Update catalog for TreeOfLife-10M

Catalog with all entries we could realign, corresponding license file, and manifest with full information for the realigned entries.

.gitattributes

@@ -74,3 +74,4 @@ eol_realign/data/full_owner_manifest.csv filter=lfs diff=lfs merge=lfs -text
 rare_species/data/rarespecies-catalog.csv filter=lfs diff=lfs merge=lfs -text
 eol_realign/data/combined_manifest.csv filter=lfs diff=lfs merge=lfs -text
 eol_realign/data/combined-manifest-licenses.csv filter=lfs diff=lfs merge=lfs -text
+data/licenses.csv filter=lfs diff=lfs merge=lfs -text

data/catalog.csv

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:ef5edf6a6e6048c98e74787cc143981095efaa27ba0aa4cebbac8116b24c9735
-size 2024176607
+oid sha256:215d0080ebf9016e0f471aa037b4201b5a611c2675c85dfec02a23dae03bbaee
+size 2043627688

data/licenses.csv

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:0486ac72f6c2654913bf81b187b34c466a6e13ef8db036b583c286bb9845e2f4
+size 2216478840

eol_realign/data/full_owner_manifest.csv

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:fefc8cf285771ca37febd6817da856bb592e356c80a9e0ec6f4a76d53f1866f8
-size 4871898541
+oid sha256:0961941b5fcae87f2a4dfacb7d7c29c64d5ef95679c62d16a46fa54d6c0a0f77
+size 3208683463

