basedb-users — General BASE mailing list

Re: [base] Schema

[Nicklas N. <ni...@th...>]

On 2012-11-13 03:32, Paulo Nuin wrote:
> Hi
>
> Is there any available image/diagram of the current schema?

Not really. The closest thing is the diagrams that can be found in each 
of the subsections at 
http://base.thep.lu.se/chrome/site/latest/html/developer/api/data_api.html

The diagrams give an object-centric view with some (but not complete) 
information to how everything is mapped to the underlying database. To 
find out about the details you would need to check the code or a real 
database after installation.

/Nicklas

[base] Schema

[Paulo N. <nu...@ge...>]

Hi

Is there any available image/diagram of the current schema?

Thanks in advance

Paulo

Re: [base] DataQuery.order(...) 2.x API question

[Nicklas N. <ni...@th...>]

On 2012-10-09 17:24, Bob MacCallum wrote:
> Just for closure, I am now in business.
>
> [mysqld]
> tmp_table_size = 5G
>
>
> Background for whoever cares:
>
> I'm running something reporter-wise in parallel (4 threads) and wanted
> roughly equal workload per "chunk" of reporters (some reporters have
> more experiments+data than others) so having them in random order
> before chunking does the trick.
>
> The tmp tables that the SELECT * FROM Reporters ORDER BY RAND(123)
> creates are 3.2G each (times 4) and while doing this there's some
> serious I/O clogging the machine but it pulls through.  If only gnu
> parallel had a -stagger [secs] option!


ORDER BY RAND() is known for performance issues once the number of rows 
grows large. I guess it is because MySQL need to create a temporary 
table with *all* the original data plus the random number for each row 
before the data can be sorted.

It might be more efficient to first do 'select id from Reporters' 
(you'll need to use the Reporter.getDynamicQuery() for this), put all 
id's in an array, randomize that in memory and then bring in the actual 
reporter data one by one (or 100 by 100 or something). That should at 
least avoid the temporary table issue since the id's can be pulled in 
directly from the primary key index. In theory it should be quicker, but 
I guess it has to be verified in practice as well.

/Nicklas

Re: [base] DataQuery.order(...) 2.x API question

[Bob M. <r.m...@im...>]

Just for closure, I am now in business.

[mysqld]
tmp_table_size = 5G


Background for whoever cares:

I'm running something reporter-wise in parallel (4 threads) and wanted
roughly equal workload per "chunk" of reporters (some reporters have
more experiments+data than others) so having them in random order
before chunking does the trick.

The tmp tables that the SELECT * FROM Reporters ORDER BY RAND(123)
creates are 3.2G each (times 4) and while doing this there's some
serious I/O clogging the machine but it pulls through.  If only gnu
parallel had a -stagger [secs] option!




On Tue, Oct 9, 2012 at 3:46 PM, Bob MacCallum
<r.m...@im...> wrote:
> Getting closer - I have set up a custom dialect:
>
> package org.vectorbase.funcgen.hibernate;
> import org.hibernate.Hibernate;
> import org.hibernate.dialect.MySQLInnoDBDialect;
> import org.hibernate.dialect.function.StandardSQLFunction;
>
> public class CustomDialect extends MySQLInnoDBDialect {
>   public CustomDialect()  {
>     super();
>     registerFunction("srand", new StandardSQLFunction("rand",
> Hibernate.DOUBLE) );
>   }
> }
>
> configure this in base.config
>
> And it all goes fine until some tmp tables run out of disk space or something
> (We have around 400k reporters FYI.)
>
> Looks like Nicklas has seen this before :-)
> https://forum.hibernate.org/viewtopic.php?f=1&t=994753
>
> I reckon I'll get it to work sooner or later.
>
> cheers,
> Bob.
>
> On Tue, Oct 9, 2012 at 2:15 PM, Bob MacCallum
> <r.m...@im...> wrote:
>> Hi Nicklas,
>> Thanks very much for the quick reply.  I am *so* close to getting this
>> working - it seems that the argument-less rand() is available in HQL
>> but I will have to jump through a few hoops to provide the seeded
>> version.
>> I'll post an update later...
>> cheers,
>> Bob.
>>
>> On Tue, Oct 9, 2012 at 12:50 PM, Nicklas Nordborg <ni...@th...> wrote:
>>> On 2012-10-09 13:11, Bob MacCallum wrote:
>>>> Hi all,
>>>>
>>>> I'm trying to get a Reporter query from the BASE2.x API which is
>>>> basically "ORDER BY RAND(123)" - to get reproducible "random" order (I
>>>> can explain *why* in another email if anyone cares to know).
>>>>
>>>> I tried this
>>>>
>>>> DataQuery<net.sf.basedb.core.data.ReporterData> repQuery =
>>>> net.sf.basedb.core.Reporter.getQuery();
>>>>
>>>> repQuery.order(Orders.asc(new HqlExpression("RAND(123)", "xxx")));
>>>>
>>>> But it seems that HqlExpression isn't for public use.  I can't find
>>>> something like "Expressions.hql".
>>>
>>> This can be found in net.sf.basedb.core.query.Hql.expression(...)
>>>
>>>> Could somebody please save me a ton of time and tell me how to put
>>>> some arbitrary SQL into the ORDER BY clause of a DataQuery?
>>>
>>> Note that it is not SQL that is needed but HQL (Hibernate Query
>>> Language). Don't know if RAND() is available in HQL. If not, it should
>>> be possible to create a custom Hibernate dialect and use that in the
>>> 'db.dialect' setting in base.config. I have never done that so I don't
>>> know any details or how hard/easy it is.
>>>
>>> Another possibility is to use Reporter.getDynamicQuery() instead which
>>> lets you work with SQL, but code-wise it's a bit harder to work with
>>> since you have to process the result row-by-row and column-by-column
>>> instead of as ReporterData objects.
>>>
>>> /Nicklas
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Don't let slow site performance ruin your business. Deploy New Relic APM
>>> Deploy New Relic app performance management and know exactly
>>> what is happening inside your Ruby, Python, PHP, Java, and .NET app
>>> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
>>> http://p.sf.net/sfu/newrelic-dev2dev
>>> _______________________________________________
>>> The BASE general discussion mailing list
>>> bas...@li...
>>> unsubscribe: send a mail with subject "unsubscribe" to
>>> bas...@li...

