{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "RS_FILEPATH = \"../../rare_species/data/\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Read in Links CSV file\n",
    "\n",
    "Full cargo archive has some more content than the [original `links_manifest_cargo_on_md5.csv`](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/fa08e0f6692a013e4e4f5ca30dd0e8883c0021d8/eol_realign/data/links_manifest_cargo_on_md5.csv)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "links_manifest_cargo = pd.read_csv(\"../data/eol-cargo-archive_combined-manifest-checksums_links.csv\", low_memory=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<class 'pandas.core.frame.DataFrame'>\n",
      "RangeIndex: 7514001 entries, 0 to 7514000\n",
      "Data columns (total 17 columns):\n",
      " #   Column                           Non-Null Count    Dtype \n",
      "---  ------                           --------------    ----- \n",
      " 0   filename_archive                 7514001 non-null  object\n",
      " 1   md5_archive                      7514001 non-null  object\n",
      " 2   combined_id_archive              7514001 non-null  object\n",
      " 3   filename_manifest                7514001 non-null  object\n",
      " 4   md5_combined_manifest            7514001 non-null  object\n",
      " 5   combined_id_manifest_redownload  7514001 non-null  object\n",
      " 6   eol_content_id                   7514001 non-null  int64 \n",
      " 7   eol_page_id                      7514001 non-null  int64 \n",
      " 8   medium_source_url                7514001 non-null  object\n",
      " 9   eol_full_size_copy_url           7514001 non-null  object\n",
      " 10  license_name                     7514001 non-null  object\n",
      " 11  copyright_owner                  6860825 non-null  object\n",
      " 12  expected_image_filename          7514001 non-null  object\n",
      " 13  source_0706                      7514001 non-null  bool  \n",
      " 14  source_0726                      7514001 non-null  bool  \n",
      " 15  source_1206                      7514001 non-null  bool  \n",
      " 16  combined_id_full_manifest        7514001 non-null  object\n",
      "dtypes: bool(3), int64(2), object(12)\n",
      "memory usage: 824.1+ MB\n"
     ]
    }
   ],
   "source": [
    "links_manifest_cargo.info(show_counts=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Check on Rare Species Catalog"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<class 'pandas.core.frame.DataFrame'>\n",
      "RangeIndex: 12000 entries, 0 to 11999\n",
      "Data columns (total 11 columns):\n",
      " #   Column          Non-Null Count  Dtype \n",
      "---  ------          --------------  ----- \n",
      " 0   rarespecies_id  12000 non-null  object\n",
      " 1   eol_content_id  12000 non-null  int64 \n",
      " 2   eol_page_id     12000 non-null  int64 \n",
      " 3   kingdom         12000 non-null  object\n",
      " 4   phylum          12000 non-null  object\n",
      " 5   class           12000 non-null  object\n",
      " 6   order           12000 non-null  object\n",
      " 7   family          12000 non-null  object\n",
      " 8   genus           12000 non-null  object\n",
      " 9   species         12000 non-null  object\n",
      " 10  sciName         12000 non-null  object\n",
      "dtypes: int64(2), object(9)\n",
      "memory usage: 1.0+ MB\n"
     ]
    }
   ],
   "source": [
    "rs_catalog = pd.read_csv(RS_FILEPATH + \"rarespecies-catalog.csv\",\n",
    "                         low_memory=False,\n",
    "                         dtype = {\"eol_content_id\": \"int64\", \"eol_page_id\": \"int64\"})\n",
    "rs_catalog.info(show_counts = True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "rs_catalog[\"combined_id_rs\"] = rs_catalog[\"eol_content_id\"].astype(str) + \"_\" + rs_catalog[\"eol_page_id\"].astype(str)\n",
    "rs_catalog.rename(columns={'eol_content_id': 'eol_content_id_rs', 'eol_page_id': 'eol_page_id_rs'}, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<class 'pandas.core.frame.DataFrame'>\n",
      "RangeIndex: 12552 entries, 0 to 12551\n",
      "Data columns (total 29 columns):\n",
      " #   Column                           Non-Null Count  Dtype \n",
      "---  ------                           --------------  ----- \n",
      " 0   rarespecies_id                   12552 non-null  object\n",
      " 1   eol_content_id_rs                12552 non-null  int64 \n",
      " 2   eol_page_id_rs                   12552 non-null  int64 \n",
      " 3   kingdom                          12552 non-null  object\n",
      " 4   phylum                           12552 non-null  object\n",
      " 5   class                            12552 non-null  object\n",
      " 6   order                            12552 non-null  object\n",
      " 7   family                           12552 non-null  object\n",
      " 8   genus                            12552 non-null  object\n",
      " 9   species                          12552 non-null  object\n",
      " 10  sciName                          12552 non-null  object\n",
      " 11  combined_id_rs                   12552 non-null  object\n",
      " 12  filename_archive                 12552 non-null  object\n",
      " 13  md5_archive                      12552 non-null  object\n",
      " 14  combined_id_archive              12552 non-null  object\n",
      " 15  filename_manifest                12552 non-null  object\n",
      " 16  md5_combined_manifest            12552 non-null  object\n",
      " 17  combined_id_manifest_redownload  12552 non-null  object\n",
      " 18  eol_content_id                   12552 non-null  int64 \n",
      " 19  eol_page_id                      12552 non-null  int64 \n",
      " 20  medium_source_url                12552 non-null  object\n",
      " 21  eol_full_size_copy_url           12552 non-null  object\n",
      " 22  license_name                     12552 non-null  object\n",
      " 23  copyright_owner                  11171 non-null  object\n",
      " 24  expected_image_filename          12552 non-null  object\n",
      " 25  source_0706                      12552 non-null  bool  \n",
      " 26  source_0726                      12552 non-null  bool  \n",
      " 27  source_1206                      12552 non-null  bool  \n",
      " 28  combined_id_full_manifest        12552 non-null  object\n",
      "dtypes: bool(3), int64(4), object(22)\n",
      "memory usage: 2.5+ MB\n"
     ]
    }
   ],
   "source": [
    "rs_links = pd.merge(rs_catalog,\n",
    "                    links_manifest_cargo,\n",
    "                    left_on = \"combined_id_rs\",\n",
    "                    right_on = \"combined_id_archive\", # merge on archive (replaced cargo)\n",
    "                    how = \"inner\")\n",
    "rs_links.info(show_counts = True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "rarespecies_id                     11826\n",
       "eol_content_id_rs                  11826\n",
       "eol_page_id_rs                       400\n",
       "kingdom                                1\n",
       "phylum                                 5\n",
       "class                                 15\n",
       "order                                 85\n",
       "family                               202\n",
       "genus                                316\n",
       "species                              385\n",
       "sciName                              400\n",
       "combined_id_rs                     11826\n",
       "filename_archive                   11826\n",
       "md5_archive                        11663\n",
       "combined_id_archive                11826\n",
       "filename_manifest                  12221\n",
       "md5_combined_manifest              11663\n",
       "combined_id_manifest_redownload    12221\n",
       "eol_content_id                     12221\n",
       "eol_page_id                          447\n",
       "medium_source_url                  12056\n",
       "eol_full_size_copy_url             12119\n",
       "license_name                          15\n",
       "copyright_owner                     3724\n",
       "expected_image_filename            12221\n",
       "source_0706                            2\n",
       "source_0726                            2\n",
       "source_1206                            2\n",
       "combined_id_full_manifest          12221\n",
       "dtype: int64"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rs_links.nunique()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "All these numbers match our check with the cargo file."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Let's check the mismatched cargo/manifest entries for those last 174..."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "matched_rs_ids = list(rs_links.combined_id_rs.unique())\n",
    "len(matched_rs_ids)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['22519448_914532',\n",
       " '28677580_1057176',\n",
       " '20714475_47047909',\n",
       " '29975068_45509269']"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "matched_rs_ids[:4]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "5890       20469929_326451\n",
       "11023    28478387_46559744\n",
       "409      22582812_51263523\n",
       "5166      22180215_2984557\n",
       "Name: combined_id_rs, dtype: object"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rs_catalog[\"combined_id_rs\"].sample(4)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<class 'pandas.core.frame.DataFrame'>\n",
      "Index: 174 entries, 163 to 11990\n",
      "Data columns (total 12 columns):\n",
      " #   Column             Non-Null Count  Dtype \n",
      "---  ------             --------------  ----- \n",
      " 0   rarespecies_id     174 non-null    object\n",
      " 1   eol_content_id_rs  174 non-null    int64 \n",
      " 2   eol_page_id_rs     174 non-null    int64 \n",
      " 3   kingdom            174 non-null    object\n",
      " 4   phylum             174 non-null    object\n",
      " 5   class              174 non-null    object\n",
      " 6   order              174 non-null    object\n",
      " 7   family             174 non-null    object\n",
      " 8   genus              174 non-null    object\n",
      " 9   species            174 non-null    object\n",
      " 10  sciName            174 non-null    object\n",
      " 11  combined_id_rs     174 non-null    object\n",
      "dtypes: int64(2), object(10)\n",
      "memory usage: 17.7+ KB\n"
     ]
    }
   ],
   "source": [
    "mismatched_rs = rs_catalog.loc[~rs_catalog[\"combined_id_rs\"].isin(matched_rs_ids)]\n",
    "mismatched_rs.info(show_counts = True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "rarespecies_id       174\n",
       "eol_content_id_rs    174\n",
       "eol_page_id_rs        34\n",
       "kingdom                1\n",
       "phylum                 2\n",
       "class                  7\n",
       "order                 22\n",
       "family                28\n",
