Demystifying APIs for Researchers: Live-Coding

Playing around with the commonchemistry API

Author

Eric R. Scott

These are notes for the participatory live-coding portion of a workshop. Slides are here: https://cct-datascience.quarto.pub/demystifying-apis-slides/

library(httr2)
library(tidyverse) #used later on for wrangling results
── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
✔ dplyr     1.1.4     ✔ readr     2.1.4
✔ forcats   1.0.0     ✔ stringr   1.5.1
✔ ggplot2   3.4.4     ✔ tibble    3.2.1
✔ lubridate 1.9.3     ✔ tidyr     1.3.0
✔ purrr     1.0.2     
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors

Detail

Now let’s get more information with the /detail endpoint

Build the query

We can pass the registry number directly from our first query into this one.

req_detail <-
  request("https://commonchemistry.cas.org/api") |> 
  req_url_path_append("detail") |> 
  req_url_query(cas_rn = caffeine$rn)
req_detail
<httr2_request>
GET https://commonchemistry.cas.org/api/detail?cas_rn=58-08-2
Body: empty

Perform the request

resp_detail <-
  req_detail |> 
  req_perform()
resp_detail
<httr2_response>
GET https://commonchemistry.cas.org/api/detail?cas_rn=58-08-2
Status: 200 OK
Content-Type: application/json
Body: In memory (5523 bytes)

Get the results

caffeine_detail <- 
  resp_detail |>
  resp_body_json()
caffeine_detail
$uri
[1] "substance/pt/58082"

$rn
[1] "58-08-2"

$name
[1] "Caffeine"

