{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "TOL_FILEPATH = \"../../data/\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Read in Links CSV files\n",
    "\n",
    "Full cargo archives have some more content than the [original `links_inner` file](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/fa08e0f6692a013e4e4f5ca30dd0e8883c0021d8/eol_realign/data/links_inner.csv) and 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).\n",
    "\n",
    "From Matt:\n",
    "> It represents a series of inner merges:\n",
    "> 1. The list of images in the EOL cargo archive (used to create the webdatasets) with the EOL portion of `catalog.csv`\n",
    ">  - Merged on a combined identifier of `eol_content_id` and `eol_page_id`.\n",
    "> Result from 1) with the list of images redownloaded from all 3 media manifests we touched around the original download time (identified [here](https://huggingface.co/datasets/imageomics/ToL-EDA/discussions/5#6584808d92eba5ad69b8379f)).\n",
    ">  - Merged on MD5\n",
    ">\n",
    "> The result has 6,219,674 unique `treeoflife_id` entries and 6,146,917 unique `md5` entries. It has the combined `eol_content_id` and `eol_page_id` identifiers used at each stage:\n",
    "- `combined_id_catalog`: represents what's in the original catalog \n",
    "- `combined_id_manifest_full_manifest`: represents what's in the combined manifest from all 3 dates \n",
    "> It also has an indicator of which of the three media manifest files each entry was present in (one or more) in columns representing retreival date (eg., `source_0706`: indicates if it was present in the manifest retrieved on July 6, 2023). It also has the copyright owner and license information as contained in the media manifest files.\n",
    ">\n",
    "> Still needs to be run through the owner name finding code. ([owner_match](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/71ad5b49226a3a49634931005eeb340b3c96db13/scripts/match_owners.py) --note: this version uses inner merges, so will remove entries without media info. Probably should adjust this.)\n",
    "\n",
    "For reference on the numbers, there are 6,250,420 EOL images in TreeOfLife-10M (the catalog). Comparing with `links_inner` previously (from [`links_inner.csv`](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/fa08e0f6692a013e4e4f5ca30dd0e8883c0021d8/eol_realign/data/links_inner.csv)) we were missing 31,376 images, 29 of which were identified in [`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_inner = pd.read_csv(\"../data/eol-cargo-archive_catalog_combined-manifest-checksums_links.csv\", low_memory=False)\n",
    "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: 6841202 entries, 0 to 6841201\n",
      "Data columns (total 30 columns):\n",
      " #   Column                           Non-Null Count    Dtype  \n",
      "---  ------                           --------------    -----  \n",
      " 0   filename_archive                 6841202 non-null  object \n",
      " 1   md5                              6841202 non-null  object \n",
      " 2   combined_id_archive              6841202 non-null  object \n",
      " 3   split                            6841202 non-null  object \n",
      " 4   treeoflife_id                    6841202 non-null  object \n",
      " 5   bioscan_part                     0 non-null        float64\n",
      " 6   bioscan_filename                 0 non-null        float64\n",
      " 7   inat21_filename                  0 non-null        float64\n",
      " 8   inat21_cls_name                  0 non-null        float64\n",
      " 9   inat21_cls_num                   0 non-null        float64\n",
      " 10  kingdom                          6551473 non-null  object \n",
      " 11  phylum                           6553206 non-null  object \n",
      " 12  class                            6532009 non-null  object \n",
      " 13  order                            6525621 non-null  object \n",
      " 14  family                           6506076 non-null  object \n",
      " 15  genus                            6486130 non-null  object \n",
      " 16  species                          6406307 non-null  object \n",
      " 17  common                           6841202 non-null  object \n",
      " 18  combined_id_catalog              6841202 non-null  object \n",
      " 19  filename_manifest                6841202 non-null  object \n",
      " 20  combined_id_manifest_redownload  6841202 non-null  object \n",
      " 21  medium_source_url                6841202 non-null  object \n",
      " 22  eol_full_size_copy_url           6841202 non-null  object \n",
      " 23  license_name                     6841202 non-null  object \n",
      " 24  copyright_owner                  6208498 non-null  object \n",
      " 25  expected_image_filename          6841202 non-null  object \n",
      " 26  source_0706                      6841202 non-null  bool   \n",
      " 27  source_0726                      6841202 non-null  bool   \n",
      " 28  source_1206                      6841202 non-null  bool   \n",
      " 29  combined_id_full_manifest        6841202 non-null  object \n",
      "dtypes: bool(3), float64(5), object(22)\n",
      "memory usage: 1.4+ GB\n"
     ]
    }
   ],
   "source": [
    "links_inner.info(show_counts=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "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": [
    "These both have about 600-700 more entries than the earlier files."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "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",
       "    </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]\n",
       "Index: []"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# These should be the same\n",
    "links_manifest_cargo.loc[links_manifest_cargo[\"combined_id_manifest_redownload\"] != links_manifest_cargo[\"combined_id_full_manifest\"]]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<class 'pandas.core.frame.DataFrame'>\n",
      "Index: 822558 entries, 2 to 7513999\n",
      "Data columns (total 17 columns):\n",
      " #   Column                           Non-Null Count   Dtype \n",
      "---  ------                           --------------   ----- \n",
      " 0   filename_archive                 822558 non-null  object\n",
      " 1   md5_archive                      822558 non-null  object\n",
      " 2   combined_id_archive              822558 non-null  object\n",
      " 3   filename_manifest                822558 non-null  object\n",
      " 4   md5_combined_manifest            822558 non-null  object\n",
      " 5   combined_id_manifest_redownload  822558 non-null  object\n",
      " 6   eol_content_id                   822558 non-null  int64 \n",
      " 7   eol_page_id                      822558 non-null  int64 \n",
      " 8   medium_source_url                822558 non-null  object\n",
      " 9   eol_full_size_copy_url           822558 non-null  object\n",
      " 10  license_name                     822558 non-null  object\n",
      " 11  copyright_owner                  797147 non-null  object\n",
      " 12  expected_image_filename          822558 non-null  object\n",
      " 13  source_0706                      822558 non-null  bool  \n",
      " 14  source_0726                      822558 non-null  bool  \n",
      " 15  source_1206                      822558 non-null  bool  \n",
      " 16  combined_id_full_manifest        822558 non-null  object\n",
      "dtypes: bool(3), int64(2), object(12)\n",
      "memory usage: 96.5+ MB\n"
     ]
    }
   ],
   "source": [
    "# archive has replaced cargo\n",
    "# full manifest or manifest redownload to replace manifest checksums -- they are equal\n",
    "links_mismatch = links_manifest_cargo.loc[links_manifest_cargo[\"combined_id_archive\"] != links_manifest_cargo[\"combined_id_full_manifest\"]]\n",
    "links_mismatch.info(show_counts = True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "There are 42 more mismatched entries. Only 13 additional unique images (MD5s)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "md5_archive                  624574\n",
       "combined_id_full_manifest    712540\n",
       "combined_id_archive          703446\n",
       "dtype: int64"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "links_mismatch[[\"md5_archive\", \"combined_id_full_manifest\", \"combined_id_archive\"]].nunique()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "# This is archive manifest mismatch\n",
    "links_mismatch.to_csv(\"../data/links_archive_manifest_IDmismatch.csv\", index = False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "catalog = pd.read_csv(TOL_FILEPATH + \"catalog.csv\", low_memory=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "# remove train_small and all non-EOL entries\n",
    "catalog = catalog.loc[catalog.split != \"train_small\"]\n",
    "eol_catalog = catalog.loc[catalog.eol_content_id.notna()]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "split                   2\n",
       "treeoflife_id     6250420\n",
       "eol_content_id    6250420\n",
       "eol_page_id        503589\n",
       "dtype: int64"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "eol_catalog[list(eol_catalog.columns)[:4]].nunique()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "eol_cols = [col for col in list(eol_catalog.columns) if \"bioscan\" not in col and \"inat\" not in col]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<class 'pandas.core.frame.DataFrame'>\n",
      "Index: 6250420 entries, 956715 to 11000930\n",
      "Data columns (total 12 columns):\n",
      " #   Column          Non-Null Count    Dtype  \n",
      "---  ------          --------------    -----  \n",
      " 0   split           6250420 non-null  object \n",
      " 1   treeoflife_id   6250420 non-null  object \n",
      " 2   eol_content_id  6250420 non-null  float64\n",
      " 3   eol_page_id     6250420 non-null  float64\n",
      " 4   kingdom         5989611 non-null  object \n",
      " 5   phylum          5991207 non-null  object \n",