       "genus                 31\n",
       "species               33\n",
       "sciName               34\n",
       "combined_id_rs       174\n",
       "dtype: int64"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mismatched_rs.nunique()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "sciName\n",
       "Aonyx capensis                27\n",
       "Zoogoneticus tequila          27\n",
       "Sousa plumbea                 17\n",
       "Sylvilagus transitionalis     16\n",
       "Scaphirhynchus albus          16\n",
       "Raja asterias                  9\n",
       "Tursiops aduncus               6\n",
       "Dalatias licha                 6\n",
       "Alopias vulpinus               5\n",
       "Hexanchus griseus              5\n",
       "Myliobatis aquila              5\n",
       "Bathytoshia centroura          4\n",
       "Rostroraja alba                3\n",
       "Sylvilagus brasiliensis        3\n",
       "Microcebus rufus               2\n",
       "Glyptemys muhlenbergii         2\n",
       "Crocodylus rhombifer           2\n",
       "Cercopithecus mona             2\n",
       "Harpia harpyja                 2\n",
       "Certhidea olivacea             1\n",
       "Lachnolaimus maximus           1\n",
       "Carcharhinus amblyrhynchos     1\n",
       "Mantella aurantiaca            1\n",
       "Piliocolobus tephrosceles      1\n",
       "Raja undulata                  1\n",
       "Luehdorfia japonica            1\n",
       "Trogon bairdii                 1\n",
       "Phoebastria albatrus           1\n",
       "Carcharhinus melanopterus      1\n",
       "Cetorhinus maximus             1\n",
       "Desmognathus imitator          1\n",
       "Phyllobates vittatus           1\n",
       "Centrochelys sulcata           1\n",
       "Eulemur fulvus                 1\n",
       "Name: count, dtype: int64"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mismatched_rs.sciName.value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "big_sciNames_missing = [\"Aonyx capensis\",\n",
    "                        \"Zoogoneticus tequila\",\n",
    "                        \"Sousa plumbea\",\n",
    "                        \"Sylvilagus transitionalis\",\n",
    "                        \"Scaphirhynchus albus\",\n",
    "                        \"Raja asterias\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[array([46559139]),\n",
       " array([208913]),\n",
       " array([46559307]),\n",
       " array([1011315]),\n",
       " array([205909]),\n",
       " array([46560546])]"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pg_ids = []\n",
    "for sciName in big_sciNames_missing:\n",
    "    pg_ids.append(rs_links.loc[rs_links[\"sciName\"] == sciName, \"eol_page_id\"].unique())\n",
    "pg_ids"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[(46559139, 16),\n",
       " (208913, 4),\n",
       " (46559307, 22),\n",
       " (1011315, 22),\n",
       " (205909, 28),\n",
       " (46560546, 24)]"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "num_images_by_pg = []\n",
    "for pg_id in pg_ids:\n",
    "    num_images = links_manifest_cargo.loc[links_manifest_cargo[\"eol_page_id\"] == pg_id[0]].shape[0]\n",
    "    num_images_by_pg.append((pg_id[0], num_images))\n",
    "\n",
    "num_images_by_pg"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The media for both of these last two is online: https://eol.org/pages/46560546/media, https://eol.org/pages/205909/media"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "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>rarespecies_id</th>\n",
       "      <th>eol_content_id_rs</th>\n",
       "      <th>eol_page_id_rs</th>\n",
       "      <th>kingdom</th>\n",
       "      <th>phylum</th>\n",
       "      <th>class</th>\n",
       "      <th>order</th>\n",
       "      <th>family</th>\n",
       "      <th>genus</th>\n",
       "      <th>species</th>\n",
       "      <th>sciName</th>\n",
       "      <th>combined_id_rs</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>1413</th>\n",
       "      <td>d239159f-cb15-4c30-8aeb-d8177f8cf34a</td>\n",
       "      <td>30098492</td>\n",
       "      <td>205909</td>\n",
       "      <td>Animalia</td>\n",
       "      <td>Chordata</td>\n",
       "      <td>Actinopterygii</td>\n",
       "      <td>Acipenseriformes</td>\n",
       "      <td>Acipenseridae</td>\n",
       "      <td>Scaphirhynchus</td>\n",
       "      <td>albus</td>\n",
       "      <td>Scaphirhynchus albus</td>\n",
       "      <td>30098492_205909</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7619</th>\n",
       "      <td>4d7436d1-82de-416b-8a51-6452efd45f44</td>\n",
       "      <td>30098515</td>\n",
       "      <td>205909</td>\n",
       "      <td>Animalia</td>\n",
       "      <td>Chordata</td>\n",
       "      <td>Actinopterygii</td>\n",
       "      <td>Acipenseriformes</td>\n",
       "      <td>Acipenseridae</td>\n",
       "      <td>Scaphirhynchus</td>\n",
       "      <td>albus</td>\n",
       "      <td>Scaphirhynchus albus</td>\n",
       "      <td>30098515_205909</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7916</th>\n",
       "      <td>2d342a7c-7e0c-4981-9630-019bb90183be</td>\n",
       "      <td>30098499</td>\n",
       "      <td>205909</td>\n",
       "      <td>Animalia</td>\n",
       "      <td>Chordata</td>\n",
       "      <td>Actinopterygii</td>\n",
       "      <td>Acipenseriformes</td>\n",
       "      <td>Acipenseridae</td>\n",
       "      <td>Scaphirhynchus</td>\n",
       "      <td>albus</td>\n",
       "      <td>Scaphirhynchus albus</td>\n",
       "      <td>30098499_205909</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11026</th>\n",
       "      <td>a9560f41-403d-46a0-a92a-9694cceffe96</td>\n",
       "      <td>30098523</td>\n",
       "      <td>205909</td>\n",
       "      <td>Animalia</td>\n",
       "      <td>Chordata</td>\n",
       "      <td>Actinopterygii</td>\n",
       "      <td>Acipenseriformes</td>\n",
       "      <td>Acipenseridae</td>\n",
       "      <td>Scaphirhynchus</td>\n",
       "      <td>albus</td>\n",
       "      <td>Scaphirhynchus albus</td>\n",
       "      <td>30098523_205909</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>193</th>\n",
       "      <td>ba2857c7-f02d-44f9-a116-8a450dc53e14</td>\n",
       "      <td>30098516</td>\n",
       "      <td>205909</td>\n",
       "      <td>Animalia</td>\n",
       "      <td>Chordata</td>\n",
       "      <td>Actinopterygii</td>\n",
       "      <td>Acipenseriformes</td>\n",
       "      <td>Acipenseridae</td>\n",
       "      <td>Scaphirhynchus</td>\n",
       "      <td>albus</td>\n",
       "      <td>Scaphirhynchus albus</td>\n",
       "      <td>30098516_205909</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                             rarespecies_id  eol_content_id_rs  \\\n",
       "1413   d239159f-cb15-4c30-8aeb-d8177f8cf34a           30098492   \n",
       "7619   4d7436d1-82de-416b-8a51-6452efd45f44           30098515   \n",
       "7916   2d342a7c-7e0c-4981-9630-019bb90183be           30098499   \n",
       "11026  a9560f41-403d-46a0-a92a-9694cceffe96           30098523   \n",
       "193    ba2857c7-f02d-44f9-a116-8a450dc53e14           30098516   \n",
       "\n",
       "       eol_page_id_rs   kingdom    phylum           class             order  \\\n",
       "1413           205909  Animalia  Chordata  Actinopterygii  Acipenseriformes   \n",
       "7619           205909  Animalia  Chordata  Actinopterygii  Acipenseriformes   \n",
       "7916           205909  Animalia  Chordata  Actinopterygii  Acipenseriformes   \n",
       "11026          205909  Animalia  Chordata  Actinopterygii  Acipenseriformes   \n",
       "193            205909  Animalia  Chordata  Actinopterygii  Acipenseriformes   \n",
       "\n",
       "              family           genus species               sciName  \\\n",
       "1413   Acipenseridae  Scaphirhynchus   albus  Scaphirhynchus albus   \n",
       "7619   Acipenseridae  Scaphirhynchus   albus  Scaphirhynchus albus   \n",
       "7916   Acipenseridae  Scaphirhynchus   albus  Scaphirhynchus albus   \n",
       "11026  Acipenseridae  Scaphirhynchus   albus  Scaphirhynchus albus   \n",
       "193    Acipenseridae  Scaphirhynchus   albus  Scaphirhynchus albus   \n",
       "\n",
       "        combined_id_rs  \n",
       "1413   30098492_205909  \n",
       "7619   30098515_205909  \n",
       "7916   30098499_205909  \n",
       "11026  30098523_205909  \n",
       "193    30098516_205909  "
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "big_mismatch = mismatched_rs.loc[mismatched_rs[\"sciName\"].isin(big_sciNames_missing)]\n",
    "big_mismatch.loc[big_mismatch[\"eol_page_id_rs\"] == 205909].sample(5)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "sampling some, they're \"not in any collections\": https://eol.org/media/30098484"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "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>rarespecies_id</th>\n",
       "      <th>eol_content_id_rs</th>\n",
       "      <th>eol_page_id_rs</th>\n",
       "      <th>kingdom</th>\n",
       "      <th>phylum</th>\n",
       "      <th>class</th>\n",
       "      <th>order</th>\n",
       "      <th>family</th>\n",
       "      <th>genus</th>\n",
       "      <th>species</th>\n",
       "      <th>sciName</th>\n",
       "      <th>combined_id_rs</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>9702</th>\n",
       "      <td>92da8fa4-fb94-42b3-9483-86d2672d6644</td>\n",
       "      <td>27648165</td>\n",
       "      <td>46560546</td>\n",
       "      <td>Animalia</td>\n",
       "      <td>Chordata</td>\n",
       "      <td>Chondrichthyes</td>\n",
       "      <td>Rajiformes</td>\n",
       "      <td>Rajidae</td>\n",
       "      <td>Raja</td>\n",
       "      <td>asterias</td>\n",
       "      <td>Raja asterias</td>\n",
       "      <td>27648165_46560546</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3655</th>\n",
       "      <td>12633820-3a3a-4c77-bd38-7221bd18b747</td>\n",
       "      <td>27648157</td>\n",
       "      <td>46560546</td>\n",
       "      <td>Animalia</td>\n",
       "      <td>Chordata</td>\n",
       "      <td>Chondrichthyes</td>\n",
       "      <td>Rajiformes</td>\n",
       "      <td>Rajidae</td>\n",
       "      <td>Raja</td>\n",
       "      <td>asterias</td>\n",
       "      <td>Raja asterias</td>\n",
       "      <td>27648157_46560546</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2025</th>\n",
       "      <td>6cb50905-48ee-4770-9605-91a95e3d027c</td>\n",
       "      <td>27648159</td>\n",
       "      <td>46560546</td>\n",
       "      <td>Animalia</td>\n",
       "      <td>Chordata</td>\n",
       "      <td>Chondrichthyes</td>\n",
       "      <td>Rajiformes</td>\n",
       "      <td>Rajidae</td>\n",
       "      <td>Raja</td>\n",
       "      <td>asterias</td>\n",
       "      <td>Raja asterias</td>\n",
