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Some files missing from value returned by osf_ls_files() #142

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mpjashby opened this issue Jul 23, 2022 · 3 comments
Open

Some files missing from value returned by osf_ls_files() #142

mpjashby opened this issue Jul 23, 2022 · 3 comments

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@mpjashby
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mpjashby commented Jul 23, 2022 •
edited

osf_ls_files() appears to be not listing some files in osfr version 0.2.8. The files that are missing are consistent (i.e. if I call the code again the same files are missing), but otherwise I can't see any pattern why some files are returned and not others. From the osfr documentation, setting n_max = Inf should ensure all files are returned, but this does not appear to work.

library(osfr)

# Trying to retrieve the file "crime_open_database_sample_detroit_2020.Rds" from
# https://osf.io/42tfc both directly and via listing the files in the directory

# Retrieving the file directly works as expected
osfr::osf_retrieve_file("https://osf.io/42tfc")
#> # A tibble: 1 × 3
#>   name                                        id    meta            
#>   <chr>                                       <chr> <list>          
#> 1 crime_open_database_sample_detroit_2020.Rds 42tfc <named list [3]>

# But retrieving a list of files that should include the file retrieves other
# files from the same directory but not the file above
osfr::osf_retrieve_node("https://osf.io/zyaqn") %>% 
  osfr::osf_ls_files(path = "Data for R package", n_max = Inf) %>% 
  dplyr::filter(stringr::str_detect(name, "sample_detroit")) %>% 
  dplyr::arrange(name)
#> # A tibble: 11 × 3
#>    name                                        id                   meta        
#>    <chr>                                       <chr>                <list>      
#>  1 crime_open_database_sample_detroit_2009.Rds 5bbde41c7cb181001a3… <named list>
#>  2 crime_open_database_sample_detroit_2010.Rds 5bbde41c7cb18100183… <named list>
#>  3 crime_open_database_sample_detroit_2011.Rds 5bbde41aec292c00192… <named list>
#>  4 crime_open_database_sample_detroit_2012.Rds 5bbde4147cb181001a3… <named list>
#>  5 crime_open_database_sample_detroit_2013.Rds 5bbde411ec292c00172… <named list>
#>  6 crime_open_database_sample_detroit_2014.Rds 5bbde40f7cb18100173… <named list>
#>  7 crime_open_database_sample_detroit_2015.Rds 5bbde40cec292c00182… <named list>
#>  8 crime_open_database_sample_detroit_2016.Rds 5bbde40aec292c00182… <named list>
#>  9 crime_open_database_sample_detroit_2017.Rds 5bbde407ec292c00172… <named list>
#> 10 crime_open_database_sample_detroit_2018.Rds 5c92a57da743a900176… <named list>
#> 11 crime_open_database_sample_detroit_2019.Rds 5f0092ddaf115601743… <named list>

# Retreiving a list of files via the OSF API returns the file as expected:
# https://api.osf.io/v2/nodes/zyaqn/files/osfstorage/5bbde32b7cb18100193c778a/?filter%5Bname%5D=sample_detroit_2020

Created on 2022-07-23 by the reprex package (v2.0.1)

Session info:

sessionInfo()
#> R version 4.1.2 (2021-11-01)
#> Platform: aarch64-apple-darwin20 (64-bit)
#> Running under: macOS Monterey 12.4
#> 
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRlapack.dylib
#> 
#> locale:
#> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> loaded via a namespace (and not attached):
#>  [1] rstudioapi_0.13   knitr_1.39        magrittr_2.0.3    R.cache_0.16.0   
#>  [5] rlang_1.0.4       fastmap_1.1.0     fansi_1.0.3       stringr_1.4.0    
#>  [9] styler_1.7.0      highr_0.9         tools_4.1.2       xfun_0.31        
#> [13] R.oo_1.25.0       utf8_1.2.2        cli_3.3.0         withr_2.5.0      
#> [17] htmltools_0.5.3   ellipsis_0.3.2    yaml_2.3.5        digest_0.6.29    
#> [21] tibble_3.1.7      lifecycle_1.0.1   purrr_0.3.4       R.utils_2.12.0   
#> [25] vctrs_0.4.1       fs_1.5.2          glue_1.6.2        evaluate_0.15    
#> [29] rmarkdown_2.14    reprex_2.0.1      stringi_1.7.8     compiler_4.1.2   
#> [33] pillar_1.8.0      R.methodsS3_1.8.2 pkgconfig_2.0.3
@aaronwolen
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Thanks for reporting and the excellent reprex! However, I'm not able to reproduce the issue with the current CRAN release of osfr (v0.2.8).