eol_realign/notebooks/re-gen_tol_catalog.ipynb

@@ -0,0 +1,926 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pandas as pd"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "TOL_FILEPATH = \"../../data/\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Read in Complete EOL TreeOfLife-10M Manifest\n",
+    "\n",
+    "[`combined-manifest-licenses.csv`](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/48af9b74b7a05a03b9a807a5b7b591fbf574eaec/eol_realign/data/combined-manifest-licenses.csv) is [`eol-cargo-archive_catalog_combined-manifest-checksums_links.csv`](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/48af9b74b7a05a03b9a807a5b7b591fbf574eaec/eol_realign/data/eol-cargo-archive_catalog_combined-manifest-checksums_links.csv) run through the `owner_match` and `make_licenses` scripts."
+   ]
+  },
+  {
+   "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 32 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                  6841202 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",
+      " 30  title                            6841202 non-null  object \n",
+      " 31  license_link                     6809751 non-null  object \n",
+      "dtypes: bool(3), float64(5), object(24)\n",
+      "memory usage: 1.5+ GB\n"
+     ]
+    }
+   ],
+   "source": [
+    "manifest = pd.read_csv(\"../data/combined-manifest-licenses.csv\",\n",
+    "                          low_memory=False,\n",
+    "                          dtype = {\"eol_content_id\": \"int64\", \"eol_page_id\": \"int64\"})\n",
+    "manifest.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "treeoflife_id                6219674\n",
+       "md5                          6146917\n",
+       "filename_archive             6219674\n",
+       "filename_manifest            6608194\n",
+       "expected_image_filename      6608194\n",
+       "combined_id_full_manifest    6608194\n",
+       "dtype: int64"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "manifest[[\"treeoflife_id\", \"md5\", \"filename_archive\", \"filename_manifest\",\"expected_image_filename\", \"combined_id_full_manifest\"]].nunique()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Read in TreeOfLife-10M Catalog"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Note that we will use [`catalog`](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/main/data/catalog.csv) from v3.3 EDA update [commit](https://huggingface.co/datasets/imageomics/ToL-EDA/commit/5260e84802d2910eedc2a206e7be035cf28f64d4). This is the version reported in the paper and in visualizations that will be included with the initial dataset publication; the patch will have updated visuals to match with this version.\n",
+    "(renamed locally to `catalog-orig-v3-3.csv`)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 11021779 entries, 0 to 11021778\n",
+      "Data columns (total 17 columns):\n",
+      " #   Column            Non-Null Count     Dtype  \n",
+      "---  ------            --------------     -----  \n",
+      " 0   split             11021779 non-null  object \n",
+      " 1   treeoflife_id     11021779 non-null  object \n",
+      " 2   eol_content_id    6844184 non-null   float64\n",
+      " 3   eol_page_id       6844184 non-null   float64\n",
+      " 4   bioscan_part      1235502 non-null   float64\n",
+      " 5   bioscan_filename  1235502 non-null   object \n",
+      " 6   inat21_filename   2942093 non-null   object \n",
+      " 7   inat21_cls_name   2942093 non-null   object \n",
+      " 8   inat21_cls_num    2942093 non-null   float64\n",
+      " 9   kingdom           10736334 non-null  object \n",
+      " 10  phylum            10738087 non-null  object \n",
+      " 11  class             10716389 non-null  object \n",
+      " 12  order             10709733 non-null  object \n",
+      " 13  family            10674746 non-null  object \n",
+      " 14  genus             9725443 non-null   object \n",
+      " 15  species           9551602 non-null   object \n",
+      " 16  common            11021779 non-null  object \n",
+      "dtypes: float64(4), object(13)\n",
+      "memory usage: 1.4+ GB\n"
+     ]
+    }
+   ],
+   "source": [
+    "catalog_orig = pd.read_csv(TOL_FILEPATH + \"catalog-orig-v3-3.csv\",\n",
+    "                         low_memory=False\n",
+    "                         )\n",
+    "catalog_orig.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Separate out the EOL portion from the BIOSCAN & iNat21 portion, that way we can merge the EOL part with the manifest (requires casting the EOL content & page IDs to `int64` and combining them with an underscore to merge on the `combined_id_full_manifest`) to get the licenses and create a clear `ToL_manifest` like with rarespecies. Then we can concatenate the adjusted EOL portion with the BIOSCAN & iNat21 portion to reconstruct the catalog."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# EOL portion of the catalog\n",
