Error message after second run of a query, with different parameters from the first run
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Nicolas
Mar 15, 2013, 2:25:27 AM3/15/13
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Hello,
I am a new member of this group. I am working on the varDB project and we would like to use the sWDK.
We have setup the sWDK on our server, however, we are encountering a problem with executing the same query with different parameters, after the initial run. When we try the query a second time, with a different parameter, we get an error.
Our setup:
We are working with sWDK version 2.2.
Our database uses PostgreSQL 9.1.6.
Our test site can be viewed here: http://fullent-dev.genome.ad.jp/gus_home/
Our problem:
When we run a second query, with different parameters from the initial query, we get this error message:
“Sequence Records by taxon: ERROR: relation "queryresult2" already exists”
As an example:
You should see the error message at this point.
[I have also attached a log of the postgresql output.]
Not attached: for some reason, I get an error #340 when trying to attach a file.
If you would like to see the log, let me know and I'll past in into a reply.
Do you have any suggestions of what the problem might be?
Best regards,
Nicolas
I am a new member of this group. I am working on the varDB project and we would like to use the sWDK.
We have setup the sWDK on our server, however, we are encountering a problem with executing the same query with different parameters, after the initial run. When we try the query a second time, with a different parameter, we get an error.
Our setup:
We are working with sWDK version 2.2.
Our database uses PostgreSQL 9.1.6.
Our test site can be viewed here: http://fullent-dev.genome.ad.jp/gus_home/
Our problem:
When we run a second query, with different parameters from the initial query, we get this error message:
“Sequence Records by taxon: ERROR: relation "queryresult2" already exists”
As an example:
- Go to http://fullent-dev.genome.ad.jp/gus_home/
- Select “Search for sequences by taxon”
- Leave default selection
- Click “Get Answer”
- Select “New Search”
- Select “Search for sequences by taxon”
- Select different parameters from the previous search
- Click “Get Answer”
You should see the error message at this point.
[I have also attached a log of the postgresql output.]
Not attached: for some reason, I get an error #340 when trying to attach a file.
If you would like to see the log, let me know and I'll past in into a reply.
Do you have any suggestions of what the problem might be?
Best regards,
Nicolas
Steve Fischer
Mar 15, 2013, 8:59:20 AM3/15/13
to strategies...@googlegroups.com
Hi Nicolas,
Great that you have gotten that far!
This might be a postgres specific issue.� The good news is that another wdk project here at penn is gearing up to use postgres too.�� they are a few steps behind you.�� when they catch up, if we see that same bug we should be able to debug it in house.
that said, perhaps another of the wdk developers will know what is causing your problem and might respond.
steve
Great that you have gotten that far!
This might be a postgres specific issue.� The good news is that another wdk project here at penn is gearing up to use postgres too.�� they are a few steps behind you.�� when they catch up, if we see that same bug we should be able to debug it in house.
that said, perhaps another of the wdk developers will know what is causing your problem and might respond.
steve
On 3/15/2013 2:25 AM, Nicolas wrote:
Hello,
I am a new member of this group. I am working on the varDB project and we would like to use the sWDK.
We have setup the sWDK on our server, however, we are encountering a problem with executing the same query with different parameters, after the initial run. When we try the query a second time, with a different parameter, we get an error.
Our setup:
We are working with sWDK version 2.2.
Our database uses PostgreSQL 9.1.6.
Our test site can be viewed here: http://fullent-dev.genome.ad.jp/gus_home/
Our problem:
When we run a second query, with different parameters from the initial query, we get this error message:
�Sequence Records by taxon: ERROR: relation "queryresult2" already exists�
As an example:
- Go to http://fullent-dev.genome.ad.jp/gus_home/
- Select �Search for sequences by taxon�
- Leave default selection
- Click �Get Answer�
- Select �New Search�
- Select �Search for sequences by taxon�
- Select different parameters from the previous search
- Click �Get Answer�
You should see the error message at this point.
[I have also attached a log of the postgresql output.]
Not attached: for some reason, I get an error #340 when trying to attach a file.
If you would like to see the log, let me know and I'll past in into a reply.
Do you have any suggestions of what the problem might be?
Best regards,
Nicolas --
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John Iodice
Mar 15, 2013, 9:36:36 AM3/15/13
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Hi Nicolas,
I'm the developer on the project Steve mentioned, using the S-WDK on PostgreSQL. I will indeed let you know whether I encounter the same bug. If I do, then I'll post the solution once I find it. Meanwhile, I have two requests to make of you:
- Can you reply to this list with the error messages that are logged when the error occurs? One of the log files (possibly catalina.out) should include the exception and stack trace that accompany it. Those can be useful.
- I'm following the installation doc to build my own WDK template site, and (as I mentioned in a separate post), I've gotten as far as the last step, "start up the application in Tomcat". Can you tell me how you did that part? That will help me with my own project, and hasten my arrival at the step that's giving you trouble. (Misery loves company!)
Thanks,
John
On Fri, Mar 15, 2013 at 8:59 AM, Steve Fischer <sfis...@pcbi.upenn.edu> wrote:
Hi Nicolas,
Great that you have gotten that far!
This might be a postgres specific issue. The good news is that another wdk project here at penn is gearing up to use postgres too. they are a few steps behind you. when they catch up, if we see that same bug we should be able to debug it in house.
that said, perhaps another of the wdk developers will know what is causing your problem and might respond.
steve
On 3/15/2013 2:25 AM, Nicolas wrote:
Hello,
I am a new member of this group. I am working on the varDB project and we would like to use the sWDK.