When I run

code_pkg_files <- osfr::osf_retrieve_node("https://osf.io/zyaqn") %>%
  osfr::osf_ls_files(path = "Data for R package", n_max = Inf)

The resulting osf_tbl_file includes 630 rows, which matches the number of files in Data for R package, and includes file crime_open_database_sample_detroit_2020.Rds.

I'm guessing this was caused by an intermittent server error. Although I would have expected the function to return an error rather than a partial result. If it occurs again you can enable verbose logging by defining the environment variable OSF_LOG to point to a logfile. For example:

OSF_PAT=osfr.log

This should give us more insight into what's happening at the request level.

@aaronwolen aaronwolen reopened this Sep 24, 2022
@mpjashby
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mpjashby commented Nov 6, 2023

I've tried to investigate this in further detail, but not got much further. As far as I can tell is is either a problem with osf_ls_files() or the OSF API (rather than a connection error or similar) since I've run the examples below over several hours (and multiple R sessions) and got the same results. Of note is that as well as some files being missing, osf_ls_files() reports other files multiple times (38 times in the case shown below).

library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
library(osfr)
#> <Logging enabled: osfr.log>

# Trying to download a file directly using `osf_retrieve_file()` works as 
# expected:
osf_retrieve_file("https://osf.io/avj2k")
#> # A tibble: 1 × 3
#>   name                                   id    meta            
#>   <chr>                                  <chr> <list>          
#> 1 crime_open_database_core_mesa_2022.Rds avj2k <named list [3]>

# But the same file (`crime_open_database_core_mesa_2022.Rds`) is missing when
# we try to retrieve a list of files with `osf_ls_files()`:
osf_retrieve_node("https://osf.io/zyaqn") |> 
  osf_ls_files(path = "Data for R package", n_max = Inf) |> 
  filter(stringr::str_detect(name, "core_mesa")) |> 
  arrange(name)
#> # A tibble: 6 × 3
#>   name                                   id                       meta        
#>   <chr>                                  <chr>                    <list>      
#> 1 crime_open_database_core_mesa_2016.Rds 5c926f5d4712b400173cc144 <named list>
#> 2 crime_open_database_core_mesa_2017.Rds 5c926f5da743a900176287aa <named list>
#> 3 crime_open_database_core_mesa_2018.Rds 5c926f5d2286e80018c62e36 <named list>
#> 4 crime_open_database_core_mesa_2019.Rds 5f009012af1156016e3b61ca <named list>
#> 5 crime_open_database_core_mesa_2020.Rds 614da1c7ec7885002840fb0d <named list>
#> 6 crime_open_database_core_mesa_2021.Rds 6347e653ec7f3f2df2f5f524 <named list>

# Just to check, if we list the same files using the API directly, the 2022 file
# is there as expected:
jsonlite::fromJSON("https://api.osf.io/v2/nodes/zyaqn/files/osfstorage/5bbde32b7cb18100193c778a/?filter%5Bname%5D=core_mesa") |> 
  purrr::pluck("data", "attributes", "name")
#> [1] "crime_open_database_core_mesa_2016.Rds"
#> [2] "crime_open_database_core_mesa_2017.Rds"
#> [3] "crime_open_database_core_mesa_2018.Rds"
#> [4] "crime_open_database_core_mesa_2019.Rds"
#> [5] "crime_open_database_core_mesa_2020.Rds"
#> [6] "crime_open_database_core_mesa_2021.Rds"
#> [7] "crime_open_database_core_mesa_2022.Rds"

# And an extra twist: in some cases the same file is reported by 
# `osf_ls_files()` multiple times:
osfr::osf_retrieve_node("https://osf.io/zyaqn") |> 
  osfr::osf_ls_files(path = "Data for R package", n_max = Inf) |> 
  dplyr::filter(stringr::str_detect(name, "core_st_louis_2009")) |> 
  dplyr::arrange(name)
#> # A tibble: 38 × 3
#>    name                                       id                    meta        
#>    <chr>                                      <chr>                 <list>      
#>  1 crime_open_database_core_st_louis_2009.Rds 5f009039af1156016a3b… <named list>
#>  2 crime_open_database_core_st_louis_2009.Rds 5f009039af1156016a3b… <named list>
#>  3 crime_open_database_core_st_louis_2009.Rds 5f009039af1156016a3b… <named list>
#>  4 crime_open_database_core_st_louis_2009.Rds 5f009039af1156016a3b… <named list>
#>  5 crime_open_database_core_st_louis_2009.Rds 5f009039af1156016a3b… <named list>
#>  6 crime_open_database_core_st_louis_2009.Rds 5f009039af1156016a3b… <named list>
#>  7 crime_open_database_core_st_louis_2009.Rds 5f009039af1156016a3b… <named list>
#>  8 crime_open_database_core_st_louis_2009.Rds 5f009039af1156016a3b… <named list>
#>  9 crime_open_database_core_st_louis_2009.Rds 5f009039af1156016a3b… <named list>
#> 10 crime_open_database_core_st_louis_2009.Rds 5f009039af1156016a3b… <named list>
#> # ℹ 28 more rows

