Add notebooks exploring the link files, combining with catalogs

RS for rare species and align reduced looks at catalog and predicted catalog

eol_realign/notebooks/links_align_reduced.ipynb

@@ -0,0 +1,938 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pandas as pd"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Read in Links CSV files"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "links_inner = pd.read_csv(\"../data/links_inner.csv\", low_memory=False)\n",
+    "links_manifest_cargo = pd.read_csv(\"../data/links_manifest_cargo_on_md5.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: 6840530 entries, 0 to 6840529\n",
+      "Data columns (total 34 columns):\n",
+      " #   Column                          Non-Null Count    Dtype  \n",
+      "---  ------                          --------------    -----  \n",
+      " 0   eol_content_id                  6840530 non-null  int64  \n",
+      " 1   eol_page_id                     6840530 non-null  int64  \n",
+      " 2   medium_source_url               6840530 non-null  object \n",
+      " 3   eol_full_size_copy_url          6840530 non-null  object \n",
+      " 4   license_name                    6840530 non-null  object \n",
+      " 5   copyright_owner                 6207911 non-null  object \n",
+      " 6   expected_image_filename         6840530 non-null  object \n",
+      " 7   source_0706                     6840530 non-null  bool   \n",
+      " 8   source_0726                     6840530 non-null  bool   \n",
+      " 9   source_1206                     6840530 non-null  bool   \n",
+      " 10  combined_id_manifest            6840530 non-null  object \n",
+      " 11  md5                             6840530 non-null  object \n",
+      " 12  combined_id_manifest_checksums  6840530 non-null  object \n",
+      " 13  eol_content_id_cargo            6840530 non-null  int64  \n",
+      " 14  eol_page_id_cargo               6840530 non-null  int64  \n",
+      " 15  combined_id_cargo               6840530 non-null  object \n",
+      " 16  split                           6840530 non-null  object \n",
+      " 17  treeoflife_id                   6840530 non-null  object \n",
+      " 18  eol_content_id_catalog          6840530 non-null  int64  \n",
+      " 19  eol_page_id_catalog             6840530 non-null  int64  \n",
+      " 20  bioscan_part                    0 non-null        float64\n",
+      " 21  bioscan_filename                0 non-null        float64\n",
+      " 22  inat21_filename                 0 non-null        float64\n",
+      " 23  inat21_cls_name                 0 non-null        float64\n",
+      " 24  inat21_cls_num                  0 non-null        float64\n",
+      " 25  kingdom                         6550801 non-null  object \n",
+      " 26  phylum                          6552534 non-null  object \n",
+      " 27  class                           6531337 non-null  object \n",
+      " 28  order                           6524949 non-null  object \n",
+      " 29  family                          6505404 non-null  object \n",
+      " 30  genus                           6485458 non-null  object \n",
+      " 31  species                         6405635 non-null  object \n",
+      " 32  common                          6840530 non-null  object \n",
+      " 33  combined_id_catalog             6840530 non-null  object \n",
+      "dtypes: bool(3), float64(5), int64(6), object(20)\n",
+      "memory usage: 1.6+ 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: 7513329 entries, 0 to 7513328\n",
+      "Data columns (total 16 columns):\n",
+      " #   Column                          Non-Null Count    Dtype \n",
+      "---  ------                          --------------    ----- \n",
+      " 0   eol_content_id                  7513329 non-null  int64 \n",
+      " 1   eol_page_id                     7513329 non-null  int64 \n",
+      " 2   medium_source_url               7513329 non-null  object\n",
+      " 3   eol_full_size_copy_url          7513329 non-null  object\n",
+      " 4   license_name                    7513329 non-null  object\n",
+      " 5   copyright_owner                 6860238 non-null  object\n",
+      " 6   expected_image_filename         7513329 non-null  object\n",
+      " 7   source_0706                     7513329 non-null  bool  \n",
+      " 8   source_0726                     7513329 non-null  bool  \n",
+      " 9   source_1206                     7513329 non-null  bool  \n",
+      " 10  combined_id_manifest            7513329 non-null  object\n",
+      " 11  md5                             7513329 non-null  object\n",
+      " 12  combined_id_manifest_checksums  7513329 non-null  object\n",
+      " 13  eol_content_id_cargo            7513329 non-null  int64 \n",
+      " 14  eol_page_id_cargo               7513329 non-null  int64 \n",
+      " 15  combined_id_cargo               7513329 non-null  object\n",
+      "dtypes: bool(3), int64(4), object(9)\n",
+      "memory usage: 766.7+ MB\n"
+     ]
+    }
+   ],
+   "source": [
+    "links_manifest_cargo.info(show_counts=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "Index: 822516 entries, 93 to 7513188\n",
+      "Data columns (total 16 columns):\n",
+      " #   Column                          Non-Null Count   Dtype \n",
+      "---  ------                          --------------   ----- \n",
+      " 0   eol_content_id                  822516 non-null  int64 \n",
+      " 1   eol_page_id                     822516 non-null  int64 \n",
+      " 2   medium_source_url               822516 non-null  object\n",
+      " 3   eol_full_size_copy_url          822516 non-null  object\n",
+      " 4   license_name                    822516 non-null  object\n",
+      " 5   copyright_owner                 797108 non-null  object\n",
+      " 6   expected_image_filename         822516 non-null  object\n",
+      " 7   source_0706                     822516 non-null  bool  \n",
+      " 8   source_0726                     822516 non-null  bool  \n",
+      " 9   source_1206                     822516 non-null  bool  \n",
+      " 10  combined_id_manifest            822516 non-null  object\n",
+      " 11  md5                             822516 non-null  object\n",
+      " 12  combined_id_manifest_checksums  822516 non-null  object\n",
+      " 13  eol_content_id_cargo            822516 non-null  int64 \n",
+      " 14  eol_page_id_cargo               822516 non-null  int64 \n",
+      " 15  combined_id_cargo               822516 non-null  object\n",
+      "dtypes: bool(3), int64(4), object(9)\n",
+      "memory usage: 90.2+ MB\n"
+     ]
+    }
+   ],
+   "source": [
+    "links_mismatch = links_manifest_cargo.loc[links_manifest_cargo[\"combined_id_cargo\"] != links_manifest_cargo[\"combined_id_manifest_checksums\"]]\n",
+    "links_mismatch.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "md5                               624561\n",
+       "combined_id_manifest_checksums    712504\n",
+       "combined_id_cargo                 703409\n",
+       "dtype: int64"
+      ]
+     },
+     "execution_count": 7,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "links_mismatch[[\"md5\", \"combined_id_manifest_checksums\", \"combined_id_cargo\"]].nunique()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "links_mismatch.to_csv(\"../data/links_cargo_manifest_IDmismatch.csv\", index = False)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 46,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "catalog = pd.read_csv(\"../../data/catalog.csv\", low_memory=False)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 47,
+   "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": 48,
