glodap_to_geoparquet.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "9ea89116-4160-43b7-833f-91d10428c774",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Import pandas and geopandas\n",
    "import pandas as pd\n",
    "import geopandas as gpd\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "54edce5e-564d-43ae-89ad-e8706841f265",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "--2024-07-04 16:44:18--  https://glodap.info/glodap_files/v2.2023/GLODAPv2.2023_Merged_Master_File.csv.zip\n",
      "Resolving glodap.info (glodap.info)... 212.201.155.241\n",
      "Connecting to glodap.info (glodap.info)|212.201.155.241|:443... connected.\n",
      "HTTP request sent, awaiting response... 200 OK\n",
      "Length: 110353886 (105M) [application/zip]\n",
      "Saving to: ‘GLODAPv2.2023_Merged_Master_File.csv.zip’\n",
      "\n",
      "GLODAPv2.2023_Merge 100%[===================>] 105.24M  11.2MB/s    in 9.6s    \n",
      "\n",
      "2024-07-04 16:44:28 (10.9 MB/s) - ‘GLODAPv2.2023_Merged_Master_File.csv.zip’ saved [110353886/110353886]\n",
      "\n"
     ]
    }
   ],
   "source": [
    "# use wget to download the GLODAPv2.2023 master file zip archive \"GLODAPv2.2023_Merged_Master_File.csv.zip\"\n",
    "!wget https://glodap.info/glodap_files/v2.2023/GLODAPv2.2023_Merged_Master_File.csv.zip"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "9d2ba428-fa8a-44cb-9565-09c031bc2b90",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Load Glodap data into a pandas dataframe \n",
    "# hinting at datatypes in the glodap csv file fields\n",
    "\n",
    "df = pd.read_csv('GLODAPv2.2023_Merged_Master_File.csv.zip',dtype={'G2expocode' : str, 'G2Cruise' : int, 'G2region' :int , 'G2cast' :int ,'G2year': int,'G2month' : int,'G2day' : int,\t'G2hour': int, 'G2minute' : int, 'G2bottle' : int, 'G2doi' : str})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "f69438e7-f43f-4cea-936a-1011775f10f8",
   "metadata": {},
   "outputs": [
    {
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       "      <th></th>\n",
       "      <th>G2expocode</th>\n",
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       "      <th>G2station</th>\n",
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       "      <th>G2cast</th>\n",
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       "      <th>G2tdnf</th>\n",
       "      <th>G2chla</th>\n",
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       "      <td>9.0</td>\n",
       "      <td>-9999.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>-9999.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>-9999.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>https://doi.org/10.3334/cdiac/otg.carina_06aq1...</td>\n",
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       "    <tr>\n",
       "      <th>3</th>\n",
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       "      <td>9.0</td>\n",
       "      <td>-9999.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>https://doi.org/10.3334/cdiac/otg.carina_06aq1...</td>\n",
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       "      <th>4</th>\n",
       "      <td>06AQ19840719</td>\n",
       "      <td>1.0</td>\n",
       "      <td>319.0</td>\n",
       "      <td>4</td>\n",
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       "      <td>1984</td>\n",
       "      <td>7</td>\n",
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       "      <td>-9999.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>-9999.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>https://doi.org/10.3334/cdiac/otg.carina_06aq1...</td>\n",
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       "      <td>9.0</td>\n",
       "      <td>-9999.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>https://doi.org/10.3334/cdiac/otg.carina_06aq1...</td>\n",
