v3.3-meta-link

.gitattributes

@@ -63,3 +63,15 @@ data/predicted-catalog.csv filter=lfs diff=lfs merge=lfs -text
 notebooks/BioCLIP_taxa_viz.ipynb filter=lfs diff=lfs merge=lfs -text
 visuals/kingdom_ToL_tree.pdf filter=lfs diff=lfs merge=lfs -text
 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_catalog_combined-manifest-checksums_links.csv filter=lfs diff=lfs merge=lfs -text
+eol_realign/data/checksums_media_cargo_archive.csv filter=lfs diff=lfs merge=lfs -text
+eol_realign/data/combined_manifest_with_checksums.csv filter=lfs diff=lfs merge=lfs -text
+eol_realign/data/full_owner_manifest.csv filter=lfs diff=lfs merge=lfs -text
+rare_species/data/rarespecies-catalog.csv filter=lfs diff=lfs merge=lfs -text
+eol_realign/data/combined_manifest.csv filter=lfs diff=lfs merge=lfs -text
+eol_realign/data/combined-manifest-licenses.csv filter=lfs diff=lfs merge=lfs -text
+data/licenses.csv filter=lfs diff=lfs merge=lfs -text

README.md

@@ -7,30 +7,61 @@ pretty_name: TreeOfLife10M EDA
 
 This repo contains the analysis of the TreeOfLife10M dataset as it's being crafted and refined.
 
-### Data
+## Data
 
 The `data` folder contains
- - `catalog.csv`: the metadata and identifiers for all images in the dataset. This includes original data source, unique identifier within TreeOfLife10M, and the associated taxa information for the image. This is the file that will be updated, while preserving the `catalog-v1-dev.csv` file for ease of comparison.
-- `stats_avg_std_byClass.csv`: average and standard distribution of images given by class in `catalog.csv`. This is for both all 
+ - `catalog.csv`: the metadata and identifiers for all images in the dataset. This includes original data source, unique identifier within TreeOfLife10M, and the associated taxa information for the image. This is the file that will be updated, while preserving the `catalog-v1-dev.csv` file for ease of comparison. [`v3.3`](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/d6b583841aed8c0df314e718735756b76164a933/data/catalog.csv) is the version of the catalog that was used for training [BioCLIP v1](https://doi.org/10.57967/hf/1511) (it has the ~30K images we could not re-align).
+ - `stats_avg_std_byClass.csv`: average and standard distribution of images given by class in `catalog.csv`. This is for both all 
 images, and images that have labels.
-- `predicted-catalog.csv`: the metadata and identifiers for all entries expected in the dataset, prior to webdataset creation. This includes original data source, unique identifier within TreeOfLife10M, and the associated taxa information. In version 3.3 (first time it was generated), it showed 27K more entries than in the webdataset and they all had full taxonomic rank filled.
-
+ - `predicted-catalog.csv`: the metadata and identifiers for all entries expected in the dataset, prior to webdataset creation. This includes original data source, unique identifier within TreeOfLife10M, and the associated taxa information. In version 3.3 (first time it was generated), it showed 27K more entries than in the webdataset and they all had full taxonomic rank filled.
  - `catalog-v1-dev.csv`: the metadata and identifiers for all images in the dataset. This includes original data source, unique identifier within TreeOfLife10M, and the associated taxa information for the image. This file will be maintained for v1 reference, and as such will not be updated.
  - `taxa_counts.csv`: count of distinct lower taxa within each higher taxon from `kingdom` down to 
 `genus` in `catalog-v1-dev.csv`, though the genus count was interrupted and therefore is incomplete.
  - `avg_std_byClass.csv`: average and standard distribution of images in `catalog-v1-dev.csv` given by class (taxonomic rank). This is for both all images, and images that have labels. Note that kingdoms had not been merged and no standardization was performed on the taxonomic hierarchy prior to creation of this file.
  - `tol_hierarchy_test.csv`: Subset of `catalog-v1-dev.csv` for testing the [`check_taxa` script](https://github.com/Imageomics/open_clip/blob/main/scripts/evobio10m/check_taxa.py) to ensure the hierarchy is properly filled in after data generation. 
 
+## Rare Species 
+All these files were generated in `eol_realign/notebooks/re-gen_rs_catalog.ipynb`.
+ - `licenses.csv`: Licensing information for all rarespecies images (includes MD5s and links to catalog and manifest on `rarespecies_id`).
+ - `rarespecies_manifest.csv`: Full manifest information for all images included in rarespecies catalog (may have some extra info from realign).
+ - `rarespecies-catalog.csv`: Catalog of all images included in [Rare Species dataset](https://huggingface.co/imageomics/rare-species).
+For evaluation, Lisa generated a `metadata.csv` that cut the `rarespecies-catalog.csv` down to just the taxonomic columns with index, changing `class` to `cls`, `common` to `common_name`, and creating a `filepath` column (`"2024-03-20/" + <eol_content_id> + "_" + <eol_page_id> + "_eol-full-size-copy.jpg"`), with a `class` column indicating the `sciName` (though this could use a different ID depending on the evaluation).
+
+
+## EOL Re-align
+
+  More detail on the background of this process can be found in the `links_align_reduced` and `links_rs_duplicates` notebooks, as well as [PR #5](https://huggingface.co/datasets/imageomics/ToL-EDA/discussions/5).
+  
+ * **Data:**
+    More information on all the datacan be found in the `links_align_reduced` and `links_rs_duplicates` notebooks. Just those of primary import and potential continued use are listed here.
 
-### Notebooks
+    - `checksums_media_cargo_archive.csv`: MD5 of all EOL images in our cargo archive.
+    - `full_owner_manifset.csv`: Record of all images from EOL that could potentially be used in the TreeOfLife-10M dataset, this has all the non-taxonomic EOL metadata for the EOL images included in the TreeOfLife-10M catalog (12,330,062 entries, gets reduced down during catalog re-generation), with MD5s aligned to `filename` (`<eol_content_id>_<eol_page_id>_eol-full-size-copy.jpg`).
+    - `rarespecies_full_manifest.csv`: Record of all images from EOL that could potentially be used in the Rare Species dataset, i.e., manifest of all images from EOL of the 400 selected species, with MD5s aligned to `filename` (`<eol_content_id>_<eol_page_id>_eol-full-size-copy.jpg`). 
+
+ * **Notebooks:** (Require `pandas`).
+  
+     - `catalog-cargo-manifest_test.ipynb`: Generates `eol_realign/data/full_owner_manifest.csv`, this has all the non-taxonomic EOL metadata for the EOL images included in the TreeOfLife-10M catalog (12,330,062 entries, gets reduced down during catalog re-generation).
+     - `links_align_reduced.ipynb`: Exploration of the degree to which we could realign the EOL files in our TreeOfLife-10M catalog to their associated metadata. There was some recovery from our original loss. Associated `py` file: `links_align_reduced.py`.
+     - `links_rs_duplicates.ipynb`: Documentation of mismatches in the Rare Species dataset and suggestion for fixing them. Saves these in `eol_realign/data/archive_mismatched_rarespecies.csv`, and generates `eol_realign/data/rarespecies_full_manifest.csv`. Uses `eol_realign/data/eol-cargo-archive_combined-manifest-checksums_links.csv`, [`rarespecies-catalog-orig.csv`](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/5db838a9db980f4cf96027b326b06e0f42df0c65/rare_species/data/rarespecies-catalog.csv), `eol_realign/data/rarespecies_missing_pages_md5s.csv`, `eol_realign/data/eol_media_manifest_2024-03-11.csv`, and [`media_manifest_missing_licenses_jul26_owners.csv`](https://huggingface.co/datasets/imageomics/eol/blob/main/owners_info_fix/media_manifest_missing_licenses_jul26_owners.csv). Associated `py` file: `links_rs_duplicates.py`.
+     - `re-gen_rs_catalog.ipynb`: Notebook generating the updated rare species catalog, lisences, and manifest files. Generates new `rarespecies_id`; these are still distinct from `treeoflife_id`s in TreeOfLife-10M. Uses `eol_realign/data/rarespecies_full_manifest.csv`and [`rarespecies-catalog-orig.csv`](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/5db838a9db980f4cf96027b326b06e0f42df0c65/rare_species/data/rarespecies-catalog.csv).
+    Outputs: `rare_species/data/rarespecies_manifest.csv`, `rare_species/data/licenses.csv`, and `rare_species/data/rarespecies-catalog.csv`.
+     - `re-gen_tol_catalog.ipynb`: Notebook updating catalog for TreeOfLife-10M (all EOL entries we could realign), along with the corresponding license file, and manifest with full information for the realigned entries. Uses `eol_realign/data/combined-manifest-licenses.csv`, [`catalog-orig-v3-3.csv`](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/d6b583841aed8c0df314e718735756b76164a933/data/catalog.csv).
+    Outputs: `eol_realign/data/full_owner_manifest.csv`, `data/licenses.csv`, and `data/catalog.csv`.
+
+ * **Scripts:** (Require `pandas`).
+    
+     - `make_licenses.py`: Adds license URLs to make the full manifest and license file.
+     - `match_owners.py`: Adds extra licensing information toward making the full manifest. Uses `eol_realign/data/eol-cargo-archive_catalog_combined-manifest-checksums_links.csv`, makes `eol_realign/data/combined_manifest.csv` for generating final catalog.
+
+## Notebooks
 
 The `notebooks` folder contains
  - `ToL_catalog_EDA.ipynb`: more full EDA of TreeOfLife10M dataset using `catalog.csv`. To be updated as `catalog.csv` is updated, i.e., as the dataset is updated.
  - `ToL_catalog_EDA.py`: py file paired to `ToL_catalog_EDA.ipynb` to facilitate diff checking in case of cell text changes in notebook.
  - `ToL_predicted-catalog_EDA.ipynb`: more full EDA of TreeOfLife10M dataset using `predicted-catalog.csv`. To be updated as `predicted-catalog.csv` is updated, i.e., as the dataset is updated.
  - `ToL_predicted-catalog_EDA.py`: py file paired to `ToL_predicted-catalog_EDA.ipynb` to facilitate diff checking in case of cell text changes in notebook.
-- `BioCLIP_taxa_viz.ipynb`: generates data visualizations, in particular, the generation of treemaps in `visuals` folder; also includes a histogram of kingdoms. The treemaps produced in the notebook are interactive and `HTML` interactive versions can also be found in [`visuals`](https://huggingface.co/datasets/imageomics/ToL-EDA/tree/main/visuals).
-
+ - `BioCLIP_taxa_viz.ipynb`: generates data visualizations, in particular, the generation of treemaps in `visuals` folder; also includes a histogram of kingdoms. The treemaps produced in the notebook are interactive and `HTML` interactive versions can also be found in [`visuals`](https://huggingface.co/datasets/imageomics/ToL-EDA/tree/main/visuals).
  - `BioCLIP_data_viz.ipynb`: notebook with quick basic stats for `catalog-v1-dev.csv`, generates `taxa_counts.csv`.
  - `BioCLIP_taxa_viz_bySource.ipynb`: generates data visualizations, in particular, the generation of visualizations in `visuals` folder and some histograms. The treemaps produced in the notebook are interactive.
  - `ToL_EDA.ipynb`: more full EDA of TreeOfLife10M dataset. Explores the labeling inconsistencies for 
@@ -39,7 +70,7 @@ direction of standardization efforts. Maintained for v1 reference, should not be
 
 **Note:** run `pip install -r requirements.txt` before starting the visualization notebooks. EDA notebooks only require `pandas` and `seaborn`.
 
-### Visuals
+## Visuals
 
 Visualizations generated to demonstrate the distribution and diversity within the phyla of TreeOfLife10M. 
 - `category-v1-visuals`: visualizations made for the original `catalog-v1-dev.csv` using `BioCLIP_taxa_viz_bySource.ipynb`.

data/catalog.csv

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:ef5edf6a6e6048c98e74787cc143981095efaa27ba0aa4cebbac8116b24c9735
-size 2024176607
+oid sha256:215d0080ebf9016e0f471aa037b4201b5a611c2675c85dfec02a23dae03bbaee
+size 2043627688

data/licenses.csv

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:0486ac72f6c2654913bf81b187b34c466a6e13ef8db036b583c286bb9845e2f4
+size 2216478840

eol_realign/data/checksums_media_cargo_archive.csv

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:f5b30008ba49fd342881e7ecd47c248d2a1c9b39960913518fcb78896bef3805
+size 490626452

eol_realign/data/combined-manifest-licenses.csv

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:5ccd5290be9d8d2ab0953774d804d8b436ceef791aca57647a523be5c92cc9c0
+size 4380387723

eol_realign/data/combined_manifest.csv

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:1bf620f9b11854d2551f06f5f01e33c6817d7c74187ed4423af1ae9a415e2ef5
+size 4057029393

eol_realign/data/combined_manifest_with_checksums.csv

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:03c75970541ad805c8f308dbe19d5b71642b724ced6324b240db41cd3e37b045
+size 4655278768

eol_realign/data/eol-cargo-archive_catalog_combined-manifest-checksums_links.csv

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:fc0cc8d4555ed4cf3e5bba2f0c88339bc605ca30982e427d7288e1eb0e74071e
+size 3921517771

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/data/full_owner_manifest.csv

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:0961941b5fcae87f2a4dfacb7d7c29c64d5ef95679c62d16a46fa54d6c0a0f77
+size 3208683463

eol_realign/data/links_cargo_manifest_IDmismatch.csv

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d62a33290d4a96f34c4970104530ea9f97f343babe8e4a766402236c753bdf66
+size 330698785

eol_realign/data/links_inner.csv

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:9cd1db106c3cc456aac9605623eaa728fc70ce48b31d91f3f2242e3a15b6b676
+size 3721927423

eol_realign/data/links_manifest_cargo_on_md5.csv

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:c9d5eea48c971a3c2c2cfeb8afa1708f19806bad5d44938b20e1dc379a37c24f
+size 2824039443

