Check media manifests from July 6 and 26 to confirm coverage of all listed images; 113K missing link to media manifest.

notebooks/ToL_license_check.ipynb

@@ -29,7 +29,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/var/folders/nv/f0fq1p1n1_3b11x579py_0q80000gq/T/ipykernel_88306/4112647395.py:1: DtypeWarning: Columns (5,6,7,14,15) have mixed types. Specify dtype option on import or set low_memory=False.\n",
+      "/var/folders/nv/f0fq1p1n1_3b11x579py_0q80000gq/T/ipykernel_74901/4112647395.py:1: DtypeWarning: Columns (5,6,7,14,15) have mixed types. Specify dtype option on import or set low_memory=False.\n",
       "  df = pd.read_csv(\"../data/predicted-catalog.csv\")\n"
      ]
     }
@@ -290,7 +290,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -309,7 +309,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -318,7 +318,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
@@ -509,7 +509,7 @@
        "4         EOL  "
       ]
      },
-     "execution_count": 5,
+     "execution_count": 7,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -527,51 +527,260 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "Index(['split', 'treeoflife_id', 'eol_content_id', 'eol_page_id'], dtype='object')"
+       "Index(['treeoflife_id', 'eol_content_id', 'eol_page_id'], dtype='object')"
       ]
      },
-     "execution_count": 6,
+     "execution_count": 9,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
-    "eol_license_cols = eol_df.columns[:4]\n",
+    "eol_license_cols = eol_df.columns[1:4]\n",
     "eol_license_cols"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "eol_license_df = eol_df[eol_license_cols]\n",
+    "#eol_license_df[\"license\"] = None"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "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>treeoflife_id</th>\n",
+       "      <th>eol_content_id</th>\n",
+       "      <th>eol_page_id</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>f2f0aa29-e87b-469c-bf5b-51a3611ab001</td>\n",
+       "      <td>22131926.0</td>\n",
+       "      <td>269504.0</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>5faa4f55-32e9-4872-953d-567e5d232e52</td>\n",
+       "      <td>22291283.0</td>\n",
+       "      <td>6101931.0</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>2282f2bf-2b52-4522-b588-dd6f356d5fd6</td>\n",
+       "      <td>21802775.0</td>\n",
+       "      <td>45513632.0</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3</th>\n",
+       "      <td>76b57c36-2181-4e6d-a5c4-b40e22a09449</td>\n",
+       "      <td>12784812.0</td>\n",
+       "      <td>51655800.0</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>4</th>\n",
+       "      <td>f57d3ab6-2cf5-484b-a590-e2a3d49a3ca2</td>\n",
+       "      <td>29713643.0</td>\n",
+       "      <td>45515896.0</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "                          treeoflife_id  eol_content_id  eol_page_id\n",
+       "0  f2f0aa29-e87b-469c-bf5b-51a3611ab001      22131926.0     269504.0\n",
+       "1  5faa4f55-32e9-4872-953d-567e5d232e52      22291283.0    6101931.0\n",
+       "2  2282f2bf-2b52-4522-b588-dd6f356d5fd6      21802775.0   45513632.0\n",
+       "3  76b57c36-2181-4e6d-a5c4-b40e22a09449      12784812.0   51655800.0\n",
+       "4  f57d3ab6-2cf5-484b-a590-e2a3d49a3ca2      29713643.0   45515896.0"
+      ]
+     },
+     "execution_count": 11,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "eol_license_df.head()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#eol_license_df.to_csv(\"../data/eol_licenses.csv\", index = False)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Merge with Media Manifest to Check for Licenses\n",
+    "Previous license files (retained below) are missing files, let's merge with the [media manifest](https://huggingface.co/datasets/imageomics/eol/blob/be7b7e6c372f6547e30030e9576d9cc638320099/data/interim/media_manifest.csv) all these images should have been downloaded from to see if there are any here that don't exist in it. From there we'll check licensing info."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
    "metadata": {},
    "outputs": [
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/var/folders/nv/f0fq1p1n1_3b11x579py_0q80000gq/T/ipykernel_88306/3674968623.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",
-      "  eol_license_df[\"license\"] = None\n"
+      "/var/folders/nv/f0fq1p1n1_3b11x579py_0q80000gq/T/ipykernel_74901/2809897267.py:1: DtypeWarning: Columns (5) have mixed types. Specify dtype option on import or set low_memory=False.\n",
+      "  media = pd.read_csv(\"../data/media_manifest (july 26).csv\")\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 6574224 entries, 0 to 6574223\n",
+      "Data columns (total 6 columns):\n",
+      " #   Column                  Non-Null Count    Dtype \n",
+      "---  ------                  --------------    ----- \n",
+      " 0   EOL content ID          6574224 non-null  int64 \n",
+      " 1   EOL page ID             6574224 non-null  int64 \n",
+      " 2   Medium Source URL       6574222 non-null  object\n",
+      " 3   EOL Full-Size Copy URL  6574224 non-null  object\n",
+      " 4   License Name            6574224 non-null  object\n",
+      " 5   Copyright Owner         5942181 non-null  object\n",
+      "dtypes: int64(2), object(4)\n",
+      "memory usage: 300.9+ MB\n"
      ]
     }
    ],
    "source": [
-    "eol_license_df = eol_df[eol_license_cols]\n",
-    "eol_license_df[\"license\"] = None"
+    "media = pd.read_csv(\"../data/media_manifest (july 26).csv\")\n",
+    "media.info(show_counts = True)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 19,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "(6277374, 3)"
+      ]
+     },
+     "execution_count": 19,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "eol_license_df.shape"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Notice that we have about 300K more entries in the media manifest, which is about expected from the [comparison of predicted-catalog to the original full list](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/main/notebooks/ToL_predicted-catalog_EDA.ipynb)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 16,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "media.rename(columns = {\"EOL content ID\": \"eol_content_id\"}, inplace = True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 20,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "eol_df_media = pd.merge(eol_license_df, media, how = \"left\", on = \"eol_content_id\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 21,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 6277374 entries, 0 to 6277373\n",
+      "Data columns (total 8 columns):\n",
+      " #   Column                  Non-Null Count    Dtype  \n",
+      "---  ------                  --------------    -----  \n",
+      " 0   treeoflife_id           6277374 non-null  object \n",
+      " 1   eol_content_id          6277374 non-null  float64\n",
+      " 2   eol_page_id             6277374 non-null  float64\n",
+      " 3   EOL page ID             6163903 non-null  float64\n",
+      " 4   Medium Source URL       6163903 non-null  object \n",
+      " 5   EOL Full-Size Copy URL  6163903 non-null  object \n",
+      " 6   License Name            6163903 non-null  object \n",
+      " 7   Copyright Owner         5549428 non-null  object \n",
+      "dtypes: float64(3), object(5)\n",
+      "memory usage: 383.1+ MB\n"
+     ]
+    }
+   ],
+   "source": [
+    "eol_df_media.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Clearly we have about 113K images whose content ID's are not in the media manifest, and thus we'er missing the URL and license info."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 22,
    "metadata": {},
    "outputs": [
     {
@@ -595,90 +804,353 @@
        "  <thead>\n",
        "    <tr style=\"text-align: right;\">\n",
        "      <th></th>\n",
-       "      <th>split</th>\n",
        "      <th>treeoflife_id</th>\n",
        "      <th>eol_content_id</th>\n",
        "      <th>eol_page_id</th>\n",
-       "      <th>license</th>\n",
+       "      <th>EOL page ID</th>\n",
+       "      <th>Medium Source URL</th>\n",
+       "      <th>EOL Full-Size Copy URL</th>\n",
+       "      <th>License Name</th>\n",
+       "      <th>Copyright Owner</th>\n",
        "    </tr>\n",
        "  </thead>\n",
        "  <tbody>\n",
        "    <tr>\n",
        "      <th>0</th>\n",
-       "      <td>train</td>\n",
        "      <td>f2f0aa29-e87b-469c-bf5b-51a3611ab001</td>\n",
        "      <td>22131926.0</td>\n",
        "      <td>269504.0</td>\n",
-       "      <td>None</td>\n",
+       "      <td>269504.0</td>\n",
+       "      <td>https://inaturalist-open-data.s3.amazonaws.com...</td>\n",
+       "      <td>https://content.eol.org/data/media/6a/ed/7a/18...</td>\n",
+       "      <td>cc-by-nc-4.0</td>\n",
+       "      <td>洪廷維</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>1</th>\n",
-       "      <td>train</td>\n",
        "      <td>5faa4f55-32e9-4872-953d-567e5d232e52</td>\n",
        "      <td>22291283.0</td>\n",
        "      <td>6101931.0</td>\n",
-       "      <td>None</td>\n",
+       "      <td>6101931.0</td>\n",
+       "      <td>https://inaturalist-open-data.s3.amazonaws.com...</td>\n",
+       "      <td>https://content.eol.org/data/media/7b/bc/92/18...</td>\n",
+       "      <td>cc-by-nc-4.0</td>\n",
+       "      <td>Игорь Поспелов</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>2</th>\n",
-       "      <td>train</td>\n",
        "      <td>2282f2bf-2b52-4522-b588-dd6f356d5fd6</td>\n",
        "      <td>21802775.0</td>\n",
        "      <td>45513632.0</td>\n",
-       "      <td>None</td>\n",
+       "      <td>45513632.0</td>\n",
+       "      <td>https://inaturalist-open-data.s3.amazonaws.com...</td>\n",
+       "      <td>https://content.eol.org/data/media/66/be/16/18...</td>\n",
+       "      <td>cc-by-nc-4.0</td>\n",
+       "      <td>Marina Gorbunova</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>3</th>\n",
-       "      <td>train</td>\n",
        "      <td>76b57c36-2181-4e6d-a5c4-b40e22a09449</td>\n",
        "      <td>12784812.0</td>\n",
        "      <td>51655800.0</td>\n",
-       "      <td>None</td>\n",
+       "      <td>51655800.0</td>\n",
+       "      <td>http://www.femorale.com/shellphotos/photos15/3...</td>\n",
+       "      <td>https://content.eol.org/data/media/c4/79/dc/14...</td>\n",
+       "      <td>cc-by-nc</td>\n",
+       "      <td>Femorale</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>4</th>\n",
-       "      <td>train</td>\n",
        "      <td>f57d3ab6-2cf5-484b-a590-e2a3d49a3ca2</td>\n",
        "      <td>29713643.0</td>\n",
        "      <td>45515896.0</td>\n",
-       "      <td>None</td>\n",
+       "      <td>45515896.0</td>\n",
+       "      <td>https://upload.wikimedia.org/wikipedia/commons...</td>\n",
+       "      <td>https://content.eol.org/data/media/5f/ef/95/50...</td>\n",
+       "      <td>cc-by-sa-3.0</td>\n",
+       "      <td>NaN</td>\n",
        "    </tr>\n",
        "  </tbody>\n",
        "</table>\n",
        "</div>"
       ],
       "text/plain": [
-       "   split                         treeoflife_id  eol_content_id  eol_page_id   \n",
-       "0  train  f2f0aa29-e87b-469c-bf5b-51a3611ab001      22131926.0     269504.0  \\\n",
-       "1  train  5faa4f55-32e9-4872-953d-567e5d232e52      22291283.0    6101931.0   \n",
-       "2  train  2282f2bf-2b52-4522-b588-dd6f356d5fd6      21802775.0   45513632.0   \n",
-       "3  train  76b57c36-2181-4e6d-a5c4-b40e22a09449      12784812.0   51655800.0   \n",
-       "4  train  f57d3ab6-2cf5-484b-a590-e2a3d49a3ca2      29713643.0   45515896.0   \n",
+       "                          treeoflife_id  eol_content_id  eol_page_id   \n",
+       "0  f2f0aa29-e87b-469c-bf5b-51a3611ab001      22131926.0     269504.0  \\\n",
+       "1  5faa4f55-32e9-4872-953d-567e5d232e52      22291283.0    6101931.0   \n",
+       "2  2282f2bf-2b52-4522-b588-dd6f356d5fd6      21802775.0   45513632.0   \n",
+       "3  76b57c36-2181-4e6d-a5c4-b40e22a09449      12784812.0   51655800.0   \n",