+   "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": 48,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "eol_catalog[list(eol_catalog.columns)[:4]].nunique()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 49,
+   "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": 50,
+   "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": 51,
+   "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": 52,
+   "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": 53,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "6219044"
+      ]
+     },
+     "execution_count": 53,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "matched_catalog_ids = list(links_inner.combined_id_catalog.unique())\n",
+    "len(matched_catalog_ids)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 54,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "['100_45516037',\n",
+       " '10000_45511252',\n",
+       " '10001_45509451',\n",
+       " '10002_45509648',\n",
+       " '10003_45510902']"
+      ]
+     },
+     "execution_count": 54,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "matched_catalog_ids[:5]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "So we have about 30K unmatched, let's find those in the catalog and then we'll try to merge with our mismatched cargo & manifest."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 55,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "10017874    20995677_64638554\n",
+       "8964610       21191962_130898\n",
+       "8441264      14142414_1117599\n",
+       "9354726      28866899_2762658\n",
+       "10681937     20538304_2752336\n",
+       "Name: combined_id_catalog, dtype: object"
+      ]
+     },
+     "execution_count": 55,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "eol_catalog['combined_id_catalog'].sample(5)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 56,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "Index: 31376 entries, 956874 to 10996978\n",
+      "Data columns (total 13 columns):\n",
+      " #   Column                  Non-Null Count  Dtype \n",
+      "---  ------                  --------------  ----- \n",
+      " 0   split                   31376 non-null  object\n",
+      " 1   treeoflife_id           31376 non-null  object\n",
+      " 2   eol_content_id_catalog  31376 non-null  int64 \n",
+      " 3   eol_page_id_catalog     31376 non-null  int64 \n",
+      " 4   kingdom                 31203 non-null  object\n",
+      " 5   phylum                  31208 non-null  object\n",
+      " 6   class                   30783 non-null  object\n",
+      " 7   order                   31158 non-null  object\n",
+      " 8   family                  30924 non-null  object\n",
+      " 9   genus                   30822 non-null  object\n",
+      " 10  species                 30029 non-null  object\n",
+      " 11  common                  31376 non-null  object\n",
+      " 12  combined_id_catalog     31376 non-null  object\n",
+      "dtypes: int64(2), object(11)\n",
+      "memory usage: 3.4+ 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": 57,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "split                         2\n",
+       "treeoflife_id             31376\n",
+       "eol_content_id_catalog    31376\n",
+       "eol_page_id_catalog        7531\n",
+       "kingdom                       7\n",
+       "phylum                       33\n",
+       "class                        88\n",
+       "order                       374\n",
+       "family                     1269\n",
+       "genus                      3827\n",
+       "species                    5550\n",
+       "common                     7372\n",
+       "combined_id_catalog       31376\n",
+       "dtype: int64"
+      ]
+     },
+     "execution_count": 57,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "mismatched_catalog.nunique()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Merge with Mismatched Cargo-Manifest\n",
+    "\n",
+    "let's merge with `links_mismatch` to see if the mismatched cargo and manifest combined IDs can be linked up."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 58,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 29 entries, 0 to 28\n",
+      "Data columns (total 29 columns):\n",
+      " #   Column                          Non-Null Count  Dtype \n",
+      "---  ------                          --------------  ----- \n",
+      " 0   split                           29 non-null     object\n",
+      " 1   treeoflife_id                   29 non-null     object\n",
+      " 2   eol_content_id_catalog          29 non-null     int64 \n",
+      " 3   eol_page_id_catalog             29 non-null     int64 \n",
+      " 4   kingdom                         29 non-null     object\n",
+      " 5   phylum                          29 non-null     object\n",
+      " 6   class                           29 non-null     object\n",
+      " 7   order                           29 non-null     object\n",
+      " 8   family                          29 non-null     object\n",
+      " 9   genus                           29 non-null     object\n",
+      " 10  species                         29 non-null     object\n",
+      " 11  common                          29 non-null     object\n",
+      " 12  combined_id_catalog             29 non-null     object\n",
+      " 13  eol_content_id                  29 non-null     int64 \n",
+      " 14  eol_page_id                     29 non-null     int64 \n",
+      " 15  medium_source_url               29 non-null     object\n",
+      " 16  eol_full_size_copy_url          29 non-null     object\n",
+      " 17  license_name                    29 non-null     object\n",
+      " 18  copyright_owner                 28 non-null     object\n",
+      " 19  expected_image_filename         29 non-null     object\n",
+      " 20  source_0706                     29 non-null     bool  \n",
+      " 21  source_0726                     29 non-null     bool  \n",
+      " 22  source_1206                     29 non-null     bool  \n",
+      " 23  combined_id_manifest            29 non-null     object\n",
+      " 24  md5                             29 non-null     object\n",
+      " 25  combined_id_manifest_checksums  29 non-null     object\n",
+      " 26  eol_content_id_cargo            29 non-null     int64 \n",
+      " 27  eol_page_id_cargo               29 non-null     int64 \n",
+      " 28  combined_id_cargo               29 non-null     object\n",
+      "dtypes: bool(3), int64(6), object(20)\n",
+      "memory usage: 6.1+ KB\n"
+     ]
+    }
+   ],
+   "source": [
+    "links_catalog_mismatch = pd.merge(mismatched_catalog,\n",
+    "                                  links_mismatch,\n",
+    "                                  left_on = \"combined_id_catalog\",\n",
+    "                                  right_on = \"combined_id_manifest_checksums\",\n",
+    "                                  how = \"inner\")\n",
+    "links_catalog_mismatch.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 59,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "9251313       9447041_5660435\n",
+       "10368203      28965413_916574\n",
+       "3357181     28940017_45513086\n",
+       "10907940     10517333_3036072\n",
+       "10208533      9444575_1178182\n",
+       "5434229     10517050_46480886\n",
+       "2638483      9446016_46468616\n",
+       "Name: combined_id_catalog, dtype: object"
+      ]
+     },
+     "execution_count": 59,
+     "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": [
+    "## Check on Rare Species Catalog"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 60,
+   "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": 61,
+   "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": 62,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 12552 entries, 0 to 12551\n",
