Change set required for functionality with Cornell Birds CSV (#40)

* Handle issues with image name column data string types and extensions to match URL image data

* Extension mismatch strategy to log mismatches

* Add exponential back-off retry condition

* Fix examples to have consistent extensions; update README examples

* Increment version info to v1.0.1

---------

Co-authored-by: Elizabeth Campolongo <38985481+egrace479@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Author: 3 people

.zenodo.json

@@ -35,9 +35,9 @@
   "license": {
     "id": "MIT"
   },
-  "publication_date": "2025-04-03",
+  "publication_date": "2025-09-25",
   "title": "Cautious Robot",
-  "version": "1.0.0",
+  "version": "1.1.0",
   "grants": [
       {
           "id": "021nxhr62::2118240"

CITATION.cff

@@ -13,14 +13,14 @@ authors:
   given-names: "Hilmar"
   orcid: "https://orcid.org/0000-0001-9107-0714"
 cff-version: 1.2.0
-date-released: "2025-04-03"
+date-released: "2025-09-25"
 identifiers:
-  - description: "The GitHub release URL of tag v1.0.0."
+  - description: "The GitHub release URL of tag v1.1.0."
     type: url
-    value: "https://github.com/Imageomics/cautious-robot/releases/tag/v1.0.0"
-  - description: "The GitHub URL of the commit tagged with v1.0.0."
+    value: "https://github.com/Imageomics/cautious-robot/releases/tag/v1.1.0"
+  - description: "The GitHub URL of the commit tagged with v1.1.0."
     type: url
-    value: "https://github.com/Imageomics/cautious-robot/tree/e7d6718ce33fb4c1d71fd4e4bc1b7b809d5133b0"
+    value: "https://github.com/Imageomics/cautious-robot/tree/<commit-hash>" # update on release
 keywords:
   - imageomics
   - metadata
@@ -37,6 +37,6 @@ license: MIT
 message: "If you use this software, please cite it using the metadata from this file."
 repository-code: "https://github.com/Imageomics/cautious-robot"
 title: "Cautious Robot"
-version: "1.0.0"
+version: "1.1.0"
 doi: "10.5281/zenodo.15133580"
 type: software

README.md

@@ -86,14 +86,14 @@ head -n 9 examples/HCGSD_testNA_checksums.csv
  > Output:
  > ```console
  > filepath,filename,md5
- > examples/test_images/10429021_V_lowres.jpg,10429021_V_lowres.jpg,c6aeb9d2f6db412ff5be0eb0b5435b83
- > examples/test_images/10428595_D_lowres.jpg,10428595_D_lowres.jpg,55882a0f3fdf8a68579c07254395653b
- > examples/test_images/10428972_V_lowres.jpg,10428972_V_lowres.jpg,0047e7454ce444f67fee1c90cc3ba9cb
- > examples/test_images/10428803_D_lowres.jpg,10428803_D_lowres.jpg,d8bfb73f2d3556390de04aa98822b815
- > examples/test_images/10428169_V_lowres.jpg,10428169_V_lowres.jpg,042c9dc294d589ce3f140f14ddab0166
- > examples/test_images/10428321_D_lowres.jpg,10428321_D_lowres.jpg,fbeeed30274e424831b06360b587ceb3
- > examples/test_images/10428140_V_lowres.jpg,10428140_V_lowres.jpg,c11538f2de5a5e2d6013fc800848d43a
- > examples/test_images/10428250_V_lowres.jpg,10428250_V_lowres.jpg,14ac99b1a9913a9d420f21b94d6136d6
+ > examples/test_images/10429021_V_lowres.png,10429021_V_lowres.png,c6aeb9d2f6db412ff5be0eb0b5435b83
+ > examples/test_images/10428595_D_lowres.png,10428595_D_lowres.png,55882a0f3fdf8a68579c07254395653b
+ > examples/test_images/10428321_D_lowres.png,10428321_D_lowres.png,fbeeed30274e424831b06360b587ceb3
+ > examples/test_images/10428250_V_lowres.png,10428250_V_lowres.png,14ac99b1a9913a9d420f21b94d6136d6
+ > examples/test_images/10428140_V_lowres.png,10428140_V_lowres.png,c11538f2de5a5e2d6013fc800848d43a
+ > examples/test_images/10428803_D_lowres.png,10428803_D_lowres.png,d8bfb73f2d3556390de04aa98822b815
+ > examples/test_images/10428169_V_lowres.png,10428169_V_lowres.png,042c9dc294d589ce3f140f14ddab0166
+ > examples/test_images/10428972_V_lowres.png,10428972_V_lowres.png,0047e7454ce444f67fee1c90cc3ba9cb
  > ```
 