      " 6   class           5971438 non-null  object \n",
      " 7   order           5965299 non-null  object \n",
      " 8   family          5948728 non-null  object \n",
      " 9   genus           5940313 non-null  object \n",
      " 10  species         5951613 non-null  object \n",
      " 11  common          6250420 non-null  object \n",
      "dtypes: float64(2), object(10)\n",
      "memory usage: 619.9+ MB\n"
     ]
    }
   ],
   "source": [
    "eol_catalog = eol_catalog[eol_cols]\n",
    "eol_catalog.info(show_counts=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Must recast IDs as `int64`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<class 'pandas.core.frame.DataFrame'>\n",
      "Index: 6250420 entries, 956715 to 11000930\n",
      "Data columns (total 4 columns):\n",
      " #   Column          Dtype \n",
      "---  ------          ----- \n",
      " 0   split           object\n",
      " 1   treeoflife_id   object\n",
      " 2   eol_content_id  int64 \n",
      " 3   eol_page_id     int64 \n",
      "dtypes: int64(2), object(2)\n",
      "memory usage: 238.4+ MB\n"
     ]
    }
   ],
   "source": [
    "eol_catalog = eol_catalog.astype({\"eol_content_id\": \"int64\", \"eol_page_id\": \"int64\"})\n",
    "eol_catalog[eol_cols[:4]].info()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
    "lines_to_next_cell": 2
   },
   "outputs": [],
   "source": [
    "# make combined ID for catalog and add suffix to eol content and page IDs\n",
    "eol_catalog['combined_id_catalog'] = eol_catalog['eol_content_id'].astype(str) + '_' + eol_catalog['eol_page_id'].astype(str)\n",
    "eol_catalog.rename(columns={'eol_content_id': 'eol_content_id_catalog', 'eol_page_id': 'eol_page_id_catalog'}, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "6219674"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "matched_catalog_ids = list(links_inner.combined_id_catalog.unique())\n",
    "len(matched_catalog_ids)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Here we go, we got an additional 630 matched IDs!"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['29538374_65414274',\n",
       " '27793900_888015',\n",
       " '29121641_5618956',\n",
       " '27596176_607817',\n",
       " '20300703_267922']"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "matched_catalog_ids[:5]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We still have about 30K unmatched (as shown below, it's down to 30,746 from 31,376), let's find those in the catalog and then we'll try to merge with our mismatched cargo & manifest."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "5842839       28875844_579175\n",
       "7715090       21712402_702458\n",
       "10112940     27938371_3091824\n",
       "8606944     27597441_49820955\n",
       "1247592      14852900_2896866\n",
       "Name: combined_id_catalog, dtype: object"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "eol_catalog['combined_id_catalog'].sample(5)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<class 'pandas.core.frame.DataFrame'>\n",
      "Index: 30746 entries, 956874 to 10996978\n",
      "Data columns (total 13 columns):\n",
      " #   Column                  Non-Null Count  Dtype \n",
      "---  ------                  --------------  ----- \n",
      " 0   split                   30746 non-null  object\n",
      " 1   treeoflife_id           30746 non-null  object\n",
      " 2   eol_content_id_catalog  30746 non-null  int64 \n",
      " 3   eol_page_id_catalog     30746 non-null  int64 \n",
      " 4   kingdom                 30573 non-null  object\n",
      " 5   phylum                  30578 non-null  object\n",
      " 6   class                   30153 non-null  object\n",
      " 7   order                   30528 non-null  object\n",
      " 8   family                  30294 non-null  object\n",
      " 9   genus                   30192 non-null  object\n",
      " 10  species                 29399 non-null  object\n",
      " 11  common                  30746 non-null  object\n",
      " 12  combined_id_catalog     30746 non-null  object\n",
      "dtypes: int64(2), object(11)\n",
      "memory usage: 3.3+ MB\n"
     ]
    }
   ],
   "source": [
    "mismatched_catalog = eol_catalog.loc[~eol_catalog[\"combined_id_catalog\"].isin(matched_catalog_ids)]\n",
    "mismatched_catalog.info(show_counts = True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "split                         2\n",
       "treeoflife_id             30746\n",
       "eol_content_id_catalog    30746\n",
       "eol_page_id_catalog        7042\n",
       "kingdom                       7\n",
       "phylum                       33\n",
       "class                        87\n",
       "order                       355\n",
       "family                     1165\n",
       "genus                      3503\n",
       "species                    5174\n",
       "common                     6884\n",
       "combined_id_catalog       30746\n",