+      "Data columns (total 28 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  eol_content_id                  12552 non-null  int64 \n",
+      " 13  eol_page_id                     12552 non-null  int64 \n",
+      " 14  medium_source_url               12552 non-null  object\n",
+      " 15  eol_full_size_copy_url          12552 non-null  object\n",
+      " 16  license_name                    12552 non-null  object\n",
+      " 17  copyright_owner                 11171 non-null  object\n",
+      " 18  expected_image_filename         12552 non-null  object\n",
+      " 19  source_0706                     12552 non-null  bool  \n",
+      " 20  source_0726                     12552 non-null  bool  \n",
+      " 21  source_1206                     12552 non-null  bool  \n",
+      " 22  combined_id_manifest            12552 non-null  object\n",
+      " 23  md5                             12552 non-null  object\n",
+      " 24  combined_id_manifest_checksums  12552 non-null  object\n",
+      " 25  eol_content_id_cargo            12552 non-null  int64 \n",
+      " 26  eol_page_id_cargo               12552 non-null  int64 \n",
+      " 27  combined_id_cargo               12552 non-null  object\n",
+      "dtypes: bool(3), int64(6), object(19)\n",
+      "memory usage: 2.4+ MB\n"
+     ]
+    }
+   ],
+   "source": [
+    "rs_links = pd.merge(rs_catalog,\n",
+    "                    links_manifest_cargo,\n",
+    "                    left_on = \"combined_id_rs\",\n",
+    "                    right_on = \"combined_id_cargo\",\n",
+    "                    how = \"inner\")\n",
+    "rs_links.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 63,
+   "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",
+       "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_manifest              12221\n",
+       "md5                               11663\n",
+       "combined_id_manifest_checksums    12221\n",
+       "eol_content_id_cargo              11826\n",
+       "eol_page_id_cargo                   400\n",
+       "combined_id_cargo                 11826\n",
+       "dtype: int64"
+      ]
+     },
+     "execution_count": 63,
+     "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": 64,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "11826"
+      ]
+     },
+     "execution_count": 64,
+     "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": 65,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "['22519448_914532',\n",
+       " '28677580_1057176',\n",
+       " '20714475_47047909',\n",
+       " '29975068_45509269']"
+      ]
+     },
+     "execution_count": 65,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "matched_rs_ids[:4]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 66,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "4010      20184952_311570\n",
+       "8096      29473123_323892\n",
+       "5217    29580624_45514697\n",
+       "890     21629967_46559745\n",
+       "Name: combined_id_rs, dtype: object"
+      ]
+     },
+     "execution_count": 66,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "rs_catalog[\"combined_id_rs\"].sample(4)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 67,
+   "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": 68,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 0 entries\n",
+      "Data columns (total 28 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  eol_content_id                  0 non-null      int64 \n",
+      " 13  eol_page_id                     0 non-null      int64 \n",
+      " 14  medium_source_url               0 non-null      object\n",
+      " 15  eol_full_size_copy_url          0 non-null      object\n",
+      " 16  license_name                    0 non-null      object\n",
+      " 17  copyright_owner                 0 non-null      object\n",
+      " 18  expected_image_filename         0 non-null      object\n",
+      " 19  source_0706                     0 non-null      bool  \n",
+      " 20  source_0726                     0 non-null      bool  \n",
+      " 21  source_1206                     0 non-null      bool  \n",
+      " 22  combined_id_manifest            0 non-null      object\n",
+      " 23  md5                             0 non-null      object\n",
+      " 24  combined_id_manifest_checksums  0 non-null      object\n",
+      " 25  eol_content_id_cargo            0 non-null      int64 \n",
+      " 26  eol_page_id_cargo               0 non-null      int64 \n",
+      " 27  combined_id_cargo               0 non-null      object\n",
+      "dtypes: bool(3), int64(6), object(19)\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_manifest_checksums\",\n",
+    "                             how = \"inner\")\n",
+    "links_rs_mismatch.info(show_counts = True)"
+   ]
+  },
+  {
+   "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
+}

eol_realign/notebooks/links_align_reduced.py

@@ -0,0 +1,161 @@
+# ---
+# jupyter:
+#   jupytext:
+#     formats: ipynb,py:percent
+#     text_representation:
+#       extension: .py
+#       format_name: percent
+#       format_version: '1.3'
+#       jupytext_version: 1.16.0
+#   kernelspec:
+#     display_name: tol
+#     language: python
+#     name: python3
+# ---
+
+# %%
+import pandas as pd
+
+# %% [markdown]
+# ### Read in Links CSV files
+
+# %%
+links_inner = pd.read_csv("../data/links_inner.csv", low_memory=False)
+links_manifest_cargo = pd.read_csv("../data/links_manifest_cargo_on_md5.csv", low_memory=False)
+
+# %%
+links_inner.info(show_counts=True)
+
+# %%
+links_manifest_cargo.info(show_counts=True)
+
+# %%
+links_mismatch = links_manifest_cargo.loc[links_manifest_cargo["combined_id_cargo"] != links_manifest_cargo["combined_id_manifest_checksums"]]
+links_mismatch.info(show_counts = True)
+
+# %%
+links_mismatch[["md5", "combined_id_manifest_checksums", "combined_id_cargo"]].nunique()
+
+# %%
+links_mismatch.to_csv("../data/links_cargo_manifest_IDmismatch.csv", index = False)
+
+# %%
+catalog = pd.read_csv("../../data/catalog.csv", low_memory=False)
+
+# %%
+# remove train_small and all non-EOL entries
+catalog = catalog.loc[catalog.split != "train_small"]
+eol_catalog = catalog.loc[catalog.eol_content_id.notna()]
+
+# %%
+eol_catalog[list(eol_catalog.columns)[:4]].nunique()
+
+# %%
+eol_cols = [col for col in list(eol_catalog.columns) if "bioscan" not in col and "inat" not in col]
+
+# %%
+eol_catalog = eol_catalog[eol_cols]
+eol_catalog.info(show_counts=True)
+
+# %% [markdown]
+# Must recast IDs as `int64`
+
+# %%
+eol_catalog = eol_catalog.astype({"eol_content_id": "int64", "eol_page_id": "int64"})
+eol_catalog[eol_cols[:4]].info()
+
+# %%
+# make combined ID for catalog and add suffix to eol content and page IDs
+eol_catalog['combined_id_catalog'] = eol_catalog['eol_content_id'].astype(str) + '_' + eol_catalog['eol_page_id'].astype(str)
+eol_catalog.rename(columns={'eol_content_id': 'eol_content_id_catalog', 'eol_page_id': 'eol_page_id_catalog'}, inplace=True)
+
+
+# %%
+matched_catalog_ids = list(links_inner.combined_id_catalog.unique())
+len(matched_catalog_ids)
+
+# %%
+matched_catalog_ids[:5]
+
+# %% [markdown]
+# So we have about 30K unmatched, let's find those in the catalog and then we'll try to merge with our mismatched cargo & manifest.
+
+# %%
+eol_catalog['combined_id_catalog'].sample(5)
+
+# %%
+mismatched_catalog = eol_catalog.loc[~eol_catalog["combined_id_catalog"].isin(matched_catalog_ids)]
+mismatched_catalog.info(show_counts = True)
+
+# %%
+mismatched_catalog.nunique()
+
+# %% [markdown]
+# ## Merge with Mismatched Cargo-Manifest
+#
+# let's merge with `links_mismatch` to see if the mismatched cargo and manifest combined IDs can be linked up.
