Any suggestions on this error message when creating a new list?

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Any suggestions on this error message when creating a new list?

Sam Hokin-3
Hi, devs. I'm totally confounded by this error message. Often it's not "real", in that if I close the error message, the Create List
button is re-enabled and I can save the list just fine. But other times the error returns without saving the list.

I can't for the life of me seem to get anything to appear in Tomcat's log files; the HTTP logs just give a 500.

Is there a way to get some more info out of this? I'm logged in as admin, so any server-side exceptions reserved for admins would
presumably appear, but this has the markings of a client-side error.

Thanks!
Sam

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Re: Any suggestions on this error message when creating a new list?

Sam Hokin-3
Oh, I forgot to mention, and this may matter a lot: I'm running the current dev branch.

commit 1395d518c96c9780c1a6cd282980e8276df9bab1
Author: julie-sullivan <[hidden email]>
Date:   Mon Jul 4 14:20:24 2016 +0100

On 07/09/2016 07:26 AM, Sam Hokin wrote:

> Hi, devs. I'm totally confounded by this error message. Often it's not "real", in that if I close the error message, the Create List
> button is re-enabled and I can save the list just fine. But other times the error returns without saving the list.
>
> I can't for the life of me seem to get anything to appear in Tomcat's log files; the HTTP logs just give a 500.
>
> Is there a way to get some more info out of this? I'm logged in as admin, so any server-side exceptions reserved for admins would
> presumably appear, but this has the markings of a client-side error.
>
> Thanks!
> Sam
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev
>
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Re: Any suggestions on this error message when creating a new list?

Joel Richardson-2
In reply to this post by Sam Hokin-3

Hi Sam,

Check intermine.log in the same directory as the tomcat logs.

Joel

--
Joel E. Richardson, Ph.D.
Sr. Research Scientist
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, Maine 04609
207-288-6435
[hidden email]





On 7/9/16, 9:26 AM, "dev on behalf of Sam Hokin"
<[hidden email] on behalf of [hidden email]> wrote:

>Hi, devs. I'm totally confounded by this error message. Often it's not
>"real", in that if I close the error message, the Create List
>button is re-enabled and I can save the list just fine. But other times
>the error returns without saving the list.
>
>I can't for the life of me seem to get anything to appear in Tomcat's log
>files; the HTTP logs just give a 500.
>
>Is there a way to get some more info out of this? I'm logged in as admin,
>so any server-side exceptions reserved for admins would
>presumably appear, but this has the markings of a client-side error.
>
>Thanks!
>Sam

---

The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

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Re: Any suggestions on this error message when creating a new list?

joe carlson
Do you know how to attach a debugger to the web app?

Works for me. Many, many times.

Joe

> On Jul 9, 2016, at 11:22 AM, Joel Richardson <[hidden email]> wrote:
>
>
> Hi Sam,
>
> Check intermine.log in the same directory as the tomcat logs.
>
> Joel
>
> --
> Joel E. Richardson, Ph.D.
> Sr. Research Scientist
> Mouse Genome Informatics
> The Jackson Laboratory
> 600 Main Street
> Bar Harbor, Maine 04609
> 207-288-6435
> [hidden email]
>
>
>
>
>
> On 7/9/16, 9:26 AM, "dev on behalf of Sam Hokin"
> <[hidden email] on behalf of [hidden email]> wrote:
>
>> Hi, devs. I'm totally confounded by this error message. Often it's not
>> "real", in that if I close the error message, the Create List
>> button is re-enabled and I can save the list just fine. But other times
>> the error returns without saving the list.
>>
>> I can't for the life of me seem to get anything to appear in Tomcat's log
>> files; the HTTP logs just give a 500.
>>
>> Is there a way to get some more info out of this? I'm logged in as admin,
>> so any server-side exceptions reserved for admins would
>> presumably appear, but this has the markings of a client-side error.
>>
>> Thanks!
>> Sam
>
> ---
>
> The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev
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Re: Any suggestions on this error message when creating a new list?

