Certain result documents are causing an error: "No such file or directory"

[zhengzheli]

Please see the below code to reproduce:

 dbc <- nodbi::src_mongo(collection = "test2", db = "db")
 q <- "https://www.clinicaltrialsregister.eu/ctr-search/search?query=2014-001203-50"
 ctrLoadQueryIntoDb(
   queryterm = q,
   con = dbc,
   euctrresults = TRUE,
   documents.path = "d",
   verbose = TRUE,
 )

• Found search query from EUCTR: query=2014-001203-50 Checking helper binaries: done
• Checking trials in EUCTR... DEBUG: queryterm is https://www.clinicaltrialsregister.eu/ctr-search/search?query=2014-001203-50 Retrieved overview, multiple records of 1 trial(s) from 1 page(s) to be downloaded (estimate: 0.05 MB) Created directory d (1/3) Downloading trials... Note: register server cannot compress data, transfer takes longer, about 0.5s per trial Download status: 1 done; 0 in progress. Total size: 26.00 Kb (100%)... done!
  (2/3) Converting to JSON, 1 records converted DEBUG: c:\cygwin\bin\bash.exe --noprofile --norc --noediting -c "PATH=/usr/local/bin:/usr/bin; \"/cygdrive/C/Users/ES-PHI~1/AppData/Local/R/WIN-LI~1/4.2/ctrdata/exec/EUCTR2~1.SH\" /cygdrive/C/Users/ES-PHI~1/AppData/Local/Temp/RTMPKF~1/CTRDAT~4" (3/3) Importing JSON records into database... DEBUG: C:\Users\ES-Philip\AppData\Local\Temp\Rtmpkf8Xvs\ctrDATA4838515e7a2b = Imported or updated 1 records on 1 trial(s)
• Checking results if available from EUCTR for 1 trials: (1/4) Downloading and extracting results (. = data, F = file[s] and data, x = none): Download status: 1 done; 0 in progress. Total size: 992.96 Kb (100%)... done!
  Error in utils::unzip(zipfile = f, exdir = tempDir) : cannot open file 'C:/Users/ES-Philip/AppData/Local/Temp/Rtmpkf8Xvs/ctrDATA4838515e7a2b/Cartier.2019.Repeated Full-Face Aesthetic Combination Treatment With AbobotulinumtoxinA, Hyaluronic Acid Filler, and Skin-Boosting Hyaluronic Acid After Monotherapy With AbobotulinumtoxinA or Hyaluronic Acid Filler.pdf': No such file or directory

I believe it is related to this code in main.R

          tmp <- utils::unzip(
            zipfile = f,
            exdir = tempDir)
          if (is.null(tmp)) return(NULL)

[rfhb]

• Thank you for reporting the issue. This is related to file names that are too long under / for MS Windows.
• In R, run usethis::edit_r_environ() and add / edit to read, e.g. TMPDIR=c:/tmp in order to set R's directory for temporary files to a short pathname. Note this should be an absolute pathname and the folder should exist. Restart R before running the example above.
• Code has been modified to to not error when extracting files and to better inform on subsequent errors (see https://github.com/rfhb/ctrdata/blob/master/R/main.R#L1707)
• Try ctrdata 27d68d00ae28867764e6f40800a6008394b78385 by running devtools::install_github("rfhb/ctrdata"), followed by the example above.

[zhengzheli]

@rfhb Thank you for your quick response and fix! I can confirm it works now.

[rfhb]

R 4.3 may permit much longer file path names, see https://blog.r-project.org/2023/03/07/path-length-limit-on-windows/index.html, hence the issue reported here may also be addressed.