Re: [base] DataQuery.order(...) 2.x API question

[Bob M. <r.m...@im...>]

Getting closer - I have set up a custom dialect:

package org.vectorbase.funcgen.hibernate;
import org.hibernate.Hibernate;
import org.hibernate.dialect.MySQLInnoDBDialect;
import org.hibernate.dialect.function.StandardSQLFunction;

public class CustomDialect extends MySQLInnoDBDialect {
  public CustomDialect()  {
    super();
    registerFunction("srand", new StandardSQLFunction("rand",
Hibernate.DOUBLE) );
  }
}

configure this in base.config

And it all goes fine until some tmp tables run out of disk space or something
(We have around 400k reporters FYI.)

Looks like Nicklas has seen this before :-)
https://forum.hibernate.org/viewtopic.php?f=1&t=994753

I reckon I'll get it to work sooner or later.

cheers,
Bob.

On Tue, Oct 9, 2012 at 2:15 PM, Bob MacCallum
<r.m...@im...> wrote:
> Hi Nicklas,
> Thanks very much for the quick reply.  I am *so* close to getting this
> working - it seems that the argument-less rand() is available in HQL
> but I will have to jump through a few hoops to provide the seeded
> version.
> I'll post an update later...
> cheers,
> Bob.
>
> On Tue, Oct 9, 2012 at 12:50 PM, Nicklas Nordborg <ni...@th...> wrote:
>> On 2012-10-09 13:11, Bob MacCallum wrote:
>>> Hi all,
>>>
>>> I'm trying to get a Reporter query from the BASE2.x API which is
>>> basically "ORDER BY RAND(123)" - to get reproducible "random" order (I
>>> can explain *why* in another email if anyone cares to know).
>>>
>>> I tried this
>>>
>>> DataQuery<net.sf.basedb.core.data.ReporterData> repQuery =
>>> net.sf.basedb.core.Reporter.getQuery();
>>>
>>> repQuery.order(Orders.asc(new HqlExpression("RAND(123)", "xxx")));
>>>
>>> But it seems that HqlExpression isn't for public use.  I can't find
>>> something like "Expressions.hql".
>>
>> This can be found in net.sf.basedb.core.query.Hql.expression(...)
>>
>>> Could somebody please save me a ton of time and tell me how to put
>>> some arbitrary SQL into the ORDER BY clause of a DataQuery?
>>
>> Note that it is not SQL that is needed but HQL (Hibernate Query
>> Language). Don't know if RAND() is available in HQL. If not, it should
>> be possible to create a custom Hibernate dialect and use that in the
>> 'db.dialect' setting in base.config. I have never done that so I don't
>> know any details or how hard/easy it is.
>>
>> Another possibility is to use Reporter.getDynamicQuery() instead which
>> lets you work with SQL, but code-wise it's a bit harder to work with
>> since you have to process the result row-by-row and column-by-column
>> instead of as ReporterData objects.
>>
>> /Nicklas
>>
>>
>> ------------------------------------------------------------------------------
>> Don't let slow site performance ruin your business. Deploy New Relic APM
>> Deploy New Relic app performance management and know exactly
>> what is happening inside your Ruby, Python, PHP, Java, and .NET app
>> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
>> http://p.sf.net/sfu/newrelic-dev2dev
>> _______________________________________________
>> The BASE general discussion mailing list
>> bas...@li...
>> unsubscribe: send a mail with subject "unsubscribe" to
>> bas...@li...

Re: [base] DataQuery.order(...) 2.x API question

[Bob M. <r.m...@im...>]

Hi Nicklas,
Thanks very much for the quick reply.  I am *so* close to getting this
working - it seems that the argument-less rand() is available in HQL
but I will have to jump through a few hoops to provide the seeded
version.
I'll post an update later...
cheers,
Bob.

On Tue, Oct 9, 2012 at 12:50 PM, Nicklas Nordborg <ni...@th...> wrote:
> On 2012-10-09 13:11, Bob MacCallum wrote:
>> Hi all,
>>
>> I'm trying to get a Reporter query from the BASE2.x API which is
>> basically "ORDER BY RAND(123)" - to get reproducible "random" order (I
>> can explain *why* in another email if anyone cares to know).
>>
>> I tried this
>>
>> DataQuery<net.sf.basedb.core.data.ReporterData> repQuery =
>> net.sf.basedb.core.Reporter.getQuery();
>>
>> repQuery.order(Orders.asc(new HqlExpression("RAND(123)", "xxx")));
>>
>> But it seems that HqlExpression isn't for public use.  I can't find
>> something like "Expressions.hql".
>
> This can be found in net.sf.basedb.core.query.Hql.expression(...)
>
>> Could somebody please save me a ton of time and tell me how to put
>> some arbitrary SQL into the ORDER BY clause of a DataQuery?
>
> Note that it is not SQL that is needed but HQL (Hibernate Query
> Language). Don't know if RAND() is available in HQL. If not, it should
> be possible to create a custom Hibernate dialect and use that in the
> 'db.dialect' setting in base.config. I have never done that so I don't
> know any details or how hard/easy it is.
>
> Another possibility is to use Reporter.getDynamicQuery() instead which
> lets you work with SQL, but code-wise it's a bit harder to work with
> since you have to process the result row-by-row and column-by-column
> instead of as ReporterData objects.
>
> /Nicklas
>
>
> ------------------------------------------------------------------------------
> Don't let slow site performance ruin your business. Deploy New Relic APM
> Deploy New Relic app performance management and know exactly
> what is happening inside your Ruby, Python, PHP, Java, and .NET app
> Try New Relic at no cost today and get our sweet Data Nerd shirt too!
> http://p.sf.net/sfu/newrelic-dev2dev
> _______________________________________________
> The BASE general discussion mailing list
> bas...@li...
> unsubscribe: send a mail with subject "unsubscribe" to
> bas...@li...

Re: [base] DataQuery.order(...) 2.x API question

[Nicklas N. <ni...@th...>]

On 2012-10-09 13:11, Bob MacCallum wrote:
> Hi all,
>
> I'm trying to get a Reporter query from the BASE2.x API which is
> basically "ORDER BY RAND(123)" - to get reproducible "random" order (I
> can explain *why* in another email if anyone cares to know).
>
> I tried this
>
> DataQuery<net.sf.basedb.core.data.ReporterData> repQuery =
> net.sf.basedb.core.Reporter.getQuery();
>
> repQuery.order(Orders.asc(new HqlExpression("RAND(123)", "xxx")));
>
> But it seems that HqlExpression isn't for public use.  I can't find
> something like "Expressions.hql".

This can be found in net.sf.basedb.core.query.Hql.expression(...)

> Could somebody please save me a ton of time and tell me how to put
> some arbitrary SQL into the ORDER BY clause of a DataQuery?

Note that it is not SQL that is needed but HQL (Hibernate Query 
Language). Don't know if RAND() is available in HQL. If not, it should 
be possible to create a custom Hibernate dialect and use that in the 
'db.dialect' setting in base.config. I have never done that so I don't 
know any details or how hard/easy it is.

Another possibility is to use Reporter.getDynamicQuery() instead which 
lets you work with SQL, but code-wise it's a bit harder to work with 
since you have to process the result row-by-row and column-by-column 
instead of as ReporterData objects.

/Nicklas

[base] DataQuery.order(...) 2.x API question

[Bob M. <r.m...@im...>]

Hi all,

I'm trying to get a Reporter query from the BASE2.x API which is
basically "ORDER BY RAND(123)" - to get reproducible "random" order (I
can explain *why* in another email if anyone cares to know).