+    "eol_catalog = catalog_orig.loc[catalog_orig[\"eol_content_id\"].notna()]\n",
+    "\n",
+    "# BIOSCAN & iNat portion of the catalog\n",
+    "bin_catalog = catalog_orig.loc[catalog_orig[\"eol_content_id\"].isna()]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Recast EOL content and page IDs as `int64` in combined ID generation. Need to leave them as they are for re-concatenating with the other portion of the catalog."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/var/folders/nv/f0fq1p1n1_3b11x579py_0q80000gq/T/ipykernel_59366/112309718.py:1: 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",
+      "  eol_catalog[\"combined_id_catalog\"] = eol_catalog[\"eol_content_id\"].astype(int).astype(str) + \"_\" + eol_catalog[\"eol_page_id\"].astype(int).astype(str)\n"
+     ]
+    },
+    {
+     "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>split</th>\n",
+       "      <th>treeoflife_id</th>\n",
+       "      <th>eol_content_id</th>\n",
+       "      <th>eol_page_id</th>\n",
+       "      <th>bioscan_part</th>\n",
+       "      <th>bioscan_filename</th>\n",
+       "      <th>inat21_filename</th>\n",
+       "      <th>inat21_cls_name</th>\n",
+       "      <th>inat21_cls_num</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>common</th>\n",
+       "      <th>combined_id_catalog</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>train_small</td>\n",
+       "      <td>a87c78c0-eb7c-45ee-9a98-681f61292d6b</td>\n",
+       "      <td>29586132.0</td>\n",
+       "      <td>65441690.0</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>Animalia</td>\n",
+       "      <td>Arthropoda</td>\n",
+       "      <td>Insecta</td>\n",
+       "      <td>Lepidoptera</td>\n",
+       "      <td>Nymphalidae</td>\n",
+       "      <td>Acraea</td>\n",
+       "      <td>terpsicore</td>\n",
+       "      <td>Tawny Coster</td>\n",
+       "      <td>29586132_65441690</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>train_small</td>\n",
+       "      <td>f8158395-d663-4f0f-b38d-1c6ecb16a8ca</td>\n",
+       "      <td>29811010.0</td>\n",
+       "      <td>45510040.0</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>Animalia</td>\n",
+       "      <td>Chordata</td>\n",
+       "      <td>Aves</td>\n",
+       "      <td>Passeriformes</td>\n",
+       "      <td>Pycnonotidae</td>\n",
+       "      <td>Pycnonotus</td>\n",
+       "      <td>cafer</td>\n",
+       "      <td>Red-vented Bulbul</td>\n",
+       "      <td>29811010_45510040</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>train_small</td>\n",
+       "      <td>63aab6e3-b01d-4259-be13-9dd41becaf29</td>\n",
+       "      <td>28563112.0</td>\n",
+       "      <td>736062.0</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>Animalia</td>\n",
+       "      <td>Arthropoda</td>\n",
+       "      <td>Insecta</td>\n",
+       "      <td>Diptera</td>\n",
+       "      <td>Empididae</td>\n",
+       "      <td>Rhamphomyia</td>\n",
+       "      <td>limbata</td>\n",
+       "      <td>Rhamphomyia limbata</td>\n",
+       "      <td>28563112_736062</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3</th>\n",
+       "      <td>train_small</td>\n",
+       "      <td>cf2d58e1-d504-489c-80dd-e99407f8c13d</td>\n",
+       "      <td>29002118.0</td>\n",
+       "      <td>349296.0</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>Animalia</td>\n",
+       "      <td>Arthropoda</td>\n",
+       "      <td>Insecta</td>\n",
+       "      <td>Lepidoptera</td>\n",
+       "      <td>Geometridae</td>\n",
+       "      <td>Exelis</td>\n",
+       "      <td>pyrolaria</td>\n",
+       "      <td>Fine Lined Gray</td>\n",
+       "      <td>29002118_349296</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "         split                         treeoflife_id  eol_content_id  \\\n",
+       "0  train_small  a87c78c0-eb7c-45ee-9a98-681f61292d6b      29586132.0   \n",
+       "1  train_small  f8158395-d663-4f0f-b38d-1c6ecb16a8ca      29811010.0   \n",
+       "2  train_small  63aab6e3-b01d-4259-be13-9dd41becaf29      28563112.0   \n",
+       "3  train_small  cf2d58e1-d504-489c-80dd-e99407f8c13d      29002118.0   \n",
+       "\n",
+       "   eol_page_id  bioscan_part bioscan_filename inat21_filename inat21_cls_name  \\\n",
+       "0   65441690.0           NaN              NaN             NaN             NaN   \n",
+       "1   45510040.0           NaN              NaN             NaN             NaN   \n",
+       "2     736062.0           NaN              NaN             NaN             NaN   \n",
+       "3     349296.0           NaN              NaN             NaN             NaN   \n",
+       "\n",
+       "   inat21_cls_num   kingdom      phylum    class          order        family  \\\n",
+       "0             NaN  Animalia  Arthropoda  Insecta    Lepidoptera   Nymphalidae   \n",