+       "4  f57d3ab6-2cf5-484b-a590-e2a3d49a3ca2      29713643.0   45515896.0   \n",
+       "\n",
+       "   EOL page ID                                  Medium Source URL   \n",
+       "0     269504.0  https://inaturalist-open-data.s3.amazonaws.com...  \\\n",
+       "1    6101931.0  https://inaturalist-open-data.s3.amazonaws.com...   \n",
+       "2   45513632.0  https://inaturalist-open-data.s3.amazonaws.com...   \n",
+       "3   51655800.0  http://www.femorale.com/shellphotos/photos15/3...   \n",
+       "4   45515896.0  https://upload.wikimedia.org/wikipedia/commons...   \n",
+       "\n",
+       "                              EOL Full-Size Copy URL  License Name   \n",
+       "0  https://content.eol.org/data/media/6a/ed/7a/18...  cc-by-nc-4.0  \\\n",
+       "1  https://content.eol.org/data/media/7b/bc/92/18...  cc-by-nc-4.0   \n",
+       "2  https://content.eol.org/data/media/66/be/16/18...  cc-by-nc-4.0   \n",
+       "3  https://content.eol.org/data/media/c4/79/dc/14...      cc-by-nc   \n",
+       "4  https://content.eol.org/data/media/5f/ef/95/50...  cc-by-sa-3.0   \n",
        "\n",
-       "  license  \n",
-       "0    None  \n",
-       "1    None  \n",
-       "2    None  \n",
-       "3    None  \n",
-       "4    None  "
+       "    Copyright Owner  \n",
+       "0               洪廷維  \n",
+       "1    Игорь Поспелов  \n",
+       "2  Marina Gorbunova  \n",
+       "3          Femorale  \n",
+       "4               NaN  "
       ]
      },
-     "execution_count": 9,
+     "execution_count": 22,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
-    "eol_license_df.head()"
+    "eol_df_media.head()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Save Record of Missing Content IDs & Compare to Older Media Manifest\n",
+    "Let's save a record of the missing content IDs, then we'll compare them to the [July 6 media manifest](https://huggingface.co/datasets/imageomics/eol/blob/eaa00a48fa188f12906c5b8074d60aa8e67eb135/data/interim/media_manifest.csv) to see if any are in there. The July 6 media manifest is smaller, but we'll still check."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 23,
+   "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>treeoflife_id</th>\n",
+       "      <th>eol_content_id</th>\n",
+       "      <th>eol_page_id</th>\n",
+       "      <th>EOL page ID</th>\n",
+       "      <th>Medium Source URL</th>\n",
+       "      <th>EOL Full-Size Copy URL</th>\n",
+       "      <th>License Name</th>\n",
+       "      <th>Copyright Owner</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>126</th>\n",
+       "      <td>4b56e165-c4d5-49f9-a321-ac9474d099f3</td>\n",
+       "      <td>2753529.0</td>\n",
+       "      <td>1225965.0</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>174</th>\n",
+       "      <td>421678a0-c8ec-43c8-815c-fc5888835068</td>\n",
+       "      <td>16288.0</td>\n",
+       "      <td>45514264.0</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>177</th>\n",
+       "      <td>be81bd8c-16a7-4911-8279-431245d67195</td>\n",
+       "      <td>2730639.0</td>\n",
+       "      <td>1034220.0</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>259</th>\n",
+       "      <td>fc765c82-84e6-437e-b9a5-1c7601c5be81</td>\n",
+       "      <td>2717906.0</td>\n",
+       "      <td>1052077.0</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>322</th>\n",
+       "      <td>8c1e6878-47ac-4f7b-8475-73e71c0e99c3</td>\n",
+       "      <td>2836995.0</td>\n",
+       "      <td>957074.0</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "                            treeoflife_id  eol_content_id  eol_page_id   \n",
+       "126  4b56e165-c4d5-49f9-a321-ac9474d099f3       2753529.0    1225965.0  \\\n",
+       "174  421678a0-c8ec-43c8-815c-fc5888835068         16288.0   45514264.0   \n",
+       "177  be81bd8c-16a7-4911-8279-431245d67195       2730639.0    1034220.0   \n",
+       "259  fc765c82-84e6-437e-b9a5-1c7601c5be81       2717906.0    1052077.0   \n",