$image
[1] "<svg width=\"199.89\" viewBox=\"0 0 6663 5080\" text-rendering=\"auto\" stroke-width=\"1\" stroke-opacity=\"1\" stroke-miterlimit=\"10\" stroke-linejoin=\"miter\" stroke-linecap=\"square\" stroke-dashoffset=\"0\" stroke-dasharray=\"none\" stroke=\"black\" shape-rendering=\"auto\" image-rendering=\"auto\" height=\"152.4\" font-weight=\"normal\" font-style=\"normal\" font-size=\"12\" font-family=\"'Dialog'\" fill-opacity=\"1\" fill=\"black\" color-rendering=\"auto\" color-interpolation=\"auto\" xmlns=\"http://www.w3.org/2000/svg\"><g><g stroke=\"white\" fill=\"white\"><rect y=\"0\" x=\"0\" width=\"6663\" stroke=\"none\" height=\"5080\"/></g><g transform=\"translate(32866,32758)\" text-rendering=\"geometricPrecision\" stroke-width=\"44\" stroke-linejoin=\"round\" stroke-linecap=\"round\"><line y2=\"-29668\" y1=\"-30807\" x2=\"-29642\" x1=\"-29642\" fill=\"none\"/><line y2=\"-29810\" y1=\"-30665\" x2=\"-29813\" x1=\"-29813\" fill=\"none\"/><line y2=\"-29099\" y1=\"-29668\" x2=\"-30625\" x1=\"-29642\" fill=\"none\"/><line y2=\"-29668\" y1=\"-29668\" x2=\"-29642\" x1=\"-27860\" fill=\"none\"/><line y2=\"-30807\" y1=\"-31266\" x2=\"-29642\" x1=\"-30437\" fill=\"none\"/><line y2=\"-31266\" y1=\"-30807\" x2=\"-28842\" x1=\"-29642\" fill=\"none\"/><line y2=\"-29562\" y1=\"-29099\" x2=\"-31425\" x1=\"-30625\" fill=\"none\"/><line y2=\"-29888\" y1=\"-30807\" x2=\"-27672\" x1=\"-27672\" fill=\"none\"/><line y2=\"-31266\" y1=\"-30807\" x2=\"-30815\" x1=\"-31613\" fill=\"none\"/><line y2=\"-30807\" y1=\"-31266\" x2=\"-27672\" x1=\"-28467\" fill=\"none\"/><line y2=\"-30717\" y1=\"-31061\" x2=\"-27857\" x1=\"-28452\" fill=\"none\"/><line y2=\"-30807\" y1=\"-29888\" x2=\"-31613\" x1=\"-31613\" fill=\"none\"/><line y2=\"-29117\" y1=\"-29481\" x2=\"-27120\" x1=\"-27484\" fill=\"none\"/><line y2=\"-32202\" y1=\"-31595\" x2=\"-30625\" x1=\"-30625\" fill=\"none\"/><line y2=\"-29313\" y1=\"-29562\" x2=\"-32231\" x1=\"-31800\" fill=\"none\"/><line y2=\"-28273\" y1=\"-29099\" x2=\"-30555\" x1=\"-30555\" fill=\"none\"/><line y2=\"-28273\" y1=\"-29099\" x2=\"-30697\" x1=\"-30697\" fill=\"none\"/><line y2=\"-31162\" y1=\"-30746\" x2=\"-32367\" x1=\"-31647\" fill=\"none\"/><line