Re: Intermine webapp deployment

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Re: Intermine webapp deployment

InterMine mailing list
Hello Julie,

It seems your solution works! I will let you know if I have any further question.

Thanks very much!

Best regards,

Guanqun Cao
Graduate Student
Department of Computer Science and Information Systems
Bradley University

On Fri, Oct 17, 2014 at 4:20 AM, Julie Sullivan <[hidden email]> wrote:
Hi Guanqun,

Yes I think so! You should be able to just copy the WAR file to the tomcat webapps directory.

So something like:

cp $HOME/intermine/tetramine/webapp/dist/tetramine-webapp.war $TOMCAT/webapps/tetramine.war

The WAR file won't be named correctly I don't think, so you'll have to make it match whatever you put in your tetramine.properties file for the base URL. (or else your queries won't work)

Try that? I've never done this so let me know how you get on!

Cheers
Julie


On 15/10/14 19:05, Guan-Qun Cao wrote:
Dear developers,

My name is Guanqun and I am working on Tetrahymena Genome Database
Project (TGD). Recently I need to build intermine for tetrahymena, but I
have problem with deploying webapp. It returns the error

    Server returned HTTP response code: 403 for URL:
    http://localhost:8080/manager/deploy?path=%2Ftetramine

when I use the command:

    ant default remove-webapp release-webapp


And I have found in the mailing list that the possible solution can be
to set up a manager role in Tomcat config file, but that would yield
security problem. I have contacted the administrators of TGD web server
and they are reluctant to solve it in this way due to the security
issue. Now I am writing to you to ask whether this problem can be solved
otherwise.

Thanks!

Best regards,

Guanqun Cao
Graduate Student
Department of Computer Science and Information Systems
Bradley University
E-mail: [hidden email] <mailto:[hidden email]>



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Re: Intermine webapp deployment

Julie Sullivan
Hello!

Sorry, that popup is annoying. Yes, those settings should have solved
your problem, I didn't realise they were the default now. But now I'm
not too sure how to fix! Are you using Tomcat 7?

You are getting the session error because the request URL doesn't match
what's expected.

* Can you tell me what your cookie says the URL is?
* What settings do you have in your .intermine/tetramine.properties
file? Specifically the baseUrl?

Julie

On 31/10/14 01:47, Guan-Qun Cao wrote:

> Hello Julie,
>
> There is actually another problem with tetramine. When I open the
> webapp, there will pop up a JS alert box saying session error. In
> following link, it gives solution that 2 attributes should be added into
> the config file:
> http://intermine.readthedocs.org/en/latest/system-requirements/software/tomcat/#session-errors
>
> I checked the server and it looks like the settings are already in place
> by default. In $TOMCAT/catalina.out file, the error below is always
> generated after opening the webapp:
> ERROR org.directwebremoting.dwrp.Batch  - A request has been denied as a
> potential CSRF attack
>
> So is there any way to tackle this problem? Or a patch for it?
>
> Thanks!
>
> Best regards,
>
> Guanqun Cao
> Graduate Student
> Department of Computer Science and Information Systems
> Bradley University
> E-mail: [hidden email] <mailto:[hidden email]>
>
>
> On Fri, Oct 17, 2014 at 4:20 AM, Julie Sullivan <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hi Guanqun,
>
>     Yes I think so! You should be able to just copy the WAR file to the
>     tomcat webapps directory.
>
>     So something like:
>
>     cp $HOME/intermine/tetramine/__webapp/dist/tetramine-webapp.__war
>     $TOMCAT/webapps/tetramine.war
>
>     The WAR file won't be named correctly I don't think, so you'll have
>     to make it match whatever you put in your tetramine.properties file
>     for the base URL. (or else your queries won't work)
>
>     Try that? I've never done this so let me know how you get on!
>
>     Cheers
>     Julie
>
>
>     On 15/10/14 19:05, Guan-Qun Cao wrote:
>
>         Dear developers,
>
>         My name is Guanqun and I am working on Tetrahymena Genome Database
>         Project (TGD). Recently I need to build intermine for
>         tetrahymena, but I
>         have problem with deploying webapp. It returns the error
>
>              Server returned HTTP response code: 403 for URL:
>         http://localhost:8080/manager/__deploy?path=%2Ftetramine
>         <http://localhost:8080/manager/deploy?path=%2Ftetramine>
>
>         when I use the command:
>
>              ant default remove-webapp release-webapp
>
>
>         And I have found in the mailing list that the possible solution
>         can be
>         to set up a manager role in Tomcat config file, but that would yield
>         security problem. I have contacted the administrators of TGD web
>         server
>         and they are reluctant to solve it in this way due to the security
>         issue. Now I am writing to you to ask whether this problem can
>         be solved
>         otherwise.
>
>         Thanks!
>
>         Best regards,
>
>         Guanqun Cao
>         Graduate Student
>         Department of Computer Science and Information Systems
>         Bradley University
>         E-mail: [hidden email] <mailto:[hidden email]>
>         <mailto:[hidden email] <mailto:[hidden email]>>
>
>
>
>         _________________________________________________
>         dev mailing list
>         [hidden email] <mailto:[hidden email]>
>         http://mail.intermine.org/cgi-__bin/mailman/listinfo/dev
>         <http://mail.intermine.org/cgi-bin/mailman/listinfo/dev>
>
>