+       "1             NaN  Animalia    Chordata     Aves  Passeriformes  Pycnonotidae   \n",
+       "2             NaN  Animalia  Arthropoda  Insecta        Diptera     Empididae   \n",
+       "3             NaN  Animalia  Arthropoda  Insecta    Lepidoptera   Geometridae   \n",
+       "\n",
+       "         genus     species               common combined_id_catalog  \n",
+       "0       Acraea  terpsicore         Tawny Coster   29586132_65441690  \n",
+       "1   Pycnonotus       cafer    Red-vented Bulbul   29811010_45510040  \n",
+       "2  Rhamphomyia     limbata  Rhamphomyia limbata     28563112_736062  \n",
+       "3       Exelis   pyrolaria      Fine Lined Gray     29002118_349296  "
+      ]
+     },
+     "execution_count": 8,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "eol_catalog[\"combined_id_catalog\"] = eol_catalog[\"eol_content_id\"].astype(int).astype(str) + \"_\" + eol_catalog[\"eol_page_id\"].astype(int).astype(str)\n",
+    "eol_catalog.head(4)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Keep in mind, we will have some repeated entries due to the `train_small` split, so we will merge on just `split != \"train_small\"`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "train_val_eol_catalog = eol_catalog.loc[eol_catalog[\"split\"] != \"train_small\"]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "We should have 6250420 entries in our merge, minus the approximately 30K we couldn't match.\n"
+     ]
+    }
+   ],
+   "source": [
+    "print(f\"We should have {train_val_eol_catalog.shape[0]} entries in our merge, minus the approximately 30K we couldn't match.\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We should have 6,250,420 entries in our merge, minus the approximately 30K we couldn't match.. The expectation is that this will be 6,219,674 entries. Details on this expectation & the `train_small` implications can be found in [`eol_realign/notebooks/links_align_reduced.ipynb`](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/3438fe9a88c0f377a4d8ac4c6c0de796858a08ac/eol_realign/notebooks/links_align_reduced.ipynb)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Catalog Columns\n",
+    "id_cols = [\"treeoflife_id\", \"eol_content_id\", \"eol_page_id\", \"combined_id_catalog\"]\n",
+    "\n",
+    "# Manifest Columns\n",
+    "manifest_cols = [\"treeoflife_id\",\n",
+    "                \"md5\",\n",
+    "                \"medium_source_url\",\n",
+    "                \"eol_full_size_copy_url\",\n",
+    "                \"license_name\",\n",
+    "                \"copyright_owner\",\n",
+    "                \"license_link\",\n",
+    "                \"title\",\n",
+    "                \"filename_archive\",\n",
+    "                \"filename_manifest\",\n",
+    "                \"expected_image_filename\",\n",
+    "                \"combined_id_full_manifest\"]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 6841202 entries, 0 to 6841201\n",
+      "Data columns (total 15 columns):\n",
+      " #   Column                     Non-Null Count    Dtype  \n",
+      "---  ------                     --------------    -----  \n",
+      " 0   treeoflife_id              6841202 non-null  object \n",
+      " 1   eol_content_id             6841202 non-null  float64\n",
+      " 2   eol_page_id                6841202 non-null  float64\n",
+      " 3   combined_id_catalog        6841202 non-null  object \n",
+      " 4   md5                        6841202 non-null  object \n",
+      " 5   medium_source_url          6841202 non-null  object \n",
+      " 6   eol_full_size_copy_url     6841202 non-null  object \n",
+      " 7   license_name               6841202 non-null  object \n",
+      " 8   copyright_owner            6841202 non-null  object \n",
+      " 9   license_link               6809751 non-null  object \n",
+      " 10  title                      6841202 non-null  object \n",
+      " 11  filename_archive           6841202 non-null  object \n",
+      " 12  filename_manifest          6841202 non-null  object \n",
+      " 13  expected_image_filename    6841202 non-null  object \n",
+      " 14  combined_id_full_manifest  6841202 non-null  object \n",
+      "dtypes: float64(2), object(13)\n",
+      "memory usage: 782.9+ MB\n"
+     ]
+    }
+   ],
+   "source": [
+    "tol_manifest = pd.merge(train_val_eol_catalog[id_cols],\n",
+    "                        manifest[manifest_cols],\n",
+    "                        on = \"treeoflife_id\",\n",
+    "                        how = \"inner\")\n",
+    "tol_manifest.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "treeoflife_id                6219674\n",
+       "eol_content_id               6219674\n",
+       "eol_page_id                   501807\n",
+       "combined_id_catalog          6219674\n",
+       "md5                          6146917\n",
+       "medium_source_url            6217871\n",
+       "eol_full_size_copy_url       6247692\n",
