Re: [basedb-devel] Feedback to BASE information

[Jari Häkkinen]

Hi Philipp,

Thank you for your interest in BASE.

Some of the information you listed is outdated. Here are updates
you can use.


1) Brief description of BASE:

BASE is a comprehensive free web-based database LIMS solution for
tracking of information and data generated in sequencing and
microarray experiments from sample to analysis. BASE is released under
the ​GNU General Public License version 3.


2) The reference list could be updated to include

- Häkkinen et al. 2016, https://doi.org/10.1101/038976
- Vallon-Christersson et al. 2009, PMID: 19822003

If only one reference can be retained then you should use
Vallon-Christersson et al.


3) Under miscellaneous you might add that source code is available at
http://base.thep.lu.se? It is open, browsable, searchable, has issue
tracking, and more. Actually predates GitHub ;-)


4) Regarding compliance to standards. We are not actively pursuing
(MIAME) standards compliance, and the public repository upload
functionality is semi-automatic at best.


Cheers,

Jari


On 2019-06-16 14:54, Pugliese, Philipp wrote:

Dear support team,

briefly to me: my name is Philipp Pugliese and I researched for the 
Friedrich-Alexander-Universität Erlangen-Nürnberg about functions that 
BASE seems to fulfill.


For a congress publication I created a matrix in which BASE is 
mentioned. Could you please give me some feedback as to whether the 
information I found in the literature is correct or up to date?


The information is:

Brief description of BASE: Is an information and analysis tool for 
microarrays that tracks all materials from biosource to raw data to 
analyses. The elements can be annotated and used as factors in the 
downstream analysis



General
  Abbreviation: BioArray Software Environment
  FAIR reference: unknown
  Note: -

Community
  Institution: Lund University
  Reference: Saal et al. 2002
  PMID: 12186655
  Software availability: open source
  License: GNU
  User mailing list or support: Yes
  URL: http://base.thep.lu.se

System requirements
  Operating system: Platform independent
  DB managing System: MySQL,PostgreSQL
  Main programming language: Java
  Client-side interface: web browser

Support
  Installation procedures: Yes
  Configuration documentation: Yes
  User documentation: Yes
  Regular maintenance: Yes

Miscellaneous
  GitHub availability: -
  Demo server availability: Yes

Requirements for data management in system biology
  Compliance to standards: MIAME
  Metadata model: MIAME-related
  Automation of data collection: batch import
  Upload to public repositories: ArrayExpress, GEO, CIBEX
  Extensibility: Java plugins / extentions
  Integration with other DMS: via java servlets



Please give me feedback by 30th June 2019 so that your feedback can be 
considered until publication.


Thanks in advance and best regards,
Philipp Pugliese
mailto:phil.pugli...@fau.de

P.S.: hope you are the right contact person. If not, could you provide 
me the right contact person?



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Re: [basedb-devel] Tab2Mage exporter plugin

[Jari Häkkinen]

Forgot this in my previous post.


I have committed the code to the repository. Building Tab2MageExporter 
causes a few warnings of which all but is complaining about use of 
deprecated BASE2Core calls. There is one warning about unchecked cast:

src/uk/ac/ebi/nugo/plugins/ta2mageexport/Tab2MageValidator.java:216: 
warning: [unchecked] unchecked cast
 [javac] found   : net.sf.basedb.core.ItemResultList
 [javac] required: 
net.sf.basedb.core.ItemResultList
 [javac] 
rba.getScan().getHybridization().getCreationEvent().getSources().list(dc);

But that is probably okay?

Also, the patch you provided has a reference to a file 
Tab2MageExporter/lib/BASE2WSClient.jar that is not in the repository. 
The file is not required for a successful compile of the 
Tab2MageExporter. Maybe it is a stray file in your working copy?