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Re: Intermine webapp deployment

Guan-Qun Cao
Hello,

Sorry about replying late. These days I have been trying to solve it myself, but it still does not work.

Yes, I am using Tomcat7. And the server for hosting tetramine is adenine.bradley.edu, and the URL to open the webapp is adenine.bradley.edu/tetramine. When it is visited, the following cookies are set:
and several domain names of google.com

I tried the following URLs when setting for baseUrl in tetramine.properties file, but none of them worked:

Is above all the information you need? Please let me know when you have an idea of a solution.

Many thanks! 


Best regards,

Guanqun Cao
Graduate Student
Department of Computer Science and Information Systems
Bradley University

On Fri, Oct 31, 2014 at 4:20 AM, Julie Sullivan <[hidden email]> wrote:
Hello!

Sorry, that popup is annoying. Yes, those settings should have solved your problem, I didn't realise they were the default now. But now I'm not too sure how to fix! Are you using Tomcat 7?

You are getting the session error because the request URL doesn't match what's expected.

* Can you tell me what your cookie says the URL is?
* What settings do you have in your .intermine/tetramine.properties file? Specifically the baseUrl?

Julie

On 31/10/14 01:47, Guan-Qun Cao wrote:
Hello Julie,

There is actually another problem with tetramine. When I open the
webapp, there will pop up a JS alert box saying session error. In
following link, it gives solution that 2 attributes should be added into
the config file:
http://intermine.readthedocs.org/en/latest/system-requirements/software/tomcat/#session-errors

I checked the server and it looks like the settings are already in place
by default. In $TOMCAT/catalina.out file, the error below is always
generated after opening the webapp:
ERROR org.directwebremoting.dwrp.Batch  - A request has been denied as a
potential CSRF attack

So is there any way to tackle this problem? Or a patch for it?

Thanks!

Best regards,

Guanqun Cao
Graduate Student
Department of Computer Science and Information Systems
Bradley University
E-mail: [hidden email] <mailto:[hidden email]>


On Fri, Oct 17, 2014 at 4:20 AM, Julie Sullivan <[hidden email]
<mailto:[hidden email]>> wrote:

    Hi Guanqun,

    Yes I think so! You should be able to just copy the WAR file to the
    tomcat webapps directory.

    So something like:

    cp $HOME/intermine/tetramine/__webapp/dist/tetramine-webapp.__war
    $TOMCAT/webapps/tetramine.war

    The WAR file won't be named correctly I don't think, so you'll have
    to make it match whatever you put in your tetramine.properties file
    for the base URL. (or else your queries won't work)

    Try that? I've never done this so let me know how you get on!