       "      <td>27648159_46560546</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1358</th>\n",
       "      <td>d436ec20-202d-44ec-9081-ca59afef356f</td>\n",
       "      <td>27648166</td>\n",
       "      <td>46560546</td>\n",
       "      <td>Animalia</td>\n",
       "      <td>Chordata</td>\n",
       "      <td>Chondrichthyes</td>\n",
       "      <td>Rajiformes</td>\n",
       "      <td>Rajidae</td>\n",
       "      <td>Raja</td>\n",
       "      <td>asterias</td>\n",
       "      <td>Raja asterias</td>\n",
       "      <td>27648166_46560546</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6574</th>\n",
       "      <td>a7c43306-6a3a-4d94-b7f0-147ad9f20a73</td>\n",
       "      <td>27648160</td>\n",
       "      <td>46560546</td>\n",
       "      <td>Animalia</td>\n",
       "      <td>Chordata</td>\n",
       "      <td>Chondrichthyes</td>\n",
       "      <td>Rajiformes</td>\n",
       "      <td>Rajidae</td>\n",
       "      <td>Raja</td>\n",
       "      <td>asterias</td>\n",
       "      <td>Raja asterias</td>\n",
       "      <td>27648160_46560546</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                            rarespecies_id  eol_content_id_rs  eol_page_id_rs  \\\n",
       "9702  92da8fa4-fb94-42b3-9483-86d2672d6644           27648165        46560546   \n",
       "3655  12633820-3a3a-4c77-bd38-7221bd18b747           27648157        46560546   \n",
       "2025  6cb50905-48ee-4770-9605-91a95e3d027c           27648159        46560546   \n",
       "1358  d436ec20-202d-44ec-9081-ca59afef356f           27648166        46560546   \n",
       "6574  a7c43306-6a3a-4d94-b7f0-147ad9f20a73           27648160        46560546   \n",
       "\n",
       "       kingdom    phylum           class       order   family genus   species  \\\n",
       "9702  Animalia  Chordata  Chondrichthyes  Rajiformes  Rajidae  Raja  asterias   \n",
       "3655  Animalia  Chordata  Chondrichthyes  Rajiformes  Rajidae  Raja  asterias   \n",
       "2025  Animalia  Chordata  Chondrichthyes  Rajiformes  Rajidae  Raja  asterias   \n",
       "1358  Animalia  Chordata  Chondrichthyes  Rajiformes  Rajidae  Raja  asterias   \n",
       "6574  Animalia  Chordata  Chondrichthyes  Rajiformes  Rajidae  Raja  asterias   \n",
       "\n",
       "            sciName     combined_id_rs  \n",
       "9702  Raja asterias  27648165_46560546  \n",
       "3655  Raja asterias  27648157_46560546  \n",
       "2025  Raja asterias  27648159_46560546  \n",
       "1358  Raja asterias  27648166_46560546  \n",
       "6574  Raja asterias  27648160_46560546  "
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "big_mismatch.loc[big_mismatch[\"eol_page_id_rs\"] == 46560546].sample(5)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Meanwhile, these are giving me 404's: 27648160, 27648159, 27648164, 27648161, 27648166"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "def get_archive_content(combined_id):\n",
    "    return combined_id.split(\"_\")[0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "links_manifest_cargo[\"eol_content_id_archive\"] = links_manifest_cargo[\"combined_id_archive\"].apply(get_archive_content)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "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>filename_archive</th>\n",
       "      <th>md5_archive</th>\n",
       "      <th>combined_id_archive</th>\n",
       "      <th>filename_manifest</th>\n",
       "      <th>md5_combined_manifest</th>\n",
       "      <th>combined_id_manifest_redownload</th>\n",
       "      <th>eol_content_id</th>\n",
       "      <th>eol_page_id</th>\n",
       "      <th>medium_source_url</th>\n",
       "      <th>eol_full_size_copy_url</th>\n",
       "      <th>license_name</th>\n",
       "      <th>copyright_owner</th>\n",
       "      <th>expected_image_filename</th>\n",
       "      <th>source_0706</th>\n",
       "      <th>source_0726</th>\n",
       "      <th>source_1206</th>\n",
       "      <th>combined_id_full_manifest</th>\n",
       "      <th>eol_content_id_archive</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "Empty DataFrame\n",
       "Columns: [filename_archive, md5_archive, combined_id_archive, filename_manifest, md5_combined_manifest, combined_id_manifest_redownload, eol_content_id, eol_page_id, medium_source_url, eol_full_size_copy_url, license_name, copyright_owner, expected_image_filename, source_0706, source_0726, source_1206, combined_id_full_manifest, eol_content_id_archive]\n",
       "Index: []"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# check if content IDs get recycled, content ID: 27648165, now online as: 30223317\n",
    "# is eol_content_id the archive content ID?\n",
    "links_manifest_cargo.loc[links_manifest_cargo[\"eol_content_id_archive\"] == 30223317]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "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>filename_archive</th>\n",
       "      <th>md5_archive</th>\n",
       "      <th>combined_id_archive</th>\n",
       "      <th>filename_manifest</th>\n",
       "      <th>md5_combined_manifest</th>\n",
       "      <th>combined_id_manifest_redownload</th>\n",
       "      <th>eol_content_id</th>\n",
       "      <th>eol_page_id</th>\n",
       "      <th>medium_source_url</th>\n",
       "      <th>eol_full_size_copy_url</th>\n",
       "      <th>license_name</th>\n",
       "      <th>copyright_owner</th>\n",
       "      <th>expected_image_filename</th>\n",
       "      <th>source_0706</th>\n",
       "      <th>source_0726</th>\n",
       "      <th>source_1206</th>\n",
       "      <th>combined_id_full_manifest</th>\n",
       "      <th>eol_content_id_archive</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "Empty DataFrame\n",
       "Columns: [filename_archive, md5_archive, combined_id_archive, filename_manifest, md5_combined_manifest, combined_id_manifest_redownload, eol_content_id, eol_page_id, medium_source_url, eol_full_size_copy_url, license_name, copyright_owner, expected_image_filename, source_0706, source_0726, source_1206, combined_id_full_manifest, eol_content_id_archive]\n",
       "Index: []"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Is it in manifest?\n",
    "links_manifest_cargo.loc[links_manifest_cargo[\"eol_content_id\"] == 30223317]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "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>filename_archive</th>\n",
       "      <th>md5_archive</th>\n",
       "      <th>combined_id_archive</th>\n",
       "      <th>filename_manifest</th>\n",
       "      <th>md5_combined_manifest</th>\n",
       "      <th>combined_id_manifest_redownload</th>\n",
       "      <th>eol_content_id</th>\n",
       "      <th>eol_page_id</th>\n",
       "      <th>medium_source_url</th>\n",
       "      <th>eol_full_size_copy_url</th>\n",
       "      <th>license_name</th>\n",
       "      <th>copyright_owner</th>\n",
       "      <th>expected_image_filename</th>\n",
       "      <th>source_0706</th>\n",
       "      <th>source_0726</th>\n",
       "      <th>source_1206</th>\n",
       "      <th>combined_id_full_manifest</th>\n",
       "      <th>eol_content_id_archive</th>\n",
       "      <th>eol_content_id_manifest</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "Empty DataFrame\n",
       "Columns: [filename_archive, md5_archive, combined_id_archive, filename_manifest, md5_combined_manifest, combined_id_manifest_redownload, eol_content_id, eol_page_id, medium_source_url, eol_full_size_copy_url, license_name, copyright_owner, expected_image_filename, source_0706, source_0726, source_1206, combined_id_full_manifest, eol_content_id_archive, eol_content_id_manifest]\n",
       "Index: []"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# to be sure we check manifest\n",
    "links_manifest_cargo[\"eol_content_id_manifest\"] = links_manifest_cargo[\"combined_id_full_manifest\"].apply(get_archive_content)\n",
    "\n",
    "links_manifest_cargo.loc[links_manifest_cargo[\"eol_content_id_manifest\"] == 30223317]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This tracks with all eol content IDs being unique across manifest versions...would there be some other intermediate stage where it changed IDs _again_?!"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Save CSV of mismatched, they should be salvageable.\n",
    "# We saw these images both online and in our cargo, just with different IDs\n",
    "\n",
    "mismatched_rs.to_csv(\"../data/archive_mismatched_rarespecies.csv\", index=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Most of our images for some of these species are missing their metadata. For the vast majority of the species, it's just 1 or 2 images."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Investigate Duplication\n",
    "\n",
    "Now I want some more info on those duplicated MD5's."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "rs_links[\"md5_dupes\"] = rs_links.duplicated(subset = \"md5_archive\", keep = \"first\")\n",
    "rs_links[\"rs_id_dupes\"] = rs_links.duplicated(subset = \"rarespecies_id\", keep = \"first\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "md5_dupes\n",
       "True    726\n",
       "Name: count, dtype: int64"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rs_links.loc[rs_links[\"rs_id_dupes\"], \"md5_dupes\"].value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "md5_dupes\n",
       "False    11663\n",
       "True       163\n",
       "Name: count, dtype: int64"
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rs_links.loc[~rs_links[\"rs_id_dupes\"], \"md5_dupes\"].value_counts()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Looks like we have 163 duplicated images in Rare Species..."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "rarespecies_id                     163\n",
       "eol_content_id_rs                  163\n",
       "eol_page_id_rs                      80\n",
       "kingdom                              1\n",
       "phylum                               4\n",
       "class                                9\n",
       "order                               37\n",
       "family                              56\n",
       "genus                               73\n",
       "species                             80\n",
       "sciName                             80\n",
       "combined_id_rs                     163\n",
       "filename_archive                   163\n",
       "md5_archive                        163\n",
       "combined_id_archive                163\n",
       "filename_manifest                  163\n",
       "md5_combined_manifest              163\n",
       "combined_id_manifest_redownload    163\n",
       "eol_content_id                     163\n",
       "eol_page_id                         80\n",
       "medium_source_url                  163\n",
       "eol_full_size_copy_url             163\n",
       "license_name                        10\n",
       "copyright_owner                     54\n",
       "expected_image_filename            163\n",