y2=\"-31283\" y1=\"-30867\" x2=\"-32297\" x1=\"-31578\" fill=\"none\"/><text y=\"-27874\" xml:space=\"preserve\" x=\"-30778\" stroke=\"none\" font-size=\"433.3333\" font-family=\"sans-serif\">O</text><text y=\"-28750\" xml:space=\"preserve\" x=\"-27083\" stroke=\"none\" font-size=\"433.3333\" font-family=\"sans-serif\">CH</text><text y=\"-28660\" xml:space=\"preserve\" x=\"-26505\" stroke=\"none\" font-size=\"313.3333\" font-family=\"sans-serif\">3</text><text y=\"-32242\" xml:space=\"preserve\" x=\"-30778\" stroke=\"none\" font-size=\"433.3333\" font-family=\"sans-serif\">CH</text><text y=\"-32153\" xml:space=\"preserve\" x=\"-30200\" stroke=\"none\" font-size=\"313.3333\" font-family=\"sans-serif\">3</text><text y=\"-28914\" xml:space=\"preserve\" x=\"-32762\" stroke=\"none\" font-size=\"433.3333\" font-family=\"sans-serif\">CH</text><text y=\"-28825\" xml:space=\"preserve\" x=\"-32185\" stroke=\"none\" font-size=\"313.3333\" font-family=\"sans-serif\">3</text><text y=\"-31150\" xml:space=\"preserve\" x=\"-32673\" stroke=\"none\" font-size=\"433.3333\" font-family=\"sans-serif\">O</text><text y=\"-29489\" xml:space=\"preserve\" x=\"-27822\" stroke=\"none\" font-size=\"433.3333\" font-family=\"sans-serif\">N</text><text y=\"-31197\" xml:space=\"preserve\" x=\"-30778\" stroke=\"none\" font-size=\"433.3333\" font-family=\"sans-serif\">N</text><text y=\"-31197\" xml:space=\"preserve\" x=\"-28808\" stroke=\"none\" font-size=\"433.3333\" font-family=\"sans-serif\">N</text><text y=\"-29489\" xml:space=\"preserve\" x=\"-31766\" stroke=\"none\" font-size=\"433.3333\" font-family=\"sans-serif\">N</text></g></g></svg>"

$inchi
[1] "InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3"

$inchiKey
[1] "InChIKey=RYYVLZVUVIJVGH-UHFFFAOYSA-N"

$smile
[1] "O=C1C2=C(N(C)C(=O)N1C)N=CN2C"

$canonicalSmile
[1] "O=C1C2=C(N=CN2C)N(C(=O)N1C)C"

$molecularFormula
[1] "C<sub>8</sub>H<sub>10</sub>N<sub>4</sub>O<sub>2</sub>"

$molecularMass
[1] "194.19"

$experimentalProperties
$experimentalProperties[[1]]
$experimentalProperties[[1]]$name
[1] "Melting Point"

$experimentalProperties[[1]]$property
[1] "238 °C"

$experimentalProperties[[1]]$sourceNumber
[1] 1


$experimentalProperties[[2]]
$experimentalProperties[[2]]$name
[1] "Density"

$experimentalProperties[[2]]$property
[1] "1.23 g/cm³ @ Temp: 18 °C"

$experimentalProperties[[2]]$sourceNumber
[1] 2



$propertyCitations
$propertyCitations[[1]]
$propertyCitations[[1]]$docUri
[1] ""

$propertyCitations[[1]]$sourceNumber
[1] 1

$propertyCitations[[1]]$source
[1] "International Chemical Safety Cards data were obtained from the National Institute for Occupational Safety and Health (US)"


$propertyCitations[[2]]
$propertyCitations[[2]]$docUri
[1] ""

$propertyCitations[[2]]$sourceNumber
[1] 2

$propertyCitations[[2]]$source
[1] "Hazardous Substances Data Bank data were obtained from the National Library of Medicine (US)"



$synonyms
$synonyms[[1]]
[1] "1<em>H</em>-Purine-2,6-dione, 3,7-dihydro-1,3,7-trimethyl-"

$synonyms[[2]]
[1] "Caffeine"

$synonyms[[3]]
[1] "3,7-Dihydro-1,3,7-trimethyl-1<em>H</em>-purine-2,6-dione"

$synonyms[[4]]
[1] "Guaranine"

$synonyms[[5]]
[1] "Methyltheobromine"

$synonyms[[6]]
[1] "No-Doz"

$synonyms[[7]]
[1] "Thein"

$synonyms[[8]]
[1] "Theine"

$synonyms[[9]]
[1] "1,3,7-Trimethyl-2,6-dioxopurine"

$synonyms[[10]]
[1] "1,3,7-Trimethylxanthine"

$synonyms[[11]]
[1] "Caffein"

$synonyms[[12]]
[1] "Cafipel"

$synonyms[[13]]
[1] "Alert-Pep"

$synonyms[[14]]
[1] "Koffein"

$synonyms[[15]]
[1] "Cafeina"

$synonyms[[16]]
[1] "Mateina"

$synonyms[[17]]
[1] "Refresh'n"

$synonyms[[18]]
[1] "Stim"

$synonyms[[19]]
[1] "Tri-Aqua"

$synonyms[[20]]
[1] "7-Methyltheophylline"

$synonyms[[21]]
[1] "Shape Plus"

$synonyms[[22]]
[1] "Caffedrine"

$synonyms[[23]]
[1] "Diurex"

$synonyms[[24]]
[1] "Stay Alert"

$synonyms[[25]]
[1] "Synalgos"

$synonyms[[26]]
[1] "Miudol"

$synonyms[[27]]
[1] "Wigraine"

$synonyms[[28]]
[1] "Dasin"

$synonyms[[29]]
[1] "Phensal"

$synonyms[[30]]
[1] "DHCplus"

$synonyms[[31]]
[1] "NSC 5036"

$synonyms[[32]]
[1] "Durvitan"

$synonyms[[33]]
[1] "Cafalgine"

$synonyms[[34]]
[1] "Midron extra"

$synonyms[[35]]
[1] "New Cetamol"

$synonyms[[36]]
[1] "Asia migrine"

$synonyms[[37]]
[1] "Palergot-C"

$synonyms[[38]]
[1] "Vivarin"

$synonyms[[39]]
[1] "1,3,7-Trimethyl-7<em>H</em>-purine-2,6-dione"

$synonyms[[40]]
[1] "1,3,7-Trimethyl-2,3,6,7-tetrahydro-1<em>H</em>-purine-2,6-dione"

$synonyms[[41]]
[1] "1,3,7-Trimethyl-3,7-dihydro-purine-2,6-dione"

$synonyms[[42]]
[1] "MeSH ID: D002110"


$replacedRns
$replacedRns[[1]]
[1] "95789-13-2"

$replacedRns[[2]]
[1] "71701-02-5"


$hasMolfile
[1] TRUE

Wrangle the results

Lists are hard to work with! Let’s try to turn this into a tibble.

as_tibble(caffeine_detail)
Error in `recycle_columns()`:
! Tibble columns must have compatible sizes.
• Size 2: Columns `experimentalProperties`, `propertyCitations`, and
  `replacedRns`.
• Size 42: Column `synonyms`.
ℹ Only values of size one are recycled.

