Analysis of EOL license file, missing content and some missing licenses.

notebooks/ToL_license_check.ipynb

@@ -681,6 +681,529 @@
     "eol_license_df.to_csv(\"../data/eol_licenses.csv\", index = False)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Check EOL License file(s) \n",
+    "\n",
+    "First we'll look at `eol_licenses.csv` from Sam, which only covers `catalog.csv`, so load both these in to make sure we've got full coverage for all included images (Matt's first match attempt from file created above couldn't find ~113K based on `eol_content_id`)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "cat_df = pd.read_csv(\"../data/catalog.csv\", low_memory = False)\n",
+    "license_df = pd.read_csv(\"../data/eol_licenses.csv\", low_memory = False)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Add data_source column for easier slicing\n",
+    "cat_df.loc[cat_df['inat21_filename'].notna(), 'data_source'] = 'iNat21'\n",
+    "cat_df.loc[cat_df['bioscan_filename'].notna(), 'data_source'] = 'BIOSCAN'\n",
+    "cat_df.loc[cat_df['eol_content_id'].notna(), 'data_source'] = 'EOL'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "eol_df = cat_df.loc[cat_df.data_source == \"EOL\"]"
+   ]
+  },
+  {
+   "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>treeoflife10m_id</th>\n",
+       "      <th>eol_content_id</th>\n",
+       "      <th>eol_page_id</th>\n",
+       "      <th>license</th>\n",
+       "      <th>owner</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>5a1daf92-60b2-4d23-9916-4c45ec796167</td>\n",
+       "      <td>5470022</td>\n",
+       "      <td>500901</td>\n",
+       "      <td>cc-by-nc-sa-3.0</td>\n",
+       "      <td>Susan A. Wineriter/Singing Insects of North Am...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>de10bc79-c46c-4b5b-bc75-64d569b9bf4a</td>\n",
+       "      <td>5470023</td>\n",
+       "      <td>858799</td>\n",
+       "      <td>cc-by-nc-sa-3.0</td>\n",
+       "      <td>Thomas J. Walker/Singing Insects of North America</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>b68e1a7b-b294-4cfd-b423-1eed359f7c94</td>\n",
+       "      <td>5470024</td>\n",
+       "      <td>598702</td>\n",
+       "      <td>cc-by-nc-sa-3.0</td>\n",
+       "      <td>Thomas J. Walker/Singing Insects of North America</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3</th>\n",
+       "      <td>dcc46822-ffa6-46de-a639-bc5e296f50cf</td>\n",
+       "      <td>5470025</td>\n",
+       "      <td>598703</td>\n",
+       "      <td>cc-by-nc-sa-3.0</td>\n",
+       "      <td>Thomas J. Walker/Singing Insects of North America</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>4</th>\n",
+       "      <td>112d0571-c2dc-442b-9b2e-6665226b0942</td>\n",
+       "      <td>5470026</td>\n",
+       "      <td>598703</td>\n",
+       "      <td>cc-by-nc-sa-3.0</td>\n",
+       "      <td>Thomas J. Walker/Singing Insects of North America</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "                       treeoflife10m_id  eol_content_id  eol_page_id   \n",
+       "0  5a1daf92-60b2-4d23-9916-4c45ec796167         5470022       500901  \\\n",
+       "1  de10bc79-c46c-4b5b-bc75-64d569b9bf4a         5470023       858799   \n",
+       "2  b68e1a7b-b294-4cfd-b423-1eed359f7c94         5470024       598702   \n",
+       "3  dcc46822-ffa6-46de-a639-bc5e296f50cf         5470025       598703   \n",
+       "4  112d0571-c2dc-442b-9b2e-6665226b0942         5470026       598703   \n",
+       "\n",
+       "           license                                              owner  \n",
+       "0  cc-by-nc-sa-3.0  Susan A. Wineriter/Singing Insects of North Am...  \n",
+       "1  cc-by-nc-sa-3.0  Thomas J. Walker/Singing Insects of North America  \n",
+       "2  cc-by-nc-sa-3.0  Thomas J. Walker/Singing Insects of North America  \n",
+       "3  cc-by-nc-sa-3.0  Thomas J. Walker/Singing Insects of North America  \n",
+       "4  cc-by-nc-sa-3.0  Thomas J. Walker/Singing Insects of North America  "
