Sanity check on catalog to cargo archive match

Everything in the catalog matches to the cargo archive.
The combined manifests can't pull in all the images from that merge (this is where the missing images come in).

.gitattributes

@@ -68,3 +68,5 @@ eol_realign/data/links_manifest_cargo_on_md5.csv filter=lfs diff=lfs merge=lfs -
 eol_realign/data/links_cargo_manifest_IDmismatch.csv filter=lfs diff=lfs merge=lfs -text
 eol_realign/data/eol-cargo-archive_combined-manifest-checksums_links.csv filter=lfs diff=lfs merge=lfs -text
 eol_realign/data/eol-cargo-archive_catalog_combined-manifest-checksums_links.csv filter=lfs diff=lfs merge=lfs -text
+eol_realign/data/checksums_media_cargo_archive.csv filter=lfs diff=lfs merge=lfs -text
+eol_realign/data/combined_manifest_with_checksums.csv filter=lfs diff=lfs merge=lfs -text

eol_realign/data/checksums_media_cargo_archive.csv

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:f5b30008ba49fd342881e7ecd47c248d2a1c9b39960913518fcb78896bef3805
+size 490626452

eol_realign/data/combined_manifest_with_checksums.csv

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:03c75970541ad805c8f308dbe19d5b71642b724ced6324b240db41cd3e37b045
+size 4655278768