       "source_0706                          2\n",
       "source_0726                          2\n",
       "source_1206                          2\n",
       "combined_id_full_manifest          163\n",
       "md5_dupes                            1\n",
       "rs_id_dupes                          1\n",
       "dtype: int64"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rs = rs_links.loc[~rs_links[\"rs_id_dupes\"]]\n",
    "rs_dupes = rs.loc[rs[\"md5_dupes\"]]\n",
    "rs_dupes.nunique()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "sciName\n",
       "Calumma ambreense             7\n",
       "Acanthochelys macrocephala    7\n",
       "Polyergus nigerrimus          7\n",
       "Pheidole elecebra             6\n",
       "Nothomyrmecia macrops         6\n",
       "Callorhinchus callorynchus    5\n",
       "Atelopus flavescens           5\n",
       "Adetomyrma venatrix           5\n",
       "Pleurodeles waltl             4\n",
       "Orcaella brevirostris         4\n",
       "Name: count, dtype: int64"
      ]
     },
     "execution_count": 27,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rs_dupes.sciName.value_counts()[:10]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We have 30 images per species, so we have about a fourth duplicated for some. Note that the counts here are the number of duplicate images, so the total number of times these particular images appear is N + 1."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Let's see how many images we have for each of these duplicated images."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[4453333, 460289, 45277122, 46561158, 1286909, 45510188, 45510548, 791049]"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rs_sci_dupe_pgs = list(rs_dupes.eol_page_id.unique())\n",
    "rs_sci_dupe_pgs[:8]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {
    "lines_to_next_cell": 2
   },
   "outputs": [],
   "source": [
    "num_images_by_pg = {}\n",
    "#list with unique by md5\n",
    "num_unique_imgs_by_pg = {}\n",
    "for pg_id in rs_sci_dupe_pgs:\n",
    "    num_images = links_manifest_cargo.loc[links_manifest_cargo[\"eol_page_id\"] == pg_id].shape[0]\n",
    "    num_images_by_pg[pg_id] = num_images\n",
    "    num_unique_images = links_manifest_cargo.loc[links_manifest_cargo[\"eol_page_id\"] == pg_id, \"md5_archive\"].nunique()\n",
    "    num_unique_imgs_by_pg[pg_id] = num_unique_images"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "80"
      ]
     },
     "execution_count": 30,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(num_images_by_pg)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "page ID 1286909 has less than 30 unique images; it has 27 unique images\n",
      "page ID 791049 has less than 30 unique images; it has 27 unique images\n",
      "page ID 485420 has less than 30 unique images; it has 24 unique images\n",
      "page ID 914531 has less than 30 unique images; it has 29 unique images\n",
      "page ID 205714 has less than 30 unique images; it has 29 unique images\n"
     ]
    }
   ],
   "source": [
    "for pg_id in num_unique_imgs_by_pg.keys():\n",
    "    if num_unique_imgs_by_pg[pg_id] < 30:\n",
    "        print(f\"page ID {pg_id} has less than 30 unique images; it has {num_unique_imgs_by_pg[pg_id]} unique images\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "https://eol.org/pages/485420/media has only 21 true images, since 3 are post-its."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "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>rarespecies_id</th>\n",
       "      <th>eol_content_id_rs</th>\n",
       "      <th>eol_page_id_rs</th>\n",
       "      <th>kingdom</th>\n",
       "      <th>phylum</th>\n",
       "      <th>class</th>\n",
       "      <th>order</th>\n",
       "      <th>family</th>\n",
       "      <th>genus</th>\n",
       "      <th>species</th>\n",
       "      <th>sciName</th>\n",
       "      <th>combined_id_rs</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>8e649092-3e9a-470d-8fe2-1a679e8dbfa9</td>\n",
       "      <td>22519448</td>\n",
       "      <td>914532</td>\n",
       "      <td>Animalia</td>\n",
       "      <td>Chordata</td>\n",
       "      <td>Aves</td>\n",
       "      <td>Anseriformes</td>\n",
       "      <td>Anatidae</td>\n",
       "      <td>Anser</td>\n",
       "      <td>canagicus</td>\n",
       "      <td>Anser canagicus</td>\n",
       "      <td>22519448_914532</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>9ceb3c09-a43a-4f43-9462-a61cea102f0a</td>\n",
       "      <td>28677580</td>\n",
       "      <td>1057176</td>\n",
       "      <td>Animalia</td>\n",
       "      <td>Chordata</td>\n",
       "      <td>Reptilia</td>\n",
       "      <td>Squamata</td>\n",
       "      <td>Dactyloidae</td>\n",
       "      <td>Anolis</td>\n",
       "      <td>koopmani</td>\n",
       "      <td>Anolis koopmani</td>\n",
       "      <td>28677580_1057176</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>d0a34ead-c4f2-4a5b-bf57-00e2a9f9f4af</td>\n",
       "      <td>20714475</td>\n",
       "      <td>47047909</td>\n",
       "      <td>Animalia</td>\n",
       "      <td>Chordata</td>\n",
       "      <td>Reptilia</td>\n",
       "      <td>Squamata</td>\n",
       "      <td>Scincidae</td>\n",
       "      <td>Oligosoma</td>\n",
       "      <td>macgregori</td>\n",
       "      <td>Oligosoma macgregori</td>\n",
       "      <td>20714475_47047909</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>4ef2a6eb-9910-488b-8fd1-b68ae49ce4da</td>\n",
       "      <td>29975068</td>\n",
       "      <td>45509269</td>\n",
       "      <td>Animalia</td>\n",
       "      <td>Chordata</td>\n",
       "      <td>Aves</td>\n",
       "      <td>Charadriiformes</td>\n",
       "      <td>Laridae</td>\n",
       "      <td>Pagophila</td>\n",
       "      <td>eburnea</td>\n",
       "      <td>Pagophila eburnea</td>\n",
       "      <td>29975068_45509269</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>095c3a37-6921-401c-b55c-67c5e80096c3</td>\n",
       "      <td>29462184</td>\n",
       "      <td>331080</td>\n",
       "      <td>Animalia</td>\n",
       "      <td>Chordata</td>\n",
       "      <td>Mammalia</td>\n",
       "      <td>Artiodactyla</td>\n",
       "      <td>Bovidae</td>\n",
       "      <td>Oryx</td>\n",
       "      <td>leucoryx</td>\n",
       "      <td>Oryx leucoryx</td>\n",
       "      <td>29462184_331080</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                         rarespecies_id  eol_content_id_rs  eol_page_id_rs  \\\n",
       "0  8e649092-3e9a-470d-8fe2-1a679e8dbfa9           22519448          914532   \n",
       "1  9ceb3c09-a43a-4f43-9462-a61cea102f0a           28677580         1057176   \n",
       "2  d0a34ead-c4f2-4a5b-bf57-00e2a9f9f4af           20714475        47047909   \n",
       "3  4ef2a6eb-9910-488b-8fd1-b68ae49ce4da           29975068        45509269   \n",
       "4  095c3a37-6921-401c-b55c-67c5e80096c3           29462184          331080   \n",
       "\n",
       "    kingdom    phylum     class            order       family      genus  \\\n",
       "0  Animalia  Chordata      Aves     Anseriformes     Anatidae      Anser   \n",
       "1  Animalia  Chordata  Reptilia         Squamata  Dactyloidae     Anolis   \n",
       "2  Animalia  Chordata  Reptilia         Squamata    Scincidae  Oligosoma   \n",
       "3  Animalia  Chordata      Aves  Charadriiformes      Laridae  Pagophila   \n",
       "4  Animalia  Chordata  Mammalia     Artiodactyla      Bovidae       Oryx   \n",
       "\n",
       "      species               sciName     combined_id_rs  \n",
       "0   canagicus       Anser canagicus    22519448_914532  \n",
       "1    koopmani       Anolis koopmani   28677580_1057176  \n",
       "2  macgregori  Oligosoma macgregori  20714475_47047909  \n",
       "3     eburnea     Pagophila eburnea  29975068_45509269  \n",
       "4    leucoryx         Oryx leucoryx    29462184_331080  "
      ]
     },
     "execution_count": 32,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rs_catalog.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "7228     30077892_46559947_eol-full-size-copy.jpg\n",
       "10774    29485438_46559780_eol-full-size-copy.jpg\n",
       "60         28672110_795859_eol-full-size-copy.jpg\n",
       "1640     12835827_46454284_eol-full-size-copy.jpg\n",
       "536      22066842_45511093_eol-full-size-copy.jpg\n",
       "5669       20495364_205910_eol-full-size-copy.jpg\n",
       "3543     13992854_45518912_eol-full-size-copy.jpg\n",
       "Name: file_name, dtype: object"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rs_catalog[\"file_name\"] = rs_catalog[\"combined_id_rs\"].astype(str) + \"_eol-full-size-copy.jpg\"\n",
    "rs_catalog[\"file_name\"].sample(7)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [],
   "source": [
    "# save filelist for easier fetching\n",
    "#rs_catalog[\"file_name\"].to_csv(\"../data/rs_file_list.txt\", index = False)\n",
    "# Not needed now"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Save `rs_links` to file for adjusting Rare Species images for uniqueness."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [],
   "source": [
    "rs_links.to_csv(\"../data/rs_links.csv\", index = False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Get MD5s of Images on Misalgined Pages\n",
    "\n",
    "Relevant background from Matt (with some notes for context here):\n",
    "- I have a CSV called `rarespecies_catalog_missing_manifest___archive.csv` with 174 entries (I double-checked that the entries in the \"sciName\" column all look good ... there are duplicates there, but all are valid Genus species binomials)\n",
    "  - This file is from `archive_mismatched_rarespecies.csv` created above.\n",
    "- Filtered that for all the unique page IDs.\n",
    "- Downloaded a media manifest current as of today (March 11)\n",
    "- There are 1,929 entries in today's media manifest with page IDs from the filtered list mentioned above\n",
    "- Downloaded them to `eol_data_cleanup/data/rare_species_pageids/` (on OSC)\n",
    "- Logged downloads with errors (there were 2), so we have 1,927 JPGs\n",
    "- Took MD5s as well, which are in `eol_data_cleanup/data/rare_species_pageids/md5s.csv` (on OSC. Here this file is `rarespecies_missing_pages_md5s.csv`).\n",
    "  - Has \"filename\" and \"md5\" columns, and filenames are `<contentID>_<pageID>_eol-full-size-copy.jpg`."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<class 'pandas.core.frame.DataFrame'>\n",
      "RangeIndex: 1927 entries, 0 to 1926\n",
      "Data columns (total 2 columns):\n",
      " #   Column    Non-Null Count  Dtype \n",
      "---  ------    --------------  ----- \n",
      " 0   filename  1927 non-null   object\n",
      " 1   md5       1927 non-null   object\n",
      "dtypes: object(2)\n",
      "memory usage: 30.2+ KB\n"
     ]
    }
   ],
   "source": [
