Autocomplete limit?

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Autocomplete limit?

Hans Vasquez-Gross
Hi All,

     Is there a limit for the number of sequences autocomplete works with?  Two example data sources are provided below, which work fine with autocomplete.   


    However, testing autocomplete on a new load of an early v0.8 assembly of a ~22Gbp genome with ~16.5 million individual sequences has not been successful.   If I try to type the first few characters of a scaffold (ie jcf), a list never drops down.  

I continued typing a sequence name reasoning that maybe there was a limit to how many results could be returned, but it never autocompleted.  In fact, I'm fairly certain when testing this assembly performance with autocomplete in GBrowse caused my webserver to become unresponsive and had to be restarted.  I'd like to have the autocomplete return a minimal number of scaffolds (20+-) so it'll stay responsive and not crash the server, but continue filtering that set as the user types more of the scaffold name.

   Any comments or suggestions would be greatly appreciated.

Thanks,
-Hans

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Re: Autocomplete limit?

Lincoln Stein
In fact there is a hard-coded limit of 100 on the number of feature names that can be returned by autocomplete, so I suspect that there is a bug in the way that prefix-matching is implemented in the database adapter you are happening to be using. This would also explain why your server is crashing -- it is probably filling up memory. 

What adapter is attached to your assembly?

Lincoln


On Tue, Apr 30, 2013 at 3:47 PM, Hans Vasquez-Gross <[hidden email]> wrote:
Hi All,

     Is there a limit for the number of sequences autocomplete works with?  Two example data sources are provided below, which work fine with autocomplete.   


    However, testing autocomplete on a new load of an early v0.8 assembly of a ~22Gbp genome with ~16.5 million individual sequences has not been successful.   If I try to type the first few characters of a scaffold (ie jcf), a list never drops down.  

I continued typing a sequence name reasoning that maybe there was a limit to how many results could be returned, but it never autocompleted.  In fact, I'm fairly certain when testing this assembly performance with autocomplete in GBrowse caused my webserver to become unresponsive and had to be restarted.  I'd like to have the autocomplete return a minimal number of scaffolds (20+-) so it'll stay responsive and not crash the server, but continue filtering that set as the user types more of the scaffold name.

   Any comments or suggestions would be greatly appreciated.

Thanks,
-Hans

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Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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Re: Autocomplete limit?

Hans Vasquez-Gross
If that is what's happening, I could see it filling up memory.  The webserver has 32gb of RAM available which should be plenty though.   All adapters are configured as follows in the individual datasource.conf files.

[scaffolds:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::Pg
                -dsn dbname=****************;host=**************
                -user *********************
                -pass *********************
search options = exact, -fulltext, +autocomplete



The Gbrowse.conf is also configured for these same default search options.  Thanks for the help Lincoln. 

Cheers,
-Hans



On Tue, Apr 30, 2013 at 1:33 PM, Lincoln Stein <[hidden email]> wrote:
In fact there is a hard-coded limit of 100 on the number of feature names that can be returned by autocomplete, so I suspect that there is a bug in the way that prefix-matching is implemented in the database adapter you are happening to be using. This would also explain why your server is crashing -- it is probably filling up memory. 

What adapter is attached to your assembly?

Lincoln


On Tue, Apr 30, 2013 at 3:47 PM, Hans Vasquez-Gross <[hidden email]> wrote:
Hi All,

     Is there a limit for the number of sequences autocomplete works with?  Two example data sources are provided below, which work fine with autocomplete.   


    However, testing autocomplete on a new load of an early v0.8 assembly of a ~22Gbp genome with ~16.5 million individual sequences has not been successful.   If I try to type the first few characters of a scaffold (ie jcf), a list never drops down.  

I continued typing a sequence name reasoning that maybe there was a limit to how many results could be returned, but it never autocompleted.  In fact, I'm fairly certain when testing this assembly performance with autocomplete in GBrowse caused my webserver to become unresponsive and had to be restarted.  I'd like to have the autocomplete return a minimal number of scaffolds (20+-) so it'll stay responsive and not crash the server, but continue filtering that set as the user types more of the scaffold name.

   Any comments or suggestions would be greatly appreciated.

Thanks,
-Hans

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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
<a href="tel:416%20673-8514" value="+14166738514" target="_blank">416 673-8514
Assistant: Renata Musa <[hidden email]>



--
----------
Hans Vasquez-Gross
iPlant Developer
Neale Lab - Robbins Hall 262
Department of Plant Science
University of California at Davis
Phone: (530) 752-0609
Skype: hansvg.ucd

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Re: Autocomplete limit?

Lincoln Stein
Do you see the webserver process getting larger?

Lincoln


On Tue, Apr 30, 2013 at 5:09 PM, Hans Vasquez-Gross <[hidden email]> wrote:
If that is what's happening, I could see it filling up memory.  The webserver has 32gb of RAM available which should be plenty though.   All adapters are configured as follows in the individual datasource.conf files.

