Upload archive analysis and data for rare species

No additional images were matched, rs_links CSV is for adjusting Rare Species dataset to avoid duplicate images within species

.gitattributes

@@ -66,3 +66,4 @@ visuals/phyla_ToL_tree.pdf filter=lfs diff=lfs merge=lfs -text
 eol_realign/data/links_inner.csv filter=lfs diff=lfs merge=lfs -text
 eol_realign/data/links_manifest_cargo_on_md5.csv filter=lfs diff=lfs merge=lfs -text
 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_combined-manifest-checksums_links.csv

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:0c53ba3c261089abe0ce8fc7e21fc21baa111db3e06333aaedc090f66c5a9519
+size 3545231521

eol_realign/notebooks/links_rs_duplicates.ipynb

@@ -9,25 +9,36 @@
     "import pandas as pd"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "RS_FILEPATH = \"../../rare_species/data/\""
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Read in Links CSV file"
+    "### Read in Links CSV file\n",
+    "\n",
+    "Full cargo archive has some more content than the [original `links_manifest_cargo_on_md5.csv`](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/fa08e0f6692a013e4e4f5ca30dd0e8883c0021d8/eol_realign/data/links_manifest_cargo_on_md5.csv)."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
-    "links_manifest_cargo = pd.read_csv(\"../data/links_manifest_cargo_on_md5.csv\", low_memory=False)"
+    "links_manifest_cargo = pd.read_csv(\"../data/eol-cargo-archive_combined-manifest-checksums_links.csv\", low_memory=False)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
@@ -35,28 +46,29 @@
      "output_type": "stream",
      "text": [
       "<class 'pandas.core.frame.DataFrame'>\n",
-      "RangeIndex: 7513329 entries, 0 to 7513328\n",
-      "Data columns (total 16 columns):\n",
-      " #   Column                          Non-Null Count    Dtype \n",
-      "---  ------                          --------------    ----- \n",
-      " 0   eol_content_id                  7513329 non-null  int64 \n",
-      " 1   eol_page_id                     7513329 non-null  int64 \n",
-      " 2   medium_source_url               7513329 non-null  object\n",
-      " 3   eol_full_size_copy_url          7513329 non-null  object\n",
-      " 4   license_name                    7513329 non-null  object\n",
-      " 5   copyright_owner                 6860238 non-null  object\n",
-      " 6   expected_image_filename         7513329 non-null  object\n",
-      " 7   source_0706                     7513329 non-null  bool  \n",
-      " 8   source_0726                     7513329 non-null  bool  \n",
-      " 9   source_1206                     7513329 non-null  bool  \n",
-      " 10  combined_id_manifest            7513329 non-null  object\n",
-      " 11  md5                             7513329 non-null  object\n",
-      " 12  combined_id_manifest_checksums  7513329 non-null  object\n",
-      " 13  eol_content_id_cargo            7513329 non-null  int64 \n",
-      " 14  eol_page_id_cargo               7513329 non-null  int64 \n",
-      " 15  combined_id_cargo               7513329 non-null  object\n",
-      "dtypes: bool(3), int64(4), object(9)\n",
-      "memory usage: 766.7+ MB\n"
+      "RangeIndex: 7514001 entries, 0 to 7514000\n",
+      "Data columns (total 17 columns):\n",
+      " #   Column                           Non-Null Count    Dtype \n",
+      "---  ------                           --------------    ----- \n",
+      " 0   filename_archive                 7514001 non-null  object\n",
+      " 1   md5_archive                      7514001 non-null  object\n",
+      " 2   combined_id_archive              7514001 non-null  object\n",
+      " 3   filename_manifest                7514001 non-null  object\n",
+      " 4   md5_combined_manifest            7514001 non-null  object\n",
+      " 5   combined_id_manifest_redownload  7514001 non-null  object\n",
+      " 6   eol_content_id                   7514001 non-null  int64 \n",
+      " 7   eol_page_id                      7514001 non-null  int64 \n",
+      " 8   medium_source_url                7514001 non-null  object\n",
+      " 9   eol_full_size_copy_url           7514001 non-null  object\n",
+      " 10  license_name                     7514001 non-null  object\n",
+      " 11  copyright_owner                  6860825 non-null  object\n",
+      " 12  expected_image_filename          7514001 non-null  object\n",
+      " 13  source_0706                      7514001 non-null  bool  \n",
+      " 14  source_0726                      7514001 non-null  bool  \n",
+      " 15  source_1206                      7514001 non-null  bool  \n",
+      " 16  combined_id_full_manifest        7514001 non-null  object\n",
+      "dtypes: bool(3), int64(2), object(12)\n",
+      "memory usage: 824.1+ MB\n"
      ]
     }
    ],
@@ -73,7 +85,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
@@ -102,7 +114,7 @@
     }
    ],
    "source": [
-    "rs_catalog = pd.read_csv(\"../../rare_species/data/rarespecies-catalog.csv\",\n",
+    "rs_catalog = pd.read_csv(RS_FILEPATH + \"rarespecies-catalog.csv\",\n",
     "                         low_memory=False,\n",
     "                         dtype = {\"eol_content_id\": \"int64\", \"eol_page_id\": \"int64\"})\n",
     "rs_catalog.info(show_counts = True)"
@@ -110,7 +122,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -120,7 +132,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
@@ -129,39 +141,40 @@
      "text": [
       "<class 'pandas.core.frame.DataFrame'>\n",
       "RangeIndex: 12552 entries, 0 to 12551\n",
-      "Data columns (total 28 columns):\n",
-      " #   Column                          Non-Null Count  Dtype \n",
-      "---  ------                          --------------  ----- \n",
-      " 0   rarespecies_id                  12552 non-null  object\n",
-      " 1   eol_content_id_rs               12552 non-null  int64 \n",
-      " 2   eol_page_id_rs                  12552 non-null  int64 \n",
-      " 3   kingdom                         12552 non-null  object\n",
-      " 4   phylum                          12552 non-null  object\n",
-      " 5   class                           12552 non-null  object\n",
-      " 6   order                           12552 non-null  object\n",
-      " 7   family                          12552 non-null  object\n",
-      " 8   genus                           12552 non-null  object\n",
-      " 9   species                         12552 non-null  object\n",
-      " 10  sciName                         12552 non-null  object\n",
-      " 11  combined_id_rs                  12552 non-null  object\n",
-      " 12  eol_content_id                  12552 non-null  int64 \n",
-      " 13  eol_page_id                     12552 non-null  int64 \n",
-      " 14  medium_source_url               12552 non-null  object\n",
-      " 15  eol_full_size_copy_url          12552 non-null  object\n",
-      " 16  license_name                    12552 non-null  object\n",
-      " 17  copyright_owner                 11171 non-null  object\n",
-      " 18  expected_image_filename         12552 non-null  object\n",
-      " 19  source_0706                     12552 non-null  bool  \n",
-      " 20  source_0726                     12552 non-null  bool  \n",
-      " 21  source_1206                     12552 non-null  bool  \n",
-      " 22  combined_id_manifest            12552 non-null  object\n",
-      " 23  md5                             12552 non-null  object\n",
-      " 24  combined_id_manifest_checksums  12552 non-null  object\n",
-      " 25  eol_content_id_cargo            12552 non-null  int64 \n",
-      " 26  eol_page_id_cargo               12552 non-null  int64 \n",
-      " 27  combined_id_cargo               12552 non-null  object\n",
-      "dtypes: bool(3), int64(6), object(19)\n",
-      "memory usage: 2.4+ MB\n"
+      "Data columns (total 29 columns):\n",
+      " #   Column                           Non-Null Count  Dtype \n",
+      "---  ------                           --------------  ----- \n",
+      " 0   rarespecies_id                   12552 non-null  object\n",
+      " 1   eol_content_id_rs                12552 non-null  int64 \n",
+      " 2   eol_page_id_rs                   12552 non-null  int64 \n",
+      " 3   kingdom                          12552 non-null  object\n",
+      " 4   phylum                           12552 non-null  object\n",
+      " 5   class                            12552 non-null  object\n",
+      " 6   order                            12552 non-null  object\n",
+      " 7   family                           12552 non-null  object\n",
+      " 8   genus                            12552 non-null  object\n",
