Re: Bug Report: BioMart 0.8 release candidate 3

classic Classic list List threaded Threaded
4 messages Options
Reply | Threaded
Open this post in threaded view
|

Re: Bug Report: BioMart 0.8 release candidate 3

Syed Haider
Hi Phil,

Have you tried deploying it through command line ? Just wondering
whether its just the deploy button or a general problem.
Also, are you running MartConfigurator over X client ?

Best,
Syed

PS: please note the new mailing list :)


On 13/01/2011 11:52, Phil Jones @ EBI wrote:

> Hi BioMart developers,
>
> Thank you for the announcement of release candidate 3.  I have just attempted to follow the instructions in the documentation.  At the point of clicking the "Deploy" button for the MSD Protein Structure data set (page 7 of the docs), repeated stack traces are being displayed in the console (no error message from the interface however) as follows:
>
> java.net.ConnectException: Connection refused
> at java.net.PlainSocketImpl.socketConnect(Native Method)
> at java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:333)
> at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:195)
> at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:182)
> at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366)
> at java.net.Socket.connect(Socket.java:529)
> at java.net.Socket.connect(Socket.java:478)
> at sun.net.NetworkClient.doConnect(NetworkClient.java:163)
> at sun.net.www.http.HttpClient.openServer(HttpClient.java:394)
> at sun.net.www.http.HttpClient.openServer(HttpClient.java:529)
> at sun.net.www.http.HttpClient.<init>(HttpClient.java:233)
> at sun.net.www.http.HttpClient.New(HttpClient.java:306)
> at sun.net.www.http.HttpClient.New(HttpClient.java:323)
> at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:975)
> at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:916)
> at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:841)
> at org.biomart.configurator.utils.McUtils.isHttpServerAvailable(McUtils.java:851)
> at org.biomart.configurator.view.menu.McMenus.deploy(McMenus.java:654)
> at org.biomart.configurator.view.menu.McMenus.access$200(McMenus.java:76)
> at org.biomart.configurator.view.menu.McMenus$3.construct(McMenus.java:538)
> at org.biomart.common.view.gui.SwingWorker$2.run(SwingWorker.java:128)
> at java.lang.Thread.run(Thread.java:662)
>
> My platform is:
> Ubuntu 10.04
> Java 1.6.0_22
> ant 1.7.1 (not that there were any problems with the build reported, so this is probably irrelevant.
>
> best regards,
>
> Phil.
>
> On 18 December 2010 18:29, Syed Haider<[hidden email]<mailto:[hidden email]>>  wrote:
> Hello everyone,
>
> The BioMart 0.8 rc3 is now available for deployer testing. The new version is a Java based, out-of-the-box single integrated application to facilitate mart building, configuration and web server deployment.
>
> For installation and a user instructions, please see a deployer's guide available here:
>
> http://www.biomart.org/rc3_documentation.pdf
>
> This release is tested on Mac OS X (Leopard and Snow Leapord), Linux (Debian 4.1.1-21), Java 6. See docs for details.
>
> The following features are now available for your testing:
>
> 1- Support for 5 database platforms (MySQL, Oracle, PgSQL, MS SQL, DB2)
>
> 2- Virtual Marts (non-materialised querying against source database)
>
> 4- A range of different web interfaces from Basic Form to
> Advanced Querying interfaces (MartAnalysis, MartForm, MartWizard, MartExplorer) and a Report page  (MartReport)
>
> 5- Backwards compatibility for BioMart 0.7 sources
>
> 6- Secure access
>
> 7- Multi-dataset linking with Link-Indices for faster and scalable joins
>
> 8- Processor framework for specialised data visualisations (e.g charts)
>
> FEATURES NOT AVAILABLE YET:
> - Full Mbuilder component including source schema modifications
> - Updates
> - Processors (Genomic Sequence, GFF, DAS, WSDL, Gzip, Excel)
>
> Please send your feedback and bug reports to [hidden email]<mailto:[hidden email]>
>
> Best Wishes,
> Syed Haider on behalf of the BioMart Team.
>
>
>
> --
> Phil Jones
> Software Development Coordinator
> InterPro Team
> PANDA Group, EMBL-EBI
> Wellcome Trust Genome Campus
> Hinxton, Cambridge, CB10 1SD
> UK.
>
> Work phone: +44 1223 492685
> Mobile: +44 7789 900964
> Skype: philip-jones
>
_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: Bug Report: BioMart 0.8 release candidate 3

