tomcat version requirement

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tomcat version requirement

joe carlson
Hello,

I’ve been wrestling with a page that is hanging (buildBag.do). I’m basically watching the wheel spin while the identifiers got verified.

I was running my tomcat through the debugger and seeing that it looked like all the intermine code was executing just fine; it looked like some internal java calls in making threads were the problem. I checked to see if my java was up to date, but then I noticed that you are now saying version 7 of tomcat is now the minimum. Did this just recently change on or about 1.3? In the past couple weeks I merged with the main branch again and essentially went from 1.1 to 1.3.

Are there known issues that demand tomcat-7, or is this just your configuration?

I’ve deployed on a tomcat-7 here but I’m still seeing the page hang at ‘verifying identifiers’. Have there been other reports of this problem? I’m still working on that.

Thanks,

Joe Carlson
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Re: tomcat version requirement

Alex Kalderimis-2
Hi Joe,

InterMine continues to work well with Tomcat-6. You are welcome to keep
using this version of Tomcat for as long as it meets your requirements.
Obviously it is getting a bit old now, and with the release of Tomcat 8
we made the decision to focus support on Tomcat 7. Documentation for
supporting Tomcat 8 should be up shortly.

As for the issue you report with verifying identifiers, that is unlikely
to be anything to do with Tomcat - if you can get to the home page then
you have configured Tomcat just fine; anything beyond there is our issue.

If your application is publicly accessible, it would help to debug it if
you could provide a link to the problematic release. If that is not
possible, then if you could open the development console (CTL-SHIFT-K in
Firefox, CTL-SHIFT-J in Chrom(e|ium)) and see if any errors are
reported, specifically to do with network requests, that would be very
helpful.

All best,

Alex Kalderimis



On 20/08/14 21:18, Joe Carlson wrote:

> Hello,
>
> I’ve been wrestling with a page that is hanging (buildBag.do). I’m basically watching the wheel spin while the identifiers got verified.
>
> I was running my tomcat through the debugger and seeing that it looked like all the intermine code was executing just fine; it looked like some internal java calls in making threads were the problem. I checked to see if my java was up to date, but then I noticed that you are now saying version 7 of tomcat is now the minimum. Did this just recently change on or about 1.3? In the past couple weeks I merged with the main branch again and essentially went from 1.1 to 1.3.
>
> Are there known issues that demand tomcat-7, or is this just your configuration?
>
> I’ve deployed on a tomcat-7 here but I’m still seeing the page hang at ‘verifying identifiers’. Have there been other reports of this problem? I’m still working on that.
>
> Thanks,
>
> Joe Carlson
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

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Re: tomcat version requirement

joe carlson
Hi Alex,

Thanks for the reply. It's good to hear that tomcat-6 should still work.
We were going to make the transition to 7 relatively soon anyway. But
it's good to hear that my weekend will not be in panic mode now. Since
writing I spent some time with java 6/7 and tomcat 6/7 combinations and
do not think that is my problem.

Our mine is accessible: phytozome.jgi.doe.gov/phytomine. Type in a
poplar gene like Potri.001G027800 in the analyze box and you can see the
phenomenon. We had our first report from a user about this yesterday
from Gos.

Here's a random collection of facts. Some of which may be relevant:

1. We had an earlier version of the mine running since January and
creating a list by pasting in values worked quite well. This was based
on a fork of 1.1

2. Between then and now, I had redeployed webapp and replaced the
objectstore database a few times - and did not touch the userprofile
database. This always seemed to work. I had noticed that if an old list
contained an item that disappeared, a verification screen came up and
reported some things had disappeared. This all looked good to me. And I
liked how the verification happened. The webapp code was all based on a
fork of 1.1

3. About a week ago, I deployed a new webapp after a merge with 1.3.
Again, there was a new objectstore database and user profile database
was not touched.

4. The bug is that pasting values into the analyze box hangs at the
'verifying identifiers' step. Another thing I've seen is that if I look
at my gene lists that I had saved before the reload, they all say '0
genes'. But by manually looking at the userprofile database I can see
that the lists are still there.