    "rs_mp = pd.read_csv(\"../data/rarespecies_missing_pages_md5s.csv\", low_memory=False)\n",
    "rs_mp.info(show_counts = True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "filename    1927\n",
       "md5         1899\n",
       "dtype: int64"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rs_mp.nunique()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "So, how many of these are in the archive?"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<class 'pandas.core.frame.DataFrame'>\n",
      "RangeIndex: 1835 entries, 0 to 1834\n",
      "Data columns (total 5 columns):\n",
      " #   Column             Non-Null Count  Dtype \n",
      "---  ------             --------------  ----- \n",
      " 0   filename           1835 non-null   object\n",
      " 1   md5                1835 non-null   object\n",
      " 2   filename_archive   1835 non-null   object\n",
      " 3   md5_archive        1835 non-null   object\n",
      " 4   filename_manifest  1835 non-null   object\n",
      "dtypes: object(5)\n",
      "memory usage: 71.8+ KB\n"
     ]
    }
   ],
   "source": [
    "rs_mp_archive = pd.merge(rs_mp,\n",
    "                         links_manifest_cargo[[\"filename_archive\", \"md5_archive\", \"filename_manifest\"]],\n",
    "                         left_on = \"md5\",\n",
    "                         right_on = \"md5_archive\",\n",
    "                         how = \"inner\")\n",
    "rs_mp_archive.info(show_counts = True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Interesting, most of these are actually in the archive."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "filename             1595\n",
       "md5                  1568\n",
       "filename_archive     1616\n",
       "md5_archive          1568\n",
       "filename_manifest    1631\n",
       "dtype: int64"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rs_mp_archive.nunique()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Though it's mostly duplicates, so that makes sense with our earlier numbers."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "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>filename</th>\n",
       "      <th>md5</th>\n",
       "      <th>filename_archive</th>\n",
       "      <th>md5_archive</th>\n",
       "      <th>filename_manifest</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>14192835_1010637_eol-full-size-copy.jpg</td>\n",
       "      <td>bcf9f23cfbd8f872e94a022789995c56</td>\n",
       "      <td>14192835_1010637_eol-full-size-copy.jpg</td>\n",
       "      <td>bcf9f23cfbd8f872e94a022789995c56</td>\n",
       "      <td>14192835_1010637_eol-full-size-copy.jpg</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>22662179_45511624_eol-full-size-copy.jpg</td>\n",
       "      <td>9e4dddfc2afc130953f8fbc0d61b52fb</td>\n",
       "      <td>22662179_45511624_eol-full-size-copy.jpg</td>\n",
       "      <td>9e4dddfc2afc130953f8fbc0d61b52fb</td>\n",
       "      <td>22662179_45511624_eol-full-size-copy.jpg</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                   filename                               md5  \\\n",
       "0   14192835_1010637_eol-full-size-copy.jpg  bcf9f23cfbd8f872e94a022789995c56   \n",
       "1  22662179_45511624_eol-full-size-copy.jpg  9e4dddfc2afc130953f8fbc0d61b52fb   \n",
       "\n",
       "                           filename_archive                       md5_archive  \\\n",
       "0   14192835_1010637_eol-full-size-copy.jpg  bcf9f23cfbd8f872e94a022789995c56   \n",
       "1  22662179_45511624_eol-full-size-copy.jpg  9e4dddfc2afc130953f8fbc0d61b52fb   \n",
       "\n",
       "                          filename_manifest  \n",
       "0   14192835_1010637_eol-full-size-copy.jpg  \n",
       "1  22662179_45511624_eol-full-size-copy.jpg  "
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rs_mp_archive.head(2)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Ensure uniqueness across available images\n",
    "\n",
    "Let's reduce the archive DataFrame down to just EOL page IDs from the Rare Species Catalog. We'll match on the archive page ID's (pulled from `filename_archive`). Then we need to merge `rs_mp` with `eol_media_manifest_2024-03-11.csv` to get the source info and concatenate the two DataFrames."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "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>EOL content ID</th>\n",
       "      <th>EOL page ID</th>\n",
       "      <th>Medium Source URL</th>\n",
       "      <th>EOL Full-Size Copy URL</th>\n",
       "      <th>License Name</th>\n",
       "      <th>Copyright Owner</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>5470022</td>\n",
       "      <td>500901</td>\n",
       "      <td>http://entnemdept.ufl.edu/walker/buzz/487dmj.gif</td>\n",
       "      <td>https://content.eol.org/data/media/54/67/bb/80...</td>\n",
       "      <td>cc-by-nc-sa-3.0</td>\n",
       "      <td>Susan A. Wineriter/Singing Insects of North Am...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>5470023</td>\n",
       "      <td>858799</td>\n",
       "      <td>http://entnemdept.ufl.edu/walker/buzz/291pm.jpg</td>\n",
       "      <td>https://content.eol.org/data/media/54/67/6a/80...</td>\n",
       "      <td>cc-by-nc-sa-3.0</td>\n",
       "      <td>Thomas J. Walker/Singing Insects of North America</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   EOL content ID  EOL page ID  \\\n",
       "0         5470022       500901   \n",
       "1         5470023       858799   \n",
       "\n",
       "                                  Medium Source URL  \\\n",
       "0  http://entnemdept.ufl.edu/walker/buzz/487dmj.gif   \n",
       "1   http://entnemdept.ufl.edu/walker/buzz/291pm.jpg   \n",
       "\n",
       "                              EOL Full-Size Copy URL     License Name  \\\n",
       "0  https://content.eol.org/data/media/54/67/bb/80...  cc-by-nc-sa-3.0   \n",
       "1  https://content.eol.org/data/media/54/67/6a/80...  cc-by-nc-sa-3.0   \n",
       "\n",
       "                                     Copyright Owner  \n",
       "0  Susan A. Wineriter/Singing Insects of North Am...  \n",
       "1  Thomas J. Walker/Singing Insects of North America  "
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mp_manifest = pd.read_csv(\"../data/eol_media_manifest_2024-03-11.csv\",\n",
    "                          low_memory=False,\n",
    "                          dtype = {\"EOL content ID\": \"int64\", \"EOL page ID\": \"int64\"})\n",
    "mp_manifest.head(2)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Rename columns to match the archive file."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "mp_manifest.rename(columns={\"EOL content ID\": \"eol_content_id\",\n",
    "                            \"EOL page ID\": \"eol_page_id\",\n",
    "                            \"Medium Source URL\": \"medium_source_url\",\n",
    "                            \"EOL Full-Size Copy URL\": \"eol_full_size_copy_url\",\n",
    "                            \"License Name\": \"license_name\",\n",
    "                            \"Copyright Owner\": \"copyright_owner\"},\n",
    "                   inplace = True)\n",
    "mp_manifest[\"filename\"] = mp_manifest[\"eol_content_id\"].astype(str) + \"_\" + mp_manifest[\"eol_page_id\"].astype(str) + \"_eol-full-size-copy.jpg\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "filename                  1927\n",
       "md5                       1899\n",
       "eol_content_id            1927\n",
       "eol_page_id                 34\n",
       "medium_source_url         1927\n",
       "eol_full_size_copy_url    1927\n",
       "license_name                14\n",
       "copyright_owner            618\n",
       "dtype: int64"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rs_mp_manifest = pd.merge(rs_mp,\n",
    "                          mp_manifest,\n",
    "                          on = \"filename\",\n",
    "                          how = \"inner\")\n",
    "rs_mp_manifest.nunique()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Good, everything merged as expected. Let's cut down the `links_manifest_cargo` DataFrame to just Rare Species pages, then we can concatenate these."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "400"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rs_pages = list(rs_catalog.eol_page_id_rs.unique())\n",
    "len(rs_pages) # should be 400"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [],
   "source": [
    "def get_page_id(combined_id):\n",
    "    # want to use the archive combined ID to ensure match\n",
    "    # combined ID is eolContentID_eolPageID\n",
    "    return int(combined_id.split(\"_\")[1])\n",
    "\n",
    "links_manifest_cargo[\"eol_page_id_archive\"] = links_manifest_cargo[\"combined_id_archive\"].apply(get_page_id)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "filename_archive                   22231\n",
       "md5_archive                        21815\n",
       "combined_id_archive                22231\n",
       "filename_manifest                  22747\n",
       "md5_combined_manifest              21815\n",
       "combined_id_manifest_redownload    22747\n",
       "eol_content_id                     22747\n",
       "eol_page_id                          467\n",
       "medium_source_url                  22369\n",
       "eol_full_size_copy_url             22560\n",
       "license_name                          15\n",
       "copyright_owner                     5286\n",
       "expected_image_filename            22747\n",
       "source_0706                            2\n",
       "source_0726                            2\n",
       "source_1206                            2\n",
       "combined_id_full_manifest          22747\n",
       "eol_page_id_archive                  400\n",
       "dtype: int64"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rs_links_cargo = links_manifest_cargo.loc[links_manifest_cargo[\"eol_page_id_archive\"].isin(rs_pages)]\n",
    "rs_links_cargo.nunique()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/var/folders/nv/f0fq1p1n1_3b11x579py_0q80000gq/T/ipykernel_11036/4189562674.py:6: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame.\n",
      "Try using .loc[row_indexer,col_indexer] = value instead\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  rs_links_cargo[\"eol_content_id_archive\"] = rs_links_cargo[\"combined_id_archive\"].apply(get_content_id)\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "filename_archive                   22231\n",
       "md5_archive                        21815\n",
       "combined_id_archive                22231\n",
       "filename_manifest                  22747\n",
       "md5_combined_manifest              21815\n",
       "combined_id_manifest_redownload    22747\n",
       "eol_content_id                     22747\n",
       "eol_page_id                          467\n",
       "medium_source_url                  22369\n",
       "eol_full_size_copy_url             22560\n",
       "license_name                          15\n",