eol_realign/data/mismatched_rarespecies.csv

@@ -0,0 +1,175 @@
+rarespecies_id,eol_content_id_rs,eol_page_id_rs,kingdom,phylum,class,order,family,genus,species,sciName,combined_id_rs
+9f8a41bb-8660-452a-a6b4-77c62b50549d,9474947,46559139,Animalia,Chordata,Mammalia,Carnivora,Mustelidae,Aonyx,capensis,Aonyx capensis,9474947_46559139
+ba2857c7-f02d-44f9-a116-8a450dc53e14,30098516,205909,Animalia,Chordata,Actinopterygii,Acipenseriformes,Acipenseridae,Scaphirhynchus,albus,Scaphirhynchus albus,30098516_205909
+865985be-bc20-406b-afc9-042029f0538d,29734616,1011315,Animalia,Chordata,Mammalia,Lagomorpha,Leporidae,Sylvilagus,transitionalis,Sylvilagus transitionalis,29734616_1011315
+78c2767b-b0d8-4f91-a176-017ca0053237,29707495,46559297,Animalia,Chordata,Mammalia,Cetacea,Delphinidae,Tursiops,aduncus,Tursiops aduncus,29707495_46559297
+66d569b3-da18-4a26-89c0-9400a1de61ca,9485028,46559307,Animalia,Chordata,Mammalia,Cetacea,Delphinidae,Sousa,plumbea,Sousa plumbea,9485028_46559307
+ea6afe07-67ac-498a-b80b-2e2aca041c26,27592105,46560177,Animalia,Chordata,Chondrichthyes,Squaliformes,Dalatiidae,Dalatias,licha,Dalatias licha,27592105_46560177
+3fe63299-e900-4d4f-b79d-d4261c66aeec,29859204,208913,Animalia,Chordata,Actinopterygii,Cyprinodontiformes,Goodeidae,Zoogoneticus,tequila,Zoogoneticus tequila,29859204_208913
+ea60af4a-c726-40e0-9c50-1ff1b130d53a,9474904,46559139,Animalia,Chordata,Mammalia,Carnivora,Mustelidae,Aonyx,capensis,Aonyx capensis,9474904_46559139
+f8620fb6-a9ad-4b66-985d-77129744cd84,9485033,46559307,Animalia,Chordata,Mammalia,Cetacea,Delphinidae,Sousa,plumbea,Sousa plumbea,9485033_46559307
+95642535-20e8-472d-ba52-dadb9fd4a7a5,29859220,208913,Animalia,Chordata,Actinopterygii,Cyprinodontiformes,Goodeidae,Zoogoneticus,tequila,Zoogoneticus tequila,29859220_208913
+0a61e001-b413-496f-a52c-ff861b97ed9b,29734622,1011315,Animalia,Chordata,Mammalia,Lagomorpha,Leporidae,Sylvilagus,transitionalis,Sylvilagus transitionalis,29734622_1011315
+c10a1491-a937-4355-b80c-e0ad00c6772b,29859198,208913,Animalia,Chordata,Actinopterygii,Cyprinodontiformes,Goodeidae,Zoogoneticus,tequila,Zoogoneticus tequila,29859198_208913
+be2d753c-4079-4409-9f49-4e49fb605003,27592101,46560177,Animalia,Chordata,Chondrichthyes,Squaliformes,Dalatiidae,Dalatias,licha,Dalatias licha,27592101_46560177
+83dd55d9-0599-4527-a546-806a31877c98,30098519,205909,Animalia,Chordata,Actinopterygii,Acipenseriformes,Acipenseridae,Scaphirhynchus,albus,Scaphirhynchus albus,30098519_205909
+89371754-476c-449d-8ae7-f2c5c70a68ee,9484693,46559297,Animalia,Chordata,Mammalia,Cetacea,Delphinidae,Tursiops,aduncus,Tursiops aduncus,9484693_46559297
+e59c07d0-e70b-436b-ad80-4f8cf44d1b42,29620709,794282,Animalia,Chordata,Reptilia,Testudines,Testudinidae,Centrochelys,sulcata,Centrochelys sulcata,29620709_794282
+0e4e8f48-a0de-493b-93d2-f2353358ca5b,9485042,46559307,Animalia,Chordata,Mammalia,Cetacea,Delphinidae,Sousa,plumbea,Sousa plumbea,9485042_46559307
+8bbc0ddf-e234-4de1-a188-e47c71b21982,9485046,46559307,Animalia,Chordata,Mammalia,Cetacea,Delphinidae,Sousa,plumbea,Sousa plumbea,9485046_46559307
+fa50fced-f9fe-49b1-aee0-fef9dd10e6ae,9445585,1019162,Animalia,Chordata,Amphibia,Anura,Dendrobatidae,Phyllobates,vittatus,Phyllobates vittatus,9445585_1019162
+8838c823-d1e4-4523-bd8f-2aa8cdb764cc,27941416,46561008,Animalia,Chordata,Chondrichthyes,Myliobatiformes,Myliobatidae,Myliobatis,aquila,Myliobatis aquila,27941416_46561008
+d436ec20-202d-44ec-9081-ca59afef356f,27648166,46560546,Animalia,Chordata,Chondrichthyes,Rajiformes,Rajidae,Raja,asterias,Raja asterias,27648166_46560546
+d239159f-cb15-4c30-8aeb-d8177f8cf34a,30098492,205909,Animalia,Chordata,Actinopterygii,Acipenseriformes,Acipenseridae,Scaphirhynchus,albus,Scaphirhynchus albus,30098492_205909
+d5c2a6bd-7278-4163-8361-7b24af2670e5,29859207,208913,Animalia,Chordata,Actinopterygii,Cyprinodontiformes,Goodeidae,Zoogoneticus,tequila,Zoogoneticus tequila,29859207_208913
+8fbd2e19-e365-4526-8bb8-dcdd75f0bd6b,9474887,46559139,Animalia,Chordata,Mammalia,Carnivora,Mustelidae,Aonyx,capensis,Aonyx capensis,9474887_46559139
+75ba5701-7e0d-4003-a32d-8c7bffccdd72,9443811,118008,Animalia,Chordata,Mammalia,Lagomorpha,Leporidae,Sylvilagus,brasiliensis,Sylvilagus brasiliensis,9443811_118008
+51fc27c8-892d-4884-90ab-5b04c16efde3,9444372,45511531,Animalia,Chordata,Aves,Accipitriformes,Accipitridae,Harpia,harpyja,Harpia harpyja,9444372_45511531
+b74d1ed5-39cb-4b99-9dc1-987cea96d0d4,30102018,331381,Animalia,Chordata,Amphibia,Caudata,Plethodontidae,Desmognathus,imitator,Desmognathus imitator,30102018_331381
+4856f506-1446-4a00-be45-6f1dd0fb6305,9474917,46559139,Animalia,Chordata,Mammalia,Carnivora,Mustelidae,Aonyx,capensis,Aonyx capensis,9474917_46559139
+1935e9cd-a291-4b8a-ac49-0381e590ec14,27592100,46560177,Animalia,Chordata,Chondrichthyes,Squaliformes,Dalatiidae,Dalatias,licha,Dalatias licha,27592100_46560177
+e899bede-284b-4332-b63f-59f195d789ee,9474899,46559139,Animalia,Chordata,Mammalia,Carnivora,Mustelidae,Aonyx,capensis,Aonyx capensis,9474899_46559139
+c22cc2bd-fe54-4a24-a611-b68ef771baf0,29734641,1011315,Animalia,Chordata,Mammalia,Lagomorpha,Leporidae,Sylvilagus,transitionalis,Sylvilagus transitionalis,29734641_1011315
+6cb50905-48ee-4770-9605-91a95e3d027c,27648159,46560546,Animalia,Chordata,Chondrichthyes,Rajiformes,Rajidae,Raja,asterias,Raja asterias,27648159_46560546
+83bdf16f-aec8-4d0f-99bc-b8706612d52c,29734617,1011315,Animalia,Chordata,Mammalia,Lagomorpha,Leporidae,Sylvilagus,transitionalis,Sylvilagus transitionalis,29734617_1011315
+a3658a31-667e-4899-ad95-1aaa86843cc3,9484692,46559297,Animalia,Chordata,Mammalia,Cetacea,Delphinidae,Tursiops,aduncus,Tursiops aduncus,9484692_46559297
+c7b23b7e-ae67-4e53-85ad-c7eaf14dfdd9,9485035,46559307,Animalia,Chordata,Mammalia,Cetacea,Delphinidae,Sousa,plumbea,Sousa plumbea,9485035_46559307
+de4a6ca0-6fc2-40de-907e-c99b98a9ca3e,27648164,46560546,Animalia,Chordata,Chondrichthyes,Rajiformes,Rajidae,Raja,asterias,Raja asterias,27648164_46560546
+4b9e099c-da80-490d-8557-50bce4b78eb0,29859197,208913,Animalia,Chordata,Actinopterygii,Cyprinodontiformes,Goodeidae,Zoogoneticus,tequila,Zoogoneticus tequila,29859197_208913
+cf5c65b1-fff0-46fc-9aa9-c6851f074b1d,14044906,46559748,Animalia,Chordata,Chondrichthyes,Lamniformes,Cetorhinidae,Cetorhinus,maximus,Cetorhinus maximus,14044906_46559748
+f16f275e-d112-400b-a166-a2b7235bdf00,27640830,46559744,Animalia,Chordata,Chondrichthyes,Lamniformes,Alopiidae,Alopias,vulpinus,Alopias vulpinus,27640830_46559744
+3d60ffa3-3622-4716-bbba-4862cb44e1cf,9485040,46559307,Animalia,Chordata,Mammalia,Cetacea,Delphinidae,Sousa,plumbea,Sousa plumbea,9485040_46559307
+30982c26-de59-48dc-81f6-e2a6cdd981fa,9474916,46559139,Animalia,Chordata,Mammalia,Carnivora,Mustelidae,Aonyx,capensis,Aonyx capensis,9474916_46559139
+fc76a950-5cd6-4d7f-aacd-adbf9bce2856,29734635,1011315,Animalia,Chordata,Mammalia,Lagomorpha,Leporidae,Sylvilagus,transitionalis,Sylvilagus transitionalis,29734635_1011315
+8d780e6e-5565-4930-b772-41c0746c6c7d,29980060,46559786,Animalia,Chordata,Chondrichthyes,Carcharhiniformes,Carcharhinidae,Carcharhinus,melanopterus,Carcharhinus melanopterus,29980060_46559786
+a7ed9423-c335-4f7b-aea7-654f0ad4c380,30098503,205909,Animalia,Chordata,Actinopterygii,Acipenseriformes,Acipenseridae,Scaphirhynchus,albus,Scaphirhynchus albus,30098503_205909
+16262d9d-b99d-47ce-9eba-5282cbda539e,29734624,1011315,Animalia,Chordata,Mammalia,Lagomorpha,Leporidae,Sylvilagus,transitionalis,Sylvilagus transitionalis,29734624_1011315
+2bcba9f3-a3a4-4a2b-a4f4-84e35be0e35f,27648163,46560546,Animalia,Chordata,Chondrichthyes,Rajiformes,Rajidae,Raja,asterias,Raja asterias,27648163_46560546
+d4206d7e-5f1c-4b7d-9e5f-77533e76397e,27592104,46560177,Animalia,Chordata,Chondrichthyes,Squaliformes,Dalatiidae,Dalatias,licha,Dalatias licha,27592104_46560177
+682f09af-fd52-48c3-a1c9-517d3ac19e11,9484694,46559297,Animalia,Chordata,Mammalia,Cetacea,Delphinidae,Tursiops,aduncus,Tursiops aduncus,9484694_46559297
+2ccd58d0-e23b-4d5a-9801-ae01d810657e,27734034,46560555,Animalia,Chordata,Chondrichthyes,Rajiformes,Rajidae,Raja,undulata,Raja undulata,27734034_46560555
+d618c15c-aabc-444a-8c44-09ce76377fd8,9485038,46559307,Animalia,Chordata,Mammalia,Cetacea,Delphinidae,Sousa,plumbea,Sousa plumbea,9485038_46559307
+ed766585-5418-4147-8543-a31304f591ca,30098514,205909,Animalia,Chordata,Actinopterygii,Acipenseriformes,Acipenseridae,Scaphirhynchus,albus,Scaphirhynchus albus,30098514_205909
+12633820-3a3a-4c77-bd38-7221bd18b747,27648157,46560546,Animalia,Chordata,Chondrichthyes,Rajiformes,Rajidae,Raja,asterias,Raja asterias,27648157_46560546
+92d425c4-0667-4df4-9977-31c16ade233e,30070655,45511267,Animalia,Chordata,Aves,Procellariiformes,Diomedeidae,Phoebastria,albatrus,Phoebastria albatrus,30070655_45511267
+41c425c2-0db1-45b9-a27d-855dc9426d2a,9474945,46559139,Animalia,Chordata,Mammalia,Carnivora,Mustelidae,Aonyx,capensis,Aonyx capensis,9474945_46559139
+3bb2a37c-d33d-4f8b-a1ae-ae70fad3ec47,9444423,45511624,Animalia,Chordata,Aves,Trogoniformes,Trogonidae,Trogon,bairdii,Trogon bairdii,9444423_45511624
+4a733627-6adb-4700-9b85-d3d352b5d2f3,29859199,208913,Animalia,Chordata,Actinopterygii,Cyprinodontiformes,Goodeidae,Zoogoneticus,tequila,Zoogoneticus tequila,29859199_208913
+266fed3d-0002-43da-93e6-39a3897d93e6,9474924,46559139,Animalia,Chordata,Mammalia,Carnivora,Mustelidae,Aonyx,capensis,Aonyx capensis,9474924_46559139
+f422aa72-40b3-4f0a-82fa-6cf519aea5c9,29972857,1056842,Animalia,Chordata,Reptilia,Testudines,Emydidae,Glyptemys,muhlenbergii,Glyptemys muhlenbergii,29972857_1056842
+26b11b35-9752-4ce9-8dbb-98e12bcd0b0d,29859202,208913,Animalia,Chordata,Actinopterygii,Cyprinodontiformes,Goodeidae,Zoogoneticus,tequila,Zoogoneticus tequila,29859202_208913
+b30b1b0f-7dd7-46ca-833a-313b2dc6efde,9474953,46559139,Animalia,Chordata,Mammalia,Carnivora,Mustelidae,Aonyx,capensis,Aonyx capensis,9474953_46559139
+8a7eae46-57af-4132-b914-78556479db67,27648161,46560546,Animalia,Chordata,Chondrichthyes,Rajiformes,Rajidae,Raja,asterias,Raja asterias,27648161_46560546
+f6b1a72f-6e1f-47fc-b303-918da4e2232b,27941417,46561008,Animalia,Chordata,Chondrichthyes,Myliobatiformes,Myliobatidae,Myliobatis,aquila,Myliobatis aquila,27941417_46561008
+9b80b959-e80f-4356-b16e-0540612fbbc3,27592102,46560177,Animalia,Chordata,Chondrichthyes,Squaliformes,Dalatiidae,Dalatias,licha,Dalatias licha,27592102_46560177
+98cb12e1-2f03-4866-a452-1c0b98049bd2,30098524,205909,Animalia,Chordata,Actinopterygii,Acipenseriformes,Acipenseridae,Scaphirhynchus,albus,Scaphirhynchus albus,30098524_205909
+8f593774-d837-452f-80d7-5865bb148e6d,29859193,208913,Animalia,Chordata,Actinopterygii,Cyprinodontiformes,Goodeidae,Zoogoneticus,tequila,Zoogoneticus tequila,29859193_208913
+b4f2cd0b-4d59-4e08-a04f-9021bb06442f,27559496,52572074,Animalia,Chordata,Chondrichthyes,Myliobatiformes,Dasyatidae,Bathytoshia,centroura,Bathytoshia centroura,27559496_52572074
+d23ece02-4cce-4c25-88b9-c3926039b3c2,29510035,130548,Animalia,Arthropoda,Insecta,Lepidoptera,Papilionidae,Luehdorfia,japonica,Luehdorfia japonica,29510035_130548
+c41ed523-e9ed-405f-9335-aa828ea60be6,9484689,46559297,Animalia,Chordata,Mammalia,Cetacea,Delphinidae,Tursiops,aduncus,Tursiops aduncus,9484689_46559297
+431abd61-10a8-481b-85fd-8d4624da9611,30098512,205909,Animalia,Chordata,Actinopterygii,Acipenseriformes,Acipenseridae,Scaphirhynchus,albus,Scaphirhynchus albus,30098512_205909
+3b00b8ea-bca8-4b10-b66f-010f7d853ebc,27559495,52572074,Animalia,Chordata,Chondrichthyes,Myliobatiformes,Dasyatidae,Bathytoshia,centroura,Bathytoshia centroura,27559495_52572074
+6916deca-f92a-4200-bd79-0b201cef23f9,29859210,208913,Animalia,Chordata,Actinopterygii,Cyprinodontiformes,Goodeidae,Zoogoneticus,tequila,Zoogoneticus tequila,29859210_208913
+5c5188e3-0061-4982-a36d-80108e1700c3,30098482,205909,Animalia,Chordata,Actinopterygii,Acipenseriformes,Acipenseridae,Scaphirhynchus,albus,Scaphirhynchus albus,30098482_205909
+88e8ca3d-07f2-40f3-9580-75088f1c3680,29734631,1011315,Animalia,Chordata,Mammalia,Lagomorpha,Leporidae,Sylvilagus,transitionalis,Sylvilagus transitionalis,29734631_1011315
+9346e1e6-aa08-4f9b-aeb6-5a3703f41cac,9474918,46559139,Animalia,Chordata,Mammalia,Carnivora,Mustelidae,Aonyx,capensis,Aonyx capensis,9474918_46559139
+b0f9408a-79e8-4b22-8e84-955f3756e13c,27586446,46560594,Animalia,Chordata,Chondrichthyes,Rajiformes,Rajidae,Rostroraja,alba,Rostroraja alba,27586446_46560594
+598cadc6-9dec-4dd7-8599-158287ecf2f2,9485045,46559307,Animalia,Chordata,Mammalia,Cetacea,Delphinidae,Sousa,plumbea,Sousa plumbea,9485045_46559307
+0587179f-cae6-40b0-8042-018680b6b024,29734629,1011315,Animalia,Chordata,Mammalia,Lagomorpha,Leporidae,Sylvilagus,transitionalis,Sylvilagus transitionalis,29734629_1011315
+31d02182-7226-4d3e-bbaa-b0d7fef674cf,30098507,205909,Animalia,Chordata,Actinopterygii,Acipenseriformes,Acipenseridae,Scaphirhynchus,albus,Scaphirhynchus albus,30098507_205909
+d57c662e-52db-42da-97e1-7547e2307282,27648158,46560546,Animalia,Chordata,Chondrichthyes,Rajiformes,Rajidae,Raja,asterias,Raja asterias,27648158_46560546
+88835f27-da8a-49cc-8b53-60de1e8dd3a6,29859191,208913,Animalia,Chordata,Actinopterygii,Cyprinodontiformes,Goodeidae,Zoogoneticus,tequila,Zoogoneticus tequila,29859191_208913
+d50ab51c-6771-462d-94fe-5de142240b87,29859221,208913,Animalia,Chordata,Actinopterygii,Cyprinodontiformes,Goodeidae,Zoogoneticus,tequila,Zoogoneticus tequila,29859221_208913
+536f3c1d-e0a4-4a0f-ba63-4970763ae762,29859215,208913,Animalia,Chordata,Actinopterygii,Cyprinodontiformes,Goodeidae,Zoogoneticus,tequila,Zoogoneticus tequila,29859215_208913
+0f1ba847-060e-4349-b557-3fca25387b94,30098501,205909,Animalia,Chordata,Actinopterygii,Acipenseriformes,Acipenseridae,Scaphirhynchus,albus,Scaphirhynchus albus,30098501_205909
+592e1992-7891-49b0-a484-ca3e075b5178,29270483,46559793,Animalia,Chordata,Chondrichthyes,Carcharhiniformes,Carcharhinidae,Carcharhinus,amblyrhynchos,Carcharhinus amblyrhynchos,29270483_46559793
+9806169f-b895-4943-9d9e-7d21ada7b9d3,9474972,46559139,Animalia,Chordata,Mammalia,Carnivora,Mustelidae,Aonyx,capensis,Aonyx capensis,9474972_46559139
+5765f247-60bc-4d22-bac2-903d7da45793,9485047,46559307,Animalia,Chordata,Mammalia,Cetacea,Delphinidae,Sousa,plumbea,Sousa plumbea,9485047_46559307
+913a4ab5-2dbe-4c98-8552-fc9b9c155774,9466096,1010637,Animalia,Chordata,Mammalia,Primates,Cercopithecidae,Cercopithecus,mona,Cercopithecus mona,9466096_1010637
+e1048070-ade5-4c62-bc6a-d1aa7958dcec,9474902,46559139,Animalia,Chordata,Mammalia,Carnivora,Mustelidae,Aonyx,capensis,Aonyx capensis,9474902_46559139
+09f03a21-01b3-41c4-9d79-1acf20449b07,9474876,46559139,Animalia,Chordata,Mammalia,Carnivora,Mustelidae,Aonyx,capensis,Aonyx capensis,9474876_46559139
+ff230c11-7fe7-4d9f-be34-8545dc1c8d22,9485036,46559307,Animalia,Chordata,Mammalia,Cetacea,Delphinidae,Sousa,plumbea,Sousa plumbea,9485036_46559307
+3d8684c9-94c2-4100-8ee7-f3495bb5fb6c,9474898,46559139,Animalia,Chordata,Mammalia,Carnivora,Mustelidae,Aonyx,capensis,Aonyx capensis,9474898_46559139
+5710e528-e246-4b5e-b8dc-2bd2d34fff2d,9467381,4453917,Animalia,Chordata,Mammalia,Primates,Cercopithecidae,Piliocolobus,tephrosceles,Piliocolobus tephrosceles,9467381_4453917
+f23ead6e-807f-47db-9ae6-5cfd2244cc17,28043084,46560148,Animalia,Chordata,Chondrichthyes,Hexanchiformes,Hexanchidae,Hexanchus,griseus,Hexanchus griseus,28043084_46560148
+fee8030c-e05b-4acd-b728-3ef6a73e410a,9474910,46559139,Animalia,Chordata,Mammalia,Carnivora,Mustelidae,Aonyx,capensis,Aonyx capensis,9474910_46559139
+0c1f17f2-f02a-44f4-8f74-a874e5c8cdc8,29859196,208913,Animalia,Chordata,Actinopterygii,Cyprinodontiformes,Goodeidae,Zoogoneticus,tequila,Zoogoneticus tequila,29859196_208913
+90a6003e-9e0f-4c1e-96c9-320633425173,29859203,208913,Animalia,Chordata,Actinopterygii,Cyprinodontiformes,Goodeidae,Zoogoneticus,tequila,Zoogoneticus tequila,29859203_208913
+dda8a68a-ad8f-4c4a-8bf7-96b083fb3945,29859223,208913,Animalia,Chordata,Actinopterygii,Cyprinodontiformes,Goodeidae,Zoogoneticus,tequila,Zoogoneticus tequila,29859223_208913
+bd27fc74-caa5-4fe3-9dbc-776127bd03e7,30098489,205909,Animalia,Chordata,Actinopterygii,Acipenseriformes,Acipenseridae,Scaphirhynchus,albus,Scaphirhynchus albus,30098489_205909
+a7c43306-6a3a-4d94-b7f0-147ad9f20a73,27648160,46560546,Animalia,Chordata,Chondrichthyes,Rajiformes,Rajidae,Raja,asterias,Raja asterias,27648160_46560546
+06f59f63-99e7-4b44-a868-d478cb6409f2,29859205,208913,Animalia,Chordata,Actinopterygii,Cyprinodontiformes,Goodeidae,Zoogoneticus,tequila,Zoogoneticus tequila,29859205_208913
+44087ce6-531e-42cc-a64b-450f42f6bead,29734621,1011315,Animalia,Chordata,Mammalia,Lagomorpha,Leporidae,Sylvilagus,transitionalis,Sylvilagus transitionalis,29734621_1011315
+d33f93de-31ec-434a-985e-a9cdeb79b557,30098484,205909,Animalia,Chordata,Actinopterygii,Acipenseriformes,Acipenseridae,Scaphirhynchus,albus,Scaphirhynchus albus,30098484_205909
+6e3ea9d1-24dc-4c31-a893-ee66e1e7dad1,28043087,46560148,Animalia,Chordata,Chondrichthyes,Hexanchiformes,Hexanchidae,Hexanchus,griseus,Hexanchus griseus,28043087_46560148
+acc6b0a9-7b58-4696-a4ff-4116f702fb9b,27640829,46559744,Animalia,Chordata,Chondrichthyes,Lamniformes,Alopiidae,Alopias,vulpinus,Alopias vulpinus,27640829_46559744
+d6956958-da73-457e-97f2-86101109ef8e,28043085,46560148,Animalia,Chordata,Chondrichthyes,Hexanchiformes,Hexanchidae,Hexanchus,griseus,Hexanchus griseus,28043085_46560148
+aba17319-737e-4b71-9cc0-587dbb1ac8d8,29734639,1011315,Animalia,Chordata,Mammalia,Lagomorpha,Leporidae,Sylvilagus,transitionalis,Sylvilagus transitionalis,29734639_1011315
+e9648a9a-db26-42dd-9bbf-bcd194d15235,29859214,208913,Animalia,Chordata,Actinopterygii,Cyprinodontiformes,Goodeidae,Zoogoneticus,tequila,Zoogoneticus tequila,29859214_208913
+5a51fdd0-99c5-4f4d-9fda-303f523c4896,9474883,46559139,Animalia,Chordata,Mammalia,Carnivora,Mustelidae,Aonyx,capensis,Aonyx capensis,9474883_46559139
+b34a8904-570d-46b9-99b1-0ad29dc94853,9474949,46559139,Animalia,Chordata,Mammalia,Carnivora,Mustelidae,Aonyx,capensis,Aonyx capensis,9474949_46559139
+45a14e5c-9d2e-402a-9289-2f23a9e51922,9485026,46559307,Animalia,Chordata,Mammalia,Cetacea,Delphinidae,Sousa,plumbea,Sousa plumbea,9485026_46559307
+cf8f3c23-eb83-40a5-979c-e9359b2b9df9,27640828,46559744,Animalia,Chordata,Chondrichthyes,Lamniformes,Alopiidae,Alopias,vulpinus,Alopias vulpinus,27640828_46559744
+dc918a92-ebe9-4a1e-b409-9e439b30115a,9485048,46559307,Animalia,Chordata,Mammalia,Cetacea,Delphinidae,Sousa,plumbea,Sousa plumbea,9485048_46559307
+1bbc4d67-196b-42e9-9adb-732b1a00ac58,29859208,208913,Animalia,Chordata,Actinopterygii,Cyprinodontiformes,Goodeidae,Zoogoneticus,tequila,Zoogoneticus tequila,29859208_208913
+4d7436d1-82de-416b-8a51-6452efd45f44,30098515,205909,Animalia,Chordata,Actinopterygii,Acipenseriformes,Acipenseridae,Scaphirhynchus,albus,Scaphirhynchus albus,30098515_205909
+ef260410-a53c-4c31-b5e6-963bf056420c,29859186,208913,Animalia,Chordata,Actinopterygii,Cyprinodontiformes,Goodeidae,Zoogoneticus,tequila,Zoogoneticus tequila,29859186_208913
+667586ab-145a-4076-9669-535447aa2b6c,30098504,205909,Animalia,Chordata,Actinopterygii,Acipenseriformes,Acipenseridae,Scaphirhynchus,albus,Scaphirhynchus albus,30098504_205909
+c7174eb2-e49f-4db3-a2d7-9bb050fd2646,27586444,46560594,Animalia,Chordata,Chondrichthyes,Rajiformes,Rajidae,Rostroraja,alba,Rostroraja alba,27586444_46560594
+c3dd1f33-9099-444f-9f8f-edf5f5d0991d,29859227,208913,Animalia,Chordata,Actinopterygii,Cyprinodontiformes,Goodeidae,Zoogoneticus,tequila,Zoogoneticus tequila,29859227_208913
+2d342a7c-7e0c-4981-9630-019bb90183be,30098499,205909,Animalia,Chordata,Actinopterygii,Acipenseriformes,Acipenseridae,Scaphirhynchus,albus,Scaphirhynchus albus,30098499_205909
+d8fca198-63e2-4b93-8905-87a1c2713aaa,9485037,46559307,Animalia,Chordata,Mammalia,Cetacea,Delphinidae,Sousa,plumbea,Sousa plumbea,9485037_46559307
+7cc1773c-3595-4bc7-8817-d33299036a53,29734638,1011315,Animalia,Chordata,Mammalia,Lagomorpha,Leporidae,Sylvilagus,transitionalis,Sylvilagus transitionalis,29734638_1011315
+754bf208-0891-46db-807d-bdc5290169c8,27640831,46559744,Animalia,Chordata,Chondrichthyes,Lamniformes,Alopiidae,Alopias,vulpinus,Alopias vulpinus,27640831_46559744
+46328a46-c77c-407b-b5a3-49e457ce8e27,9485027,46559307,Animalia,Chordata,Mammalia,Cetacea,Delphinidae,Sousa,plumbea,Sousa plumbea,9485027_46559307
+3b2af1eb-0672-48b2-91b9-35d982bd592e,28043079,46560148,Animalia,Chordata,Chondrichthyes,Hexanchiformes,Hexanchidae,Hexanchus,griseus,Hexanchus griseus,28043079_46560148
+17668f81-e13e-467a-8343-c8a8400d56bf,28043082,46560148,Animalia,Chordata,Chondrichthyes,Hexanchiformes,Hexanchidae,Hexanchus,griseus,Hexanchus griseus,28043082_46560148
+2a7befd0-9abc-40fc-a4dd-473f724a477b,27592103,46560177,Animalia,Chordata,Chondrichthyes,Squaliformes,Dalatiidae,Dalatias,licha,Dalatias licha,27592103_46560177
+98f5aea6-b0d8-4b66-8dda-042d3140b203,27559497,52572074,Animalia,Chordata,Chondrichthyes,Myliobatiformes,Dasyatidae,Bathytoshia,centroura,Bathytoshia centroura,27559497_52572074
+9a96a903-61e5-41a3-9dc2-8f0bd906f82f,9474934,46559139,Animalia,Chordata,Mammalia,Carnivora,Mustelidae,Aonyx,capensis,Aonyx capensis,9474934_46559139
+a33feafd-0954-4d71-a7e5-331a28abe1ec,9443813,118008,Animalia,Chordata,Mammalia,Lagomorpha,Leporidae,Sylvilagus,brasiliensis,Sylvilagus brasiliensis,9443813_118008
+ef9fdea8-45e3-4037-8b8a-aa30381bd9f8,9466102,1010637,Animalia,Chordata,Mammalia,Primates,Cercopithecidae,Cercopithecus,mona,Cercopithecus mona,9466102_1010637
+3c5c82b0-1a3a-4c0b-ade7-a8bf32fdac10,9474932,46559139,Animalia,Chordata,Mammalia,Carnivora,Mustelidae,Aonyx,capensis,Aonyx capensis,9474932_46559139
+88b4f4e8-f5f9-4977-8f2b-8be6f5c62da5,29859200,208913,Animalia,Chordata,Actinopterygii,Cyprinodontiformes,Goodeidae,Zoogoneticus,tequila,Zoogoneticus tequila,29859200_208913
+5c7fc0d0-52ab-4e8a-aada-583702c22d1b,29734620,1011315,Animalia,Chordata,Mammalia,Lagomorpha,Leporidae,Sylvilagus,transitionalis,Sylvilagus transitionalis,29734620_1011315
+8f53eebf-d878-49df-8bda-89f31bb0c8f1,27559498,52572074,Animalia,Chordata,Chondrichthyes,Myliobatiformes,Dasyatidae,Bathytoshia,centroura,Bathytoshia centroura,27559498_52572074
+9bccfc8e-714a-476f-ba72-c063d9369fe2,29859219,208913,Animalia,Chordata,Actinopterygii,Cyprinodontiformes,Goodeidae,Zoogoneticus,tequila,Zoogoneticus tequila,29859219_208913
+2046eca8-c21b-4f9b-a36c-6827bd598e0e,9465816,324405,Animalia,Chordata,Mammalia,Primates,Cheirogaleidae,Microcebus,rufus,Microcebus rufus,9465816_324405
+5d93a2dc-2341-4ecd-a357-71a996e46af1,9485039,46559307,Animalia,Chordata,Mammalia,Cetacea,Delphinidae,Sousa,plumbea,Sousa plumbea,9485039_46559307
+77f98914-c53e-4506-b076-7a1e13abf4ed,9474952,46559139,Animalia,Chordata,Mammalia,Carnivora,Mustelidae,Aonyx,capensis,Aonyx capensis,9474952_46559139
+88ec953f-2adf-4cb2-b984-abb1949c3165,9474895,46559139,Animalia,Chordata,Mammalia,Carnivora,Mustelidae,Aonyx,capensis,Aonyx capensis,9474895_46559139
+f25b5a17-6bc1-47cb-91f6-b3ed1edd3f31,29859222,208913,Animalia,Chordata,Actinopterygii,Cyprinodontiformes,Goodeidae,Zoogoneticus,tequila,Zoogoneticus tequila,29859222_208913
+ccda992d-6452-412f-a626-7af8f36bcea2,27941420,46561008,Animalia,Chordata,Chondrichthyes,Myliobatiformes,Myliobatidae,Myliobatis,aquila,Myliobatis aquila,27941420_46561008
+24c7c44b-cdb5-4eeb-808a-9f55d6dadf8c,9485043,46559307,Animalia,Chordata,Mammalia,Cetacea,Delphinidae,Sousa,plumbea,Sousa plumbea,9485043_46559307
+2de51d63-b717-4695-8d2c-ba2fdb6d5315,9444371,45511531,Animalia,Chordata,Aves,Accipitriformes,Accipitridae,Harpia,harpyja,Harpia harpyja,9444371_45511531
+92da8fa4-fb94-42b3-9483-86d2672d6644,27648165,46560546,Animalia,Chordata,Chondrichthyes,Rajiformes,Rajidae,Raja,asterias,Raja asterias,27648165_46560546
+db166886-1dad-43b1-aae6-7f2ef13e467a,27586445,46560594,Animalia,Chordata,Chondrichthyes,Rajiformes,Rajidae,Rostroraja,alba,Rostroraja alba,27586445_46560594
+1ebedee8-eacd-44db-a97c-b9ec7e5c70a2,9474925,46559139,Animalia,Chordata,Mammalia,Carnivora,Mustelidae,Aonyx,capensis,Aonyx capensis,9474925_46559139
+44ab910b-1d77-4161-b646-de56b366be3e,9484696,46559297,Animalia,Chordata,Mammalia,Cetacea,Delphinidae,Tursiops,aduncus,Tursiops aduncus,9484696_46559297
+e202b109-b3bf-41ea-acf5-050ed671884c,9474957,46559139,Animalia,Chordata,Mammalia,Carnivora,Mustelidae,Aonyx,capensis,Aonyx capensis,9474957_46559139
+30e91837-7b30-4aaa-9071-602c12f7d64f,29859190,208913,Animalia,Chordata,Actinopterygii,Cyprinodontiformes,Goodeidae,Zoogoneticus,tequila,Zoogoneticus tequila,29859190_208913
+97a64450-ec40-4d53-8b0f-20c32290e9a3,9474944,46559139,Animalia,Chordata,Mammalia,Carnivora,Mustelidae,Aonyx,capensis,Aonyx capensis,9474944_46559139
+94598086-9752-4f5f-84e8-31b1480de2c1,9474908,46559139,Animalia,Chordata,Mammalia,Carnivora,Mustelidae,Aonyx,capensis,Aonyx capensis,9474908_46559139
+069eec43-535e-48de-a93d-711a64221800,29859218,208913,Animalia,Chordata,Actinopterygii,Cyprinodontiformes,Goodeidae,Zoogoneticus,tequila,Zoogoneticus tequila,29859218_208913
+a25bc949-92b6-4cb7-b583-06aea68fdd85,29734627,1011315,Animalia,Chordata,Mammalia,Lagomorpha,Leporidae,Sylvilagus,transitionalis,Sylvilagus transitionalis,29734627_1011315
+3960c9c5-5ff3-4990-bb88-52d695dedc65,29859206,208913,Animalia,Chordata,Actinopterygii,Cyprinodontiformes,Goodeidae,Zoogoneticus,tequila,Zoogoneticus tequila,29859206_208913
+9630b0fa-0d44-4238-bfad-52bca531b552,28940905,46571820,Animalia,Chordata,Actinopterygii,Labriformes,Labridae,Lachnolaimus,maximus,Lachnolaimus maximus,28940905_46571820
+a9560f41-403d-46a0-a92a-9694cceffe96,30098523,205909,Animalia,Chordata,Actinopterygii,Acipenseriformes,Acipenseridae,Scaphirhynchus,albus,Scaphirhynchus albus,30098523_205909
+f6d75624-6581-4bc4-826f-4c7bc30bde4b,29445364,1050315,Animalia,Chordata,Aves,Passeriformes,Thraupidae,Certhidea,olivacea,Certhidea olivacea,29445364_1050315
+a4ae6563-4aa1-41f7-ab5a-b042d23eee9b,27640833,46559744,Animalia,Chordata,Chondrichthyes,Lamniformes,Alopiidae,Alopias,vulpinus,Alopias vulpinus,27640833_46559744
+8bcc9b8a-de04-42dc-83e6-e79b433f5ab5,9443812,118008,Animalia,Chordata,Mammalia,Lagomorpha,Leporidae,Sylvilagus,brasiliensis,Sylvilagus brasiliensis,9443812_118008
+22906c73-8288-4eb0-bb06-8b6bfae40b13,9485041,46559307,Animalia,Chordata,Mammalia,Cetacea,Delphinidae,Sousa,plumbea,Sousa plumbea,9485041_46559307
+557dc6bf-d462-4ff7-9cbd-50197114af5f,27941422,46561008,Animalia,Chordata,Chondrichthyes,Myliobatiformes,Myliobatidae,Myliobatis,aquila,Myliobatis aquila,27941422_46561008
+915e1291-ecaa-4e09-a3be-8e171b841278,29859226,208913,Animalia,Chordata,Actinopterygii,Cyprinodontiformes,Goodeidae,Zoogoneticus,tequila,Zoogoneticus tequila,29859226_208913
+83a4f5ac-5d48-45bc-ba94-0f63d3238177,29734628,1011315,Animalia,Chordata,Mammalia,Lagomorpha,Leporidae,Sylvilagus,transitionalis,Sylvilagus transitionalis,29734628_1011315
+59ae92b5-a679-482c-9ff7-ea8d189e8ba2,9474974,46559139,Animalia,Chordata,Mammalia,Carnivora,Mustelidae,Aonyx,capensis,Aonyx capensis,9474974_46559139
+a40ccf8f-a0ea-4590-8815-35a1b0bb5e86,30025401,333429,Animalia,Chordata,Amphibia,Anura,Mantellidae,Mantella,aurantiaca,Mantella aurantiaca,30025401_333429
+e67db980-b824-445d-9fcd-ff5b645e6524,9465815,324405,Animalia,Chordata,Mammalia,Primates,Cheirogaleidae,Microcebus,rufus,Microcebus rufus,9465815_324405
+44bc35e0-f37c-490b-a78f-acf403dc6a7c,29972861,1056842,Animalia,Chordata,Reptilia,Testudines,Emydidae,Glyptemys,muhlenbergii,Glyptemys muhlenbergii,29972861_1056842
+845eef8e-5108-4793-8113-0fdf4ef0f7ce,22564200,795274,Animalia,Chordata,Reptilia,Crocodilia,Crocodylidae,Crocodylus,rhombifer,Crocodylus rhombifer,22564200_795274
+aac57174-8b33-4f98-a9ba-3c467e4297ad,22564199,795274,Animalia,Chordata,Reptilia,Crocodilia,Crocodylidae,Crocodylus,rhombifer,Crocodylus rhombifer,22564199_795274
+dc2ba6ca-df57-4a26-9041-422939415a86,29734626,1011315,Animalia,Chordata,Mammalia,Lagomorpha,Leporidae,Sylvilagus,transitionalis,Sylvilagus transitionalis,29734626_1011315
+f3f30b6c-b9ec-4714-857e-e89631a5b9ca,29734618,1011315,Animalia,Chordata,Mammalia,Lagomorpha,Leporidae,Sylvilagus,transitionalis,Sylvilagus transitionalis,29734618_1011315
+b5872a8f-b253-4df9-b080-92cf8b8d7396,9474963,46559139,Animalia,Chordata,Mammalia,Carnivora,Mustelidae,Aonyx,capensis,Aonyx capensis,9474963_46559139
+9fc4e15d-85c8-49eb-b083-c339551ef1e4,27941421,46561008,Animalia,Chordata,Chondrichthyes,Myliobatiformes,Myliobatidae,Myliobatis,aquila,Myliobatis aquila,27941421_46561008
+54d324c0-0cf4-4ecb-a8a5-5738bc8e1f8a,9465817,326525,Animalia,Chordata,Mammalia,Primates,Lemuridae,Eulemur,fulvus,Eulemur fulvus,9465817_326525

eol_realign/notebooks/catalog-cargo-manifest_test.ipynb

@@ -0,0 +1,851 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pandas as pd"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "TOL_FILEPATH = \"../../data/\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "tol = pd.read_csv(TOL_FILEPATH + \"catalog.csv\", low_memory=False)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "Index: 6250420 entries, 956715 to 11000930\n",
+      "Data columns (total 12 columns):\n",
+      " #   Column          Non-Null Count    Dtype \n",
+      "---  ------          --------------    ----- \n",
+      " 0   split           6250420 non-null  object\n",
+      " 1   treeoflife_id   6250420 non-null  object\n",
+      " 2   eol_content_id  6250420 non-null  int64 \n",
+      " 3   eol_page_id     6250420 non-null  int64 \n",
+      " 4   kingdom         5989611 non-null  object\n",
+      " 5   phylum          5991207 non-null  object\n",
+      " 6   class           5971438 non-null  object\n",
+      " 7   order           5965299 non-null  object\n",
+      " 8   family          5948728 non-null  object\n",
+      " 9   genus           5940313 non-null  object\n",
+      " 10  species         5951613 non-null  object\n",
+      " 11  common          6250420 non-null  object\n",
+      "dtypes: int64(2), object(10)\n",
+      "memory usage: 619.9+ MB\n"
+     ]
+    }
+   ],
+   "source": [
+    "# Remove duplicates\n",
+    "tol = tol.loc[tol.split != 'train_small']\n",
+    "\n",
+    "# Reduce to just EOL data & columns\n",
+    "eol = tol.loc[tol[\"eol_content_id\"].notna()]\n",
+    "eol_cols = [col for col in list(eol.columns) if \"bioscan\" not in col and \"inat\" not in col]\n",
+    "eol_catalog = eol[eol_cols]\n",
+    "\n",
+    "# Cast EOL content & page IDs as ints\n",
+    "eol_catalog = eol_catalog.astype({\"eol_content_id\": \"int64\", \"eol_page_id\": \"int64\"})\n",
+    "eol_catalog.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "archive = pd.read_csv(\"../data/checksums_media_cargo_archive.csv\", low_memory=False)"
+   ]
+  },
+  {
+   "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>split</th>\n",
+       "      <th>treeoflife_id</th>\n",
+       "      <th>eol_content_id_catalog</th>\n",
+       "      <th>eol_page_id_catalog</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>combined_id_catalog</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>956715</th>\n",
+       "      <td>train</td>\n",
+       "      <td>aa563519-6d97-47c3-bcda-c72cdf19a1bf</td>\n",
+       "      <td>14855758</td>\n",
+       "      <td>788082</td>\n",
+       "      <td>Animalia</td>\n",
+       "      <td>Arthropoda</td>\n",
+       "      <td>Insecta</td>\n",
+       "      <td>Diptera</td>\n",
+       "      <td>Cecidomyiidae</td>\n",
+       "      <td>Geocrypta</td>\n",
+       "      <td>galii</td>\n",
+       "      <td>Geocrypta galii</td>\n",
+       "      <td>14855758_788082</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>956716</th>\n",
+       "      <td>train</td>\n",
+       "      <td>e3253a67-7114-41d5-ac55-1696d6c7f6f3</td>\n",
+       "      <td>22807070</td>\n",
+       "      <td>639017</td>\n",
+       "      <td>Plantae</td>\n",
+       "      <td>Tracheophyta</td>\n",
+       "      <td>Magnoliopsida</td>\n",
+       "      <td>Fabales</td>\n",
+       "      <td>Fabaceae</td>\n",
+       "      <td>Psoralea</td>\n",
+       "      <td>lupinella</td>\n",
+       "      <td>Psoralea lupinella</td>\n",
+       "      <td>22807070_639017</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "        split                         treeoflife_id  eol_content_id_catalog  \\\n",
+       "956715  train  aa563519-6d97-47c3-bcda-c72cdf19a1bf                14855758   \n",
+       "956716  train  e3253a67-7114-41d5-ac55-1696d6c7f6f3                22807070   \n",
+       "\n",
+       "        eol_page_id_catalog   kingdom        phylum          class    order  \\\n",
+       "956715               788082  Animalia    Arthropoda        Insecta  Diptera   \n",
+       "956716               639017   Plantae  Tracheophyta  Magnoliopsida  Fabales   \n",
+       "\n",
+       "               family      genus    species              common  \\\n",
+       "956715  Cecidomyiidae  Geocrypta      galii     Geocrypta galii   \n",
+       "956716       Fabaceae   Psoralea  lupinella  Psoralea lupinella   \n",
+       "\n",
+       "       combined_id_catalog  \n",
+       "956715     14855758_788082  \n",
+       "956716     22807070_639017  "
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# make combined ID for catalog and add suffix to eol content and page IDs\n",
+    "eol_catalog['combined_id_catalog'] = eol_catalog['eol_content_id'].astype(str) + '_' + eol_catalog['eol_page_id'].astype(str)\n",
+    "eol_catalog.rename(columns={'eol_content_id': 'eol_content_id_catalog', 'eol_page_id': 'eol_page_id_catalog'}, inplace=True)\n",
+    "eol_catalog.head(2)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "archive has 6725471 entries, with columns: ['Filename', 'MD5']\n"
+     ]
+    }
+   ],
+   "source": [
+    "# Cargo had 6,724,838 entries\n",
+    "print(f\"archive has {archive.shape[0]} entries, with columns: {list(archive.columns)}\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "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</th>\n",
+       "      <th>MD5</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>29538374_65414274_eol-full-size-copy.jpg</td>\n",
+       "      <td>98b1ed1430620ad50a6126cb2f9fcc74</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>27793900_888015_eol-full-size-copy.jpg</td>\n",
+       "      <td>2de2ff12d5f339fe9d81a170749f9cb6</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "                                   Filename                               MD5\n",
+       "0  29538374_65414274_eol-full-size-copy.jpg  98b1ed1430620ad50a6126cb2f9fcc74\n",
+       "1    27793900_888015_eol-full-size-copy.jpg  2de2ff12d5f339fe9d81a170749f9cb6"
+      ]
+     },
+     "execution_count": 8,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "archive.head(2)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def get_combined_id(filename):\n",
+    "    return filename.split(\"_e\")[0]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "archive[\"combined_id\"] = archive[\"Filename\"].apply(get_combined_id)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Merge catalog with archive (sanity check on our images since the cargo didn't match with all of catalog)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 6250420 entries, 0 to 6250419\n",
+      "Data columns (total 16 columns):\n",
+      " #   Column                  Non-Null Count    Dtype \n",
+      "---  ------                  --------------    ----- \n",
+      " 0   split                   6250420 non-null  object\n",
+      " 1   treeoflife_id           6250420 non-null  object\n",
+      " 2   eol_content_id_catalog  6250420 non-null  int64 \n",
+      " 3   eol_page_id_catalog     6250420 non-null  int64 \n",
+      " 4   kingdom                 5989611 non-null  object\n",
+      " 5   phylum                  5991207 non-null  object\n",
+      " 6   class                   5971438 non-null  object\n",
+      " 7   order                   5965299 non-null  object\n",
+      " 8   family                  5948728 non-null  object\n",
+      " 9   genus                   5940313 non-null  object\n",
+      " 10  species                 5951613 non-null  object\n",
+      " 11  common                  6250420 non-null  object\n",
+      " 12  combined_id_catalog     6250420 non-null  object\n",
+      " 13  Filename                6250420 non-null  object\n",
+      " 14  MD5                     6250420 non-null  object\n",
+      " 15  combined_id             6250420 non-null  object\n",
+      "dtypes: int64(2), object(14)\n",
+      "memory usage: 763.0+ MB\n"
+     ]
+    }
+   ],
+   "source": [
+    "catalog_archive = pd.merge(eol_catalog,\n",
+    "                           archive,\n",
+    "                           left_on = \"combined_id_catalog\",\n",
+    "                           right_on = \"combined_id\",\n",
+    "                           how=\"inner\"\n",
+    "                           )\n",
+    "catalog_archive.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Sanity check confirmed: Everything in the catalog is captured in our cargo archive."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Pull in combined manifest with checksums to merge on the archive checksums."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "Index(['filename_manifest', 'md5_combined_manifest',\n",
+       "       'combined_id_manifest_redownload', 'eol_content_id', 'eol_page_id',\n",
+       "       'medium_source_url', 'eol_full_size_copy_url', 'license_name',\n",
+       "       'copyright_owner', 'expected_image_filename', 'source_0706',\n",
+       "       'source_0726', 'source_1206', 'combined_id_full_manifest'],\n",
+       "      dtype='object')"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "manifests = pd.read_csv(\"../data/combined_manifest_with_checksums.csv\", low_memory=False)\n",
+    "manifests.columns"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 6841202 entries, 0 to 6841201\n",
+      "Data columns (total 30 columns):\n",
+      " #   Column                           Non-Null Count    Dtype \n",
+      "---  ------                           --------------    ----- \n",
+      " 0   split                            6841202 non-null  object\n",
+      " 1   treeoflife_id                    6841202 non-null  object\n",
+      " 2   eol_content_id_catalog           6841202 non-null  int64 \n",
+      " 3   eol_page_id_catalog              6841202 non-null  int64 \n",
+      " 4   kingdom                          6551473 non-null  object\n",
+      " 5   phylum                           6553206 non-null  object\n",
+      " 6   class                            6532009 non-null  object\n",
+      " 7   order                            6525621 non-null  object\n",
+      " 8   family                           6506076 non-null  object\n",
+      " 9   genus                            6486130 non-null  object\n",
+      " 10  species                          6406307 non-null  object\n",
+      " 11  common                           6841202 non-null  object\n",
+      " 12  combined_id_catalog              6841202 non-null  object\n",
+      " 13  Filename                         6841202 non-null  object\n",
+      " 14  MD5                              6841202 non-null  object\n",
+      " 15  combined_id                      6841202 non-null  object\n",
+      " 16  filename_manifest                6841202 non-null  object\n",
+      " 17  md5_combined_manifest            6841202 non-null  object\n",
+      " 18  combined_id_manifest_redownload  6841202 non-null  object\n",
+      " 19  eol_content_id                   6841202 non-null  int64 \n",
+      " 20  eol_page_id                      6841202 non-null  int64 \n",
+      " 21  medium_source_url                6841202 non-null  object\n",
+      " 22  eol_full_size_copy_url           6841202 non-null  object\n",
+      " 23  license_name                     6841202 non-null  object\n",
+      " 24  copyright_owner                  6208498 non-null  object\n",
+      " 25  expected_image_filename          6841202 non-null  object\n",
+      " 26  source_0706                      6841202 non-null  bool  \n",
+      " 27  source_0726                      6841202 non-null  bool  \n",
+      " 28  source_1206                      6841202 non-null  bool  \n",
+      " 29  combined_id_full_manifest        6841202 non-null  object\n",
+      "dtypes: bool(3), int64(4), object(23)\n",
+      "memory usage: 1.4+ GB\n"
+     ]
+    }
+   ],
+   "source": [
+    "catalog_archive_manifest = pd.merge(catalog_archive,\n",
+    "                                    manifests,\n",
+    "                                    left_on = \"MD5\",\n",
+    "                                    right_on = \"md5_combined_manifest\",\n",
+    "                                    how = \"inner\",\n",
+    "                                    suffixes=(\"\",\"_manifests\")\n",
+    "                                    )\n",
+    "catalog_archive_manifest.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "6219674"
+      ]
+     },
+     "execution_count": 14,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "catalog_archive_manifest.treeoflife_id.nunique()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Only 6,219,674 of our 6,250,420 images were able to be pulled through the combined manifests."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Align Owners to Manifest"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "owner_df = pd.read_csv(\"../data/media_manifest_missing_licenses_jul26_owners.csv\",\n",
+    "                       low_memory=False,\n",
+    "                       dtype={\"EOL content ID\": \"int64\", \"EOL page ID\": \"int64\"},)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "try merge then fill and concatenate."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "['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']\n",
+      "['EOL content ID', 'EOL page ID', 'Medium Source URL', 'EOL Full-Size Copy URL', 'License Name', 'Copyright Owner', 'license_link', 'title']\n"
+     ]
+    }
+   ],
+   "source": [
+    "print(list(manifests.columns))\n",
+    "print(list(owner_df.columns))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 23,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "There are 12330062 entries in the combined manifest\n",
+      "There are 632043 entries in the owner match CSV\n"
+     ]
+    }
+   ],
+   "source": [
+    "print(f\"There are {manifests.shape[0]} entries in the combined manifest\")\n",
+    "print(f\"There are {owner_df.shape[0]} entries in the owner match CSV\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "owner_df[\"combined_id_owner\"] = owner_df[\"EOL content ID\"].astype(str) + \"_\" + owner_df[\"EOL page ID\"].astype(str)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 630056 entries, 0 to 630055\n",
+      "Data columns (total 23 columns):\n",
+      " #   Column                           Non-Null Count   Dtype \n",
+      "---  ------                           --------------   ----- \n",
+      " 0   EOL content ID                   630056 non-null  int64 \n",
+      " 1   EOL page ID                      630056 non-null  int64 \n",
+      " 2   Medium Source URL                630056 non-null  object\n",
+      " 3   EOL Full-Size Copy URL           630056 non-null  object\n",
+      " 4   License Name                     630056 non-null  object\n",
+      " 5   Copyright Owner                  611829 non-null  object\n",
+      " 6   license_link                     619741 non-null  object\n",
+      " 7   title                            604447 non-null  object\n",
+      " 8   combined_id_owner                630056 non-null  object\n",
+      " 9   filename_manifest                630056 non-null  object\n",
+      " 10  md5_combined_manifest            630056 non-null  object\n",
+      " 11  combined_id_manifest_redownload  630056 non-null  object\n",
+      " 12  eol_content_id                   630056 non-null  int64 \n",
+      " 13  eol_page_id                      630056 non-null  int64 \n",
+      " 14  medium_source_url                630056 non-null  object\n",
+      " 15  eol_full_size_copy_url           630056 non-null  object\n",
+      " 16  license_name                     630056 non-null  object\n",
+      " 17  copyright_owner                  0 non-null       object\n",
+      " 18  expected_image_filename          630056 non-null  object\n",
+      " 19  source_0706                      630056 non-null  bool  \n",
+      " 20  source_0726                      630056 non-null  bool  \n",
+      " 21  source_1206                      630056 non-null  bool  \n",
+      " 22  combined_id_full_manifest        630056 non-null  object\n",
+      "dtypes: bool(3), int64(4), object(16)\n",
+      "memory usage: 97.9+ MB\n"
+     ]
+    }
+   ],
+   "source": [
+    "owners_manifest = pd.merge(owner_df,\n",
+    "                           manifests,\n",
+    "                           left_on=\"combined_id_owner\",\n",
+    "                           right_on = \"combined_id_full_manifest\",\n",
+    "                           how = \"inner\")\n",
+    "owners_manifest.info()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 16,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 630056 entries, 0 to 630055\n",
+      "Data columns (total 23 columns):\n",
+      " #   Column                           Non-Null Count   Dtype \n",
+      "---  ------                           --------------   ----- \n",
+      " 0   EOL content ID                   630056 non-null  int64 \n",
+      " 1   EOL page ID                      630056 non-null  int64 \n",
+      " 2   Medium Source URL                630056 non-null  object\n",
+      " 3   EOL Full-Size Copy URL           630056 non-null  object\n",
+      " 4   License Name                     630056 non-null  object\n",
+      " 5   Copyright Owner                  611829 non-null  object\n",
+      " 6   license_link                     619741 non-null  object\n",
+      " 7   title                            604447 non-null  object\n",
+      " 8   combined_id_owner                630056 non-null  object\n",
+      " 9   filename_manifest                630056 non-null  object\n",
+      " 10  md5_combined_manifest            630056 non-null  object\n",
+      " 11  combined_id_manifest_redownload  630056 non-null  object\n",
+      " 12  eol_content_id                   630056 non-null  int64 \n",
+      " 13  eol_page_id                      630056 non-null  int64 \n",
+      " 14  medium_source_url                630056 non-null  object\n",
+      " 15  eol_full_size_copy_url           630056 non-null  object\n",
+      " 16  license_name                     630056 non-null  object\n",
+      " 17  copyright_owner                  611829 non-null  object\n",
+      " 18  expected_image_filename          630056 non-null  object\n",
+      " 19  source_0706                      630056 non-null  bool  \n",
+      " 20  source_0726                      630056 non-null  bool  \n",
+      " 21  source_1206                      630056 non-null  bool  \n",
+      " 22  combined_id_full_manifest        630056 non-null  object\n",
+      "dtypes: bool(3), int64(4), object(16)\n",
+      "memory usage: 97.9+ MB\n"
+     ]
+    }
+   ],
+   "source": [
+    "owners_manifest[\"copyright_owner\"] = owners_manifest[\"Copyright Owner\"]\n",
+    "owners_manifest.info(show_counts=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 17,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "Index(['filename_manifest', 'md5_combined_manifest',\n",
+       "       'combined_id_manifest_redownload', 'eol_content_id', 'eol_page_id',\n",
+       "       'medium_source_url', 'eol_full_size_copy_url', 'license_name',\n",
+       "       'copyright_owner', 'expected_image_filename', 'source_0706',\n",
+       "       'source_0726', 'source_1206', 'combined_id_full_manifest', 'title'],\n",
+       "      dtype='object')"
+      ]
+     },
+     "execution_count": 17,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "license_cols = list(manifests.columns)\n",
+    "license_cols.append(\"title\")\n",
+    "owners_manifest = owners_manifest[license_cols]\n",
+    "owners_manifest.columns"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "630056"
+      ]
+     },
+     "execution_count": 13,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "rematched_owner_ids = list(owners_manifest.combined_id_full_manifest.unique())\n",
+    "len(rematched_owner_ids)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "(11700006, 14)"
+      ]
+     },
+     "execution_count": 14,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "un_matched_owner_manifest = manifests.loc[~manifests.combined_id_full_manifest.isin(rematched_owner_ids)]\n",
+    "un_matched_owner_manifest.shape"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 18,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/var/folders/nv/f0fq1p1n1_3b11x579py_0q80000gq/T/ipykernel_4207/1002247400.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",
+      "  un_matched_owner_manifest[\"title\"] = \"not provided\"\n"
+     ]
+    }
+   ],
+   "source": [
+    "un_matched_owner_manifest[\"title\"] = \"not provided\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 19,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 12330062 entries, 0 to 12330061\n",
+      "Data columns (total 15 columns):\n",
+      " #   Column                           Non-Null Count     Dtype \n",
+      "---  ------                           --------------     ----- \n",
+      " 0   filename_manifest                12330062 non-null  object\n",
+      " 1   md5_combined_manifest            12330062 non-null  object\n",
+      " 2   combined_id_manifest_redownload  12330062 non-null  object\n",
+      " 3   eol_content_id                   12330062 non-null  int64 \n",
+      " 4   eol_page_id                      12330062 non-null  int64 \n",
+      " 5   medium_source_url                12330062 non-null  object\n",
+      " 6   eol_full_size_copy_url           12330062 non-null  object\n",
+      " 7   license_name                     12330062 non-null  object\n",
+      " 8   copyright_owner                  11544885 non-null  object\n",
+      " 9   expected_image_filename          12330062 non-null  object\n",
+      " 10  source_0706                      12330062 non-null  bool  \n",
+      " 11  source_0726                      12330062 non-null  bool  \n",
+      " 12  source_1206                      12330062 non-null  bool  \n",
+      " 13  combined_id_full_manifest        12330062 non-null  object\n",
+      " 14  title                            12304453 non-null  object\n",
+      "dtypes: bool(3), int64(2), object(10)\n",
+      "memory usage: 1.1+ GB\n"
+     ]
+    }
+   ],
+   "source": [
+    "full_owner_manifest = pd.concat([un_matched_owner_manifest, owners_manifest], ignore_index=True)\n",
+    "full_owner_manifest.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 20,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Licenses still missing Copyright Owners: \n",
+      " license_name\n",
+      "cc-by-3.0                          262894\n",
+      "cc-publicdomain                    262803\n",
+      "cc-by-nc-sa-3.0                    122493\n",
+      "cc-by-sa-3.0                        93303\n",
+      "No known copyright restrictions     31025\n",
+      "cc-by-nc                            12619\n",
+      "cc-0-1.0                               32\n",
+      "cc-by-nc-2.0                            5\n",
+      "cc-by-nc-4.0                            2\n",
+      "cc-by-nc-sa                             1\n",
+      "Name: count, dtype: int64\n"
+     ]
+    }
+   ],
+   "source": [
+    "print(\n",
+    "        \"Licenses still missing Copyright Owners: \\n\",\n",
+    "        full_owner_manifest.loc[\n",
+    "            full_owner_manifest[\"copyright_owner\"].isna(), \"license_name\"\n",
+    "        ].value_counts(),\n",
+    "    )"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 21,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "full_owner_manifest[\"copyright_owner\"].fillna(\"not provided\", inplace=True)\n",
+    "full_owner_manifest[\"title\"].fillna(\"not provided\", inplace=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 22,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "full_owner_manifest.to_csv(\"../data/full_owner_manifest.csv\", index = False)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "std",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