+       "license_name                      16\n",
+       "copyright_owner               403215\n",
+       "license_link                      11\n",
+       "title                         482137\n",
+       "filename_archive             6219674\n",
+       "filename_manifest            6608194\n",
+       "expected_image_filename      6608194\n",
+       "combined_id_full_manifest    6608194\n",
+       "dtype: int64"
+      ]
+     },
+     "execution_count": 13,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "tol_manifest.nunique()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Let's reduce this down to just the unique `treeoflife_id`s. All URLs are valid and the EOL content and page IDs (plus `combined_id_catalog` will match the filenames we have saved)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "(6219674, 16)\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "treeoflife_id                6219674\n",
+       "eol_content_id               6219674\n",
+       "eol_page_id                   501807\n",
+       "combined_id_catalog          6219674\n",
+       "md5                          6146917\n",
+       "medium_source_url            6144920\n",
+       "eol_full_size_copy_url       6146917\n",
+       "license_name                      16\n",
+       "copyright_owner               398253\n",
+       "license_link                      11\n",
+       "title                         475702\n",
+       "filename_archive             6219674\n",
+       "filename_manifest            6146917\n",
+       "expected_image_filename      6146917\n",
+       "combined_id_full_manifest    6146917\n",
+       "duplicate_tol_id                   1\n",
+       "dtype: int64"
+      ]
+     },
+     "execution_count": 14,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "tol_manifest[\"duplicate_tol_id\"] = tol_manifest.duplicated(\"treeoflife_id\", keep = \"first\")\n",
+    "tol_manifest = tol_manifest.loc[~tol_manifest[\"duplicate_tol_id\"]]\n",
+    "\n",
+    "print(tol_manifest.shape)\n",
+    "tol_manifest.nunique()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Clearly, these match with the archive filenames.\n",
+    "\n",
+    "Our numbers match the expected count. Let's check our `copyright_owner` and `title` coverage. "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "license_name\n",
+       "No known copyright restrictions    7389\n",
+       "cc-by-nc-sa-3.0                    4247\n",
+       "cc-publicdomain                    3422\n",
+       "cc-by-nc                           3029\n",
+       "cc-by-3.0                           470\n",
+       "cc-by-sa-3.0                        171\n",
+       "cc-0-1.0                             32\n",
+       "cc-by-nc-2.0                          2\n",
+       "cc-by-nc-4.0                          1\n",
+       "Name: count, dtype: int64"
+      ]
+     },
+     "execution_count": 15,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "tol_manifest.loc[tol_manifest[\"copyright_owner\"] == \"not provided\", \"license_name\"].value_counts()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 16,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "license_name\n",
+       "cc-by-nc-4.0                       2401921\n",
+       "cc-by-sa-3.0                        760953\n",
+       "cc-by-nc-sa-3.0                     664194\n",
+       "cc-by-3.0                           439653\n",
+       "cc-by-4.0                           368046\n",
+       "cc-by-nc                            316103\n",
+       "cc-by-nc-sa-4.0                     184204\n",
+       "cc-by-nc-sa                         154761\n",
+       "cc-publicdomain                     129257\n",
+       "cc-by-sa-4.0                         65003\n",
+       "cc-by                                58303\n",
+       "cc-by-sa-2.0                         30157\n",
+       "cc-by-nc-2.0                         27718\n",
+       "cc-0-1.0                             20358\n",
+       "No known copyright restrictions      16042\n",
+       "cc-by-nc-sa-2.5                        315\n",
+       "Name: count, dtype: int64"
+      ]
+     },
+     "execution_count": 16,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "tol_manifest.loc[tol_manifest[\"title\"] == \"not provided\", \"license_name\"].value_counts()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "At least most unmatched lack of copyright restrictions or are CC0; we did what we could."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Save Full Owner Manifest\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 17,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "tol_manifest.to_csv(\"../data/full_owner_manifest.csv\", index = False)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Make and Save License File"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 18,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "licesne_cols = [\"treeoflife_id\",\n",