eol_realign/notebooks/catalog-cargo-manifest_test.ipynb

@@ -0,0 +1,497 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pandas as pd"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "TOL_FILEPATH = \"../../data/\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "tol = pd.read_csv(TOL_FILEPATH + \"catalog.csv\", low_memory=False)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "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  int64 \n",
+      " 3   eol_page_id     6250420 non-null  int64 \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: int64(2), object(10)\n",
+      "memory usage: 619.9+ MB\n"
+     ]
+    }
+   ],
+   "source": [
+    "# Remove duplicates\n",
+    "tol = tol.loc[tol.split != 'train_small']\n",
+    "\n",
+    "# Reduce to just EOL data & columns\n",
+    "eol = tol.loc[tol[\"eol_content_id\"].notna()]\n",
+    "eol_cols = [col for col in list(eol.columns) if \"bioscan\" not in col and \"inat\" not in col]\n",
+    "eol_catalog = eol[eol_cols]\n",
+    "\n",
+    "# Cast EOL content & page IDs as ints\n",
+    "eol_catalog = eol_catalog.astype({\"eol_content_id\": \"int64\", \"eol_page_id\": \"int64\"})\n",
+    "eol_catalog.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "archive = pd.read_csv(\"../data/checksums_media_cargo_archive.csv\", low_memory=False)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>split</th>\n",
+       "      <th>treeoflife_id</th>\n",
+       "      <th>eol_content_id_catalog</th>\n",
+       "      <th>eol_page_id_catalog</th>\n",
+       "      <th>kingdom</th>\n",
+       "      <th>phylum</th>\n",
+       "      <th>class</th>\n",
+       "      <th>order</th>\n",
+       "      <th>family</th>\n",
+       "      <th>genus</th>\n",
+       "      <th>species</th>\n",
+       "      <th>common</th>\n",
+       "      <th>combined_id_catalog</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>956715</th>\n",
+       "      <td>train</td>\n",
+       "      <td>aa563519-6d97-47c3-bcda-c72cdf19a1bf</td>\n",
+       "      <td>14855758</td>\n",
+       "      <td>788082</td>\n",
+       "      <td>Animalia</td>\n",
+       "      <td>Arthropoda</td>\n",
+       "      <td>Insecta</td>\n",
+       "      <td>Diptera</td>\n",
+       "      <td>Cecidomyiidae</td>\n",
+       "      <td>Geocrypta</td>\n",
+       "      <td>galii</td>\n",
+       "      <td>Geocrypta galii</td>\n",
+       "      <td>14855758_788082</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>956716</th>\n",
+       "      <td>train</td>\n",
+       "      <td>e3253a67-7114-41d5-ac55-1696d6c7f6f3</td>\n",
+       "      <td>22807070</td>\n",
+       "      <td>639017</td>\n",
+       "      <td>Plantae</td>\n",
+       "      <td>Tracheophyta</td>\n",
+       "      <td>Magnoliopsida</td>\n",
+       "      <td>Fabales</td>\n",
+       "      <td>Fabaceae</td>\n",
+       "      <td>Psoralea</td>\n",
+       "      <td>lupinella</td>\n",
+       "      <td>Psoralea lupinella</td>\n",
+       "      <td>22807070_639017</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "        split                         treeoflife_id  eol_content_id_catalog  \\\n",
+       "956715  train  aa563519-6d97-47c3-bcda-c72cdf19a1bf                14855758   \n",
+       "956716  train  e3253a67-7114-41d5-ac55-1696d6c7f6f3                22807070   \n",
+       "\n",
+       "        eol_page_id_catalog   kingdom        phylum          class    order  \\\n",
+       "956715               788082  Animalia    Arthropoda        Insecta  Diptera   \n",
+       "956716               639017   Plantae  Tracheophyta  Magnoliopsida  Fabales   \n",
+       "\n",
+       "               family      genus    species              common  \\\n",
+       "956715  Cecidomyiidae  Geocrypta      galii     Geocrypta galii   \n",
+       "956716       Fabaceae   Psoralea  lupinella  Psoralea lupinella   \n",
+       "\n",
+       "       combined_id_catalog  \n",
+       "956715     14855758_788082  \n",
+       "956716     22807070_639017  "
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "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)\n",
+    "eol_catalog.head(2)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "archive has 6725471 entries, with columns: ['Filename', 'MD5']\n"
+     ]
+    }
+   ],
+   "source": [
+    "# Cargo had 6,724,838 entries\n",
+    "print(f\"archive has {archive.shape[0]} entries, with columns: {list(archive.columns)}\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>Filename</th>\n",
+       "      <th>MD5</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>29538374_65414274_eol-full-size-copy.jpg</td>\n",
+       "      <td>98b1ed1430620ad50a6126cb2f9fcc74</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>27793900_888015_eol-full-size-copy.jpg</td>\n",
+       "      <td>2de2ff12d5f339fe9d81a170749f9cb6</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "                                   Filename                               MD5\n",
+       "0  29538374_65414274_eol-full-size-copy.jpg  98b1ed1430620ad50a6126cb2f9fcc74\n",
+       "1    27793900_888015_eol-full-size-copy.jpg  2de2ff12d5f339fe9d81a170749f9cb6"
+      ]
+     },
+     "execution_count": 8,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "archive.head(2)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def get_combined_id(filename):\n",
+    "    return filename.split(\"_e\")[0]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "archive[\"combined_id\"] = archive[\"Filename\"].apply(get_combined_id)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Merge catalog with archive (sanity check on our images since the cargo didn't match with all of catalog)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 6250420 entries, 0 to 6250419\n",