+      " 9   species                          12552 non-null  object\n",
+      " 10  sciName                          12552 non-null  object\n",
+      " 11  combined_id_rs                   12552 non-null  object\n",
+      " 12  filename_archive                 12552 non-null  object\n",
+      " 13  md5_archive                      12552 non-null  object\n",
+      " 14  combined_id_archive              12552 non-null  object\n",
+      " 15  filename_manifest                12552 non-null  object\n",
+      " 16  md5_combined_manifest            12552 non-null  object\n",
+      " 17  combined_id_manifest_redownload  12552 non-null  object\n",
+      " 18  eol_content_id                   12552 non-null  int64 \n",
+      " 19  eol_page_id                      12552 non-null  int64 \n",
+      " 20  medium_source_url                12552 non-null  object\n",
+      " 21  eol_full_size_copy_url           12552 non-null  object\n",
+      " 22  license_name                     12552 non-null  object\n",
+      " 23  copyright_owner                  11171 non-null  object\n",
+      " 24  expected_image_filename          12552 non-null  object\n",
+      " 25  source_0706                      12552 non-null  bool  \n",
+      " 26  source_0726                      12552 non-null  bool  \n",
+      " 27  source_1206                      12552 non-null  bool  \n",
+      " 28  combined_id_full_manifest        12552 non-null  object\n",
+      "dtypes: bool(3), int64(4), object(22)\n",
+      "memory usage: 2.5+ MB\n"
      ]
     }
    ],
@@ -169,51 +182,52 @@
     "rs_links = pd.merge(rs_catalog,\n",
     "                    links_manifest_cargo,\n",
     "                    left_on = \"combined_id_rs\",\n",
-    "                    right_on = \"combined_id_cargo\",\n",
+    "                    right_on = \"combined_id_archive\", # merge on archive (replaced cargo)\n",
     "                    how = \"inner\")\n",
     "rs_links.info(show_counts = True)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "rarespecies_id                    11826\n",
-       "eol_content_id_rs                 11826\n",
-       "eol_page_id_rs                      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",
-       "combined_id_rs                    11826\n",
-       "eol_content_id                    12221\n",
-       "eol_page_id                         447\n",
-       "medium_source_url                 12056\n",
-       "eol_full_size_copy_url            12119\n",
-       "license_name                         15\n",
-       "copyright_owner                    3724\n",
-       "expected_image_filename           12221\n",
-       "source_0706                           2\n",
-       "source_0726                           2\n",
-       "source_1206                           2\n",
-       "combined_id_manifest              12221\n",
-       "md5                               11663\n",
-       "combined_id_manifest_checksums    12221\n",
-       "eol_content_id_cargo              11826\n",
-       "eol_page_id_cargo                   400\n",
-       "combined_id_cargo                 11826\n",
+       "rarespecies_id                     11826\n",
+       "eol_content_id_rs                  11826\n",
+       "eol_page_id_rs                       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",
+       "combined_id_rs                     11826\n",
+       "filename_archive                   11826\n",
+       "md5_archive                        11663\n",
+       "combined_id_archive                11826\n",
+       "filename_manifest                  12221\n",
+       "md5_combined_manifest              11663\n",
+       "combined_id_manifest_redownload    12221\n",
+       "eol_content_id                     12221\n",
+       "eol_page_id                          447\n",
+       "medium_source_url                  12056\n",
+       "eol_full_size_copy_url             12119\n",
+       "license_name                          15\n",
+       "copyright_owner                     3724\n",
+       "expected_image_filename            12221\n",
+       "source_0706                            2\n",
+       "source_0726                            2\n",
+       "source_1206                            2\n",
+       "combined_id_full_manifest          12221\n",
        "dtype: int64"
       ]
      },
-     "execution_count": 7,
+     "execution_count": 8,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -222,6 +236,13 @@
     "rs_links.nunique()"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "All these numbers match our check with the cargo file."
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -231,7 +252,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [
     {
@@ -240,7 +261,7 @@
        "11826"
       ]
      },
-     "execution_count": 8,
+     "execution_count": 9,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -252,7 +273,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [
     {
@@ -264,7 +285,7 @@
        " '29975068_45509269']"
       ]
      },
-     "execution_count": 9,
+     "execution_count": 10,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -275,20 +296,20 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "4310    20080369_46579618\n",
-       "842     27592101_46560177\n",
-       "1111      20945361_570181\n",
-       "3609    10819533_46516728\n",
+       "7687      21071827_355546\n",
+       "6923    27808045_46570095\n",
+       "7019    20599607_45513966\n",
+       "873       28902910_311199\n",
        "Name: combined_id_rs, dtype: object"
       ]
      },
-     "execution_count": 10,
+     "execution_count": 11,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -299,7 +320,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [
     {
@@ -335,7 +356,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [
     {
@@ -356,7 +377,7 @@
        "dtype: int64"
       ]
      },
-     "execution_count": 12,
+     "execution_count": 13,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -367,7 +388,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 14,
    "metadata": {},
    "outputs": [
     {
@@ -411,7 +432,7 @@
        "Name: count, dtype: int64"
       ]
      },
-     "execution_count": 13,
+     "execution_count": 14,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -422,7 +443,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 15,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -436,7 +457,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 16,
    "metadata": {},
    "outputs": [
     {
@@ -450,7 +471,7 @@
        " array([46560546])]"
       ]
      },
-     "execution_count": 15,
+     "execution_count": 16,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -464,7 +485,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 17,
    "metadata": {},
    "outputs": [
     {
@@ -478,7 +499,7 @@
        " (46560546, 24)]"
       ]
      },
-     "execution_count": 16,
+     "execution_count": 17,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -501,7 +522,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 18,
    "metadata": {},
    "outputs": [
     {
@@ -541,9 +562,9 @@
        "  </thead>\n",
        "  <tbody>\n",
        "    <tr>\n",
-       "      <th>7726</th>\n",
-       "      <td>667586ab-145a-4076-9669-535447aa2b6c</td>\n",
-       "      <td>30098504</td>\n",
+       "      <th>1413</th>\n",
+       "      <td>d239159f-cb15-4c30-8aeb-d8177f8cf34a</td>\n",
+       "      <td>30098492</td>\n",
        "      <td>205909</td>\n",
        "      <td>Animalia</td>\n",
        "      <td>Chordata</td>\n",
@@ -553,12 +574,12 @@
        "      <td>Scaphirhynchus</td>\n",
        "      <td>albus</td>\n",
        "      <td>Scaphirhynchus albus</td>\n",
-       "      <td>30098504_205909</td>\n",
+       "      <td>30098492_205909</td>\n",
        "    </tr>\n",
        "    <tr>\n",
-       "      <th>1413</th>\n",
-       "      <td>d239159f-cb15-4c30-8aeb-d8177f8cf34a</td>\n",
-       "      <td>30098492</td>\n",
+       "      <th>7619</th>\n",
+       "      <td>4d7436d1-82de-416b-8a51-6452efd45f44</td>\n",
+       "      <td>30098515</td>\n",
        "      <td>205909</td>\n",
        "      <td>Animalia</td>\n",
        "      <td>Chordata</td>\n",
@@ -568,7 +589,7 @@
        "      <td>Scaphirhynchus</td>\n",
        "      <td>albus</td>\n",
        "      <td>Scaphirhynchus albus</td>\n",
-       "      <td>30098492_205909</td>\n",
+       "      <td>30098515_205909</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>7916</th>\n",
@@ -586,9 +607,9 @@
        "      <td>30098499_205909</td>\n",
        "    </tr>\n",
        "    <tr>\n",
-       "      <th>6909</th>\n",
-       "      <td>d33f93de-31ec-434a-985e-a9cdeb79b557</td>\n",
