages (from jsonschema>=4.18.0->dapi==1.0.0) (23.1.0)\n",
+      "Requirement already satisfied: jsonschema-specifications>=2023.03.6 in /opt/conda/lib/python3.11/site-packages (from jsonschema>=4.18.0->dapi==1.0.0) (2023.7.1)\n",
+      "Requirement already satisfied: referencing>=0.28.4 in /opt/conda/lib/python3.11/site-packages (from jsonschema>=4.18.0->dapi==1.0.0) (0.30.2)\n",
+      "Requirement already satisfied: rpds-py>=0.7.1 in /opt/conda/lib/python3.11/site-packages (from jsonschema>=4.18.0->dapi==1.0.0) (0.10.6)\n",
+      "Requirement already satisfied: python-dateutil>=2.8.2 in /opt/conda/lib/python3.11/site-packages (from pandas<3.0.0,>=2.2.3->dapi==1.0.0) (2.8.2)\n",
+      "Requirement already satisfied: pytz>=2020.1 in /opt/conda/lib/python3.11/site-packages (from pandas<3.0.0,>=2.2.3->dapi==1.0.0) (2023.3.post1)\n",
+      "Requirement already satisfied: tzdata>=2022.7 in /home/jupyter/.local/lib/python3.11/site-packages (from pandas<3.0.0,>=2.2.3->dapi==1.0.0) (2025.2)\n",
+      "Requirement already satisfied: greenlet>=1 in /opt/conda/lib/python3.11/site-packages (from sqlalchemy<3.0.0,>=2.0.23->dapi==1.0.0) (3.0.0)\n",
+      "Requirement already satisfied: typing-extensions>=4.6.0 in /opt/conda/lib/python3.11/site-packages (from sqlalchemy<3.0.0,>=2.0.23->dapi==1.0.0) (4.8.0)\n",
+      "Requirement already satisfied: PyJWT>=1.7.1 in /opt/conda/lib/python3.11/site-packages (from tapipy<2.0.0,>=1.6.3->dapi==1.0.0) (2.8.0)\n",
+      "Requirement already satisfied: atomicwrites<2.0.0,>=1.4.0 in /opt/conda/lib/python3.11/site-packages (from tapipy<2.0.0,>=1.6.3->dapi==1.0.0) (1.4.1)\n",
+      "Requirement already satisfied: certifi>=2020.11.8 in /opt/conda/lib/python3.11/site-packages (from tapipy<2.0.0,>=1.6.3->dapi==1.0.0) (2023.7.22)\n",
+      "Requirement already satisfied: cloudpickle>=1.6.0 in /opt/conda/lib/python3.11/site-packages (from tapipy<2.0.0,>=1.6.3->dapi==1.0.0) (3.1.0)\n",
+      "Requirement already satisfied: cryptography>=3.3.2 in /opt/conda/lib/python3.11/site-packages (from tapipy<2.0.0,>=1.6.3->dapi==1.0.0) (41.0.4)\n",
+      "Requirement already satisfied: openapi_core==0.16.0 in /opt/conda/lib/python3.11/site-packages (from tapipy<2.0.0,>=1.6.3->dapi==1.0.0) (0.16.0)\n",
+      "Requirement already satisfied: openapi_spec_validator<0.6.0,>=0.5.0 in /opt/conda/lib/python3.11/site-packages (from tapipy<2.0.0,>=1.6.3->dapi==1.0.0) (0.5.4)\n",
+      "Requirement already satisfied: pyyaml>=5.4 in /opt/conda/lib/python3.11/site-packages (from tapipy<2.0.0,>=1.6.3->dapi==1.0.0) (6.0.1)\n",
+      "Requirement already satisfied: requests<3.0.0,>=2.20.0 in /opt/conda/lib/python3.11/site-packages (from tapipy<2.0.0,>=1.6.3->dapi==1.0.0) (2.31.0)\n",
+      "Requirement already satisfied: setuptools>=21.0.0 in /opt/conda/lib/python3.11/site-packages (from tapipy<2.0.0,>=1.6.3->dapi==1.0.0) (68.2.2)\n",
+      "Requirement already satisfied: six<2.0,>=1.10 in /opt/conda/lib/python3.11/site-packages (from tapipy<2.0.0,>=1.6.3->dapi==1.0.0) (1.16.0)\n",
+      "Requirement already satisfied: urllib3<2.0.0,>=1.26.5 in /opt/conda/lib/python3.11/site-packages (from tapipy<2.0.0,>=1.6.3->dapi==1.0.0) (1.26.20)\n",
+      "Requirement already satisfied: isodate in /opt/conda/lib/python3.11/site-packages (from openapi_core==0.16.0->tapipy<2.0.0,>=1.6.3->dapi==1.0.0) (0.7.2)\n",
+      "Requirement already satisfied: jsonschema-spec<0.2.0,>=0.1.1 in /home/jupyter/.local/lib/python3.11/site-packages (from openapi_core==0.16.0->tapipy<2.0.0,>=1.6.3->dapi==1.0.0) (0.1.3)\n",
+      "Requirement already satisfied: more-itertools in /opt/conda/lib/python3.11/site-packages (from openapi_core==0.16.0->tapipy<2.0.0,>=1.6.3->dapi==1.0.0) (10.5.0)\n",
+      "Requirement already satisfied: openapi-schema-validator<0.4.0,>=0.3.0 in /opt/conda/lib/python3.11/site-packages (from openapi_core==0.16.0->tapipy<2.0.0,>=1.6.3->dapi==1.0.0) (0.3.4)\n",
+      "Requirement already satisfied: parse in /opt/conda/lib/python3.11/site-packages (from openapi_core==0.16.0->tapipy<2.0.0,>=1.6.3->dapi==1.0.0) (1.20.2)\n",
+      "Requirement already satisfied: pathable<0.5.0,>=0.4.0 in /opt/conda/lib/python3.11/site-packages (from openapi_core==0.16.0->tapipy<2.0.0,>=1.6.3->dapi==1.0.0) (0.4.3)\n",