+
+# %%
+links_catalog_mismatch = pd.merge(mismatched_catalog,
+                                  links_mismatch,
+                                  left_on = "combined_id_catalog",
+                                  right_on = "combined_id_manifest_checksums",
+                                  how = "inner")
+links_catalog_mismatch.info(show_counts = True)
+
+# %%
+mismatched_catalog.combined_id_catalog.sample(7)
+
+# %% [markdown]
+# These pages are reasonably full too: [5660435](https://eol.org/pages/5660435).
+
+# %% [markdown]
+# ## Check on Rare Species Catalog
+
+# %%
+rs_catalog = pd.read_csv("../../rare_species/data/rarespecies-catalog.csv",
+                         low_memory=False,
+                         dtype = {"eol_content_id": "int64", "eol_page_id": "int64"})
+rs_catalog.info(show_counts = True)
+
+# %%
+rs_catalog["combined_id_rs"] = rs_catalog["eol_content_id"].astype(str) + "_" + rs_catalog["eol_page_id"].astype(str)
+rs_catalog.rename(columns={'eol_content_id': 'eol_content_id_rs', 'eol_page_id': 'eol_page_id_rs'}, inplace=True)
+
+# %%
+rs_links = pd.merge(rs_catalog,
+                    links_manifest_cargo,
+                    left_on = "combined_id_rs",
+                    right_on = "combined_id_cargo",
+                    how = "inner")
+rs_links.info(show_counts = True)
+
+# %%
+rs_links.nunique()
+
+# %% [markdown]
+# Let's check the mismatched cargo/manifest entries for those last 174...
+
+# %%
+matched_rs_ids = list(rs_links.combined_id_rs.unique())
+len(matched_rs_ids)
+
+# %%
+matched_rs_ids[:4]
+
+# %%
+rs_catalog["combined_id_rs"].sample(4)
+
+# %%
+mismatched_rs = rs_catalog.loc[~rs_catalog["combined_id_rs"].isin(matched_rs_ids)]
+mismatched_rs.info(show_counts = True)
+
+# %%
+links_rs_mismatch = pd.merge(mismatched_rs,
+                             links_mismatch,
+                             left_on = "combined_id_rs",
+                             right_on = "combined_id_manifest_checksums",
+                             how = "inner")
+links_rs_mismatch.info(show_counts = True)
+
+# %%

eol_realign/notebooks/links_rs_duplicates.ipynb

@@ -0,0 +1,1742 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pandas as pd"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Read in Links CSV file"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "links_manifest_cargo = pd.read_csv(\"../data/links_manifest_cargo_on_md5.csv\", low_memory=False)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 7513329 entries, 0 to 7513328\n",
+      "Data columns (total 16 columns):\n",
+      " #   Column                          Non-Null Count    Dtype \n",
+      "---  ------                          --------------    ----- \n",
+      " 0   eol_content_id                  7513329 non-null  int64 \n",
+      " 1   eol_page_id                     7513329 non-null  int64 \n",
+      " 2   medium_source_url               7513329 non-null  object\n",
+      " 3   eol_full_size_copy_url          7513329 non-null  object\n",
+      " 4   license_name                    7513329 non-null  object\n",
+      " 5   copyright_owner                 6860238 non-null  object\n",
+      " 6   expected_image_filename         7513329 non-null  object\n",
+      " 7   source_0706                     7513329 non-null  bool  \n",
+      " 8   source_0726                     7513329 non-null  bool  \n",
+      " 9   source_1206                     7513329 non-null  bool  \n",
+      " 10  combined_id_manifest            7513329 non-null  object\n",
+      " 11  md5                             7513329 non-null  object\n",
+      " 12  combined_id_manifest_checksums  7513329 non-null  object\n",
+      " 13  eol_content_id_cargo            7513329 non-null  int64 \n",
+      " 14  eol_page_id_cargo               7513329 non-null  int64 \n",
+      " 15  combined_id_cargo               7513329 non-null  object\n",
+      "dtypes: bool(3), int64(4), object(9)\n",
+      "memory usage: 766.7+ 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(\"../../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": 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 28 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  eol_content_id                  12552 non-null  int64 \n",
+      " 13  eol_page_id                     12552 non-null  int64 \n",
+      " 14  medium_source_url               12552 non-null  object\n",
+      " 15  eol_full_size_copy_url          12552 non-null  object\n",
+      " 16  license_name                    12552 non-null  object\n",
+      " 17  copyright_owner                 11171 non-null  object\n",
+      " 18  expected_image_filename         12552 non-null  object\n",
+      " 19  source_0706                     12552 non-null  bool  \n",
+      " 20  source_0726                     12552 non-null  bool  \n",
+      " 21  source_1206                     12552 non-null  bool  \n",
+      " 22  combined_id_manifest            12552 non-null  object\n",
+      " 23  md5                             12552 non-null  object\n",
+      " 24  combined_id_manifest_checksums  12552 non-null  object\n",
+      " 25  eol_content_id_cargo            12552 non-null  int64 \n",
+      " 26  eol_page_id_cargo               12552 non-null  int64 \n",
+      " 27  combined_id_cargo               12552 non-null  object\n",
+      "dtypes: bool(3), int64(6), object(19)\n",
+      "memory usage: 2.4+ MB\n"
+     ]
+    }
+   ],
+   "source": [
+    "rs_links = pd.merge(rs_catalog,\n",
+    "                    links_manifest_cargo,\n",
+    "                    left_on = \"combined_id_rs\",\n",
+    "                    right_on = \"combined_id_cargo\",\n",
+    "                    how = \"inner\")\n",
+    "rs_links.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "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",
+       "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_manifest              12221\n",
+       "md5                               11663\n",
+       "combined_id_manifest_checksums    12221\n",
+       "eol_content_id_cargo              11826\n",
+       "eol_page_id_cargo                   400\n",
+       "combined_id_cargo                 11826\n",
+       "dtype: int64"
+      ]
+     },
+     "execution_count": 7,
+     "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": 8,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "11826"
+      ]
+     },
+     "execution_count": 8,
+     "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": 9,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "['22519448_914532',\n",
+       " '28677580_1057176',\n",
+       " '20714475_47047909',\n",
+       " '29975068_45509269']"
+      ]
+     },
+     "execution_count": 9,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "matched_rs_ids[:4]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "4310    20080369_46579618\n",
+       "842     27592101_46560177\n",
+       "1111      20945361_570181\n",
+       "3609    10819533_46516728\n",
+       "Name: combined_id_rs, dtype: object"
+      ]
+     },
+     "execution_count": 10,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "rs_catalog[\"combined_id_rs\"].sample(4)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "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": 12,
+   "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": 12,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "mismatched_rs.nunique()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "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": 13,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "mismatched_rs.sciName.value_counts()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "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": 15,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "[array([46559139]),\n",