I tried this

DataQuery<net.sf.basedb.core.data.ReporterData> repQuery =
net.sf.basedb.core.Reporter.getQuery();

repQuery.order(Orders.asc(new HqlExpression("RAND(123)", "xxx")));

But it seems that HqlExpression isn't for public use.  I can't find
something like "Expressions.hql".
Could somebody please save me a ton of time and tell me how to put
some arbitrary SQL into the ORDER BY clause of a DataQuery?

many thanks,
Bob.

Re: [base] Setting up a new root bioassay set

[Nicklas N. <ni...@th...>]

On 2012-10-02 00:27, McClelland, Erin wrote:
>
> Hi
> Tried to post this earlier but it didn't seem to work - apologies if
> this is a duplicate message.
>
> We have run into a problem setting up a new root bioassay set - we
> continually get an error message similar to the following: Duplicate
> entry '22-1' for key 'PRIMARY' -  (see stack trace below).  Initially we
> did not have a reporter map imported for the new array we are using and
> had some problems with that importation - not sure if that would affect
> the root bioassay set as the reporters now seem to be in BASE. We are
> using data output from ImaGene. We are unsure how to address this
> problem and wondered if you have any suggestions.


It's difficult to say exactly what has happened here, but the error 
indicates some kind of duplicate position/reporter information in the 
raw data. This can be checked by going to the "Raw data" tab of one of 
the raw bioassays. Each entry in this table should have a unique 
"position", but possibly there are at least two with position=1.

If that is the case, new raw bioassays has to be created and the raw 
data has to be re-imported. Make sure that the array design has imported 
reporters since that is required to make the positions unique.

Hope this helps.

/Nicklas

[base] Setting up a new root bioassay set

[McClelland, E. <Eri...@df...>]

> Hi
> Tried to post this earlier but it didn't seem to work - apologies if
> this is a duplicate message.
> 
> We have run into a problem setting up a new root bioassay set - we
> continually get an error message similar to the following: Duplicate
> entry '22-1' for key 'PRIMARY' -  (see stack trace below).  Initially
> we did not have a reporter map imported for the new array we are using
> and had some problems with that importation - not sure if that would
> affect the root bioassay set as the reporters now seem to be in BASE.
> We are using data output from ImaGene. We are unsure how to address
> this problem and wondered if you have any suggestions.
> 
> 
> Thanks,
> 
> Erin
> 
> 
> 
> Message -- Error: Run plugin: Formula intensity calculator
> javascript:Main.openTabControlHelp('417022294046a3ae', 'main', 'null')
> Subject	 Error: Run plugin: Formula intensity calculator
> 
> From	 SYSTEM	 
> Time sent	 2012-09-18 14:59:23	 
> Message	 Duplicate entry '22-1' for key 'PRIMARY'	
> 
> net.sf.basedb.core.BaseException: Duplicate entry '22-1' for key
> 'PRIMARY'
> at
> net.sf.basedb.core.QueryExecutor.getFutureResult(QueryExecutor.java:19
> 4)
> at
> net.sf.basedb.core.QueryExecutor.executeUpdate(QueryExecutor.java:105)
> at
> net.sf.basedb.core.hibernate.ExecuteUpdateWork.execute(ExecuteUpdateWo
> rk.java:77)
> at org.hibernate.impl.SessionImpl.doWork(SessionImpl.java:1873)
> at net.sf.basedb.core.HibernateUtil.doJdbcWork(HibernateUtil.java:994)
> at net.sf.basedb.core.PositionBatcher.insert(PositionBatcher.java:251)
> at
> net.sf.basedb.util.IntensityCalculatorUtil.createRootBioAssaySet(Inten
> sityCalculatorUtil.java:208)
> at
> net.sf.basedb.plugins.IntensityCalculatorPlugin.run(IntensityCalculato
> rPlugin.java:259)
> at
> net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionReques
> t.java:110)
> at
> net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.jav
> a:506)
> at java.lang.Thread.run(Thread.java:619)
> Caused by:
> com.mysql.jdbc.exceptions.jdbc4.MySQLIntegrityConstraintViolationExcep
> tion: Duplicate entry '22-1' for key 'PRIMARY'
> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
> Method)
> at
> sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructo
> rAccessorImpl.java:39)
> at
> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingCo
> nstructorAccessorImpl.java:27)
> at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
> at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
> at com.mysql.jdbc.Util.getInstance(Util.java:381)
> at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1015)
> at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:956)
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3491)
> at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3423)
> at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1936)
> at
> com.mysql.jdbc.ServerPreparedStatement.serverExecute(ServerPreparedSta
> tement.java:1328)
> at
> com.mysql.jdbc.ServerPreparedStatement.executeInternal(ServerPreparedS
> tatement.java:838)
> at
> com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:
> 2019)
> at
> com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:
> 1937)
> at
> com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:
> 1922)
> at
> com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeUpdate(NewPr
> oxyPreparedStatement.java:105)
> at
> net.sf.basedb.core.QueryExecutor$FutureUpdate.call(QueryExecutor.java:
> 269)
> at
> net.sf.basedb.core.QueryExecutor$FutureUpdate.call(QueryExecutor.java:
> 257)
> at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
> at java.util.concurrent.FutureTask.run(FutureTask.java:138)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecu
> tor.java:886)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.
> java:908)
> ... 1 more
> 

Re: [base] Can BASE (v2.12.1) import files directly from the server it's running on?

