[R] web scraping tables generated in multiple server pages
boB Rudis
bob at rudis.net
Wed May 11 20:26:55 CEST 2016
I upgraded ffox to the 46-series and intermittently received the same
error. But by adding a `Sys.sleep(1)` to the final `if`:
if ((i %% 10) == 0) {
ref <- remDr$findElements("xpath", ".//a[.='...']")
ref[[length(ref)]]$clickElement()
Sys.sleep(1)
}
I was able to reproduce my original, successful outcome. I think it
has something to do with the page not being fully loaded when the the
driver tries to get the page content. Go multithreading! My choice of
1s was arbitrary. Longer == better chance of it working more often.
This <http://stackoverflow.com/questions/27080920/how-to-check-if-page-finished-loading-in-rselenium>
would probably also be better (waiting for a full page load signal),
but I try to not use [R]Selenium at all if it can be helped.
-Bob
On Wed, May 11, 2016 at 2:00 PM, boB Rudis <bob at rudis.net> wrote:
> Hey David,
>
> I'm on a Mac as well but have never had to tweak anything to get
> [R]Selenium to work (but this is one reason I try to avoid solutions
> involving RSelenium as they are pretty fragile IMO).
>
> The site itself has "Página 1 de 69" at the top which is where i got
> the "69" from and I just re-ran the code in a 100% clean env (on a
> completely different Mac) and it worked fine.
>
> I did neglect to put my session info up before (apologies):
>
> Session info
> ------------------------------------------------------------------------------------
> setting value
> version R version 3.3.0 RC (2016-05-01 r70572)
> system x86_64, darwin13.4.0
> ui RStudio (0.99.1172)
> language (EN)
> collate en_US.UTF-8
> tz America/New_York
> date 2016-05-11
>
> Packages ----------------------------------------------------------------------------------------
> package * version date source
> assertthat 0.1 2013-12-06 CRAN (R 3.3.0)
> bitops * 1.0-6 2013-08-17 CRAN (R 3.3.0)
> caTools 1.17.1 2014-09-10 CRAN (R 3.3.0)
> DBI 0.4 2016-05-02 CRAN (R 3.3.0)
> devtools * 1.11.1 2016-04-21 CRAN (R 3.3.0)
> digest 0.6.9 2016-01-08 CRAN (R 3.3.0)
> dplyr * 0.4.3 2015-09-01 CRAN (R 3.3.0)
> httr 1.1.0 2016-01-28 CRAN (R 3.3.0)
> magrittr 1.5 2014-11-22 CRAN (R 3.3.0)
> memoise 1.0.0 2016-01-29 CRAN (R 3.3.0)
> pbapply * 1.2-1 2016-04-19 CRAN (R 3.3.0)
> R6 2.1.2 2016-01-26 CRAN (R 3.3.0)
> Rcpp 0.12.4 2016-03-26 CRAN (R 3.3.0)
> RCurl * 1.95-4.8 2016-03-01 CRAN (R 3.3.0)
> RJSONIO * 1.3-0 2014-07-28 CRAN (R 3.3.0)
> RSelenium * 1.3.5 2014-10-26 CRAN (R 3.3.0)
> rvest * 0.3.1 2015-11-11 CRAN (R 3.3.0)
> selectr 0.2-3 2014-12-24 CRAN (R 3.3.0)
> stringi 1.0-1 2015-10-22 CRAN (R 3.3.0)
> stringr 1.0.0 2015-04-30 CRAN (R 3.3.0)
> withr 1.0.1 2016-02-04 CRAN (R 3.3.0)
> XML * 3.98-1.4 2016-03-01 CRAN (R 3.3.0)
> xml2 * 0.1.2 2015-09-01 CRAN (R 3.3.0)
>
> (and, wow, does that tiny snippet of code end up using alot of pkgs)
>
> I had actually started with smaller snippets to test. The code got
> uglier due to the way the site paginates (it loads 10-entries worth of
> data on to a single page but requires a server call for the next 10).
>
> I also keep firefox scarily out-of-date (back in the 33's rev) b/c I
> only use it with RSelenium (not a big fan of the browser). Let me
> update to the 46-series and see if I can replicate.