-       "      <td>30098484</td>\n",
+       "      <th>11026</th>\n",
+       "      <td>a9560f41-403d-46a0-a92a-9694cceffe96</td>\n",
+       "      <td>30098523</td>\n",
        "      <td>205909</td>\n",
        "      <td>Animalia</td>\n",
        "      <td>Chordata</td>\n",
@@ -598,12 +619,12 @@
        "      <td>Scaphirhynchus</td>\n",
        "      <td>albus</td>\n",
        "      <td>Scaphirhynchus albus</td>\n",
-       "      <td>30098484_205909</td>\n",
+       "      <td>30098523_205909</td>\n",
        "    </tr>\n",
        "    <tr>\n",
-       "      <th>6564</th>\n",
-       "      <td>bd27fc74-caa5-4fe3-9dbc-776127bd03e7</td>\n",
-       "      <td>30098489</td>\n",
+       "      <th>193</th>\n",
+       "      <td>ba2857c7-f02d-44f9-a116-8a450dc53e14</td>\n",
+       "      <td>30098516</td>\n",
        "      <td>205909</td>\n",
        "      <td>Animalia</td>\n",
        "      <td>Chordata</td>\n",
@@ -613,36 +634,43 @@
        "      <td>Scaphirhynchus</td>\n",
        "      <td>albus</td>\n",
        "      <td>Scaphirhynchus albus</td>\n",
-       "      <td>30098489_205909</td>\n",
+       "      <td>30098516_205909</td>\n",
        "    </tr>\n",
        "  </tbody>\n",
        "</table>\n",
        "</div>"
       ],
       "text/plain": [
-       "                            rarespecies_id  eol_content_id_rs  eol_page_id_rs  \\\n",
-       "7726  667586ab-145a-4076-9669-535447aa2b6c           30098504          205909   \n",
-       "1413  d239159f-cb15-4c30-8aeb-d8177f8cf34a           30098492          205909   \n",
-       "7916  2d342a7c-7e0c-4981-9630-019bb90183be           30098499          205909   \n",
-       "6909  d33f93de-31ec-434a-985e-a9cdeb79b557           30098484          205909   \n",
-       "6564  bd27fc74-caa5-4fe3-9dbc-776127bd03e7           30098489          205909   \n",
+       "                             rarespecies_id  eol_content_id_rs  \\\n",
+       "1413   d239159f-cb15-4c30-8aeb-d8177f8cf34a           30098492   \n",
+       "7619   4d7436d1-82de-416b-8a51-6452efd45f44           30098515   \n",
+       "7916   2d342a7c-7e0c-4981-9630-019bb90183be           30098499   \n",
+       "11026  a9560f41-403d-46a0-a92a-9694cceffe96           30098523   \n",
+       "193    ba2857c7-f02d-44f9-a116-8a450dc53e14           30098516   \n",
        "\n",
-       "       kingdom    phylum           class             order         family  \\\n",
-       "7726  Animalia  Chordata  Actinopterygii  Acipenseriformes  Acipenseridae   \n",
-       "1413  Animalia  Chordata  Actinopterygii  Acipenseriformes  Acipenseridae   \n",
-       "7916  Animalia  Chordata  Actinopterygii  Acipenseriformes  Acipenseridae   \n",
-       "6909  Animalia  Chordata  Actinopterygii  Acipenseriformes  Acipenseridae   \n",
-       "6564  Animalia  Chordata  Actinopterygii  Acipenseriformes  Acipenseridae   \n",
+       "       eol_page_id_rs   kingdom    phylum           class             order  \\\n",
+       "1413           205909  Animalia  Chordata  Actinopterygii  Acipenseriformes   \n",
+       "7619           205909  Animalia  Chordata  Actinopterygii  Acipenseriformes   \n",
+       "7916           205909  Animalia  Chordata  Actinopterygii  Acipenseriformes   \n",
+       "11026          205909  Animalia  Chordata  Actinopterygii  Acipenseriformes   \n",
+       "193            205909  Animalia  Chordata  Actinopterygii  Acipenseriformes   \n",
        "\n",
-       "               genus species               sciName   combined_id_rs  \n",
-       "7726  Scaphirhynchus   albus  Scaphirhynchus albus  30098504_205909  \n",
-       "1413  Scaphirhynchus   albus  Scaphirhynchus albus  30098492_205909  \n",
-       "7916  Scaphirhynchus   albus  Scaphirhynchus albus  30098499_205909  \n",
-       "6909  Scaphirhynchus   albus  Scaphirhynchus albus  30098484_205909  \n",
-       "6564  Scaphirhynchus   albus  Scaphirhynchus albus  30098489_205909  "
+       "              family           genus species               sciName  \\\n",
+       "1413   Acipenseridae  Scaphirhynchus   albus  Scaphirhynchus albus   \n",
+       "7619   Acipenseridae  Scaphirhynchus   albus  Scaphirhynchus albus   \n",
+       "7916   Acipenseridae  Scaphirhynchus   albus  Scaphirhynchus albus   \n",
+       "11026  Acipenseridae  Scaphirhynchus   albus  Scaphirhynchus albus   \n",
+       "193    Acipenseridae  Scaphirhynchus   albus  Scaphirhynchus albus   \n",
+       "\n",
+       "        combined_id_rs  \n",
+       "1413   30098492_205909  \n",
+       "7619   30098515_205909  \n",
+       "7916   30098499_205909  \n",
+       "11026  30098523_205909  \n",
+       "193    30098516_205909  "
       ]
      },
-     "execution_count": 17,
+     "execution_count": 18,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -661,7 +689,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 19,
    "metadata": {},
    "outputs": [
     {
@@ -701,9 +729,9 @@
        "  </thead>\n",
        "  <tbody>\n",
        "    <tr>\n",
-       "      <th>3655</th>\n",
-       "      <td>12633820-3a3a-4c77-bd38-7221bd18b747</td>\n",
-       "      <td>27648157</td>\n",
+       "      <th>9702</th>\n",
+       "      <td>92da8fa4-fb94-42b3-9483-86d2672d6644</td>\n",
+       "      <td>27648165</td>\n",
        "      <td>46560546</td>\n",
        "      <td>Animalia</td>\n",
        "      <td>Chordata</td>\n",
@@ -713,12 +741,12 @@
        "      <td>Raja</td>\n",
        "      <td>asterias</td>\n",
        "      <td>Raja asterias</td>\n",
-       "      <td>27648157_46560546</td>\n",
+       "      <td>27648165_46560546</td>\n",
        "    </tr>\n",
        "    <tr>\n",
-       "      <th>4243</th>\n",
-       "      <td>8a7eae46-57af-4132-b914-78556479db67</td>\n",
-       "      <td>27648161</td>\n",
+       "      <th>3655</th>\n",
+       "      <td>12633820-3a3a-4c77-bd38-7221bd18b747</td>\n",
+       "      <td>27648157</td>\n",
        "      <td>46560546</td>\n",
        "      <td>Animalia</td>\n",
        "      <td>Chordata</td>\n",
@@ -728,12 +756,12 @@
        "      <td>Raja</td>\n",
        "      <td>asterias</td>\n",
        "      <td>Raja asterias</td>\n",
-       "      <td>27648161_46560546</td>\n",
+       "      <td>27648157_46560546</td>\n",
        "    </tr>\n",
        "    <tr>\n",
-       "      <th>2347</th>\n",
-       "      <td>de4a6ca0-6fc2-40de-907e-c99b98a9ca3e</td>\n",
-       "      <td>27648164</td>\n",
+       "      <th>2025</th>\n",
+       "      <td>6cb50905-48ee-4770-9605-91a95e3d027c</td>\n",
+       "      <td>27648159</td>\n",
        "      <td>46560546</td>\n",
        "      <td>Animalia</td>\n",
        "      <td>Chordata</td>\n",
@@ -743,12 +771,12 @@
        "      <td>Raja</td>\n",
        "      <td>asterias</td>\n",
        "      <td>Raja asterias</td>\n",
-       "      <td>27648164_46560546</td>\n",
+       "      <td>27648159_46560546</td>\n",
        "    </tr>\n",
        "    <tr>\n",
-       "      <th>3481</th>\n",
-       "      <td>2bcba9f3-a3a4-4a2b-a4f4-84e35be0e35f</td>\n",
-       "      <td>27648163</td>\n",
+       "      <th>1358</th>\n",
+       "      <td>d436ec20-202d-44ec-9081-ca59afef356f</td>\n",
+       "      <td>27648166</td>\n",
        "      <td>46560546</td>\n",
        "      <td>Animalia</td>\n",
        "      <td>Chordata</td>\n",
@@ -758,12 +786,12 @@
        "      <td>Raja</td>\n",
        "      <td>asterias</td>\n",
        "      <td>Raja asterias</td>\n",
-       "      <td>27648163_46560546</td>\n",
+       "      <td>27648166_46560546</td>\n",
        "    </tr>\n",
        "    <tr>\n",
-       "      <th>1358</th>\n",
-       "      <td>d436ec20-202d-44ec-9081-ca59afef356f</td>\n",
-       "      <td>27648166</td>\n",
+       "      <th>6574</th>\n",
+       "      <td>a7c43306-6a3a-4d94-b7f0-147ad9f20a73</td>\n",
+       "      <td>27648160</td>\n",
        "      <td>46560546</td>\n",
        "      <td>Animalia</td>\n",
        "      <td>Chordata</td>\n",
@@ -773,7 +801,7 @@
        "      <td>Raja</td>\n",
        "      <td>asterias</td>\n",
        "      <td>Raja asterias</td>\n",
-       "      <td>27648166_46560546</td>\n",
+       "      <td>27648160_46560546</td>\n",
        "    </tr>\n",
        "  </tbody>\n",
        "</table>\n",
@@ -781,28 +809,28 @@
       ],
       "text/plain": [
        "                            rarespecies_id  eol_content_id_rs  eol_page_id_rs  \\\n",
+       "9702  92da8fa4-fb94-42b3-9483-86d2672d6644           27648165        46560546   \n",
        "3655  12633820-3a3a-4c77-bd38-7221bd18b747           27648157        46560546   \n",
-       "4243  8a7eae46-57af-4132-b914-78556479db67           27648161        46560546   \n",