       "dtype: int64"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mismatched_catalog.nunique()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Seems one class got resolved (equals more orders and down)."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Merge with Mismatched CargoArchive-Manifest\n",
    "\n",
    "let's merge with `links_mismatch` to see if the mismatched archive and manifest combined IDs can be linked up."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<class 'pandas.core.frame.DataFrame'>\n",
      "RangeIndex: 0 entries\n",
      "Data columns (total 30 columns):\n",
      " #   Column                           Non-Null Count  Dtype \n",
      "---  ------                           --------------  ----- \n",
      " 0   split                            0 non-null      object\n",
      " 1   treeoflife_id                    0 non-null      object\n",
      " 2   eol_content_id_catalog           0 non-null      int64 \n",
      " 3   eol_page_id_catalog              0 non-null      int64 \n",
      " 4   kingdom                          0 non-null      object\n",
      " 5   phylum                           0 non-null      object\n",
      " 6   class                            0 non-null      object\n",
      " 7   order                            0 non-null      object\n",
      " 8   family                           0 non-null      object\n",
      " 9   genus                            0 non-null      object\n",
      " 10  species                          0 non-null      object\n",
      " 11  common                           0 non-null      object\n",
      " 12  combined_id_catalog              0 non-null      object\n",
      " 13  filename_archive                 0 non-null      object\n",
      " 14  md5_archive                      0 non-null      object\n",
      " 15  combined_id_archive              0 non-null      object\n",
      " 16  filename_manifest                0 non-null      object\n",
      " 17  md5_combined_manifest            0 non-null      object\n",
      " 18  combined_id_manifest_redownload  0 non-null      object\n",
      " 19  eol_content_id                   0 non-null      int64 \n",
      " 20  eol_page_id                      0 non-null      int64 \n",
      " 21  medium_source_url                0 non-null      object\n",
      " 22  eol_full_size_copy_url           0 non-null      object\n",
      " 23  license_name                     0 non-null      object\n",
      " 24  copyright_owner                  0 non-null      object\n",
      " 25  expected_image_filename          0 non-null      object\n",
      " 26  source_0706                      0 non-null      bool  \n",
      " 27  source_0726                      0 non-null      bool  \n",
      " 28  source_1206                      0 non-null      bool  \n",
      " 29  combined_id_full_manifest        0 non-null      object\n",
      "dtypes: bool(3), int64(4), object(23)\n",
      "memory usage: 132.0+ bytes\n"
     ]
    }
   ],
   "source": [
    "# replace manifest checksums with full manifest as above\n",
    "links_catalog_mismatch = pd.merge(mismatched_catalog,\n",
    "                                  links_mismatch,\n",
    "                                  left_on = \"combined_id_catalog\",\n",
    "                                  right_on = \"combined_id_full_manifest\",\n",
    "                                  how = \"inner\")\n",
    "links_catalog_mismatch.info(show_counts = True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now there's no gain from the mismatch file, but that was only 29 images, so we've captured them from the archive (plus more!)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "2003559      15270321_240065\n",
       "8751466       29485627_17806\n",
       "4818957       27965287_35726\n",
       "8697796       9483753_328724\n",
       "1049389      9446784_5019858\n",
       "8364678      9467133_2925218\n",
       "5119903    28880812_10305215\n",
       "Name: combined_id_catalog, dtype: object"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mismatched_catalog.combined_id_catalog.sample(7)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "These pages are reasonably full too: [5660435](https://eol.org/pages/5660435)."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Final Catalog\n",
    "\n",
    "Our final EOL catalog is thus going to be the `treeoflife_id`s in `links_inner`.\n",
    "\n",
    "Finall question is just how does this look for our `train_small`?"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<class 'pandas.core.frame.DataFrame'>\n",
      "Index: 593764 entries, 0 to 918500\n",
      "Data columns (total 12 columns):\n",
      " #   Column          Non-Null Count   Dtype  \n",
      "---  ------          --------------   -----  \n",
      " 0   split           593764 non-null  object \n",
      " 1   treeoflife_id   593764 non-null  object \n",
      " 2   eol_content_id  593764 non-null  float64\n",
      " 3   eol_page_id     593764 non-null  float64\n",