We have setup the sWDK on our server, however, we are encountering a problem with executing the same query with different parameters, after the initial run. When we try the query a second time, with a different parameter, we get an error.
Our setup:
We are working with sWDK version 2.2.
Our database uses PostgreSQL 9.1.6.
Our test site can be viewed here: http://fullent-dev.genome.ad.jp/gus_home/
Our problem:
When we run a second query, with different parameters from the initial query, we get this error message:
“Sequence Records by taxon: ERROR: relation "queryresult2" already exists”
As an example:
- Select “Search for sequences by taxon”
- Leave default selection
- Click “Get Answer”
- Select “New Search”
- Select “Search for sequences by taxon”
- Select different parameters from the previous search
- Click “Get Answer”
You should see the error message at this point.
[I have also attached a log of the postgresql output.]
Not attached: for some reason, I get an error #340 when trying to attach a file.
If you would like to see the log, let me know and I'll past in into a reply.
Do you have any suggestions of what the problem might be?
Best regards,
Nicolas
--
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Steve Fischer
Mar 15, 2013, 10:29:03 AM3/15/13
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nicolas, by the way, what version of the wdk are you using?
steve
On 3/15/2013 2:25 AM, Nicolas wrote:
Hello,
I am a new member of this group. I am working on the varDB project and we would like to use the sWDK.
We have setup the sWDK on our server, however, we are encountering a problem with executing the same query with different parameters, after the initial run. When we try the query a second time, with a different parameter, we get an error.
Our setup:
We are working with sWDK version 2.2.
Our database uses PostgreSQL 9.1.6.
Our test site can be viewed here: http://fullent-dev.genome.ad.jp/gus_home/
Our problem:
When we run a second query, with different parameters from the initial query, we get this error message:
�Sequence Records by taxon: ERROR: relation "queryresult2" already exists�
As an example:
- Select �Search for sequences by taxon�
- Leave default selection
- Click �Get Answer�
- Select �New Search�
- Select �Search for sequences by taxon�
- Select different parameters from the previous search
- Click �Get Answer�
You should see the error message at this point.
[I have also attached a log of the postgresql output.]
Not attached: for some reason, I get an error #340 when trying to attach a file.
If you would like to see the log, let me know and I'll past in into a reply.
Do you have any suggestions of what the problem might be?
Best regards,
Nicolas --
You received this message because you are subscribed to the Google Groups "strategies-wdk-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to strategies-wdk-u...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.
�
�
Nicolas Joannin
Mar 16, 2013, 10:02:33 AM3/16/13
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Hi Steve and John,
Thanks for looking into this, and I do hope our experience will be useful...
(Just so you know, I am based in Japan, which means that we currently have 13 hours time difference, so morning for you is evening for me.)
Quick answer for Steve: we are using version 2.2... It's probably not the latest, but we weren't sure where to find the absolute latest.
John, to answer your questions, I won't be able to fully answer before Monday or Tuesday, as it's already the week end here and I'm not the one who handled the Tomcat part of it.
- I've abbreviated the log files for Tomcat and Postgres, and marked them at the times I did each query, the FIRST QUERY being the one that returns a result and the SECOND QUERY the one that give an error message.
- In the Tomcat log, I don't recognize any exception (but that might just be that I don't know what to look for), but the entries related to the second query are much fewer than for the first.
- In the Postgres log, there is the error message we get in the UI.
- This is the part that I didn't take care of (I handled the configuration of the model), so I can't say much about it. But I'll email ask him for those details and will post them as soon as possible. That said, whenever I modify the config files, I need to re-build and install the model and webapp. To do so, I first stop Tomcat with "catalina.sh stop", I re-build/install my model, refresh the cache, build webinstall, and finally restart Tomcat with "catalina.sh start".
Will post again when I have more info!
Cheers,
Nicolas
On Fri, Mar 15, 2013 at 11:29 PM, Steve Fischer <sfis...@pcbi.upenn.edu> wrote:
nicolas, by the way, what version of the wdk are you using?
steve
On 3/15/2013 2:25 AM, Nicolas wrote:
Hello,
I am a new member of this group. I am working on the varDB project and we would like to use the sWDK.
We have setup the sWDK on our server, however, we are encountering a problem with executing the same query with different parameters, after the initial run. When we try the query a second time, with a different parameter, we get an error.
Our setup:
We are working with sWDK version 2.2.
Our database uses PostgreSQL 9.1.6.
Our test site can be viewed here: http://fullent-dev.genome.ad.jp/gus_home/
Our problem:
When we run a second query, with different parameters from the initial query, we get this error message:
“Sequence Records by taxon: ERROR: relation "queryresult2" already exists”
As an example:
- Select “Search for sequences by taxon”
- Leave default selection
- Click “Get Answer”
- Select “New Search”
- Select “Search for sequences by taxon”
- Select different parameters from the previous search
- Click “Get Answer”
You should see the error message at this point.
[I have also attached a log of the postgresql output.]
Not attached: for some reason, I get an error #340 when trying to attach a file.
If you would like to see the log, let me know and I'll past in into a reply.
Do you have any suggestions of what the problem might be?
Best regards,
Nicolas
--
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