-       "2347  de4a6ca0-6fc2-40de-907e-c99b98a9ca3e           27648164        46560546   \n",
-       "3481  2bcba9f3-a3a4-4a2b-a4f4-84e35be0e35f           27648163        46560546   \n",
+       "2025  6cb50905-48ee-4770-9605-91a95e3d027c           27648159        46560546   \n",
        "1358  d436ec20-202d-44ec-9081-ca59afef356f           27648166        46560546   \n",
+       "6574  a7c43306-6a3a-4d94-b7f0-147ad9f20a73           27648160        46560546   \n",
        "\n",
        "       kingdom    phylum           class       order   family genus   species  \\\n",
+       "9702  Animalia  Chordata  Chondrichthyes  Rajiformes  Rajidae  Raja  asterias   \n",
        "3655  Animalia  Chordata  Chondrichthyes  Rajiformes  Rajidae  Raja  asterias   \n",
-       "4243  Animalia  Chordata  Chondrichthyes  Rajiformes  Rajidae  Raja  asterias   \n",
-       "2347  Animalia  Chordata  Chondrichthyes  Rajiformes  Rajidae  Raja  asterias   \n",
-       "3481  Animalia  Chordata  Chondrichthyes  Rajiformes  Rajidae  Raja  asterias   \n",
+       "2025  Animalia  Chordata  Chondrichthyes  Rajiformes  Rajidae  Raja  asterias   \n",
        "1358  Animalia  Chordata  Chondrichthyes  Rajiformes  Rajidae  Raja  asterias   \n",
+       "6574  Animalia  Chordata  Chondrichthyes  Rajiformes  Rajidae  Raja  asterias   \n",
        "\n",
        "            sciName     combined_id_rs  \n",
+       "9702  Raja asterias  27648165_46560546  \n",
        "3655  Raja asterias  27648157_46560546  \n",
-       "4243  Raja asterias  27648161_46560546  \n",
-       "2347  Raja asterias  27648164_46560546  \n",
-       "3481  Raja asterias  27648163_46560546  \n",
-       "1358  Raja asterias  27648166_46560546  "
+       "2025  Raja asterias  27648159_46560546  \n",
+       "1358  Raja asterias  27648166_46560546  \n",
+       "6574  Raja asterias  27648160_46560546  "
       ]
      },
-     "execution_count": 18,
+     "execution_count": 19,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -820,7 +848,26 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": 20,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def get_archive_content(combined_id):\n",
+    "    return combined_id.split(\"_\")[0]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 21,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "links_manifest_cargo[\"eol_content_id_archive\"] = links_manifest_cargo[\"combined_id_archive\"].apply(get_archive_content)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 22,
    "metadata": {},
    "outputs": [
     {
@@ -844,6 +891,12 @@
        "  <thead>\n",
        "    <tr style=\"text-align: right;\">\n",
        "      <th></th>\n",
+       "      <th>filename_archive</th>\n",
+       "      <th>md5_archive</th>\n",
+       "      <th>combined_id_archive</th>\n",
+       "      <th>filename_manifest</th>\n",
+       "      <th>md5_combined_manifest</th>\n",
+       "      <th>combined_id_manifest_redownload</th>\n",
        "      <th>eol_content_id</th>\n",
        "      <th>eol_page_id</th>\n",
        "      <th>medium_source_url</th>\n",
@@ -854,12 +907,8 @@
        "      <th>source_0706</th>\n",
        "      <th>source_0726</th>\n",
        "      <th>source_1206</th>\n",
-       "      <th>combined_id_manifest</th>\n",
-       "      <th>md5</th>\n",
-       "      <th>combined_id_manifest_checksums</th>\n",
-       "      <th>eol_content_id_cargo</th>\n",
-       "      <th>eol_page_id_cargo</th>\n",
-       "      <th>combined_id_cargo</th>\n",
+       "      <th>combined_id_full_manifest</th>\n",
+       "      <th>eol_content_id_archive</th>\n",
        "    </tr>\n",
        "  </thead>\n",
        "  <tbody>\n",
@@ -869,23 +918,24 @@
       ],
       "text/plain": [
        "Empty DataFrame\n",
-       "Columns: [eol_content_id, eol_page_id, medium_source_url, eol_full_size_copy_url, license_name, copyright_owner, expected_image_filename, source_0706, source_0726, source_1206, combined_id_manifest, md5, combined_id_manifest_checksums, eol_content_id_cargo, eol_page_id_cargo, combined_id_cargo]\n",
+       "Columns: [filename_archive, md5_archive, combined_id_archive, filename_manifest, md5_combined_manifest, combined_id_manifest_redownload, eol_content_id, eol_page_id, medium_source_url, eol_full_size_copy_url, license_name, copyright_owner, expected_image_filename, source_0706, source_0726, source_1206, combined_id_full_manifest, eol_content_id_archive]\n",
        "Index: []"
       ]
      },
-     "execution_count": 19,
+     "execution_count": 22,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
     "# check if content IDs get recycled, content ID: 27648165, now online as: 30223317\n",
-    "links_manifest_cargo.loc[links_manifest_cargo[\"eol_content_id_cargo\"] == 30223317]"
+    "# is eol_content_id the archive content ID?\n",
+    "links_manifest_cargo.loc[links_manifest_cargo[\"eol_content_id_archive\"] == 30223317]"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 20,
+   "execution_count": 23,
    "metadata": {},
    "outputs": [
     {
@@ -909,6 +959,12 @@
        "  <thead>\n",
        "    <tr style=\"text-align: right;\">\n",
        "      <th></th>\n",
+       "      <th>filename_archive</th>\n",
+       "      <th>md5_archive</th>\n",
+       "      <th>combined_id_archive</th>\n",
+       "      <th>filename_manifest</th>\n",
+       "      <th>md5_combined_manifest</th>\n",
+       "      <th>combined_id_manifest_redownload</th>\n",
        "      <th>eol_content_id</th>\n",
        "      <th>eol_page_id</th>\n",
        "      <th>medium_source_url</th>\n",
@@ -919,12 +975,8 @@
        "      <th>source_0706</th>\n",
        "      <th>source_0726</th>\n",
        "      <th>source_1206</th>\n",
-       "      <th>combined_id_manifest</th>\n",
-       "      <th>md5</th>\n",
-       "      <th>combined_id_manifest_checksums</th>\n",
-       "      <th>eol_content_id_cargo</th>\n",
-       "      <th>eol_page_id_cargo</th>\n",
-       "      <th>combined_id_cargo</th>\n",
+       "      <th>combined_id_full_manifest</th>\n",
+       "      <th>eol_content_id_archive</th>\n",
        "    </tr>\n",
        "  </thead>\n",
        "  <tbody>\n",
@@ -934,11 +986,11 @@
       ],
       "text/plain": [
        "Empty DataFrame\n",
-       "Columns: [eol_content_id, eol_page_id, medium_source_url, eol_full_size_copy_url, license_name, copyright_owner, expected_image_filename, source_0706, source_0726, source_1206, combined_id_manifest, md5, combined_id_manifest_checksums, eol_content_id_cargo, eol_page_id_cargo, combined_id_cargo]\n",
+       "Columns: [filename_archive, md5_archive, combined_id_archive, filename_manifest, md5_combined_manifest, combined_id_manifest_redownload, eol_content_id, eol_page_id, medium_source_url, eol_full_size_copy_url, license_name, copyright_owner, expected_image_filename, source_0706, source_0726, source_1206, combined_id_full_manifest, eol_content_id_archive]\n",
        "Index: []"
       ]
      },
-     "execution_count": 20,
+     "execution_count": 23,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -948,6 +1000,76 @@
     "links_manifest_cargo.loc[links_manifest_cargo[\"eol_content_id\"] == 30223317]"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 24,
+   "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_archive</th>\n",
+       "      <th>md5_archive</th>\n",
+       "      <th>combined_id_archive</th>\n",
+       "      <th>filename_manifest</th>\n",
+       "      <th>md5_combined_manifest</th>\n",
+       "      <th>combined_id_manifest_redownload</th>\n",
+       "      <th>eol_content_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",
+       "      <th>expected_image_filename</th>\n",
+       "      <th>source_0706</th>\n",
+       "      <th>source_0726</th>\n",
+       "      <th>source_1206</th>\n",
+       "      <th>combined_id_full_manifest</th>\n",
+       "      <th>eol_content_id_archive</th>\n",
+       "      <th>eol_content_id_manifest</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "Empty DataFrame\n",
+       "Columns: [filename_archive, md5_archive, combined_id_archive, filename_manifest, md5_combined_manifest, combined_id_manifest_redownload, eol_content_id, eol_page_id, medium_source_url, eol_full_size_copy_url, license_name, copyright_owner, expected_image_filename, source_0706, source_0726, source_1206, combined_id_full_manifest, eol_content_id_archive, eol_content_id_manifest]\n",
+       "Index: []"
+      ]
+     },
+     "execution_count": 24,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# to be sure we check manifest\n",
+    "links_manifest_cargo[\"eol_content_id_manifest\"] = links_manifest_cargo[\"combined_id_full_manifest\"].apply(get_archive_content)\n",