The list isn’t a nice rectangle, so it can’t be easily converted into a tibble.

We can take subsets of the list where all elements are the same length and make those into data frames

One way to “drill down” into lists is with purrr::pluck()

caffeine_detail |> pluck("name")
[1] "Caffeine"
caffeine_detail |> pluck(1)
[1] "substance/pt/58082"
caffeine_detail |> pluck("experimentalProperties", 1, "property")
[1] "238 °C"

We can instead use purrr::keep() to supply a function to determine which elements to extract. For example, let’s take all the elements with length == 1 and turn those into a data frame.

caffeine_basics <- caffeine_detail |> 
  purrr::keep(\(x) length(x) == 1) |> 
  as_tibble()

This uses an anonymous function, \(x) length(x) == 1, which is saying “for list element x, is the length of x 1?”. keep() iterates like a for loop where x is representing caffeine_detail[[1]] through caffeine_detail[[15]].

Bonus

Now that we have a data frame, we can make a table with gt that displays the SVG data as an image of the molecule!

library(gt)
gt(caffeine_basics) |> 
  fmt_markdown(columns = c(image, molecularFormula)) #molecular formula was also HTML
uri rn name image inchi inchiKey smile canonicalSmile molecularFormula molecularMass hasMolfile
substance/pt/58082 58-08-2 Caffeine

OCH3CH3CH3ONNNN

InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3 InChIKey=RYYVLZVUVIJVGH-UHFFFAOYSA-N O=C1C2=C(N(C)C(=O)N1C)N=CN2C O=C1C2=C(N=CN2C)N(C(=O)N1C)C

C8H10N4O2

 194.19 TRUE

Nice! This isn’t a gt workshop, but there is a lot you can do with gt to make publication quality tables.

Iterating

The true power of accessing APIs programatically is that we can iterate! For example, we can take a list of chemicals, search for the registry number for all of them, get the results for all of them, and turn it into a single output table.

Important

Many APIs have a rate limit that limits how quickly you can make requests (e.g. 10 per minute). Sometimes this rate limit is documented on the API website, sometimes you’ll just get errors if you make too many requests (surprise!). Slow down your requests with req_throttle().

chemical_names <- c("caffeine", "vanillin", "bergamotene") #vanilla earl grey anyone?

All queries will start like this

req_search_base <-
  request("https://commonchemistry.cas.org/api") |> 
  req_url_path_append("search")

Then we want to generate queries for each of the chemicals by plugging the elements of chemical_names into req_url_query(q = <chemical_name>). We can do that with map() from the purr package. The first argument is the thing to iterate over—chemical_names in our case. The second argument is a function to perform. Here I’ve again used R’s “shortcut” for creating an anonymous function: \(arg_name) do_things_to(arg_name)

req_list <- 
  map(chemical_names, \(x) req_search_base |> req_url_query(q = x))
req_list
[[1]]
<httr2_request>
GET https://commonchemistry.cas.org/api/search?q=caffeine
Body: empty

[[2]]
<httr2_request>
GET https://commonchemistry.cas.org/api/search?q=vanillin
Body: empty

[[3]]
<httr2_request>
GET https://commonchemistry.cas.org/api/search?q=bergamotene
Body: empty

So now we have a list of three queries. We can use map() again to perform all of them. This time, we don’t even need the anonymous function because req_perform() just takes the request as it’s first unnamed argument.

resp_list <- map(req_list, req_perform)
resp_list
[[1]]
<httr2_response>
GET https://commonchemistry.cas.org/api/search?q=caffeine
Status: 200 OK
Content-Type: application/json
Body: In memory (3893 bytes)

[[2]]
<httr2_response>
GET https://commonchemistry.cas.org/api/search?q=vanillin
Status: 200 OK
Content-Type: application/json
Body: In memory (2682 bytes)

