CODEWITHSUNDEEP
rpostgethttr
ava
ava

Reputation: 996

how to write a correct request (httr::GET or httr::POST)

I would like to extract the links listed under "Information" on a webpage using R. The data is publicly available and scraping is not prohibitet.

With an empty search on https://fsca.swissmedic.ch/mep/#/ and >export results I get a CSV. However, this CSV does not include what I need (links under "Information"). I thought that I could use this CSV (with unique identifiers, e.g., Vk_20220224_16) to programmatically open the pages separately (e.g., https://fsca.swissmedic.ch/mep/#/?q=Vk_20220224_16) and then extract these links (with a function using html_attr("href") etc.).

Unfortunately, I fail to get the content of the separate pages. I get an error message (400 Bad Request) when I use httr:GET(url).

I think I get this error message because my request does not include all parameter that the server needs. Is there a way to check which parameter are needed so that the server understands my request?

Example:

#library
library(httr)

# read html
html <- GET("https://fsca.swissmedic.ch/mep/#/?q=Vk_20220224_16")
html
#> Response [https://fsca.swissmedic.ch/mep/#/?q=Vk_20220224_16]
#>   Date: 2022-12-22 23:13
#>   Status: 400
#>   Content-Type: text/html; charset=iso-8859-1
#>   Size: 347 B
#> <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
#> <html><head>
#> <title>400 Bad Request</title>
#> </head><body>
#> <h1>Bad Request</h1>
#> <p>Your browser sent a request that this server could not understand.<br />
#> </p>
#> <p>Additionally, a 400 Bad Request
#> error was encountered while trying to use an ErrorDocument to handle the requ...
#> </body></html>

Created on 2022-12-23 with reprex v2.0.2

Update

I just learned that I can check the parameter needed using firefox: enter image description here

So I tried using httr::POST but I still do not get the page content/table, I only get "Loading..."

#library
library(httr)
library(jsonlite)
library(rvest)


# set parameter
body <- list(
  queryTerm="Vk_20220224_16",
  fromDate="",
  toDate="")

# POST
res <- POST(
       "https://fsca.swissmedic.ch/",
       body = jsonlite::toJSON(body),
       encode = "form",
       verbose()
       )

# get results
read_html(res)
#> {html_document}
#> <html>
#> [1] <head>\n<meta http-equiv="Content-Type" content="text/html; charset=UTF-8 ...
#> [2] <body>\n<mep-app>Loading...</mep-app><script type="text/javascript" src=" ...

Created on 2022-12-23 with reprex v2.0.2

Upvotes: 0

Views: 252

Answers (1)

HoelR
HoelR

Reputation: 6563

How to request with httr2

library(httr2)
library(tidyverse)

"https://fsca.swissmedic.ch/mep/api/publications/search?pageNumber=0&sortingProperty=PUBLICATION_DATE&direction=DESC" %>%
  request() %>%
  req_body_json(
    list(
      fromDate = "2022-12-04",
      toDate = "2022-12-20",
      queryTerm = NULL,
      onlyUpdates = "false"
    )
  ) %>%
  req_perform() %>%
  resp_body_json(simplifyVector = T) %>%
  pluck("content") %>%
  as_tibble()

# A tibble: 37 × 9
   publikationsDatum swissmedicRef  hersteller                status status…¹ begru…² devices freig…³ docum…⁴
   <chr>             <chr>          <chr>                     <chr>  <chr>    <chr>   <list>  <lgl>   <list> 
 1 2022-12-07        Vk_20221202_03 Medtronic CoreValve LLC   UPDATE 2022-12… "Added… <df>    TRUE    <df>   
 2 2022-12-20        Vk_20221216_12 Biocartis NV              UPDATE 2022-12… "Added… <df>    TRUE    <df>   
 3 2022-12-20        Vk_20221219_01 Siemens Healthcare GmbH   FIRST  2022-12… ""      <df>    TRUE    <df>   
 4 2022-12-20        Vk_20221216_19 Medicvent AB              FIRST  2022-12… ""      <df>    TRUE    <df>   
 5 2022-12-20        Vk_20221213_25 Macopharma                FIRST  2022-12… ""      <df>    TRUE    <df>   
 6 2022-12-20        Vk_20221208_26 Spiegelberg GmbH & Co. KG FIRST  2022-12… ""      <df>    TRUE    <df>   
 7 2022-12-06        Vk_20221201_21 Fujifilm Corporation      UPDATE 2022-12… "Rewor… <df>    TRUE    <df>   
 8 2022-12-20        Vk_20221216_15 Maquet Critical Care AB   FIRST  2022-12… ""      <df>    TRUE    <df>   
 9 2022-12-20        Vk_20221216_17 Siemens Healthcare GmbH   FIRST  2022-12… ""      <df>    TRUE    <df>   
10 2022-12-20        Vk_20221215_03 custo med GmbH            FIRST  2022-12… ""      <df>    TRUE    <df>   
# … with 27 more rows, and abbreviated variable names ¹​statusDatum, ²​begruendung, ³​freigeschaltet,
#   ⁴​documents
# ℹ Use `print(n = ...)` to see more rows

With search parameter

"https://fsca.swissmedic.ch/mep/api/publications/search?pageNumber=0&sortingProperty=PUBLICATION_DATE&direction=DESC" %>%
  request() %>%
  req_body_json(list(
    fromDate = NULL,
    toDate = NULL,
    queryTerm = "Vk_20220224_16",
    onlyUpdates = "false"
  )) %>%
  req_perform() %>%
  resp_body_json(simplifyVector = TRUE) %>%
  pluck("content") %>%
  as_tibble() %>%
  unnest(everything()) 

# A tibble: 3 × 16
  publikatio…¹ swiss…² herst…³ status statu…⁴ begru…⁵ hande…⁶ sn    lot   swVer…⁷ model besch…⁸ freig…⁹ title
  <chr>        <chr>   <chr>   <chr>  <chr>   <chr>   <chr>   <chr> <chr> <chr>   <chr> <chr>   <lgl>   <chr>
1 2022-03-07   Vk_202… Siemen… FIRST  2022-0… ""      Artis … ""    ""    ""      ""    MD: St… TRUE    DE-1 
2 2022-03-07   Vk_202… Siemen… FIRST  2022-0… ""      Artis Q ""    ""    ""      ""    MD: St… TRUE    FR-1 
3 2022-03-07   Vk_202… Siemen… FIRST  2022-0… ""      Artis … ""    ""    ""      ""    MD: St… TRUE    IT-1 
# … with 2 more variables: language <chr>, version <chr>, and abbreviated variable names ¹​publikationsDatum,
#   ²​swissmedicRef, ³​hersteller, ⁴​statusDatum, ⁵​begruendung, ⁶​handelsname, ⁷​swVersion, ⁸​beschreibungKlasse,
#   ⁹​freigeschaltet
# ℹ Use `colnames()` to see all variable names

Download links of the documents, which can be looped/mapped to auto download:

str_c("https://fsca.swissmedic.ch/mep/api/publications/", "Vk_20220224_16", 
      "/documents/", 0:(number_of_documents - 1))  

[1] "https://fsca.swissmedic.ch/mep/api/publications/Vk_20220224_16/documents/0"
[2] "https://fsca.swissmedic.ch/mep/api/publications/Vk_20220224_16/documents/1"
[3] "https://fsca.swissmedic.ch/mep/api/publications/Vk_20220224_16/documents/2"

Upvotes: 1

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