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Question: Suggestion: spinning wheel for AnnotationHub
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gravatar for Michael Love
3 months ago by
Michael Love14k
United States
Michael Love14k wrote:

I'm putting together teaching material for using AnnotationHub, and I noticed it takes some time to do some searches edit: using display(ah). For example, species: Homo sapiens, and global search for "chip-seq". After putting in "chip-seq" it takes 30-50 seconds on my machine. Putting "chip-seq" in the Description field takes 10-15 seconds for me, similarly "peaks" in the tags field. I guess this just has to do with more things being added to AnnotationHub (I feel like it was faster when I've tried it in the past). My suggestion is that it would help to have a visual indicator that it's "working", so that users know to let the browser sit while it's looking for records.

> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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] parallel  stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
[1] shiny_1.0.4          AnnotationHub_2.8.2  BiocGenerics_0.22.0  BiocInstaller_1.26.0 rmarkdown_1.6      
[6] testthat_1.0.2       devtools_1.13.2     

loaded via a namespace (and not attached):
[1] Rcpp_0.12.11                  AnnotationDbi_1.38.1          knitr_1.16                  
[4] magrittr_1.5                  IRanges_2.10.2                xtable_1.8-2                
[7] R6_2.2.1                      stringr_1.2.0                 httr_1.2.1                  
[10] tools_3.4.0                   Biobase_2.36.2                DBI_0.6-1                   
[13] withr_1.0.2                   htmltools_0.3.6               yaml_2.1.14                 
[16] rprojroot_1.2                 digest_0.6.12                 interactiveDisplayBase_1.14.0
[19] crayon_1.3.2                  S4Vectors_0.14.3              curl_2.6                    
[22] mime_0.5                      memoise_1.1.0                 evaluate_0.10               
[25] RSQLite_1.1-2                 stringi_1.1.5                 compiler_3.4.0              
[28] backports_1.1.0               stats4_3.4.0                  jsonlite_1.5                
[31] httpuv_1.3.3    
ADD COMMENTlink modified 8 weeks ago by shepherl ♦♦ 510 • written 3 months ago by Michael Love14k

Hi Mike -- actually a little unclear what you're talking about. I guess after display(AnnotationHub()) ? or query(AnnotationHub(), "chip-seq") ?

ADD REPLYlink written 3 months ago by Martin Morgan ♦♦ 20k
2

The spinning wheel is so... MacOS centric. Can't we have something more universal?

ADD REPLYlink written 3 months ago by James W. MacDonald45k

Oh sorry, forgot to say using display(ah).

I tried using release and devel, and Chrome and Firefox on Mac and experienced similar wait times.

ADD REPLYlink written 3 months ago by Michael Love14k

Actually just "Loading..." 

I found this:

https://shiny.rstudio.com/reference/shiny/latest/Progress.html

ADD REPLYlink written 3 months ago by Michael Love14k
2
gravatar for shepherl
8 weeks ago by
shepherl ♦♦ 510
shepherl ♦♦ 510 wrote:

We made some changes to AnnotationHub display that seems to help with the speed of searches.  We are still investigating solutions to adding a progress/busy notification.  

ADD COMMENTlink written 8 weeks ago by shepherl ♦♦ 510

Thanks. I just tried out the latest version in devel, using Chrome. Here were some timings:

start with species: Homo sapiens, then:

search                    previous timing current timing
Global search: "chip-seq" 30-50 s         ~1 min  
Description: "chip-seq"   10-15 s         ~1 s
Tags: "peaks"             10-15 s         30 s

So a lot faster for searching Description, but seemingly slower for other fields. Let me know if you'd like me to try it out more (or maybe a specific version of AHub which isn't the one I'm using below?)

 R Under development (unstable) (2017-08-07 r73058)
 Platform: x86_64-apple-darwin15.6.0 (64-bit)
 Running under: OS X El Capitan 10.11.6

 Matrix products: default
 BLAS: /Users/love/bin/R/lib/libRblas.dylib
 LAPACK: /Users/love/bin/R/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] parallel  stats     graphics  grDevices datasets  utils     methods
 [8] base

 other attached packages:
 [1] shiny_1.0.5          AnnotationHub_2.9.12 BiocGenerics_0.23.1
 [4] BiocInstaller_1.27.4 rmarkdown_1.6        testthat_1.0.2
 [7] devtools_1.13.3
ADD REPLYlink written 8 weeks ago by Michael Love14k

I guess Lori's commits are in git, not yet available via biocLite?

git clone https://git.bioconductor.org/packages/AnnotationHub

which has version 2.9.13.

ADD REPLYlink written 8 weeks ago by Martin Morgan ♦♦ 20k

Got it. Thanks. I'll try again 

ADD REPLYlink written 8 weeks ago by Michael Love14k

That's great, it's much faster now using v2.9.13! Thanks

start with species: Homo sapiens, then:

search                    previous timing current timing
Global search: "chip-seq" 30-50 s         8 s
Description: "chip-seq"   10-15 s         ~1 s
Tags: "peaks"             10-15 s         ~1 s
ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by Michael Love14k

Great to hear! 

ADD REPLYlink written 8 weeks ago by shepherl ♦♦ 510
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