Julie Sullivan-2
In reply to this post by Sam Hokin-3
Hi Sam,

Yes, seems like a client-side issue definitely. To track those down, I
usually use the dev console in my browser. Try that? Look in the console
panel, do you see any errors?

Can you reproduce the issue on beta flymine? beta.flymine.org is on the
dev branch too. I wasn't able to get an errors to appear.

Make a ticket?

Cheers
Julie

On 07/09/2016 02:26 PM, Sam Hokin wrote:

> Hi, devs. I'm totally confounded by this error message. Often it's not
> "real", in that if I close the error message, the Create List button is
> re-enabled and I can save the list just fine. But other times the error
> returns without saving the list.
>
> I can't for the life of me seem to get anything to appear in Tomcat's
> log files; the HTTP logs just give a 500.
>
> Is there a way to get some more info out of this? I'm logged in as
> admin, so any server-side exceptions reserved for admins would
> presumably appear, but this has the markings of a client-side error.
>
> Thanks!
> Sam
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev
>
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[hidden email]
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Re: Any suggestions on this error message when creating a new list?

Sam Hokin-3
Thanks, Julie. Yeah, It's not reproducing on beta.flymine; because I can't make outgoing HTTP connections to cdn.intermine.org on
this rather locked-down public server. I'll have to lock our sysadmin in a closet without food until he gives in.... Thanks for the tip!

Using //@ to indicate sourceMappingURL pragmas is deprecated. Use //# instead jquery.min.js:1:0

ƒ InterMine JavaScript Library loaded intermine.js:1:365
mutating the [[Prototype]] of an object will cause your code to run very slowly; instead create the object with the correct initial
[[Prototype]] value using Object.create imtables.js:29647:3

Using imtables: 2.0.0 results.do:875:9

Webservice is at version 19 results.do:904:5

Use of getPreventDefault() is deprecated.  Use defaultPrevented instead. jquery.min.js:5:12747

Error: Service failed. Please contact support.
Stack trace:
[3]</</blocking/</<@http://cdn.intermine.org/js/intermine/imjs/3.15.0/im.js:139:31
[29]</EventEmitter.prototype.emit@http://cdn.intermine.org/js/intermine/imjs/3.15.0/im.js:8281:9
[54]</Response.prototype.handle@http://cdn.intermine.org/js/intermine/imjs/3.15.0/im.js:13263:14
[53]</module.exports/xhr.onreadystatechange@http://cdn.intermine.org/js/intermine/imjs/3.15.0/im.js:13026:9
imtables.js:18173:18

null
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Re: Any suggestions on this error message when creating a new list?

joe carlson
In reply to this post by joe carlson


On 07/11/2016 09:02 AM, Sam Hokin wrote:
> I do not. You mean a JVM debugger? Or something that spits client-side
> stuff out? Either way I'm all ears.

I have found this to be essential.

I work in eclipse. I know other people may like intellij or netbeans
better, but they're not for me. So I can only give the recipe for
eclipse but I suspect the other IDEs have similar capabilities.

First, import the intermine codebase into eclipse. It is not necessary
to get everything absolutely perfect. I still have some places where the
classpaths are not completely set up; but that's OK. I don't use eclipse
to build or deploy the code. Intermine must be built with debugging
information - check that imbuild/library.xml has <property
name="javac.debug" value="on"/> and <property name="javac.debuglevel"
value="lines,vars,source"/> and that the source you're looking at agrees
with what was used to build the deployed code.

I'm using tomcat-7 on the webserver. On the server side, take whatever
script you use for starting tomcat and define the environment variable
JDPA_OPTS. For me I use
> export JPDA_OPTS=-agentlib:jdwp=transport=dt_socket,address=<web
> server host>:8069,server=y,suspend=y
(Obviously replace <web server host> with the name of your host. I'm
using 8069 as the debug port. You can use any free port)

and start tomcat with:

>     $CATALINA_HOME/bin/catalina.sh jpda start

After you issue that command, you'll probably get a 503 response if you
point your browser to the webapp. You need to get eclipse to connect
first. You do not need to be on the same host as the web server.