+       "322  8c1e6878-47ac-4f7b-8475-73e71c0e99c3       2836995.0     957074.0   \n",
+       "\n",
+       "     EOL page ID Medium Source URL EOL Full-Size Copy URL License Name   \n",
+       "126          NaN               NaN                    NaN          NaN  \\\n",
+       "174          NaN               NaN                    NaN          NaN   \n",
+       "177          NaN               NaN                    NaN          NaN   \n",
+       "259          NaN               NaN                    NaN          NaN   \n",
+       "322          NaN               NaN                    NaN          NaN   \n",
+       "\n",
+       "    Copyright Owner  \n",
+       "126             NaN  \n",
+       "174             NaN  \n",
+       "177             NaN  \n",
+       "259             NaN  \n",
+       "322             NaN  "
+      ]
+     },
+     "execution_count": 23,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "eol_missing_content_ids = eol_df_media.loc[eol_df_media[\"Medium Source URL\"].isna()]\n",
+    "eol_missing_content_ids.head()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 24,
    "metadata": {},
    "outputs": [],
    "source": [
-    "eol_license_df.to_csv(\"../data/eol_licenses.csv\", index = False)"
+    "eol_missing_content_ids.to_csv(\"../data/eol_missing_content_ids.csv\", index = False)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 25,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/var/folders/nv/f0fq1p1n1_3b11x579py_0q80000gq/T/ipykernel_74901/610094471.py:1: DtypeWarning: Columns (0,1) have mixed types. Specify dtype option on import or set low_memory=False.\n",
+      "  media_old = pd.read_csv(\"../data/media_manifest.csv\")\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 5712231 entries, 0 to 5712230\n",
+      "Data columns (total 6 columns):\n",
+      " #   Column                  Non-Null Count    Dtype \n",
+      "---  ------                  --------------    ----- \n",
+      " 0   EOL content ID          5712231 non-null  object\n",
+      " 1   EOL page ID             5712163 non-null  object\n",
+      " 2   Medium Source URL       5712163 non-null  object\n",
+      " 3   EOL Full-Size Copy URL  5709587 non-null  object\n",
+      " 4   License Name            5709587 non-null  object\n",
+      " 5   Copyright Owner         4921801 non-null  object\n",
+      "dtypes: object(6)\n",
+      "memory usage: 261.5+ MB\n"
+     ]
+    }
+   ],
+   "source": [
+    "media_old = pd.read_csv(\"../data/media_manifest.csv\")\n",
+    "media_old.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 26,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "media_old.rename(columns = {\"EOL content ID\": \"eol_content_id\"}, inplace = True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 27,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "eol_df_media_old = pd.merge(eol_missing_content_ids[eol_license_cols], media_old, how = \"left\", on = \"eol_content_id\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 28,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 113471 entries, 0 to 113470\n",
+      "Data columns (total 8 columns):\n",
+      " #   Column                  Non-Null Count   Dtype  \n",
+      "---  ------                  --------------   -----  \n",
+      " 0   treeoflife_id           113471 non-null  object \n",
+      " 1   eol_content_id          113471 non-null  object \n",
+      " 2   eol_page_id             113471 non-null  float64\n",
+      " 3   EOL page ID             0 non-null       object \n",
+      " 4   Medium Source URL       0 non-null       object \n",
+      " 5   EOL Full-Size Copy URL  0 non-null       object \n",
+      " 6   License Name            0 non-null       object \n",
+      " 7   Copyright Owner         0 non-null       object \n",
+      "dtypes: float64(1), object(7)\n",
+      "memory usage: 6.9+ MB\n"
+     ]
+    }
+   ],
+   "source": [
+    "eol_df_media_old.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "No, we do not have any of the missing ones in the older media manifest."