 - **Download Images to Subfolders Based on Column Value:**
@@ -110,7 +110,7 @@ cautious-robot -i examples/HCGSD_testNA.csv -o examples/test_images_subdirs --su
  > 8 images were downloaded to examples/test_images_subdirs of the 8 expected.
  > ```
 ```
-ls examples/test_images
+ls examples/test_images_subdirs
 ```
  > Output:
  > ```console
@@ -123,14 +123,14 @@ head -n 9 examples/HCGSD_testNA_checksums.csv
  > Output:
  > ```console
  > filepath,filename,md5
- > examples/test_images_subdirs/erato/10429021_V_lowres.jpg,10429021_V_lowres.jpg,c6aeb9d2f6db412ff5be0eb0b5435b83
- > examples/test_images_subdirs/erato/10428595_D_lowres.jpg,10428595_D_lowres.jpg,55882a0f3fdf8a68579c07254395653b
- > examples/test_images_subdirs/erato/10428972_V_lowres.jpg,10428972_V_lowres.jpg,0047e7454ce444f67fee1c90cc3ba9cb
- > examples/test_images_subdirs/erato/10428803_D_lowres.jpg,10428803_D_lowres.jpg,d8bfb73f2d3556390de04aa98822b815
- > examples/test_images_subdirs/melpomene/10428169_V_lowres.jpg,10428169_V_lowres.jpg,042c9dc294d589ce3f140f14ddab0166
- > examples/test_images_subdirs/melpomene/10428321_D_lowres.jpg,10428321_D_lowres.jpg,fbeeed30274e424831b06360b587ceb3
- > examples/test_images_subdirs/melpomene/10428140_V_lowres.jpg,10428140_V_lowres.jpg,c11538f2de5a5e2d6013fc800848d43a
- > examples/test_images_subdirs/melpomene/10428250_V_lowres.jpg,10428250_V_lowres.jpg,14ac99b1a9913a9d420f21b94d6136d6
+ > examples/test_images_subdirs/melpomene/10428321_D_lowres.png,10428321_D_lowres.png,fbeeed30274e424831b06360b587ceb3
+ > examples/test_images_subdirs/melpomene/10428250_V_lowres.png,10428250_V_lowres.png,14ac99b1a9913a9d420f21b94d6136d6
+ > examples/test_images_subdirs/melpomene/10428140_V_lowres.png,10428140_V_lowres.png,c11538f2de5a5e2d6013fc800848d43a
+ > examples/test_images_subdirs/melpomene/10428169_V_lowres.png,10428169_V_lowres.png,042c9dc294d589ce3f140f14ddab0166
+ > examples/test_images_subdirs/erato/10429021_V_lowres.png,10429021_V_lowres.png,c6aeb9d2f6db412ff5be0eb0b5435b83
+ > examples/test_images_subdirs/erato/10428595_D_lowres.png,10428595_D_lowres.png,55882a0f3fdf8a68579c07254395653b
+ > examples/test_images_subdirs/erato/10428803_D_lowres.png,10428803_D_lowres.png,d8bfb73f2d3556390de04aa98822b815
+ > examples/test_images_subdirs/erato/10428972_V_lowres.png,10428972_V_lowres.png,0047e7454ce444f67fee1c90cc3ba9cb
  > ```
 
 - **Image Checksum Mismatch:** one value is intentionally altered in the source CSV
@@ -154,7 +154,7 @@ head -n 2 examples/HCGSD_test_MD5_mismatch_missing.csv
  > Output:
  > ```console
  > nhm_specimen,species,subspecies,sex,file_url,filename,md5
- > 10428972,erato,petiverana,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10428972_V_lowres.png,10428972_V_lowres.jpg,mismatch
+ > 10428972,erato,petiverana,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10428972_V_lowres.png,10428972_V_lowres.png,mismatch
  > ```
 