5. I can make new lists. If I save the results of a query into a list,
it works. And those show up on the list page with the proper number of
genes.

6. We're using the intermine lists as a way of storing our 'shopping
cart' in our main web portal
http://phytozome.jgi.doe.gov/pz/portal.html. List creation and retrieval
works here, indicating the webservice list operations are OK. (This was
the workaround that I suggested to Gos yesterday. If he puts things into
the shopping cart from the main portal, he can use that list in
intermine later.)

7. I spent time running the webapp through the debugger yesterday. I
verified that the queries in BagQueryRunner are being executed and
returning proper results. I've walk the code through the end of that
thread and all looked OK. But I still need to figure out which thread to
look at after that.

8. Here is the output of the web console for things marked with
javascript. I did not include the css messages:

> [09:44:56.016] The Web Console logging API (console.log, console.info,
> console.warn, console.error) has been disabled by a script on this page.
> [09:44:47.166] Use of Mutation Events is deprecated. Use
> MutationObserver instead. @
> chrome://firebug/content/chrome/tabContext.js:589
> --
> [09:45:20.663] Use of Mutation Events is deprecated. Use
> MutationObserver instead. @
> chrome://firebug/content/chrome/tabContext.js:589
> [09:45:21.457] ReferenceError: require is not defined @
> http://phytozome.jgi.doe.gov/phytomine/buildBag.do:648
The suspicious thing is the last line.

That's where I stand right now. I need to see what should happen after
BagQueryRunner and track that. I'd appreciate any comments.

Joe Carlson


 Alex Kalderimis wrote:

> Hi Joe,
>
> InterMine continues to work well with Tomcat-6. You are welcome to keep
> using this version of Tomcat for as long as it meets your requirements.
> Obviously it is getting a bit old now, and with the release of Tomcat 8
> we made the decision to focus support on Tomcat 7. Documentation for
> supporting Tomcat 8 should be up shortly.
>
> As for the issue you report with verifying identifiers, that is unlikely
> to be anything to do with Tomcat - if you can get to the home page then
> you have configured Tomcat just fine; anything beyond there is our issue.
>
> If your application is publicly accessible, it would help to debug it if
> you could provide a link to the problematic release. If that is not
> possible, then if you could open the development console (CTL-SHIFT-K in
> Firefox, CTL-SHIFT-J in Chrom(e|ium)) and see if any errors are
> reported, specifically to do with network requests, that would be very
> helpful.
>
> All best,
>
> Alex Kalderimis
>
>
>
> On 20/08/14 21:18, Joe Carlson wrote:
>  
>> Hello,
>>
>> I’ve been wrestling with a page that is hanging (buildBag.do). I’m basically watching the wheel spin while the identifiers got verified.
>>
>> I was running my tomcat through the debugger and seeing that it looked like all the intermine code was executing just fine; it looked like some internal java calls in making threads were the problem. I checked to see if my java was up to date, but then I noticed that you are now saying version 7 of tomcat is now the minimum. Did this just recently change on or about 1.3? In the past couple weeks I merged with the main branch again and essentially went from 1.1 to 1.3.
>>
>> Are there known issues that demand tomcat-7, or is this just your configuration?
>>
>> I’ve deployed on a tomcat-7 here but I’m still seeing the page hang at ‘verifying identifiers’. Have there been other reports of this problem? I’m still working on that.
>>
>> Thanks,
>>
>> Joe Carlson
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>
>>    


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Re: tomcat version requirement

Julie Sullivan
Hi Joe!

I just tested this and it worked fine. How did you fix the problem?