[Nicklas N. <ni...@th...>]

On 2012-09-20 01:26, Hugh Brown wrote:
> Hi everyone -- my department is running BASE version 2.12.1.  We have
> some users outside our department, and their network connection is
> rather slow.  At the moment, they're importing files rather
> circuitously: uploading them to our server for pre-processing,
> downloading the results, then uploading them to BASE via their
> browser.  The end result is many round trips for large data files.
 >
> I'm wondering if BASE, perhaps through a plugin, supports importing
> files from the server it's running on.  I found a message from 2007
> about this idea
>
> 	http://www.mail-archive.com/bas...@li.../msg00218.html
>
> but as far as I can see, this is not in BASE2.  Have I missed anything?

No, you have not missed anything. There is no functionality for 
importing files directly from the server. Although it would be possible 
to implement this as a plug-in or as an "External file extension" (but 
this require at least BASE 3.0). In any case, I can imagine all sorts of 
security/permission-related issues with this.

> About the only other alternative I can think of is installing the FTP
> server plugin, then have the users connect via FTP from the server
> itself (ie, over the loopback interface).  Is there any reason that
> would not work?

I think this would work very well. And if you only need the FTP support 
locally then there is no need to open up firewalls, etc. which is always 
a hassle with FTP.

/Nicklas

[base] Can BASE (v2.12.1) import files directly from the server it's running on?

[Hugh B. <hb...@ch...>]

Hi everyone -- my department is running BASE version 2.12.1.  We have
some users outside our department, and their network connection is
rather slow.  At the moment, they're importing files rather
circuitously: uploading them to our server for pre-processing,
downloading the results, then uploading them to BASE via their
browser.  The end result is many round trips for large data files.

I'm wondering if BASE, perhaps through a plugin, supports importing
files from the server it's running on.  I found a message from 2007
about this idea

	http://www.mail-archive.com/bas...@li.../msg00218.html

but as far as I can see, this is not in BASE2.  Have I missed anything?

About the only other alternative I can think of is installing the FTP
server plugin, then have the users connect via FTP from the server
itself (ie, over the loopback interface).  Is there any reason that
would not work?

Apologies if this question has been asked before, but I couldn't find
any other mention of "local import" on the -users or -devel mailing
list.  If I've left out any info, please let me know.

Thanks in advance for any help!

--
Hugh Brown, Systems Manager
The Centre for High-Throughput Biology
hb...@ch...

[base] BASE 3.2 has been released

[Nicklas N. <ni...@th...>]

Hello all,

We are happy to announce the release of BASE 3.2. It is a new major
release that includes several new features and enhancements.

   * Several new extension possibilities in table listings,
     the item overview and other places.

   * A new parent/child structure for derived bioassays that makes
     it possible to merge bioassays from multiple physical bioassays.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.2&group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

Re: [base] Change BASE's HTML title

[Nicklas N. <ni...@th...>]

On 2012-08-20 21:01, Paulo Nuin wrote:

> How can this be solved?

I don't know. My guess is that something on that server is incorrectly 
configured that has to do with networking and/or DNS lookup.

/Nicklas

Re: [base] Change BASE's HTML title

[Paulo N. <nu...@ge...>]

Noticed that domain and hostname were identical, don't know why, and reset it, but it still shows me the same thing.

Paulo


On 2012-08-20, at 3:01 PM, Paulo Nuin <nu...@ge...> wrote:

> Indeed there's some error getting localhost
> 
> 13:40:29,172 ERROR Cache:202 - Unable to set localhost. This prevents creation of a GUID. Cause was: braincode-linux: braincode-linux
> java.net.UnknownHostException: braincode-linux: braincode-linux
> 	at java.net.InetAddress.getLocalHost(InetAddress.java:1426)
> 	at net.sf.ehcache.Cache.<clinit>(Cache.java:200)
> 	at net.sf.ehcache.config.ConfigurationHelper.createCache(ConfigurationHelper.java:302)
> 	at net.sf.ehcache.config.ConfigurationHelper.createDefaultCache(ConfigurationHelper.java:218)
> 	at net.sf.ehcache.CacheManager.configure(CacheManager.java:618)
> 	at net.sf.ehcache.CacheManager.init(CacheManager.java:361)
> 	at net.sf.ehcache.CacheManager.<init>(CacheManager.java:302)
> 	at org.hibernate.cache.EhCacheProvider.start(EhCacheProvider.java:131)
> 	at org.hibernate.cache.impl.bridge.RegionFactoryCacheProviderBridge.start(RegionFactoryCacheProviderBridge.java:72)
> 	at org.hibernate.impl.SessionFactoryImpl.<init>(SessionFactoryImpl.java:238)
> 	at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1872)
> 	at net.sf.basedb.core.HibernateUtil.init2(HibernateUtil.java:210)
> 	at net.sf.basedb.core.Application.start(Application.java:507)
> 	at net.sf.basedb.core.Application.start(Application.java:399)
> 	at net.sf.basedb.clients.web.servlet.StartStopServlet.init(StartStopServlet.java:58)
> 	at javax.servlet.GenericServlet.init(GenericServlet.java:212)
> 	at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1173)
> 	at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:993)
> 	at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:4421)
> 	at org.apache.catalina.core.StandardContext.start(StandardContext.java:4734)
> 	at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:799)
> 	at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:779)
> 	at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:601)
> 	at org.apache.catalina.startup.HostConfig.deployDirectory(HostConfig.java:1079)
> 	at org.apache.catalina.startup.HostConfig.deployDirectories(HostConfig.java:1002)
> 	at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:506)
> 	at org.apache.catalina.startup.HostConfig.check(HostConfig.java:1385)
> 	at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:306)
> 	at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:142)
> 	at org.apache.catalina.core.ContainerBase.backgroundProcess(ContainerBase.java:1389)
> 	at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1653)
> 	at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1662)
> 	at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.run(ContainerBase.java:1642)
> 	at java.lang.Thread.run(Thread.java:679)
> 
> 
> How can this be solved?
> 
> Thanks
> Paulo
> 
> 
> On 2012-08-20, at 1:57 PM, Nicklas Nordborg <ni...@th...> wrote:
> 
>> On 2012-08-20 18:56, Paulo Nuin wrote:
>>> Hi
>>> 
>>> The computer has a name under /etc/HOSTNAME running SuSE, and network is fine.
>> 
>> Check Tomcat's log file if there are any error messages. The name is set 
>> to 'unknown' if the name can't be retrieved from the system.
>> 
>> /Nicklas
>> 
>> 
>> ------------------------------------------------------------------------------
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and 
>> threat landscape has changed and how IT managers can respond. Discussions 
>> will include endpoint security, mobile security and the latest in malware 
>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>> _______________________________________________
>> The BASE general discussion mailing list
>> bas...@li...
>> unsubscribe: send a mail with subject "unsubscribe" to
>> bas...@li...
> 
> 
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and 
> threat landscape has changed and how IT managers can respond. Discussions 
> will include endpoint security, mobile security and the latest in malware 
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> The BASE general discussion mailing list
> bas...@li...
> unsubscribe: send a mail with subject "unsubscribe" to
> bas...@li...

Re: [base] Change BASE's HTML title

[Paulo N. <nu...@ge...>]

Indeed there's some error getting localhost

13:40:29,172 ERROR Cache:202 - Unable to set localhost. This prevents creation of a GUID. Cause was: braincode-linux: braincode-linux
java.net.UnknownHostException: braincode-linux: braincode-linux
	at java.net.InetAddress.getLocalHost(InetAddress.java:1426)
	at net.sf.ehcache.Cache.<clinit>(Cache.java:200)
	at net.sf.ehcache.config.ConfigurationHelper.createCache(ConfigurationHelper.java:302)
	at net.sf.ehcache.config.ConfigurationHelper.createDefaultCache(ConfigurationHelper.java:218)
	at net.sf.ehcache.CacheManager.configure(CacheManager.java:618)
	at net.sf.ehcache.CacheManager.init(CacheManager.java:361)
	at net.sf.ehcache.CacheManager.<init>(CacheManager.java:302)
	at org.hibernate.cache.EhCacheProvider.start(EhCacheProvider.java:131)
	at org.hibernate.cache.impl.bridge.RegionFactoryCacheProviderBridge.start(RegionFactoryCacheProviderBridge.java:72)
	at org.hibernate.impl.SessionFactoryImpl.<init>(SessionFactoryImpl.java:238)
	at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1872)
	at net.sf.basedb.core.HibernateUtil.init2(HibernateUtil.java:210)
	at net.sf.basedb.core.Application.start(Application.java:507)
	at net.sf.basedb.core.Application.start(Application.java:399)
	at net.sf.basedb.clients.web.servlet.StartStopServlet.init(StartStopServlet.java:58)
	at javax.servlet.GenericServlet.init(GenericServlet.java:212)
	at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1173)
	at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:993)
	at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:4421)
	at org.apache.catalina.core.StandardContext.start(StandardContext.java:4734)
	at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:799)
	at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:779)
	at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:601)
	at org.apache.catalina.startup.HostConfig.deployDirectory(HostConfig.java:1079)
	at org.apache.catalina.startup.HostConfig.deployDirectories(HostConfig.java:1002)
	at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:506)
	at org.apache.catalina.startup.HostConfig.check(HostConfig.java:1385)
	at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:306)
	at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:142)
	at org.apache.catalina.core.ContainerBase.backgroundProcess(ContainerBase.java:1389)
	at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1653)
	at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1662)
	at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.run(ContainerBase.java:1642)
	at java.lang.Thread.run(Thread.java:679)


