Add common name to rarespecies-catalog

Done at end of re-gen_rs_catalog notebook.

eol_realign/notebooks/re-gen_rs_catalog.ipynb

@@ -1087,6 +1087,411 @@
     "updated_catalog.to_csv(RS_FILEPATH + \"rarespecies-catalog.csv\", index = False)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Add common name column\n",
+    "\n",
+    "Common names have now been requested, so we'll pull those in (from [`predicted-catalog.csv`](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/main/data/predicted-catalog.csv), [v3.3](https://huggingface.co/datasets/imageomics/ToL-EDA/commit/5260e84802d2910eedc2a206e7be035cf28f64d4)).\n",
+    "\n",
+    "Updating [`rarespecies-catalog.csv`](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/49400c376e62866be1c5038b673d2ebb002c0540/rare_species/data/rarespecies-catalog.csv)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# pull our updated catalog back in\n",
+    "updated_catalog = pd.read_csv(RS_FILEPATH + \"rarespecies-catalog.csv\",\n",
+    "                              low_memory=False,\n",
+    "                              dtype = {\"eol_content_id\": \"int64\", \"eol_page_id\": \"int64\"})"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "pred_cat = pd.read_csv(\"../../data/predicted-catalog.csv\", low_memory=False)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Reduce to just images sourced from EOL, cast content and page ids to `int64` for proper matching (will check there aren't different common name labels for some entries), then reduce to just Rare Species pages."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "eol_content_id    22580\n",
+       "eol_page_id         400\n",
+       "kingdom               1\n",
+       "phylum                5\n",
+       "class                15\n",
+       "order                85\n",
+       "family              202\n",
+       "genus               316\n",
+       "species             385\n",
+       "common              398\n",
+       "dtype: int64"
+      ]
+     },
+     "execution_count": 7,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "eol_pred = pred_cat.loc[pred_cat[\"eol_content_id\"].notna()]\n",
+    "eol_pred = eol_pred.astype({\"eol_content_id\": \"int64\", \"eol_page_id\": \"int64\"})\n",
+    "rs_pred = eol_pred.loc[eol_pred[\"eol_page_id\"].isin(list(updated_catalog.eol_page_id.unique()))]\n",
+    "\n",
+    "cols_interest = list(updated_catalog.columns)[1:-1]\n",
+    "cols_interest.append(\"common\")\n",
+    "rs_pred[cols_interest].nunique()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We don't seem to have unique common names for all of these entries. Let's find out what's duplicated."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/var/folders/nv/f0fq1p1n1_3b11x579py_0q80000gq/T/ipykernel_63935/2578193768.py:1: 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",
+      "  rs_pred[\"duplicate_page\"] = rs_pred.duplicated(\"eol_page_id\", keep = \"first\")\n"
+     ]
+    },
+    {
+     "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>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>duplicate_common</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>53510</th>\n",
+       "      <td>14217127</td>\n",
+       "      <td>45276300</td>\n",
+       "      <td>Animalia</td>\n",
+       "      <td>Cnidaria</td>\n",
+       "      <td>Anthozoa</td>\n",
+       "      <td>Scleractinia</td>\n",
+       "      <td>Acroporidae</td>\n",
+       "      <td>Acropora</td>\n",
+       "      <td>millepora</td>\n",
+       "      <td>staghorn coral</td>\n",
+       "      <td>True</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>95841</th>\n",
+       "      <td>28509006</td>\n",
+       "      <td>332461</td>\n",
+       "      <td>Animalia</td>\n",
+       "      <td>Chordata</td>\n",
+       "      <td>Amphibia</td>\n",
+       "      <td>Caudata</td>\n",
+       "      <td>Salamandridae</td>\n",
+       "      <td>Tylototriton</td>\n",
+       "      <td>verrucosus</td>\n",
+       "      <td>Yunnan Newt</td>\n",
+       "      <td>True</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "       eol_content_id  eol_page_id   kingdom    phylum     class  \\\n",
+       "53510        14217127     45276300  Animalia  Cnidaria  Anthozoa   \n",
+       "95841        28509006       332461  Animalia  Chordata  Amphibia   \n",
+       "\n",
+       "              order         family         genus     species          common  \\\n",
+       "53510  Scleractinia    Acroporidae      Acropora   millepora  staghorn coral   \n",
+       "95841       Caudata  Salamandridae  Tylototriton  verrucosus     Yunnan Newt   \n",
+       "\n",
+       "       duplicate_common  \n",
+       "53510              True  \n",
+       "95841              True  "
+      ]
+     },
+     "execution_count": 9,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "rs_pred[\"duplicate_page\"] = rs_pred.duplicated(\"eol_page_id\", keep = \"first\")\n",
+    "single_page = rs_pred.loc[~rs_pred[\"duplicate_page\"]]\n",
+    "single_page = single_page[cols_interest]\n",
+    "single_page[\"duplicate_common\"] = rs_pred.duplicated(\"common\", keep = \"first\")\n",