Julie

> Hi Alex,
>
> Thanks for the reply. It's good to hear that tomcat-6 should still work.
> We were going to make the transition to 7 relatively soon anyway. But
> it's good to hear that my weekend will not be in panic mode now. Since
> writing I spent some time with java 6/7 and tomcat 6/7 combinations and
> do not think that is my problem.
>
> Our mine is accessible: phytozome.jgi.doe.gov/phytomine. Type in a
> poplar gene like Potri.001G027800 in the analyze box and you can see the
> phenomenon. We had our first report from a user about this yesterday
> from Gos.
>
> Here's a random collection of facts. Some of which may be relevant:
>
> 1. We had an earlier version of the mine running since January and
> creating a list by pasting in values worked quite well. This was based
> on a fork of 1.1
>
> 2. Between then and now, I had redeployed webapp and replaced the
> objectstore database a few times - and did not touch the userprofile
> database. This always seemed to work. I had noticed that if an old list
> contained an item that disappeared, a verification screen came up and
> reported some things had disappeared. This all looked good to me. And I
> liked how the verification happened. The webapp code was all based on a
> fork of 1.1
>
> 3. About a week ago, I deployed a new webapp after a merge with 1.3.
> Again, there was a new objectstore database and user profile database
> was not touched.
>
> 4. The bug is that pasting values into the analyze box hangs at the
> 'verifying identifiers' step. Another thing I've seen is that if I look
> at my gene lists that I had saved before the reload, they all say '0
> genes'. But by manually looking at the userprofile database I can see
> that the lists are still there.
>
> 5. I can make new lists. If I save the results of a query into a list,
> it works. And those show up on the list page with the proper number of
> genes.
>
> 6. We're using the intermine lists as a way of storing our 'shopping
> cart' in our main web portal
> http://phytozome.jgi.doe.gov/pz/portal.html. List creation and retrieval
> works here, indicating the webservice list operations are OK. (This was
> the workaround that I suggested to Gos yesterday. If he puts things into
> the shopping cart from the main portal, he can use that list in
> intermine later.)
>
> 7. I spent time running the webapp through the debugger yesterday. I
> verified that the queries in BagQueryRunner are being executed and
> returning proper results. I've walk the code through the end of that
> thread and all looked OK. But I still need to figure out which thread to
> look at after that.
>
> 8. Here is the output of the web console for things marked with
> javascript. I did not include the css messages:
>> [09:44:56.016] The Web Console logging API (console.log, console.info,
>> console.warn, console.error) has been disabled by a script on this page.
>> [09:44:47.166] Use of Mutation Events is deprecated. Use
>> MutationObserver instead. @
>> chrome://firebug/content/chrome/tabContext.js:589
>> --
>> [09:45:20.663] Use of Mutation Events is deprecated. Use
>> MutationObserver instead. @
>> chrome://firebug/content/chrome/tabContext.js:589
>> [09:45:21.457] ReferenceError: require is not defined @
>> http://phytozome.jgi.doe.gov/phytomine/buildBag.do:648
> The suspicious thing is the last line.
>
> That's where I stand right now. I need to see what should happen after
> BagQueryRunner and track that. I'd appreciate any comments.
>
> Joe Carlson
>
>
>  Alex Kalderimis wrote:
>> Hi Joe,
>>
>> InterMine continues to work well with Tomcat-6. You are welcome to keep
>> using this version of Tomcat for as long as it meets your requirements.
>> Obviously it is getting a bit old now, and with the release of Tomcat 8
>> we made the decision to focus support on Tomcat 7. Documentation for
>> supporting Tomcat 8 should be up shortly.
>>
>> As for the issue you report with verifying identifiers, that is unlikely
>> to be anything to do with Tomcat - if you can get to the home page then
>> you have configured Tomcat just fine; anything beyond there is our
>> issue.
>>
>> If your application is publicly accessible, it would help to debug it if
>> you could provide a link to the problematic release. If that is not
>> possible, then if you could open the development console (CTL-SHIFT-K in
>> Firefox, CTL-SHIFT-J in Chrom(e|ium)) and see if any errors are
>> reported, specifically to do with network requests, that would be very
>> helpful.
>>
>> All best,
>>
>> Alex Kalderimis
>>
>>
>>
>> On 20/08/14 21:18, Joe Carlson wrote:
>>
>>> Hello,
>>>
>>> I’ve been wrestling with a page that is hanging (buildBag.do). I’m
>>> basically watching the wheel spin while the identifiers got verified.
>>>
>>> I was running my tomcat through the debugger and seeing that it looked
>>> like all the intermine code was executing just fine; it looked like
>>> some internal java calls in making threads were the problem. I checked
>>> to see if my java was up to date, but then I noticed that you are now
>>> saying version 7 of tomcat is now the minimum. Did this just recently
>>> change on or about 1.3? In the past couple weeks I merged with the main
>>> branch again and essentially went from 1.1 to 1.3.
>>>
>>> Are there known issues that demand tomcat-7, or is this just your
>>> configuration?
>>>
>>> I’ve deployed on a tomcat-7 here but I’m still seeing the page hang at
>>> ‘verifying identifiers’. Have there been other reports of this problem?
>>> I’m still working on that.
>>>
>>> Thanks,
>>>
>>> Joe Carlson
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>>
>>>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>
>