+      "Requirement already satisfied: werkzeug in /opt/conda/lib/python3.11/site-packages (from openapi_core==0.16.0->tapipy<2.0.0,>=1.6.3->dapi==1.0.0) (3.1.2)\n",
+      "Requirement already satisfied: cffi>=1.12 in /opt/conda/lib/python3.11/site-packages (from cryptography>=3.3.2->tapipy<2.0.0,>=1.6.3->dapi==1.0.0) (1.16.0)\n",
+      "Requirement already satisfied: lazy-object-proxy<2.0.0,>=1.7.1 in /opt/conda/lib/python3.11/site-packages (from openapi_spec_validator<0.6.0,>=0.5.0->tapipy<2.0.0,>=1.6.3->dapi==1.0.0) (1.10.0)\n",
+      "Requirement already satisfied: charset-normalizer<4,>=2 in /opt/conda/lib/python3.11/site-packages (from requests<3.0.0,>=2.20.0->tapipy<2.0.0,>=1.6.3->dapi==1.0.0) (3.3.0)\n",
+      "Requirement already satisfied: idna<4,>=2.5 in /opt/conda/lib/python3.11/site-packages (from requests<3.0.0,>=2.20.0->tapipy<2.0.0,>=1.6.3->dapi==1.0.0) (3.4)\n",
+      "Requirement already satisfied: pycparser in /opt/conda/lib/python3.11/site-packages (from cffi>=1.12->cryptography>=3.3.2->tapipy<2.0.0,>=1.6.3->dapi==1.0.0) (2.21)\n",
+      "Requirement already satisfied: MarkupSafe>=2.1.1 in /opt/conda/lib/python3.11/site-packages (from werkzeug->openapi_core==0.16.0->tapipy<2.0.0,>=1.6.3->dapi==1.0.0) (2.1.3)\n",
+      "Building wheels for collected packages: dapi\n",
+      "  Building wheel for dapi (pyproject.toml) ... \u001b[?25ldone\n",
+      "\u001b[?25h  Created wheel for dapi: filename=dapi-1.0.0-py3-none-any.whl size=24062 sha256=cf0ff0df24ae1cb99cf56a627d1fdcd6d5d91e53a3c9eae6e99b8f3ab519713a\n",
+      "  Stored in directory: /tmp/pip-ephem-wheel-cache-58or_9hm/wheels/e1/79/c6/a9ec0b77e5349b798d57dca8ea213ee48626dea9e159e67fdc\n",
+      "Successfully built dapi\n",
+      "Installing collected packages: dapi\n",
+      "Successfully installed dapi-1.0.0\n"
+     ]
+    }
+   ],
+   "source": [
+    "!pip uninstall dapi --yes\n",
+    "!pip install git+https://github.com/DesignSafe-CI/dapi.git@t3 --user"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
    "id": "06f33aaa",
    "metadata": {},
    "outputs": [],
@@ -29,7 +110,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 3,
    "id": "abc973d4",
    "metadata": {},
    "outputs": [
@@ -57,7 +138,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "id": "3c1d34e8",
    "metadata": {},
    "outputs": [
@@ -100,10 +181,41 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
    "id": "80a7fa20",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "Querying NGL Database using 'ngl' variable...\n",
+      "Executing query on 'ngl'...\n",
+      "--- NGL Data (DataFrame) ---\n",
+      "   SITE_ID            SITE_NAME   SITE_LAT    SITE_LON  \\\n",
+      "0      147            Amagasaki  34.715560  135.400750   \n",
+      "1      148         Bonds Corner  32.693100 -115.338200   \n",
+      "2      149          Hachirogata  39.850000  140.017000   \n",
+      "3      150  Higashi-Kobe Bridge  34.710214  135.293345   \n",
+      "4      151   Hanshin Expressway  34.724834  135.301489   \n",
+      "\n",
+      "                    SITE_GEOL  \\\n",
+      "0                         Qal   \n",
+      "1  Qal, deep, Imperial Valley   \n",
+      "2                   Af (Fill)   \n",
+      "3                   Af (Fill)   \n",
+      "4                               \n",
+      "\n",
+      "                                            SITE_REM  SITE_STAT  SITE_REVW  \n",
+      "0  Industrial site near Yomoga River.  Coordinate...          1          2  \n",
+      "1                                                             1          2  \n",
+      "2  Gingery indicates the geology near the strong ...          1          2  \n",
+      "3  A geologic map of the area (Geological Survey ...          1          2  \n",
+      "4         Hanshin Expressway (Mylonakis et al. 2006)          1          2  \n"
+     ]
+    }
+   ],
    "source": [
     "## Database Example Usage (Using convenience variables)\n",
     "if ngl:  # Check if ngl variable was successfully created\n",
@@ -123,7 +235,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "dapi-ptztLUqK-py3.13",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -137,7 +249,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.13.3"
+   "version": "3.11.6"
   }
  },
  "nbformat": 4,