+    "\n",
+    "single_page.loc[single_page[\"duplicate_common\"]]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "(400, 11)"
+      ]
+     },
+     "execution_count": 10,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "single_page.shape"
+   ]
+  },
+  {
+   "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>eol_content_id</th>\n",
+       "      <th>eol_page_id</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>duplicate_common</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>5280</th>\n",
+       "      <td>28261341</td>\n",
+       "      <td>45276299</td>\n",
+       "      <td>Animalia</td>\n",
+       "      <td>Cnidaria</td>\n",
+       "      <td>Anthozoa</td>\n",
+       "      <td>Scleractinia</td>\n",
+       "      <td>Acroporidae</td>\n",
+       "      <td>Acropora</td>\n",
+       "      <td>acuminata</td>\n",
+       "      <td>staghorn coral</td>\n",
+       "      <td>False</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>17074</th>\n",
+       "      <td>8777107</td>\n",
+       "      <td>331513</td>\n",
+       "      <td>Animalia</td>\n",
+       "      <td>Chordata</td>\n",
+       "      <td>Amphibia</td>\n",
+       "      <td>Caudata</td>\n",
+       "      <td>Salamandridae</td>\n",
+       "      <td>Tylototriton</td>\n",
+       "      <td>shanjing</td>\n",
+       "      <td>Yunnan Newt</td>\n",
+       "      <td>False</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>53510</th>\n",
+       "      <td>14217127</td>\n",
+       "      <td>45276300</td>\n",
+       "      <td>Animalia</td>\n",
+       "      <td>Cnidaria</td>\n",
+       "      <td>Anthozoa</td>\n",
+       "      <td>Scleractinia</td>\n",
+       "      <td>Acroporidae</td>\n",
+       "      <td>Acropora</td>\n",
+       "      <td>millepora</td>\n",
+       "      <td>staghorn coral</td>\n",
+       "      <td>True</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>95841</th>\n",
+       "      <td>28509006</td>\n",
+       "      <td>332461</td>\n",
+       "      <td>Animalia</td>\n",
+       "      <td>Chordata</td>\n",
+       "      <td>Amphibia</td>\n",
+       "      <td>Caudata</td>\n",
+       "      <td>Salamandridae</td>\n",
+       "      <td>Tylototriton</td>\n",
+       "      <td>verrucosus</td>\n",
+       "      <td>Yunnan Newt</td>\n",
+       "      <td>True</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "       eol_content_id  eol_page_id   kingdom    phylum     class  \\\n",
+       "5280         28261341     45276299  Animalia  Cnidaria  Anthozoa   \n",
+       "17074         8777107       331513  Animalia  Chordata  Amphibia   \n",
+       "53510        14217127     45276300  Animalia  Cnidaria  Anthozoa   \n",
+       "95841        28509006       332461  Animalia  Chordata  Amphibia   \n",
+       "\n",
+       "              order         family         genus     species          common  \\\n",
+       "5280   Scleractinia    Acroporidae      Acropora   acuminata  staghorn coral   \n",
+       "17074       Caudata  Salamandridae  Tylototriton    shanjing     Yunnan Newt   \n",
+       "53510  Scleractinia    Acroporidae      Acropora   millepora  staghorn coral   \n",
+       "95841       Caudata  Salamandridae  Tylototriton  verrucosus     Yunnan Newt   \n",
+       "\n",
+       "       duplicate_common  \n",
+       "5280              False  \n",
+       "17074             False  \n",
+       "53510              True  \n",
+       "95841              True  "
+      ]
+     },
+     "execution_count": 11,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "duplicated_common_names = [\"staghorn coral\", \"Yunnan Newt\"]\n",
+    "single_page.loc[single_page[\"common\"].isin(duplicated_common_names)]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "So we have two common names that are each used for two species (within the same genus). That's not terribly unusual, but good to know.\n",
+    "\n",
+    "### Add the Common Name Column"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "rarespecies_id    11983\n",
+       "eol_content_id    11983\n",
+       "eol_page_id         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",
+       "common              398\n",
+       "dtype: int64"
+      ]
+     },
+     "execution_count": 14,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "def get_common_name(page_id):\n",
+    "    return single_page.loc[single_page[\"eol_page_id\"] == page_id, \"common\"].values[0]\n",
+    "\n",
+    "updated_catalog[\"common\"] = updated_catalog[\"eol_page_id\"].apply(get_common_name)\n",
+    "updated_catalog.nunique()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Save Updated Version with Common Names"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "updated_catalog.to_csv(RS_FILEPATH + \"rarespecies-catalog.csv\", index = False)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,

rare_species/data/rarespecies-catalog.csv

@@ -1,3 +1,3 @@
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-size 1734117
+oid sha256:96c458bd580caf5df4743c639eb38490e62eddef44b92be519d6771bdc2bf8fa
+size 1953805