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       "      <td>9.0</td>\n",
       "      <td>-9999.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>-9999.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>-9999.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>https://doi.org/10.3334/cdiac/otg.carina_06aq1...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>06AQ19840719</td>\n",
       "      <td>1.0</td>\n",
       "      <td>319.0</td>\n",
       "      <td>4</td>\n",
       "      <td>1</td>\n",
       "      <td>1984</td>\n",
       "      <td>7</td>\n",
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       "      <td>https://doi.org/10.3334/cdiac/otg.carina_06aq1...</td>\n",
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       "      <td>9.0</td>\n",
       "      <td>-9999.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>-9999.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>-9999.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>https://doi.org/10.3334/cdiac/otg.carina_06aq1...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>06AQ19840719</td>\n",
       "      <td>1.0</td>\n",
       "      <td>319.0</td>\n",
       "      <td>4</td>\n",
       "      <td>1</td>\n",
       "      <td>1984</td>\n",
       "      <td>7</td>\n",
       "      <td>20</td>\n",
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       "      <td>9.0</td>\n",
       "      <td>-9999.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>-9999.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>-9999.0</td>\n",
       "      <td>9.0</td>\n",
       "      <td>https://doi.org/10.3334/cdiac/otg.carina_06aq1...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>10 rows × 109 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     G2expocode  G2cruise  G2station  G2region  G2cast  G2year  G2month  \\\n",
       "0  06AQ19840719       1.0      319.0         4       1    1984        7   \n",
       "1  06AQ19840719       1.0      319.0         4       1    1984        7   \n",
       "2  06AQ19840719       1.0      319.0         4       1    1984        7   \n",
       "3  06AQ19840719       1.0      319.0         4       1    1984        7   \n",
       "4  06AQ19840719       1.0      319.0         4       1    1984        7   \n",
       "5  06AQ19840719       1.0      319.0         4       1    1984        7   \n",
       "6  06AQ19840719       1.0      319.0         4       1    1984        7   \n",
       "7  06AQ19840719       1.0      319.0         4       1    1984        7   \n",
       "8  06AQ19840719       1.0      319.0         4       1    1984        7   \n",
       "9  06AQ19840719       1.0      319.0         4       1    1984        7   \n",
       "\n",
       "   G2day  G2hour  G2minute  ...  G2tocf   G2doc  G2docf   G2don  G2donf  \\\n",
       "0     20      14        46  ...     9.0 -9999.0     9.0 -9999.0     9.0   \n",
       "1     20      14        46  ...     9.0 -9999.0     9.0 -9999.0     9.0   \n",
       "2     20      14        46  ...     9.0 -9999.0     9.0 -9999.0     9.0   \n",
       "3     20      14        46  ...     9.0 -9999.0     9.0 -9999.0     9.0   \n",
       "4     20      14        46  ...     9.0 -9999.0     9.0 -9999.0     9.0   \n",
       "5     20      14        46  ...     9.0 -9999.0     9.0 -9999.0     9.0   \n",
       "6     20      14        46  ...     9.0 -9999.0     9.0 -9999.0     9.0   \n",
       "7     20      14        46  ...     9.0 -9999.0     9.0 -9999.0     9.0   \n",
       "8     20      14        46  ...     9.0 -9999.0     9.0 -9999.0     9.0   \n",
       "9     20      14        46  ...     9.0 -9999.0     9.0 -9999.0     9.0   \n",
       "\n",
       "    G2tdn  G2tdnf  G2chla  G2chlaf  \\\n",
       "0 -9999.0     9.0 -9999.0      9.0   \n",