[[3]]
<httr2_response>
GET https://commonchemistry.cas.org/api/search?q=bergamotene
Status: 200 OK
Content-Type: application/json
Body: In memory (2270 bytes)

And again, we can use map to extract all the results

map(resp_list, resp_body_json)
[[1]]
[[1]]$count
[1] 1

[[1]]$results
[[1]]$results[[1]]
[[1]]$results[[1]]$rn
[1] "58-08-2"

[[1]]$results[[1]]$name
[1] "Caffeine"

[[1]]$results[[1]]$image
[1] "<svg width=\"199.89\" viewBox=\"0 0 6663 5080\" text-rendering=\"auto\" stroke-width=\"1\" stroke-opacity=\"1\" stroke-miterlimit=\"10\" stroke-linejoin=\"miter\" stroke-linecap=\"square\" stroke-dashoffset=\"0\" stroke-dasharray=\"none\" stroke=\"black\" shape-rendering=\"auto\" image-rendering=\"auto\" height=\"152.4\" font-weight=\"normal\" font-style=\"normal\" font-size=\"12\" font-family=\"'Dialog'\" fill-opacity=\"1\" fill=\"black\" color-rendering=\"auto\" color-interpolation=\"auto\" xmlns=\"http://www.w3.org/2000/svg\"><g><g stroke=\"white\" fill=\"white\"><rect y=\"0\" x=\"0\" width=\"6663\" stroke=\"none\" height=\"5080\"/></g><g transform=\"translate(32866,32758)\" text-rendering=\"geometricPrecision\" stroke-width=\"44\" stroke-linejoin=\"round\" stroke-linecap=\"round\"><line y2=\"-29668\" y1=\"-30807\" x2=\"-29642\" x1=\"-29642\" fill=\"none\"/><line y2=\"-29810\" y1=\"-30665\" x2=\"-29813\" x1=\"-29813\" fill=\"none\"/><line y2=\"-29099\" y1=\"-29668\" x2=\"-30625\" x1=\"-29642\" fill=\"none\"/><line y2=\"-29668\" y1=\"-29668\" x2=\"-29642\" x1=\"-27860\" fill=\"none\"/><line y2=\"-30807\" y1=\"-31266\" x2=\"-29642\" x1=\"-30437\" fill=\"none\"/><line y2=\"-31266\" y1=\"-30807\" x2=\"-28842\" x1=\"-29642\" fill=\"none\"/><line y2=\"-29562\" y1=\"-29099\" x2=\"-31425\" x1=\"-30625\" fill=\"none\"/><line y2=\"-29888\" y1=\"-30807\" x2=\"-27672\" x1=\"-27672\" fill=\"none\"/><line y2=\"-31266\" y1=\"-30807\" x2=\"-30815\" x1=\"-31613\" fill=\"none\"/><line y2=\"-30807\" y1=\"-31266\" x2=\"-27672\" x1=\"-28467\" fill=\"none\"/><line y2=\"-30717\" y1=\"-31061\" x2=\"-27857\" x1=\"-28452\" fill=\"none\"/><line y2=\"-30807\" y1=\"-29888\" x2=\"-31613\" x1=\"-31613\" fill=\"none\"/><line y2=\"-29117\" y1=\"-29481\" x2=\"-27120\" x1=\"-27484\" fill=\"none\"/><line y2=\"-32202\" y1=\"-31595\" x2=\"-30625\" x1=\"-30625\" fill=\"none\"/><line y2=\"-29313\" y1=\"-29562\" x2=\"-32231\" x1=\"-31800\" fill=\"none\"/><line y2=\"-28273\" y1=\"-29099\" x2=\"-30555\" x1=\"-30555\" fill=\"none\"/><line y2=\"-28273\" y1=\"-29099\" x2=\"-30697\" x1=\"-30697\" fill=\"none\"/><line y2=\"-31162\" y1=\"-30746\" x2=\"-32367\" x1=\"-31647\" fill=\"none\"/><line y2=\"-31283\" y1=\"-30867\" x2=\"-32297\" x1=\"-31578\" fill=\"none\"/><text y=\"-27874\" xml:space=\"preserve\" x=\"-30778\" stroke=\"none\" font-size=\"433.3333\" font-family=\"sans-serif\">O</text><text y=\"-28750\" xml:space=\"preserve\" x=\"-27083\" stroke=\"none\" font-size=\"433.3333\" font-family=\"sans-serif\">CH</text><text y=\"-28660\" xml:space=\"preserve\" x=\"-26505\" stroke=\"none\" font-size=\"313.3333\" font-family=\"sans-serif\">3</text><text y=\"-32242\" xml:space=\"preserve\" x=\"-30778\" stroke=\"none\" font-size=\"433.3333\" font-family=\"sans-serif\">CH</text><text y=\"-32153\" xml:space=\"preserve\" x=\"-30200\" stroke=\"none\" font-size=\"313.3333\" font-family=\"sans-serif\">3</text><text y=\"-28914\" xml:space=\"preserve\" x=\"-32762\" stroke=\"none\" font-size=\"433.3333\" font-family=\"sans-serif\">CH</text><text y=\"-28825\" xml:space=\"preserve\" x=\"-32185\" stroke=\"none\" font-size=\"313.3333\" font-family=\"sans-serif\">3</text><text y=\"-31150\" xml:space=\"preserve\" x=\"-32673\" stroke=\"none\" font-size=\"433.3333\" font-family=\"sans-serif\">O</text><text y=\"-29489\" xml:space=\"preserve\" x=\"-27822\" stroke=\"none\" font-size=\"433.3333\" font-family=\"sans-serif\">N</text><text y=\"-31197\" xml:space=\"preserve\" x=\"-30778\" stroke=\"none\" font-size=\"433.3333\" font-family=\"sans-serif\">N</text><text y=\"-31197\" xml:space=\"preserve\" x=\"-28808\" stroke=\"none\" font-size=\"433.3333\" font-family=\"sans-serif\">N</text><text y=\"-29489\" xml:space=\"preserve\" x=\"-31766\" stroke=\"none\" font-size=\"433.3333\" font-family=\"sans-serif\">N</text></g></g></svg>"