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Re: tomcat version requirement

joe carlson
Hi Julie,

Yes, I was floundering a bit trying to find the source of the problem.
It turned out to be some missing components in the CDN.

We're hosting our own CDN and had synced up with your github, but there
are a couple of things not included (pomme and component-400). It took a
while to see that this was the issue since they are loaded dynamically.
If there had been a <script src=...> I would have seen that the file was
not found in the firebug console. But there was no error reporting from
the require('pomme'). (I think if I were grading this coding project, I
would have knocked off a few points for checking the return status of
the 'require'.)

But things are still not totally fixed. I can make a list, but if I type
in identifiers into the 'Create a new list' box that do not exist in
that class - or just type in nonsense - I get back the the infinite spin
during the 'verifying identifiers' step.

Another thing I see, and I don't know if this is related, is that I've
lost old lists. In the past, I've successfully swapped out the mine db
and kept the userprofile db. When I looked at a list that I had stored
using the earlier mine, I got a verification page that showed items that
were no longer found. That was all great and I had been happy to see
that you took care of this situation. But now all I see are '0 genes'
next to my old lists. They still have valid identifiers. What is the
processing that happens when a mine db get updated?

Thanks,

joe


On 09/02/2014 02:45 AM, [hidden email] wrote:

> Hi Joe!
>
> I just tested this and it worked fine. How did you fix the problem?
>
> Julie
>
>> Hi Alex,
>>
>> Thanks for the reply. It's good to hear that tomcat-6 should still work.
>> We were going to make the transition to 7 relatively soon anyway. But
>> it's good to hear that my weekend will not be in panic mode now. Since
>> writing I spent some time with java 6/7 and tomcat 6/7 combinations and
>> do not think that is my problem.
>>
>> Our mine is accessible: phytozome.jgi.doe.gov/phytomine. Type in a
>> poplar gene like Potri.001G027800 in the analyze box and you can see the
>> phenomenon. We had our first report from a user about this yesterday
>> from Gos.
>>
>> Here's a random collection of facts. Some of which may be relevant:
>>
>> 1. We had an earlier version of the mine running since January and
>> creating a list by pasting in values worked quite well. This was based
>> on a fork of 1.1
>>
>> 2. Between then and now, I had redeployed webapp and replaced the
>> objectstore database a few times - and did not touch the userprofile
>> database. This always seemed to work. I had noticed that if an old list
>> contained an item that disappeared, a verification screen came up and
>> reported some things had disappeared. This all looked good to me. And I
>> liked how the verification happened. The webapp code was all based on a
>> fork of 1.1
>>
>> 3. About a week ago, I deployed a new webapp after a merge with 1.3.
>> Again, there was a new objectstore database and user profile database
>> was not touched.
>>
>> 4. The bug is that pasting values into the analyze box hangs at the
>> 'verifying identifiers' step. Another thing I've seen is that if I look
>> at my gene lists that I had saved before the reload, they all say '0
>> genes'. But by manually looking at the userprofile database I can see
>> that the lists are still there.
>>
>> 5. I can make new lists. If I save the results of a query into a list,
>> it works. And those show up on the list page with the proper number of
>> genes.
>>
>> 6. We're using the intermine lists as a way of storing our 'shopping
>> cart' in our main web portal
>> http://phytozome.jgi.doe.gov/pz/portal.html. List creation and retrieval
>> works here, indicating the webservice list operations are OK. (This was
>> the workaround that I suggested to Gos yesterday. If he puts things into