+       " array([208913]),\n",
+       " array([46559307]),\n",
+       " array([1011315]),\n",
+       " array([205909]),\n",
+       " array([46560546])]"
+      ]
+     },
+     "execution_count": 15,
+     "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": 16,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "[(46559139, 16),\n",
+       " (208913, 4),\n",
+       " (46559307, 22),\n",
+       " (1011315, 22),\n",
+       " (205909, 28),\n",
+       " (46560546, 24)]"
+      ]
+     },
+     "execution_count": 16,
+     "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": 17,
+   "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>7726</th>\n",
+       "      <td>667586ab-145a-4076-9669-535447aa2b6c</td>\n",
+       "      <td>30098504</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>30098504_205909</td>\n",
+       "    </tr>\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>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>6909</th>\n",
+       "      <td>d33f93de-31ec-434a-985e-a9cdeb79b557</td>\n",
+       "      <td>30098484</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>30098484_205909</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>6564</th>\n",
+       "      <td>bd27fc74-caa5-4fe3-9dbc-776127bd03e7</td>\n",
+       "      <td>30098489</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>30098489_205909</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "                            rarespecies_id  eol_content_id_rs  eol_page_id_rs  \\\n",
+       "7726  667586ab-145a-4076-9669-535447aa2b6c           30098504          205909   \n",
+       "1413  d239159f-cb15-4c30-8aeb-d8177f8cf34a           30098492          205909   \n",
+       "7916  2d342a7c-7e0c-4981-9630-019bb90183be           30098499          205909   \n",
+       "6909  d33f93de-31ec-434a-985e-a9cdeb79b557           30098484          205909   \n",
+       "6564  bd27fc74-caa5-4fe3-9dbc-776127bd03e7           30098489          205909   \n",
+       "\n",
+       "       kingdom    phylum           class             order         family  \\\n",
+       "7726  Animalia  Chordata  Actinopterygii  Acipenseriformes  Acipenseridae   \n",
+       "1413  Animalia  Chordata  Actinopterygii  Acipenseriformes  Acipenseridae   \n",
+       "7916  Animalia  Chordata  Actinopterygii  Acipenseriformes  Acipenseridae   \n",
+       "6909  Animalia  Chordata  Actinopterygii  Acipenseriformes  Acipenseridae   \n",
+       "6564  Animalia  Chordata  Actinopterygii  Acipenseriformes  Acipenseridae   \n",
+       "\n",
+       "               genus species               sciName   combined_id_rs  \n",
+       "7726  Scaphirhynchus   albus  Scaphirhynchus albus  30098504_205909  \n",
+       "1413  Scaphirhynchus   albus  Scaphirhynchus albus  30098492_205909  \n",
+       "7916  Scaphirhynchus   albus  Scaphirhynchus albus  30098499_205909  \n",
+       "6909  Scaphirhynchus   albus  Scaphirhynchus albus  30098484_205909  \n",
+       "6564  Scaphirhynchus   albus  Scaphirhynchus albus  30098489_205909  "
+      ]
+     },
+     "execution_count": 17,
+     "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": 18,
+   "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>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>4243</th>\n",
+       "      <td>8a7eae46-57af-4132-b914-78556479db67</td>\n",
+       "      <td>27648161</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>27648161_46560546</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2347</th>\n",
+       "      <td>de4a6ca0-6fc2-40de-907e-c99b98a9ca3e</td>\n",
+       "      <td>27648164</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>27648164_46560546</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3481</th>\n",
+       "      <td>2bcba9f3-a3a4-4a2b-a4f4-84e35be0e35f</td>\n",
+       "      <td>27648163</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>27648163_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",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "                            rarespecies_id  eol_content_id_rs  eol_page_id_rs  \\\n",
+       "3655  12633820-3a3a-4c77-bd38-7221bd18b747           27648157        46560546   \n",
+       "4243  8a7eae46-57af-4132-b914-78556479db67           27648161        46560546   \n",
+       "2347  de4a6ca0-6fc2-40de-907e-c99b98a9ca3e           27648164        46560546   \n",
+       "3481  2bcba9f3-a3a4-4a2b-a4f4-84e35be0e35f           27648163        46560546   \n",
+       "1358  d436ec20-202d-44ec-9081-ca59afef356f           27648166        46560546   \n",
+       "\n",
+       "       kingdom    phylum           class       order   family genus   species  \\\n",
+       "3655  Animalia  Chordata  Chondrichthyes  Rajiformes  Rajidae  Raja  asterias   \n",
+       "4243  Animalia  Chordata  Chondrichthyes  Rajiformes  Rajidae  Raja  asterias   \n",
+       "2347  Animalia  Chordata  Chondrichthyes  Rajiformes  Rajidae  Raja  asterias   \n",
+       "3481  Animalia  Chordata  Chondrichthyes  Rajiformes  Rajidae  Raja  asterias   \n",
+       "1358  Animalia  Chordata  Chondrichthyes  Rajiformes  Rajidae  Raja  asterias   \n",
+       "\n",
+       "            sciName     combined_id_rs  \n",
+       "3655  Raja asterias  27648157_46560546  \n",
+       "4243  Raja asterias  27648161_46560546  \n",
+       "2347  Raja asterias  27648164_46560546  \n",
+       "3481  Raja asterias  27648163_46560546  \n",
+       "1358  Raja asterias  27648166_46560546  "
+      ]
+     },
+     "execution_count": 18,
+     "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": 19,
+   "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",
+       "      <th>expected_image_filename</th>\n",
+       "      <th>source_0706</th>\n",
+       "      <th>source_0726</th>\n",
+       "      <th>source_1206</th>\n",
+       "      <th>combined_id_manifest</th>\n",
+       "      <th>md5</th>\n",
+       "      <th>combined_id_manifest_checksums</th>\n",
+       "      <th>eol_content_id_cargo</th>\n",
+       "      <th>eol_page_id_cargo</th>\n",
+       "      <th>combined_id_cargo</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "Empty DataFrame\n",
+       "Columns: [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_manifest, md5, combined_id_manifest_checksums, eol_content_id_cargo, eol_page_id_cargo, combined_id_cargo]\n",
+       "Index: []"
+      ]
+     },
+     "execution_count": 19,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# check if content IDs get recycled, content ID: 27648165, now online as: 30223317\n",
+    "links_manifest_cargo.loc[links_manifest_cargo[\"eol_content_id_cargo\"] == 30223317]"
+   ]
+  },
+  {
+   "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>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_manifest</th>\n",
+       "      <th>md5</th>\n",
+       "      <th>combined_id_manifest_checksums</th>\n",
+       "      <th>eol_content_id_cargo</th>\n",
+       "      <th>eol_page_id_cargo</th>\n",
+       "      <th>combined_id_cargo</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "Empty DataFrame\n",
+       "Columns: [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_manifest, md5, combined_id_manifest_checksums, eol_content_id_cargo, eol_page_id_cargo, combined_id_cargo]\n",
+       "Index: []"
+      ]
+     },
+     "execution_count": 20,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# Is it in manifest?\n",