Esposito, Anthony
I just tried both- with the command line, starts and stops without the connection exceptions; using deploy button in MConf (using X forwarding from a remote box) I get the connection exceptions, on both a first-run and a redeploy after starting/stopping from the CLI.  

tj
                                                                                                 _____
T.J. Esposito
La Jolla Research Business Technology - Bioinformatics & Innovation
Please consider the environment before printing email.


-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Syed Haider
Sent: Thursday, January 13, 2011 4:05 AM
To: Phil Jones @ EBI
Cc: [hidden email]
Subject: Re: [Users] Bug Report: BioMart 0.8 release candidate 3

Hi Phil,

Have you tried deploying it through command line ? Just wondering whether its just the deploy button or a general problem.
Also, are you running MartConfigurator over X client ?

Best,
Syed

PS: please note the new mailing list :)


On 13/01/2011 11:52, Phil Jones @ EBI wrote:

> Hi BioMart developers,
>
> Thank you for the announcement of release candidate 3.  I have just attempted to follow the instructions in the documentation.  At the point of clicking the "Deploy" button for the MSD Protein Structure data set (page 7 of the docs), repeated stack traces are being displayed in the console (no error message from the interface however) as follows:
>
> java.net.ConnectException: Connection refused at
> java.net.PlainSocketImpl.socketConnect(Native Method) at
> java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:333)
> at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:195)
> at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:182)
> at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366)
> at java.net.Socket.connect(Socket.java:529)
> at java.net.Socket.connect(Socket.java:478)
> at sun.net.NetworkClient.doConnect(NetworkClient.java:163)
> at sun.net.www.http.HttpClient.openServer(HttpClient.java:394)
> at sun.net.www.http.HttpClient.openServer(HttpClient.java:529)
> at sun.net.www.http.HttpClient.<init>(HttpClient.java:233)
> at sun.net.www.http.HttpClient.New(HttpClient.java:306)
> at sun.net.www.http.HttpClient.New(HttpClient.java:323)
> at
> sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLCo
> nnection.java:975) at
> sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnec
> tion.java:916) at
> sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.
> java:841) at
> org.biomart.configurator.utils.McUtils.isHttpServerAvailable(McUtils.j
> ava:851) at
> org.biomart.configurator.view.menu.McMenus.deploy(McMenus.java:654)
> at
> org.biomart.configurator.view.menu.McMenus.access$200(McMenus.java:76)
> at
> org.biomart.configurator.view.menu.McMenus$3.construct(McMenus.java:53
> 8) at
> org.biomart.common.view.gui.SwingWorker$2.run(SwingWorker.java:128)
> at java.lang.Thread.run(Thread.java:662)
>
> My platform is:
> Ubuntu 10.04
> Java 1.6.0_22
> ant 1.7.1 (not that there were any problems with the build reported, so this is probably irrelevant.
>
> best regards,
>
> Phil.
>
> On 18 December 2010 18:29, Syed Haider<[hidden email]<mailto:[hidden email]>>  wrote:
> Hello everyone,
>
> The BioMart 0.8 rc3 is now available for deployer testing. The new version is a Java based, out-of-the-box single integrated application to facilitate mart building, configuration and web server deployment.
>
> For installation and a user instructions, please see a deployer's guide available here:
>
> http://www.biomart.org/rc3_documentation.pdf
>
> This release is tested on Mac OS X (Leopard and Snow Leapord), Linux (Debian 4.1.1-21), Java 6. See docs for details.
>
> The following features are now available for your testing:
>
> 1- Support for 5 database platforms (MySQL, Oracle, PgSQL, MS SQL,
> DB2)
>
> 2- Virtual Marts (non-materialised querying against source database)
>
> 4- A range of different web interfaces from Basic Form to Advanced
> Querying interfaces (MartAnalysis, MartForm, MartWizard, MartExplorer)
> and a Report page  (MartReport)
>
> 5- Backwards compatibility for BioMart 0.7 sources
>
> 6- Secure access
>
> 7- Multi-dataset linking with Link-Indices for faster and scalable
> joins
>
> 8- Processor framework for specialised data visualisations (e.g
> charts)
>
> FEATURES NOT AVAILABLE YET:
> - Full Mbuilder component including source schema modifications
> - Updates
> - Processors (Genomic Sequence, GFF, DAS, WSDL, Gzip, Excel)
>
> Please send your feedback and bug reports to
> [hidden email]<mailto:[hidden email]>
>
> Best Wishes,
> Syed Haider on behalf of the BioMart Team.
>
>
>
> --
> Phil Jones
> Software Development Coordinator
> InterPro Team
> PANDA Group, EMBL-EBI
> Wellcome Trust Genome Campus
> Hinxton, Cambridge, CB10 1SD
> UK.
>
> Work phone: +44 1223 492685
> Mobile: +44 7789 900964
> Skype: philip-jones
>
_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: Bug Report: BioMart 0.8 release candidate 3