>> the shopping cart from the main portal, he can use that list in
>> intermine later.)
>>
>> 7. I spent time running the webapp through the debugger yesterday. I
>> verified that the queries in BagQueryRunner are being executed and
>> returning proper results. I've walk the code through the end of that
>> thread and all looked OK. But I still need to figure out which thread to
>> look at after that.
>>
>> 8. Here is the output of the web console for things marked with
>> javascript. I did not include the css messages:
>>> [09:44:56.016] The Web Console logging API (console.log, console.info,
>>> console.warn, console.error) has been disabled by a script on this page.
>>> [09:44:47.166] Use of Mutation Events is deprecated. Use
>>> MutationObserver instead. @
>>> chrome://firebug/content/chrome/tabContext.js:589
>>> --
>>> [09:45:20.663] Use of Mutation Events is deprecated. Use
>>> MutationObserver instead. @
>>> chrome://firebug/content/chrome/tabContext.js:589
>>> [09:45:21.457] ReferenceError: require is not defined @
>>> http://phytozome.jgi.doe.gov/phytomine/buildBag.do:648
>> The suspicious thing is the last line.
>>
>> That's where I stand right now. I need to see what should happen after
>> BagQueryRunner and track that. I'd appreciate any comments.
>>
>> Joe Carlson
>>
>>
>>   Alex Kalderimis wrote:
>>> Hi Joe,
>>>
>>> InterMine continues to work well with Tomcat-6. You are welcome to keep
>>> using this version of Tomcat for as long as it meets your requirements.
>>> Obviously it is getting a bit old now, and with the release of Tomcat 8
>>> we made the decision to focus support on Tomcat 7. Documentation for
>>> supporting Tomcat 8 should be up shortly.
>>>
>>> As for the issue you report with verifying identifiers, that is unlikely
>>> to be anything to do with Tomcat - if you can get to the home page then
>>> you have configured Tomcat just fine; anything beyond there is our
>>> issue.
>>>
>>> If your application is publicly accessible, it would help to debug it if
>>> you could provide a link to the problematic release. If that is not
>>> possible, then if you could open the development console (CTL-SHIFT-K in
>>> Firefox, CTL-SHIFT-J in Chrom(e|ium)) and see if any errors are
>>> reported, specifically to do with network requests, that would be very
>>> helpful.
>>>
>>> All best,
>>>
>>> Alex Kalderimis
>>>
>>>
>>>
>>> On 20/08/14 21:18, Joe Carlson wrote:
>>>
>>>> Hello,
>>>>
>>>> I’ve been wrestling with a page that is hanging (buildBag.do). I’m
>>>> basically watching the wheel spin while the identifiers got verified.
>>>>
>>>> I was running my tomcat through the debugger and seeing that it looked
>>>> like all the intermine code was executing just fine; it looked like
>>>> some internal java calls in making threads were the problem. I checked
>>>> to see if my java was up to date, but then I noticed that you are now
>>>> saying version 7 of tomcat is now the minimum. Did this just recently
>>>> change on or about 1.3? In the past couple weeks I merged with the main
>>>> branch again and essentially went from 1.1 to 1.3.
>>>>
>>>> Are there known issues that demand tomcat-7, or is this just your
>>>> configuration?
>>>>
>>>> I’ve deployed on a tomcat-7 here but I’m still seeing the page hang at
>>>> ‘verifying identifiers’. Have there been other reports of this problem?
>>>> I’m still working on that.
>>>>
>>>> Thanks,
>>>>
>>>> Joe Carlson
>>>> _______________________________________________
>>>> dev mailing list
>>>> [hidden email]
>>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>>>
>>>>
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>
>>


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Re: tomcat version requirement

Julie Sullivan
Hi Joe

Sorry you are having so much trouble!

1. list upload with bad IDs

The list upload is executing the "ID resolution" web service call:

http://iodocs.labs.intermine.org/phytomine/docs

I tried it directly in the docs, and got the same behaviour. The job
never returns if the ID is not in the database.