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "license_df.head()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "(6020135, 5)"
+      ]
+     },
+     "execution_count": 8,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "license_df.shape"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "(6844184, 18)"
+      ]
+     },
+     "execution_count": 9,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "eol_df.shape"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Yeah, we're missing about 82K images in the license file."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 6020135 entries, 0 to 6020134\n",
+      "Data columns (total 5 columns):\n",
+      " #   Column            Non-Null Count    Dtype \n",
+      "---  ------            --------------    ----- \n",
+      " 0   treeoflife10m_id  6020135 non-null  object\n",
+      " 1   eol_content_id    6020135 non-null  int64 \n",
+      " 2   eol_page_id       6020135 non-null  int64 \n",
+      " 3   license           6020135 non-null  object\n",
+      " 4   owner             5402786 non-null  object\n",
+      "dtypes: int64(2), object(3)\n",
+      "memory usage: 229.7+ MB\n"
+     ]
+    }
+   ],
+   "source": [
+    "license_df.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "license\n",
+       "cc-0-1.0                           282812\n",
+       "cc-publicdomain                    172641\n",
+       "cc-by-nc-sa-3.0                    130678\n",
+       "cc-by-nc                            14160\n",
+       "cc-by-sa-3.0                        11622\n",
+       "cc-by-3.0                            5430\n",
+       "cc-by-nc-2.0                            2\n",
+       "No known copyright restrictions         2\n",
+       "cc-by-nc-sa                             1\n",
+       "cc-by                                   1\n",
+       "Name: count, dtype: int64"
+      ]
+     },
+     "execution_count": 11,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "license_df.loc[license_df[\"owner\"].isna(), \"license\"].value_counts()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "CC BY licenses without `owner` indicated is rather problematic."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "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>treeoflife10m_id</th>\n",
+       "      <th>eol_content_id</th>\n",
+       "      <th>eol_page_id</th>\n",
+       "      <th>license</th>\n",
+       "      <th>owner</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>4396225</th>\n",
+       "      <td>f86dbf9d-8402-471f-9772-ccb418b6f8fe</td>\n",
+       "      <td>28351223</td>\n",
+       "      <td>51902011</td>\n",
+       "      <td>cc-0-1.0</td>\n",
+       "      <td>NaN</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1072047</th>\n",
+       "      <td>2cd83c40-1fd8-44f8-867b-57aef25ff281</td>\n",
+       "      <td>14796160</td>\n",
+       "      <td>160017</td>\n",
+       "      <td>cc-by-nc-sa-3.0</td>\n",
+       "      <td>NaN</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>4356765</th>\n",
+       "      <td>3df036ca-631d-4795-9079-d85b8fcef3c1</td>\n",
+       "      <td>28311652</td>\n",
+       "      <td>1249103</td>\n",
+       "      <td>cc-0-1.0</td>\n",
+       "      <td>NaN</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1162697</th>\n",
+       "      <td>883e002f-fa75-4e96-9b78-7dce34a3a4e1</td>\n",
+       "      <td>14888539</td>\n",
+       "      <td>11486400</td>\n",
+       "      <td>cc-by-nc-sa-3.0</td>\n",
+       "      <td>NaN</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>377813</th>\n",
+       "      <td>5babc816-d142-434b-b505-997de27a87b2</td>\n",
+       "      <td>10646391</td>\n",
+       "      <td>52251608</td>\n",
+       "      <td>cc-by-nc</td>\n",
+       "      <td>NaN</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "                             treeoflife10m_id  eol_content_id  eol_page_id   \n",
+       "4396225  f86dbf9d-8402-471f-9772-ccb418b6f8fe        28351223     51902011  \\\n",
+       "1072047  2cd83c40-1fd8-44f8-867b-57aef25ff281        14796160       160017   \n",
+       "4356765  3df036ca-631d-4795-9079-d85b8fcef3c1        28311652      1249103   \n",
+       "1162697  883e002f-fa75-4e96-9b78-7dce34a3a4e1        14888539     11486400   \n",
+       "377813   5babc816-d142-434b-b505-997de27a87b2        10646391     52251608   \n",
+       "\n",
+       "                 license owner  \n",
+       "4396225         cc-0-1.0   NaN  \n",
+       "1072047  cc-by-nc-sa-3.0   NaN  \n",
+       "4356765         cc-0-1.0   NaN  \n",
+       "1162697  cc-by-nc-sa-3.0   NaN  \n",
+       "377813          cc-by-nc   NaN  "
+      ]
+     },
+     "execution_count": 14,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "license_df.loc[license_df[\"owner\"].isna()].sample(5)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Tracked down `eol_content_id` [14796160](https://eol.org/media/14796160), original source is [BioImages](https://www.bioimages.org.uk/image.php?id=79950) with copyright Malcolm Storey (like 99% of the images on the site (see their [conditions of use](https://www.bioimages.org.uk/cright.htm))). He is listed as \"compiler\" on the EOL media page."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "license\n",
+       "cc-by-nc-4.0                       2431101\n",
+       "cc-by-sa-3.0                        776696\n",
+       "cc-by-nc-sa-3.0                     559160\n",
+       "cc-by-3.0                           428137\n",
+       "cc-by-4.0                           379862\n",
+       "cc-by-nc                            327467\n",
+       "cc-publicdomain                     299235\n",
+       "cc-0-1.0                            299119\n",
+       "cc-by-nc-sa-4.0                     191967\n",
+       "cc-by-nc-sa                         153033\n",
+       "cc-by-sa-4.0                         66743\n",
+       "cc-by                                47300\n",
+       "cc-by-sa-2.0                         31019\n",
+       "cc-by-nc-2.0                         28175\n",
+       "No known copyright restrictions        801\n",
+       "cc-by-nc-sa-2.5                        315\n",
+       "public domain                            5\n",
+       "Name: count, dtype: int64"
+      ]
+     },
+     "execution_count": 12,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "license_df.license.value_counts()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
+   "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>treeoflife10m_id</th>\n",
+       "      <th>eol_content_id</th>\n",
+       "      <th>eol_page_id</th>\n",
+       "      <th>license</th>\n",
+       "      <th>owner</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>4937687</th>\n",
+       "      <td>a19281ef-3c49-4bec-b7b0-b7b4027d6237</td>\n",
+       "      <td>29043581</td>\n",
+       "      <td>46576133</td>\n",
+       "      <td>No known copyright restrictions</td>\n",
+       "      <td>Smithsonian Institution</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>5298480</th>\n",
+       "      <td>4d4c7538-9cbd-4ac6-9f4c-fc73bf0c260f</td>\n",
+       "      <td>29405472</td>\n",
+       "      <td>1178661</td>\n",
+       "      <td>No known copyright restrictions</td>\n",
+       "      <td>Internet Archive Book Images</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>5452574</th>\n",
+       "      <td>74a636d7-b681-47be-bed7-5a726de5c9d1</td>\n",
+       "      <td>29560411</td>\n",
+       "      <td>964204</td>\n",
+       "      <td>No known copyright restrictions</td>\n",
+       "      <td>current</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>4959929</th>\n",
+       "      <td>b012b50b-04c2-4ca9-9078-18351897e3b9</td>\n",
+       "      <td>29065898</td>\n",
+       "      <td>126217</td>\n",
+       "      <td>No known copyright restrictions</td>\n",
+       "      <td>Biologicheskii institut (Akademiia nauk SSSR);...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>5073633</th>\n",
+       "      <td>4a2c6dd6-1dd4-4a0c-9a9d-0f219f3a4069</td>\n",
+       "      <td>29179854</td>\n",
+       "      <td>65417018</td>\n",
+       "      <td>No known copyright restrictions</td>\n",
+       "      <td>OSU Special Collections &amp; Archives : Commons</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "                             treeoflife10m_id  eol_content_id  eol_page_id   \n",
+       "4937687  a19281ef-3c49-4bec-b7b0-b7b4027d6237        29043581     46576133  \\\n",
+       "5298480  4d4c7538-9cbd-4ac6-9f4c-fc73bf0c260f        29405472      1178661   \n",
+       "5452574  74a636d7-b681-47be-bed7-5a726de5c9d1        29560411       964204   \n",
+       "4959929  b012b50b-04c2-4ca9-9078-18351897e3b9        29065898       126217   \n",
+       "5073633  4a2c6dd6-1dd4-4a0c-9a9d-0f219f3a4069        29179854     65417018   \n",
+       "\n",
+       "                                 license   \n",
+       "4937687  No known copyright restrictions  \\\n",
+       "5298480  No known copyright restrictions   \n",
+       "5452574  No known copyright restrictions   \n",
+       "4959929  No known copyright restrictions   \n",
+       "5073633  No known copyright restrictions   \n",
+       "\n",
+       "                                                     owner  \n",
+       "4937687                            Smithsonian Institution  \n",
+       "5298480                       Internet Archive Book Images  \n",
+       "5452574                                            current  \n",
+       "4959929  Biologicheskii institut (Akademiia nauk SSSR);...  \n",
+       "5073633       OSU Special Collections & Archives : Commons  "
+      ]
+     },
+     "execution_count": 15,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "license_df.loc[license_df[\"license\"] == \"No known copyright restrictions\"].sample(5)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 16,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "license_df.loc[license_df[\"owner\"].isna()].to_csv(\"../data/eol_licenses_missing_owner.csv\", index = False)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,

notebooks/ToL_license_check.py

@@ -73,4 +73,58 @@ eol_license_df.head()
 # %%
 eol_license_df.to_csv("../data/eol_licenses.csv", index = False)
 
+# %% [markdown]
+# ## Check EOL License file(s) 
+#
+# First we'll look at `eol_licenses.csv` from Sam, which only covers `catalog.csv`, so load both these in to make sure we've got full coverage for all included images (Matt's first match attempt from file created above couldn't find ~113K based on `eol_content_id`).
+
+# %%
+cat_df = pd.read_csv("../data/catalog.csv", low_memory = False)
+license_df = pd.read_csv("../data/eol_licenses.csv", low_memory = False)
+
+# %%
+# Add data_source column for easier slicing
+cat_df.loc[cat_df['inat21_filename'].notna(), 'data_source'] = 'iNat21'
+cat_df.loc[cat_df['bioscan_filename'].notna(), 'data_source'] = 'BIOSCAN'
+cat_df.loc[cat_df['eol_content_id'].notna(), 'data_source'] = 'EOL'
+
+# %%
+eol_df = cat_df.loc[cat_df.data_source == "EOL"]
+
+# %%
+license_df.head()
+
+# %%
+license_df.shape
+
+# %%
+eol_df.shape
+
+# %% [markdown]
+# Yeah, we're missing about 82K images in the license file.
+
+# %%
+license_df.info(show_counts = True)
+
+# %%
+license_df.loc[license_df["owner"].isna(), "license"].value_counts()
+
+# %% [markdown]
+# CC BY licenses without `owner` indicated is rather problematic.
+
+# %%
+license_df.loc[license_df["owner"].isna()].sample(5)
+
+# %% [markdown]
+# Tracked down `eol_content_id` [14796160](https://eol.org/media/14796160), original source is [BioImages](https://www.bioimages.org.uk/image.php?id=79950) with copyright Malcolm Storey (like 99% of the images on the site (see their [conditions of use](https://www.bioimages.org.uk/cright.htm))). He is listed as "compiler" on the EOL media page.
+
+# %%
+license_df.license.value_counts()
+
+# %%
+license_df.loc[license_df["license"] == "No known copyright restrictions"].sample(5)
+
+# %%
+license_df.loc[license_df["owner"].isna()].to_csv("../data/eol_licenses_missing_owner.csv", index = False)
+
 # %%