      " 4   kingdom         569128 non-null  object \n",
      " 5   phylum          569285 non-null  object \n",
      " 6   class           567356 non-null  object \n",
      " 7   order           566839 non-null  object \n",
      " 8   family          565269 non-null  object \n",
      " 9   genus           564605 non-null  object \n",
      " 10  species         565399 non-null  object \n",
      " 11  common          593764 non-null  object \n",
      "dtypes: float64(2), object(10)\n",
      "memory usage: 58.9+ MB\n"
     ]
    }
   ],
   "source": [
    "cat_2 = pd.read_csv(TOL_FILEPATH + \"catalog.csv\", low_memory=False)\n",
    "\n",
    "# reduce to just train_small and all non-EOL entries\n",
    "cat_2 = cat_2.loc[cat_2.split == \"train_small\"]\n",
    "eol_cat_2 = cat_2.loc[cat_2.eol_content_id.notna()]\n",
    "\n",
    "eol_cat_2 = eol_cat_2[eol_cols]\n",
    "eol_cat_2.info(show_counts=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "So `train_small` has 593,764 images from EOL. \n",
    "\n",
    "Let's recast IDs as ints to match up with `links_inner` and check we have info for all of them."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<class 'pandas.core.frame.DataFrame'>\n",
      "Index: 593764 entries, 0 to 918500\n",
      "Data columns (total 4 columns):\n",
      " #   Column          Non-Null Count   Dtype \n",
      "---  ------          --------------   ----- \n",
      " 0   split           593764 non-null  object\n",
      " 1   treeoflife_id   593764 non-null  object\n",
      " 2   eol_content_id  593764 non-null  int64 \n",
      " 3   eol_page_id     593764 non-null  int64 \n",
      "dtypes: int64(2), object(2)\n",
      "memory usage: 22.7+ MB\n"
     ]
    }
   ],
   "source": [
    "eol_cat_2 = eol_cat_2.astype({\"eol_content_id\": \"int64\", \"eol_page_id\": \"int64\"})\n",
    "eol_cat_2[eol_cols[:4]].info()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {},
   "outputs": [],
   "source": [
    "# make combined ID for catalog and add suffix to eol content and page IDs\n",
    "eol_cat_2['combined_id_catalog'] = eol_cat_2['eol_content_id'].astype(str) + '_' + eol_cat_2['eol_page_id'].astype(str)\n",
    "eol_cat_2.rename(columns={'eol_content_id': 'eol_content_id_catalog', 'eol_page_id': 'eol_page_id_catalog'}, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<class 'pandas.core.frame.DataFrame'>\n",
      "RangeIndex: 612614 entries, 0 to 612613\n",
      "Data columns (total 25 columns):\n",
      " #   Column                           Non-Null Count   Dtype \n",
      "---  ------                           --------------   ----- \n",
      " 0   split                            612614 non-null  object\n",
      " 1   treeoflife_id                    612614 non-null  object\n",
      " 2   eol_content_id_catalog           612614 non-null  int64 \n",
      " 3   eol_page_id_catalog              612614 non-null  int64 \n",
      " 4   kingdom                          584979 non-null  object\n",
      " 5   phylum                           585140 non-null  object\n",
      " 6   class                            583235 non-null  object\n",
      " 7   order                            582668 non-null  object\n",
      " 8   family                           581082 non-null  object\n",
      " 9   genus                            580464 non-null  object\n",
      " 10  species                          579943 non-null  object\n",
      " 11  common                           612614 non-null  object\n",
      " 12  combined_id_catalog_x            612614 non-null  object\n",
      " 13  combined_id_catalog_y            612614 non-null  object\n",
      " 14  filename_manifest                612614 non-null  object\n",
      " 15  combined_id_manifest_redownload  612614 non-null  object\n",
      " 16  medium_source_url                612614 non-null  object\n",
      " 17  eol_full_size_copy_url           612614 non-null  object\n",
      " 18  license_name                     612614 non-null  object\n",
      " 19  copyright_owner                  554029 non-null  object\n",
      " 20  expected_image_filename          612614 non-null  object\n",
      " 21  source_0706                      612614 non-null  bool  \n",
      " 22  source_0726                      612614 non-null  bool  \n",
      " 23  source_1206                      612614 non-null  bool  \n",
      " 24  combined_id_full_manifest        612614 non-null  object\n",
      "dtypes: bool(3), int64(2), object(20)\n",
      "memory usage: 104.6+ MB\n"
     ]
    }
   ],
   "source": [
    "eol_ts_links = pd.merge(eol_cat_2,\n",
    "                        links_inner[list(links_inner.columns)[18:]],\n",
    "                        left_on = \"combined_id_catalog\",\n",
    "                        right_on = \"combined_id_full_manifest\",\n",
    "                        how = \"inner\")\n",
    "eol_ts_links.info(show_counts = True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "590730"
      ]
     },
