Code here written by Erica Krimmel. Please see Use Case: Download media based on specimen record search for context.

If you are running this code on your own computer, you may wish to create a new folder for the working directory and save this file to it. This code will create two new subdirectories and save media files to them.

# Load core libraries; install these packages if you have not already
library(ridigbio)
library(tidyverse)

# Load library for making nice HTML output
library(kableExtra)

Write a query to search for specimen records

First, you need to find all the media records for which you are interested in downloading media files. Do this using the idig_search_media function from the ridigbio package, which allows you to search for media records based on data contained in linked specimen records, like species or collecting locality. You can learn more about this function from the iDigBio API documentation and ridigbio documentation. In this example, we want to search for images of herbarium specimens of species in the genus Acer that were collected in the United States.

# Edit the fields (e.g. `genus`) and values (e.g. "manis") in `list()` 
# to adjust your query and the fields (e.g. `uuid`) in `fields` to adjust the
# columns returned in your results; edit the number after `limit` to adjust the
# number of records you will retrieve images for
records <- idig_search_media(rq = list(genus = "acer",
                                       country = "united states"), 
            fields = c("uuid",
                       "accessuri",
                       "rights",
                       "format",
                       "records"),
            limit = 10)

The result of the code above is a data frame called records:

uuid accessuri rights format records
00008f34-9a3a-4ecb-8477-17fad7c56441 https://bisque.cyverse.org/image_service/image/00-ogmgjEJqzTLFVgViaw3tZS?resize=4000&format=jpeg CC0 image/jpeg 96fa9d9a-7bb3-41d9-8ec8-110265d0b41c
0000b146-6fd2-4a6a-bf78-9e709cc995e9 http://mam.ansp.org/image/CM/Fullsize/345/CM345773.jpg CC0 image/jpeg 8af932f6-24c1-4c9c-9963-10b9b584b632
0000d1cd-8211-45c6-8dfa-bd4a9a001aad http://mam.ansp.org/image/TAWES/Fullsize/0005/TAWES0005954.jpg CC0 image/jpeg 0a18cad9-2e85-4ae1-8274-68274b058b61
00023a90-46a8-4af4-95ef-be5b8a63fc44 http://collections.nmnh.si.edu/media/index.php?irn=13725474 NA image/jpeg 7e3e7561-042e-4216-800a-7873fe7c9a2e
000277e9-659b-4e0c-a61b-c5262d33969b http://www.pnwherbaria.org/images/jpeg.php?Image=WTU-V-023351.jpg NA image/jpeg ac4d39f6-8775-48ea-b1d1-cd14c6f60e08
0003200a-261d-43d5-ae3e-ef39b6f5e2e9 https://bisque.cyverse.org/image_service/image/00-GUe6j3wkiqQDHA2Q8XFmD7/resize:4000/format:jpeg BY-NC image/jpeg 09157ffe-1a92-4f89-b90f-9c17c2f9dacc
000495be-df5c-4c01-a951-5656a3fe5ef5 http://bgbaseserver.eeb.uconn.edu/DATABASEIMAGES/CONN00075691.JPG BY-NC-SA image/jpeg 2642a89e-bcda-4c8c-8b20-3753b37ab990
00056e02-50b6-4c62-a975-306cc870dd83 http://www.mississippiplants.org/images/specimens/MISS0038464/MISS0038464.JPG BY-NC image/jpeg 04764068-999e-4902-b30b-4e1d0d23d214
00068ad5-816c-425e-8e81-8a2f808043e8 http://mam.ansp.org/image/PH/Fullsize/00436/PH00436926.jpg BY-NC image/jpeg 1ac7a558-1450-4ea4-941e-7aed2d95c768
00082dc9-d98d-4ced-84b8-3ba5d9d2368a https://bisque.cyverse.org/image_service/image/00-umMPpFdh5R2CtTUbESrMnJ/resize:4000/format:jpeg BY-NC image/jpeg 14ebb959-fdc2-4788-800b-296fdb6991f6

Generate a list of URLs to download media from

Now that we know what media records are of interest to us, we need to isolate the URLs that link to the actual media files so that we can download them. In this example, we will demonstrate how to download files that are cached on the iDigBio server, as well as the original files hosted externally by the data provider. You likely do not need to download two sets of images, so can choose to comment out the steps related to either "_iDigBio" or "_external" depending on your preference.