eol_realign/notebooks/links_align_reduced.ipynb

@@ -0,0 +1,1253 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pandas as pd"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "TOL_FILEPATH = \"../../data/\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Read in Links CSV files\n",
+    "\n",
+    "Full cargo archives have some more content than the [original `links_inner` file](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/fa08e0f6692a013e4e4f5ca30dd0e8883c0021d8/eol_realign/data/links_inner.csv) and 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).\n",
+    "\n",
+    "From Matt:\n",
+    "> It represents a series of inner merges:\n",
+    "> 1. The list of images in the EOL cargo archive (used to create the webdatasets) with the EOL portion of `catalog.csv`\n",
+    ">  - Merged on a combined identifier of `eol_content_id` and `eol_page_id`.\n",
+    "> Result from 1) with the list of images redownloaded from all 3 media manifests we touched around the original download time (identified [here](https://huggingface.co/datasets/imageomics/ToL-EDA/discussions/5#6584808d92eba5ad69b8379f)).\n",
+    ">  - Merged on MD5\n",
+    ">\n",
+    "> The result has 6,219,674 unique `treeoflife_id` entries and 6,146,917 unique `md5` entries. It has the combined `eol_content_id` and `eol_page_id` identifiers used at each stage:\n",
+    "- `combined_id_catalog`: represents what's in the original catalog \n",
+    "- `combined_id_manifest_full_manifest`: represents what's in the combined manifest from all 3 dates \n",
+    "> It also has an indicator of which of the three media manifest files each entry was present in (one or more) in columns representing retreival date (eg., `source_0706`: indicates if it was present in the manifest retrieved on July 6, 2023). It also has the copyright owner and license information as contained in the media manifest files.\n",
+    ">\n",
+    "> Still needs to be run through the owner name finding code. ([owner_match](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/71ad5b49226a3a49634931005eeb340b3c96db13/scripts/match_owners.py) --note: this version uses inner merges, so will remove entries without media info. Probably should adjust this.)\n",
+    "\n",
+    "For reference on the numbers, there are 6,250,420 EOL images in TreeOfLife-10M (the catalog). Comparing with `links_inner` previously (from [`links_inner.csv`](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/fa08e0f6692a013e4e4f5ca30dd0e8883c0021d8/eol_realign/data/links_inner.csv)) we were missing 31,376 images, 29 of which were identified in [`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": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "links_inner = pd.read_csv(\"../data/eol-cargo-archive_catalog_combined-manifest-checksums_links.csv\", low_memory=False)\n",
+    "links_manifest_cargo = pd.read_csv(\"../data/eol-cargo-archive_combined-manifest-checksums_links.csv\", low_memory=False)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 6841202 entries, 0 to 6841201\n",
+      "Data columns (total 30 columns):\n",
+      " #   Column                           Non-Null Count    Dtype  \n",
+      "---  ------                           --------------    -----  \n",
+      " 0   filename_archive                 6841202 non-null  object \n",
+      " 1   md5                              6841202 non-null  object \n",
+      " 2   combined_id_archive              6841202 non-null  object \n",
+      " 3   split                            6841202 non-null  object \n",
+      " 4   treeoflife_id                    6841202 non-null  object \n",
+      " 5   bioscan_part                     0 non-null        float64\n",
+      " 6   bioscan_filename                 0 non-null        float64\n",
+      " 7   inat21_filename                  0 non-null        float64\n",
+      " 8   inat21_cls_name                  0 non-null        float64\n",
+      " 9   inat21_cls_num                   0 non-null        float64\n",
+      " 10  kingdom                          6551473 non-null  object \n",
+      " 11  phylum                           6553206 non-null  object \n",
+      " 12  class                            6532009 non-null  object \n",
+      " 13  order                            6525621 non-null  object \n",
+      " 14  family                           6506076 non-null  object \n",
+      " 15  genus                            6486130 non-null  object \n",
+      " 16  species                          6406307 non-null  object \n",
+      " 17  common                           6841202 non-null  object \n",
+      " 18  combined_id_catalog              6841202 non-null  object \n",
+      " 19  filename_manifest                6841202 non-null  object \n",
+      " 20  combined_id_manifest_redownload  6841202 non-null  object \n",
+      " 21  medium_source_url                6841202 non-null  object \n",
+      " 22  eol_full_size_copy_url           6841202 non-null  object \n",
+      " 23  license_name                     6841202 non-null  object \n",
+      " 24  copyright_owner                  6208498 non-null  object \n",
+      " 25  expected_image_filename          6841202 non-null  object \n",
+      " 26  source_0706                      6841202 non-null  bool   \n",
+      " 27  source_0726                      6841202 non-null  bool   \n",
+      " 28  source_1206                      6841202 non-null  bool   \n",
+      " 29  combined_id_full_manifest        6841202 non-null  object \n",
+      "dtypes: bool(3), float64(5), object(22)\n",
+      "memory usage: 1.4+ GB\n"
+     ]
+    }
+   ],
+   "source": [
+    "links_inner.info(show_counts=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\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"
+     ]
+    }
+   ],
+   "source": [
+    "links_manifest_cargo.info(show_counts=True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "These both have about 600-700 more entries than the earlier files."
+   ]
+  },
+  {
+   "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>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",
+       "    </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]\n",
+       "Index: []"
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# These should be the same\n",
+    "links_manifest_cargo.loc[links_manifest_cargo[\"combined_id_manifest_redownload\"] != links_manifest_cargo[\"combined_id_full_manifest\"]]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "Index: 822558 entries, 2 to 7513999\n",
+      "Data columns (total 17 columns):\n",
+      " #   Column                           Non-Null Count   Dtype \n",
+      "---  ------                           --------------   ----- \n",
+      " 0   filename_archive                 822558 non-null  object\n",
+      " 1   md5_archive                      822558 non-null  object\n",
+      " 2   combined_id_archive              822558 non-null  object\n",
+      " 3   filename_manifest                822558 non-null  object\n",
+      " 4   md5_combined_manifest            822558 non-null  object\n",
+      " 5   combined_id_manifest_redownload  822558 non-null  object\n",
+      " 6   eol_content_id                   822558 non-null  int64 \n",
+      " 7   eol_page_id                      822558 non-null  int64 \n",
+      " 8   medium_source_url                822558 non-null  object\n",
+      " 9   eol_full_size_copy_url           822558 non-null  object\n",
+      " 10  license_name                     822558 non-null  object\n",
+      " 11  copyright_owner                  797147 non-null  object\n",
+      " 12  expected_image_filename          822558 non-null  object\n",
+      " 13  source_0706                      822558 non-null  bool  \n",
+      " 14  source_0726                      822558 non-null  bool  \n",
+      " 15  source_1206                      822558 non-null  bool  \n",
+      " 16  combined_id_full_manifest        822558 non-null  object\n",
+      "dtypes: bool(3), int64(2), object(12)\n",
+      "memory usage: 96.5+ MB\n"
+     ]
+    }
+   ],
+   "source": [
+    "# archive has replaced cargo\n",
+    "# full manifest or manifest redownload to replace manifest checksums -- they are equal\n",
+    "links_mismatch = links_manifest_cargo.loc[links_manifest_cargo[\"combined_id_archive\"] != links_manifest_cargo[\"combined_id_full_manifest\"]]\n",
+    "links_mismatch.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "There are 42 more mismatched entries. Only 13 additional unique images (MD5s)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "md5_archive                  624574\n",
+       "combined_id_full_manifest    712540\n",
+       "combined_id_archive          703446\n",
+       "dtype: int64"
+      ]
+     },
+     "execution_count": 9,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "links_mismatch[[\"md5_archive\", \"combined_id_full_manifest\", \"combined_id_archive\"]].nunique()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# This is archive manifest mismatch\n",
+    "links_mismatch.to_csv(\"../data/links_archive_manifest_IDmismatch.csv\", index = False)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "catalog = pd.read_csv(TOL_FILEPATH + \"catalog.csv\", low_memory=False)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# remove train_small and all non-EOL entries\n",
+    "catalog = catalog.loc[catalog.split != \"train_small\"]\n",
+    "eol_catalog = catalog.loc[catalog.eol_content_id.notna()]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "split                   2\n",
+       "treeoflife_id     6250420\n",
+       "eol_content_id    6250420\n",
+       "eol_page_id        503589\n",
+       "dtype: int64"
+      ]
+     },
+     "execution_count": 13,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "eol_catalog[list(eol_catalog.columns)[:4]].nunique()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "eol_cols = [col for col in list(eol_catalog.columns) if \"bioscan\" not in col and \"inat\" not in col]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "Index: 6250420 entries, 956715 to 11000930\n",
+      "Data columns (total 12 columns):\n",
+      " #   Column          Non-Null Count    Dtype  \n",
+      "---  ------          --------------    -----  \n",
+      " 0   split           6250420 non-null  object \n",
+      " 1   treeoflife_id   6250420 non-null  object \n",
+      " 2   eol_content_id  6250420 non-null  float64\n",
+      " 3   eol_page_id     6250420 non-null  float64\n",
+      " 4   kingdom         5989611 non-null  object \n",
+      " 5   phylum          5991207 non-null  object \n",
+      " 6   class           5971438 non-null  object \n",
+      " 7   order           5965299 non-null  object \n",
+      " 8   family          5948728 non-null  object \n",
+      " 9   genus           5940313 non-null  object \n",
+      " 10  species         5951613 non-null  object \n",
+      " 11  common          6250420 non-null  object \n",
+      "dtypes: float64(2), object(10)\n",
+      "memory usage: 619.9+ MB\n"
+     ]
+    }
+   ],
+   "source": [
+    "eol_catalog = eol_catalog[eol_cols]\n",
+    "eol_catalog.info(show_counts=True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Must recast IDs as `int64`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 16,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "Index: 6250420 entries, 956715 to 11000930\n",
+      "Data columns (total 4 columns):\n",
+      " #   Column          Dtype \n",
+      "---  ------          ----- \n",
+      " 0   split           object\n",
+      " 1   treeoflife_id   object\n",
+      " 2   eol_content_id  int64 \n",
+      " 3   eol_page_id     int64 \n",
+      "dtypes: int64(2), object(2)\n",
+      "memory usage: 238.4+ MB\n"
+     ]
+    }
+   ],
+   "source": [
+    "eol_catalog = eol_catalog.astype({\"eol_content_id\": \"int64\", \"eol_page_id\": \"int64\"})\n",
+    "eol_catalog[eol_cols[:4]].info()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 17,
+   "metadata": {
+    "lines_to_next_cell": 2
+   },
+   "outputs": [],
+   "source": [
+    "# make combined ID for catalog and add suffix to eol content and page IDs\n",
+    "eol_catalog['combined_id_catalog'] = eol_catalog['eol_content_id'].astype(str) + '_' + eol_catalog['eol_page_id'].astype(str)\n",
+    "eol_catalog.rename(columns={'eol_content_id': 'eol_content_id_catalog', 'eol_page_id': 'eol_page_id_catalog'}, inplace=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 18,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "6219674"
+      ]
+     },
+     "execution_count": 18,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "matched_catalog_ids = list(links_inner.combined_id_catalog.unique())\n",
+    "len(matched_catalog_ids)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Here we go, we got an additional 630 matched IDs!"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 19,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "['29538374_65414274',\n",
+       " '27793900_888015',\n",
+       " '29121641_5618956',\n",
+       " '27596176_607817',\n",
+       " '20300703_267922']"
+      ]
+     },
+     "execution_count": 19,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "matched_catalog_ids[:5]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We still have about 30K unmatched (as shown below, it's down to 30,746 from 31,376), let's find those in the catalog and then we'll try to merge with our mismatched cargo & manifest."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 20,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "5842839       28875844_579175\n",
+       "7715090       21712402_702458\n",
+       "10112940     27938371_3091824\n",
+       "8606944     27597441_49820955\n",
+       "1247592      14852900_2896866\n",
+       "Name: combined_id_catalog, dtype: object"
+      ]
+     },
+     "execution_count": 20,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "eol_catalog['combined_id_catalog'].sample(5)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 21,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "Index: 30746 entries, 956874 to 10996978\n",
+      "Data columns (total 13 columns):\n",
+      " #   Column                  Non-Null Count  Dtype \n",
+      "---  ------                  --------------  ----- \n",
+      " 0   split                   30746 non-null  object\n",
+      " 1   treeoflife_id           30746 non-null  object\n",
+      " 2   eol_content_id_catalog  30746 non-null  int64 \n",
+      " 3   eol_page_id_catalog     30746 non-null  int64 \n",
+      " 4   kingdom                 30573 non-null  object\n",
+      " 5   phylum                  30578 non-null  object\n",
+      " 6   class                   30153 non-null  object\n",
+      " 7   order                   30528 non-null  object\n",
+      " 8   family                  30294 non-null  object\n",
+      " 9   genus                   30192 non-null  object\n",
+      " 10  species                 29399 non-null  object\n",
+      " 11  common                  30746 non-null  object\n",
+      " 12  combined_id_catalog     30746 non-null  object\n",
+      "dtypes: int64(2), object(11)\n",
+      "memory usage: 3.3+ MB\n"
+     ]
+    }
+   ],
+   "source": [
+    "mismatched_catalog = eol_catalog.loc[~eol_catalog[\"combined_id_catalog\"].isin(matched_catalog_ids)]\n",
+    "mismatched_catalog.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 22,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "split                         2\n",
+       "treeoflife_id             30746\n",
+       "eol_content_id_catalog    30746\n",
+       "eol_page_id_catalog        7042\n",
+       "kingdom                       7\n",
+       "phylum                       33\n",
+       "class                        87\n",
+       "order                       355\n",
+       "family                     1165\n",
+       "genus                      3503\n",
+       "species                    5174\n",
+       "common                     6884\n",
+       "combined_id_catalog       30746\n",
+       "dtype: int64"
+      ]
+     },
+     "execution_count": 22,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "mismatched_catalog.nunique()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Seems one class got resolved (equals more orders and down)."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Merge with Mismatched CargoArchive-Manifest\n",
+    "\n",
+    "let's merge with `links_mismatch` to see if the mismatched archive and manifest combined IDs can be linked up."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 23,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 0 entries\n",
+      "Data columns (total 30 columns):\n",
+      " #   Column                           Non-Null Count  Dtype \n",
+      "---  ------                           --------------  ----- \n",
+      " 0   split                            0 non-null      object\n",
+      " 1   treeoflife_id                    0 non-null      object\n",
+      " 2   eol_content_id_catalog           0 non-null      int64 \n",
+      " 3   eol_page_id_catalog              0 non-null      int64 \n",
+      " 4   kingdom                          0 non-null      object\n",
+      " 5   phylum                           0 non-null      object\n",
+      " 6   class                            0 non-null      object\n",
+      " 7   order                            0 non-null      object\n",
+      " 8   family                           0 non-null      object\n",
+      " 9   genus                            0 non-null      object\n",
+      " 10  species                          0 non-null      object\n",
+      " 11  common                           0 non-null      object\n",
+      " 12  combined_id_catalog              0 non-null      object\n",
+      " 13  filename_archive                 0 non-null      object\n",
+      " 14  md5_archive                      0 non-null      object\n",
+      " 15  combined_id_archive              0 non-null      object\n",
+      " 16  filename_manifest                0 non-null      object\n",
+      " 17  md5_combined_manifest            0 non-null      object\n",
+      " 18  combined_id_manifest_redownload  0 non-null      object\n",
+      " 19  eol_content_id                   0 non-null      int64 \n",
+      " 20  eol_page_id                      0 non-null      int64 \n",
+      " 21  medium_source_url                0 non-null      object\n",
+      " 22  eol_full_size_copy_url           0 non-null      object\n",
+      " 23  license_name                     0 non-null      object\n",
+      " 24  copyright_owner                  0 non-null      object\n",
+      " 25  expected_image_filename          0 non-null      object\n",
+      " 26  source_0706                      0 non-null      bool  \n",
+      " 27  source_0726                      0 non-null      bool  \n",
+      " 28  source_1206                      0 non-null      bool  \n",
+      " 29  combined_id_full_manifest        0 non-null      object\n",
+      "dtypes: bool(3), int64(4), object(23)\n",
+      "memory usage: 132.0+ bytes\n"
+     ]
+    }
+   ],
+   "source": [
+    "# replace manifest checksums with full manifest as above\n",
+    "links_catalog_mismatch = pd.merge(mismatched_catalog,\n",
+    "                                  links_mismatch,\n",
+    "                                  left_on = \"combined_id_catalog\",\n",
+    "                                  right_on = \"combined_id_full_manifest\",\n",
+    "                                  how = \"inner\")\n",
+    "links_catalog_mismatch.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Now there's no gain from the mismatch file, but that was only 29 images, so we've captured them from the archive (plus more!)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 24,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "2003559      15270321_240065\n",
+       "8751466       29485627_17806\n",
+       "4818957       27965287_35726\n",
+       "8697796       9483753_328724\n",
+       "1049389      9446784_5019858\n",
+       "8364678      9467133_2925218\n",
+       "5119903    28880812_10305215\n",
+       "Name: combined_id_catalog, dtype: object"
+      ]
+     },
+     "execution_count": 24,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "mismatched_catalog.combined_id_catalog.sample(7)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "These pages are reasonably full too: [5660435](https://eol.org/pages/5660435)."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Final Catalog\n",
+    "\n",
+    "Our final EOL catalog is thus going to be the `treeoflife_id`s in `links_inner`.\n",
+    "\n",
+    "Finall question is just how does this look for our `train_small`?"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 34,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "Index: 593764 entries, 0 to 918500\n",
+      "Data columns (total 12 columns):\n",
+      " #   Column          Non-Null Count   Dtype  \n",
+      "---  ------          --------------   -----  \n",
+      " 0   split           593764 non-null  object \n",
+      " 1   treeoflife_id   593764 non-null  object \n",
+      " 2   eol_content_id  593764 non-null  float64\n",
+      " 3   eol_page_id     593764 non-null  float64\n",
+      " 4   kingdom         569128 non-null  object \n",
+      " 5   phylum          569285 non-null  object \n",
+      " 6   class           567356 non-null  object \n",
+      " 7   order           566839 non-null  object \n",
+      " 8   family          565269 non-null  object \n",
+      " 9   genus           564605 non-null  object \n",
+      " 10  species         565399 non-null  object \n",
+      " 11  common          593764 non-null  object \n",
+      "dtypes: float64(2), object(10)\n",
+      "memory usage: 58.9+ MB\n"
+     ]
+    }
+   ],
+   "source": [
+    "cat_2 = pd.read_csv(TOL_FILEPATH + \"catalog.csv\", low_memory=False)\n",
+    "\n",
+    "# reduce to just train_small and all non-EOL entries\n",
+    "cat_2 = cat_2.loc[cat_2.split == \"train_small\"]\n",
+    "eol_cat_2 = cat_2.loc[cat_2.eol_content_id.notna()]\n",
+    "\n",
+    "eol_cat_2 = eol_cat_2[eol_cols]\n",
+    "eol_cat_2.info(show_counts=True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "So `train_small` has 593,764 images from EOL. \n",
+    "\n",
+    "Let's recast IDs as ints to match up with `links_inner` and check we have info for all of them."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 35,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "Index: 593764 entries, 0 to 918500\n",
+      "Data columns (total 4 columns):\n",
+      " #   Column          Non-Null Count   Dtype \n",
+      "---  ------          --------------   ----- \n",
+      " 0   split           593764 non-null  object\n",
+      " 1   treeoflife_id   593764 non-null  object\n",
+      " 2   eol_content_id  593764 non-null  int64 \n",
+      " 3   eol_page_id     593764 non-null  int64 \n",
+      "dtypes: int64(2), object(2)\n",
+      "memory usage: 22.7+ MB\n"
+     ]
+    }
+   ],
+   "source": [
+    "eol_cat_2 = eol_cat_2.astype({\"eol_content_id\": \"int64\", \"eol_page_id\": \"int64\"})\n",
+    "eol_cat_2[eol_cols[:4]].info()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 36,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# make combined ID for catalog and add suffix to eol content and page IDs\n",
+    "eol_cat_2['combined_id_catalog'] = eol_cat_2['eol_content_id'].astype(str) + '_' + eol_cat_2['eol_page_id'].astype(str)\n",
+    "eol_cat_2.rename(columns={'eol_content_id': 'eol_content_id_catalog', 'eol_page_id': 'eol_page_id_catalog'}, inplace=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 40,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 612614 entries, 0 to 612613\n",
+      "Data columns (total 25 columns):\n",
+      " #   Column                           Non-Null Count   Dtype \n",
+      "---  ------                           --------------   ----- \n",
+      " 0   split                            612614 non-null  object\n",
+      " 1   treeoflife_id                    612614 non-null  object\n",
+      " 2   eol_content_id_catalog           612614 non-null  int64 \n",
+      " 3   eol_page_id_catalog              612614 non-null  int64 \n",
+      " 4   kingdom                          584979 non-null  object\n",
+      " 5   phylum                           585140 non-null  object\n",
+      " 6   class                            583235 non-null  object\n",
+      " 7   order                            582668 non-null  object\n",
+      " 8   family                           581082 non-null  object\n",
+      " 9   genus                            580464 non-null  object\n",
+      " 10  species                          579943 non-null  object\n",
+      " 11  common                           612614 non-null  object\n",
+      " 12  combined_id_catalog_x            612614 non-null  object\n",
+      " 13  combined_id_catalog_y            612614 non-null  object\n",
+      " 14  filename_manifest                612614 non-null  object\n",
+      " 15  combined_id_manifest_redownload  612614 non-null  object\n",
+      " 16  medium_source_url                612614 non-null  object\n",
+      " 17  eol_full_size_copy_url           612614 non-null  object\n",
+      " 18  license_name                     612614 non-null  object\n",
+      " 19  copyright_owner                  554029 non-null  object\n",
+      " 20  expected_image_filename          612614 non-null  object\n",
+      " 21  source_0706                      612614 non-null  bool  \n",
+      " 22  source_0726                      612614 non-null  bool  \n",
+      " 23  source_1206                      612614 non-null  bool  \n",
+      " 24  combined_id_full_manifest        612614 non-null  object\n",
+      "dtypes: bool(3), int64(2), object(20)\n",
+      "memory usage: 104.6+ MB\n"
+     ]
+    }
+   ],
+   "source": [
+    "eol_ts_links = pd.merge(eol_cat_2,\n",
+    "                        links_inner[list(links_inner.columns)[18:]],\n",
+    "                        left_on = \"combined_id_catalog\",\n",
+    "                        right_on = \"combined_id_full_manifest\",\n",
+    "                        how = \"inner\")\n",
+    "eol_ts_links.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 41,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "590730"
+      ]
+     },
+     "execution_count": 41,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "eol_ts_links.treeoflife_id.nunique()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "So we are missing the metadata for 3,734 of these images."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Check on Rare Species Catalog"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 25,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 12000 entries, 0 to 11999\n",
+      "Data columns (total 11 columns):\n",
+      " #   Column          Non-Null Count  Dtype \n",
+      "---  ------          --------------  ----- \n",
+      " 0   rarespecies_id  12000 non-null  object\n",
+      " 1   eol_content_id  12000 non-null  int64 \n",
+      " 2   eol_page_id     12000 non-null  int64 \n",
+      " 3   kingdom         12000 non-null  object\n",
+      " 4   phylum          12000 non-null  object\n",
+      " 5   class           12000 non-null  object\n",
+      " 6   order           12000 non-null  object\n",
+      " 7   family          12000 non-null  object\n",
+      " 8   genus           12000 non-null  object\n",
+      " 9   species         12000 non-null  object\n",
+      " 10  sciName         12000 non-null  object\n",
+      "dtypes: int64(2), object(9)\n",
+      "memory usage: 1.0+ MB\n"
+     ]
+    }
+   ],
+   "source": [
+    "rs_catalog = pd.read_csv(\"../../rare_species/data/rarespecies-catalog.csv\",\n",
+    "                         low_memory=False,\n",
+    "                         dtype = {\"eol_content_id\": \"int64\", \"eol_page_id\": \"int64\"})\n",
+    "rs_catalog.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 26,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "rs_catalog[\"combined_id_rs\"] = rs_catalog[\"eol_content_id\"].astype(str) + \"_\" + rs_catalog[\"eol_page_id\"].astype(str)\n",
+    "rs_catalog.rename(columns={'eol_content_id': 'eol_content_id_rs', 'eol_page_id': 'eol_page_id_rs'}, inplace=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 27,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 12552 entries, 0 to 12551\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"
+     ]
+    }
+   ],
+   "source": [
+    "rs_links = pd.merge(rs_catalog,\n",
+    "                    links_manifest_cargo,\n",
+    "                    left_on = \"combined_id_rs\",\n",
+    "                    right_on = \"combined_id_archive\", # looking at archive\n",
+    "                    how = \"inner\")\n",
+    "rs_links.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 28,
+   "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",
+       "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": 28,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "rs_links.nunique()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Let's check the mismatched cargo/manifest entries for those last 174..."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 29,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "11826"
+      ]
+     },
+     "execution_count": 29,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "matched_rs_ids = list(rs_links.combined_id_rs.unique())\n",
+    "len(matched_rs_ids)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 30,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "['22519448_914532',\n",
+       " '28677580_1057176',\n",
+       " '20714475_47047909',\n",
+       " '29975068_45509269']"
+      ]
+     },
+     "execution_count": 30,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "matched_rs_ids[:4]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 31,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "1473     29538601_46580048\n",
+       "11127     29447084_1019571\n",
+       "6578       20398296_328017\n",
+       "11583     29772112_1049135\n",
+       "Name: combined_id_rs, dtype: object"
+      ]
+     },
+     "execution_count": 31,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "rs_catalog[\"combined_id_rs\"].sample(4)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 32,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "Index: 174 entries, 163 to 11990\n",
+      "Data columns (total 12 columns):\n",
+      " #   Column             Non-Null Count  Dtype \n",
+      "---  ------             --------------  ----- \n",
+      " 0   rarespecies_id     174 non-null    object\n",
+      " 1   eol_content_id_rs  174 non-null    int64 \n",
+      " 2   eol_page_id_rs     174 non-null    int64 \n",
+      " 3   kingdom            174 non-null    object\n",
+      " 4   phylum             174 non-null    object\n",
+      " 5   class              174 non-null    object\n",
+      " 6   order              174 non-null    object\n",
+      " 7   family             174 non-null    object\n",
+      " 8   genus              174 non-null    object\n",
+      " 9   species            174 non-null    object\n",
+      " 10  sciName            174 non-null    object\n",
+      " 11  combined_id_rs     174 non-null    object\n",
+      "dtypes: int64(2), object(10)\n",
+      "memory usage: 17.7+ KB\n"
+     ]
+    }
+   ],
+   "source": [
+    "mismatched_rs = rs_catalog.loc[~rs_catalog[\"combined_id_rs\"].isin(matched_rs_ids)]\n",
+    "mismatched_rs.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 33,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 0 entries\n",
+      "Data columns (total 29 columns):\n",
+      " #   Column                           Non-Null Count  Dtype \n",
+      "---  ------                           --------------  ----- \n",
+      " 0   rarespecies_id                   0 non-null      object\n",
+      " 1   eol_content_id_rs                0 non-null      int64 \n",
+      " 2   eol_page_id_rs                   0 non-null      int64 \n",
+      " 3   kingdom                          0 non-null      object\n",
+      " 4   phylum                           0 non-null      object\n",
+      " 5   class                            0 non-null      object\n",
+      " 6   order                            0 non-null      object\n",
+      " 7   family                           0 non-null      object\n",
+      " 8   genus                            0 non-null      object\n",
+      " 9   species                          0 non-null      object\n",
+      " 10  sciName                          0 non-null      object\n",
+      " 11  combined_id_rs                   0 non-null      object\n",
+      " 12  filename_archive                 0 non-null      object\n",
+      " 13  md5_archive                      0 non-null      object\n",
+      " 14  combined_id_archive              0 non-null      object\n",
+      " 15  filename_manifest                0 non-null      object\n",
+      " 16  md5_combined_manifest            0 non-null      object\n",
+      " 17  combined_id_manifest_redownload  0 non-null      object\n",
+      " 18  eol_content_id                   0 non-null      int64 \n",
+      " 19  eol_page_id                      0 non-null      int64 \n",
+      " 20  medium_source_url                0 non-null      object\n",
+      " 21  eol_full_size_copy_url           0 non-null      object\n",
+      " 22  license_name                     0 non-null      object\n",
+      " 23  copyright_owner                  0 non-null      object\n",
+      " 24  expected_image_filename          0 non-null      object\n",
+      " 25  source_0706                      0 non-null      bool  \n",
+      " 26  source_0726                      0 non-null      bool  \n",
+      " 27  source_1206                      0 non-null      bool  \n",
+      " 28  combined_id_full_manifest        0 non-null      object\n",
+      "dtypes: bool(3), int64(4), object(22)\n",
+      "memory usage: 132.0+ bytes\n"
+     ]
+    }
+   ],
+   "source": [
+    "links_rs_mismatch = pd.merge(mismatched_rs,\n",
+    "                             links_mismatch,\n",
+    "                             left_on = \"combined_id_rs\",\n",
+    "                             right_on = \"combined_id_full_manifest\",\n",
+    "                             how = \"inner\")\n",
+    "links_rs_mismatch.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "jupytext": {
+   "formats": "ipynb,py:percent"
+  },
+  "kernelspec": {
+   "display_name": "tol",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

