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Question: Suggestion: spinning wheel for AnnotationHub
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gravatar for Michael Love
11 months ago by
Michael Love18k
United States
Michael Love18k 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 10 months ago by shepherl ♦♦ 640 • written 11 months ago by Michael Love18k

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

ADD REPLYlink written 11 months ago by Martin Morgan ♦♦ 22k
2

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

ADD REPLYlink written 11 months ago by James W. MacDonald46k

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 11 months ago by Michael Love18k

Actually just "Loading..." 

I found this:

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

ADD REPLYlink written 11 months ago by Michael Love18k
2
gravatar for shepherl
10 months ago by
shepherl ♦♦ 640
United States
shepherl ♦♦ 640 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 10 months ago by shepherl ♦♦ 640

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 10 months ago by Michael Love18k

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 10 months ago by Martin Morgan ♦♦ 22k

Got it. Thanks. I'll try again 

ADD REPLYlink written 10 months ago by Michael Love18k

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 10 months ago • written 10 months ago by Michael Love18k

Great to hear! 

ADD REPLYlink written 10 months ago by shepherl ♦♦ 640
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