       "1 -9999.0     9.0 -9999.0      9.0   \n",
       "2 -9999.0     9.0 -9999.0      9.0   \n",
       "3 -9999.0     9.0 -9999.0      9.0   \n",
       "4 -9999.0     9.0 -9999.0      9.0   \n",
       "5 -9999.0     9.0 -9999.0      9.0   \n",
       "6 -9999.0     9.0 -9999.0      9.0   \n",
       "7 -9999.0     9.0 -9999.0      9.0   \n",
       "8 -9999.0     9.0 -9999.0      9.0   \n",
       "9 -9999.0     9.0 -9999.0      9.0   \n",
       "\n",
       "                                               G2doi  \n",
       "0  https://doi.org/10.3334/cdiac/otg.carina_06aq1...  \n",
       "1  https://doi.org/10.3334/cdiac/otg.carina_06aq1...  \n",
       "2  https://doi.org/10.3334/cdiac/otg.carina_06aq1...  \n",
       "3  https://doi.org/10.3334/cdiac/otg.carina_06aq1...  \n",
       "4  https://doi.org/10.3334/cdiac/otg.carina_06aq1...  \n",
       "5  https://doi.org/10.3334/cdiac/otg.carina_06aq1...  \n",
       "6  https://doi.org/10.3334/cdiac/otg.carina_06aq1...  \n",
       "7  https://doi.org/10.3334/cdiac/otg.carina_06aq1...  \n",
       "8  https://doi.org/10.3334/cdiac/otg.carina_06aq1...  \n",
       "9  https://doi.org/10.3334/cdiac/otg.carina_06aq1...  \n",
       "\n",
       "[10 rows x 109 columns]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# examine the data frame\n",
    "df.head(10)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "0c696051-7df3-4b5c-9240-d916a244dc2a",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<class 'pandas.core.frame.DataFrame'>\n",
      "RangeIndex: 1402829 entries, 0 to 1402828\n",
      "Columns: 109 entries, G2expocode to G2doi\n",
      "dtypes: float64(99), int64(8), object(2)\n",
      "memory usage: 1.1+ GB\n"
     ]
    }
   ],
   "source": [
    "df.info()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "ec60dfc7-3ef3-4382-94ea-ff5747f72120",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "       expocode  cruise  station  region  cast  year  month  day  hour  \\\n",
      "0  06AQ19840719     1.0    319.0       4     1  1984      7   20    14   \n",
      "1  06AQ19840719     1.0    319.0       4     1  1984      7   20    14   \n",
      "2  06AQ19840719     1.0    319.0       4     1  1984      7   20    14   \n",
      "3  06AQ19840719     1.0    319.0       4     1  1984      7   20    14   \n",
      "4  06AQ19840719     1.0    319.0       4     1  1984      7   20    14   \n",
      "\n",
      "   minute  ...  tocf     doc  docf     don  donf     tdn  tdnf    chla  chlaf  \\\n",
      "0      46  ...   9.0 -9999.0   9.0 -9999.0   9.0 -9999.0   9.0 -9999.0    9.0   \n",
      "1      46  ...   9.0 -9999.0   9.0 -9999.0   9.0 -9999.0   9.0 -9999.0    9.0   \n",
      "2      46  ...   9.0 -9999.0   9.0 -9999.0   9.0 -9999.0   9.0 -9999.0    9.0   \n",
      "3      46  ...   9.0 -9999.0   9.0 -9999.0   9.0 -9999.0   9.0 -9999.0    9.0   \n",
      "4      46  ...   9.0 -9999.0   9.0 -9999.0   9.0 -9999.0   9.0 -9999.0    9.0   \n",
      "\n",
      "                                                 doi  \n",
      "0  https://doi.org/10.3334/cdiac/otg.carina_06aq1...  \n",
      "1  https://doi.org/10.3334/cdiac/otg.carina_06aq1...  \n",
      "2  https://doi.org/10.3334/cdiac/otg.carina_06aq1...  \n",
      "3  https://doi.org/10.3334/cdiac/otg.carina_06aq1...  \n",
      "4  https://doi.org/10.3334/cdiac/otg.carina_06aq1...  \n",
      "\n",
      "[5 rows x 109 columns]\n"
     ]
    }
   ],
   "source": [
    "# Remove the first 2 \"G2\" characters from column names\n",
    "df.columns = df.columns.str[2:]\n",
    "# examine the fields and sample data\n",
    "print(df.head())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "3705ef05-f60d-4396-932b-6da5fc5ba7c0",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Combine year, month, day, hour, and minute columns into a new datetime column\n",