Cheers,

Jari


On 2/9/10 2:29 PM, Gildas Le Corguillé wrote:
> Hi,
>
> I join you my patch for Tab2MageExporter. Is it what you expected in
> your email ?
>
> Until now, I've never participated to an open project. Thus don't be
> affraid if you see my name everywhere, it's because I wanted to sign and
> assume what I changed if there were troubles with my updates.
>
> I might have to make modifications later (bugs) or adapt this current
> script for a MAGE-TAB exporter because Tab2Mage format don't allow
> pooling like Base does :
> - Base : n samples in 1 sample
> - Tab2Mage : n sampels in 1 extract
> It will depend of my free times among my own projects.
>
> Excerpt from ChangeLog.txt :
>
> version 1.01 : 08/02/2010 - lecorguille
> - Fix a problem with pooling which was not supported ... for me
> - Modification : Filenames are use instead of RawBioAssays' names
> for File[raw] column in the Hybridization section
> - Add the possibility to have several Files[raw] per RawBioAssay (ex
> : one cy3 and one cy5)
> - Add a scan column in the Hybridization section
> - Add a BioSourceDescription column in the Hybridization section
> - Fix a problem with protocols in the Hybridization section
>
>
> Cheers
>
> Gildas
>
>
>
> Le 05/02/2010 11:27, Jari Häkkinen a écrit :
>> Hi Gildas,
>>
>> Great to see work done on the Tab2Mage exporter. The original author has
>> left for other tasks and the Tab2Mage code is currently without a
>> maintainer but lives under the GPL2 license so it is free to modify and
>> improve.
>>
>> You can submit your patches to me and I make sure that they are
>> committed to the repository. If you checked out the source from
>> subversion then you can simply create a patch diff. Excerpt from
>> http://base.thep.lu.se/wiki/DeveloperInformation:
>>
>> ... send an email to the developers list containing your log message and
>> the output of svn diff (from the top of your Subversion working copy) ...
>>
>> Send the patch to me.
>>
>> For the new method usage we simply increase the BASE version requirement
>> on the plug-in. I'll find out when the new method appeared in BASE.
>> Changing the Tab2Mage plugin will not affect already installed servers
>> but rather new users of the Tab2Mage plugin. Of course, users wanting to
>> use your new features must of course upgrade their BASE if it is
>> obsolete.
>>
>>
>> Cheers,
>>
>> Jari
>>
>>
>> On 2/5/10 10:07 AM, Gildas Le Corguillé wrote:
>>> Dear colleagues,
>>>
>>> I had a problem with Tab2Mage exporter plugin about polling.
>>> Then to know if it was my fault or its fault, I downloaded the sources
>>> to study the pooling implications.
>>>
>>> And finally, I tried to fix what I thought be a bug.
>>>
>>> Now Tab2Mage_exporter :
>>> - supports pooling
>>> - creates a scan column in the output file
>>> - uses the filemane name in the "File[raw]" column instead of the
>>> RawBioAssay name
>>> - supports several files per RawBioAssay
>>>
>>>
>>> I hope I didn't add bug !?
>>> And now, what is your policy about submiting an update ? Must I contact
>>> the original author ?
>>>
>>> For the last point, I had to use the method RawBioAssay.setFileSet().
>>> Which is implement in a newer BASE2Core than Tab2Mage_exporter
>>> previously used.
>>> But I don't know from which version of Base, this method appear ? Then
>>> if we propose my update, old version of base will show troubles.
>>>
>>> Thank you for your attention
>>>
>>> Best regards
>>>
>>> Gildas
>>

Re: [basedb-devel] Tab2Mage exporter plugin

[Jari Häkkinen]

Committed in http://baseplugins.thep.lu.se/changeset/1188 and the 
plug-in wiki page is updated accordingly.