Which version of InterMine are you using? An updated version of the
master branch? Are you using what's on github?

This may take some investigation as I'm not totally certain what's going on.

2. lists with 0 entries

Here are the docs for the list upgrade:

http://intermine.readthedocs.org/en/latest/webapp/lists/list-upgrade/#serial-number-overview

A list shouldn't have zero entries, not with still-valid identifiers.

You've logged in and these lists were marked as upgraded but then have
zero members? Is that the situation?

Maybe you could look in the userprofile to see what the lists' status are:

        select * from savedbag where userprofileid = SUPER_USER_ID;

I'd like to know how this happened, as it really shouldn't!

Julie

On 02/09/14 17:53, Joe Carlson wrote:

> Hi Julie,
>
> Yes, I was floundering a bit trying to find the source of the problem.
> It turned out to be some missing components in the CDN.
>
> We're hosting our own CDN and had synced up with your github, but there
> are a couple of things not included (pomme and component-400). It took a
> while to see that this was the issue since they are loaded dynamically.
> If there had been a <script src=...> I would have seen that the file was
> not found in the firebug console. But there was no error reporting from
> the require('pomme'). (I think if I were grading this coding project, I
> would have knocked off a few points for checking the return status of
> the 'require'.)
>
> But things are still not totally fixed. I can make a list, but if I type
> in identifiers into the 'Create a new list' box that do not exist in
> that class - or just type in nonsense - I get back the the infinite spin
> during the 'verifying identifiers' step.
>
> Another thing I see, and I don't know if this is related, is that I've
> lost old lists. In the past, I've successfully swapped out the mine db
> and kept the userprofile db. When I looked at a list that I had stored
> using the earlier mine, I got a verification page that showed items that
> were no longer found. That was all great and I had been happy to see
> that you took care of this situation. But now all I see are '0 genes'
> next to my old lists. They still have valid identifiers. What is the
> processing that happens when a mine db get updated?
>
> Thanks,
>
> joe
>
>
> On 09/02/2014 02:45 AM, [hidden email] wrote:
>> Hi Joe!
>>
>> I just tested this and it worked fine. How did you fix the problem?
>>
>> Julie
>>
>>> Hi Alex,
>>>
>>> Thanks for the reply. It's good to hear that tomcat-6 should still work.
>>> We were going to make the transition to 7 relatively soon anyway. But
>>> it's good to hear that my weekend will not be in panic mode now. Since
>>> writing I spent some time with java 6/7 and tomcat 6/7 combinations and
>>> do not think that is my problem.
>>>
>>> Our mine is accessible: phytozome.jgi.doe.gov/phytomine. Type in a
>>> poplar gene like Potri.001G027800 in the analyze box and you can see the
>>> phenomenon. We had our first report from a user about this yesterday
>>> from Gos.
>>>
>>> Here's a random collection of facts. Some of which may be relevant:
>>>
>>> 1. We had an earlier version of the mine running since January and
>>> creating a list by pasting in values worked quite well. This was based
>>> on a fork of 1.1
>>>
>>> 2. Between then and now, I had redeployed webapp and replaced the
>>> objectstore database a few times - and did not touch the userprofile
>>> database. This always seemed to work. I had noticed that if an old list
>>> contained an item that disappeared, a verification screen came up and
>>> reported some things had disappeared. This all looked good to me. And I
>>> liked how the verification happened. The webapp code was all based on a
>>> fork of 1.1
>>>
>>> 3. About a week ago, I deployed a new webapp after a merge with 1.3.
>>> Again, there was a new objectstore database and user profile database
>>> was not touched.
>>>
>>> 4. The bug is that pasting values into the analyze box hangs at the
>>> 'verifying identifiers' step. Another thing I've seen is that if I look
>>> at my gene lists that I had saved before the reload, they all say '0
>>> genes'. But by manually looking at the userprofile database I can see
>>> that the lists are still there.
>>>