       "copyright_owner                     5286\n",
       "expected_image_filename            22747\n",
       "source_0706                            2\n",
       "source_0726                            2\n",
       "source_1206                            2\n",
       "combined_id_full_manifest          22747\n",
       "eol_page_id_archive                  400\n",
       "eol_content_id_archive             22231\n",
       "dtype: int64"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "def get_content_id(combined_id):\n",
    "    # want to use the archive combined ID to ensure match\n",
    "    # combined ID is eolContentID_eolPageID\n",
    "    return int(combined_id.split(\"_\")[0])\n",
    "\n",
    "rs_links_cargo[\"eol_content_id_archive\"] = rs_links_cargo[\"combined_id_archive\"].apply(get_content_id)\n",
    "rs_links_cargo.nunique()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['filename_archive',\n",
       " 'md5_archive',\n",
       " 'combined_id_archive',\n",
       " 'eol_content_id_archive',\n",
       " 'eol_page_id_archive',\n",
       " 'medium_source_url',\n",
       " 'eol_full_size_copy_url',\n",
       " 'license_name',\n",
       " 'copyright_owner']"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cols_to_match = list(rs_links_cargo.columns)[:3] + [\"eol_content_id_archive\", \"eol_page_id_archive\"] + list(rs_mp_manifest.columns)[4:]\n",
    "cols_to_match"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Index(['filename', 'md5', 'combined_id', 'eol_content_id', 'eol_page_id',\n",
       "       'medium_source_url', 'eol_full_size_copy_url', 'license_name',\n",
       "       'copyright_owner'],\n",
       "      dtype='object')"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rs_links_cargo = rs_links_cargo[cols_to_match]\n",
    "rs_links_cargo.rename(columns={\"filename_archive\": \"filename\",\n",
    "                               \"md5_archive\": \"md5\",\n",
    "                               \"combined_id_archive\": \"combined_id\",\n",
    "                               \"eol_content_id_archive\": \"eol_content_id\",\n",
    "                               \"eol_page_id_archive\": \"eol_page_id\"},\n",
    "                               inplace = True)\n",
    "rs_links_cargo.columns"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now we just need to add `combined_id` to `rs_mp_manifest` and we'll be able to concatenate them."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "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>filename</th>\n",
       "      <th>md5</th>\n",
       "      <th>eol_content_id</th>\n",
       "      <th>eol_page_id</th>\n",
       "      <th>medium_source_url</th>\n",
       "      <th>eol_full_size_copy_url</th>\n",
       "      <th>license_name</th>\n",
       "      <th>copyright_owner</th>\n",
       "      <th>combined_id</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>14192835_1010637_eol-full-size-copy.jpg</td>\n",
       "      <td>bcf9f23cfbd8f872e94a022789995c56</td>\n",
       "      <td>14192835</td>\n",
       "      <td>1010637</td>\n",
       "      <td>https://farm5.staticflickr.com/4036/4450466800...</td>\n",
       "      <td>https://content.eol.org/data/media/d7/1c/ce/54...</td>\n",
       "      <td>cc-by-nc-sa</td>\n",
       "      <td>Mark Stevens</td>\n",
       "      <td>14192835_1010637</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>22662179_45511624_eol-full-size-copy.jpg</td>\n",
       "      <td>9e4dddfc2afc130953f8fbc0d61b52fb</td>\n",
       "      <td>22662179</td>\n",
       "      <td>45511624</td>\n",
       "      <td>https://inaturalist-open-data.s3.amazonaws.com...</td>\n",
       "      <td>https://content.eol.org/data/media/55/a1/bf/18...</td>\n",
       "      <td>cc-by-nc-4.0</td>\n",
       "      <td>oscarcubero</td>\n",
       "      <td>22662179_45511624</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>28915133_1010637_eol-full-size-copy.jpg</td>\n",
       "      <td>e3d3c433af26fd4dfef43e32459d1d81</td>\n",
       "      <td>28915133</td>\n",
       "      <td>1010637</td>\n",
       "      <td>https://upload.wikimedia.org/wikipedia/commons...</td>\n",
       "      <td>https://content.eol.org/data/media/3a/46/66/50...</td>\n",
       "      <td>cc-by-sa-3.0</td>\n",
       "      <td>Profgkay</td>\n",
       "      <td>28915133_1010637</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>22310543_46559744_eol-full-size-copy.jpg</td>\n",
       "      <td>b2919b9a5273d9091cd7b5b5e682b53c</td>\n",
       "      <td>22310543</td>\n",
       "      <td>46559744</td>\n",
       "      <td>https://inaturalist-open-data.s3.amazonaws.com...</td>\n",
       "      <td>https://content.eol.org/data/media/58/f8/88/18...</td>\n",
       "      <td>cc-by-nc-4.0</td>\n",
       "      <td>Amy Jaecker-Jones</td>\n",
       "      <td>22310543_46559744</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>30025399_333429_eol-full-size-copy.jpg</td>\n",
       "      <td>1a1be33aeb1b694b26838416e2dedb80</td>\n",
       "      <td>30025399</td>\n",
       "      <td>333429</td>\n",
       "      <td>https://upload.wikimedia.org/wikipedia/commons...</td>\n",
       "      <td>https://content.eol.org/data/media/59/10/02/50...</td>\n",
       "      <td>cc-by-sa-3.0</td>\n",
       "      <td>User:Winnerhominid</td>\n",
       "      <td>30025399_333429</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                   filename                               md5  \\\n",
       "0   14192835_1010637_eol-full-size-copy.jpg  bcf9f23cfbd8f872e94a022789995c56   \n",
       "1  22662179_45511624_eol-full-size-copy.jpg  9e4dddfc2afc130953f8fbc0d61b52fb   \n",
       "2   28915133_1010637_eol-full-size-copy.jpg  e3d3c433af26fd4dfef43e32459d1d81   \n",
       "3  22310543_46559744_eol-full-size-copy.jpg  b2919b9a5273d9091cd7b5b5e682b53c   \n",
       "4    30025399_333429_eol-full-size-copy.jpg  1a1be33aeb1b694b26838416e2dedb80   \n",
       "\n",
       "   eol_content_id  eol_page_id  \\\n",
       "0        14192835      1010637   \n",
       "1        22662179     45511624   \n",
       "2        28915133      1010637   \n",
       "3        22310543     46559744   \n",
       "4        30025399       333429   \n",
       "\n",
       "                                   medium_source_url  \\\n",
       "0  https://farm5.staticflickr.com/4036/4450466800...   \n",
       "1  https://inaturalist-open-data.s3.amazonaws.com...   \n",
       "2  https://upload.wikimedia.org/wikipedia/commons...   \n",
       "3  https://inaturalist-open-data.s3.amazonaws.com...   \n",
       "4  https://upload.wikimedia.org/wikipedia/commons...   \n",
       "\n",
       "                              eol_full_size_copy_url  license_name  \\\n",
       "0  https://content.eol.org/data/media/d7/1c/ce/54...   cc-by-nc-sa   \n",
       "1  https://content.eol.org/data/media/55/a1/bf/18...  cc-by-nc-4.0   \n",
       "2  https://content.eol.org/data/media/3a/46/66/50...  cc-by-sa-3.0   \n",
       "3  https://content.eol.org/data/media/58/f8/88/18...  cc-by-nc-4.0   \n",
       "4  https://content.eol.org/data/media/59/10/02/50...  cc-by-sa-3.0   \n",
       "\n",
       "      copyright_owner        combined_id  \n",
       "0        Mark Stevens   14192835_1010637  \n",
       "1         oscarcubero  22662179_45511624  \n",
       "2            Profgkay   28915133_1010637  \n",
       "3   Amy Jaecker-Jones  22310543_46559744  \n",
       "4  User:Winnerhominid    30025399_333429  "
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rs_mp_manifest[\"combined_id\"] = rs_mp_manifest[\"eol_content_id\"].astype(str) + \"_\" + rs_mp_manifest[\"eol_page_id\"].astype(str)\n",
    "rs_mp_manifest.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "filename                  22570\n",
       "md5                       22146\n",
       "combined_id               22570\n",
       "eol_content_id            22570\n",
       "eol_page_id                 400\n",
       "medium_source_url         22701\n",
       "eol_full_size_copy_url    22892\n",
       "license_name                 15\n",
       "copyright_owner            5326\n",
       "dtype: int64"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rs_full_manifest = pd.concat([rs_links_cargo, rs_mp_manifest], ignore_index=True)\n",
    "rs_full_manifest.nunique()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(25515, 9)"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rs_full_manifest.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "25515"
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# does that match?\n",
    "rs_links_cargo.shape[0] + rs_mp_manifest.shape[0]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Let's reduce this down to just unique MD5s. I think we'll have to regenerate rarespecies IDs, since we can't necessarily match all the ones we had before."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<class 'pandas.core.frame.DataFrame'>\n",
      "Index: 22146 entries, 0 to 25513\n",
      "Data columns (total 10 columns):\n",
      " #   Column                  Non-Null Count  Dtype \n",
      "---  ------                  --------------  ----- \n",
      " 0   filename                22146 non-null  object\n",
      " 1   md5                     22146 non-null  object\n",
      " 2   combined_id             22146 non-null  object\n",
      " 3   eol_content_id          22146 non-null  int64 \n",
      " 4   eol_page_id             22146 non-null  int64 \n",
      " 5   medium_source_url       22146 non-null  object\n",
      " 6   eol_full_size_copy_url  22146 non-null  object\n",
      " 7   license_name            22146 non-null  object\n",
      " 8   copyright_owner         18958 non-null  object\n",
      " 9   duplicate_img           22146 non-null  bool  \n",
      "dtypes: bool(1), int64(2), object(7)\n",
      "memory usage: 1.7+ MB\n"
     ]
    }
   ],
   "source": [
    "rs_full_manifest[\"duplicate_img\"] = rs_full_manifest.duplicated(subset = \"md5\", keep = \"first\")\n",
    "rs_full_manifest_unique = rs_full_manifest.loc[~rs_full_manifest[\"duplicate_img\"]]\n",
    "rs_full_manifest_unique.info(show_counts = True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now I need to reduce to just 30 images per page. Let's save this as a CSV first actually and then generate that in a new notebook. I can realign the labels based on the page IDs from the `rarespecies_catalog`, but I won't be able to properly rematch the `rarespecies_id`, so that will need to be regenerated...\n",
    "\n",
    "### Run Owner match script on this before saving\n",
    "\n",
    "Let's match any missing owners where possible to make sure this is a full-info DataFrame before saving it to a CSV."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [],
   "source": [
    "from tqdm import tqdm"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [],
   "source": [
    "def get_owners_titles(manifest, owners):\n",
    "    \"\"\"\n",