    "df['recordedtime'] = pd.to_datetime(df[['year', 'month', 'day', 'hour', 'minute']])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "7de158c9-46b1-4e74-8746-0bfe7aa9407c",
   "metadata": {},
   "outputs": [],
   "source": [
    "from shapely.geometry import Point\n",
    "\n",
    "# Create a GeoPandas GeoDataFrame with Point geometries\n",
    "gdf = gpd.GeoDataFrame(df, \n",
    "                        geometry=gpd.points_from_xy(df['longitude'], df['latitude']),\n",
    "                        crs='EPSG:4326')  # Set the coordinate reference system (CRS)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "3080525c-bd39-462e-abbb-d83b0d74a812",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Collecting pyarrow\n",
      "  Downloading pyarrow-16.1.0-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (3.0 kB)\n",
      "Requirement already satisfied: numpy>=1.16.6 in /opt/conda/lib/python3.11/site-packages (from pyarrow) (1.26.4)\n",
      "Downloading pyarrow-16.1.0-cp311-cp311-manylinux_2_28_x86_64.whl (40.8 MB)\n",
      "\u001b[2K   \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m40.8/40.8 MB\u001b[0m \u001b[31m9.6 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m:00:01\u001b[0m00:01\u001b[0m\n",
      "\u001b[?25hInstalling collected packages: pyarrow\n",
      "Successfully installed pyarrow-16.1.0\n",
      "Note: you may need to restart the kernel to use updated packages.\n"
     ]
    }
   ],
   "source": [
    "# Install the pyarrow library dependency for geoparquet export from geopandas\n",
    "%pip install pyarrow"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "c95e2b29-f7b0-45dc-8bd4-ec878aee63bc",
   "metadata": {},
   "outputs": [],
   "source": [
    "# export the geopandas dataframe as geoparquet\n",
    "gdf.to_parquet('glodap_v2_2023_merged_master.parquet')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "14f50710-aaab-42dd-929d-989c9cbcc517",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "GLODAPv2.2023_Merged_Master_File.csv.zip  glodap_v2_2023_merged_master.parquet\n",
      "glodap_to_geoparquet.ipynb                \u001b[0m\u001b[01;34mwork\u001b[0m/\n"
     ]
    }
   ],
   "source": [
    "# show the local directory workspace contents to see the new geoparquet file\n",
    "%ls"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "82c3dac6-4973-4147-ae98-f64af815af49",
   "metadata": {},
   "outputs": [],
   "source": [
    "#GLODAPv2.2023\n",
    "\n",
    "#Olsen, A., R. M. Key, S. van Heuven, S. K. Lauvset, A. Velo, X. Lin, C. Schirnick, A. Kozyr, T. Tanhua, M. Hoppema, S. Jutterström, R. Steinfeldt,\n",
    "#E. Jeansson, M. Ishii, F. F. Pérez and T. Suzuki. The Global Ocean Data Analysis Project version 2 (GLODAPv2) – an internally consistent data\n",
    "#product for the world ocean, Earth Syst. Sci. Data, 8, 297–323, 2016, doi:10.5194/essd-8-297-2016\n",
    "\n",
    "#Lauvset, S. K, R. M. Key, A. Olsen, S. van Heuven, A. Velo, X. Lin, C. Schirnick, A. Kozyr, T. Tanhua, M. Hoppema, S. Jutterström, R. Steinfeldt, E.\n",
    "#Jeansson, M. Ishii, F. F. Pérez, T. Suzuki and S. Watelet. A new global interior ocean mapped climatology: the 1°x1° GLODAP version 2, Earth Syst.\n",
    "#Sci. Data, 8, 325–340, 2016, doi:10.5194/essd-8-325-2016\n",
    "\n",
    "#Key, R.M., A. Olsen, S. van Heuven, S. K. Lauvset, A. Velo, X. Lin, C. Schirnick, A. Kozyr, T. Tanhua, M. Hoppema, S. Jutterström, R. Steinfeldt, E.\n",
    "#Jeansson, M. Ishii, F. F. Perez, and T. Suzuki. 2015. Global Ocean Data Analysis Project, Version 2 (GLODAPv2), ORNL/CDIAC-162, NDP-093. Carbon\n",
    "#Dioxide Information Analysis Center, Oak Ridge National Laboratory, US Department of Energy, Oak Ridge, Tennessee. doi:10.3334/CDIAC/OTG.\n",
    "#NDP093_GLODAPv2"
   ]
  }
 ],
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