Select Debug -> Debug Configuration -> Remote Java Application.

Enter the name of the project (Intermine), Connection Type: Standard
(Socket Attach) The connection properties are Host: <web server host>
and port 8069. Then click debug.

Now the web server will respond, a bit slower than normal, but certainly
usable. Browse over the the bag creation code and set a breakpoint by
right clicking on the line number or ctrl-shift-B. As soon as the hit
this code, eclipse should automatically switch into the debug
perspective and you can step through the code line by line.

Hours of fun!

Joe
>
> On 07/09/2016 01:13 PM, Joe Carlson wrote:
>> Do you know how to attach a debugger to the web app?
>>
>> Works for me. Many, many times.
>>
>> Joe

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Re: Any suggestions on this error message when creating a new list?

Yo Yehudi-2
Hey Sam,

Is this happening on the live mines? I've still been having performance issues in general whilst trying to browse the beany mines (this is after you upgraded the server instance), with a lot of timeouts and 500s. I've tried to replicate the situation on the beany mines to see if I can find out any more myself but I can't actually get that far - might it be that the front end is simply reflecting the back end performance issues? I suspect Joe's suggestion may be the way forward.

Thanks,

Yo

On 11 July 2016 at 18:06, Joe Carlson <[hidden email]> wrote:


On 07/11/2016 09:02 AM, Sam Hokin wrote:
I do not. You mean a JVM debugger? Or something that spits client-side stuff out? Either way I'm all ears.

I have found this to be essential.

I work in eclipse. I know other people may like intellij or netbeans better, but they're not for me. So I can only give the recipe for eclipse but I suspect the other IDEs have similar capabilities.

First, import the intermine codebase into eclipse. It is not necessary to get everything absolutely perfect. I still have some places where the classpaths are not completely set up; but that's OK. I don't use eclipse to build or deploy the code. Intermine must be built with debugging information - check that imbuild/library.xml has <property name="javac.debug" value="on"/> and <property name="javac.debuglevel" value="lines,vars,source"/> and that the source you're looking at agrees with what was used to build the deployed code.

I'm using tomcat-7 on the webserver. On the server side, take whatever script you use for starting tomcat and define the environment variable JDPA_OPTS. For me I use
export JPDA_OPTS=-agentlib:jdwp=transport=dt_socket,address=<web server host>:8069,server=y,suspend=y
(Obviously replace <web server host> with the name of your host. I'm using 8069 as the debug port. You can use any free port)

and start tomcat with:

    $CATALINA_HOME/bin/catalina.sh jpda start

After you issue that command, you'll probably get a 503 response if you point your browser to the webapp. You need to get eclipse to connect first. You do not need to be on the same host as the web server.

Select Debug -> Debug Configuration -> Remote Java Application.

Enter the name of the project (Intermine), Connection Type: Standard (Socket Attach) The connection properties are Host: <web server host> and port 8069. Then click debug.

Now the web server will respond, a bit slower than normal, but certainly usable. Browse over the the bag creation code and set a breakpoint by right clicking on the line number or ctrl-shift-B. As soon as the hit this code, eclipse should automatically switch into the debug perspective and you can step through the code line by line.

Hours of fun!

Joe


On 07/09/2016 01:13 PM, Joe Carlson wrote:
Do you know how to attach a debugger to the web app?

Works for me. Many, many times.

Joe

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev


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Re: Any suggestions on this error message when creating a new list?

Joel Richardson-2

I still wonder if the relevant error messages aren’t being logged in intermine.log – wherever it is.