+    "                \"eol_content_id\",\n",
+    "                \"eol_page_id\",\n",
+    "                \"md5\",\n",
+    "                \"medium_source_url\",\n",
+    "                \"eol_full_size_copy_url\",\n",
+    "                \"license_name\",\n",
+    "                \"copyright_owner\",\n",
+    "                \"license_link\",\n",
+    "                \"title\"]\n",
+    "\n",
+    "licenses = tol_manifest[licesne_cols]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 19,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "licenses.to_csv(TOL_FILEPATH + \"licenses.csv\", index = False)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Make Updated Catalog\n",
+    "\n",
+    "Reconnect the EOL portion of the catalog to the BIOSCAN and iNat21 portion."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 20,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "['split',\n",
+       " 'treeoflife_id',\n",
+       " 'eol_content_id',\n",
+       " 'eol_page_id',\n",
+       " 'bioscan_part',\n",
+       " 'bioscan_filename',\n",
+       " 'inat21_filename',\n",
+       " 'inat21_cls_name',\n",
+       " 'inat21_cls_num',\n",
+       " 'kingdom',\n",
+       " 'phylum',\n",
+       " 'class',\n",
+       " 'order',\n",
+       " 'family',\n",
+       " 'genus',\n",
+       " 'species',\n",
+       " 'common']"
+      ]
+     },
+     "execution_count": 20,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "cat_cols = list(catalog_orig.columns)\n",
+    "cat_cols"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Need to first reduce the `eol_catalog` (still has the `train_small` split we want to keep).\n",
+    "\n",
+    "BIOSCAN & iNat portion of the catalog: `bin_catalog`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 21,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "(6810437, 18)\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "6219674"
+      ]
+     },
+     "execution_count": 21,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "matched_tol_ids = list(tol_manifest.treeoflife_id)\n",
+    "\n",
+    "reduced_eol_cat = eol_catalog.loc[eol_catalog[\"treeoflife_id\"].isin(matched_tol_ids)]\n",
+    "\n",
+    "#check we have expected numbers (6,219,674 + 590,730 = 6,810,404, still only 6,219,674 unique)\n",
+    "print(reduced_eol_cat.shape)\n",
+    "reduced_eol_cat.treeoflife_id.nunique()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Looks like we recovered 33 more from the small train set than we expected. These came from the archive recovery (had we merged on `combined_id_archive` instead of `combined_id_full_manifest` in [`links_align_reduced.ipynb`](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/3438fe9a88c0f377a4d8ac4c6c0de796858a08ac/eol_realign/notebooks/links_align_reduced.ipynb), would have seen that difference)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 24,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "The BIOSCAN & iNate portion have 4177595 total images, with 3815156 unique entries.\n"
+     ]
+    }
+   ],
+   "source": [
+    "print(f\"The BIOSCAN & iNate portion have {bin_catalog.shape[0]} total images, with {bin_catalog.treeoflife_id.nunique()} unique entries.\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We have expected 10,034,830 unique entries in the final set, 10,988,032 total entries."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 25,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "(10988032, 17)\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "split                      3\n",
+       "treeoflife_id       10034830\n",
+       "eol_content_id       6219674\n",
+       "eol_page_id           501807\n",
+       "bioscan_part             113\n",
+       "bioscan_filename     1128313\n",
+       "inat21_filename      2686843\n",
+       "inat21_cls_name        10000\n",
+       "inat21_cls_num         10000\n",
+       "kingdom                   12\n",
+       "phylum                   108\n",
+       "class                    347\n",
+       "order                   1495\n",
+       "family                  7954\n",
+       "genus                  73687\n",
+       "species               163001\n",
+       "common                442253\n",
+       "dtype: int64"
+      ]
+     },
+     "execution_count": 25,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "updated_catalog = pd.concat([reduced_eol_cat[cat_cols], bin_catalog], ignore_index = True)\n",
+    "\n",
+    "print(updated_catalog.shape)\n",
+    "updated_catalog.nunique()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Looks good, precisely as expected. Let's save this to a CSV now."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 26,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "updated_catalog.to_csv(TOL_FILEPATH + \"catalog.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
+}