[scaffolds:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::Pg
                -dsn dbname=****************;host=**************
                -user *********************
                -pass *********************
search options = exact, -fulltext, +autocomplete



The Gbrowse.conf is also configured for these same default search options.  Thanks for the help Lincoln. 

Cheers,
-Hans



On Tue, Apr 30, 2013 at 1:33 PM, Lincoln Stein <[hidden email]> wrote:
In fact there is a hard-coded limit of 100 on the number of feature names that can be returned by autocomplete, so I suspect that there is a bug in the way that prefix-matching is implemented in the database adapter you are happening to be using. This would also explain why your server is crashing -- it is probably filling up memory. 

What adapter is attached to your assembly?

Lincoln


On Tue, Apr 30, 2013 at 3:47 PM, Hans Vasquez-Gross <[hidden email]> wrote:
Hi All,

     Is there a limit for the number of sequences autocomplete works with?  Two example data sources are provided below, which work fine with autocomplete.   


    However, testing autocomplete on a new load of an early v0.8 assembly of a ~22Gbp genome with ~16.5 million individual sequences has not been successful.   If I try to type the first few characters of a scaffold (ie jcf), a list never drops down.  

I continued typing a sequence name reasoning that maybe there was a limit to how many results could be returned, but it never autocompleted.  In fact, I'm fairly certain when testing this assembly performance with autocomplete in GBrowse caused my webserver to become unresponsive and had to be restarted.  I'd like to have the autocomplete return a minimal number of scaffolds (20+-) so it'll stay responsive and not crash the server, but continue filtering that set as the user types more of the scaffold name.

   Any comments or suggestions would be greatly appreciated.

Thanks,
-Hans

------------------------------------------------------------------------------
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Code-level diagnostics for performance bottlenecks with <2% overhead
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_______________________________________________
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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
<a href="tel:416%20673-8514" value="+14166738514" target="_blank">416 673-8514
Assistant: Renata Musa <[hidden email]>



--
----------
Hans Vasquez-Gross
iPlant Developer
Neale Lab - Robbins Hall 262
Department of Plant Science
University of California at Davis
Phone: <a href="tel:%28530%29%20752-0609" value="+15307520609" target="_blank">(530) 752-0609
Skype: hansvg.ucd



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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Re: Autocomplete limit?

Hans Vasquez-Gross
Yes, I do see the process getting larger and spawning more pids.  When testing auto complete , I can see as I type characters, there is a POST that happens from prototype.js line 1530.   Below you can find some system information.

Thanks,
-Hans

havasquezgross@dendrome:~$ free -m
             total       used       free     shared    buffers     cached
Mem:         32178      31927        251          0          1         33
-/+ buffers/cache:      31892        286
Swap:         4095       3179        916