[[2]]
[[2]]$count
[1] 1

[[2]]$results
[[2]]$results[[1]]
[[2]]$results[[1]]$rn
[1] "121-33-5"

[[2]]$results[[1]]$name
[1] "Vanillin"

[[2]]$results[[1]]$image
[1] "<svg width=\"186.99\" viewBox=\"0 0 6233 2898\" text-rendering=\"auto\" stroke-width=\"1\" stroke-opacity=\"1\" stroke-miterlimit=\"10\" stroke-linejoin=\"miter\" stroke-linecap=\"square\" stroke-dashoffset=\"0\" stroke-dasharray=\"none\" stroke=\"black\" shape-rendering=\"auto\" image-rendering=\"auto\" height=\"86.94\" font-weight=\"normal\" font-style=\"normal\" font-size=\"12\" font-family=\"'Dialog'\" fill-opacity=\"1\" fill=\"black\" color-rendering=\"auto\" color-interpolation=\"auto\" xmlns=\"http://www.w3.org/2000/svg\"><g><g stroke=\"white\" fill=\"white\"><rect y=\"0\" x=\"0\" width=\"6233\" stroke=\"none\" height=\"2898\"/></g><g transform=\"translate(32866,32758)\" text-rendering=\"geometricPrecision\" stroke-width=\"44\" stroke-linejoin=\"round\" stroke-linecap=\"round\"><line y2=\"-32465\" y1=\"-31896\" x2=\"-29720\" x1=\"-30706\" fill=\"none\"/><line y2=\"-32245\" y1=\"-31821\" x2=\"-29758\" x1=\"-30498\" fill=\"none\"/><line y2=\"-31896\" y1=\"-30758\" x2=\"-30706\" x1=\"-30706\" fill=\"none\"/><line y2=\"-31896\" y1=\"-32465\" x2=\"-28735\" x1=\"-29720\" fill=\"none\"/><line y2=\"-30758\" y1=\"-30191\" x2=\"-30706\" x1=\"-29720\" fill=\"none\"/><line y2=\"-30836\" y1=\"-30408\" x2=\"-30498\" x1=\"-29758\" fill=\"none\"/><line y2=\"-30758\" y1=\"-31896\" x2=\"-28735\" x1=\"-28735\" fill=\"none\"/><line y2=\"-30902\" y1=\"-31754\" x2=\"-28906\" x1=\"-28906\" fill=\"none\"/><line y2=\"-30191\" y1=\"-30758\" x2=\"-29720\" x1=\"-28735\" fill=\"none\"/><line y2=\"-32422\" y1=\"-31896\" x2=\"-27828\" x1=\"-28735\" fill=\"none\"/><line y2=\"-32006\" y1=\"-32422\" x2=\"-27109\" x1=\"-27828\" fill=\"none\"/><line y2=\"-31936\" y1=\"-32248\" x2=\"-27268\" x1=\"-27808\" fill=\"none\"/><line y2=\"-32312\" y1=\"-31896\" x2=\"-31425\" x1=\"-30706\" fill=\"none\"/><line y2=\"-32063\" y1=\"-32312\" x2=\"-32231\" x1=\"-31800\" fill=\"none\"/><line y2=\"-30454\" y1=\"-30758\" x2=\"-31234\" x1=\"-30706\" fill=\"none\"/><text y=\"-32242\" xml:space=\"preserve\" x=\"-31766\" stroke=\"none\" font-size=\"433.3333\" font-family=\"sans-serif\">O</text><text y=\"-31665\" xml:space=\"preserve\" x=\"-32762\" stroke=\"none\" font-size=\"433.3333\" font-family=\"sans-serif\">CH</text><text y=\"-31575\" xml:space=\"preserve\" x=\"-32185\" stroke=\"none\" font-size=\"313.3333\" font-family=\"sans-serif\">3</text><text y=\"-30056\" xml:space=\"preserve\" x=\"-31766\" stroke=\"none\" font-size=\"433.3333\" font-family=\"sans-serif\">OH</text><text y=\"-31717\" xml:space=\"preserve\" x=\"-27074\" stroke=\"none\" font-size=\"433.3333\" font-family=\"sans-serif\">O</text></g></g></svg>"




[[3]]
[[3]]$count
[1] 1

[[3]]$results
[[3]]$results[[1]]
[[3]]$results[[1]]$rn
[1] "6895-56-3"

[[3]]$results[[1]]$name
[1] "Bergamotene"

