Confirmed that content IDs that don't match to media manifest are in both TreeOfLife-10M and Rare Species datasets.

notebooks/ToL_license_check.ipynb

@@ -913,6 +913,41 @@
     "eol_df_media.head()"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 34,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "treeoflife_id             113471\n",
+       "eol_content_id            113471\n",
+       "eol_page_id                 9762\n",
+       "EOL page ID                    0\n",
+       "Medium Source URL              0\n",
+       "EOL Full-Size Copy URL         0\n",
+       "License Name                   0\n",
+       "Copyright Owner                0\n",
+       "dtype: int64"
+      ]
+     },
+     "execution_count": 34,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "eol_df_media.loc[eol_df_media[\"Medium Source URL\"].isna()].nunique()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "The missing info is distributed across 9,762 pages."
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -1153,6 +1188,120 @@
     "No, we do not have any of the missing ones in the older media manifest."
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Check how this compares to Catalog \n",
+    "Let's see if these are all images in TreeOfLife-10M, or a mix between it and Rare Species."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 29,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "cat_df = pd.read_csv(\"../data/catalog.csv\", low_memory = False)\n",
+    "# Remove duplicates in train_small\n",
+    "cat_df = cat_df.loc[cat_df.split != 'train_small']"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 30,
+   "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": 31,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "eol_cat_df = cat_df.loc[cat_df.data_source == \"EOL\"]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 32,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 6250420 entries, 0 to 6250419\n",
+      "Data columns (total 8 columns):\n",
+      " #   Column                  Non-Null Count    Dtype  \n",
+      "---  ------                  --------------    -----  \n",
+      " 0   treeoflife_id           6250420 non-null  object \n",
+      " 1   eol_content_id          6250420 non-null  float64\n",
+      " 2   eol_page_id             6250420 non-null  float64\n",
+      " 3   EOL page ID             6137845 non-null  float64\n",
+      " 4   Medium Source URL       6137845 non-null  object \n",
+      " 5   EOL Full-Size Copy URL  6137845 non-null  object \n",
+      " 6   License Name            6137845 non-null  object \n",
+      " 7   Copyright Owner         5527063 non-null  object \n",
+      "dtypes: float64(3), object(5)\n",
+      "memory usage: 381.5+ MB\n"
+     ]
+    }
+   ],
+   "source": [
+    "eol_cat_df_media = pd.merge(eol_cat_df[eol_license_cols], media, how = \"left\", on = \"eol_content_id\")\n",
+    "eol_cat_df_media.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Looks like the problem is distributed across both datasets."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 33,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "treeoflife_id             112575\n",
+       "eol_content_id            112575\n",
+       "eol_page_id                 9634\n",
+       "EOL page ID                    0\n",
+       "Medium Source URL              0\n",
+       "EOL Full-Size Copy URL         0\n",
+       "License Name                   0\n",
+       "Copyright Owner                0\n",
+       "dtype: int64"
+      ]
+     },
+     "execution_count": 33,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "eol_cat_df_media.loc[eol_cat_df_media[\"Medium Source URL\"].isna()].nunique()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "For `catalog` the missing information is distributed across 9,634 pages, so that's 128 pages (of 400) in the Rare Species dataset that we can't currently match."
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

notebooks/ToL_license_check.py

@@ -102,6 +102,12 @@ eol_df_media.info(show_counts = True)
 # %%
 eol_df_media.head()
 
+# %%
+eol_df_media.loc[eol_df_media["Medium Source URL"].isna()].nunique()
+
+# %% [markdown]
+# The missing info is distributed across 9,762 pages.
+
 # %% [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.
@@ -129,6 +135,37 @@ 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 how this compares to Catalog 
+# Let's see if these are all images in TreeOfLife-10M, or a mix between it and Rare Species.
+
+# %%
+cat_df = pd.read_csv("../data/catalog.csv", low_memory = False)
+# Remove duplicates in train_small
+cat_df = cat_df.loc[cat_df.split != 'train_small']
+
+# %%
+# 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_cat_df = cat_df.loc[cat_df.data_source == "EOL"]
+
+# %%
+eol_cat_df_media = pd.merge(eol_cat_df[eol_license_cols], media, how = "left", on = "eol_content_id")
+eol_cat_df_media.info(show_counts = True)
+
+# %% [markdown]
+# Looks like the problem is distributed across both datasets.
+
+# %%
+eol_cat_df_media.loc[eol_cat_df_media["Medium Source URL"].isna()].nunique()
+
+# %% [markdown]
+# For `catalog` the missing information is distributed across 9,634 pages, so that's 128 pages (of 400) in the Rare Species dataset that we can't currently match.
+
 # %% [markdown]
 # ## Check EOL License file(s) 
 #