+      "Data columns (total 16 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_catalog  6250420 non-null  int64 \n",
+      " 3   eol_page_id_catalog     6250420 non-null  int64 \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",
+      " 12  combined_id_catalog     6250420 non-null  object\n",
+      " 13  Filename                6250420 non-null  object\n",
+      " 14  MD5                     6250420 non-null  object\n",
+      " 15  combined_id             6250420 non-null  object\n",
+      "dtypes: int64(2), object(14)\n",
+      "memory usage: 763.0+ MB\n"
+     ]
+    }
+   ],
+   "source": [
+    "catalog_archive = pd.merge(eol_catalog,\n",
+    "                           archive,\n",
+    "                           left_on = \"combined_id_catalog\",\n",
+    "                           right_on = \"combined_id\",\n",
+    "                           how=\"inner\"\n",
+    "                           )\n",
+    "catalog_archive.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Sanity check confirmed: Everything in the catalog is captured in our cargo archive."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Pull in combined manifest with checksums to merge on the archive checksums."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "Index(['filename_manifest', 'md5_combined_manifest',\n",
+       "       'combined_id_manifest_redownload', 'eol_content_id', 'eol_page_id',\n",
+       "       'medium_source_url', 'eol_full_size_copy_url', 'license_name',\n",
+       "       'copyright_owner', 'expected_image_filename', 'source_0706',\n",
+       "       'source_0726', 'source_1206', 'combined_id_full_manifest'],\n",
+       "      dtype='object')"
+      ]
+     },
+     "execution_count": 12,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "manifests = pd.read_csv(\"../data/combined_manifest_with_checksums.csv\", low_memory=False)\n",
+    "manifests.columns"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 6841202 entries, 0 to 6841201\n",
+      "Data columns (total 30 columns):\n",
+      " #   Column                           Non-Null Count    Dtype \n",
+      "---  ------                           --------------    ----- \n",
+      " 0   split                            6841202 non-null  object\n",
+      " 1   treeoflife_id                    6841202 non-null  object\n",
+      " 2   eol_content_id_catalog           6841202 non-null  int64 \n",
+      " 3   eol_page_id_catalog              6841202 non-null  int64 \n",
+      " 4   kingdom                          6551473 non-null  object\n",
+      " 5   phylum                           6553206 non-null  object\n",
+      " 6   class                            6532009 non-null  object\n",
+      " 7   order                            6525621 non-null  object\n",
+      " 8   family                           6506076 non-null  object\n",
+      " 9   genus                            6486130 non-null  object\n",
+      " 10  species                          6406307 non-null  object\n",
+      " 11  common                           6841202 non-null  object\n",
+      " 12  combined_id_catalog              6841202 non-null  object\n",
+      " 13  Filename                         6841202 non-null  object\n",
+      " 14  MD5                              6841202 non-null  object\n",
+      " 15  combined_id                      6841202 non-null  object\n",
+      " 16  filename_manifest                6841202 non-null  object\n",
+      " 17  md5_combined_manifest            6841202 non-null  object\n",
+      " 18  combined_id_manifest_redownload  6841202 non-null  object\n",
+      " 19  eol_content_id                   6841202 non-null  int64 \n",
+      " 20  eol_page_id                      6841202 non-null  int64 \n",
+      " 21  medium_source_url                6841202 non-null  object\n",
+      " 22  eol_full_size_copy_url           6841202 non-null  object\n",
+      " 23  license_name                     6841202 non-null  object\n",
+      " 24  copyright_owner                  6208498 non-null  object\n",
+      " 25  expected_image_filename          6841202 non-null  object\n",
+      " 26  source_0706                      6841202 non-null  bool  \n",
+      " 27  source_0726                      6841202 non-null  bool  \n",
+      " 28  source_1206                      6841202 non-null  bool  \n",
+      " 29  combined_id_full_manifest        6841202 non-null  object\n",
+      "dtypes: bool(3), int64(4), object(23)\n",
+      "memory usage: 1.4+ GB\n"
+     ]
+    }
+   ],
+   "source": [
+    "catalog_archive_manifest = pd.merge(catalog_archive,\n",
+    "                                    manifests,\n",
+    "                                    left_on = \"MD5\",\n",
+    "                                    right_on = \"md5_combined_manifest\",\n",
+    "                                    how = \"inner\",\n",
+    "                                    suffixes=(\"\",\"_manifests\")\n",
+    "                                    )\n",
+    "catalog_archive_manifest.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "6219674"
+      ]
+     },
+     "execution_count": 14,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "catalog_archive_manifest.treeoflife_id.nunique()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Only 6,219,674 of our 6,250,420 images were able to be pulled through the combined manifests."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "std",
+   "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
+}