havasquezgross@dendrome:~$ ps aux | grep gbrow
root      1076  0.0  0.0 153044    16 ?        Ss   12:24   0:00 /usr/bin/perl /usr/bin/gbrowse_slave --port 8101 --verbose 2 --log /var/log/gbrowse/gbrowse_slave --prefork 3 --pid /var/run/gbrowse/gbrowse-slave.8101.pid --preload /etc/gbrowse/slave_preload.conf
root      1080  0.0  0.0 153040    16 ?        Ss   12:24   0:00 /usr/bin/perl /usr/bin/gbrowse_slave --port 8102 --verbose 2 --log /var/log/gbrowse/gbrowse_slave --prefork 3 --pid /var/run/gbrowse/gbrowse-slave.8102.pid --preload /etc/gbrowse/slave_preload.conf
root      1084  0.0  0.0 153044     4 ?        S    12:24   0:00 /usr/bin/perl /usr/bin/gbrowse_slave --port 8101 --verbose 2 --log /var/log/gbrowse/gbrowse_slave --prefork 3 --pid /var/run/gbrowse/gbrowse-slave.8101.pid --preload /etc/gbrowse/slave_preload.conf
root      1085  0.0  0.0 153044     4 ?        S    12:24   0:00 /usr/bin/perl /usr/bin/gbrowse_slave --port 8101 --verbose 2 --log /var/log/gbrowse/gbrowse_slave --prefork 3 --pid /var/run/gbrowse/gbrowse-slave.8101.pid --preload /etc/gbrowse/slave_preload.conf
root      1086  0.0  0.0 153044     4 ?        S    12:24   0:00 /usr/bin/perl /usr/bin/gbrowse_slave --port 8101 --verbose 2 --log /var/log/gbrowse/gbrowse_slave --prefork 3 --pid /var/run/gbrowse/gbrowse-slave.8101.pid --preload /etc/gbrowse/slave_preload.conf
root      1087  0.0  0.0 153040    16 ?        Ss   12:24   0:00 /usr/bin/perl /usr/bin/gbrowse_slave --port 8103 --verbose 2 --log /var/log/gbrowse/gbrowse_slave --prefork 3 --pid /var/run/gbrowse/gbrowse-slave.8103.pid --preload /etc/gbrowse/slave_preload.conf
root      1120  0.0  0.0 153040     4 ?        S    12:24   0:00 /usr/bin/perl /usr/bin/gbrowse_slave --port 8102 --verbose 2 --log /var/log/gbrowse/gbrowse_slave --prefork 3 --pid /var/run/gbrowse/gbrowse-slave.8102.pid --preload /etc/gbrowse/slave_preload.conf
root      1121  0.0  0.0 153040     4 ?        S    12:24   0:00 /usr/bin/perl /usr/bin/gbrowse_slave --port 8102 --verbose 2 --log /var/log/gbrowse/gbrowse_slave --prefork 3 --pid /var/run/gbrowse/gbrowse-slave.8102.pid --preload /etc/gbrowse/slave_preload.conf
root      1122  0.0  0.0 153040     4 ?        S    12:24   0:00 /usr/bin/perl /usr/bin/gbrowse_slave --port 8102 --verbose 2 --log /var/log/gbrowse/gbrowse_slave --prefork 3 --pid /var/run/gbrowse/gbrowse-slave.8102.pid --preload /etc/gbrowse/slave_preload.conf
root      1207  0.0  0.0 153040     4 ?        S    12:24   0:00 /usr/bin/perl /usr/bin/gbrowse_slave --port 8103 --verbose 2 --log /var/log/gbrowse/gbrowse_slave --prefork 3 --pid /var/run/gbrowse/gbrowse-slave.8103.pid --preload /etc/gbrowse/slave_preload.conf
root      1208  0.0  0.0 153040     4 ?        S    12:24   0:00 /usr/bin/perl /usr/bin/gbrowse_slave --port 8103 --verbose 2 --log /var/log/gbrowse/gbrowse_slave --prefork 3 --pid /var/run/gbrowse/gbrowse-slave.8103.pid --preload /etc/gbrowse/slave_preload.conf
root      1209  0.0  0.0 153040     4 ?        S    12:24   0:00 /usr/bin/perl /usr/bin/gbrowse_slave --port 8103 --verbose 2 --log /var/log/gbrowse/gbrowse_slave --prefork 3 --pid /var/run/gbrowse/gbrowse-slave.8103.pid --preload /etc/gbrowse/slave_preload.conf
www-data  2104  0.8  2.3 4283484 762728 ?      S    12:28   1:07 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 13813  4.2  8.2 4283484 2725036 ?     D    14:35   0:24 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 13814  4.1  8.2 4283484 2716056 ?     D    14:35   0:24 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 13819  4.0  7.9 4283484 2611684 ?     D    14:35   0:23 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 13820  3.9  7.4 4283484 2468304 ?     D    14:35   0:22 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 13821  0.9  0.1 317808 64464 ?        S    14:36   0:05 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 13822  3.8  7.5 4283484 2472632 ?     D    14:36   0:21 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 13823  3.8  7.5 4283484 2473848 ?     D    14:36   0:21 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 13825  3.8  7.4 4283484 2465132 ?     D    14:36   0:21 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 13827  0.6  0.1 315132 61404 ?        S    14:36   0:03 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 13832  3.9  7.5 4283484 2473244 ?     D    14:36   0:22 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 13838  0.6  0.1 312984 59172 ?        S    14:36   0:03 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 13846  4.0  7.4 4283484 2454240 ?     D    14:36   0:22 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 13852  0.3  0.1 313544 60520 ?        S    14:36   0:02 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 13862  3.9  7.4 4283484 2465432 ?     D    14:36   0:22 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 13867  0.2  0.1 312016 56292 ?        S    14:36   0:01 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 13888  3.9  7.4 4283484 2453824 ?     D    14:36   0:21 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 13890  0.3  0.1 314408 61808 ?        S    14:36   0:01 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 13899  2.7  4.6 4283484 1540232 ?     D    14:37   0:13 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 13900  2.8  4.6 4283484 1529644 ?     D    14:37   0:14 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 13901  2.8  4.5 4283484 1500076 ?     R    14:37   0:14 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 13925  2.1  3.5 4283484 1182944 ?     D    14:37   0:10 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 14012  0.3  0.1 144420 36404 ?        S    14:40   0:01 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 14015  0.3  0.1 144420 36408 ?        S    14:40   0:00 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 14020  0.3  0.1 144420 36408 ?        S    14:40   0:01 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 14032  0.3  0.1 144420 36408 ?        S    14:40   0:00 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 14046  0.3  0.1 144420 36408 ?        S    14:40   0:00 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 14060  0.3  0.1 144420 36408 ?        S    14:40   0:00 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 14065  0.3  0.1 144420 36412 ?        S    14:40   0:00 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 14108  0.3  0.1 144420 36408 ?        S    14:40   0:00 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 14114  0.3  0.1 144420 36412 ?        S    14:40   0:00 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 14130  0.3  0.1 144420 36408 ?        S    14:41   0:00 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 14135  0.3  0.1 144420 36408 ?        S    14:41   0:00 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 14143  0.2  0.1 144420 36408 ?        S    14:41   0:00 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 14967  5.2  0.1 245536 58488 ?        D    14:45   0:01 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 15047  4.0  0.1 147556 41948 ?        D    14:45   0:00 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
www-data 15055  1.0  0.0  35224  6768 ?        D    14:45   0:00 /usr/bin/perl /usr/lib/cgi-bin/gbrowse/gbrowse
1009     15061  0.0  0.0   9388   848 pts/4    S+   14:45   0:00 grep gbrow