How can this be solved?

Thanks
Paulo


On 2012-08-20, at 1:57 PM, Nicklas Nordborg <ni...@th...> wrote:

> On 2012-08-20 18:56, Paulo Nuin wrote:
>> Hi
>> 
>> The computer has a name under /etc/HOSTNAME running SuSE, and network is fine.
> 
> Check Tomcat's log file if there are any error messages. The name is set 
> to 'unknown' if the name can't be retrieved from the system.
> 
> /Nicklas
> 
> 
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and 
> threat landscape has changed and how IT managers can respond. Discussions 
> will include endpoint security, mobile security and the latest in malware 
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> The BASE general discussion mailing list
> bas...@li...
> unsubscribe: send a mail with subject "unsubscribe" to
> bas...@li...

Re: [base] Change BASE's HTML title

[Nicklas N. <ni...@th...>]

On 2012-08-20 18:56, Paulo Nuin wrote:
> Hi
>
> The computer has a name under /etc/HOSTNAME running SuSE, and network is fine.

Check Tomcat's log file if there are any error messages. The name is set 
to 'unknown' if the name can't be retrieved from the system.

/Nicklas

Re: [base] Change BASE's HTML title

[Paulo N. <nu...@ge...>]

Hi

The computer has a name under /etc/HOSTNAME running SuSE, and network is fine.

Thanks
Paulo


On 2012-08-20, at 12:32 PM, Nicklas Nordborg <ni...@th...> wrote:

> On 2012-08-20 17:09, Paulo Nuin wrote:
>> Hi
>> 
>> I have a quick question on configuring BASE's HTML page title. In the
>> server we have installed now it appears
>> 
>> BASE 3.1.1 @ unknown
>> 
>> I found the jsp pages in the www directory but it is not clear to me
>> where this title is coming from. I was able to add a value to the
>> title variable in the jsp, but the unknown still appears.
> 
> The title is generated from the current BASE version and the name of the 
> computer it is installed on. I have never seen the string 'unknown' 
> there. Usually, if the computer doesn't have a name the title will be 
> something like: 'BASE x.y.z @ 127.0.0.1' or 'BASE x.y.z @ localhost'
> 
> Maybe it is an indication that there is no network connection...
> 
> Or maybe the computer's name is 'unknown'?
> 
> /Nicklas
> 
> 
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and 
> threat landscape has changed and how IT managers can respond. Discussions 
> will include endpoint security, mobile security and the latest in malware 
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> The BASE general discussion mailing list
> bas...@li...
> unsubscribe: send a mail with subject "unsubscribe" to
> bas...@li...

Re: [base] Change BASE's HTML title

[Nicklas N. <ni...@th...>]

On 2012-08-20 17:09, Paulo Nuin wrote:
> Hi
>
> I have a quick question on configuring BASE's HTML page title. In the
> server we have installed now it appears
>
> BASE 3.1.1 @ unknown
>
> I found the jsp pages in the www directory but it is not clear to me
> where this title is coming from. I was able to add a value to the
> title variable in the jsp, but the unknown still appears.

The title is generated from the current BASE version and the name of the 
computer it is installed on. I have never seen the string 'unknown' 
there. Usually, if the computer doesn't have a name the title will be 
something like: 'BASE x.y.z @ 127.0.0.1' or 'BASE x.y.z @ localhost'

Maybe it is an indication that there is no network connection...

Or maybe the computer's name is 'unknown'?

/Nicklas

[base] Change BASE's HTML title

[Paulo N. <nu...@ge...>]

Hi

I have a quick question on configuring BASE's HTML page title. In the server we have installed now it appears

BASE 3.1.1 @ unknown

I found the jsp pages in the www directory but it is not clear to me where this title is coming from. I was able to add a value to the title variable in the jsp, but the unknown still appears.

Any help is appreciated.

Thanks in advance

Paulo

[base] BASE 3.1.2 has been released

[Nicklas N. <ni...@th...>]

Hello all,

We have released BASE 3.1.2 today. This is a bugfix release that
fixes a few minor problems.