>
> -Bob
>
> On Wed, May 11, 2016 at 1:48 PM, David Winsemius <dwinsemius at comcast.net> wrote:
>>
>>> On May 10, 2016, at 1:11 PM, boB Rudis <bob at rudis.net> wrote:
>>>
>>> Unfortunately, it's a wretched, vile, SharePoint-based site. That
>>> means it doesn't use traditional encoding methods to do the pagination
>>> and one of the only ways to do this effectively is going to be to use
>>> RSelenium:
>>>
>>> library(RSelenium)
>>> library(rvest)
>>> library(dplyr)
>>> library(pbapply)
>>>
>>> URL <- "http://outorgaonerosa.prefeitura.sp.gov.br/relatorios/RelSituacaoGeralProcessos.aspx"
>>>
>>> checkForServer()
>>> startServer()
>>> remDr <- remoteDriver$new()
>>> remDr$open()
>>
>> Thanks Bob/hrbrmstr;
>>
>> At this point I got an error:
>>
>>> startServer()
>>> remDr <- remoteDriver$new()
>>> remDr$open()
>> [1] "Connecting to remote server"
>> Undefined error in RCurl call.Error in queryRD(paste0(serverURL, "/session"), "POST", qdata = toJSON(serverOpts)) :
>>
>> Running R 3.0.0 on a Mac (El Cap) in the R.app GUI.
>> $ java -version
>> java version "1.8.0_65"
>> Java(TM) SE Runtime Environment (build 1.8.0_65-b17)
>> Java HotSpot(TM) 64-Bit Server VM (build 25.65-b01, mixed mode)
>>
>> I asked myself: What additional information is needed to debug this? But then I thought I had a responsibility to search for earlier reports of this error on a Mac, and there were many. After reading this thread: https://github.com/ropensci/RSelenium/issues/54 I decided to try creating an "alias", mac-speak for a symlink, and put that symlink in my working directory (with no further chmod security efforts). I restarted R and re-ran the code which opened a Firefox browser window and then proceeded to page through many pages. Eventually, however it errors out with this message:
>>
>>> pblapply(1:69, function(i) {
>> +
>> + if (i %in% seq(1, 69, 10)) {
>> + pg <- read_html(remDr$getPageSource()[[1]])
>> + ret <- html_table(html_nodes(pg, "table")[[3]], header=TRUE)
>> +
>> + } else {
>> + ref <- remDr$findElements("xpath",
>> + sprintf(".//a[contains(@href, 'javascript:__doPostBack') and .='%s']",
>> + i))
>> + ref[[1]]$clickElement()
>> + pg <- read_html(remDr$getPageSource()[[1]])
>> + ret <- html_table(html_nodes(pg, "table")[[3]], header=TRUE)
>> +
>> + }
>> + if ((i %% 10) == 0) {
>> + ref <- remDr$findElements("xpath", ".//a[.='...']")
>> + ref[[length(ref)]]$clickElement()
>> + }
>> +
>> + ret
>> +
>> + }) -> tabs
>> |+++++++++++ | 22% ~54s Error in html_nodes(pg, "table")[[3]] : subscript out of bounds
>>>
>>> final_dat <- bind_rows(tabs)
>> Error in bind_rows(tabs) : object 'tabs' not found
>>
>>
>> There doesn't seem to be any trace of objects from all the downloading efforts that I could find. When I changed both instances of '69' to '30' it no longer errors out. Is there supposed to be an initial step of finding out how many pages are actually there befor setting the two iteration limits? I'm wondering if that code could be modified to return some intermediate values that would be amenable to further assembly efforts in the event of errors?
>>
>> Sincerely;
>> David.
>>
>>
>>> remDr$navigate(URL)
>>>
>>> pblapply(1:69, function(i) {
>>>
>>> if (i %in% seq(1, 69, 10)) {
>>>
>>> # the first item on the page is not a link but we can just grab the page
>>>
>>> pg <- read_html(remDr$getPageSource()[[1]])
>>> ret <- html_table(html_nodes(pg, "table")[[3]], header=TRUE)
>>>
>>> } else {
>>>
>>> # we can get the rest of them by the link text directly
>>>
>>> ref <- remDr$findElements("xpath",
>>> sprintf(".//a[contains(@href, 'javascript:__doPostBack') and .='%s']",
>>> i))
>>> ref[[1]]$clickElement()
>>> pg <- read_html(remDr$getPageSource()[[1]])
>>> ret <- html_table(html_nodes(pg, "table")[[3]], header=TRUE)
>>>
>>> }
>>>
>>> # we have to move to the next actual page of data after every 10 links
>>>
>>> if ((i %% 10) == 0) {
>>> ref <- remDr$findElements("xpath", ".//a[.='...']")