eol_realign/notebooks/links_align_reduced.py

@@ -0,0 +1,250 @@
+# ---
+# jupyter:
+#   jupytext:
+#     formats: ipynb,py:percent
+#     text_representation:
+#       extension: .py
+#       format_name: percent
+#       format_version: '1.3'
+#       jupytext_version: 1.16.0
+#   kernelspec:
+#     display_name: tol
+#     language: python
+#     name: python3
+# ---
+
+# %%
+import pandas as pd
+
+# %%
+TOL_FILEPATH = "../../data/"
+
+# %% [markdown]
+# ### Read in Links CSV files
+#
+# Full cargo archives have some more content than the [original `links_inner` file](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/fa08e0f6692a013e4e4f5ca30dd0e8883c0021d8/eol_realign/data/links_inner.csv) and 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).
+#
+# From Matt:
+# > It represents a series of inner merges:
+# > 1. The list of images in the EOL cargo archive (used to create the webdatasets) with the EOL portion of `catalog.csv`
+# >  - Merged on a combined identifier of `eol_content_id` and `eol_page_id`.
+# > Result from 1) with the list of images redownloaded from all 3 media manifests we touched around the original download time (identified [here](https://huggingface.co/datasets/imageomics/ToL-EDA/discussions/5#6584808d92eba5ad69b8379f)).
+# >  - Merged on MD5
+# >
+# > The result has 6,219,674 unique `treeoflife_id` entries and 6,146,917 unique `md5` entries. It has the combined `eol_content_id` and `eol_page_id` identifiers used at each stage:
+# - `combined_id_catalog`: represents what's in the original catalog 
+# - `combined_id_manifest_full_manifest`: represents what's in the combined manifest from all 3 dates 
+# > It also has an indicator of which of the three media manifest files each entry was present in (one or more) in columns representing retreival date (eg., `source_0706`: indicates if it was present in the manifest retrieved on July 6, 2023). It also has the copyright owner and license information as contained in the media manifest files.
+# >
+# > Still needs to be run through the owner name finding code. ([owner_match](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/71ad5b49226a3a49634931005eeb340b3c96db13/scripts/match_owners.py) --note: this version uses inner merges, so will remove entries without media info. Probably should adjust this.)
+#
+# For reference on the numbers, there are 6,250,420 EOL images in TreeOfLife-10M (the catalog). Comparing with `links_inner` previously (from [`links_inner.csv`](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/fa08e0f6692a013e4e4f5ca30dd0e8883c0021d8/eol_realign/data/links_inner.csv)) we were missing 31,376 images, 29 of which were identified in [`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_inner = pd.read_csv("../data/eol-cargo-archive_catalog_combined-manifest-checksums_links.csv", low_memory=False)
+links_manifest_cargo = pd.read_csv("../data/eol-cargo-archive_combined-manifest-checksums_links.csv", low_memory=False)
+
+# %%
+links_inner.info(show_counts=True)
+
+# %%
+links_manifest_cargo.info(show_counts=True)
+
+# %% [markdown]
+# These both have about 600-700 more entries than the earlier files.
+
+# %%
+# These should be the same
+links_manifest_cargo.loc[links_manifest_cargo["combined_id_manifest_redownload"] != links_manifest_cargo["combined_id_full_manifest"]]
+
+# %%
+# archive has replaced cargo
+# full manifest or manifest redownload to replace manifest checksums -- they are equal
+links_mismatch = links_manifest_cargo.loc[links_manifest_cargo["combined_id_archive"] != links_manifest_cargo["combined_id_full_manifest"]]
+links_mismatch.info(show_counts = True)
+
+# %% [markdown]
+# There are 42 more mismatched entries. Only 13 additional unique images (MD5s).
+
+# %%
+links_mismatch[["md5_archive", "combined_id_full_manifest", "combined_id_archive"]].nunique()
+
+# %%
+# This is archive manifest mismatch
+links_mismatch.to_csv("../data/links_archive_manifest_IDmismatch.csv", index = False)
+
+# %%
+catalog = pd.read_csv(TOL_FILEPATH + "catalog.csv", low_memory=False)
+
+# %%
+# remove train_small and all non-EOL entries
+catalog = catalog.loc[catalog.split != "train_small"]
+eol_catalog = catalog.loc[catalog.eol_content_id.notna()]
+
+# %%
+eol_catalog[list(eol_catalog.columns)[:4]].nunique()
+
+# %%
+eol_cols = [col for col in list(eol_catalog.columns) if "bioscan" not in col and "inat" not in col]
+
+# %%
+eol_catalog = eol_catalog[eol_cols]
+eol_catalog.info(show_counts=True)
+
+# %% [markdown]
+# Must recast IDs as `int64`
+
+# %%
+eol_catalog = eol_catalog.astype({"eol_content_id": "int64", "eol_page_id": "int64"})
+eol_catalog[eol_cols[:4]].info()
+
+# %%
+# make combined ID for catalog and add suffix to eol content and page IDs
+eol_catalog['combined_id_catalog'] = eol_catalog['eol_content_id'].astype(str) + '_' + eol_catalog['eol_page_id'].astype(str)
+eol_catalog.rename(columns={'eol_content_id': 'eol_content_id_catalog', 'eol_page_id': 'eol_page_id_catalog'}, inplace=True)
+
+
+# %%
+matched_catalog_ids = list(links_inner.combined_id_catalog.unique())
+len(matched_catalog_ids)
+
+# %% [markdown]
+# Here we go, we got an additional 630 matched IDs!
+
+# %%
+matched_catalog_ids[:5]
+
+# %% [markdown]
+# We still have about 30K unmatched (as shown below, it's down to 30,746 from 31,376), let's find those in the catalog and then we'll try to merge with our mismatched cargo & manifest.
+
+# %%
+eol_catalog['combined_id_catalog'].sample(5)
+
+# %%
+mismatched_catalog = eol_catalog.loc[~eol_catalog["combined_id_catalog"].isin(matched_catalog_ids)]
+mismatched_catalog.info(show_counts = True)
+
+# %%
+mismatched_catalog.nunique()
+
+# %% [markdown]
+# Seems one class got resolved (equals more orders and down).
+
+# %% [markdown]
+# ## Merge with Mismatched CargoArchive-Manifest
+#
+# let's merge with `links_mismatch` to see if the mismatched archive and manifest combined IDs can be linked up.
+
+# %%
+# replace manifest checksums with full manifest as above
+links_catalog_mismatch = pd.merge(mismatched_catalog,
+                                  links_mismatch,
+                                  left_on = "combined_id_catalog",
+                                  right_on = "combined_id_full_manifest",
+                                  how = "inner")
+links_catalog_mismatch.info(show_counts = True)
+
+# %% [markdown]
+# Now there's no gain from the mismatch file, but that was only 29 images, so we've captured them from the archive (plus more!).
+
+# %%
+mismatched_catalog.combined_id_catalog.sample(7)
+
+# %% [markdown]
+# These pages are reasonably full too: [5660435](https://eol.org/pages/5660435).
+
+# %% [markdown]
+# ### Final Catalog
+#
+# Our final EOL catalog is thus going to be the `treeoflife_id`s in `links_inner`.
+#
+# Finall question is just how does this look for our `train_small`?
+
+# %%
+cat_2 = pd.read_csv(TOL_FILEPATH + "catalog.csv", low_memory=False)
+
+# reduce to just train_small and all non-EOL entries
+cat_2 = cat_2.loc[cat_2.split == "train_small"]
+eol_cat_2 = cat_2.loc[cat_2.eol_content_id.notna()]
+
+eol_cat_2 = eol_cat_2[eol_cols]
+eol_cat_2.info(show_counts=True)
+
+# %% [markdown]
+# So `train_small` has 593,764 images from EOL. 
+#
+# Let's recast IDs as ints to match up with `links_inner` and check we have info for all of them.
+
+# %%
+eol_cat_2 = eol_cat_2.astype({"eol_content_id": "int64", "eol_page_id": "int64"})
+eol_cat_2[eol_cols[:4]].info()
+
+# %%
+# make combined ID for catalog and add suffix to eol content and page IDs
+eol_cat_2['combined_id_catalog'] = eol_cat_2['eol_content_id'].astype(str) + '_' + eol_cat_2['eol_page_id'].astype(str)
+eol_cat_2.rename(columns={'eol_content_id': 'eol_content_id_catalog', 'eol_page_id': 'eol_page_id_catalog'}, inplace=True)
+
+# %%
+eol_ts_links = pd.merge(eol_cat_2,
+                        links_inner[list(links_inner.columns)[18:]],
+                        left_on = "combined_id_catalog",
+                        right_on = "combined_id_full_manifest",
+                        how = "inner")
+eol_ts_links.info(show_counts = True)
+
+# %%
+eol_ts_links.treeoflife_id.nunique()
+
+# %% [markdown]
+# So we are missing the metadata for 3,734 of these images.
+
+# %% [markdown]
+# ## Check on Rare Species Catalog
+
+# %%
+rs_catalog = pd.read_csv("../../rare_species/data/rarespecies-catalog.csv",
+                         low_memory=False,
+                         dtype = {"eol_content_id": "int64", "eol_page_id": "int64"})
+rs_catalog.info(show_counts = True)
+
+# %%
+rs_catalog["combined_id_rs"] = rs_catalog["eol_content_id"].astype(str) + "_" + rs_catalog["eol_page_id"].astype(str)
+rs_catalog.rename(columns={'eol_content_id': 'eol_content_id_rs', 'eol_page_id': 'eol_page_id_rs'}, inplace=True)
+
+# %%
+rs_links = pd.merge(rs_catalog,
+                    links_manifest_cargo,
+                    left_on = "combined_id_rs",
+                    right_on = "combined_id_archive", # looking at archive
+                    how = "inner")
+rs_links.info(show_counts = True)
+
+# %%
+rs_links.nunique()
+
+# %% [markdown]
+# Let's check the mismatched cargo/manifest entries for those last 174...
+
+# %%
+matched_rs_ids = list(rs_links.combined_id_rs.unique())
+len(matched_rs_ids)
+
+# %%
+matched_rs_ids[:4]
+
+# %%
+rs_catalog["combined_id_rs"].sample(4)
+
+# %%
+mismatched_rs = rs_catalog.loc[~rs_catalog["combined_id_rs"].isin(matched_rs_ids)]
+mismatched_rs.info(show_counts = True)
+
+# %%
+links_rs_mismatch = pd.merge(mismatched_rs,
+                             links_mismatch,
+                             left_on = "combined_id_rs",
+                             right_on = "combined_id_full_manifest",
+                             how = "inner")
+links_rs_mismatch.info(show_counts = True)
+
+# %%