Joel
— 
Joel E. Richardson, Ph.D.
Sr. Research Scientist
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, Maine 04609
207-288-6435

From: Yo Yehudi <[hidden email]>
Reply-To: "[hidden email]" <[hidden email]>
Date: Tuesday, July 12, 2016 at 6:12 AM
To: Joe Carlson <[hidden email]>
Cc: Sam Hokin <[hidden email]>, Joel Richardson <[hidden email]>, "[hidden email]" <[hidden email]>
Subject: Re: [InterMine Dev] Any suggestions on this error message when creating a new list?

Hey Sam,

Is this happening on the live mines? I've still been having performance issues in general whilst trying to browse the beany mines (this is after you upgraded the server instance), with a lot of timeouts and 500s. I've tried to replicate the situation on the beany mines to see if I can find out any more myself but I can't actually get that far - might it be that the front end is simply reflecting the back end performance issues? I suspect Joe's suggestion may be the way forward.

Thanks,

Yo

On 11 July 2016 at 18:06, Joe Carlson <[hidden email]> wrote:


On 07/11/2016 09:02 AM, Sam Hokin wrote:
I do not. You mean a JVM debugger? Or something that spits client-side stuff out? Either way I'm all ears.

I have found this to be essential.

I work in eclipse. I know other people may like intellij or netbeans better, but they're not for me. So I can only give the recipe for eclipse but I suspect the other IDEs have similar capabilities.

First, import the intermine codebase into eclipse. It is not necessary to get everything absolutely perfect. I still have some places where the classpaths are not completely set up; but that's OK. I don't use eclipse to build or deploy the code. Intermine must be built with debugging information - check that imbuild/library.xml has <property name="javac.debug" value="on"/> and <property name="javac.debuglevel" value="lines,vars,source"/> and that the source you're looking at agrees with what was used to build the deployed code.

I'm using tomcat-7 on the webserver. On the server side, take whatever script you use for starting tomcat and define the environment variable JDPA_OPTS. For me I use
export JPDA_OPTS=-agentlib:jdwp=transport=dt_socket,address=<web server host>:8069,server=y,suspend=y
(Obviously replace <web server host> with the name of your host. I'm using 8069 as the debug port. You can use any free port)

and start tomcat with:

    $CATALINA_HOME/bin/catalina.sh jpda start

After you issue that command, you'll probably get a 503 response if you point your browser to the webapp. You need to get eclipse to connect first. You do not need to be on the same host as the web server.

Select Debug -> Debug Configuration -> Remote Java Application.

Enter the name of the project (Intermine), Connection Type: Standard (Socket Attach) The connection properties are Host: <web server host> and port 8069. Then click debug.

Now the web server will respond, a bit slower than normal, but certainly usable. Browse over the the bag creation code and set a breakpoint by right clicking on the line number or ctrl-shift-B. As soon as the hit this code, eclipse should automatically switch into the debug perspective and you can step through the code line by line.

Hours of fun!

Joe


On 07/09/2016 01:13 PM, Joe Carlson wrote:
Do you know how to attach a debugger to the web app?

Works for me. Many, many times.

Joe

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev

---

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Re: Any suggestions on this error message when creating a new list?

Sam Hokin-3
Yeah, I'm still working on it. Joel, I found intermine.log under /usr/share/tomcat. Not a particularly appropriate place, but it's
there and there's plenty of exception messages to ponder.

Yo, it's definitely back-end performance issues. We need more RAM. The mines work pretty well after a reboot or Tomcat restart, and
then things degrade over a half day to the point that 500s start being thrown, presumably due to timeouts. But now that I've found
the realtime log I can start to chip away at the causes of the exceptions. Should have things running better soon, I think, and
especially after we get more RAM on the VM.

Thanks for all the help, guys!

On 07/12/2016 04:26 AM, Joel Richardson wrote:
>
> I still wonder if the relevant error messages aren’t being logged in intermine.log – wherever it is.
>
> Joel
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