Error: "failed to retrieve file size" when browsing through indexed vcf tracks

[russellmyers]

JBrowse version: JBrowse 1.16.6 Web browser: Chrome (also reproducible in other browsers)

Error encountered "failed to retrieve file size" when browsing through indexed vcf tracks - see attached images.

The issue appears to be very similar to issue #1252 on github (which is marked as closed).

Steps to reproduce:

• go to http://pseudobase-test.biology.duke.edu/jb?data=pse
• Select all tracks (or at least all tracks in the "D.Pseudoobscura" category)
• zoom in a few times, until the error starts to appear.

[cmdcolin]

Possible fix here https://github.com/rbuels/http-range-fetcher/pull/7

If you are interested in testing, here is a way you can

git clone https://github.com/rbuels/http-range-fetcher
cd http-range-fetcher
git checkout fix_stat_undefined_error
yarn
yarn build
yarn link
cd ..

git clone https://github.com/gmod/jbrowse
cd jbrowse
yarn
yarn link http-range-fetcher
yarn watch

[cmdcolin]

After yarn watch, jbrowse is rebuilt and you can open the index.html or run yarn start in the jbrowse folder

[russellmyers]

Thanks @cmdcolin, will check out the potential fix above and will report back here

[russellmyers]

Hi @cmdcolin - I've installed a test version as per above. It's here: http://pseudobase-test.biology.duke.edu/jb_rf/jbrowse/?data=pse

However, I'm still able to reproduce the error.

NOTE - I tried putting a breakpoint in httpRangeFetcher.js to ensure it was actually reaching the new code, but something is puzzling me - I must have done something wrong, as the source code in the debugger for httpRangeFetcher.js doesn't seem to match the code on Github. (Caveat: I'm no expert on Dojo, or even Javascript - I have Python/Java background).

For example, the definition of the HTTPRangeFetcher class at the start of the source code of httpRangeFetcher.js is defined in "var ... function()" syntax in the debugger (see second pic below) however it is defined with "class" syntax in the actual master souce code on github. So, I seem to have completely the wrong source code for httpRangeFetcher.js somehow (or else I'm misunderstanding something). What might I have done wrong? Any clues?

Cheers, Russell

[cmdcolin]

@russellmyers I am not seeing the error happen when I visit this link. I can confirm you have the right http-range-fetcher installed there too

[cmdcolin]

Can you clear browser cache and ensure that you are still seeing the error with your updated link?

[russellmyers]

@cmdcolin Thanks for confirmation of the correct http-range-fetcher installation in the test jbrowse link I set up (jb_rf/jbrowse..). I've tried clearing the cache, and from what I can see the error certainly seems to be happening less, however I can still reproduce the error in certain situations.

For example:

1) Clear cache

2) go to: http://pseudobase-test.biology.duke.edu/jb_rf/jbrowse/?data=pse&loc=2%3A1188..7007&tracks=ref%2Cgenes%2CAFC12_VCF%2CPP1137_VCF%2CMSH24_VCF%2CFS18_VCF%2CMAT32_VCF%2CMATTL_VCF%2CMSH9_VCF%2CPP1134_VCF%2CS10-A47_VCF%2CS11-A14_VCF%2CS1-A56_VCF%2CS3-M14_VCF%2CS4-A60_VCF%2CS5-M17_VCF%2CS6-A19_VCF%2CS7-Flag14_VCF%2CS9-A12_VCF%2CS12-M27_VCF%2CS13-A48_VCF%2CS14-A49_VCF%2CS15-A57_VCF%2CS16-A30_VCF%2CS17-M20_VCF%2CS18-M15_VCF%2CS19-A24_VCF%2CS21-M6_VCF%2CS22-A6_VCF%2CS20-M13_VCF%2CDpseSR_VCF%2CDpseST_VCF%2CBogotana-SCinv_VCF%2CSuta3_VCF%2CToro1_VCF%2CToro4_VCF%2CWhiteER_VCF%2CMSH1993_VCF%2CMSH39_VCF%2CSC04_VCF%2CDperSR_VCF%2CDperST_VCF%2CSRR1925735_VCF%2CSRR1873753_VCF%2CSRR1873751_VCF%2CSRR1873754_VCF%2CSRR1873755_VCF%2CSRR2042916_VCF%2CSRR1873752_VCF%2CSRR1925734_VCF%2CSRR1925723_VCF%2CML16_VCF%2CSP235_VCF%2Clowei_VCF&highlight=

3) Then once all tracks are loaded successfully, hit the big zoom out button once.

Result: I still get the "failed to retrieve file size error".

Would you be able to try the above as well? Do you get the same error?

Cheers, Russell

[cmdcolin]

I can reproduce, and can see where there is a possible problem

[cmdcolin]

Ref here https://github.com/rbuels/http-range-fetcher/issues/12

[cmdcolin]

No fix yet but will keep you posted

[russellmyers]

Great, thanks @cmdcolin !

[cmdcolin]

@russellmyers if you want to try a new fix

cd http-range-fetcher
git fetch
git checkout perform_record_stats_in_stat
yarn
yarn build
cd ../jbrowse
yarn
yarn watch

This should create a new instance with the new http-range-fetcher incorporated

[russellmyers]

Excellent, seems to have done the trick! Thanks heaps @cmdcolin

[cmdcolin]

This was fixed on dev branch, pending next release