 ## Development

examples/HCGSD_testNA.csv

@@ -1,11 +1,11 @@
 NHM_Specimen,Species,Subspecies,Sex,file_url,filename
-10429021,erato,notabilis,female,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10429021_V_lowres.png,10429021_V_lowres.jpg
-10428972,erato,petiverana,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10428972_V_lowres.png,10428972_V_lowres.jpg
+10429021,erato,notabilis,female,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10429021_V_lowres.png,10429021_V_lowres.png
+10428972,erato,petiverana,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10428972_V_lowres.png,10428972_V_lowres.png
 10429172,erato,petiverana,male,,
-10428595,erato,phyllis,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/dorsal_images/10428595_D_lowres.png,10428595_D_lowres.jpg
-10428140,melpomene,plesseni,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10428140_V_lowres.png,10428140_V_lowres.jpg
-10428250,melpomene,schunkei,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10428250_V_lowres.png,10428250_V_lowres.jpg
+10428595,erato,phyllis,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/dorsal_images/10428595_D_lowres.png,10428595_D_lowres.png
+10428140,melpomene,plesseni,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10428140_V_lowres.png,10428140_V_lowres.png
+10428250,melpomene,schunkei,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10428250_V_lowres.png,10428250_V_lowres.png
 10427979,melpomene,rosina_S,male,,
-10428803,erato,guarica,female,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/dorsal_images/10428803_D_lowres.png,10428803_D_lowres.jpg
-10428169,melpomene,plesseni,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10428169_V_lowres.png,10428169_V_lowres.jpg
-10428321,melpomene,nanna,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/dorsal_images/10428321_D_lowres.png,10428321_D_lowres.jpg
+10428803,erato,guarica,female,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/dorsal_images/10428803_D_lowres.png,10428803_D_lowres.png
+10428169,melpomene,plesseni,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10428169_V_lowres.png,10428169_V_lowres.png
+10428321,melpomene,nanna,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/dorsal_images/10428321_D_lowres.png,10428321_D_lowres.png

examples/HCGSD_testNA_wMD5.csv

@@ -1,11 +1,11 @@
 NHM_Specimen,Species,Subspecies,Sex,file_url,filename,md5
-10429021,erato,notabilis,female,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10429021_V_lowres.png,10429021_V_lowres.jpg,c6aeb9d2f6db412ff5be0eb0b5435b83
-10428972,erato,petiverana,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10428972_V_lowres.png,10428972_V_lowres.jpg,0047e7454ce444f67fee1c90cc3ba9cb
+10429021,erato,notabilis,female,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10429021_V_lowres.png,10429021_V_lowres.png,c6aeb9d2f6db412ff5be0eb0b5435b83
+10428972,erato,petiverana,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10428972_V_lowres.png,10428972_V_lowres.png,0047e7454ce444f67fee1c90cc3ba9cb
 10429172,erato,petiverana,male,,,
-10428595,erato,phyllis,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/dorsal_images/10428595_D_lowres.png,10428595_D_lowres.jpg,55882a0f3fdf8a68579c07254395653b
-10428140,melpomene,plesseni,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10428140_V_lowres.png,10428140_V_lowres.jpg,c11538f2de5a5e2d6013fc800848d43a
-10428250,melpomene,schunkei,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10428250_V_lowres.png,10428250_V_lowres.jpg,14ac99b1a9913a9d420f21b94d6136d6
+10428595,erato,phyllis,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/dorsal_images/10428595_D_lowres.png,10428595_D_lowres.png,55882a0f3fdf8a68579c07254395653b
+10428140,melpomene,plesseni,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10428140_V_lowres.png,10428140_V_lowres.png,c11538f2de5a5e2d6013fc800848d43a
+10428250,melpomene,schunkei,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10428250_V_lowres.png,10428250_V_lowres.png,14ac99b1a9913a9d420f21b94d6136d6
 10427979,melpomene,rosina_S,male,,,
-10428803,erato,guarica,female,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/dorsal_images/10428803_D_lowres.png,10428803_D_lowres.jpg,d8bfb73f2d3556390de04aa98822b815
-10428169,melpomene,plesseni,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10428169_V_lowres.png,10428169_V_lowres.jpg,042c9dc294d589ce3f140f14ddab0166
-10428321,melpomene,nanna,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/dorsal_images/10428321_D_lowres.png,10428321_D_lowres.jpg,fbeeed30274e424831b06360b587ceb3
+10428803,erato,guarica,female,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/dorsal_images/10428803_D_lowres.png,10428803_D_lowres.png,d8bfb73f2d3556390de04aa98822b815
+10428169,melpomene,plesseni,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10428169_V_lowres.png,10428169_V_lowres.png,042c9dc294d589ce3f140f14ddab0166
+10428321,melpomene,nanna,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/dorsal_images/10428321_D_lowres.png,10428321_D_lowres.png,fbeeed30274e424831b06360b587ceb3