[[3]]$results[[1]]$image
[1] "<svg width=\"230.52\" viewBox=\"0 0 7684 2975\" text-rendering=\"auto\" stroke-width=\"1\" stroke-opacity=\"1\" stroke-miterlimit=\"10\" stroke-linejoin=\"miter\" stroke-linecap=\"square\" stroke-dashoffset=\"0\" stroke-dasharray=\"none\" stroke=\"black\" shape-rendering=\"auto\" image-rendering=\"auto\" height=\"89.25\" font-weight=\"normal\" font-style=\"normal\" font-size=\"12\" font-family=\"'Dialog'\" fill-opacity=\"1\" fill=\"black\" color-rendering=\"auto\" color-interpolation=\"auto\" xmlns=\"http://www.w3.org/2000/svg\"><g><g stroke=\"white\" fill=\"white\"><rect y=\"0\" x=\"0\" width=\"7684\" stroke=\"none\" height=\"2975\"/></g><g transform=\"translate(32866,32866)\" text-rendering=\"geometricPrecision\" stroke-width=\"44\" stroke-linejoin=\"round\" stroke-linecap=\"round\"><line y2=\"-32289\" y1=\"-31714\" x2=\"-27245\" x1=\"-28227\" fill=\"none\"/><line y2=\"-31142\" y1=\"-32289\" x2=\"-27245\" x1=\"-27245\" fill=\"none\"/><line y2=\"-31714\" y1=\"-32289\" x2=\"-26262\" x1=\"-27245\" fill=\"none\"/><line y2=\"-31714\" y1=\"-30570\" x2=\"-28227\" x1=\"-28227\" fill=\"none\"/><line y2=\"-30570\" y1=\"-31142\" x2=\"-28227\" x1=\"-27245\" fill=\"none\"/><line y2=\"-30570\" y1=\"-31714\" x2=\"-26262\" x1=\"-26262\" fill=\"none\"/><line y2=\"-30570\" y1=\"-29995\" x2=\"-28227\" x1=\"-27245\" fill=\"none\"/><line y2=\"-29995\" y1=\"-30570\" x2=\"-27245\" x1=\"-26262\" fill=\"none\"/><line y2=\"-32240\" y1=\"-31714\" x2=\"-29134\" x1=\"-28227\" fill=\"none\"/><line y2=\"-31714\" y1=\"-32240\" x2=\"-30041\" x1=\"-29134\" fill=\"none\"/><line y2=\"-32240\" y1=\"-31714\" x2=\"-30948\" x1=\"-30041\" fill=\"none\"/><line y2=\"-31714\" y1=\"-32240\" x2=\"-31855\" x1=\"-30948\" fill=\"none\"/><line y2=\"-31659\" y1=\"-32052\" x2=\"-31673\" x1=\"-30992\" fill=\"none\"/><line y2=\"-32762\" y1=\"-31714\" x2=\"-28227\" x1=\"-28227\" fill=\"none\"/><line y2=\"-32240\" y1=\"-31714\" x2=\"-25355\" x1=\"-26262\" fill=\"none\"/><line y2=\"-32118\" y1=\"-31595\" x2=\"-25286\" x1=\"-26193\" fill=\"none\"/><line y2=\"-32240\" y1=\"-31714\" x2=\"-32762\" x1=\"-31855\" fill=\"none\"/><line y2=\"-30668\" y1=\"-31714\" x2=\"-31855\" x1=\"-31855\" fill=\"none\"/></g></g></svg>"

Now here it’s gotten a little complicated because we now have a list of lists. So instead of just map()ing resp_body_json(), let’s do some data extraction inside of map(). It’s usually easiest to figure out how to do this by first testing it out on just a single element.

resp_list[[1]] |> 
  resp_body_json() |> 
  pluck("results", 1) |> #equivalent to x[[results]][[1]]
  as_tibble()
# A tibble: 1 × 3
  rn      name     image                                                        
  <chr>   <chr>    <chr>                                                        
1 58-08-2 Caffeine "<svg width=\"199.89\" viewBox=\"0 0 6663 5080\" text-render…

Then we can put this code inside an anonymous function \(x) and replace resp_list[[1]] with x

df_list <- map(resp_list, \(x) {
  x |> 
    resp_body_json() |> 
    pluck("results", 1) |> #equivalent to x[[results]][[1]]
    as_tibble()
})

Now we have a list of tibbles that we can combine with list_rbind()

search_results <- list_rbind(df_list)
search_results
# A tibble: 3 × 3
  rn        name        image                                                   
  <chr>     <chr>       <chr>                                                   
1 58-08-2   Caffeine    "<svg width=\"199.89\" viewBox=\"0 0 6663 5080\" text-r…
2 121-33-5  Vanillin    "<svg width=\"186.99\" viewBox=\"0 0 6233 2898\" text-r…
3 6895-56-3 Bergamotene "<svg width=\"230.52\" viewBox=\"0 0 7684 2975\" text-r…
Bonus

We can do the cool gt thing with multiple rows now

gt(search_results) |> 
  fmt_markdown(columns = image)
rn name image
58-08-2 Caffeine

OCH3CH3CH3ONNNN

121-33-5 Vanillin

OCH3OHO

6895-56-3 Bergamotene

Try it on your own!

As an exercise, use the three CAS registry numbers in search_results to search the detail/ endpoint and make a table of chemical representations (InChI, InChIKey, SMILES, and canonical SMILES) for each molecule.