tutorials/create_catalog_cesm.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "68b6b854",
   "metadata": {},
   "source": [
    "# Create Catalog for CESM output"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "519c212b",
   "metadata": {},
   "outputs": [],
   "source": [
    "import pathlib\n",
    "import os\n",
    "from os import listdir\n",
    "from os.path import isfile, join\n",
    "import shutil\n",
    "\n",
    "import intake\n",
    "from ecgtools import Builder\n",
    "from ecgtools.parsers.cesm import parse_cesm_timeseries\n",
    "\n",
    "import pandas as pd \n",
    "import xarray as xr\n",
    "import numpy as np\n",
    "import itertools"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "fae5eb96",
   "metadata": {},
   "source": [
    "## Step 0: Move Files from `data_tmp` to `data` and Create New Folders if needed"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "83f8042e",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Path of new downloaded CESM data \n",
    "path='/data/keeling/a/cristi/a/data_tmp/'\n",
    "# rootpath of target directory.\n",
    "rootpath='/data/keeling/a/cristi/a/esm_data/cesm/CESM_LME'\n",
    "\n",
    "def target_location_cmip(fname,rootpath): #generates target location \n",
    "    if rootpath[-1]!='/':\n",
    "        rootpath=rootpath+'/'\n",
    "    fname_set=fname.split('_')     \n",
    "    location=rootpath+fname_set[2]+'/'+fname_set[3]+'/'+fname_set[4]+'/'# index need change based on CESM files are named\n",
    "    return location\n",
    "\n",
    "# move files from current folder to target folders\n",
    "k_moved=0\n",
    "for j in listdir(path): #read all downlaoded files in data_tmp\n",
    "    current_dir=os.path.join(path, j) \n",
    "    target_dir= target_location_cmip(j,rootpath)\n",
    "    if target_dir!=current_dir:\n",
    "        if os.path.exists(target_dir)==False:\n",
    "            os.makedirs(target_dir) #make directories \n",
    "        shutil.move(current_dir,target_dir) #move files \n",
    "        k_moved+=1\n",
    "        \n",
    "print('moved '+str(k_moved)+' files')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "831a9e33",
   "metadata": {},
   "source": [
    "## Step 1: Get updated list of Subdirectories"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "d0187444",
   "metadata": {},
   "source": [
    "1. Log onto Keeling and go to `/data/keeling/a/cristi/a/data/cesm`\n",
    "\n",
    "2. Run the following line of code to the get the most updated list of all subdirectories\n",
    "\n",
    "`readlink -f $(find . -type d -path '*/*' -prune) > subdir_list.csv`"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f87ba44e",
   "metadata": {},
   "source": [
    "## Get list of all subdirectories in `/data/keeling/a/cristi/a/data/cesm2`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "271a5d3e",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['/data/cristi/a/cristi/esm_data/cesm/CESM_LME']"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "filepathlist = pd.read_csv('/data/keeling/a/cristi/a/esm_data/cesm/subdir_list.csv',header=None,names=['dirpaths']).values.tolist()\n",
    "\n",
    "# Transform list of lists to list of strings\n",
    "filepath=list(itertools.chain.from_iterable(filepathlist))\n",
    "filepath"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "6d98772e",
   "metadata": {
    "slideshow": {
     "slide_type": "subslide"
    }
   },
   "source": [
    "## Create Catalog Builder and Build the Catalog"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "9ff083dd",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/data/keeling/a/rytam2/miniconda3/lib/python3.9/site-packages/ecgtools/parsers/cesm.py:240: UserWarning: Using the default frequency definitions\n",
      "  warnings.warn('Using the default frequency definitions')\n",
      "/data/keeling/a/rytam2/miniconda3/lib/python3.9/site-packages/ecgtools/builder.py:202: UserWarning: Unable to parse 1 assets. A list of these assets can be found in `.invalid_assets` attribute.\n",
      "  self.get_assets().parse(\n"
     ]
    }
   ],
   "source": [
    "# Create the Builder\n",
    "cat_builder = Builder(\n",
    "    # Directory of Organized CMIP6 files \n",
    "    paths=filepath)\n",
    "\n",
    "# Build the Catalog\n",
    "catalog = cat_builder.build(parsing_func=parse_cesm_timeseries)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2ee8421e",
   "metadata": {},
   "source": [
    "# Check and Save the Catalog"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "cfba4a05",
   "metadata": {},
   "outputs": [
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       "      <td>Salinity</td>\n",
       "      <td>gram/kilogram</td>\n",
       "      <td>1.0</td>\n",
       "      <td>month_1</td>\n",
       "      <td>/data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>ocn</td>\n",
       "      <td>pop.h</td>\n",
       "      <td>b.ie12.B1850C5CN.f19_g16.LME.002</td>\n",
       "      <td>002</td>\n",
       "      <td>SALT</td>\n",
       "      <td>1500-01</td>\n",
       "      <td>1599-12</td>\n",
       "      <td>150001-159912</td>\n",
       "      <td>Salinity</td>\n",
       "      <td>gram/kilogram</td>\n",
       "      <td>1.0</td>\n",
       "      <td>month_1</td>\n",
       "      <td>/data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>ocn</td>\n",
       "      <td>pop.h</td>\n",
       "      <td>b.ie12.B1850C5CN.f19_g16.LME.002</td>\n",
       "      <td>002</td>\n",
       "      <td>SALT</td>\n",
       "      <td>1600-01</td>\n",
       "      <td>1699-12</td>\n",
       "      <td>160001-169912</td>\n",
       "      <td>Salinity</td>\n",
       "      <td>gram/kilogram</td>\n",
       "      <td>1.0</td>\n",
       "      <td>month_1</td>\n",
       "      <td>/data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>23</th>\n",
       "      <td>ocn</td>\n",
       "      <td>pop.h</td>\n",
       "      <td>b.ie12.B1850C5CN.f19_g16.LME.002</td>\n",
       "      <td>002</td>\n",
       "      <td>SALT</td>\n",
       "      <td>1700-01</td>\n",
       "      <td>1799-12</td>\n",
       "      <td>170001-179912</td>\n",
       "      <td>Salinity</td>\n",
       "      <td>gram/kilogram</td>\n",
       "      <td>1.0</td>\n",
       "      <td>month_1</td>\n",
       "      <td>/data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>ocn</td>\n",
       "      <td>pop.h</td>\n",
       "      <td>b.ie12.B1850C5CN.f19_g16.LME.002</td>\n",
       "      <td>002</td>\n",
       "      <td>SALT</td>\n",
       "      <td>1800-01</td>\n",
       "      <td>1849-12</td>\n",
       "      <td>180001-184912</td>\n",
       "      <td>Salinity</td>\n",
       "      <td>gram/kilogram</td>\n",
       "      <td>1.0</td>\n",
       "      <td>month_1</td>\n",
       "      <td>/data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>ocn</td>\n",
       "      <td>pop.h</td>\n",
       "      <td>b.ie12.B1850C5CN.f19_g16.LME.002</td>\n",
       "      <td>002</td>\n",
       "      <td>SALT</td>\n",
       "      <td>1800-01</td>\n",
       "      <td>1899-12</td>\n",
       "      <td>180001-189912</td>\n",
       "      <td>Salinity</td>\n",
       "      <td>gram/kilogram</td>\n",
       "      <td>1.0</td>\n",
       "      <td>month_1</td>\n",
       "      <td>/data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>26</th>\n",
       "      <td>ocn</td>\n",
       "      <td>pop.h</td>\n",
       "      <td>b.ie12.B1850C5CN.f19_g16.LME.002</td>\n",
       "      <td>002</td>\n",
       "      <td>SALT</td>\n",
       "      <td>1850-01</td>\n",
       "      <td>2005-12</td>\n",
       "      <td>185001-200512</td>\n",
       "      <td>Salinity</td>\n",
       "      <td>gram/kilogram</td>\n",
       "      <td>1.0</td>\n",
       "      <td>month_1</td>\n",
       "      <td>/data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   component stream                              case member_id variable  \\\n",
       "1        ocn  pop.h  b.ie12.B1850C5CN.f19_g16.LME.002       002     R18O   \n",
       "2        ocn  pop.h  b.ie12.B1850C5CN.f19_g16.LME.002       002     R18O   \n",
       "3        ocn  pop.h  b.ie12.B1850C5CN.f19_g16.LME.002       002     R18O   \n",
       "4        ocn  pop.h  b.ie12.B1850C5CN.f19_g16.LME.002       002     R18O   \n",
       "5        ocn  pop.h  b.ie12.B1850C5CN.f19_g16.LME.002       002     R18O   \n",
       "6        ocn  pop.h  b.ie12.B1850C5CN.f19_g16.LME.002       002     R18O   \n",
       "7        ocn  pop.h  b.ie12.B1850C5CN.f19_g16.LME.002       002     R18O   \n",
       "8        ocn  pop.h  b.ie12.B1850C5CN.f19_g16.LME.002       002     R18O   \n",
       "9        ocn  pop.h  b.ie12.B1850C5CN.f19_g16.LME.002       002     R18O   \n",
       "10       ocn  pop.h  b.ie12.B1850C5CN.f19_g16.LME.002       002     R18O   \n",
       "11       ocn  pop.h  b.ie12.B1850C5CN.f19_g16.LME.002       002     R18O   \n",
       "12       ocn  pop.h  b.ie12.B1850C5CN.f19_g16.LME.002       002     R18O   \n",
       "13       ocn  pop.h  b.ie12.B1850C5CN.f19_g16.LME.002       002     R18O   \n",
       "14       ocn  pop.h  b.ie12.B1850C5CN.f19_g16.LME.002       002     SALT   \n",
       "15       ocn  pop.h  b.ie12.B1850C5CN.f19_g16.LME.002       002     SALT   \n",
       "16       ocn  pop.h  b.ie12.B1850C5CN.f19_g16.LME.002       002     SALT   \n",
       "17       ocn  pop.h  b.ie12.B1850C5CN.f19_g16.LME.002       002     SALT   \n",
       "18       ocn  pop.h  b.ie12.B1850C5CN.f19_g16.LME.002       002     SALT   \n",
       "19       ocn  pop.h  b.ie12.B1850C5CN.f19_g16.LME.002       002     SALT   \n",
       "20       ocn  pop.h  b.ie12.B1850C5CN.f19_g16.LME.002       002     SALT   \n",
       "21       ocn  pop.h  b.ie12.B1850C5CN.f19_g16.LME.002       002     SALT   \n",
       "22       ocn  pop.h  b.ie12.B1850C5CN.f19_g16.LME.002       002     SALT   \n",
       "23       ocn  pop.h  b.ie12.B1850C5CN.f19_g16.LME.002       002     SALT   \n",
       "24       ocn  pop.h  b.ie12.B1850C5CN.f19_g16.LME.002       002     SALT   \n",
       "25       ocn  pop.h  b.ie12.B1850C5CN.f19_g16.LME.002       002     SALT   \n",
       "26       ocn  pop.h  b.ie12.B1850C5CN.f19_g16.LME.002       002     SALT   \n",
       "\n",
       "   start_time end_time     time_range long_name          units  \\\n",
       "1     0850-01  0899-12  085001-089912      R18O       unitless   \n",
       "2     0900-01  0999-12  090001-099912      R18O       unitless   \n",
       "3     1000-01  1099-12  100001-109912      R18O       unitless   \n",
       "4     1100-01  1199-12  110001-119912      R18O       unitless   \n",
       "5     1200-01  1299-12  120001-129912      R18O       unitless   \n",
       "6     1300-01  1399-12  130001-139912      R18O       unitless   \n",
       "7     1400-01  1499-12  140001-149912      R18O       unitless   \n",
       "8     1500-01  1599-12  150001-159912      R18O       unitless   \n",
       "9     1600-01  1699-12  160001-169912      R18O       unitless   \n",
       "10    1700-01  1799-12  170001-179912      R18O       unitless   \n",
       "11    1800-01  1849-12  180001-184912      R18O       unitless   \n",
       "12    1800-01  1899-12  180001-189912      R18O       unitless   \n",
       "13    1850-01  2005-12  185001-200512      R18O       unitless   \n",
       "14    0850-01  0899-12  085001-089912  Salinity  gram/kilogram   \n",
       "15    0900-01  0999-12  090001-099912  Salinity  gram/kilogram   \n",
       "16    1000-01  1099-12  100001-109912  Salinity  gram/kilogram   \n",
       "17    1100-01  1199-12  110001-119912  Salinity  gram/kilogram   \n",
       "18    1200-01  1299-12  120001-129912  Salinity  gram/kilogram   \n",
       "19    1300-01  1399-12  130001-139912  Salinity  gram/kilogram   \n",
       "20    1400-01  1499-12  140001-149912  Salinity  gram/kilogram   \n",
       "21    1500-01  1599-12  150001-159912  Salinity  gram/kilogram   \n",
       "22    1600-01  1699-12  160001-169912  Salinity  gram/kilogram   \n",