+    "links_manifest_cargo.loc[links_manifest_cargo[\"eol_content_id\"] == 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": 27,
+   "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/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": 21,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "rs_links[\"md5_dupes\"] = rs_links.duplicated(subset = \"md5\", keep = \"first\")\n",
+    "rs_links[\"rs_id_dupes\"] = rs_links.duplicated(subset = \"rarespecies_id\", keep = \"first\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 22,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "md5_dupes\n",
+       "True    726\n",
+       "Name: count, dtype: int64"
+      ]
+     },
+     "execution_count": 22,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "rs_links.loc[rs_links[\"rs_id_dupes\"], \"md5_dupes\"].value_counts()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 23,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "md5_dupes\n",
+       "False    11663\n",
+       "True       163\n",
+       "Name: count, dtype: int64"
+      ]
+     },
+     "execution_count": 23,
+     "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": 24,
+   "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",
+       "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                    48\n",
+       "expected_image_filename           163\n",
+       "source_0706                         2\n",
+       "source_0726                         1\n",
+       "source_1206                         2\n",
+       "combined_id_manifest              163\n",
+       "md5                               163\n",
+       "combined_id_manifest_checksums    163\n",
+       "eol_content_id_cargo              163\n",
+       "eol_page_id_cargo                  80\n",
+       "combined_id_cargo                 163\n",
+       "md5_dupes                           1\n",
+       "rs_id_dupes                         1\n",
+       "dtype: int64"
+      ]
+     },
+     "execution_count": 24,
+     "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": 25,
+   "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": 25,
+     "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": 26,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "[4453333, 460289, 45277122, 46561158, 1286909, 45510188, 45510548, 791049]"
+      ]
+     },
+     "execution_count": 26,
+     "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": 27,
+   "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\"].nunique()\n",
+    "    num_unique_imgs_by_pg[pg_id] = num_unique_images"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 28,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "80"
+      ]
+     },
+     "execution_count": 28,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "len(num_images_by_pg)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 29,
+   "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": 33,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "856        28675441_453303_eol-full-size-copy.jpg\n",
+       "3628       22574040_456490_eol-full-size-copy.jpg\n",
+       "11038    22222313_45511297_eol-full-size-copy.jpg\n",
+       "1526     20963513_45511277_eol-full-size-copy.jpg\n",
+       "3703     20080370_46579618_eol-full-size-copy.jpg\n",
+       "1991      21744553_1039032_eol-full-size-copy.jpg\n",
+       "9552     20997172_46561158_eol-full-size-copy.jpg\n",
+       "Name: file_name, dtype: object"
+      ]
+     },
+     "execution_count": 33,
+     "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": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# save filelist for easier fetching\n",
+    "rs_catalog[\"file_name\"].to_csv(\"../data/rs_file_list.txt\", index = False)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Check for number of _unique_ images per species\n",
+    "\n",
+    "We want to see if we can replace the species that don't have at least 30 unique images per species in our rare species dataset. We need the full list of options from IUCN...We did hold out all 400?\n",
+    "\n",
+    "Would require going back and checking for species in predicted catalog that aren't in catalog, then comparing that to `links_manifest_cargo_on_md5`."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 34,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "pred_cat = pd.read_csv(\"../../data/predicted-catalog.csv\", low_memory=False)\n",
+    "catalog = pd.read_csv(\"../../data/data/catalog.csv\", low_memory=False)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 35,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# process catalog\n",
+    "catalog = catalog.loc[catalog.split != \"train_small\"]\n",
+    "eol_catalog = catalog.loc[catalog.eol_content_id.notna()]\n",
+    "eol_catalog = eol_catalog.astype({\"eol_content_id\": \"int64\", \"eol_page_id\": \"int64\"})\n",
+    "\n",
+    "# process pred-cat\n",
+    "eol_pred_cat = pred_cat.loc[pred_cat.eol_content_id.notna()]\n",
+    "eol_pred_cat = eol_pred_cat.astype({\"eol_content_id\": \"int64\", \"eol_page_id\": \"int64\"})"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 39,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 6277374 entries, 0 to 6277373\n",
+      "Data columns (total 18 columns):\n",
+      " #   Column               Non-Null Count    Dtype  \n",
+      "---  ------               --------------    -----  \n",
+      " 0   split                6277374 non-null  object \n",
+      " 1   treeoflife_id        6277374 non-null  object \n",
+      " 2   eol_content_id_pred  6277374 non-null  int64  \n",
+      " 3   eol_page_id          6277374 non-null  int64  \n",
+      " 4   bioscan_part         0 non-null        float64\n",
+      " 5   bioscan_filename     0 non-null        object \n",
+      " 6   inat21_filename      0 non-null        object \n",
+      " 7   inat21_cls_name      0 non-null        object \n",
+      " 8   inat21_cls_num       0 non-null        float64\n",
+      " 9   kingdom              6016565 non-null  object \n",
+      " 10  phylum               6018161 non-null  object \n",
+      " 11  class                5998392 non-null  object \n",
+      " 12  order                5992253 non-null  object \n",
+      " 13  family               5975682 non-null  object \n",
+      " 14  genus                5967267 non-null  object \n",
+      " 15  species              5978567 non-null  object \n",
+      " 16  common               6277374 non-null  object \n",
+      " 17  eol_content_id_cat   6250420 non-null  float64\n",
+      "dtypes: float64(3), int64(2), object(13)\n",
+      "memory usage: 862.1+ MB\n"
+     ]
+    }
+   ],
+   "source": [
+    "full_pred_cat = pd.merge(eol_pred_cat, eol_catalog[[\"treeoflife_id\", \"eol_content_id\"]], on = \"treeoflife_id\", how = \"left\", suffixes = (\"_pred\", \"_cat\"))\n",
+    "full_pred_cat.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 41,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "26954"
+      ]
+     },
+     "execution_count": 41,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "non_cat_ids = list(full_pred_cat.loc[full_pred_cat[\"eol_content_id_cat\"].isna(), \"treeoflife_id\"])\n",
+    "len(non_cat_ids)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 54,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/var/folders/nv/f0fq1p1n1_3b11x579py_0q80000gq/T/ipykernel_2421/666684240.py:2: 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",
+      "  pot_imgs[\"sciName\"] = pot_imgs[\"genus\"] + \" \" + pot_imgs[\"species\"]\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "split                   2\n",
+       "treeoflife_id       26954\n",