    ]
   },
   {

notebooks/ToL_license_check.py

@@ -60,18 +60,74 @@ eol_df.head()
 # We don't need the BIOSCAN or iNat21 columns, nor the taxa columns.
 
 # %%
-eol_license_cols = eol_df.columns[:4]
+eol_license_cols = eol_df.columns[1:4]
 eol_license_cols
 
 # %%
 eol_license_df = eol_df[eol_license_cols]
-eol_license_df["license"] = None
+#eol_license_df["license"] = None
 
 # %%
 eol_license_df.head()
 
 # %%
-eol_license_df.to_csv("../data/eol_licenses.csv", index = False)
+#eol_license_df.to_csv("../data/eol_licenses.csv", index = False)
+
+# %% [markdown]
+# ### Merge with Media Manifest to Check for Licenses
+# Previous license files (retained below) are missing files, let's merge with the [media manifest](https://huggingface.co/datasets/imageomics/eol/blob/be7b7e6c372f6547e30030e9576d9cc638320099/data/interim/media_manifest.csv) all these images should have been downloaded from to see if there are any here that don't exist in it. From there we'll check licensing info.
+
+# %%
+media = pd.read_csv("../data/media_manifest (july 26).csv")
+media.info(show_counts = True)
+
+# %%
+eol_license_df.shape
+
+# %% [markdown]
+# Notice that we have about 300K more entries in the media manifest, which is about expected from the [comparison of predicted-catalog to the original full list](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/main/notebooks/ToL_predicted-catalog_EDA.ipynb).
+
+# %%
+media.rename(columns = {"EOL content ID": "eol_content_id"}, inplace = True)
+
+# %%
+eol_df_media = pd.merge(eol_license_df, media, how = "left", on = "eol_content_id")
+
+# %%
+eol_df_media.info(show_counts = True)
+
+# %% [markdown]
+# Clearly we have about 113K images whose content ID's are not in the media manifest, and thus we'er missing the URL and license info.
+
+# %%
+eol_df_media.head()
+
+# %% [markdown]
+# ### Save Record of Missing Content IDs & Compare to Older Media Manifest
+# Let's save a record of the missing content IDs, then we'll compare them to the [July 6 media manifest](https://huggingface.co/datasets/imageomics/eol/blob/eaa00a48fa188f12906c5b8074d60aa8e67eb135/data/interim/media_manifest.csv) to see if any are in there. The July 6 media manifest is smaller, but we'll still check.
+
+# %%
+eol_missing_content_ids = eol_df_media.loc[eol_df_media["Medium Source URL"].isna()]
+eol_missing_content_ids.head()
+
+# %%
+eol_missing_content_ids.to_csv("../data/eol_missing_content_ids.csv", index = False)
+
+# %%
+media_old = pd.read_csv("../data/media_manifest.csv")
+media_old.info(show_counts = True)
+
+# %%
+media_old.rename(columns = {"EOL content ID": "eol_content_id"}, inplace = True)
+
+# %%
+eol_df_media_old = pd.merge(eol_missing_content_ids[eol_license_cols], media_old, how = "left", on = "eol_content_id")
+
+# %%
+eol_df_media_old.info(show_counts = True)
+
+# %% [markdown]
+# No, we do not have any of the missing ones in the older media manifest.
 
 # %% [markdown]
 # ## Check EOL License file(s)