eol_realign/notebooks/links_rs_duplicates.py

@@ -0,0 +1,536 @@
+# ---
+# jupyter:
+#   jupytext:
+#     formats: ipynb,py:percent
+#     text_representation:
+#       extension: .py
+#       format_name: percent
+#       format_version: '1.3'
+#       jupytext_version: 1.16.0
+#   kernelspec:
+#     display_name: tol
+#     language: python
+#     name: python3
+# ---
+
+# %%
+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/eol-cargo-archive_combined-manifest-checksums_links.csv", low_memory=False)
+
+# %%
+links_manifest_cargo.info(show_counts=True)
+
+# %% [markdown]
+# ## Check on Rare Species Catalog
+
+# %%
+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)
+
+# %%
+rs_catalog["combined_id_rs"] = rs_catalog["eol_content_id"].astype(str) + "_" + rs_catalog["eol_page_id"].astype(str)
+rs_catalog.rename(columns={'eol_content_id': 'eol_content_id_rs', 'eol_page_id': 'eol_page_id_rs'}, inplace=True)
+
+# %%
+rs_links = pd.merge(rs_catalog,
+                    links_manifest_cargo,
+                    left_on = "combined_id_rs",
+                    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...
+
+# %%
+matched_rs_ids = list(rs_links.combined_id_rs.unique())
+len(matched_rs_ids)
+
+# %%
+matched_rs_ids[:4]
+
+# %%
+rs_catalog["combined_id_rs"].sample(4)
+
+# %%
+mismatched_rs = rs_catalog.loc[~rs_catalog["combined_id_rs"].isin(matched_rs_ids)]
+mismatched_rs.info(show_counts = True)
+
+# %%
+mismatched_rs.nunique()
+
+# %%
+mismatched_rs.sciName.value_counts()
+
+# %%
+big_sciNames_missing = ["Aonyx capensis",
+                        "Zoogoneticus tequila",
+                        "Sousa plumbea",
+                        "Sylvilagus transitionalis",
+                        "Scaphirhynchus albus",
+                        "Raja asterias"]
+
+# %%
+pg_ids = []
+for sciName in big_sciNames_missing:
+    pg_ids.append(rs_links.loc[rs_links["sciName"] == sciName, "eol_page_id"].unique())
+pg_ids
+
+# %%
+num_images_by_pg = []
+for pg_id in pg_ids:
+    num_images = links_manifest_cargo.loc[links_manifest_cargo["eol_page_id"] == pg_id[0]].shape[0]
+    num_images_by_pg.append((pg_id[0], num_images))
+
+num_images_by_pg
+
+# %% [markdown]
+# The media for both of these last two is online: https://eol.org/pages/46560546/media, https://eol.org/pages/205909/media
+
+# %%
+big_mismatch = mismatched_rs.loc[mismatched_rs["sciName"].isin(big_sciNames_missing)]
+big_mismatch.loc[big_mismatch["eol_page_id_rs"] == 205909].sample(5)
+
+# %% [markdown]
+# sampling some, they're "not in any collections": https://eol.org/media/30098484
+
+# %%
+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
+# 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_?!
+
+# %%
+# 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/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.
+
+# %% [markdown]
+# ## Investigate Duplication
+#
+# Now I want some more info on those duplicated MD5's.
+
+# %%
+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")
+
+# %%
+rs_links.loc[rs_links["rs_id_dupes"], "md5_dupes"].value_counts()
+
+# %%
+rs_links.loc[~rs_links["rs_id_dupes"], "md5_dupes"].value_counts()
+
+# %% [markdown]
+# Looks like we have 163 duplicated images in Rare Species...
+
+# %%
+rs = rs_links.loc[~rs_links["rs_id_dupes"]]
+rs_dupes = rs.loc[rs["md5_dupes"]]
+rs_dupes.nunique()
+
+# %%
+rs_dupes.sciName.value_counts()[:10]
+
+# %% [markdown]
+# We have 30 images per species, so we have about a fourth duplicated for some. Note that the counts here are the number of duplicate images, so the total number of times these particular images appear is N + 1.
+
+# %% [markdown]
+# Let's see how many images we have for each of these duplicated images.
+
+# %%
+rs_sci_dupe_pgs = list(rs_dupes.eol_page_id.unique())
+rs_sci_dupe_pgs[:8]
+
+# %%
+num_images_by_pg = {}
+#list with unique by md5
+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_archive"].nunique()
+    num_unique_imgs_by_pg[pg_id] = num_unique_images
+
+
+# %%
+len(num_images_by_pg)
+
+# %%
+for pg_id in num_unique_imgs_by_pg.keys():
+    if num_unique_imgs_by_pg[pg_id] < 30:
+        print(f"page ID {pg_id} has less than 30 unique images; it has {num_unique_imgs_by_pg[pg_id]} unique images")
+
+# %% [markdown]
+# https://eol.org/pages/485420/media has only 21 true images, since 3 are post-its.
+
+# %%
+rs_catalog.head()
+
+# %%
+rs_catalog["file_name"] = rs_catalog["combined_id_rs"].astype(str) + "_eol-full-size-copy.jpg"
+rs_catalog["file_name"].sample(7)
+
+# %%
+# save filelist for easier fetching
+#rs_catalog["file_name"].to_csv("../data/rs_file_list.txt", index = False)
+# Not needed now
+
+# %% [markdown]
+# Save `rs_links` to file for adjusting Rare Species images for uniqueness.
+
+# %%
+rs_links.to_csv("../data/rs_links.csv", index = False)
+
+# %% [markdown]
+# ### Get MD5s of Images on Misalgined Pages
+#
+# Relevant background from Matt (with some notes for context here):
+# - I have a CSV called `rarespecies_catalog_missing_manifest___archive.csv` with 174 entries (I double-checked that the entries in the "sciName" column all look good ... there are duplicates there, but all are valid Genus species binomials)
+#   - This file is from `archive_mismatched_rarespecies.csv` created above.
+# - Filtered that for all the unique page IDs.
+# - Downloaded a media manifest current as of today (March 11)
+# - There are 1,929 entries in today's media manifest with page IDs from the filtered list mentioned above
+# - Downloaded them to `eol_data_cleanup/data/rare_species_pageids/` (on OSC)
+# - Logged downloads with errors (there were 2), so we have 1,927 JPGs
+# - Took MD5s as well, which are in `eol_data_cleanup/data/rare_species_pageids/md5s.csv` (on OSC. Here this file is `rarespecies_missing_pages_md5s.csv`).
+#   - Has "filename" and "md5" columns, and filenames are `<contentID>_<pageID>_eol-full-size-copy.jpg`.
+
+# %%
+rs_mp = pd.read_csv("../data/rarespecies_missing_pages_md5s.csv", low_memory=False)
+rs_mp.info(show_counts = True)
+
+# %%
+rs_mp.nunique()
+
+# %% [markdown]
+# So, how many of these are in the archive?
+
+# %%
+rs_mp_archive = pd.merge(rs_mp,
+                         links_manifest_cargo[["filename_archive", "md5_archive", "filename_manifest"]],
+                         left_on = "md5",
+                         right_on = "md5_archive",
+                         how = "inner")
+rs_mp_archive.info(show_counts = True)
+
+# %% [markdown]
+# Interesting, most of these are actually in the archive.
+
+# %%
+rs_mp_archive.nunique()
+
+# %% [markdown]
+# Though it's mostly duplicates, so that makes sense with our earlier numbers.
+
+# %%
+rs_mp_archive.head(2)
+
+# %% [markdown]
+# ### Ensure uniqueness across available images
+#
+# Let's reduce the archive DataFrame down to just EOL page IDs from the Rare Species Catalog. We'll match on the archive page ID's (pulled from `filename_archive`). Then we need to merge `rs_mp` with `eol_media_manifest_2024-03-11.csv` to get the source info and concatenate the two DataFrames.
+
+# %%
+mp_manifest = pd.read_csv("../data/eol_media_manifest_2024-03-11.csv",
+                          low_memory=False,
+                          dtype = {"EOL content ID": "int64", "EOL page ID": "int64"})
+mp_manifest.head(2)
+
+# %% [markdown]
+# Rename columns to match the archive file.
+
+# %%
+mp_manifest.rename(columns={"EOL content ID": "eol_content_id",
+                            "EOL page ID": "eol_page_id",
+                            "Medium Source URL": "medium_source_url",
+                            "EOL Full-Size Copy URL": "eol_full_size_copy_url",
+                            "License Name": "license_name",
+                            "Copyright Owner": "copyright_owner"},
+                   inplace = True)
+mp_manifest["filename"] = mp_manifest["eol_content_id"].astype(str) + "_" + mp_manifest["eol_page_id"].astype(str) + "_eol-full-size-copy.jpg"
+
+# %%
+rs_mp_manifest = pd.merge(rs_mp,
+                          mp_manifest,
+                          on = "filename",
+                          how = "inner")
+rs_mp_manifest.nunique()
+
+# %% [markdown]
+# Good, everything merged as expected. Let's cut down the `links_manifest_cargo` DataFrame to just Rare Species pages, then we can concatenate these.
+
+# %%
+rs_pages = list(rs_catalog.eol_page_id_rs.unique())
+len(rs_pages) # should be 400
+
+
+# %%
+def get_page_id(combined_id):
+    # want to use the archive combined ID to ensure match
+    # combined ID is eolContentID_eolPageID
+    return int(combined_id.split("_")[1])
+
+links_manifest_cargo["eol_page_id_archive"] = links_manifest_cargo["combined_id_archive"].apply(get_page_id)
+
+# %%
+rs_links_cargo = links_manifest_cargo.loc[links_manifest_cargo["eol_page_id_archive"].isin(rs_pages)]
+rs_links_cargo.nunique()
+
+
+# %%
+def get_content_id(combined_id):
+    # want to use the archive combined ID to ensure match
+    # combined ID is eolContentID_eolPageID
+    return int(combined_id.split("_")[0])
+
+rs_links_cargo["eol_content_id_archive"] = rs_links_cargo["combined_id_archive"].apply(get_content_id)
+rs_links_cargo.nunique()
+
+# %%
+cols_to_match = list(rs_links_cargo.columns)[:3] + ["eol_content_id_archive", "eol_page_id_archive"] + list(rs_mp_manifest.columns)[4:]
+cols_to_match
+
+# %%
+rs_links_cargo = rs_links_cargo[cols_to_match]
+rs_links_cargo.rename(columns={"filename_archive": "filename",
+                               "md5_archive": "md5",
+                               "combined_id_archive": "combined_id",
+                               "eol_content_id_archive": "eol_content_id",
+                               "eol_page_id_archive": "eol_page_id"},
+                               inplace = True)
+rs_links_cargo.columns
+
+# %% [markdown]
+# Now we just need to add `combined_id` to `rs_mp_manifest` and we'll be able to concatenate them.
+
+# %%
+rs_mp_manifest["combined_id"] = rs_mp_manifest["eol_content_id"].astype(str) + "_" + rs_mp_manifest["eol_page_id"].astype(str)
+rs_mp_manifest.head()
+
+# %%
+rs_full_manifest = pd.concat([rs_links_cargo, rs_mp_manifest], ignore_index=True)
+rs_full_manifest.nunique()
+
+# %%
+rs_full_manifest.shape
+
+# %%
+# does that match?
+rs_links_cargo.shape[0] + rs_mp_manifest.shape[0]
+
+# %% [markdown]
+# Let's reduce this down to just unique MD5s. I think we'll have to regenerate rarespecies IDs, since we can't necessarily match all the ones we had before.
+
+# %%
+rs_full_manifest["duplicate_img"] = rs_full_manifest.duplicated(subset = "md5", keep = "first")
+rs_full_manifest_unique = rs_full_manifest.loc[~rs_full_manifest["duplicate_img"]]
+rs_full_manifest_unique.info(show_counts = True)
+
+# %% [markdown]
+# Now I need to reduce to just 30 images per page. Let's save this as a CSV first actually and then generate that in a new notebook. I can realign the labels based on the page IDs from the `rarespecies_catalog`, but I won't be able to properly rematch the `rarespecies_id`, so that will need to be regenerated...
+#
+# ### Run Owner match script on this before saving
+#
+# Let's match any missing owners where possible to make sure this is a full-info DataFrame before saving it to a CSV.
+
+# %%
+from tqdm import tqdm
+
+
+# %%
+def get_owners_titles(manifest, owners):
+    """
+    Function to attach owner names and image titles to manifest entries in combined manifest.
+    Fills empty "copyright_owner" and "title" values with "not provided".
+    Parameters:
+    -----------
+    manifest - rs_full_manifest_unique
+    owners - DataFrame of July 26, 2023 media manifest entries that had missing owners, updated with their information.
+    Returns:
+    --------
+    manifest - Rare Species media manifest DataFrame with missing owners resolved to extent possible.
+    """
+    missing_owners = [
+        comb_id
+        for comb_id in list(
+            manifest.loc[manifest["copyright_owner"].isna(), "combined_id"]
+        )
+    ]
+
+    for comb_id in tqdm(missing_owners):
+        temp = owners.loc[owners.combined_id_owner == comb_id]
+        copyright_owner = str(temp["Copyright Owner"].values)
+        title = str(temp.title.values)
+        manifest.loc[manifest["combined_id"] == comb_id, "copyright_owner"] = copyright_owner
+        manifest.loc[manifest["combined_id"] == comb_id, "title"] = title
+
+    # Print counts of licenses for which owner info was not resolved
+    print(
+        "Licenses still missing Copyright Owners: \n",
+        manifest.loc[
+            manifest["copyright_owner"].isna(), "license_name"
+        ].value_counts(),
+    )
+
+    # Fill null "copyright_owner" and "Title" values with "not provided"
+    manifest["copyright_owner"].fillna("not provided", inplace=True)
+    manifest["title"].fillna("not provided", inplace=True)
+
+    return manifest
+
+
+def update_owners(manifest, owners):
+    """
+    Function to fetch and attach the missing owner and title information to EOL catalog entries and save catalog-media file.
+    Parameters:
+    -----------
+    manifest - rs_full_manifest_unique.
+    owners - DataFrame of July 26, 2023 media manifest entries that had missing owners, updated with their information.
+    """
+    # Need combined IDs for the owner match file
+    # EOL content & page IDs read in as int64
+    owners["combined_id_owner"] = owners["EOL content ID"].astype(str) + "_" + owners["EOL page ID"].astype(str)
+
+    updated_manifest = get_owners_titles(manifest, owners)
+
+    return updated_manifest
+
+
+# %%
+owner_df = pd.read_csv("../data/media_manifest_missing_licenses_jul26_owners.csv",
+                        low_memory = False,
+                        dtype={"EOL content ID": "int64", "EOL page ID": "int64"},)
+
+
+# %%
+complete_rs_manifest = update_owners(rs_full_manifest_unique, owner_df)
+complete_rs_manifest.info(show_counts = True)
+
+# %%
+complete_rs_manifest.loc[complete_rs_manifest["copyright_owner"] == "not provided"].shape
+
+# %%
+complete_rs_manifest.sample(7)
+
+# %%
+complete_rs_manifest.loc[complete_rs_manifest["title"] == "not provided"].shape
+
+# %% [markdown]
+# Most don't have title, but they all have the copyright owner filled in. That's good!
+
+# %%
+cols = [col for col in list(complete_rs_manifest.columns) if col != "duplicate_img"]
+complete_rs_manifest = complete_rs_manifest[cols]
+complete_rs_manifest.head(2)
+
+# %% [markdown]
+# ### Add License URL Column for Completeness
+
+# %%
+CC_URL = "https://creativecommons.org/"
+
+
+def get_license_url(license_version):
+    """
+    Function to generate the appropriate Creative Commons URL for a given license.
+    All licenses in the media manifest are "cc-XX", a variation on "publicdomain", or "No known copyright restrictions".
+
+    Parameters:
+    -----------
+    license_version - String. License (eg., "cc-by-nc 3.0").
+
+    Returns:
+    --------
+    license_url - String. Creative Commons URL associated with the license_version.
+
+    """
+    # First check for version number and isolate it
+    if "." in license_version:
+        version = license_version.split(sep="-")[-1]
+        license_name = license_version.split(sep="-" + version)[0]
+    else:
+        # No version specified, so default to latest version (4.0)
+        license_name = license_version
+        version = "4.0"
+    # Check which type of license
+    if license_name[:5] == "cc-by":
+        by_x = license_name.split(sep="cc-")[1]
+        license_url = CC_URL + "licenses/" + by_x + "/" + version
+    elif (license_name[:4] == "cc-0") or ("public" in license_name):
+        license_url = CC_URL + "publicdomain/zero/1.0"
+    else:
+        # "No known copyright restrictions"
+        license_url = None
+    return license_url
+
+
+
+# %%
+license_col = "license_name"
+complete_rs_manifest["license_link"] = complete_rs_manifest[license_col].apply(get_license_url)
+
+# %%
+complete_rs_manifest.info(show_counts=True)
+
+# %%
+print(
+        "Licenses with no URL: \n",
+        complete_rs_manifest.loc[complete_rs_manifest["license_link"].isna(), license_col].value_counts(),
+    )
+
+# %% [markdown]
+# As expected, we're good to save this full Rare Species manifest now.
+
+# %%
+complete_rs_manifest.to_csv("../data/rarespecies_full_manifest.csv", index = False)
+
+# %%

