Unexpected end of input error with custom tracks on UCSC Genome Browser mirror

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Leung, Wilson

non lue,
5 août 2022, 14:00:4805/08/2022
à genome...@soe.ucsc.edu

Dear Sir/Madam,

 

Problem Summary:

------------------

 

We would like to request assistance with the "unexpected end of input" error with the custom track feature of the UCSC Genome Browser on our mirror site (testbrowser.thegep.org). We can consistently reproduce this issue only in cases where the custom track is hosted on the same server as the UCSC Genome Browser mirror site.

 

 

Steps to Reproduce [*]:

------------------

 

1. Example custom track:

testbrowser.thegep.org/~wilson/test/test.gff

 

 

2. Open a web browser, and navigate to the following URL with the hgt.customText parameter to load the custom track into the UCSC Genome Browser mirror:

 

testbrowser.thegep.org/cgi-bin/hgTracks?enableHighlightingDialog=0&ruler=full&pix=800&db=DyakRefSeq3&complement_DyakRefSeq3=0&position=NC_052530:19150779-19150841&hgt.customText=https://testbrowser.thegep.org/~wilson/test/test.gff

 

 

Expected Result

------------------

The UCSC Genome Browser mirror shows the genomic region at NC_052530:19150779-19150841 in the DyakRefSeq3 assembly with the "CustomModel" custom track

 

 

 

Actual Result

------------------

The UCSC Genome Browser mirror shows the error message:

"Error unexpected end of input reading http header on https://testbrowser.thegep.org/~wilson/test/test.gff"

 

 

 

To try to identify the cause of the issue, we have uploaded the same custom track to two other servers, and then use the same approach to load the custom track on the UCSC Genome Browser mirror:

 

Test case 1:

------------------

Custom track: gander.wustl.edu/~wilson/test/test.gff

 

testbrowser.thegep.org/cgi-bin/hgTracks?enableHighlightingDialog=0&ruler=full&pix=800&db=DyakRefSeq3&complement_DyakRefSeq3=0&position=NC_052530:19150779-19150841&hgt.customText=https://gander.wustl.edu/~wilson/test/test.gff

 

Test case 2:

------------------

Custom track: gander2.wustl.edu/~wilson/test/test.gff

 

testbrowser.thegep.org/cgi-bin/hgTracks?enableHighlightingDialog=0&ruler=full&pix=800&db=DyakRefSeq3&complement_DyakRefSeq3=0&position=NC_052530:19150779-19150841&hgt.customText=https://gander2.wustl.edu/~wilson/test/test.gff

 

Loading the custom tracks hosted on these servers do not trigger the "unexpected end of input" error message in the UCSC Genome Browser mirror site:

 

---

 

Server details:

------------------

Operating System: Ubuntu 20.04.4 LTS

Web Server: Apache 2.4.41 (Ubuntu)

Database: MariaDB server version: 10.3.34-MariaDB-0ubuntu0.20.04.1

 

UCSC Genome Browser version 432

 

 

Client details:

------------------

Firefox 103.0.1

Chrome 103.0.5060.134

Operating System: macOS Monterey 12.5

 

---

 

 

We would appreciate your advice on changes to the configurations of the mirror site that would enable reliable loading of custom tracks hosted on the same server as the UCSC Genome Browser mirror site.

 

Please let me know if you require additional information to reproduce the issue. Thank you for your kind attention and assistance in this matter.

 

Sincerely,

 

Wilson

 

---

 

[*] The HTTP protocol were omitted from the URLs in the message to prevent the Office 365 Safe Links feature from re-writing the URLs in the Email message

 

Hiram Clawson

non lue,
5 août 2022, 16:04:3305/08/2022
à Leung, Wilson,genome...@soe.ucsc.edu
Good Afternoon Wilson:

See if you can get a clue from the apache server logs on the system
that is causing the difficulty. This is indeed a puzzle, I do not
immediately see anything different that would be important between
your different servers there.

--Hiram

Leung, Wilson

non lue,
5 août 2022, 17:45:3305/08/2022
à Hiram Clawson,genome...@soe.ucsc.edu

Hello Hiram,

 

Thank you for your quick response, and for your help in diagnosing the cause of the custom track issue.