Esposito, Anthony
Oh and I forgot to note, both methods of starting BioMart, regardless of whether the exceptions were present or not, resulted in the app being deployed with a fully functional front end.  

tj
                                                                                                 _____
T.J. Esposito
La Jolla Research Business Technology - Bioinformatics & Innovation
Please consider the environment before printing email.


-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Esposito, Anthony
Sent: Thursday, January 13, 2011 12:26 PM
To: Syed Haider; Phil Jones @ EBI
Cc: [hidden email]
Subject: Re: [Users] Bug Report: BioMart 0.8 release candidate 3

I just tried both- with the command line, starts and stops without the connection exceptions; using deploy button in MConf (using X forwarding from a remote box) I get the connection exceptions, on both a first-run and a redeploy after starting/stopping from the CLI.  

tj
                                                                                                 _____ T.J. Esposito La Jolla Research Business Technology - Bioinformatics & Innovation Please consider the environment before printing email.


-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Syed Haider
Sent: Thursday, January 13, 2011 4:05 AM
To: Phil Jones @ EBI
Cc: [hidden email]
Subject: Re: [Users] Bug Report: BioMart 0.8 release candidate 3

Hi Phil,

Have you tried deploying it through command line ? Just wondering whether its just the deploy button or a general problem.
Also, are you running MartConfigurator over X client ?

Best,
Syed

PS: please note the new mailing list :)


On 13/01/2011 11:52, Phil Jones @ EBI wrote:

> Hi BioMart developers,
>
> Thank you for the announcement of release candidate 3.  I have just attempted to follow the instructions in the documentation.  At the point of clicking the "Deploy" button for the MSD Protein Structure data set (page 7 of the docs), repeated stack traces are being displayed in the console (no error message from the interface however) as follows:
>
> java.net.ConnectException: Connection refused at
> java.net.PlainSocketImpl.socketConnect(Native Method) at
> java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:333)
> at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:195)
> at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:182)
> at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366)
> at java.net.Socket.connect(Socket.java:529)
> at java.net.Socket.connect(Socket.java:478)
> at sun.net.NetworkClient.doConnect(NetworkClient.java:163)
> at sun.net.www.http.HttpClient.openServer(HttpClient.java:394)
> at sun.net.www.http.HttpClient.openServer(HttpClient.java:529)
> at sun.net.www.http.HttpClient.<init>(HttpClient.java:233)
> at sun.net.www.http.HttpClient.New(HttpClient.java:306)
> at sun.net.www.http.HttpClient.New(HttpClient.java:323)
> at
> sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLCo
> nnection.java:975) at
> sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnec
> tion.java:916) at
> sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.
> java:841) at
> org.biomart.configurator.utils.McUtils.isHttpServerAvailable(McUtils.j
> ava:851) at
> org.biomart.configurator.view.menu.McMenus.deploy(McMenus.java:654)
> at
> org.biomart.configurator.view.menu.McMenus.access$200(McMenus.java:76)
> at
> org.biomart.configurator.view.menu.McMenus$3.construct(McMenus.java:53
> 8) at
> org.biomart.common.view.gui.SwingWorker$2.run(SwingWorker.java:128)
> at java.lang.Thread.run(Thread.java:662)
>
> My platform is:
> Ubuntu 10.04
> Java 1.6.0_22
> ant 1.7.1 (not that there were any problems with the build reported, so this is probably irrelevant.
>
> best regards,
>
> Phil.
>
> On 18 December 2010 18:29, Syed Haider<[hidden email]<mailto:[hidden email]>>  wrote:
> Hello everyone,
>
> The BioMart 0.8 rc3 is now available for deployer testing. The new version is a Java based, out-of-the-box single integrated application to facilitate mart building, configuration and web server deployment.
>
> For installation and a user instructions, please see a deployer's guide available here:
>
> http://www.biomart.org/rc3_documentation.pdf
>
> This release is tested on Mac OS X (Leopard and Snow Leapord), Linux (Debian 4.1.1-21), Java 6. See docs for details.
>
> The following features are now available for your testing:
>
> 1- Support for 5 database platforms (MySQL, Oracle, PgSQL, MS SQL,
> DB2)
>
> 2- Virtual Marts (non-materialised querying against source database)
>
> 4- A range of different web interfaces from Basic Form to Advanced
> Querying interfaces (MartAnalysis, MartForm, MartWizard, MartExplorer)
> and a Report page  (MartReport)
>
> 5- Backwards compatibility for BioMart 0.7 sources
>
> 6- Secure access
>
> 7- Multi-dataset linking with Link-Indices for faster and scalable
> joins
>
> 8- Processor framework for specialised data visualisations (e.g
> charts)
>
> FEATURES NOT AVAILABLE YET:
> - Full Mbuilder component including source schema modifications
> - Updates
> - Processors (Genomic Sequence, GFF, DAS, WSDL, Gzip, Excel)
>
> Please send your feedback and bug reports to
> [hidden email]<mailto:[hidden email]>
>
> Best Wishes,
> Syed Haider on behalf of the BioMart Team.
>
>
>
> --
> Phil Jones
> Software Development Coordinator
> InterPro Team
> PANDA Group, EMBL-EBI
> Wellcome Trust Genome Campus
> Hinxton, Cambridge, CB10 1SD
> UK.
>
> Work phone: +44 1223 492685
> Mobile: +44 7789 900964
> Skype: philip-jones
>
_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users
Reply | Threaded
Open this post in threaded view
|

Re: Bug Report: BioMart 0.8 release candidate 3

Syed Haider
Thanks TJ :)

Phil was going to give it a go, lets see if it works for him from
command. Meanwhile, let us address the exceptions regardless.

Best,
Syed

On 13/01/2011 20:27, Esposito, Anthony wrote:

> Oh and I forgot to note, both methods of starting BioMart, regardless of whether the exceptions were present or not, resulted in the app being deployed with a fully functional front end.
>
> tj
>                                                                                                   _____
> T.J. Esposito
> La Jolla Research Business Technology - Bioinformatics&  Innovation
> Please consider the environment before printing email.
>
>
> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]] On Behalf Of Esposito, Anthony
> Sent: Thursday, January 13, 2011 12:26 PM
> To: Syed Haider; Phil Jones @ EBI
> Cc: [hidden email]
> Subject: Re: [Users] Bug Report: BioMart 0.8 release candidate 3
>
> I just tried both- with the command line, starts and stops without the connection exceptions; using deploy button in MConf (using X forwarding from a remote box) I get the connection exceptions, on both a first-run and a redeploy after starting/stopping from the CLI.
>
> tj
>                                                                                                   _____ T.J. Esposito La Jolla Research Business Technology - Bioinformatics&  Innovation Please consider the environment before printing email.
>
>
> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]] On Behalf Of Syed Haider
> Sent: Thursday, January 13, 2011 4:05 AM
> To: Phil Jones @ EBI
> Cc: [hidden email]
> Subject: Re: [Users] Bug Report: BioMart 0.8 release candidate 3
>
> Hi Phil,
>
> Have you tried deploying it through command line ? Just wondering whether its just the deploy button or a general problem.
> Also, are you running MartConfigurator over X client ?
>
> Best,
> Syed
>
> PS: please note the new mailing list :)
>
>
> On 13/01/2011 11:52, Phil Jones @ EBI wrote:
>> Hi BioMart developers,
>>
>> Thank you for the announcement of release candidate 3.  I have just attempted to follow the instructions in the documentation.  At the point of clicking the "Deploy" button for the MSD Protein Structure data set (page 7 of the docs), repeated stack traces are being displayed in the console (no error message from the interface however) as follows:
>>
>> java.net.ConnectException: Connection refused at
>> java.net.PlainSocketImpl.socketConnect(Native Method) at
>> java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:333)
>> at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:195)
>> at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:182)
>> at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366)
>> at java.net.Socket.connect(Socket.java:529)
>> at java.net.Socket.connect(Socket.java:478)
>> at sun.net.NetworkClient.doConnect(NetworkClient.java:163)
>> at sun.net.www.http.HttpClient.openServer(HttpClient.java:394)
>> at sun.net.www.http.HttpClient.openServer(HttpClient.java:529)
>> at sun.net.www.http.HttpClient.<init>(HttpClient.java:233)
>> at sun.net.www.http.HttpClient.New(HttpClient.java:306)
>> at sun.net.www.http.HttpClient.New(HttpClient.java:323)
>> at
>> sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLCo
>> nnection.java:975) at
>> sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnec
>> tion.java:916) at
>> sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.
>> java:841) at
>> org.biomart.configurator.utils.McUtils.isHttpServerAvailable(McUtils.j
>> ava:851) at
>> org.biomart.configurator.view.menu.McMenus.deploy(McMenus.java:654)
>> at
>> org.biomart.configurator.view.menu.McMenus.access$200(McMenus.java:76)
>> at
>> org.biomart.configurator.view.menu.McMenus$3.construct(McMenus.java:53
>> 8) at
>> org.biomart.common.view.gui.SwingWorker$2.run(SwingWorker.java:128)
>> at java.lang.Thread.run(Thread.java:662)
>>
>> My platform is:
>> Ubuntu 10.04
>> Java 1.6.0_22
>> ant 1.7.1 (not that there were any problems with the build reported, so this is probably irrelevant.
>>
>> best regards,
>>
>> Phil.
>>
>> On 18 December 2010 18:29, Syed Haider<[hidden email]<mailto:[hidden email]>>   wrote:
>> Hello everyone,
>>
>> The BioMart 0.8 rc3 is now available for deployer testing. The new version is a Java based, out-of-the-box single integrated application to facilitate mart building, configuration and web server deployment.
>>
>> For installation and a user instructions, please see a deployer's guide available here:
>>
>> http://www.biomart.org/rc3_documentation.pdf
>>
>> This release is tested on Mac OS X (Leopard and Snow Leapord), Linux (Debian 4.1.1-21), Java 6. See docs for details.
>>
>> The following features are now available for your testing:
>>
>> 1- Support for 5 database platforms (MySQL, Oracle, PgSQL, MS SQL,
>> DB2)
>>
>> 2- Virtual Marts (non-materialised querying against source database)
>>
>> 4- A range of different web interfaces from Basic Form to Advanced
>> Querying interfaces (MartAnalysis, MartForm, MartWizard, MartExplorer)
>> and a Report page  (MartReport)
>>
>> 5- Backwards compatibility for BioMart 0.7 sources
>>
>> 6- Secure access
>>
>> 7- Multi-dataset linking with Link-Indices for faster and scalable
>> joins
>>
>> 8- Processor framework for specialised data visualisations (e.g
>> charts)
>>
>> FEATURES NOT AVAILABLE YET:
>> - Full Mbuilder component including source schema modifications
>> - Updates
>> - Processors (Genomic Sequence, GFF, DAS, WSDL, Gzip, Excel)
>>
>> Please send your feedback and bug reports to
>> [hidden email]<mailto:[hidden email]>
>>
>> Best Wishes,
>> Syed Haider on behalf of the BioMart Team.
>>
>>
>>
>> --
>> Phil Jones
>> Software Development Coordinator
>> InterPro Team
>> PANDA Group, EMBL-EBI
>> Wellcome Trust Genome Campus
>> Hinxton, Cambridge, CB10 1SD
>> UK.
>>
>> Work phone: +44 1223 492685
>> Mobile: +44 7789 900964
>> Skype: philip-jones
>>
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users
_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users