Thanks,


Jari


On 2/9/10 2:29 PM, Gildas Le Corguillé wrote:
> Hi,
>
> I join you my patch for Tab2MageExporter. Is it what you expected in
> your email ?
>
> Until now, I've never participated to an open project. Thus don't be
> affraid if you see my name everywhere, it's because I wanted to sign and
> assume what I changed if there were troubles with my updates.
>
> I might have to make modifications later (bugs) or adapt this current
> script for a MAGE-TAB exporter because Tab2Mage format don't allow
> pooling like Base does :
> - Base : n samples in 1 sample
> - Tab2Mage : n sampels in 1 extract
> It will depend of my free times among my own projects.
>
> Excerpt from ChangeLog.txt :
>
> version 1.01 : 08/02/2010 - lecorguille
> - Fix a problem with pooling which was not supported ... for me
> - Modification : Filenames are use instead of RawBioAssays' names
> for File[raw] column in the Hybridization section
> - Add the possibility to have several Files[raw] per RawBioAssay (ex
> : one cy3 and one cy5)
> - Add a scan column in the Hybridization section
> - Add a BioSourceDescription column in the Hybridization section
> - Fix a problem with protocols in the Hybridization section
>
>
> Cheers
>
> Gildas
>
>
>
> Le 05/02/2010 11:27, Jari Häkkinen a écrit :
>> Hi Gildas,
>>
>> Great to see work done on the Tab2Mage exporter. The original author has
>> left for other tasks and the Tab2Mage code is currently without a
>> maintainer but lives under the GPL2 license so it is free to modify and
>> improve.
>>
>> You can submit your patches to me and I make sure that they are
>> committed to the repository. If you checked out the source from
>> subversion then you can simply create a patch diff. Excerpt from
>> http://base.thep.lu.se/wiki/DeveloperInformation:
>>
>> ... send an email to the developers list containing your log message and
>> the output of svn diff (from the top of your Subversion working copy) ...
>>
>> Send the patch to me.
>>
>> For the new method usage we simply increase the BASE version requirement
>> on the plug-in. I'll find out when the new method appeared in BASE.
>> Changing the Tab2Mage plugin will not affect already installed servers
>> but rather new users of the Tab2Mage plugin. Of course, users wanting to
>> use your new features must of course upgrade their BASE if it is
>> obsolete.
>>
>>
>> Cheers,
>>
>> Jari
>>
>>
>> On 2/5/10 10:07 AM, Gildas Le Corguillé wrote:
>>> Dear colleagues,
>>>
>>> I had a problem with Tab2Mage exporter plugin about polling.
>>> Then to know if it was my fault or its fault, I downloaded the sources
>>> to study the pooling implications.
>>>
>>> And finally, I tried to fix what I thought be a bug.
>>>
>>> Now Tab2Mage_exporter :
>>> - supports pooling
>>> - creates a scan column in the output file
>>> - uses the filemane name in the "File[raw]" column instead of the
>>> RawBioAssay name
>>> - supports several files per RawBioAssay
>>>
>>>
>>> I hope I didn't add bug !?
>>> And now, what is your policy about submiting an update ? Must I contact
>>> the original author ?
>>>
>>> For the last point, I had to use the method RawBioAssay.setFileSet().
>>> Which is implement in a newer BASE2Core than Tab2Mage_exporter
>>> previously used.
>>> But I don't know from which version of Base, this method appear ? Then
>>> if we propose my update, old version of base will show troubles.
>>>
>>> Thank you for your attention
>>>
>>> Best regards
>>>
>>> Gildas
>>>
>>>
>>>
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>>>
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>>> basedb-devel@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/basedb-devel
&

Re: [basedb-devel] Tab2Mage exporter plugin

[Jari Häkkinen]

Hi Gildas,

Great to see work done on the Tab2Mage exporter. The original author has 
left for other tasks and the Tab2Mage code is currently without a 
maintainer but lives under the GPL2 license so it is free to modify and 
improve.

You can submit your patches to me and I make sure that they are 
committed to the repository. If you checked out the source from 
subversion then you can simply create a patch diff. Excerpt from 
http://base.thep.lu.se/wiki/DeveloperInformation:

... send an email to the developers list containing your log message and 
the output of svn diff (from the top of your Subversion working copy) ...

Send the patch to me.