# Assemble a vector of iDigBio server download URLs from `records`
mediaurl_idigbio <- records %>% 
  mutate(mediaURL = paste("https://api.idigbio.org/v2/media/", uuid, sep = "")) %>% 
  select(mediaURL) %>% 
  pull()

# Assemble a vector of external server download URLs from `records`
mediaurl_external <- records$accessuri %>% 
  str_replace("\\?size=fullsize", "")

These vectors look like this:

mediaurl_idigbio
##  [1] "https://api.idigbio.org/v2/media/00008f34-9a3a-4ecb-8477-17fad7c56441"
##  [2] "https://api.idigbio.org/v2/media/0000b146-6fd2-4a6a-bf78-9e709cc995e9"
##  [3] "https://api.idigbio.org/v2/media/0000d1cd-8211-45c6-8dfa-bd4a9a001aad"
##  [4] "https://api.idigbio.org/v2/media/00023a90-46a8-4af4-95ef-be5b8a63fc44"
##  [5] "https://api.idigbio.org/v2/media/000277e9-659b-4e0c-a61b-c5262d33969b"
##  [6] "https://api.idigbio.org/v2/media/0003200a-261d-43d5-ae3e-ef39b6f5e2e9"
##  [7] "https://api.idigbio.org/v2/media/000495be-df5c-4c01-a951-5656a3fe5ef5"
##  [8] "https://api.idigbio.org/v2/media/00056e02-50b6-4c62-a975-306cc870dd83"
##  [9] "https://api.idigbio.org/v2/media/00068ad5-816c-425e-8e81-8a2f808043e8"
## [10] "https://api.idigbio.org/v2/media/00082dc9-d98d-4ced-84b8-3ba5d9d2368a"
mediaurl_external
##  [1] "https://bisque.cyverse.org/image_service/image/00-ogmgjEJqzTLFVgViaw3tZS?resize=4000&format=jpeg"
##  [2] "http://mam.ansp.org/image/CM/Fullsize/345/CM345773.jpg"                                          
##  [3] "http://mam.ansp.org/image/TAWES/Fullsize/0005/TAWES0005954.jpg"                                  
##  [4] "http://collections.nmnh.si.edu/media/index.php?irn=13725474"                                     
##  [5] "http://www.pnwherbaria.org/images/jpeg.php?Image=WTU-V-023351.jpg"                               
##  [6] "https://bisque.cyverse.org/image_service/image/00-GUe6j3wkiqQDHA2Q8XFmD7/resize:4000/format:jpeg"
##  [7] "http://bgbaseserver.eeb.uconn.edu/DATABASEIMAGES/CONN00075691.JPG"                               
##  [8] "http://www.mississippiplants.org/images/specimens/MISS0038464/MISS0038464.JPG"                   
##  [9] "http://mam.ansp.org/image/PH/Fullsize/00436/PH00436926.jpg"                                      
## [10] "https://bisque.cyverse.org/image_service/image/00-umMPpFdh5R2CtTUbESrMnJ/resize:4000/format:jpeg"

Download media

We can use the download URLs that we assembled in the step above to go and download each media file. For clarity, we will place files in two different folders, based on whether we downloaded them from the iDigBio server or an external server. We will name each file based on its unique identifier.

# Create new directories to save media files in
dir.create("jpgs_idigbio")
dir.create("jpgs_external")

# Assemble another vector of file paths to use when saving media downloaded 
# from iDigBio
mediapath_idigbio <- paste("jpgs_idigbio/", records$uuid, ".jpg", sep = "")

# Assemble another vector of file paths to use when saving media downloaded
# from external servers; please note that it's probably not a great idea to
# assume these files are all jpgs, as we're doing here...
mediapath_external <- paste("jpgs_external/", records$uuid, ".jpg", sep = "")

# Add a check to deal with URLs that are broken links
possibly_download.file = purrr::possibly(download.file, 
                                         otherwise = "cannot download")

# Iterate through the action of downloading whatever file is at each
# iDigBio URL
purrr::walk2(.x = mediaurl_idigbio,
             .y = mediapath_idigbio, possibly_download.file)

# Iterate through the action of downloading whatever file is at each
# external URL
purrr::walk2(.x = mediaurl_external,
             .y = mediapath_external, possibly_download.file)

You should now have two folders, each with ten images downloaded from iDigBio and external servers, respectively. Note that we only downloaded ten images here for brevity’s sake, but you can increase this using the limit argument in the first step. Here is an example of one of the images we downloaded: