gversmee/dbgap2x

dbgap2x's Issues

Password Jupyter

dbgap2x password provided in the documentation doesn't work.

Error in parallel::mclapply

Hi Authors!!

I am trying to use this package. When I run the exemplary command in R i.e. search.dbgap("Jackson") it throws the following error:

Error in parallel::mclapply(mc.cores = getOption("mc.cores", parallel::detectCores()),  : 
  'mc.cores' > 1 is not supported on Windows

Please help me understand how to deal with this?

functions is.parent() and parent.study()

On the Jupyter/mybinder, http request error.
Error in curl::curl_fetch_memory(url, handle = handle): Error in the HTTP2 framing layer Tracebak

Size of Docker image

10Gb is way too much
The Docker image took 40 min to download, and after checking, docker image is 10Gb. My understanding is that dbGaP2x only requires a jupyter server, a few dev libraries and a R environment. The image should be much less than 1Gb.

start docker automatically on the tutorial page

add installation steps for fresh R installation

library(devtools)
library(BiocInstaller)
biocLite("XML")
install.packages("data.table")
install.packages("htmlTable")```

Github repo name in tutorial

In the tutorial (chunk 1), the name of the github repository is not in accordance with the paper's

Reduce size of sratoolkit docker images

Original size: 762Mb.
Change #1: Size decreased to 369Mb.

Other ways to decrease the size:

• use alpine
• remove wget

query search.dbgap("Jackson", no.browser = TRUE)

This function is important to the tool, but only returns the URL of the dbgap page listing the studies. Would prefer to return a structured summary of those studies, so that it can be used in combination with other queries.

htmlTable

It looks like htmlTable package needs to be manually installed before installing the package via devtools

possibly speed up the queries and add as much structured data as you can

Tuning parallel functions

Need to add an option for datatables.dict and variables.dict to choose the number of cores used.

Output format from parent.study function

Hi! I observed the weird format of output from parent.study() function.

parent.study("phs000090")
[1] " 'phs000280.v6.p1" ""

(space) ' in the first element and the empty string in the second element.
Do you know why I got this? Thanks.

> sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.3

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] dbgap2x_1.0 dplyr_0.8.5

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.3        pillar_1.4.3      compiler_3.6.2    bitops_1.0-6      prettyunits_1.1.1 remotes_2.1.1    
 [7] tools_3.6.2       testthat_2.3.2    digest_0.6.25     pkgbuild_1.0.6    pkgload_1.0.2     jsonlite_1.6.1   
[13] memoise_1.1.0     tibble_2.1.3      pkgconfig_2.0.3   rlang_0.4.5       cli_2.0.2         parallel_3.6.2   
[19] curl_4.3          yaml_2.2.1        xfun_0.12         httr_1.4.1        withr_2.1.2       stringr_1.4.0    
[25] knitr_1.28        vctrs_0.2.4       desc_1.2.0        fs_1.3.2          devtools_2.2.2    rprojroot_1.3-2  
[31] tidyselect_1.0.0  data.table_1.12.8 glue_1.3.1        R6_2.4.1          processx_3.4.2    fansi_0.4.1      
[37] XML_3.99-0.3      sessioninfo_1.1.1 callr_3.4.2       purrr_0.3.3       magrittr_1.5      backports_1.1.5  
[43] ps_1.3.2          ellipsis_0.3.0    usethis_1.5.1     assertthat_0.2.1  utf8_1.1.4        stringi_1.4.6    
[49] RCurl_1.98-1.1    crayon_1.3.4  

change the option name in the "browser functions"

browse.dbgap, browse.study, search.dbgap
change for "open.browser"

start docker automatically with user root

see if we can remove "-u root" from code