On Tue, Apr 30, 2013 at 2:32 PM, Lincoln Stein <[hidden email]> wrote:
Do you see the webserver process getting larger?

Lincoln


On Tue, Apr 30, 2013 at 5:09 PM, Hans Vasquez-Gross <[hidden email]> wrote:
If that is what's happening, I could see it filling up memory.  The webserver has 32gb of RAM available which should be plenty though.   All adapters are configured as follows in the individual datasource.conf files.

[scaffolds:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::Pg
                -dsn dbname=****************;host=**************
                -user *********************
                -pass *********************
search options = exact, -fulltext, +autocomplete



The Gbrowse.conf is also configured for these same default search options.  Thanks for the help Lincoln. 

Cheers,
-Hans



On Tue, Apr 30, 2013 at 1:33 PM, Lincoln Stein <[hidden email]> wrote:
In fact there is a hard-coded limit of 100 on the number of feature names that can be returned by autocomplete, so I suspect that there is a bug in the way that prefix-matching is implemented in the database adapter you are happening to be using. This would also explain why your server is crashing -- it is probably filling up memory. 

What adapter is attached to your assembly?

Lincoln


On Tue, Apr 30, 2013 at 3:47 PM, Hans Vasquez-Gross <[hidden email]> wrote:
Hi All,

     Is there a limit for the number of sequences autocomplete works with?  Two example data sources are provided below, which work fine with autocomplete.   


    However, testing autocomplete on a new load of an early v0.8 assembly of a ~22Gbp genome with ~16.5 million individual sequences has not been successful.   If I try to type the first few characters of a scaffold (ie jcf), a list never drops down.  

I continued typing a sequence name reasoning that maybe there was a limit to how many results could be returned, but it never autocompleted.  In fact, I'm fairly certain when testing this assembly performance with autocomplete in GBrowse caused my webserver to become unresponsive and had to be restarted.  I'd like to have the autocomplete return a minimal number of scaffolds (20+-) so it'll stay responsive and not crash the server, but continue filtering that set as the user types more of the scaffold name.

   Any comments or suggestions would be greatly appreciated.

Thanks,
-Hans

------------------------------------------------------------------------------
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Get 100% visibility into your production application - at no cost.
Code-level diagnostics for performance bottlenecks with <2% overhead
Download for free and get started troubleshooting in minutes.
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Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
<a href="tel:416%20673-8514" value="+14166738514" target="_blank">416 673-8514
Assistant: Renata Musa <[hidden email]>



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Hans Vasquez-Gross
iPlant Developer
Neale Lab - Robbins Hall 262
Department of Plant Science
University of California at Davis
Phone: <a href="tel:%28530%29%20752-0609" value="+15307520609" target="_blank">(530) 752-0609
Skype: hansvg.ucd



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
<a href="tel:416%20673-8514" value="+14166738514" target="_blank">416 673-8514
Assistant: Renata Musa <[hidden email]>



--
----------
Hans Vasquez-Gross
iPlant Developer
Neale Lab - Robbins Hall 262
Department of Plant Science
University of California at Davis
Phone: (530) 752-0609
Skype: hansvg.ucd

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Re: Autocomplete limit?

Hans Vasquez-Gross
On the pages that do successfully autocomplete, the POST returns back a 200 status and populates the dropdown.  However, running on the genome assembly, I can see the status on the POST pending for a while ( more then 1 minute).   Then, after 1.7minutes of execution, it returns back a 200 OK status, but no data is in the dropdown.

Thanks,
-Hans


------------------------------------------------------------------------------
Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET
Get 100% visibility into your production application - at no cost.
Code-level diagnostics for performance bottlenecks with <2% overhead
Download for free and get started troubleshooting in minutes.
http://p.sf.net/sfu/appdyn_d2d_ap1
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