eol_realign/notebooks/re-gen_rs_catalog.ipynb

@@ -0,0 +1,1527 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "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 Complete Rare Species Manifest"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 22146 entries, 0 to 22145\n",
+      "Data columns (total 11 columns):\n",
+      " #   Column                  Non-Null Count  Dtype \n",
+      "---  ------                  --------------  ----- \n",
+      " 0   filename                22146 non-null  object\n",
+      " 1   md5                     22146 non-null  object\n",
+      " 2   combined_id             22146 non-null  object\n",
+      " 3   eol_content_id          22146 non-null  int64 \n",
+      " 4   eol_page_id             22146 non-null  int64 \n",
+      " 5   medium_source_url       22146 non-null  object\n",
+      " 6   eol_full_size_copy_url  22146 non-null  object\n",
+      " 7   license_name            22146 non-null  object\n",
+      " 8   copyright_owner         22146 non-null  object\n",
+      " 9   title                   22146 non-null  object\n",
+      " 10  license_link            22103 non-null  object\n",
+      "dtypes: int64(2), object(9)\n",
+      "memory usage: 1.9+ MB\n"
+     ]
+    }
+   ],
+   "source": [
+    "rs_manifest = pd.read_csv(\"../data/rarespecies_full_manifest.csv\",\n",
+    "                          low_memory=False,\n",
+    "                          dtype = {\"eol_content_id\": \"int64\", \"eol_page_id\": \"int64\"})\n",
+    "rs_manifest.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Read in Rare Species Catalog"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Note that the original [`rarespecies-catalog`](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/5db838a9db980f4cf96027b326b06e0f42df0c65/rare_species/data/rarespecies-catalog.csv) generation was done in [`rare_species_make_catalog.ipynb`](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/5db838a9db980f4cf96027b326b06e0f42df0c65/rare_species/notebooks/rare_species_make_catalog.ipynb). It used [`predicted-catalog.csv`](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/5db838a9db980f4cf96027b326b06e0f42df0c65/data/predicted-catalog.csv) to get the taxonomic information and align the [rare species cargo](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/5db838a9db980f4cf96027b326b06e0f42df0c65/rare_species/data/rarespecies.csv) appropriately. There were also checks that the unseen subset was indeed excluded from the [catalog](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/5db838a9db980f4cf96027b326b06e0f42df0c65/data/catalog.csv).\n",
+    "\n",
+    "We will use the [`rarespecies-catalog.csv`](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/5db838a9db980f4cf96027b326b06e0f42df0c65/rare_species/data/rarespecies-catalog.csv) generated in that notebook to align taxonomic information with the full rare species manifest (renamed locally to `rarespecies-catalog-orig.csv`)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 12000 entries, 0 to 11999\n",
+      "Data columns (total 11 columns):\n",
+      " #   Column          Non-Null Count  Dtype \n",
+      "---  ------          --------------  ----- \n",
+      " 0   rarespecies_id  12000 non-null  object\n",
+      " 1   eol_content_id  12000 non-null  int64 \n",
+      " 2   eol_page_id     12000 non-null  int64 \n",
+      " 3   kingdom         12000 non-null  object\n",
+      " 4   phylum          12000 non-null  object\n",
+      " 5   class           12000 non-null  object\n",
+      " 6   order           12000 non-null  object\n",
+      " 7   family          12000 non-null  object\n",
+      " 8   genus           12000 non-null  object\n",
+      " 9   species         12000 non-null  object\n",
+      " 10  sciName         12000 non-null  object\n",
+      "dtypes: int64(2), object(9)\n",
+      "memory usage: 1.0+ MB\n"
+     ]
+    }
+   ],
+   "source": [
+    "rs_catalog = pd.read_csv(RS_FILEPATH + \"rarespecies-catalog-orig.csv\",\n",
+    "                         low_memory=False,\n",
+    "                         dtype = {\"eol_content_id\": \"int64\", \"eol_page_id\": \"int64\"})\n",
+    "rs_catalog.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Check Number of Images per Page"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "22146"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "rs_manifest[\"md5\"].nunique()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We should have at least 30 images per species, except for 5. Let's check the number of images for each species (all now included are unique, as demonstrated above)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {
+    "lines_to_next_cell": 2
+   },
+   "outputs": [],
+   "source": [
+    "num_images_by_pg = {}\n",
+    "\n",
+    "for pg_id in list(rs_manifest.eol_page_id.unique()):\n",
+    "    num_images = rs_manifest.loc[rs_manifest[\"eol_page_id\"] == pg_id].shape[0]\n",
+    "    num_images_by_pg[pg_id] = num_images\n",
+    "    rs_manifest.loc[rs_manifest[\"eol_page_id\"] == pg_id, \"num_images\"] = num_images\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "93"
+      ]
+     },
+     "execution_count": 7,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "rs_manifest.num_images.nunique()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "There's a lot of variety in the number of images per page. We'll check again on the (expected 5) pages that have less than 30 images."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "page ID 485420 has less than 30 unique images; it has 24 unique images\n",
+      "page ID 914531 has less than 30 unique images; it has 29 unique images\n",
+      "page ID 791049 has less than 30 unique images; it has 27 unique images\n",
+      "page ID 205714 has less than 30 unique images; it has 29 unique images\n",
+      "page ID 1286909 has less than 30 unique images; it has 27 unique images\n"
+     ]
+    }
+   ],
+   "source": [
+    "for pg_id in num_images_by_pg.keys():\n",
+    "    if num_images_by_pg[pg_id] < 30:\n",
+    "        print(f\"page ID {pg_id} has less than 30 unique images; it has {num_images_by_pg[pg_id]} unique images\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "https://eol.org/pages/485420/media has only 21 true images, since 3 are post-its. These will need to be manually noted and removed."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Reduce to 30 Images per Page"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Now we need to reduce to just 30 images per page. We can realign the labels based on the page IDs from the `rarespecies_catalog`, but I won't be able to properly rematch the `rarespecies_id`, so that will need to be regenerated..."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "22146"
+      ]
+     },
+     "execution_count": 9,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# Is filename unique? --yes, 22146 is number of images in the full rarespecies manifest\n",
+    "rs_manifest.filename.nunique()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "keep\n",
+       "yes    11986\n",
+       "Name: count, dtype: int64"
+      ]
+     },
+     "execution_count": 10,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "img_list_by_page = {}\n",
+    "\n",
+    "for page_id in list(rs_manifest.eol_page_id.unique()):\n",
+    "    temp = rs_manifest.loc[rs_manifest.eol_page_id == page_id]\n",
+    "    if temp.num_images.values[0] > 30:\n",
+    "        imgs_to_keep = list(temp.filename.sample(30, random_state = 614)) #seed for reproducibility\n",
+    "    else:\n",
+    "        imgs_to_keep = list(temp.filename)\n",
+    "\n",
+    "    rs_manifest.loc[rs_manifest[\"filename\"].isin(imgs_to_keep), \"keep\"] = \"yes\"\n",
+    "    img_list_by_page[page_id] = imgs_to_keep\n",
+    "\n",
+    "rs_manifest[\"keep\"].value_counts()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "That's 14 less than 12000 images, which matches with the number of images we'd be reduced by due to the 5 pages that have less than 30 images."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "(11986, 13)\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "filename                  11986\n",
+       "md5                       11986\n",
+       "combined_id               11986\n",
+       "eol_content_id            11986\n",
+       "eol_page_id                 400\n",
+       "medium_source_url         11986\n",
+       "eol_full_size_copy_url    11986\n",
+       "license_name                 15\n",
+       "copyright_owner            4164\n",
+       "title                      1290\n",
+       "license_link                 10\n",
+       "num_images                   93\n",
+       "keep                          1\n",
+       "dtype: int64"
+      ]
+     },
+     "execution_count": 11,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "reduced_rs_manifest = rs_manifest.loc[rs_manifest[\"keep\"] == \"yes\"]\n",
+    "\n",
+    "print(reduced_rs_manifest.shape)\n",
+    "reduced_rs_manifest.nunique()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "num_images\n",
+       "30.0    11850\n",
+       "29.0       58\n",
+       "27.0       54\n",
+       "24.0       24\n",
+       "Name: count, dtype: int64"
+      ]
+     },
+     "execution_count": 12,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "for pg_id in list(reduced_rs_manifest.eol_page_id.unique()):\n",
+    "    num_images = reduced_rs_manifest.loc[reduced_rs_manifest[\"eol_page_id\"] == pg_id].shape[0]\n",
+    "    reduced_rs_manifest.loc[reduced_rs_manifest[\"eol_page_id\"] == pg_id, \"num_images\"] = num_images\n",
+    "\n",
+    "reduced_rs_manifest[\"num_images\"].value_counts()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "One page has only 24, two have 27 & 29, the remaining 395 pages have 30.\n",
+    "\n",
+    "Let's track down those 3 post-it images on page 485420."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "https://eol.org/media/29856158\n",
+      "https://eol.org/media/28605134\n",
+      "https://eol.org/media/14677205\n",
+      "https://eol.org/media/28605135\n",
+      "https://eol.org/media/29856162\n",
+      "https://eol.org/media/29856156\n",
+      "https://eol.org/media/29856167\n",
+      "https://eol.org/media/29856165\n",
+      "https://eol.org/media/29856163\n",
+      "https://eol.org/media/29856157\n",
+      "https://eol.org/media/14677203\n",
+      "https://eol.org/media/29856159\n",
+      "https://eol.org/media/28605131\n",
+      "https://eol.org/media/29856155\n",
+      "https://eol.org/media/29856151\n",
+      "https://eol.org/media/29856161\n",
+      "https://eol.org/media/14677207\n",
+      "https://eol.org/media/29856150\n",
+      "https://eol.org/media/29856164\n",
+      "https://eol.org/media/14677204\n",
+      "https://eol.org/media/28605132\n",
+      "https://eol.org/media/28605133\n",
+      "https://eol.org/media/28605130\n",
+      "https://eol.org/media/29856166\n"
+     ]
+    }
+   ],
+   "source": [
+    "for content_id in list(reduced_rs_manifest.loc[reduced_rs_manifest[\"eol_page_id\"] == 485420, \"eol_content_id\"]):\n",
+    "    print(f\"https://eol.org/media/{content_id}\")\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Post-it image EOL Content IDs (unique in this DataFrame):\n",
+    "- [28605134](https://eol.org/media/28605134)\n",
+    "- [29856159](https://eol.org/media/29856159)\n",
+    "- [29856164](https://eol.org/media/29856164)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "(11983, 13)\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "filename                  11983\n",
+       "md5                       11983\n",
+       "combined_id               11983\n",
+       "eol_content_id            11983\n",
+       "eol_page_id                 400\n",
+       "medium_source_url         11983\n",
+       "eol_full_size_copy_url    11983\n",
+       "license_name                 15\n",
+       "copyright_owner            4164\n",
+       "title                      1290\n",
+       "license_link                 10\n",
+       "num_images                    4\n",
+       "keep                          1\n",
+       "dtype: int64"
+      ]
+     },
+     "execution_count": 14,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "post_its = [28605134, 29856159, 29856164]\n",
+    "\n",
+    "rarespecies_manifest = reduced_rs_manifest.loc[~reduced_rs_manifest[\"eol_content_id\"].isin(post_its)]\n",
+    "print(rarespecies_manifest.shape)\n",
+    "rarespecies_manifest.nunique()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Remove extra columns"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "Index(['filename', 'md5', 'combined_id', 'eol_content_id', 'eol_page_id',\n",
+       "       'medium_source_url', 'eol_full_size_copy_url', 'license_name',\n",
+       "       'copyright_owner', 'title', 'license_link'],\n",
+       "      dtype='object')"
+      ]
+     },
+     "execution_count": 15,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "rarespecies_manifest = rarespecies_manifest[list(rarespecies_manifest.columns)[:-2]]\n",
+    "rarespecies_manifest.columns"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Add `uuid` (new `rarespecies_id`)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 16,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import uuid"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 17,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "11983"
+      ]
+     },
+     "execution_count": 17,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "rarespecies_manifest[\"rarespecies_id\"] = [uuid.uuid4() for i in range(rarespecies_manifest.shape[0])]\n",
+    "rarespecies_manifest.rarespecies_id.nunique()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Save Manifest with `uuid`s"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 27,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "rarespecies_manifest.to_csv(RS_FILEPATH + \"rarespecies_manifest.csv\", index = False)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Make and Save License File"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 28,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "licesne_cols = [\"rarespecies_id\",\n",
+    "                \"eol_content_id\",\n",
+    "                \"eol_page_id\",\n",
+    "                \"md5\",\n",
+    "                \"medium_source_url\",\n",
+    "                \"eol_full_size_copy_url\",\n",
+    "                \"license_name\",\n",
+    "                \"copyright_owner\",\n",
+    "                \"license_link\",\n",
+    "                \"title\"]\n",
+    "\n",
+    "licenses = rarespecies_manifest[licesne_cols]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 29,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "licenses.to_csv(RS_FILEPATH + \"licenses.csv\", index = False)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Make Rare Species Catalog\n",
+    "\n",
+    "Align taxonomic information to the IDs in the manifest.\n",
+    "\n",
+    "Pull manifest back in; something went weird with initial catalog generation."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 11983 entries, 0 to 11982\n",
+      "Data columns (total 12 columns):\n",
+      " #   Column                  Non-Null Count  Dtype \n",
+      "---  ------                  --------------  ----- \n",
+      " 0   filename                11983 non-null  object\n",
+      " 1   md5                     11983 non-null  object\n",
+      " 2   combined_id             11983 non-null  object\n",
+      " 3   eol_content_id          11983 non-null  int64 \n",
+      " 4   eol_page_id             11983 non-null  int64 \n",
+      " 5   medium_source_url       11983 non-null  object\n",
+      " 6   eol_full_size_copy_url  11983 non-null  object\n",
+      " 7   license_name            11983 non-null  object\n",
+      " 8   copyright_owner         11983 non-null  object\n",
+      " 9   title                   11983 non-null  object\n",
+      " 10  license_link            11957 non-null  object\n",
+      " 11  rarespecies_id          11983 non-null  object\n",
+      "dtypes: int64(2), object(10)\n",
+      "memory usage: 1.1+ MB\n"
+     ]
+    }
+   ],
+   "source": [
+    "rarespecies_manifest = pd.read_csv(RS_FILEPATH + \"rarespecies_manifest.csv\",\n",
+    "                                   low_memory=False,\n",
+    "                                   dtype = {\"eol_content_id\": \"int64\", \"eol_page_id\": \"int64\"})\n",
+    "rarespecies_manifest.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "id_cols = [\"rarespecies_id\", \"eol_content_id\", \"eol_page_id\"]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "['eol_page_id',\n",
+       " 'kingdom',\n",
+       " 'phylum',\n",
+       " 'class',\n",
+       " 'order',\n",
+       " 'family',\n",
+       " 'genus',\n",
+       " 'species',\n",
+       " 'sciName']"
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "cat_cols = list(rs_catalog.columns)[2:]\n",
+    "cat_cols"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "(359490, 11)\n"
+     ]
+    },
+    {
+     "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",
+       "dtype: int64"
+      ]
+     },
+     "execution_count": 8,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "updated_catalog = pd.merge(rarespecies_manifest[id_cols],\n",
+    "                           rs_catalog[cat_cols],\n",
+    "                           on = \"eol_page_id\",\n",
+    "                           how = \"left\")\n",
+    "\n",
+    "print(updated_catalog.shape)\n",
+    "updated_catalog.nunique()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Uniqueness counts are as expected, but it duplicated entries for everything in the manifest (30 copies of everything since there are multiple matches per page). We need to use just the unique values."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "duplicate_species\n",
+       "True     11600\n",
+       "False      400\n",
+       "Name: count, dtype: int64"
+      ]
+     },
+     "execution_count": 9,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "rs_catalog[\"duplicate_species\"] = rs_catalog.duplicated(subset = cat_cols, keep = \"first\")\n",
+    "rs_catalog[\"duplicate_species\"].value_counts()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "rarespecies_id       400\n",
+       "eol_content_id       400\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",
+       "duplicate_species      1\n",
+       "dtype: int64"
+      ]
+     },
+     "execution_count": 10,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "unique_rs_catalog = rs_catalog.loc[~rs_catalog[\"duplicate_species\"]]\n",
+    "unique_rs_catalog.nunique()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Now the merge shouldn't produce duplicates."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "(11983, 11)\n"
+     ]
+    },
+    {
+     "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",
+       "dtype: int64"
+      ]
+     },
+     "execution_count": 11,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "updated_catalog = pd.merge(rarespecies_manifest[id_cols],\n",
+    "                           unique_rs_catalog[cat_cols],\n",
+    "                           on = \"eol_page_id\",\n",
+    "                           how = \"left\")\n",
+    "\n",
+    "print(updated_catalog.shape)\n",
+    "updated_catalog.nunique()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "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>rarespecies_id</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>sciName</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>4462</th>\n",
+       "      <td>0022b617-0f5a-48cf-93b4-b987bc0b28d5</td>\n",
+       "      <td>30072827</td>\n",
+       "      <td>323915</td>\n",
+       "      <td>Animalia</td>\n",
+       "      <td>Chordata</td>\n",
+       "      <td>Mammalia</td>\n",
+       "      <td>Primates</td>\n",
+       "      <td>Atelidae</td>\n",
+       "      <td>Alouatta</td>\n",
+       "      <td>caraya</td>\n",
+       "      <td>Alouatta caraya</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3229</th>\n",
+       "      <td>b14f5d3c-17d0-4d05-be0f-635c32813ecf</td>\n",
+       "      <td>22894725</td>\n",
+       "      <td>1047771</td>\n",
+       "      <td>Animalia</td>\n",
+       "      <td>Chordata</td>\n",
+       "      <td>Aves</td>\n",
+       "      <td>Passeriformes</td>\n",
+       "      <td>Mimidae</td>\n",
+       "      <td>Mimus</td>\n",
+       "      <td>macdonaldi</td>\n",
+       "      <td>Mimus macdonaldi</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>5172</th>\n",
+       "      <td>a579040e-98dc-4249-b78a-94efe761770e</td>\n",
+       "      <td>22191928</td>\n",
+       "      <td>1038777</td>\n",
+       "      <td>Animalia</td>\n",
+       "      <td>Chordata</td>\n",
+       "      <td>Mammalia</td>\n",
+       "      <td>Artiodactyla</td>\n",
+       "      <td>Bovidae</td>\n",
+       "      <td>Procapra</td>\n",
+       "      <td>picticaudata</td>\n",
+       "      <td>Procapra picticaudata</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>9542</th>\n",
+       "      <td>14b76c63-f4aa-4108-bcfe-04ad7004e615</td>\n",
+       "      <td>29910658</td>\n",
+       "      <td>47363970</td>\n",
+       "      <td>Animalia</td>\n",
+       "      <td>Chordata</td>\n",
+       "      <td>Aves</td>\n",
+       "      <td>Strigiformes</td>\n",
+       "      <td>Strigidae</td>\n",
+       "      <td>Athene</td>\n",
+       "      <td>blewitti</td>\n",
+       "      <td>Athene blewitti</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>7663</th>\n",
+       "      <td>75e0f3c5-de1e-4e6a-96dc-1d3542dc5259</td>\n",
+       "      <td>15263810</td>\n",
+       "      <td>327865</td>\n",
+       "      <td>Animalia</td>\n",
+       "      <td>Chordata</td>\n",
+       "      <td>Mammalia</td>\n",
+       "      <td>Chiroptera</td>\n",
+       "      <td>Phyllostomidae</td>\n",
+       "      <td>Choeronycteris</td>\n",
+       "      <td>mexicana</td>\n",
+       "      <td>Choeronycteris mexicana</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1418</th>\n",
+       "      <td>9470b0d1-c077-41a1-ac09-6bfae0735e4f</td>\n",
+       "      <td>2647</td>\n",
+       "      <td>45511277</td>\n",
+       "      <td>Animalia</td>\n",
+       "      <td>Chordata</td>\n",
+       "      <td>Aves</td>\n",
+       "      <td>Procellariiformes</td>\n",
+       "      <td>Diomedeidae</td>\n",
+       "      <td>Thalassarche</td>\n",
+       "      <td>chlororhynchos</td>\n",
+       "      <td>Thalassarche chlororhynchos</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>8008</th>\n",
+       "      <td>07ce200b-c168-4706-9328-5aa02eee1d73</td>\n",
+       "      <td>22969028</td>\n",
+       "      <td>1012078</td>\n",
+       "      <td>Animalia</td>\n",
+       "      <td>Chordata</td>\n",
+       "      <td>Actinopterygii</td>\n",
+       "      <td>Cyprinodontiformes</td>\n",
+       "      <td>Cyprinodontidae</td>\n",
+       "      <td>Cyprinodon</td>\n",
+       "      <td>macularius</td>\n",
+       "      <td>Cyprinodon macularius</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>6762</th>\n",
+       "      <td>a1b441ac-8f72-41d5-9f89-db95ad09ea43</td>\n",
+       "      <td>29679324</td>\n",
+       "      <td>23668991</td>\n",
+       "      <td>Animalia</td>\n",
+       "      <td>Chordata</td>\n",
+       "      <td>Reptilia</td>\n",
+       "      <td>Squamata</td>\n",
+       "      <td>Dactyloidae</td>\n",
+       "      <td>Anolis</td>\n",
+       "      <td>monteverde</td>\n",
+       "      <td>Anolis monteverde</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2846</th>\n",
+       "      <td>cd86b9c7-31dc-4906-9536-05d64e2759ca</td>\n",
+       "      <td>28928692</td>\n",
+       "      <td>45518912</td>\n",
+       "      <td>Animalia</td>\n",
+       "      <td>Chordata</td>\n",
+       "      <td>Aves</td>\n",
+       "      <td>Charadriiformes</td>\n",
+       "      <td>Burhinidae</td>\n",
+       "      <td>Esacus</td>\n",
+       "      <td>recurvirostris</td>\n",
+       "      <td>Esacus recurvirostris</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>8111</th>\n",
+       "      <td>91c6b4dd-c199-45fb-97cd-6bc9e4c7fbe6</td>\n",
+       "      <td>29033057</td>\n",
+       "      <td>963751</td>\n",
+       "      <td>Animalia</td>\n",
+       "      <td>Chordata</td>\n",
+       "      <td>Reptilia</td>\n",
+       "      <td>Squamata</td>\n",
+       "      <td>Iguanidae</td>\n",
+       "      <td>Ctenosaura</td>\n",
+       "      <td>bakeri</td>\n",
+       "      <td>Ctenosaura bakeri</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "                            rarespecies_id  eol_content_id  eol_page_id  \\\n",
+       "4462  0022b617-0f5a-48cf-93b4-b987bc0b28d5        30072827       323915   \n",
+       "3229  b14f5d3c-17d0-4d05-be0f-635c32813ecf        22894725      1047771   \n",
+       "5172  a579040e-98dc-4249-b78a-94efe761770e        22191928      1038777   \n",
+       "9542  14b76c63-f4aa-4108-bcfe-04ad7004e615        29910658     47363970   \n",
+       "7663  75e0f3c5-de1e-4e6a-96dc-1d3542dc5259        15263810       327865   \n",
+       "1418  9470b0d1-c077-41a1-ac09-6bfae0735e4f            2647     45511277   \n",
+       "8008  07ce200b-c168-4706-9328-5aa02eee1d73        22969028      1012078   \n",
+       "6762  a1b441ac-8f72-41d5-9f89-db95ad09ea43        29679324     23668991   \n",
+       "2846  cd86b9c7-31dc-4906-9536-05d64e2759ca        28928692     45518912   \n",
+       "8111  91c6b4dd-c199-45fb-97cd-6bc9e4c7fbe6        29033057       963751   \n",
+       "\n",
+       "       kingdom    phylum           class               order           family  \\\n",
+       "4462  Animalia  Chordata        Mammalia            Primates         Atelidae   \n",
+       "3229  Animalia  Chordata            Aves       Passeriformes          Mimidae   \n",
+       "5172  Animalia  Chordata        Mammalia        Artiodactyla          Bovidae   \n",
+       "9542  Animalia  Chordata            Aves        Strigiformes        Strigidae   \n",
+       "7663  Animalia  Chordata        Mammalia          Chiroptera   Phyllostomidae   \n",
+       "1418  Animalia  Chordata            Aves   Procellariiformes      Diomedeidae   \n",
+       "8008  Animalia  Chordata  Actinopterygii  Cyprinodontiformes  Cyprinodontidae   \n",
+       "6762  Animalia  Chordata        Reptilia            Squamata      Dactyloidae   \n",
+       "2846  Animalia  Chordata            Aves     Charadriiformes       Burhinidae   \n",
+       "8111  Animalia  Chordata        Reptilia            Squamata        Iguanidae   \n",
+       "\n",
+       "               genus         species                      sciName  \n",
+       "4462        Alouatta          caraya              Alouatta caraya  \n",
+       "3229           Mimus      macdonaldi             Mimus macdonaldi  \n",
+       "5172        Procapra    picticaudata        Procapra picticaudata  \n",
+       "9542          Athene        blewitti              Athene blewitti  \n",
+       "7663  Choeronycteris        mexicana      Choeronycteris mexicana  \n",
+       "1418    Thalassarche  chlororhynchos  Thalassarche chlororhynchos  \n",
+       "8008      Cyprinodon      macularius        Cyprinodon macularius  \n",
+       "6762          Anolis      monteverde            Anolis monteverde  \n",
+       "2846          Esacus  recurvirostris        Esacus recurvirostris  \n",
+       "8111      Ctenosaura          bakeri            Ctenosaura bakeri  "
+      ]
+     },
+     "execution_count": 12,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "updated_catalog.sample(10)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Looks good, precisely as expected. Let's save this to a CSV now."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "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,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "jupytext": {
+   "formats": "ipynb,py:percent"
+  },
+  "kernelspec": {
+   "display_name": "tol",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