+    "\n",
+    "links_manifest_cargo.loc[links_manifest_cargo[\"eol_content_id_manifest\"] == 30223317]"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -957,14 +1079,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 27,
+   "execution_count": 25,
    "metadata": {},
    "outputs": [],
    "source": [
     "# Save CSV of mismatched, they should be salvageable.\n",
     "# We saw these images both online and in our cargo, just with different IDs\n",
     "\n",
-    "mismatched_rs.to_csv(\"../data/mismatched_rarespecies.csv\", index=False)"
+    "mismatched_rs.to_csv(\"../data/archive_mismatched_rarespecies.csv\", index=False)"
    ]
   },
   {
@@ -985,17 +1107,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 21,
+   "execution_count": 26,
    "metadata": {},
    "outputs": [],
    "source": [
-    "rs_links[\"md5_dupes\"] = rs_links.duplicated(subset = \"md5\", keep = \"first\")\n",
+    "rs_links[\"md5_dupes\"] = rs_links.duplicated(subset = \"md5_archive\", keep = \"first\")\n",
     "rs_links[\"rs_id_dupes\"] = rs_links.duplicated(subset = \"rarespecies_id\", keep = \"first\")"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 22,
+   "execution_count": 27,
    "metadata": {},
    "outputs": [
     {
@@ -1006,7 +1128,7 @@
        "Name: count, dtype: int64"
       ]
      },
-     "execution_count": 22,
+     "execution_count": 27,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1017,7 +1139,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 23,
+   "execution_count": 28,
    "metadata": {},
    "outputs": [
     {
@@ -1029,7 +1151,7 @@
        "Name: count, dtype: int64"
       ]
      },
-     "execution_count": 23,
+     "execution_count": 28,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1047,46 +1169,47 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": 29,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "rarespecies_id                    163\n",
-       "eol_content_id_rs                 163\n",
-       "eol_page_id_rs                     80\n",
-       "kingdom                             1\n",
-       "phylum                              4\n",
-       "class                               9\n",
-       "order                              37\n",
-       "family                             56\n",
-       "genus                              73\n",
-       "species                            80\n",
-       "sciName                            80\n",
-       "combined_id_rs                    163\n",
-       "eol_content_id                    163\n",
-       "eol_page_id                        80\n",
-       "medium_source_url                 163\n",
-       "eol_full_size_copy_url            163\n",
-       "license_name                       10\n",
-       "copyright_owner                    48\n",
-       "expected_image_filename           163\n",
-       "source_0706                         2\n",
-       "source_0726                         1\n",
-       "source_1206                         2\n",
-       "combined_id_manifest              163\n",
-       "md5                               163\n",
-       "combined_id_manifest_checksums    163\n",
-       "eol_content_id_cargo              163\n",
-       "eol_page_id_cargo                  80\n",
-       "combined_id_cargo                 163\n",
-       "md5_dupes                           1\n",
-       "rs_id_dupes                         1\n",
+       "rarespecies_id                     163\n",
+       "eol_content_id_rs                  163\n",
+       "eol_page_id_rs                      80\n",
+       "kingdom                              1\n",
+       "phylum                               4\n",
+       "class                                9\n",
+       "order                               37\n",
+       "family                              56\n",
+       "genus                               73\n",
+       "species                             80\n",
+       "sciName                             80\n",
+       "combined_id_rs                     163\n",
+       "filename_archive                   163\n",
+       "md5_archive                        163\n",
+       "combined_id_archive                163\n",
+       "filename_manifest                  163\n",
+       "md5_combined_manifest              163\n",
+       "combined_id_manifest_redownload    163\n",
+       "eol_content_id                     163\n",
+       "eol_page_id                         80\n",
+       "medium_source_url                  163\n",
+       "eol_full_size_copy_url             163\n",
+       "license_name                        10\n",
+       "copyright_owner                     54\n",
+       "expected_image_filename            163\n",
+       "source_0706                          2\n",
+       "source_0726                          2\n",
+       "source_1206                          2\n",
+       "combined_id_full_manifest          163\n",
+       "md5_dupes                            1\n",
+       "rs_id_dupes                          1\n",
        "dtype: int64"
       ]
      },
-     "execution_count": 24,
+     "execution_count": 29,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1099,7 +1222,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 25,
+   "execution_count": 30,
    "metadata": {},
    "outputs": [
     {
@@ -1119,7 +1242,7 @@
        "Name: count, dtype: int64"
       ]
      },
-     "execution_count": 25,
+     "execution_count": 30,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1144,7 +1267,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 26,
+   "execution_count": 31,
    "metadata": {},
    "outputs": [
     {
@@ -1153,7 +1276,7 @@
        "[4453333, 460289, 45277122, 46561158, 1286909, 45510188, 45510548, 791049]"
       ]
      },
-     "execution_count": 26,
+     "execution_count": 31,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1165,7 +1288,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 27,
+   "execution_count": 32,
    "metadata": {
     "lines_to_next_cell": 2
    },
@@ -1177,13 +1300,13 @@
     "for pg_id in rs_sci_dupe_pgs:\n",
     "    num_images = links_manifest_cargo.loc[links_manifest_cargo[\"eol_page_id\"] == pg_id].shape[0]\n",
     "    num_images_by_pg[pg_id] = num_images\n",
-    "    num_unique_images = links_manifest_cargo.loc[links_manifest_cargo[\"eol_page_id\"] == pg_id, \"md5\"].nunique()\n",
+    "    num_unique_images = links_manifest_cargo.loc[links_manifest_cargo[\"eol_page_id\"] == pg_id, \"md5_archive\"].nunique()\n",
     "    num_unique_imgs_by_pg[pg_id] = num_unique_images"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 28,
+   "execution_count": 33,
    "metadata": {},
    "outputs": [
     {
@@ -1192,7 +1315,7 @@
        "80"
       ]
      },
-     "execution_count": 28,
+     "execution_count": 33,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1203,7 +1326,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 29,
+   "execution_count": 34,
    "metadata": {},
    "outputs": [
     {
@@ -1233,7 +1356,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 32,
+   "execution_count": 35,
    "metadata": {},
    "outputs": [
     {
@@ -1374,7 +1497,7 @@
        "4    leucoryx         Oryx leucoryx    29462184_331080  "
       ]
      },
-     "execution_count": 32,
+     "execution_count": 35,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1385,23 +1508,23 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 33,
+   "execution_count": 36,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "856        28675441_453303_eol-full-size-copy.jpg\n",
-       "3628       22574040_456490_eol-full-size-copy.jpg\n",
-       "11038    22222313_45511297_eol-full-size-copy.jpg\n",
-       "1526     20963513_45511277_eol-full-size-copy.jpg\n",
-       "3703     20080370_46579618_eol-full-size-copy.jpg\n",
-       "1991      21744553_1039032_eol-full-size-copy.jpg\n",
-       "9552     20997172_46561158_eol-full-size-copy.jpg\n",
+       "11143     28913274_330971_eol-full-size-copy.jpg\n",
+       "8577      28895396_319982_eol-full-size-copy.jpg\n",
+       "9267      22765674_791137_eol-full-size-copy.jpg\n",
+       "10563    21669746_1181772_eol-full-size-copy.jpg\n",
+       "5600      8965876_1038796_eol-full-size-copy.jpg\n",
+       "9448      28905600_212582_eol-full-size-copy.jpg\n",
+       "4526     21554082_1038643_eol-full-size-copy.jpg\n",
        "Name: file_name, dtype: object"
       ]
      },
-     "execution_count": 33,
+     "execution_count": 36,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1413,298 +1536,29 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 37,
    "metadata": {},
    "outputs": [],
    "source": [