>>> 5. I can make new lists. If I save the results of a query into a list,
>>> it works. And those show up on the list page with the proper number of
>>> genes.
>>>
>>> 6. We're using the intermine lists as a way of storing our 'shopping
>>> cart' in our main web portal
>>> http://phytozome.jgi.doe.gov/pz/portal.html. List creation and retrieval
>>> works here, indicating the webservice list operations are OK. (This was
>>> the workaround that I suggested to Gos yesterday. If he puts things into
>>> the shopping cart from the main portal, he can use that list in
>>> intermine later.)
>>>
>>> 7. I spent time running the webapp through the debugger yesterday. I
>>> verified that the queries in BagQueryRunner are being executed and
>>> returning proper results. I've walk the code through the end of that
>>> thread and all looked OK. But I still need to figure out which thread to
>>> look at after that.
>>>
>>> 8. Here is the output of the web console for things marked with
>>> javascript. I did not include the css messages:
>>>> [09:44:56.016] The Web Console logging API (console.log, console.info,
>>>> console.warn, console.error) has been disabled by a script on this
>>>> page.
>>>> [09:44:47.166] Use of Mutation Events is deprecated. Use
>>>> MutationObserver instead. @
>>>> chrome://firebug/content/chrome/tabContext.js:589
>>>> --
>>>> [09:45:20.663] Use of Mutation Events is deprecated. Use
>>>> MutationObserver instead. @
>>>> chrome://firebug/content/chrome/tabContext.js:589
>>>> [09:45:21.457] ReferenceError: require is not defined @
>>>> http://phytozome.jgi.doe.gov/phytomine/buildBag.do:648
>>> The suspicious thing is the last line.
>>>
>>> That's where I stand right now. I need to see what should happen after
>>> BagQueryRunner and track that. I'd appreciate any comments.
>>>
>>> Joe Carlson
>>>
>>>
>>>   Alex Kalderimis wrote:
>>>> Hi Joe,
>>>>
>>>> InterMine continues to work well with Tomcat-6. You are welcome to keep
>>>> using this version of Tomcat for as long as it meets your requirements.
>>>> Obviously it is getting a bit old now, and with the release of Tomcat 8
>>>> we made the decision to focus support on Tomcat 7. Documentation for
>>>> supporting Tomcat 8 should be up shortly.
>>>>
>>>> As for the issue you report with verifying identifiers, that is
>>>> unlikely
>>>> to be anything to do with Tomcat - if you can get to the home page then
>>>> you have configured Tomcat just fine; anything beyond there is our
>>>> issue.
>>>>
>>>> If your application is publicly accessible, it would help to debug
>>>> it if
>>>> you could provide a link to the problematic release. If that is not
>>>> possible, then if you could open the development console
>>>> (CTL-SHIFT-K in
>>>> Firefox, CTL-SHIFT-J in Chrom(e|ium)) and see if any errors are
>>>> reported, specifically to do with network requests, that would be very
>>>> helpful.
>>>>
>>>> All best,
>>>>
>>>> Alex Kalderimis
>>>>
>>>>
>>>>
>>>> On 20/08/14 21:18, Joe Carlson wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> I’ve been wrestling with a page that is hanging (buildBag.do). I’m
>>>>> basically watching the wheel spin while the identifiers got verified.
>>>>>
>>>>> I was running my tomcat through the debugger and seeing that it looked
>>>>> like all the intermine code was executing just fine; it looked like
>>>>> some internal java calls in making threads were the problem. I checked
>>>>> to see if my java was up to date, but then I noticed that you are now
>>>>> saying version 7 of tomcat is now the minimum. Did this just recently
>>>>> change on or about 1.3? In the past couple weeks I merged with the
>>>>> main
>>>>> branch again and essentially went from 1.1 to 1.3.
>>>>>
>>>>> Are there known issues that demand tomcat-7, or is this just your
>>>>> configuration?
>>>>>
>>>>> I’ve deployed on a tomcat-7 here but I’m still seeing the page hang at
>>>>> ‘verifying identifiers’. Have there been other reports of this
>>>>> problem?
>>>>> I’m still working on that.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Joe Carlson
>>>>> _______________________________________________
>>>>> dev mailing list
>>>>> [hidden email]
>>>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>>>>
>>>>>
>>>
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>>
>>>
>
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