eol_realign/notebooks/re-gen_tol_catalog.ipynb

@@ -0,0 +1,926 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pandas as pd"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "TOL_FILEPATH = \"../../data/\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Read in Complete EOL TreeOfLife-10M Manifest\n",
+    "\n",
+    "[`combined-manifest-licenses.csv`](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/48af9b74b7a05a03b9a807a5b7b591fbf574eaec/eol_realign/data/combined-manifest-licenses.csv) is [`eol-cargo-archive_catalog_combined-manifest-checksums_links.csv`](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/48af9b74b7a05a03b9a807a5b7b591fbf574eaec/eol_realign/data/eol-cargo-archive_catalog_combined-manifest-checksums_links.csv) run through the `owner_match` and `make_licenses` scripts."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 6841202 entries, 0 to 6841201\n",
+      "Data columns (total 32 columns):\n",
+      " #   Column                           Non-Null Count    Dtype  \n",
+      "---  ------                           --------------    -----  \n",
+      " 0   filename_archive                 6841202 non-null  object \n",
+      " 1   md5                              6841202 non-null  object \n",
+      " 2   combined_id_archive              6841202 non-null  object \n",
+      " 3   split                            6841202 non-null  object \n",
+      " 4   treeoflife_id                    6841202 non-null  object \n",
+      " 5   bioscan_part                     0 non-null        float64\n",
+      " 6   bioscan_filename                 0 non-null        float64\n",
+      " 7   inat21_filename                  0 non-null        float64\n",
+      " 8   inat21_cls_name                  0 non-null        float64\n",
+      " 9   inat21_cls_num                   0 non-null        float64\n",
+      " 10  kingdom                          6551473 non-null  object \n",
+      " 11  phylum                           6553206 non-null  object \n",
+      " 12  class                            6532009 non-null  object \n",
+      " 13  order                            6525621 non-null  object \n",
+      " 14  family                           6506076 non-null  object \n",
+      " 15  genus                            6486130 non-null  object \n",
+      " 16  species                          6406307 non-null  object \n",
+      " 17  common                           6841202 non-null  object \n",
+      " 18  combined_id_catalog              6841202 non-null  object \n",
+      " 19  filename_manifest                6841202 non-null  object \n",
+      " 20  combined_id_manifest_redownload  6841202 non-null  object \n",
+      " 21  medium_source_url                6841202 non-null  object \n",
+      " 22  eol_full_size_copy_url           6841202 non-null  object \n",
+      " 23  license_name                     6841202 non-null  object \n",
+      " 24  copyright_owner                  6841202 non-null  object \n",
+      " 25  expected_image_filename          6841202 non-null  object \n",
+      " 26  source_0706                      6841202 non-null  bool   \n",
+      " 27  source_0726                      6841202 non-null  bool   \n",
+      " 28  source_1206                      6841202 non-null  bool   \n",
+      " 29  combined_id_full_manifest        6841202 non-null  object \n",
+      " 30  title                            6841202 non-null  object \n",
+      " 31  license_link                     6809751 non-null  object \n",
+      "dtypes: bool(3), float64(5), object(24)\n",
+      "memory usage: 1.5+ GB\n"
+     ]
+    }
+   ],
+   "source": [
+    "manifest = pd.read_csv(\"../data/combined-manifest-licenses.csv\",\n",
+    "                          low_memory=False,\n",
+    "                          dtype = {\"eol_content_id\": \"int64\", \"eol_page_id\": \"int64\"})\n",
+    "manifest.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "treeoflife_id                6219674\n",
+       "md5                          6146917\n",
+       "filename_archive             6219674\n",
+       "filename_manifest            6608194\n",
+       "expected_image_filename      6608194\n",
+       "combined_id_full_manifest    6608194\n",
+       "dtype: int64"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "manifest[[\"treeoflife_id\", \"md5\", \"filename_archive\", \"filename_manifest\",\"expected_image_filename\", \"combined_id_full_manifest\"]].nunique()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Read in TreeOfLife-10M Catalog"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Note that we will use [`catalog`](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/main/data/catalog.csv) from v3.3 EDA update [commit](https://huggingface.co/datasets/imageomics/ToL-EDA/commit/5260e84802d2910eedc2a206e7be035cf28f64d4). This is the version reported in the paper and in visualizations that will be included with the initial dataset publication; the patch will have updated visuals to match with this version.\n",
+    "(renamed locally to `catalog-orig-v3-3.csv`)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 11021779 entries, 0 to 11021778\n",
+      "Data columns (total 17 columns):\n",
+      " #   Column            Non-Null Count     Dtype  \n",
+      "---  ------            --------------     -----  \n",
+      " 0   split             11021779 non-null  object \n",
+      " 1   treeoflife_id     11021779 non-null  object \n",
+      " 2   eol_content_id    6844184 non-null   float64\n",
+      " 3   eol_page_id       6844184 non-null   float64\n",
+      " 4   bioscan_part      1235502 non-null   float64\n",
+      " 5   bioscan_filename  1235502 non-null   object \n",
+      " 6   inat21_filename   2942093 non-null   object \n",
+      " 7   inat21_cls_name   2942093 non-null   object \n",
+      " 8   inat21_cls_num    2942093 non-null   float64\n",
+      " 9   kingdom           10736334 non-null  object \n",
+      " 10  phylum            10738087 non-null  object \n",
+      " 11  class             10716389 non-null  object \n",
+      " 12  order             10709733 non-null  object \n",
+      " 13  family            10674746 non-null  object \n",
+      " 14  genus             9725443 non-null   object \n",
+      " 15  species           9551602 non-null   object \n",
+      " 16  common            11021779 non-null  object \n",
+      "dtypes: float64(4), object(13)\n",
+      "memory usage: 1.4+ GB\n"
+     ]
+    }
+   ],
+   "source": [
+    "catalog_orig = pd.read_csv(TOL_FILEPATH + \"catalog-orig-v3-3.csv\",\n",
+    "                         low_memory=False\n",
+    "                         )\n",
+    "catalog_orig.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Separate out the EOL portion from the BIOSCAN & iNat21 portion, that way we can merge the EOL part with the manifest (requires casting the EOL content & page IDs to `int64` and combining them with an underscore to merge on the `combined_id_full_manifest`) to get the licenses and create a clear `ToL_manifest` like with rarespecies. Then we can concatenate the adjusted EOL portion with the BIOSCAN & iNat21 portion to reconstruct the catalog."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# EOL portion of the catalog\n",
+    "eol_catalog = catalog_orig.loc[catalog_orig[\"eol_content_id\"].notna()]\n",
+    "\n",
+    "# BIOSCAN & iNat portion of the catalog\n",
+    "bin_catalog = catalog_orig.loc[catalog_orig[\"eol_content_id\"].isna()]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Recast EOL content and page IDs as `int64` in combined ID generation. Need to leave them as they are for re-concatenating with the other portion of the catalog."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/var/folders/nv/f0fq1p1n1_3b11x579py_0q80000gq/T/ipykernel_59366/112309718.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",
+      "  eol_catalog[\"combined_id_catalog\"] = eol_catalog[\"eol_content_id\"].astype(int).astype(str) + \"_\" + eol_catalog[\"eol_page_id\"].astype(int).astype(str)\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>split</th>\n",
+       "      <th>treeoflife_id</th>\n",
+       "      <th>eol_content_id</th>\n",
+       "      <th>eol_page_id</th>\n",
+       "      <th>bioscan_part</th>\n",
+       "      <th>bioscan_filename</th>\n",
+       "      <th>inat21_filename</th>\n",
+       "      <th>inat21_cls_name</th>\n",
+       "      <th>inat21_cls_num</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>combined_id_catalog</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>train_small</td>\n",
+       "      <td>a87c78c0-eb7c-45ee-9a98-681f61292d6b</td>\n",
+       "      <td>29586132.0</td>\n",
+       "      <td>65441690.0</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>Animalia</td>\n",
+       "      <td>Arthropoda</td>\n",
+       "      <td>Insecta</td>\n",
+       "      <td>Lepidoptera</td>\n",
+       "      <td>Nymphalidae</td>\n",
+       "      <td>Acraea</td>\n",
+       "      <td>terpsicore</td>\n",
+       "      <td>Tawny Coster</td>\n",
+       "      <td>29586132_65441690</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>train_small</td>\n",
+       "      <td>f8158395-d663-4f0f-b38d-1c6ecb16a8ca</td>\n",
+       "      <td>29811010.0</td>\n",
+       "      <td>45510040.0</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>Animalia</td>\n",
+       "      <td>Chordata</td>\n",
+       "      <td>Aves</td>\n",
+       "      <td>Passeriformes</td>\n",
+       "      <td>Pycnonotidae</td>\n",
+       "      <td>Pycnonotus</td>\n",
+       "      <td>cafer</td>\n",
+       "      <td>Red-vented Bulbul</td>\n",
+       "      <td>29811010_45510040</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>train_small</td>\n",
+       "      <td>63aab6e3-b01d-4259-be13-9dd41becaf29</td>\n",
+       "      <td>28563112.0</td>\n",
+       "      <td>736062.0</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>Animalia</td>\n",
+       "      <td>Arthropoda</td>\n",
+       "      <td>Insecta</td>\n",
+       "      <td>Diptera</td>\n",
+       "      <td>Empididae</td>\n",
+       "      <td>Rhamphomyia</td>\n",
+       "      <td>limbata</td>\n",
+       "      <td>Rhamphomyia limbata</td>\n",
+       "      <td>28563112_736062</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3</th>\n",
+       "      <td>train_small</td>\n",
+       "      <td>cf2d58e1-d504-489c-80dd-e99407f8c13d</td>\n",
+       "      <td>29002118.0</td>\n",
+       "      <td>349296.0</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>NaN</td>\n",
+       "      <td>Animalia</td>\n",
+       "      <td>Arthropoda</td>\n",
+       "      <td>Insecta</td>\n",
+       "      <td>Lepidoptera</td>\n",
+       "      <td>Geometridae</td>\n",
+       "      <td>Exelis</td>\n",
+       "      <td>pyrolaria</td>\n",
+       "      <td>Fine Lined Gray</td>\n",
+       "      <td>29002118_349296</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "         split                         treeoflife_id  eol_content_id  \\\n",
+       "0  train_small  a87c78c0-eb7c-45ee-9a98-681f61292d6b      29586132.0   \n",
+       "1  train_small  f8158395-d663-4f0f-b38d-1c6ecb16a8ca      29811010.0   \n",
+       "2  train_small  63aab6e3-b01d-4259-be13-9dd41becaf29      28563112.0   \n",
+       "3  train_small  cf2d58e1-d504-489c-80dd-e99407f8c13d      29002118.0   \n",
+       "\n",
+       "   eol_page_id  bioscan_part bioscan_filename inat21_filename inat21_cls_name  \\\n",
+       "0   65441690.0           NaN              NaN             NaN             NaN   \n",
+       "1   45510040.0           NaN              NaN             NaN             NaN   \n",
+       "2     736062.0           NaN              NaN             NaN             NaN   \n",
+       "3     349296.0           NaN              NaN             NaN             NaN   \n",
+       "\n",
+       "   inat21_cls_num   kingdom      phylum    class          order        family  \\\n",
+       "0             NaN  Animalia  Arthropoda  Insecta    Lepidoptera   Nymphalidae   \n",
+       "1             NaN  Animalia    Chordata     Aves  Passeriformes  Pycnonotidae   \n",
+       "2             NaN  Animalia  Arthropoda  Insecta        Diptera     Empididae   \n",
+       "3             NaN  Animalia  Arthropoda  Insecta    Lepidoptera   Geometridae   \n",
+       "\n",
+       "         genus     species               common combined_id_catalog  \n",
+       "0       Acraea  terpsicore         Tawny Coster   29586132_65441690  \n",
+       "1   Pycnonotus       cafer    Red-vented Bulbul   29811010_45510040  \n",
+       "2  Rhamphomyia     limbata  Rhamphomyia limbata     28563112_736062  \n",
+       "3       Exelis   pyrolaria      Fine Lined Gray     29002118_349296  "
+      ]
+     },
+     "execution_count": 8,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "eol_catalog[\"combined_id_catalog\"] = eol_catalog[\"eol_content_id\"].astype(int).astype(str) + \"_\" + eol_catalog[\"eol_page_id\"].astype(int).astype(str)\n",
+    "eol_catalog.head(4)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Keep in mind, we will have some repeated entries due to the `train_small` split, so we will merge on just `split != \"train_small\"`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "train_val_eol_catalog = eol_catalog.loc[eol_catalog[\"split\"] != \"train_small\"]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "We should have 6250420 entries in our merge, minus the approximately 30K we couldn't match.\n"
+     ]
+    }
+   ],
+   "source": [
+    "print(f\"We should have {train_val_eol_catalog.shape[0]} entries in our merge, minus the approximately 30K we couldn't match.\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We should have 6,250,420 entries in our merge, minus the approximately 30K we couldn't match.. The expectation is that this will be 6,219,674 entries. Details on this expectation & the `train_small` implications can be found in [`eol_realign/notebooks/links_align_reduced.ipynb`](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/3438fe9a88c0f377a4d8ac4c6c0de796858a08ac/eol_realign/notebooks/links_align_reduced.ipynb)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Catalog Columns\n",
+    "id_cols = [\"treeoflife_id\", \"eol_content_id\", \"eol_page_id\", \"combined_id_catalog\"]\n",
+    "\n",
+    "# Manifest Columns\n",
+    "manifest_cols = [\"treeoflife_id\",\n",
+    "                \"md5\",\n",
+    "                \"medium_source_url\",\n",
+    "                \"eol_full_size_copy_url\",\n",
+    "                \"license_name\",\n",
+    "                \"copyright_owner\",\n",
+    "                \"license_link\",\n",
+    "                \"title\",\n",
+    "                \"filename_archive\",\n",
+    "                \"filename_manifest\",\n",
+    "                \"expected_image_filename\",\n",
+    "                \"combined_id_full_manifest\"]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "<class 'pandas.core.frame.DataFrame'>\n",
+      "RangeIndex: 6841202 entries, 0 to 6841201\n",
+      "Data columns (total 15 columns):\n",
+      " #   Column                     Non-Null Count    Dtype  \n",
+      "---  ------                     --------------    -----  \n",
+      " 0   treeoflife_id              6841202 non-null  object \n",
+      " 1   eol_content_id             6841202 non-null  float64\n",
+      " 2   eol_page_id                6841202 non-null  float64\n",
+      " 3   combined_id_catalog        6841202 non-null  object \n",
+      " 4   md5                        6841202 non-null  object \n",
+      " 5   medium_source_url          6841202 non-null  object \n",
+      " 6   eol_full_size_copy_url     6841202 non-null  object \n",
+      " 7   license_name               6841202 non-null  object \n",
+      " 8   copyright_owner            6841202 non-null  object \n",
+      " 9   license_link               6809751 non-null  object \n",
+      " 10  title                      6841202 non-null  object \n",
+      " 11  filename_archive           6841202 non-null  object \n",
+      " 12  filename_manifest          6841202 non-null  object \n",
+      " 13  expected_image_filename    6841202 non-null  object \n",
+      " 14  combined_id_full_manifest  6841202 non-null  object \n",
+      "dtypes: float64(2), object(13)\n",
+      "memory usage: 782.9+ MB\n"
+     ]
+    }
+   ],
+   "source": [
+    "tol_manifest = pd.merge(train_val_eol_catalog[id_cols],\n",
+    "                        manifest[manifest_cols],\n",
+    "                        on = \"treeoflife_id\",\n",
+    "                        how = \"inner\")\n",
+    "tol_manifest.info(show_counts = True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "treeoflife_id                6219674\n",
+       "eol_content_id               6219674\n",
+       "eol_page_id                   501807\n",
+       "combined_id_catalog          6219674\n",
+       "md5                          6146917\n",
+       "medium_source_url            6217871\n",
+       "eol_full_size_copy_url       6247692\n",
+       "license_name                      16\n",
+       "copyright_owner               403215\n",
+       "license_link                      11\n",
+       "title                         482137\n",
+       "filename_archive             6219674\n",
+       "filename_manifest            6608194\n",
+       "expected_image_filename      6608194\n",
+       "combined_id_full_manifest    6608194\n",
+       "dtype: int64"
+      ]
+     },
+     "execution_count": 13,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "tol_manifest.nunique()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Let's reduce this down to just the unique `treeoflife_id`s. All URLs are valid and the EOL content and page IDs (plus `combined_id_catalog` will match the filenames we have saved)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "(6219674, 16)\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "treeoflife_id                6219674\n",
+       "eol_content_id               6219674\n",
+       "eol_page_id                   501807\n",
+       "combined_id_catalog          6219674\n",
+       "md5                          6146917\n",
+       "medium_source_url            6144920\n",
+       "eol_full_size_copy_url       6146917\n",
+       "license_name                      16\n",
+       "copyright_owner               398253\n",
+       "license_link                      11\n",
+       "title                         475702\n",
+       "filename_archive             6219674\n",
+       "filename_manifest            6146917\n",
+       "expected_image_filename      6146917\n",
+       "combined_id_full_manifest    6146917\n",
+       "duplicate_tol_id                   1\n",
+       "dtype: int64"
+      ]
+     },
+     "execution_count": 14,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "tol_manifest[\"duplicate_tol_id\"] = tol_manifest.duplicated(\"treeoflife_id\", keep = \"first\")\n",
+    "tol_manifest = tol_manifest.loc[~tol_manifest[\"duplicate_tol_id\"]]\n",
+    "\n",
+    "print(tol_manifest.shape)\n",
+    "tol_manifest.nunique()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Clearly, these match with the archive filenames.\n",
+    "\n",
+    "Our numbers match the expected count. Let's check our `copyright_owner` and `title` coverage. "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "license_name\n",
+       "No known copyright restrictions    7389\n",
+       "cc-by-nc-sa-3.0                    4247\n",
+       "cc-publicdomain                    3422\n",
+       "cc-by-nc                           3029\n",
+       "cc-by-3.0                           470\n",
+       "cc-by-sa-3.0                        171\n",
+       "cc-0-1.0                             32\n",
+       "cc-by-nc-2.0                          2\n",
+       "cc-by-nc-4.0                          1\n",
+       "Name: count, dtype: int64"
+      ]
+     },
+     "execution_count": 15,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "tol_manifest.loc[tol_manifest[\"copyright_owner\"] == \"not provided\", \"license_name\"].value_counts()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 16,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "license_name\n",
+       "cc-by-nc-4.0                       2401921\n",
+       "cc-by-sa-3.0                        760953\n",
+       "cc-by-nc-sa-3.0                     664194\n",
+       "cc-by-3.0                           439653\n",
+       "cc-by-4.0                           368046\n",
+       "cc-by-nc                            316103\n",
+       "cc-by-nc-sa-4.0                     184204\n",
+       "cc-by-nc-sa                         154761\n",
+       "cc-publicdomain                     129257\n",
+       "cc-by-sa-4.0                         65003\n",
+       "cc-by                                58303\n",
+       "cc-by-sa-2.0                         30157\n",
+       "cc-by-nc-2.0                         27718\n",
+       "cc-0-1.0                             20358\n",
+       "No known copyright restrictions      16042\n",
+       "cc-by-nc-sa-2.5                        315\n",
+       "Name: count, dtype: int64"
+      ]
+     },
+     "execution_count": 16,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "tol_manifest.loc[tol_manifest[\"title\"] == \"not provided\", \"license_name\"].value_counts()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "At least most unmatched lack of copyright restrictions or are CC0; we did what we could."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Save Full Owner Manifest\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 17,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "tol_manifest.to_csv(\"../data/full_owner_manifest.csv\", index = False)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Make and Save License File"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 18,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "licesne_cols = [\"treeoflife_id\",\n",
+    "                \"eol_content_id\",\n",
+    "                \"eol_page_id\",\n",
+    "                \"md5\",\n",
+    "                \"medium_source_url\",\n",
+    "                \"eol_full_size_copy_url\",\n",
+    "                \"license_name\",\n",
+    "                \"copyright_owner\",\n",
+    "                \"license_link\",\n",
+    "                \"title\"]\n",
+    "\n",
+    "licenses = tol_manifest[licesne_cols]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 19,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "licenses.to_csv(TOL_FILEPATH + \"licenses.csv\", index = False)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Make Updated Catalog\n",
+    "\n",
+    "Reconnect the EOL portion of the catalog to the BIOSCAN and iNat21 portion."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 20,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "['split',\n",
+       " 'treeoflife_id',\n",
+       " 'eol_content_id',\n",
+       " 'eol_page_id',\n",
+       " 'bioscan_part',\n",
+       " 'bioscan_filename',\n",
+       " 'inat21_filename',\n",
+       " 'inat21_cls_name',\n",
+       " 'inat21_cls_num',\n",
+       " 'kingdom',\n",
+       " 'phylum',\n",
+       " 'class',\n",
+       " 'order',\n",
+       " 'family',\n",
+       " 'genus',\n",
+       " 'species',\n",
+       " 'common']"
+      ]
+     },
+     "execution_count": 20,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "cat_cols = list(catalog_orig.columns)\n",
+    "cat_cols"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Need to first reduce the `eol_catalog` (still has the `train_small` split we want to keep).\n",
+    "\n",
+    "BIOSCAN & iNat portion of the catalog: `bin_catalog`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 21,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "(6810437, 18)\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "6219674"
+      ]
+     },
+     "execution_count": 21,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "matched_tol_ids = list(tol_manifest.treeoflife_id)\n",
+    "\n",
+    "reduced_eol_cat = eol_catalog.loc[eol_catalog[\"treeoflife_id\"].isin(matched_tol_ids)]\n",
+    "\n",
+    "#check we have expected numbers (6,219,674 + 590,730 = 6,810,404, still only 6,219,674 unique)\n",
+    "print(reduced_eol_cat.shape)\n",
+    "reduced_eol_cat.treeoflife_id.nunique()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Looks like we recovered 33 more from the small train set than we expected. These came from the archive recovery (had we merged on `combined_id_archive` instead of `combined_id_full_manifest` in [`links_align_reduced.ipynb`](https://huggingface.co/datasets/imageomics/ToL-EDA/blob/3438fe9a88c0f377a4d8ac4c6c0de796858a08ac/eol_realign/notebooks/links_align_reduced.ipynb), would have seen that difference)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 24,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "The BIOSCAN & iNate portion have 4177595 total images, with 3815156 unique entries.\n"
+     ]
+    }
+   ],
+   "source": [
+    "print(f\"The BIOSCAN & iNate portion have {bin_catalog.shape[0]} total images, with {bin_catalog.treeoflife_id.nunique()} unique entries.\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We have expected 10,034,830 unique entries in the final set, 10,988,032 total entries."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 25,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "(10988032, 17)\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "split                      3\n",
+       "treeoflife_id       10034830\n",
+       "eol_content_id       6219674\n",
+       "eol_page_id           501807\n",
+       "bioscan_part             113\n",
+       "bioscan_filename     1128313\n",
+       "inat21_filename      2686843\n",
+       "inat21_cls_name        10000\n",
+       "inat21_cls_num         10000\n",
+       "kingdom                   12\n",
+       "phylum                   108\n",
+       "class                    347\n",
+       "order                   1495\n",
+       "family                  7954\n",
+       "genus                  73687\n",
+       "species               163001\n",
+       "common                442253\n",
+       "dtype: int64"
+      ]
+     },
+     "execution_count": 25,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "updated_catalog = pd.concat([reduced_eol_cat[cat_cols], bin_catalog], ignore_index = True)\n",
+    "\n",
+    "print(updated_catalog.shape)\n",
+    "updated_catalog.nunique()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Looks good, precisely as expected. Let's save this to a CSV now."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 26,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "updated_catalog.to_csv(TOL_FILEPATH + \"catalog.csv\", index = False)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "jupytext": {
+   "formats": "ipynb,py:percent"
+  },
+  "kernelspec": {
+   "display_name": "tol",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

eol_realign/scripts/make_licenses.py

@@ -0,0 +1,101 @@
+import pandas as pd
+from pathlib import Path
+import argparse
+import sys
+
+# Output of match_owners.py (combined_manifest.csv) should be fed in.
+
+CC_URL = "https://creativecommons.org/"
+
+
+def get_license_url(license_version):
+    """
+    Function to generate the appropriate Creative Commons URL for a given license.
+    All licenses in the media manifest are "cc-XX", a variation on "publicdomain", or "No known copyright restrictions".
+
+    Parameters:
+    -----------
+    license_version - String. License (eg., "cc-by-nc 3.0").
+
+    Returns:
+    --------
+    license_url - String. Creative Commons URL associated with the license_version.
+
+    """
+    # First check for version number and isolate it
+    if "." in license_version:
+        version = license_version.split(sep="-")[-1]
+        license_name = license_version.split(sep="-" + version)[0]
+    else:
+        # No version specified, so default to latest version (4.0)
+        license_name = license_version
+        version = "4.0"
+    # Check which type of license
+    if license_name[:5] == "cc-by":
+        by_x = license_name.split(sep="cc-")[1]
+        license_url = CC_URL + "licenses/" + by_x + "/" + version
+    elif (license_name[:4] == "cc-0") or ("public" in license_name):
+        license_url = CC_URL + "publicdomain/zero/1.0"
+    else:
+        # "No known copyright restrictions"
+        license_url = None
+    return license_url
+
+
+def main(src_csv, dest_dir):
+    # Check CSV compatibility
+    try:
+        print("Reading CSV")
+        df = pd.read_csv(src_csv, low_memory=False)
+    except Exception as e:
+        sys.exit(e)
+
+    # Check for "License Name" or "license_name" column
+    print("Processing data")
+    df_cols = list(df.columns)
+    if "License Name" not in df_cols:
+        if "license_name" not in df_cols:
+            sys.exit("Source CSV does not have a column labeled License Name or license_name.")
+        license_col = "license_name"
+    else:
+        license_col = "License Name"
+
+    # Check filepath given by user
+    dest_dir_path = Path(dest_dir)
+    if not dest_dir_path.is_absolute():
+        # Use ToL-EDA as reference folder
+        base_path = Path(__file__).parent.parent.resolve()
+        filepath = base_path / dest_dir_path
+    else:
+        filepath = dest_dir_path
+
+    filepath.mkdir(parents=True, exist_ok=True)
+
+    # Add links for licenses to combined manifest
+    print("Getting URLs for licenses")
+    df["license_link"] = df[license_col].apply(get_license_url)
+
+    # Save license file
+    df.to_csv(str(filepath / "combined-manifest-licenses.csv"), index=False)
+
+    # Print counts of licenses for which URL was not resolved
+    print(
+        "Licenses with no URL: \n",
+        df.loc[df["license_link"].isna(), license_col].value_counts(),
+    )
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="Add license URLs to combined manifest file"
+    )
+    parser.add_argument("input_file", help="Path to the input CSV file")
+    parser.add_argument(
+        "--output_path",
+        default="data",
+        required=False,
+        help="Path to the folder for output license file",
+    )
+    args = parser.parse_args()
+
+    main(args.input_file, args.output_path)

eol_realign/scripts/match_owners.py

@@ -0,0 +1,136 @@
+import pandas as pd
+from pathlib import Path
+import argparse
+import sys
+
+# NOTE: column names are hard-coded to the files provided in MANIFEST_PATH & OWNER_PATH
+# It is intended to just add the extra licensing information to the combined manifest
+# Owner fix file: https://huggingface.co/datasets/imageomics/eol/blob/main/owners_info_fix/media_manifest_missing_licenses_jul26_owners.csv
+MANIFEST_PATH = "data/eol-cargo-archive_catalog_combined-manifest-checksums_links.csv"
+OWNER_PATH = "data/media_manifest_missing_licenses_jul26_owners.csv"
+
+
+def get_owners_titles(manifest, owners):
+    """
+    Function to attach owner names and image titles to manifest entries in combined manifest.
+    Fills empty "Copyright Owner" and "Title" values with "not provided".
+
+    Parameters:
+    -----------
+    manifest - DataFrame composed of manifest entries aligned on MD5s from three different manifests,
+                includes columns "md5_combined_manifest", "combined_id_full_manifest".
+    owners - DataFrame of July 26, 2023 media manifest entries that had missing owners, updated with their information.
+
+    Returns:
+    --------
+    full_owner_manifest - Media manifest DataFrame with missing owners resolved.
+    num_matched - Number of records matched with the owner fix file.
+    """
+
+    # First merge owners
+    owners_manifest = pd.merge(owners,
+                           manifest,
+                           left_on="combined_id_owner",
+                           right_on = "combined_id_full_manifest",
+                           how = "inner")
+    
+    # Set "copyright_owner" column to owners patched in owner CSV 
+    owners_manifest["copyright_owner"] = owners_manifest["Copyright Owner"]
+
+    # Preserve columns that match the combined manifest
+    license_cols = list(manifest.columns)
+    license_cols.append("title")
+    owners_manifest = owners_manifest[license_cols]
+
+    # Get matched owner IDs
+    rematched_owner_ids = list(owners_manifest.combined_id_full_manifest.unique())
+    num_matched = len(rematched_owner_ids)
+
+    # Reduce manifest to just records not matched in owner file
+    un_matched_owner_manifest = manifest.loc[~manifest.combined_id_full_manifest.isin(rematched_owner_ids)]
+    un_matched_owner_manifest["title"] = "not provided"
+
+    # Align the matched owners with the unmatched
+    full_owner_manifest = pd.concat([un_matched_owner_manifest, owners_manifest], ignore_index=True)
+
+    # Fill null "copyright_owner" and "Title" values with "not provided"
+    full_owner_manifest["copyright_owner"].fillna("not provided", inplace=True)
+    full_owner_manifest["title"].fillna("not provided", inplace=True)
+
+    return full_owner_manifest, num_matched
+
+
+def update_owners(manifest, owners, filepath):
+    """
+    Function to fetch and attach the missing owner and title information to EOL catalog entries and save catalog-media file.
+
+    Parameters:
+    -----------
+    manifest - DataFrame composed of manifest entries aligned on MD5s from three different manifests,
+                includes columns "md5_combined_manifest", "combined_id_full_manifest".
+    owners - DataFrame of July 26, 2023 media manifest entries that had missing owners, updated with their information.
+    """
+    # Need combined IDs for the owner match file
+    # EOL content & page IDs read in as int64
+    owners["combined_id_owner"] = owners["EOL content ID"].astype(str) + "_" + owners["EOL page ID"].astype(str)
+
+    updated_manifest, num_matched = get_owners_titles(manifest, owners)
+
+    # Save updated combined manifest file to chosen location
+    updated_manifest.to_csv(filepath, index=False)
+
+    # Print counts of licenses for which owner info was not resolved
+    print(f"Of the {manifest.shape[0]} entries in manifest, {num_matched} were matched to the owner fix file.")
+    print(
+        "Licenses still missing Copyright Owners: \n",
+        manifest.loc[
+            manifest["copyright_owner"].isna(), "license_name"
+        ].value_counts(),
+    )
+
+
+def main(dest_dir):
+    # Read in CSVs
+    try:
+        # Read in media manifest and owner fix CSVs with EOL content and page IDs as type "int64".
+        print("Reading combined media manifest CSV")
+        manifest = pd.read_csv(
+            MANIFEST_PATH,
+            low_memory=False,
+        )
+        print("Reading owner fix CSV")
+        owners = pd.read_csv(
+            OWNER_PATH,
+            dtype={"EOL content ID": "int64", "EOL page ID": "int64"},
+            low_memory=False,
+        )
+    except Exception as e:
+        sys.exit(e)
+
+    # Check filepath given by user
+    dest_dir_path = Path(dest_dir)
+    if not dest_dir_path.is_absolute():
+        # Use ToL-EDA as reference folder
+        base_path = Path(__file__).parent.parent.resolve()
+        filepath = base_path / dest_dir_path
+    else:
+        filepath = dest_dir_path
+
+    filepath.mkdir(parents=True, exist_ok=True)
+
+    # Make and save updated manifest to chosen filepath
+    update_owners(manifest, owners, str(filepath / "combined_manifest.csv"))
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Attach missing owner info to combined manifest")
+
+    parser.add_argument(
+        "--output_path",
+        default="data",
+        required=False,
+        help="Path to the folder for output combined manifest file",
+    )
+    args = parser.parse_args()
+
+    main(args.output_path)

rare_species/data/rarespecies-catalog.csv

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:96c458bd580caf5df4743c639eb38490e62eddef44b92be519d6771bdc2bf8fa
+size 1953805