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: [email protected] [mailto:[email protected]] On Behalf Of
Esposito, Anthony
Sent: Thursday, January 13, 2011 12:26 PM
To: Syed Haider; Phil Jones @ EBI
Cc: [email protected]
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: [email protected] [mailto:[email protected]] On Behalf Of
Syed Haider
Sent: Thursday, January 13, 2011 4:05 AM
To: Phil Jones @ EBI
Cc: [email protected]
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<[email protected]<mailto:[email protected]>> 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
[email protected]<mailto:[email protected]>
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
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