 

Below are the Apache log entries for the cases when (1) loading the custom track from the same domain as the UCSC Genome Browser mirror, and when (2) loading the custom track from a different domain than the UCSC Genome Browser mirror:

 

 

Case 1: Custom track on the same server as the UCSC Genome Browser mirror:

 

[hgTracks] [client <ip address>] [hgsid=unknown] [/cgi-bin/hgTracks?enableHighlightingDialog=0&ruler=full&pix=800&db=DyakRefSeq3&complement_DyakRefSeq3=0&position=NC_052530:

19150779-19150841&hgt.customText=https://testbrowser.thegep.org/~wilson/test/test.gff]

 

Error unexpected end of input reading http header on https://testbrowser.thegep.org/~wilson/test/test.gff

 

CGI_TIME: hgTracks: Overall total time: 20182 millis

 

 

---

 

Case 2: Custom track on a different server

 

customTrack: new 1 from https://gander.wustl.edu/~wilson/test/test.gff botDelay 0 millis

customTrack: saved 1 in ../trash/ct/ct_testbrowser_23201_d7a990.bed

CGI_TIME: hgTracks: Overall total time: 166 millis

 

 

---

 

Apache is configured with the following RequestReadTimeout settings:

 

RequestReadTimeout header=20-40,minrate=500

 

 

The "Overall total time" for case 1 is approximately 20000 millis (i.e., 20 seconds). Hence it appears that the request timed out due to the RequestReadTimeout setting (i.e., header=20-40) because the connection did not receive the request header after 20 seconds.

 

The custom track file typically completes loading in 20-30 millis when I request the file directly from the Apache web server (testbrowser.thegep.org/~wilson/test/test.gff).

 

 

 

Please let me know if you require more information. Thanks for your help.

 

Sincerely,

 

Wilson

 

---

 

On 8/5/22, 3:04 PM, "Hiram Clawson" <hi...@soe.ucsc.edu> wrote:

Good Afternoon Wilson:

 

See if you can get a clue from the apache server logs on the system

that is causing the difficulty.  This is indeed a puzzle, I do not

immediately see anything different that would be important between

your different servers there.

 

--Hiram

 

On 8/5/22 10:39 AM, Leung, Wilson wrote:

> Dear Sir/Madam,

>

> Problem Summary:

> ------------------

>

> We would like to request assistance with the "unexpected end of input" error with the custom track feature of the UCSC Genome Browser on our mirror site (testbrowser.thegep.org). We can consistently reproduce this issue only in cases where the custom track is hosted on the same server as the UCSC Genome Browser mirror site.

>

>

> Steps to Reproduce [*]:

> ------------------

>

> 1. Example custom track:

>

>

> 2. Open a web browser, and navigate to the following URL with the hgt.customText parameter to load the custom track into the UCSC Genome Browser mirror:

>

>

>

> Expected Result

> ------------------

> The UCSC Genome Browser mirror shows the genomic region at NC_052530:19150779-19150841 in the DyakRefSeq3 assembly with the "CustomModel" custom track

>

>

>

> Actual Result

> ------------------

> The UCSC Genome Browser mirror shows the error message:

>

>

>

> To try to identify the cause of the issue, we have uploaded the same custom track to two other servers, and then use the same approach to load the custom track on the UCSC Genome Browser mirror:

>

> Test case 1:

> ------------------

>

>

> Test case 2:

> ------------------

>

Gerardo Perez

non lue,
12 août 2022, 20:22:2212/08/2022
à Leung, Wilson,genome...@soe.ucsc.edu

Hello, Wilson.

Thank you for your interest in the Genome Browser.

We were unable to reproduce your issue. Was the problem resolved by increasing the number limit of opened files, increasing the number of processes, and changing the MariaDB max_connection limit? If not, could you provide us with any additional info so we can look into this further?

One of our engineers recommends turning off the Microsoft Outlook email security system since it’s making it hard for tech support. The emails seem to get corrupted by the Microsoft Outlook email security system, which makes it confusing since they all look like they are redirecting through na01.safelinks.protection.outlook.com:
https://answers.microsoft.com/en-us/outlook_com/forum/all/httpsna01safelinksprotectionoutlookcom/fd5521e6-2190-444f-a889-dea65441a6ee

Simple links like https://testbrowser.thegep.org/~wilson/test/test.gff become complex, and complex ones are even worse.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute


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