+       "eol_content_id      26954\n",
+       "eol_page_id           831\n",
+       "bioscan_part            0\n",
+       "bioscan_filename        0\n",
+       "inat21_filename         0\n",
+       "inat21_cls_name         0\n",
+       "inat21_cls_num          0\n",
+       "kingdom                 2\n",
+       "phylum                  6\n",
+       "class                  18\n",
+       "order                 106\n",
+       "family                285\n",
+       "genus                 566\n",
+       "species               749\n",
+       "common                796\n",
+       "sciName               802\n",
+       "dtype: int64"
+      ]
+     },
+     "execution_count": 54,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "pot_imgs = eol_pred_cat.loc[eol_pred_cat.treeoflife_id.isin(non_cat_ids)]\n",
+    "pot_imgs[\"sciName\"] = pot_imgs[\"genus\"] + \" \" + pot_imgs[\"species\"]\n",
+    "pot_imgs.nunique()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Interesting, we have 831 unique EOL page IDs, but only 802 unique scientific names. Wonder how that matches up with 7-tuples."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 55,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/var/folders/nv/f0fq1p1n1_3b11x579py_0q80000gq/T/ipykernel_2421/3965230711.py:2: 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",
+      "  pot_imgs[\"duplicate\"] = pot_imgs.duplicated(subset = taxa, keep = \"first\")\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "duplicate\n",
+       "True     26152\n",
+       "False      802\n",
+       "Name: count, dtype: int64"
+      ]
+     },
+     "execution_count": 55,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "taxa = list(pot_imgs.columns)[9:-2]\n",
+    "pot_imgs[\"duplicate\"] = pot_imgs.duplicated(subset = taxa, keep = \"first\")\n",
+    "\n",
+    "# our species count this way is num true in duplicate\n",
+    "pot_imgs.duplicate.value_counts()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Okay, so this matches up with our `sciName` count."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 56,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "(279370, 24)"
+      ]
+     },
+     "execution_count": 56,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "eol_cols = list(pot_imgs.columns)[1:4] + list(pot_imgs.columns)[9:]\n",
+    "\n",
+    "pot_imgs = pot_imgs[eol_cols]\n",
+    "\n",
+    "#compare to catalog sciNames\n",
+    "eol_catalog[\"sciName\"] = eol_catalog[\"genus\"] + \" \" + eol_catalog[\"species\"]\n",
+    "\n",
+    "overlap_sciNames = pd.merge(pot_imgs, eol_catalog[eol_cols[:-1]], on = \"sciName\", how = \"inner\")\n",
+    "overlap_sciNames.shape"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 58,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "treeoflife_id_x      3994\n",
+       "eol_content_id_x     3994\n",
+       "eol_page_id_x         402\n",
+       "kingdom_x               2\n",
+       "phylum_x                6\n",
+       "class_x                15\n",
+       "order_x                81\n",
+       "family_x              192\n",
+       "genus_x               320\n",
+       "species_x             390\n",
+       "common_x              402\n",
+       "sciName               402\n",
+       "duplicate               2\n",
+       "treeoflife_id_y     28738\n",
+       "eol_content_id_y    28738\n",
+       "eol_page_id_y         444\n",
+       "kingdom_y               2\n",
+       "phylum_y                6\n",
+       "class_y                15\n",
+       "order_y                81\n",
+       "family_y              192\n",
+       "genus_y               320\n",
+       "species_y             390\n",
+       "common_y              402\n",
+       "dtype: int64"
+      ]
+     },
+     "execution_count": 58,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "overlap_sciNames.nunique()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Here are our other 402 species, so we didn't hold out anything but the 400 chosen.\n",
+    "\n",
+    "We're stuck with less images for some of them unless we source images from elsewhere."
+   ]
+  },
+  {
+   "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": "3.11.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

eol_realign/notebooks/links_rs_duplicates.py

@@ -0,0 +1,268 @@
+# ---
+# jupyter:
+#   jupytext:
+#     formats: ipynb,py:percent
+#     text_representation:
+#       extension: .py
+#       format_name: percent
+#       format_version: '1.3'
+#       jupytext_version: 1.16.0
+#   kernelspec:
+#     display_name: tol
+#     language: python
+#     name: python3
+# ---
+
+# %%
+import pandas as pd
+
+# %% [markdown]
+# ### Read in Links CSV file
+
+# %%
+links_manifest_cargo = pd.read_csv("../data/links_manifest_cargo_on_md5.csv", low_memory=False)
+
+# %%
+links_manifest_cargo.info(show_counts=True)
+
+# %% [markdown]
+# ## Check on Rare Species Catalog
+
+# %%
+rs_catalog = pd.read_csv("../../rare_species/data/rarespecies-catalog.csv",
+                         low_memory=False,
+                         dtype = {"eol_content_id": "int64", "eol_page_id": "int64"})
+rs_catalog.info(show_counts = True)
+
+# %%
+rs_catalog["combined_id_rs"] = rs_catalog["eol_content_id"].astype(str) + "_" + rs_catalog["eol_page_id"].astype(str)
+rs_catalog.rename(columns={'eol_content_id': 'eol_content_id_rs', 'eol_page_id': 'eol_page_id_rs'}, inplace=True)
+
+# %%
+rs_links = pd.merge(rs_catalog,
+                    links_manifest_cargo,
+                    left_on = "combined_id_rs",
+                    right_on = "combined_id_cargo",
+                    how = "inner")
+rs_links.info(show_counts = True)
+
+# %%
+rs_links.nunique()
+
+# %% [markdown]
+# Let's check the mismatched cargo/manifest entries for those last 174...
+
+# %%
+matched_rs_ids = list(rs_links.combined_id_rs.unique())
+len(matched_rs_ids)
+
+# %%
+matched_rs_ids[:4]
+
+# %%
+rs_catalog["combined_id_rs"].sample(4)
+
+# %%
+mismatched_rs = rs_catalog.loc[~rs_catalog["combined_id_rs"].isin(matched_rs_ids)]
+mismatched_rs.info(show_counts = True)
+
+# %%
+mismatched_rs.nunique()
+
+# %%
+mismatched_rs.sciName.value_counts()
+
+# %%
+big_sciNames_missing = ["Aonyx capensis",
+                        "Zoogoneticus tequila",
+                        "Sousa plumbea",
+                        "Sylvilagus transitionalis",
+                        "Scaphirhynchus albus",
+                        "Raja asterias"]
+
+# %%
+pg_ids = []
+for sciName in big_sciNames_missing:
+    pg_ids.append(rs_links.loc[rs_links["sciName"] == sciName, "eol_page_id"].unique())
+pg_ids
+
+# %%
+num_images_by_pg = []
+for pg_id in pg_ids:
+    num_images = links_manifest_cargo.loc[links_manifest_cargo["eol_page_id"] == pg_id[0]].shape[0]
+    num_images_by_pg.append((pg_id[0], num_images))
+
+num_images_by_pg
+
+# %% [markdown]
+# The media for both of these last two is online: https://eol.org/pages/46560546/media, https://eol.org/pages/205909/media
+
+# %%
+big_mismatch = mismatched_rs.loc[mismatched_rs["sciName"].isin(big_sciNames_missing)]
+big_mismatch.loc[big_mismatch["eol_page_id_rs"] == 205909].sample(5)
+
+# %% [markdown]
+# sampling some, they're "not in any collections": https://eol.org/media/30098484
+
+# %%
+big_mismatch.loc[big_mismatch["eol_page_id_rs"] == 46560546].sample(5)
+
+# %% [markdown]
+# Meanwhile, these are giving me 404's: 27648160, 27648159, 27648164, 27648161, 27648166
+
+# %%
+# check if content IDs get recycled, content ID: 27648165, now online as: 30223317
+links_manifest_cargo.loc[links_manifest_cargo["eol_content_id_cargo"] == 30223317]
+
+# %%
+# Is it in manifest?