    Cheers
    Julie


    On 15/10/14 19:05, Guan-Qun Cao wrote:

        Dear developers,

        My name is Guanqun and I am working on Tetrahymena Genome Database
        Project (TGD). Recently I need to build intermine for
        tetrahymena, but I
        have problem with deploying webapp. It returns the error

             Server returned HTTP response code: 403 for URL:
        http://localhost:8080/manager/__deploy?path=%2Ftetramine
        <http://localhost:8080/manager/deploy?path=%2Ftetramine>

        when I use the command:

             ant default remove-webapp release-webapp


        And I have found in the mailing list that the possible solution
        can be
        to set up a manager role in Tomcat config file, but that would yield
        security problem. I have contacted the administrators of TGD web
        server
        and they are reluctant to solve it in this way due to the security
        issue. Now I am writing to you to ask whether this problem can
        be solved
        otherwise.

        Thanks!

        Best regards,

        Guanqun Cao
        Graduate Student
        Department of Computer Science and Information Systems
        Bradley University
        E-mail: [hidden email] <mailto:[hidden email]>
        <mailto:[hidden email] <mailto:[hidden email]>>



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        dev mailing list
        [hidden email] <mailto:[hidden email]>
        http://mail.intermine.org/cgi-__bin/mailman/listinfo/dev
        <http://mail.intermine.org/cgi-bin/mailman/listinfo/dev>




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Re: Intermine webapp deployment

Julie Sullivan
The base URL should be `adenine.bradley.edu` and the path should be
`tetramine`. Can you send me your updated properties? (off list!)

Can you redeploy the mine with these settings, and let me know so I can
test the site? I'll look at the errors in the browser console to see
which requests are causing the problem. The error message (CSRF attack)
means the website is getting requests from different URLs.


On 07/11/14 01:49, Guan-Qun Cao wrote:

> Hello,
>
> Sorry about replying late. These days I have been trying to solve it
> myself, but it still does not work.
>
> Yes, I am using Tomcat7. And the server for hosting tetramine is
> adenine.bradley.edu <http://adenine.bradley.edu>, and the URL to open
> the webapp is adenine.bradley.edu/tetramine
> <http://adenine.bradley.edu/tetramine>. When it is visited, the
> following cookies are set:
> www.bradley.edu <http://www.bradley.edu>
> adenine.bradley.edu <http://adenine.bradley.edu>
> and several domain names of google.com <http://google.com>
>
> I tried the following URLs when setting for baseUrl in
> tetramine.__properties file, but none of them worked:
> http://localhost:8080
> http://localhost:8080/tetramine
> http://adenine.bradley.edu
> http://adenine.bradley.edu/tetramine
> http://adenine.bradley.edu/tetramine/begin.do
>
> Is above all the information you need? Please let me know when you have
> an idea of a solution.
>
> Many thanks!
>
>
> Best regards,
>
> Guanqun Cao
> Graduate Student
> Department of Computer Science and Information Systems
> Bradley University
> E-mail: [hidden email] <mailto:[hidden email]>
>
>
> On Fri, Oct 31, 2014 at 4:20 AM, Julie Sullivan <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hello!
>
>     Sorry, that popup is annoying. Yes, those settings should have
>     solved your problem, I didn't realise they were the default now. But
>     now I'm not too sure how to fix! Are you using Tomcat 7?
>
>     You are getting the session error because the request URL doesn't
>     match what's expected.
>
>     * Can you tell me what your cookie says the URL is?
>     * What settings do you have in your
>     .intermine/tetramine.__properties file? Specifically the baseUrl?
>
>     Julie
>
>     On 31/10/14 01:47, Guan-Qun Cao wrote:
>
>         Hello Julie,
>
>         There is actually another problem with tetramine. When I open the
>         webapp, there will pop up a JS alert box saying session error. In
>         following link, it gives solution that 2 attributes should be
>         added into
>         the config file:
>         http://intermine.readthedocs.__org/en/latest/system-__requirements/software/tomcat/#__session-errors
>         <http://intermine.readthedocs.org/en/latest/system-requirements/software/tomcat/#session-errors>
>
>         I checked the server and it looks like the settings are already
>         in place
>         by default. In $TOMCAT/catalina.out file, the error below is always
>         generated after opening the webapp:
>         ERROR org.directwebremoting.dwrp.__Batch  - A request has been
>         denied as a
>         potential CSRF attack
>
>         So is there any way to tackle this problem? Or a patch for it?
>
>         Thanks!
>
>         Best regards,
>
>         Guanqun Cao
>         Graduate Student
>         Department of Computer Science and Information Systems
>         Bradley University
>         E-mail: [hidden email] <mailto:[hidden email]>
>         <mailto:[hidden email] <mailto:[hidden email]>>
>
>
>         On Fri, Oct 17, 2014 at 4:20 AM, Julie Sullivan
>         <[hidden email] <mailto:[hidden email]>
>         <mailto:[hidden email] <mailto:[hidden email]>>> wrote:
>
>              Hi Guanqun,
>
>              Yes I think so! You should be able to just copy the WAR
>         file to the
>              tomcat webapps directory.
>
>              So something like:
>
>              cp
>         $HOME/intermine/tetramine/____webapp/dist/tetramine-webapp.____war
>              $TOMCAT/webapps/tetramine.war
>
>              The WAR file won't be named correctly I don't think, so
>         you'll have
>              to make it match whatever you put in your
>         tetramine.properties file
>              for the base URL. (or else your queries won't work)
>
>              Try that? I've never done this so let me know how you get on!
>
>              Cheers
>              Julie
>
>
>              On 15/10/14 19:05, Guan-Qun Cao wrote:
>
>                  Dear developers,
>
>                  My name is Guanqun and I am working on Tetrahymena
>         Genome Database
>                  Project (TGD). Recently I need to build intermine for
>                  tetrahymena, but I
>                  have problem with deploying webapp. It returns the error
>
>                       Server returned HTTP response code: 403 for URL:
>         http://localhost:8080/manager/____deploy?path=%2Ftetramine
>         <http://localhost:8080/manager/__deploy?path=%2Ftetramine>
>
>         <<a href="http://localhost:8080/__manager/deploy?path=%__2Ftetramine">http://localhost:8080/__manager/deploy?path=%__2Ftetramine
>         <http://localhost:8080/manager/deploy?path=%2Ftetramine>>
>
>                  when I use the command:
>
>                       ant default remove-webapp release-webapp
>
>
>                  And I have found in the mailing list that the possible
>         solution
>                  can be
>                  to set up a manager role in Tomcat config file, but
>         that would yield
>                  security problem. I have contacted the administrators
>         of TGD web
>                  server
>                  and they are reluctant to solve it in this way due to
>         the security
>                  issue. Now I am writing to you to ask whether this
>         problem can
>                  be solved
>                  otherwise.
>
>                  Thanks!
>
>                  Best regards,
>
>                  Guanqun Cao
>                  Graduate Student
>                  Department of Computer Science and Information Systems
>                  Bradley University
>                  E-mail: [hidden email]
>         <mailto:[hidden email]> <mailto:[hidden email]
>         <mailto:[hidden email]>>
>                  <mailto:[hidden email]
>         <mailto:[hidden email]> <mailto:[hidden email]
>         <mailto:[hidden email]>>__>
>
>
>
>                  ___________________________________________________
>                  dev mailing list
>         [hidden email] <mailto:[hidden email]>
>         <mailto:[hidden email] <mailto:[hidden email]>>
>         http://mail.intermine.org/cgi-____bin/mailman/listinfo/dev
>         <http://mail.intermine.org/cgi-__bin/mailman/listinfo/dev>
>
>         <http://mail.intermine.org/__cgi-bin/mailman/listinfo/dev
>         <http://mail.intermine.org/cgi-bin/mailman/listinfo/dev>>
>
>
>

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