>>> ref[[length(ref)]]$clickElement()
>>> }
>>>
>>> ret
>>>
>>> }) -> tabs
>>>
>>> final_dat <- bind_rows(tabs)
>>> final_dat <- final_dat[, c(1, 2, 5, 7, 8, 13, 14)] # the cols you want
>>> final_dat <- final_dat[complete.cases(final_dat),] # take care of NAs
>>>
>>> remDr$quit()
>>>
>>>
>>> Prbly good ref code to have around, but you can grab the data & code
>>> here: https://gist.github.com/hrbrmstr/ec35ebb32c3cf0aba95f7bad28df1e98
>>>
>>> (anything to help a fellow parent out :-)
>>>
>>> -Bob
>>>
>>> On Tue, May 10, 2016 at 2:45 PM, Michael Friendly <friendly at yorku.ca> wrote:
>>>> This is my first attempt to try R web scraping tools, for a project my
>>>> daughter is working on. It concerns a data base of projects in Sao
>>>> Paulo, Brazil, listed at
>>>> http://outorgaonerosa.prefeitura.sp.gov.br/relatorios/RelSituacaoGeralProcessos.aspx,
>>>> but spread out over 69 pages accessed through a javascript menu at the
>>>> bottom of the page.
>>>>
>>>> Each web page contains 3 HTML tables, of which only the last contains
>>>> the relevant data. In this, only a subset of columns are of interest.
>>>> I tried using the XML package as illustrated on several tutorial pages,
>>>> as shown below. I have no idea how to automate this to extract these
>>>> tables from multiple web pages. Is there some other package better
>>>> suited to this task? Can someone help me solve this and other issues?
>>>>
>>>> # Goal: read the data tables contained on 69 pages generated by the link
>>>> below, where
>>>> # each page is generated by a javascript link in the menu of the bottom
>>>> of the page.
>>>> #
>>>> # Each "page" contains 3 html tables, with names "Table 1", "Table 2",
>>>> and the only one
>>>> # of interest with the data, "grdRelSitGeralProcessos"
>>>> #
>>>> # From each such table, extract the following columns:
>>>> #- Processo
>>>> #- Endereço
>>>> #- Distrito
>>>> #- Area terreno (m2)
>>>> #- Valor contrapartida ($)
>>>> #- Area excedente (m2)
>>>>
>>>> # NB: All of the numeric fields use "." as comma-separator and "," as
>>>> the decimal separator,
>>>> # but because of this are read in as character
>>>>
>>>>
>>>> library(XML)
>>>> link <-
>>>> "http://outorgaonerosa.prefeitura.sp.gov.br/relatorios/RelSituacaoGeralProcessos.aspx"
>>>>
>>>> saopaulo <- htmlParse(link)
>>>> saopaulo.tables <- readHTMLTable(saopaulo, stringsAsFactors = FALSE)
>>>> length(saopaulo.tables)
>>>>
>>>> # its the third table on this page we want
>>>> sp.tab <- saopaulo.tables[[3]]
>>>>
>>>> # columns wanted
>>>> wanted <- c(1, 2, 5, 7, 8, 13, 14)
>>>> head(sp.tab[, wanted])
>>>>
>>>>> head(sp.tab[, wanted])
>>>> Proposta Processo Endereço Distrito
>>>> 1 1 2002-0.148.242-4 R. DOMINGOS LOPES DA SILVA X R. CORNÉLIO
>>>> VAN CLEVE VILA ANDRADE
>>>> 2 2 2003-0.129.667-3 AV. DR. JOSÉ HIGINO,
>>>> 200 E 216 AGUA RASA
>>>> 3 3 2003-0.065.011-2 R. ALIANÇA LIBERAL,
>>>> 980 E 990 VILA LEOPOLDINA
>>>> 4 4 2003-0.165.806-0 R. ALIANÇA LIBERAL,
>>>> 880 E 886 VILA LEOPOLDINA
>>>> 5 5 2003-0.139.053-0 R. DR. JOSÉ DE ANDRADE
>>>> FIGUEIRA, 111 VILA ANDRADE
>>>> 6 6 2003-0.200.692-0 R. JOSÉ DE
>>>> JESUS, 66 VILA SONIA
>>>> Ã rea Terreno (m2) Ã rea Excedente (m2) Valor Contrapartida (R$)
>>>> 1 0,00 1.551,14 127.875,98
>>>> 2 0,00 3.552,13 267.075,77
>>>> 3 0,00 624,99 70.212,93
>>>> 4 0,00 395,64 44.447,18
>>>> 5 0,00 719,68 41.764,46
>>>> 6 0,00 446,52 85.152,92
>>>>
>>>> thanks,
>>>>
>>>>
>>>> --
>>>> Michael Friendly Email: friendly AT yorku DOT ca
>>>> Professor, Psychology Dept. & Chair, Quantitative Methods
>>>> York University Voice: 416 736-2100 x66249 Fax: 416 736-5814
>>>> 4700 Keele Street Web:http://www.datavis.ca
>>>> Toronto, ONT M3J 1P3 CANADA
>>>>
>>>>
>>>> [[alternative HTML version deleted]]
>>>>
>>>> ______________________________________________
>>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>
>> David Winsemius
>> Alameda, CA, USA
>>
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