Created on 2023-11-06 with reprex v2.0.2

Session info 
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.3.1 (2023-06-16)
#>  os       macOS Sonoma 14.0
#>  system   aarch64, darwin20
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       Europe/London
#>  date     2023-11-06
#>  pandoc   3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version date (UTC) lib source
#>  cachem        1.0.8   2023-05-01 [1] CRAN (R 4.3.0)
#>  cli           3.6.1   2023-03-23 [1] CRAN (R 4.3.0)
#>  crul          1.4.0   2023-05-17 [1] CRAN (R 4.3.0)
#>  curl          5.0.2   2023-08-14 [1] CRAN (R 4.3.0)
#>  digest        0.6.33  2023-07-07 [1] CRAN (R 4.3.0)
#>  dplyr       * 1.1.2   2023-04-20 [1] CRAN (R 4.3.0)
#>  evaluate      0.21    2023-05-05 [1] CRAN (R 4.3.0)
#>  fansi         1.0.4   2023-01-22 [1] CRAN (R 4.3.0)
#>  fastmap       1.1.1   2023-02-24 [1] CRAN (R 4.3.0)
#>  fs            1.6.3   2023-07-20 [1] CRAN (R 4.3.0)
#>  generics      0.1.3   2022-07-05 [1] CRAN (R 4.3.0)
#>  glue          1.6.2   2022-02-24 [1] CRAN (R 4.3.0)
#>  htmltools     0.5.6   2023-08-10 [1] CRAN (R 4.3.0)
#>  httpcode      0.3.0   2020-04-10 [1] CRAN (R 4.3.0)
#>  httr          1.4.7   2023-08-15 [1] CRAN (R 4.3.0)
#>  jsonlite      1.8.7   2023-06-29 [1] CRAN (R 4.3.0)
#>  knitr         1.43    2023-05-25 [1] CRAN (R 4.3.0)
#>  lifecycle     1.0.3   2022-10-07 [1] CRAN (R 4.3.0)
#>  logger        0.2.2   2021-10-19 [1] CRAN (R 4.3.0)
#>  magrittr      2.0.3   2022-03-30 [1] CRAN (R 4.3.0)
#>  memoise       2.0.1   2021-11-26 [1] CRAN (R 4.3.0)
#>  osfr        * 0.2.9   2022-09-25 [1] CRAN (R 4.3.0)
#>  pillar        1.9.0   2023-03-22 [1] CRAN (R 4.3.0)
#>  pkgconfig     2.0.3   2019-09-22 [1] CRAN (R 4.3.0)
#>  purrr         1.0.2   2023-08-10 [1] CRAN (R 4.3.0)
#>  R.cache       0.16.0  2022-07-21 [1] CRAN (R 4.3.0)
#>  R.methodsS3   1.8.2   2022-06-13 [1] CRAN (R 4.3.0)
#>  R.oo          1.25.0  2022-06-12 [1] CRAN (R 4.3.0)
#>  R.utils       2.12.2  2022-11-11 [1] CRAN (R 4.3.0)
#>  R6            2.5.1   2021-08-19 [1] CRAN (R 4.3.0)
#>  Rcpp          1.0.11  2023-07-06 [1] CRAN (R 4.3.0)
#>  reprex        2.0.2   2022-08-17 [1] CRAN (R 4.3.0)
#>  rlang         1.1.1   2023-04-28 [1] CRAN (R 4.3.0)
#>  rmarkdown     2.24    2023-08-14 [1] CRAN (R 4.3.0)
#>  rstudioapi    0.15.0  2023-07-07 [1] CRAN (R 4.3.0)
#>  sessioninfo   1.2.2   2021-12-06 [1] CRAN (R 4.3.0)
#>  stringi       1.7.12  2023-01-11 [1] CRAN (R 4.3.0)
#>  stringr       1.5.0   2022-12-02 [1] CRAN (R 4.3.0)
#>  styler        1.10.2  2023-08-29 [1] CRAN (R 4.3.0)
#>  tibble        3.2.1   2023-03-20 [1] CRAN (R 4.3.0)
#>  tidyselect    1.2.0   2022-10-10 [1] CRAN (R 4.3.0)
#>  triebeard     0.4.1   2023-03-04 [1] CRAN (R 4.3.0)
#>  urltools      1.7.3   2019-04-14 [1] CRAN (R 4.3.0)
#>  utf8          1.2.3   2023-01-31 [1] CRAN (R 4.3.0)
#>  vctrs         0.6.4   2023-10-12 [1] CRAN (R 4.3.1)
#>  withr         2.5.0   2022-03-03 [1] CRAN (R 4.3.0)
#>  xfun          0.40    2023-08-09 [1] CRAN (R 4.3.0)
#>  yaml          2.3.7   2023-01-23 [1] CRAN (R 4.3.0)
#> 
#>  [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────

Nothing gets written to the file specified in OSF_LOG when creating a reprex (presumably because the reprex is run in a separate session), so the following is the contents of the log file produced when running the same code as above directly after running the reprex:

Log output (collapsed because it's quite long) 
INFO [2023-11-06 17:10:43] GET https://api.osf.io/v2/files/avj2k/
INFO [2023-11-06 17:10:44] STATUS 200 - https://api.osf.io/v2/files/avj2k/ - [namelookup:0.011103, connect:0.113655, pretransfer:0.140852, starttransfer:0.615729, total:0.615888]
INFO [2023-11-06 17:10:44] GET https://api.osf.io/v2/nodes/zyaqn/
INFO [2023-11-06 17:10:44] STATUS 200 - https://api.osf.io/v2/nodes/zyaqn/ - [namelookup:0.000026, pretransfer:0.000143, starttransfer:0.465292, total:0.465445]
INFO [2023-11-06 17:10:44] GET https://api.osf.io/v2/nodes/zyaqn/files/osfstorage/?filter%5Bkind%5D=folder&filter%5Bname%5D=Data%20for%20R%20package&page=1
INFO [2023-11-06 17:10:45] STATUS 200 - https://api.osf.io/v2/nodes/zyaqn/files/osfstorage/?filter%5Bkind%5D=folder&filter%5Bname%5D=Data%20for%20R%20package&page=1 - [namelookup:0.000038, pretransfer:0.000191, starttransfer:0.496523, total:0.516179]
INFO [2023-11-06 17:10:45] GET https://api.osf.io/v2/nodes/zyaqn/files/osfstorage/5bbde32b7cb18100193c778a/?page=1
INFO [2023-11-06 17:10:46] STATUS 200 - https://api.osf.io/v2/nodes/zyaqn/files/osfstorage/5bbde32b7cb18100193c778a/?page=1 - [namelookup:0.000027, pretransfer:0.000194, starttransfer:0.817904, total:0.870050]
INFO [2023-11-06 17:10:46] GET https://api.osf.io/v2/nodes/zyaqn/files/osfstorage/5bbde32b7cb18100193c778a/?page=2
INFO [2023-11-06 17:10:48] STATUS 200 - https://api.osf.io/v2/nodes/zyaqn/files/osfstorage/5bbde32b7cb18100193c778a/?page=2 - [namelookup:0.000033, pretransfer:0.000203, starttransfer:0.698030, total:1.747944]
INFO [2023-11-06 17:10:48] GET https://api.osf.io/v2/nodes/zyaqn/files/osfstorage/5bbde32b7cb18100193c778a/?page=3
INFO [2023-11-06 17:10:49] STATUS 200 - https://api.osf.io/v2/nodes/zyaqn/files/osfstorage/5bbde32b7cb18100193c778a/?page=3 - [namelookup:0.000098, pretransfer:0.000424, starttransfer:0.778379, total:1.826785]
INFO [2023-11-06 17:10:49] GET https://api.osf.io/v2/nodes/zyaqn/files/osfstorage/5bbde32b7cb18100193c778a/?page=4
INFO [2023-11-06 17:10:50] STATUS 200 - https://api.osf.io/v2/nodes/zyaqn/files/osfstorage/5bbde32b7cb18100193c778a/?page=4 - [namelookup:0.000050, pretransfer:0.000243, starttransfer:0.707573, total:0.707735]
INFO [2023-11-06 17:10:50] GET https://api.osf.io/v2/nodes/zyaqn/files/osfstorage/5bbde32b7cb18100193c778a/?page=5
INFO [2023-11-06 17:10:51] STATUS 200 - https://api.osf.io/v2/nodes/zyaqn/files/osfstorage/5bbde32b7cb18100193c778a/?page=5 - [namelookup:0.000061, pretransfer:0.000422, starttransfer:0.818692, total:0.864945]
INFO [2023-11-06 17:10:51] GET https://api.osf.io/v2/nodes/zyaqn/files/osfstorage/5bbde32b7cb18100193c778a/?page=6
INFO [2023-11-06 17:10:53] STATUS 200 - https://api.osf.io/v2/nodes/zyaqn/files/osfstorage/5bbde32b7cb18100193c778a/?page=6 - [namelookup:0.000028, pretransfer:0.000181, starttransfer:0.688275, total:1.745620]
INFO [2023-11-06 17:10:53] GET https://api.osf.io/v2/nodes/zyaqn/files/osfstorage/5bbde32b7cb18100193c778a/?page=7
INFO [2023-11-06 17:10:54] STATUS 200 - https://api.osf.io/v2/nodes/zyaqn/files/osfstorage/5bbde32b7cb18100193c778a/?page=7 - [namelookup:0.000049, pretransfer:0.000248, starttransfer:0.908260, total:0.947111]