+links_manifest_cargo.loc[links_manifest_cargo["eol_content_id"] == 30223317]
+
+# %% [markdown]
+# This tracks with all eol content IDs being unique across manifest versions...would there be some other intermediate stage where it changed IDs _again_?!
+
+# %%
+# Save CSV of mismatched, they should be salvageable.
+# We saw these images both online and in our cargo, just with different IDs
+
+mismatched_rs.to_csv("../data/mismatched_rarespecies.csv", index=False)
+
+# %% [markdown]
+# 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.
+
+# %% [markdown]
+# ## Investigate Duplication
+#
+# Now I want some more info on those duplicated MD5's.
+
+# %%
+rs_links["md5_dupes"] = rs_links.duplicated(subset = "md5", keep = "first")
+rs_links["rs_id_dupes"] = rs_links.duplicated(subset = "rarespecies_id", keep = "first")
+
+# %%
+rs_links.loc[rs_links["rs_id_dupes"], "md5_dupes"].value_counts()
+
+# %%
+rs_links.loc[~rs_links["rs_id_dupes"], "md5_dupes"].value_counts()
+
+# %% [markdown]
+# Looks like we have 163 duplicated images in Rare Species...
+
+# %%
+rs = rs_links.loc[~rs_links["rs_id_dupes"]]
+rs_dupes = rs.loc[rs["md5_dupes"]]
+rs_dupes.nunique()
+
+# %%
+rs_dupes.sciName.value_counts()[:10]
+
+# %% [markdown]
+# 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.
+
+# %% [markdown]
+# Let's see how many images we have for each of these duplicated images.
+
+# %%
+rs_sci_dupe_pgs = list(rs_dupes.eol_page_id.unique())
+rs_sci_dupe_pgs[:8]
+
+# %%
+num_images_by_pg = {}
+#list with unique by md5
+num_unique_imgs_by_pg = {}
+for pg_id in rs_sci_dupe_pgs:
+    num_images = links_manifest_cargo.loc[links_manifest_cargo["eol_page_id"] == pg_id].shape[0]
+    num_images_by_pg[pg_id] = num_images
+    num_unique_images = links_manifest_cargo.loc[links_manifest_cargo["eol_page_id"] == pg_id, "md5"].nunique()
+    num_unique_imgs_by_pg[pg_id] = num_unique_images
+
+
+# %%
+len(num_images_by_pg)
+
+# %%
+for pg_id in num_unique_imgs_by_pg.keys():
+    if num_unique_imgs_by_pg[pg_id] < 30:
+        print(f"page ID {pg_id} has less than 30 unique images; it has {num_unique_imgs_by_pg[pg_id]} unique images")
+
+# %% [markdown]
+# https://eol.org/pages/485420/media has only 21 true images, since 3 are post-its.
+
+# %%
+rs_catalog.head()
+
+# %%
+rs_catalog["file_name"] = rs_catalog["combined_id_rs"].astype(str) + "_eol-full-size-copy.jpg"
+rs_catalog["file_name"].sample(7)
+
+# %%
+# save filelist for easier fetching
+rs_catalog["file_name"].to_csv("../data/rs_file_list.txt", index = False)
+
+# %% [markdown]
+# ### Check for number of _unique_ images per species
+#
+# We want to see if we can replace the species that don't have at least 30 unique images per species in our rare species dataset. We need the full list of options from IUCN...We did hold out all 400?
+#
+# Would require going back and checking for species in predicted catalog that aren't in catalog, then comparing that to `links_manifest_cargo_on_md5`.
+
+# %%
+pred_cat = pd.read_csv("../../data/predicted-catalog.csv", low_memory=False)
+catalog = pd.read_csv("../../data/data/catalog.csv", low_memory=False)
+
+# %%
+# process catalog
+catalog = catalog.loc[catalog.split != "train_small"]
+eol_catalog = catalog.loc[catalog.eol_content_id.notna()]
+eol_catalog = eol_catalog.astype({"eol_content_id": "int64", "eol_page_id": "int64"})
+
+# process pred-cat
+eol_pred_cat = pred_cat.loc[pred_cat.eol_content_id.notna()]
+eol_pred_cat = eol_pred_cat.astype({"eol_content_id": "int64", "eol_page_id": "int64"})
+
+# %%
+full_pred_cat = pd.merge(eol_pred_cat, eol_catalog[["treeoflife_id", "eol_content_id"]], on = "treeoflife_id", how = "left", suffixes = ("_pred", "_cat"))
+full_pred_cat.info(show_counts = True)
+
+# %%
+non_cat_ids = list(full_pred_cat.loc[full_pred_cat["eol_content_id_cat"].isna(), "treeoflife_id"])
+len(non_cat_ids)
+
+# %%
+pot_imgs = eol_pred_cat.loc[eol_pred_cat.treeoflife_id.isin(non_cat_ids)]
+pot_imgs["sciName"] = pot_imgs["genus"] + " " + pot_imgs["species"]
+pot_imgs.nunique()
+
+# %% [markdown]
+# Interesting, we have 831 unique EOL page IDs, but only 802 unique scientific names. Wonder how that matches up with 7-tuples.
+
+# %%
+taxa = list(pot_imgs.columns)[9:-2]
+pot_imgs["duplicate"] = pot_imgs.duplicated(subset = taxa, keep = "first")
+
+# our species count this way is num true in duplicate
+pot_imgs.duplicate.value_counts()
+
+# %% [markdown]
+# Okay, so this matches up with our `sciName` count.
+
+# %%
+eol_cols = list(pot_imgs.columns)[1:4] + list(pot_imgs.columns)[9:]
+
+pot_imgs = pot_imgs[eol_cols]
+
+#compare to catalog sciNames
+eol_catalog["sciName"] = eol_catalog["genus"] + " " + eol_catalog["species"]
+
+overlap_sciNames = pd.merge(pot_imgs, eol_catalog[eol_cols[:-1]], on = "sciName", how = "inner")
+overlap_sciNames.shape
+
+# %%
+overlap_sciNames.nunique()
+
+# %% [markdown]
+# Here are our other 402 species, so we didn't hold out anything but the 400 chosen.
+#
+# We're stuck with less images for some of them unless we source images from elsewhere.
+
+# %%