       "23    1700-01  1799-12  170001-179912  Salinity  gram/kilogram   \n",
       "24    1800-01  1849-12  180001-184912  Salinity  gram/kilogram   \n",
       "25    1800-01  1899-12  180001-189912  Salinity  gram/kilogram   \n",
       "26    1850-01  2005-12  185001-200512  Salinity  gram/kilogram   \n",
       "\n",
       "    vertical_levels frequency  \\\n",
       "1               1.0   month_1   \n",
       "2               1.0   month_1   \n",
       "3               1.0   month_1   \n",
       "4               1.0   month_1   \n",
       "5               1.0   month_1   \n",
       "6               1.0   month_1   \n",
       "7               1.0   month_1   \n",
       "8               1.0   month_1   \n",
       "9               1.0   month_1   \n",
       "10              1.0   month_1   \n",
       "11              1.0   month_1   \n",
       "12              1.0   month_1   \n",
       "13              1.0   month_1   \n",
       "14              1.0   month_1   \n",
       "15              1.0   month_1   \n",
       "16              1.0   month_1   \n",
       "17              1.0   month_1   \n",
       "18              1.0   month_1   \n",
       "19              1.0   month_1   \n",
       "20              1.0   month_1   \n",
       "21              1.0   month_1   \n",
       "22              1.0   month_1   \n",
       "23              1.0   month_1   \n",
       "24              1.0   month_1   \n",
       "25              1.0   month_1   \n",
       "26              1.0   month_1   \n",
       "\n",
       "                                                 path  \n",
       "1   /data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...  \n",
       "2   /data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...  \n",
       "3   /data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...  \n",
       "4   /data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...  \n",
       "5   /data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...  \n",
       "6   /data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...  \n",
       "7   /data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...  \n",
       "8   /data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...  \n",
       "9   /data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...  \n",
       "10  /data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...  \n",
       "11  /data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...  \n",
       "12  /data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...  \n",
       "13  /data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...  \n",
       "14  /data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...  \n",
       "15  /data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...  \n",
       "16  /data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...  \n",
       "17  /data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...  \n",
       "18  /data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...  \n",
       "19  /data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...  \n",
       "20  /data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...  \n",
       "21  /data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...  \n",
       "22  /data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...  \n",
       "23  /data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...  \n",
       "24  /data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...  \n",
       "25  /data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...  \n",
       "26  /data/cristi/a/cristi/data/CESM_LME/b.ie12.B18...  "
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Browse the catalog\n",
    "catalog.df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "3c247776",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Save the catalog as .csv \n",
    "catalog.df.to_csv('/data/keeling/a/cristi/a/data/cesm_lme_catalog.csv', index=False)"
   ]
  }
 ],
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