INFO [2023-11-06 17:10:54] GET https://api.osf.io/v2/nodes/zyaqn/files/osfstorage/5bbde32b7cb18100193c778a/?page=8
INFO [2023-11-06 17:10:56] STATUS 200 - https://api.osf.io/v2/nodes/zyaqn/files/osfstorage/5bbde32b7cb18100193c778a/?page=8 - [namelookup:0.000030, pretransfer:0.000153, starttransfer:0.870798, total:1.920806]
INFO [2023-11-06 17:10:56] GET https://api.osf.io/v2/nodes/zyaqn/files/osfstorage/5bbde32b7cb18100193c778a/?page=9
INFO [2023-11-06 17:10:57] STATUS 200 - https://api.osf.io/v2/nodes/zyaqn/files/osfstorage/5bbde32b7cb18100193c778a/?page=9 - [namelookup:0.000050, pretransfer:0.000294, starttransfer:1.051933, total:1.056050]
INFO [2023-11-06 17:10:57] GET https://api.osf.io/v2/nodes/zyaqn/files/osfstorage/5bbde32b7cb18100193c778a/?page=10
INFO [2023-11-06 17:10:58] STATUS 200 - https://api.osf.io/v2/nodes/zyaqn/files/osfstorage/5bbde32b7cb18100193c778a/?page=10 - [namelookup:0.000032, pretransfer:0.000181, starttransfer:1.049134, total:1.049286]
INFO [2023-11-06 17:10:58] GET https://api.osf.io/v2/nodes/zyaqn/files/osfstorage/5bbde32b7cb18100193c778a/?page=11
INFO [2023-11-06 17:11:00] STATUS 200 - https://api.osf.io/v2/nodes/zyaqn/files/osfstorage/5bbde32b7cb18100193c778a/?page=11 - [namelookup:0.000051, pretransfer:0.000266, starttransfer:0.706937, total:1.758570]
INFO [2023-11-06 17:11:00] GET https://api.osf.io/v2/nodes/zyaqn/files/osfstorage/5bbde32b7cb18100193c778a/?page=12
INFO [2023-11-06 17:11:00] STATUS 200 - https://api.osf.io/v2/nodes/zyaqn/files/osfstorage/5bbde32b7cb18100193c778a/?page=12 - [namelookup:0.000068, pretransfer:0.000421, starttransfer:0.771036, total:0.772385]
INFO [2023-11-06 17:11:00] GET https://api.osf.io/v2/nodes/zyaqn/files/osfstorage/5bbde32b7cb18100193c778a/?page=13
INFO [2023-11-06 17:11:01] STATUS 200 - https://api.osf.io/v2/nodes/zyaqn/files/osfstorage/5bbde32b7cb18100193c778a/?page=13 - [namelookup:0.000044, pretransfer:0.000272, starttransfer:0.696774, total:0.747615]
INFO [2023-11-06 17:11:01] GET https://api.osf.io/v2/nodes/zyaqn/files/osfstorage/5bbde32b7cb18100193c778a/?page=14
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Two final things to note:

  • If the logger package is not installed then logging fails silently, which is quite hard to fix. It might be worth adding a note about this to the CONTRIBUTING reprex in the osfr package.
  • The CONTRIBUTING vignette currently says "You can also enable logging by defining OSF_LOG to point to a logfile. For example: OSF_PAT=osfr.log" but I suspect this should say "You can also enable logging by defining OSF_LOG to point to a logfile. For example: OSF_LOG=osfr.log".

@mpjashby mpjashby mentioned this issue Nov 7, 2023
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@mzettersten
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Hi, we've recently been running into this same issue (missing files and folders in osf_ls_files) in some projects where we host a large amount of raw data on OSF. Are there any updates on what might be causing the issue? Happy to provide details if this is actively being investigated. Thanks!

@adriansteffan adriansteffan mentioned this issue May 23, 2024
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@aaronwolen @mpjashby @mzettersten