examples/HCGSD_test_MD5_mismatch.csv

@@ -1,11 +1,11 @@
 NHM_Specimen,Species,Subspecies,Sex,file_url,filename,md5
-10429021,erato,notabilis,female,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10429021_V_lowres.png,10429021_V_lowres.jpg,c6aeb9d2f6db412ff5be0eb0b5435b83
-10428972,erato,petiverana,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10428972_V_lowres.png,10428972_V_lowres.jpg,mismatch
+10429021,erato,notabilis,female,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10429021_V_lowres.png,10429021_V_lowres.png,c6aeb9d2f6db412ff5be0eb0b5435b83
+10428972,erato,petiverana,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10428972_V_lowres.png,10428972_V_lowres.png,mismatch
 10429172,erato,petiverana,male,,,
-10428595,erato,phyllis,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/dorsal_images/10428595_D_lowres.png,10428595_D_lowres.jpg,55882a0f3fdf8a68579c07254395653b
-10428140,melpomene,plesseni,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10428140_V_lowres.png,10428140_V_lowres.jpg,c11538f2de5a5e2d6013fc800848d43a
-10428250,melpomene,schunkei,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10428250_V_lowres.png,10428250_V_lowres.jpg,14ac99b1a9913a9d420f21b94d6136d6
+10428595,erato,phyllis,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/dorsal_images/10428595_D_lowres.png,10428595_D_lowres.png,55882a0f3fdf8a68579c07254395653b
+10428140,melpomene,plesseni,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10428140_V_lowres.png,10428140_V_lowres.png,c11538f2de5a5e2d6013fc800848d43a
+10428250,melpomene,schunkei,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10428250_V_lowres.png,10428250_V_lowres.png,14ac99b1a9913a9d420f21b94d6136d6
 10427979,melpomene,rosina_S,male,,,
-10428803,erato,guarica,female,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/dorsal_images/10428803_D_lowres.png,10428803_D_lowres.jpg,d8bfb73f2d3556390de04aa98822b815
-10428169,melpomene,plesseni,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10428169_V_lowres.png,10428169_V_lowres.jpg,042c9dc294d589ce3f140f14ddab0166
-10428321,melpomene,nanna,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/dorsal_images/10428321_D_lowres.png,10428321_D_lowres.jpg,fbeeed30274e424831b06360b587ceb3
+10428803,erato,guarica,female,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/dorsal_images/10428803_D_lowres.png,10428803_D_lowres.png,d8bfb73f2d3556390de04aa98822b815
+10428169,melpomene,plesseni,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/ventral_images/10428169_V_lowres.png,10428169_V_lowres.png,042c9dc294d589ce3f140f14ddab0166
+10428321,melpomene,nanna,male,https://github.com/Imageomics/dashboard-prototype/raw/main/test_data/images/dorsal_images/10428321_D_lowres.png,10428321_D_lowres.png,fbeeed30274e424831b06360b587ceb3

src/cautiousrobot/__about__.py

@@ -1 +1 @@
-__version__ = "1.0.0"
+__version__ = "1.1.0"