     "# save filelist for easier fetching\n",
-    "rs_catalog[\"file_name\"].to_csv(\"../data/rs_file_list.txt\", index = False)"
+    "#rs_catalog[\"file_name\"].to_csv(\"../data/rs_file_list.txt\", index = False)\n",
+    "# Not needed now"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Check for number of _unique_ images per species\n",
-    "\n",
-    "We want to see if we can replace the species that don't have at least 30 unique images per species in our rare species dataset. We need the full list of options from IUCN...We did hold out all 400?\n",
-    "\n",
-    "Would require going back and checking for species in predicted catalog that aren't in catalog, then comparing that to `links_manifest_cargo_on_md5`."
+    "Save `rs_links` to file for adjusting Rare Species images for uniqueness."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 34,
+   "execution_count": 38,
    "metadata": {},
    "outputs": [],
    "source": [
-    "pred_cat = pd.read_csv(\"../../data/predicted-catalog.csv\", low_memory=False)\n",
-    "catalog = pd.read_csv(\"../../data/data/catalog.csv\", low_memory=False)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 35,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# process catalog\n",
-    "catalog = catalog.loc[catalog.split != \"train_small\"]\n",
-    "eol_catalog = catalog.loc[catalog.eol_content_id.notna()]\n",
-    "eol_catalog = eol_catalog.astype({\"eol_content_id\": \"int64\", \"eol_page_id\": \"int64\"})\n",
-    "\n",
-    "# process pred-cat\n",
-    "eol_pred_cat = pred_cat.loc[pred_cat.eol_content_id.notna()]\n",
-    "eol_pred_cat = eol_pred_cat.astype({\"eol_content_id\": \"int64\", \"eol_page_id\": \"int64\"})"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 39,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "<class 'pandas.core.frame.DataFrame'>\n",
-      "RangeIndex: 6277374 entries, 0 to 6277373\n",
-      "Data columns (total 18 columns):\n",
-      " #   Column               Non-Null Count    Dtype  \n",
-      "---  ------               --------------    -----  \n",
-      " 0   split                6277374 non-null  object \n",
-      " 1   treeoflife_id        6277374 non-null  object \n",
-      " 2   eol_content_id_pred  6277374 non-null  int64  \n",
-      " 3   eol_page_id          6277374 non-null  int64  \n",
-      " 4   bioscan_part         0 non-null        float64\n",
-      " 5   bioscan_filename     0 non-null        object \n",
-      " 6   inat21_filename      0 non-null        object \n",
-      " 7   inat21_cls_name      0 non-null        object \n",
-      " 8   inat21_cls_num       0 non-null        float64\n",
-      " 9   kingdom              6016565 non-null  object \n",
-      " 10  phylum               6018161 non-null  object \n",
-      " 11  class                5998392 non-null  object \n",
-      " 12  order                5992253 non-null  object \n",
-      " 13  family               5975682 non-null  object \n",
-      " 14  genus                5967267 non-null  object \n",
-      " 15  species              5978567 non-null  object \n",
-      " 16  common               6277374 non-null  object \n",
-      " 17  eol_content_id_cat   6250420 non-null  float64\n",
-      "dtypes: float64(3), int64(2), object(13)\n",
-      "memory usage: 862.1+ MB\n"
-     ]
-    }
-   ],
-   "source": [
-    "full_pred_cat = pd.merge(eol_pred_cat, eol_catalog[[\"treeoflife_id\", \"eol_content_id\"]], on = \"treeoflife_id\", how = \"left\", suffixes = (\"_pred\", \"_cat\"))\n",
-    "full_pred_cat.info(show_counts = True)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 41,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "26954"
-      ]
-     },
-     "execution_count": 41,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "non_cat_ids = list(full_pred_cat.loc[full_pred_cat[\"eol_content_id_cat\"].isna(), \"treeoflife_id\"])\n",
-    "len(non_cat_ids)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 54,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/var/folders/nv/f0fq1p1n1_3b11x579py_0q80000gq/T/ipykernel_2421/666684240.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",
-      "  pot_imgs[\"sciName\"] = pot_imgs[\"genus\"] + \" \" + pot_imgs[\"species\"]\n"
-     ]
-    },
-    {
-     "data": {
-      "text/plain": [
-       "split                   2\n",
-       "treeoflife_id       26954\n",
-       "eol_content_id      26954\n",
-       "eol_page_id           831\n",
-       "bioscan_part            0\n",
-       "bioscan_filename        0\n",
-       "inat21_filename         0\n",
-       "inat21_cls_name         0\n",
-       "inat21_cls_num          0\n",
-       "kingdom                 2\n",
-       "phylum                  6\n",
-       "class                  18\n",
-       "order                 106\n",
-       "family                285\n",
-       "genus                 566\n",
-       "species               749\n",
-       "common                796\n",
-       "sciName               802\n",
-       "dtype: int64"
-      ]
-     },
-     "execution_count": 54,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "pot_imgs = eol_pred_cat.loc[eol_pred_cat.treeoflife_id.isin(non_cat_ids)]\n",
-    "pot_imgs[\"sciName\"] = pot_imgs[\"genus\"] + \" \" + pot_imgs[\"species\"]\n",
-    "pot_imgs.nunique()"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Interesting, we have 831 unique EOL page IDs, but only 802 unique scientific names. Wonder how that matches up with 7-tuples."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 55,
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/var/folders/nv/f0fq1p1n1_3b11x579py_0q80000gq/T/ipykernel_2421/3965230711.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",
-      "  pot_imgs[\"duplicate\"] = pot_imgs.duplicated(subset = taxa, keep = \"first\")\n"
-     ]
-    },
-    {
-     "data": {
-      "text/plain": [
-       "duplicate\n",
-       "True     26152\n",
-       "False      802\n",
-       "Name: count, dtype: int64"
-      ]
-     },
-     "execution_count": 55,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "taxa = list(pot_imgs.columns)[9:-2]\n",
-    "pot_imgs[\"duplicate\"] = pot_imgs.duplicated(subset = taxa, keep = \"first\")\n",
-    "\n",
-    "# our species count this way is num true in duplicate\n",
-    "pot_imgs.duplicate.value_counts()"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Okay, so this matches up with our `sciName` count."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 56,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "(279370, 24)"
-      ]
-     },
-     "execution_count": 56,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "eol_cols = list(pot_imgs.columns)[1:4] + list(pot_imgs.columns)[9:]\n",
-    "\n",
-    "pot_imgs = pot_imgs[eol_cols]\n",
-    "\n",
-    "#compare to catalog sciNames\n",
-    "eol_catalog[\"sciName\"] = eol_catalog[\"genus\"] + \" \" + eol_catalog[\"species\"]\n",
-    "\n",
-    "overlap_sciNames = pd.merge(pot_imgs, eol_catalog[eol_cols[:-1]], on = \"sciName\", how = \"inner\")\n",
-    "overlap_sciNames.shape"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 58,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "treeoflife_id_x      3994\n",
-       "eol_content_id_x     3994\n",
-       "eol_page_id_x         402\n",
-       "kingdom_x               2\n",
-       "phylum_x                6\n",
-       "class_x                15\n",
-       "order_x                81\n",
-       "family_x              192\n",
-       "genus_x               320\n",
-       "species_x             390\n",
-       "common_x              402\n",
-       "sciName               402\n",
-       "duplicate               2\n",
-       "treeoflife_id_y     28738\n",
-       "eol_content_id_y    28738\n",
-       "eol_page_id_y         444\n",
-       "kingdom_y               2\n",
-       "phylum_y                6\n",
-       "class_y                15\n",
-       "order_y                81\n",
-       "family_y              192\n",
-       "genus_y               320\n",
-       "species_y             390\n",
-       "common_y              402\n",
-       "dtype: int64"
-      ]
-     },
-     "execution_count": 58,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "overlap_sciNames.nunique()"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Here are our other 402 species, so we didn't hold out anything but the 400 chosen.\n",
-    "\n",
-    "We're stuck with less images for some of them unless we source images from elsewhere."
+    "rs_links.to_csv(\"../data/rs_links.csv\", index = False)"
    ]
   },
   {
@@ -1734,7 +1588,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.6"
+   "version": "3.11.3"
   }
  },
  "nbformat": 4,