    "    Function to attach owner names and image titles to manifest entries in combined manifest.\n",
    "    Fills empty \"copyright_owner\" and \"title\" values with \"not provided\".\n",
    "    Parameters:\n",
    "    -----------\n",
    "    manifest - rs_full_manifest_unique\n",
    "    owners - DataFrame of July 26, 2023 media manifest entries that had missing owners, updated with their information.\n",
    "    Returns:\n",
    "    --------\n",
    "    manifest - Rare Species media manifest DataFrame with missing owners resolved to extent possible.\n",
    "    \"\"\"\n",
    "    missing_owners = [\n",
    "        comb_id\n",
    "        for comb_id in list(\n",
    "            manifest.loc[manifest[\"copyright_owner\"].isna(), \"combined_id\"]\n",
    "        )\n",
    "    ]\n",
    "\n",
    "    for comb_id in tqdm(missing_owners):\n",
    "        temp = owners.loc[owners.combined_id_owner == comb_id]\n",
    "        copyright_owner = str(temp[\"Copyright Owner\"].values)\n",
    "        title = str(temp.title.values)\n",
    "        manifest.loc[manifest[\"combined_id\"] == comb_id, \"copyright_owner\"] = copyright_owner\n",
    "        manifest.loc[manifest[\"combined_id\"] == comb_id, \"title\"] = title\n",
    "\n",
    "    # Print counts of licenses for which owner info was not resolved\n",
    "    print(\n",
    "        \"Licenses still missing Copyright Owners: \\n\",\n",
    "        manifest.loc[\n",
    "            manifest[\"copyright_owner\"].isna(), \"license_name\"\n",
    "        ].value_counts(),\n",
    "    )\n",
    "\n",
    "    # Fill null \"copyright_owner\" and \"Title\" values with \"not provided\"\n",
    "    manifest[\"copyright_owner\"].fillna(\"not provided\", inplace=True)\n",
    "    manifest[\"title\"].fillna(\"not provided\", inplace=True)\n",
    "\n",
    "    return manifest\n",
    "\n",
    "\n",
    "def update_owners(manifest, owners):\n",
    "    \"\"\"\n",
    "    Function to fetch and attach the missing owner and title information to EOL catalog entries and save catalog-media file.\n",
    "    Parameters:\n",
    "    -----------\n",
    "    manifest - rs_full_manifest_unique.\n",
    "    owners - DataFrame of July 26, 2023 media manifest entries that had missing owners, updated with their information.\n",
    "    \"\"\"\n",
    "    # Need combined IDs for the owner match file\n",
    "    # EOL content & page IDs read in as int64\n",
    "    owners[\"combined_id_owner\"] = owners[\"EOL content ID\"].astype(str) + \"_\" + owners[\"EOL page ID\"].astype(str)\n",
    "\n",
    "    updated_manifest = get_owners_titles(manifest, owners)\n",
    "\n",
    "    return updated_manifest"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [],
   "source": [
    "owner_df = pd.read_csv(\"../data/media_manifest_missing_licenses_jul26_owners.csv\",\n",
    "                        low_memory = False,\n",
    "                        dtype={\"EOL content ID\": \"int64\", \"EOL page ID\": \"int64\"},)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|          | 0/3188 [00:00<?, ?it/s]/var/folders/nv/f0fq1p1n1_3b11x579py_0q80000gq/T/ipykernel_11036/1896888662.py:25: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame.\n",
      "Try using .loc[row_indexer,col_indexer] = value instead\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  manifest.loc[manifest[\"combined_id\"] == comb_id, \"title\"] = title\n",
      "100%|██████████| 3188/3188 [01:03<00:00, 50.47it/s]\n",
      "/var/folders/nv/f0fq1p1n1_3b11x579py_0q80000gq/T/ipykernel_11036/1896888662.py:36: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  manifest[\"copyright_owner\"].fillna(\"not provided\", inplace=True)\n",
      "/var/folders/nv/f0fq1p1n1_3b11x579py_0q80000gq/T/ipykernel_11036/1896888662.py:37: SettingWithCopyWarning: \n",
      "A value is trying to be set on a copy of a slice from a DataFrame\n",
      "\n",
      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
      "  manifest[\"title\"].fillna(\"not provided\", inplace=True)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Licenses still missing Copyright Owners: \n",
      " Series([], Name: count, dtype: int64)\n",
      "<class 'pandas.core.frame.DataFrame'>\n",
      "Index: 22146 entries, 0 to 25513\n",
      "Data columns (total 11 columns):\n",
      " #   Column                  Non-Null Count  Dtype \n",
      "---  ------                  --------------  ----- \n",
      " 0   filename                22146 non-null  object\n",
      " 1   md5                     22146 non-null  object\n",
      " 2   combined_id             22146 non-null  object\n",
      " 3   eol_content_id          22146 non-null  int64 \n",
      " 4   eol_page_id             22146 non-null  int64 \n",
      " 5   medium_source_url       22146 non-null  object\n",
      " 6   eol_full_size_copy_url  22146 non-null  object\n",
      " 7   license_name            22146 non-null  object\n",
      " 8   copyright_owner         22146 non-null  object\n",
      " 9   duplicate_img           22146 non-null  bool  \n",
      " 10  title                   22146 non-null  object\n",
      "dtypes: bool(1), int64(2), object(8)\n",
      "memory usage: 1.9+ MB\n"
     ]
    }
   ],
   "source": [
    "complete_rs_manifest = update_owners(rs_full_manifest_unique, owner_df)\n",
    "complete_rs_manifest.info(show_counts = True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(0, 11)"
      ]
     },
     "execution_count": 31,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "complete_rs_manifest.loc[complete_rs_manifest[\"copyright_owner\"] == \"not provided\"].shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "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>filename</th>\n",
       "      <th>md5</th>\n",
       "      <th>combined_id</th>\n",
       "      <th>eol_content_id</th>\n",
       "      <th>eol_page_id</th>\n",
       "      <th>medium_source_url</th>\n",
       "      <th>eol_full_size_copy_url</th>\n",
       "      <th>license_name</th>\n",
       "      <th>copyright_owner</th>\n",
       "      <th>duplicate_img</th>\n",
       "      <th>title</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>1371</th>\n",
       "      <td>30052484_308387_eol-full-size-copy.jpg</td>\n",
       "      <td>39bea196c9335a93a937327f04e58729</td>\n",
       "      <td>30052484_308387</td>\n",
       "      <td>30052484</td>\n",
       "      <td>308387</td>\n",
       "      <td>https://upload.wikimedia.org/wikipedia/commons...</td>\n",
       "      <td>https://content.eol.org/data/media/64/58/c6/50...</td>\n",
       "      <td>cc-by-sa-3.0</td>\n",
       "      <td>['BotMultichillT']</td>\n",
       "      <td>False</td>\n",
       "      <td>['Okapia johnstoni5.jpg']</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2524</th>\n",
       "      <td>29389820_1179513_eol-full-size-copy.jpg</td>\n",
       "      <td>ad70ce70b54302f80a78035e52c5552c</td>\n",
       "      <td>29389820_1179513</td>\n",
       "      <td>29389820</td>\n",
       "      <td>1179513</td>\n",
       "      <td>https://upload.wikimedia.org/wikipedia/commons...</td>\n",
       "      <td>https://content.eol.org/data/media/67/ce/e1/50...</td>\n",
       "      <td>cc-by-sa-3.0</td>\n",
       "      <td>Vera Buhl</td>\n",
       "      <td>False</td>\n",
       "      <td>not provided</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4327</th>\n",
       "      <td>28221214_45276460_eol-full-size-copy.jpg</td>\n",
       "      <td>d0188bee1b8e37f0e590221e37aeb8bf</td>\n",
       "      <td>28221214_45276460</td>\n",
       "      <td>28221214</td>\n",
       "      <td>45276460</td>\n",
       "      <td>http://n2t.net/ark:/65665/m3ae98ac6e-dd63-48bf...</td>\n",
       "      <td>https://content.eol.org/data/media/15/8b/b0/53...</td>\n",
       "      <td>cc-0-1.0</td>\n",
       "      <td>['Smithsonian Institution, NMNH, Invertebrate ...</td>\n",
       "      <td>False</td>\n",
       "      <td>['IZ COE 86556 whole colony top view']</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14687</th>\n",
       "      <td>14681519_403723_eol-full-size-copy.jpg</td>\n",
       "      <td>d1851dd3f010c509f719e044b8826dc9</td>\n",
       "      <td>14681519_403723</td>\n",
       "      <td>14681519</td>\n",
       "      <td>403723</td>\n",
       "      <td>https://www.antweb.org/images/casent0901314/ca...</td>\n",
       "      <td>https://content.eol.org/data/media/bf/35/96/16...</td>\n",
       "      <td>cc-by-nc-sa-4.0</td>\n",
       "      <td>California Academy of Sciences</td>\n",
       "      <td>False</td>\n",
       "      <td>not provided</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5319</th>\n",
       "      <td>29844429_45511531_eol-full-size-copy.jpg</td>\n",
       "      <td>0ea23bac2d7369f18bf14a78abf3e3e7</td>\n",
       "      <td>29844429_45511531</td>\n",
       "      <td>29844429</td>\n",
       "      <td>45511531</td>\n",
       "      <td>https://upload.wikimedia.org/wikipedia/commons...</td>\n",
       "      <td>https://content.eol.org/data/media/5f/35/51/50...</td>\n",
       "      <td>cc-by-sa-3.0</td>\n",
       "      <td>Alastair Rae</td>\n",
       "      <td>False</td>\n",
       "      <td>not provided</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10776</th>\n",
       "      <td>28913280_330971_eol-full-size-copy.jpg</td>\n",
       "      <td>f585a0ebce3aec60d30fb545ceedfe46</td>\n",
       "      <td>28913280_330971</td>\n",
       "      <td>28913280</td>\n",
       "      <td>330971</td>\n",
       "      <td>https://upload.wikimedia.org/wikipedia/commons...</td>\n",
       "      <td>https://content.eol.org/data/media/5f/ad/6c/50...</td>\n",
       "      <td>cc-by-sa-3.0</td>\n",
       "      <td>Stéphanie Bret</td>\n",
       "      <td>False</td>\n",
       "      <td>not provided</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22845</th>\n",
       "      <td>14053938_336170_eol-full-size-copy.jpg</td>\n",
       "      <td>2a652f57ca3b7dd4e7ad73ab6aef57fd</td>\n",
       "      <td>14053938_336170</td>\n",
       "      <td>14053938</td>\n",
       "      <td>336170</td>\n",
       "      <td>https://live.staticflickr.com/6045/6274545363_...</td>\n",
       "      <td>https://content.eol.org/data/media/d8/8f/86/54...</td>\n",
       "      <td>cc-by</td>\n",
       "      <td>Brian Gratwicke</td>\n",
       "      <td>False</td>\n",
       "      <td>not provided</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                       filename  \\\n",
       "1371     30052484_308387_eol-full-size-copy.jpg   \n",
       "2524    29389820_1179513_eol-full-size-copy.jpg   \n",
       "4327   28221214_45276460_eol-full-size-copy.jpg   \n",
       "14687    14681519_403723_eol-full-size-copy.jpg   \n",
       "5319   29844429_45511531_eol-full-size-copy.jpg   \n",
       "10776    28913280_330971_eol-full-size-copy.jpg   \n",
       "22845    14053938_336170_eol-full-size-copy.jpg   \n",
       "\n",