     "execution_count": 41,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "eol_ts_links.treeoflife_id.nunique()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "So we are missing the metadata for 3,734 of these images."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Check on Rare Species Catalog"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "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(\"../../rare_species/data/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": 26,
   "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": 27,
   "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\", # looking at archive\n",
    "                    how = \"inner\")\n",
    "rs_links.info(show_counts = True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "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": 28,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rs_links.nunique()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Let's check the mismatched cargo/manifest entries for those last 174..."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "11826"
      ]
     },
     "execution_count": 29,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "matched_rs_ids = list(rs_links.combined_id_rs.unique())\n",
    "len(matched_rs_ids)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['22519448_914532',\n",
       " '28677580_1057176',\n",
       " '20714475_47047909',\n",
       " '29975068_45509269']"
      ]
     },
     "execution_count": 30,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "matched_rs_ids[:4]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "1473     29538601_46580048\n",
       "11127     29447084_1019571\n",
       "6578       20398296_328017\n",
       "11583     29772112_1049135\n",
       "Name: combined_id_rs, dtype: object"
      ]
     },
     "execution_count": 31,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rs_catalog[\"combined_id_rs\"].sample(4)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "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": 33,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<class 'pandas.core.frame.DataFrame'>\n",
      "RangeIndex: 0 entries\n",
      "Data columns (total 29 columns):\n",
      " #   Column                           Non-Null Count  Dtype \n",
      "---  ------                           --------------  ----- \n",
      " 0   rarespecies_id                   0 non-null      object\n",
      " 1   eol_content_id_rs                0 non-null      int64 \n",
      " 2   eol_page_id_rs                   0 non-null      int64 \n",
      " 3   kingdom                          0 non-null      object\n",
      " 4   phylum                           0 non-null      object\n",
      " 5   class                            0 non-null      object\n",
      " 6   order                            0 non-null      object\n",
      " 7   family                           0 non-null      object\n",
      " 8   genus                            0 non-null      object\n",
      " 9   species                          0 non-null      object\n",
      " 10  sciName                          0 non-null      object\n",
      " 11  combined_id_rs                   0 non-null      object\n",
      " 12  filename_archive                 0 non-null      object\n",
      " 13  md5_archive                      0 non-null      object\n",
      " 14  combined_id_archive              0 non-null      object\n",
      " 15  filename_manifest                0 non-null      object\n",
      " 16  md5_combined_manifest            0 non-null      object\n",
      " 17  combined_id_manifest_redownload  0 non-null      object\n",
      " 18  eol_content_id                   0 non-null      int64 \n",
      " 19  eol_page_id                      0 non-null      int64 \n",
      " 20  medium_source_url                0 non-null      object\n",
      " 21  eol_full_size_copy_url           0 non-null      object\n",
      " 22  license_name                     0 non-null      object\n",
      " 23  copyright_owner                  0 non-null      object\n",
      " 24  expected_image_filename          0 non-null      object\n",
      " 25  source_0706                      0 non-null      bool  \n",
      " 26  source_0726                      0 non-null      bool  \n",
      " 27  source_1206                      0 non-null      bool  \n",
      " 28  combined_id_full_manifest        0 non-null      object\n",
      "dtypes: bool(3), int64(4), object(22)\n",
      "memory usage: 132.0+ bytes\n"
     ]
    }
   ],
   "source": [
    "links_rs_mismatch = pd.merge(mismatched_rs,\n",
    "                             links_mismatch,\n",
    "                             left_on = \"combined_id_rs\",\n",
    "                             right_on = \"combined_id_full_manifest\",\n",
    "                             how = \"inner\")\n",
    "links_rs_mismatch.info(show_counts = True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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