eol_realign/notebooks/links_rs_duplicates.py

@@ -16,11 +16,16 @@
 # %%
 import pandas as pd
 
+# %%
+RS_FILEPATH = "../../rare_species/data/"
+
 # %% [markdown]
 # ### Read in Links CSV file
+#
+# Full cargo archive has some more content than the [original `links_manifest_cargo_on_md5.csv`](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/fa08e0f6692a013e4e4f5ca30dd0e8883c0021d8/eol_realign/data/links_manifest_cargo_on_md5.csv).
 
 # %%
-links_manifest_cargo = pd.read_csv("../data/links_manifest_cargo_on_md5.csv", low_memory=False)
+links_manifest_cargo = pd.read_csv("../data/eol-cargo-archive_combined-manifest-checksums_links.csv", low_memory=False)
 
 # %%
 links_manifest_cargo.info(show_counts=True)
@@ -29,7 +34,7 @@ links_manifest_cargo.info(show_counts=True)
 # ## Check on Rare Species Catalog
 
 # %%
-rs_catalog = pd.read_csv("../../rare_species/data/rarespecies-catalog.csv",
+rs_catalog = pd.read_csv(RS_FILEPATH + "rarespecies-catalog.csv",
                          low_memory=False,
                          dtype = {"eol_content_id": "int64", "eol_page_id": "int64"})
 rs_catalog.info(show_counts = True)
@@ -42,13 +47,16 @@ rs_catalog.rename(columns={'eol_content_id': 'eol_content_id_rs', 'eol_page_id':
 rs_links = pd.merge(rs_catalog,
                     links_manifest_cargo,
                     left_on = "combined_id_rs",
-                    right_on = "combined_id_cargo",
+                    right_on = "combined_id_archive", # merge on archive (replaced cargo)
                     how = "inner")
 rs_links.info(show_counts = True)
 
 # %%
 rs_links.nunique()
 
+# %% [markdown]
+# All these numbers match our check with the cargo file.
+
 # %% [markdown]
 # Let's check the mismatched cargo/manifest entries for those last 174...
 