       "                                    md5        combined_id  eol_content_id  \\\n",
       "1371   39bea196c9335a93a937327f04e58729    30052484_308387        30052484   \n",
       "2524   ad70ce70b54302f80a78035e52c5552c   29389820_1179513        29389820   \n",
       "4327   d0188bee1b8e37f0e590221e37aeb8bf  28221214_45276460        28221214   \n",
       "14687  d1851dd3f010c509f719e044b8826dc9    14681519_403723        14681519   \n",
       "5319   0ea23bac2d7369f18bf14a78abf3e3e7  29844429_45511531        29844429   \n",
       "10776  f585a0ebce3aec60d30fb545ceedfe46    28913280_330971        28913280   \n",
       "22845  2a652f57ca3b7dd4e7ad73ab6aef57fd    14053938_336170        14053938   \n",
       "\n",
       "       eol_page_id                                  medium_source_url  \\\n",
       "1371        308387  https://upload.wikimedia.org/wikipedia/commons...   \n",
       "2524       1179513  https://upload.wikimedia.org/wikipedia/commons...   \n",
       "4327      45276460  http://n2t.net/ark:/65665/m3ae98ac6e-dd63-48bf...   \n",
       "14687       403723  https://www.antweb.org/images/casent0901314/ca...   \n",
       "5319      45511531  https://upload.wikimedia.org/wikipedia/commons...   \n",
       "10776       330971  https://upload.wikimedia.org/wikipedia/commons...   \n",
       "22845       336170  https://live.staticflickr.com/6045/6274545363_...   \n",
       "\n",
       "                                  eol_full_size_copy_url     license_name  \\\n",
       "1371   https://content.eol.org/data/media/64/58/c6/50...     cc-by-sa-3.0   \n",
       "2524   https://content.eol.org/data/media/67/ce/e1/50...     cc-by-sa-3.0   \n",
       "4327   https://content.eol.org/data/media/15/8b/b0/53...         cc-0-1.0   \n",
       "14687  https://content.eol.org/data/media/bf/35/96/16...  cc-by-nc-sa-4.0   \n",
       "5319   https://content.eol.org/data/media/5f/35/51/50...     cc-by-sa-3.0   \n",
       "10776  https://content.eol.org/data/media/5f/ad/6c/50...     cc-by-sa-3.0   \n",
       "22845  https://content.eol.org/data/media/d8/8f/86/54...            cc-by   \n",
       "\n",
       "                                         copyright_owner  duplicate_img  \\\n",
       "1371                                  ['BotMultichillT']          False   \n",
       "2524                                           Vera Buhl          False   \n",
       "4327   ['Smithsonian Institution, NMNH, Invertebrate ...          False   \n",
       "14687                     California Academy of Sciences          False   \n",
       "5319                                        Alastair Rae          False   \n",
       "10776                                     Stéphanie Bret          False   \n",
       "22845                                    Brian Gratwicke          False   \n",
       "\n",
       "                                        title  \n",
       "1371                ['Okapia johnstoni5.jpg']  \n",
       "2524                             not provided  \n",
       "4327   ['IZ COE 86556 whole colony top view']  \n",
       "14687                            not provided  \n",
       "5319                             not provided  \n",
       "10776                            not provided  \n",
       "22845                            not provided  "
      ]
     },
     "execution_count": 32,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "complete_rs_manifest.sample(7)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(18958, 11)"
      ]
     },
     "execution_count": 33,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "complete_rs_manifest.loc[complete_rs_manifest[\"title\"] == \"not provided\"].shape"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Most don't have title, but they all have the copyright owner filled in. That's good!"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "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>filename</th>\n",
       "      <th>md5</th>\n",
       "      <th>combined_id</th>\n",
       "      <th>eol_content_id</th>\n",
       "      <th>eol_page_id</th>\n",
       "      <th>medium_source_url</th>\n",
       "      <th>eol_full_size_copy_url</th>\n",
       "      <th>license_name</th>\n",
       "      <th>copyright_owner</th>\n",
       "      <th>title</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>28493296_995017_eol-full-size-copy.jpg</td>\n",
       "      <td>e83ab9a6630f01099fee7effbd7b68a7</td>\n",
       "      <td>28493296_995017</td>\n",
       "      <td>28493296</td>\n",
       "      <td>995017</td>\n",
       "      <td>http://mczbase.mcz.harvard.edu/specimen_images...</td>\n",
       "      <td>https://content.eol.org/data/media/c7/b7/04/26...</td>\n",
       "      <td>cc-by-nc-sa-3.0</td>\n",
       "      <td>Museum of Comparative Zoology, Harvard University</td>\n",
       "      <td>not provided</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>21548284_1049155_eol-full-size-copy.jpg</td>\n",
       "      <td>90545b27c992f2fbcb0edb81fbf8c042</td>\n",
       "      <td>21548284_1049155</td>\n",
       "      <td>21548284</td>\n",
       "      <td>1049155</td>\n",
       "      <td>https://inaturalist-open-data.s3.amazonaws.com...</td>\n",
       "      <td>https://content.eol.org/data/media/58/f9/6d/18...</td>\n",
       "      <td>cc-by-nc-4.0</td>\n",
       "      <td>hickeldypickleldy</td>\n",
       "      <td>not provided</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                  filename                               md5  \\\n",
       "0   28493296_995017_eol-full-size-copy.jpg  e83ab9a6630f01099fee7effbd7b68a7   \n",
       "1  21548284_1049155_eol-full-size-copy.jpg  90545b27c992f2fbcb0edb81fbf8c042   \n",
       "\n",
       "        combined_id  eol_content_id  eol_page_id  \\\n",
       "0   28493296_995017        28493296       995017   \n",
       "1  21548284_1049155        21548284      1049155   \n",
       "\n",
       "                                   medium_source_url  \\\n",
       "0  http://mczbase.mcz.harvard.edu/specimen_images...   \n",
       "1  https://inaturalist-open-data.s3.amazonaws.com...   \n",
       "\n",
       "                              eol_full_size_copy_url     license_name  \\\n",
       "0  https://content.eol.org/data/media/c7/b7/04/26...  cc-by-nc-sa-3.0   \n",
       "1  https://content.eol.org/data/media/58/f9/6d/18...     cc-by-nc-4.0   \n",
       "\n",
       "                                     copyright_owner         title  \n",
       "0  Museum of Comparative Zoology, Harvard University  not provided  \n",
       "1                                  hickeldypickleldy  not provided  "
      ]
     },
     "execution_count": 34,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cols = [col for col in list(complete_rs_manifest.columns) if col != \"duplicate_img\"]\n",
    "complete_rs_manifest = complete_rs_manifest[cols]\n",
    "complete_rs_manifest.head(2)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Add License URL Column for Completeness"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [],
   "source": [
    "CC_URL = \"https://creativecommons.org/\"\n",
    "\n",
    "\n",
    "def get_license_url(license_version):\n",
    "    \"\"\"\n",
    "    Function to generate the appropriate Creative Commons URL for a given license.\n",
    "    All licenses in the media manifest are \"cc-XX\", a variation on \"publicdomain\", or \"No known copyright restrictions\".\n",
    "\n",
    "    Parameters:\n",
    "    -----------\n",
    "    license_version - String. License (eg., \"cc-by-nc 3.0\").\n",
    "\n",
    "    Returns:\n",
    "    --------\n",
    "    license_url - String. Creative Commons URL associated with the license_version.\n",
    "\n",
    "    \"\"\"\n",
    "    # First check for version number and isolate it\n",
    "    if \".\" in license_version:\n",
    "        version = license_version.split(sep=\"-\")[-1]\n",
    "        license_name = license_version.split(sep=\"-\" + version)[0]\n",
    "    else:\n",
    "        # No version specified, so default to latest version (4.0)\n",
    "        license_name = license_version\n",
    "        version = \"4.0\"\n",
    "    # Check which type of license\n",
    "    if license_name[:5] == \"cc-by\":\n",
    "        by_x = license_name.split(sep=\"cc-\")[1]\n",
    "        license_url = CC_URL + \"licenses/\" + by_x + \"/\" + version\n",
    "    elif (license_name[:4] == \"cc-0\") or (\"public\" in license_name):\n",
    "        license_url = CC_URL + \"publicdomain/zero/1.0\"\n",
    "    else:\n",
    "        # \"No known copyright restrictions\"\n",
    "        license_url = None\n",
    "    return license_url\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [],
   "source": [
    "license_col = \"license_name\"\n",
    "complete_rs_manifest[\"license_link\"] = complete_rs_manifest[license_col].apply(get_license_url)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<class 'pandas.core.frame.DataFrame'>\n",
      "Index: 22146 entries, 0 to 25513\n",
      "Data columns (total 11 columns):\n",
      " #   Column                  Non-Null Count  Dtype \n",
      "---  ------                  --------------  ----- \n",
      " 0   filename                22146 non-null  object\n",
      " 1   md5                     22146 non-null  object\n",
      " 2   combined_id             22146 non-null  object\n",
      " 3   eol_content_id          22146 non-null  int64 \n",
      " 4   eol_page_id             22146 non-null  int64 \n",
      " 5   medium_source_url       22146 non-null  object\n",
      " 6   eol_full_size_copy_url  22146 non-null  object\n",
      " 7   license_name            22146 non-null  object\n",
      " 8   copyright_owner         22146 non-null  object\n",
      " 9   title                   22146 non-null  object\n",
      " 10  license_link            22103 non-null  object\n",
      "dtypes: int64(2), object(9)\n",
      "memory usage: 2.0+ MB\n"
     ]
    }
   ],
   "source": [
    "complete_rs_manifest.info(show_counts=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Licenses with no URL: \n",
      " license_name\n",
      "No known copyright restrictions    43\n",
      "Name: count, dtype: int64\n"
     ]
    }
   ],
   "source": [
    "print(\n",
    "        \"Licenses with no URL: \\n\",\n",
    "        complete_rs_manifest.loc[complete_rs_manifest[\"license_link\"].isna(), license_col].value_counts(),\n",
    "    )"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "As expected, we're good to save this full Rare Species manifest now."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {},
   "outputs": [],
   "source": [
    "complete_rs_manifest.to_csv(\"../data/rarespecies_full_manifest.csv\", index = False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "jupytext": {
   "formats": "ipynb,py:percent"
  },
  "kernelspec": {
   "display_name": "tol",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.11.3"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}