For a complete list of changes, see:
http://base.thep.lu.se/query?milestone=BASE+3.1.2&group=type

Installation/upgrade instructions:
http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html

As usual, the program can be downloaded from:
http://base.thep.lu.se/wiki/DownloadPage

/Nicklas

Re: [base] MeV: export bioassay set to TDMS file error

[Nicklas N. <ni...@th...>]

On 2012-06-07 08:52, Nicklas Nordborg wrote:
> On 2012-06-05 22:52, Steven Charles Fan wrote:
>> Running base v3.1.1 with mev-launcher-1.9 binary (current base version
>> and MeV version 4.7.3) on Centos6. Tried to export a bioassay set of two
>> bioassays to a TDMS file for analysis in MeV and got a unnamed error
>> with the following stack trace:
> ...
>   >  Is this a user error I can do something about or have I stumbled upon
> a bug?
>
> I can confirm that this is indeed a bug. Until a fix has been released,
> the workaround is to use the 'Clone reporters' function on the
> experiment view page.

I have now release a new version of the MeV plug-in (1.10). It fixes 
this bug and also update MeV to 4.8.1. It can be downloaded from:

http://baseplugins.thep.lu.se/wiki/net.sf.basedb.mev

/Nicklas

Re: [base] MeV: export bioassay set to TDMS file error

[Nicklas N. <ni...@th...>]

On 2012-06-05 22:52, Steven Charles Fan wrote:
> Running base v3.1.1 with mev-launcher-1.9 binary (current base version
> and MeV version 4.7.3) on Centos6. Tried to export a bioassay set of two
> bioassays to a TDMS file for analysis in MeV and got a unnamed error
> with the following stack trace:
...
 > Is this a user error I can do something about or have I stumbled upon 
a bug?

I can confirm that this is indeed a bug. Until a fix has been released, 
the workaround is to use the 'Clone reporters' function on the 
experiment view page.

> The following is unrelated, but I was wondering if reporters were best
> imported from a gpr file or GAL file or if there is a difference. I was
> also wondering if there was a way to update biological annotations
> automatically from SGD.

It shouldn't really matter since the only reporter information in gpr 
and gal files are the reporter id. Annotations need to come from a 
different source. I do not know what SGD is, but in any case there is no 
function to update annotations automatically from any external source. 
It must be done manually by exporting and importing files.

> Oh and a (possible) bug notice: in the *Genepix raw data cy5/cy3
> (cy5/cy3) import configuration* for the *raw bioassay import from file*,
> I had to change *Rgn R<superscipt 2>* to *Rgn R2* to get it to work with
> my grp extension genepix files.

It's not really a bug. The data files we have all have R² (superscript). 
My guess is that it depends on the Genepix software version and/or 
settings in the software.

/Nicklas

[base] MeV: export bioassay set to TDMS file error

[Steven C. F. <sf...@em...>]

Running base v3.1.1 with mev-launcher-1.9 binary (current base version and
MeV version 4.7.3) on Centos6. Tried to export a bioassay set of two
bioassays to a TDMS file for analysis in MeV and got a unnamed error with
the following stack trace:

java.lang.NullPointerException
  at
net.sf.basedb.mev.export.TdmsExporter.addReporterFields(TdmsExporter.java:290)
  at
net.sf.basedb.mev.export.TdmsExporter.beginExport(TdmsExporter.java:107)
  at
net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter.doExport(AbstractBioAssaySetExporter.java:277)
  at
net.sf.basedb.mev.plugin.TdmsExporterPlugin.performExport(TdmsExporterPlugin.java:263)
  at
net.sf.basedb.core.plugin.AbstractExporterPlugin.run(AbstractExporterPlugin.java:144)
  at
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:116)
  at
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:510)
  at java.lang.Thread.run(Thread.java:662)

Is this a user error I can do something about or have I stumbled upon a bug?

The following is unrelated, but I was wondering if reporters were best
imported from a gpr file or GAL file or if there is a difference. I was
also wondering if there was a way to update biological annotations
automatically from SGD.

Oh and a (possible) bug notice: in the *Genepix raw data cy5/cy3 (cy5/cy3)
import configuration* for the *raw bioassay import from file*, I had to
change *Rgn R<superscipt 2>* to *Rgn R2* to get it to work with my grp
extension genepix files.

Thanks in Advance
Steven Fan

[base] Agilent and LIMMA in BASE

[Ross C. <ros...@mo...>]

Hi

I want to analyse Agilent microarrays in BASE 2.17.2 using LIMMA methods to
perform background subtraction, normalisation and significance testing.

Does anyone know if there is a suitable plugin available to perform these
analyses?

Thanks

Ross
-- 
Dr Ross Chapman
Senior Bioinformatician
MIMR

(03) 99024719