@@ -107,17 +115,33 @@ big_mismatch.loc[big_mismatch["eol_page_id_rs"] == 205909].sample(5)
 # %%
 big_mismatch.loc[big_mismatch["eol_page_id_rs"] == 46560546].sample(5)
 
+
 # %% [markdown]
 # Meanwhile, these are giving me 404's: 27648160, 27648159, 27648164, 27648161, 27648166
 
+# %%
+def get_archive_content(combined_id):
+    return combined_id.split("_")[0]
+
+
+# %%
+links_manifest_cargo["eol_content_id_archive"] = links_manifest_cargo["combined_id_archive"].apply(get_archive_content)
+
 # %%
 # check if content IDs get recycled, content ID: 27648165, now online as: 30223317
-links_manifest_cargo.loc[links_manifest_cargo["eol_content_id_cargo"] == 30223317]
+# is eol_content_id the archive content ID?
+links_manifest_cargo.loc[links_manifest_cargo["eol_content_id_archive"] == 30223317]
 
 # %%
 # Is it in manifest?
 links_manifest_cargo.loc[links_manifest_cargo["eol_content_id"] == 30223317]
 
+# %%
+# to be sure we check manifest
+links_manifest_cargo["eol_content_id_manifest"] = links_manifest_cargo["combined_id_full_manifest"].apply(get_archive_content)
+
+links_manifest_cargo.loc[links_manifest_cargo["eol_content_id_manifest"] == 30223317]
+
 # %% [markdown]
 # This tracks with all eol content IDs being unique across manifest versions...would there be some other intermediate stage where it changed IDs _again_?!
 
@@ -125,7 +149,7 @@ links_manifest_cargo.loc[links_manifest_cargo["eol_content_id"] == 30223317]
 # Save CSV of mismatched, they should be salvageable.
 # We saw these images both online and in our cargo, just with different IDs
 
-mismatched_rs.to_csv("../data/mismatched_rarespecies.csv", index=False)
+mismatched_rs.to_csv("../data/archive_mismatched_rarespecies.csv", index=False)
 
 # %% [markdown]
 # Most of our images for some of these species are missing their metadata. For the vast majority of the species, it's just 1 or 2 images.
@@ -136,7 +160,7 @@ mismatched_rs.to_csv("../data/mismatched_rarespecies.csv", index=False)
 # Now I want some more info on those duplicated MD5's.
 
 # %%
-rs_links["md5_dupes"] = rs_links.duplicated(subset = "md5", keep = "first")
+rs_links["md5_dupes"] = rs_links.duplicated(subset = "md5_archive", keep = "first")
 rs_links["rs_id_dupes"] = rs_links.duplicated(subset = "rarespecies_id", keep = "first")
 
 # %%
@@ -173,7 +197,7 @@ num_unique_imgs_by_pg = {}
 for pg_id in rs_sci_dupe_pgs:
     num_images = links_manifest_cargo.loc[links_manifest_cargo["eol_page_id"] == pg_id].shape[0]
     num_images_by_pg[pg_id] = num_images
-    num_unique_images = links_manifest_cargo.loc[links_manifest_cargo["eol_page_id"] == pg_id, "md5"].nunique()
+    num_unique_images = links_manifest_cargo.loc[links_manifest_cargo["eol_page_id"] == pg_id, "md5_archive"].nunique()
     num_unique_imgs_by_pg[pg_id] = num_unique_images
 
 
@@ -197,72 +221,13 @@ rs_catalog["file_name"].sample(7)
 
 # %%
 # save filelist for easier fetching
-rs_catalog["file_name"].to_csv("../data/rs_file_list.txt", index = False)
-
-# %% [markdown]
-# ### Check for number of _unique_ images per species
-#
-# We want to see if we can replace the species that don't have at least 30 unique images per species in our rare species dataset. We need the full list of options from IUCN...We did hold out all 400?
-#
-# Would require going back and checking for species in predicted catalog that aren't in catalog, then comparing that to `links_manifest_cargo_on_md5`.
-
-# %%
-pred_cat = pd.read_csv("../../data/predicted-catalog.csv", low_memory=False)
-catalog = pd.read_csv("../../data/data/catalog.csv", low_memory=False)
-
-# %%
-# process catalog
-catalog = catalog.loc[catalog.split != "train_small"]
-eol_catalog = catalog.loc[catalog.eol_content_id.notna()]
-eol_catalog = eol_catalog.astype({"eol_content_id": "int64", "eol_page_id": "int64"})
-
-# process pred-cat
-eol_pred_cat = pred_cat.loc[pred_cat.eol_content_id.notna()]
-eol_pred_cat = eol_pred_cat.astype({"eol_content_id": "int64", "eol_page_id": "int64"})
-
-# %%
-full_pred_cat = pd.merge(eol_pred_cat, eol_catalog[["treeoflife_id", "eol_content_id"]], on = "treeoflife_id", how = "left", suffixes = ("_pred", "_cat"))
-full_pred_cat.info(show_counts = True)
-
-# %%
-non_cat_ids = list(full_pred_cat.loc[full_pred_cat["eol_content_id_cat"].isna(), "treeoflife_id"])
-len(non_cat_ids)
-
-# %%
-pot_imgs = eol_pred_cat.loc[eol_pred_cat.treeoflife_id.isin(non_cat_ids)]
-pot_imgs["sciName"] = pot_imgs["genus"] + " " + pot_imgs["species"]
-pot_imgs.nunique()
+#rs_catalog["file_name"].to_csv("../data/rs_file_list.txt", index = False)
+# Not needed now
 
 # %% [markdown]
-# Interesting, we have 831 unique EOL page IDs, but only 802 unique scientific names. Wonder how that matches up with 7-tuples.
+# Save `rs_links` to file for adjusting Rare Species images for uniqueness.
 
 # %%
-taxa = list(pot_imgs.columns)[9:-2]
-pot_imgs["duplicate"] = pot_imgs.duplicated(subset = taxa, keep = "first")
-
-# our species count this way is num true in duplicate
-pot_imgs.duplicate.value_counts()
-
-# %% [markdown]
-# Okay, so this matches up with our `sciName` count.
-
-# %%
-eol_cols = list(pot_imgs.columns)[1:4] + list(pot_imgs.columns)[9:]
-
-pot_imgs = pot_imgs[eol_cols]
-
-#compare to catalog sciNames
-eol_catalog["sciName"] = eol_catalog["genus"] + " " + eol_catalog["species"]
-
-overlap_sciNames = pd.merge(pot_imgs, eol_catalog[eol_cols[:-1]], on = "sciName", how = "inner")
-overlap_sciNames.shape
-
-# %%
-overlap_sciNames.nunique()
-
-# %% [markdown]
-# Here are our other 402 species, so we didn't hold out anything but the 400 chosen.
-#
-# We're stuck with less images for some of them unless we source images from elsewhere.
+rs_links.to_csv("../data/rs_links.csv", index = False)
 
 # %%