For the new method usage we simply increase the BASE version requirement 
on the plug-in. I'll find out when the new method appeared in BASE. 
Changing the Tab2Mage plugin  will not affect already installed servers 
but rather new users of the Tab2Mage plugin. Of course, users wanting to 
use your new features must of course upgrade their BASE if it is obsolete.


Cheers,

Jari


On 2/5/10 10:07 AM, Gildas Le Corguillé wrote:
> Dear colleagues,
>
> I had a problem with Tab2Mage exporter plugin about polling.
> Then to know if it was my fault or its fault, I downloaded the sources
> to study the pooling implications.
>
> And finally, I tried to fix what I thought be a bug.
>
> Now Tab2Mage_exporter :
>- supports pooling
>- creates a scan column in the output file
>- uses the filemane name in the "File[raw]" column instead of the
> RawBioAssay name
>- supports several files per RawBioAssay
>
>
> I hope I didn't add bug !?
> And now, what is your policy about submiting an update ? Must I contact
> the original author ?
>
> For the last point, I had to use the method RawBioAssay.setFileSet().
> Which is implement in a newer BASE2Core than Tab2Mage_exporter
> previously used.
> But I don't know from which version of Base, this method appear ? Then
> if we propose my update, old version of base will show troubles.
>
> Thank you for your attention
>
> Best regards
>
> Gildas
>
>
>
> --
> The Planet: dedicated and managed hosting, cloud storage, colocation
> Stay online with enterprise data centers and the best network in the business
> Choose flexible plans and management services without long-term contracts
> Personal 24x7 support from experience hosting pros just a phone call away.
> http://p.sf.net/sfu/theplanet-com
> ___
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> basedb-devel@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/basedb-devel


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[basedb-devel] BASE 2 published in BMC Bioinformatics

[Jari Häkkinen]

Hi all,

We have published a short presentation of BASE in BMC Bioinformatics 
2009, 10:330 (http://www.biomedcentral.com/1471-2105/10/330).

The article gives an brief overview of BASE and its most important 
features. The paper gives a taste of what can be accomplished with BASE 
today. Now we need that ever important tutorial material  ;-)


Cheers,

Jari

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Re: [basedb-devel] MeV

[Jari Häkkinen]

Great, we'll upgrade MeV in base after the holidays.


Jari


David Waring wrote:
> The MeV people have incorporated the servlet support changes in their  
> svn repository. So if you want to grab it from sourseforge you could  
> put it into the Base distribution.
> 
> They will likely be incorporating auto-loading features also but  
> those changes are more complicated and they want to address some  
> other issues, so that may not happen right away.
> 
> 
> 
> 
> On Dec 11, 2008, at 1:31 PM, David Waring wrote:
> 
>> I have also made another change to my version of Base. My users
>> wanted real intensities within MeV instead of ratios. But
>> unfortunately MeV does not support a multi experiment file with
>> intensities. So I made a modified BioassayExporter and added a new
>> new FileLoader in MeV based on the TDMS (Stanford) format. I'm going
>> to see if TIGR is interested in these and my other changes that allow
>> the data to be loaded automatically skipping the normal dialog.
>>
>>
>> On Dec 10, 2008, at 1:04 PM, Nicklas Nordborg wrote:
>>
>>> Thanks, this is excellent news!
>>>
>>> We were also "planning" to do this, but there has always been some
>>> other
>>> more important things that had to be done before. It is really nice
>>> that
>>> MeV has been webstart-enabled and can load files from the web. If I
>>> remember correctly the modifications we (Jari) had to do was
>>> related to
>>> make MeV work as a webstart-application and to download the file from
>>> the BASE server. It seems like it is almost possible to use MeV
>>> without
>>> modifications. The first issue can maybe be addressed on the BASE  
>>> side
>>> as well. The servlet could be changed to accept query parameters as
>>> part
>>> of the path instead. Eg something like:
>>> http://your.base.server/base2/./mev/export//
>>> 
>>>
>>> The timeout issue needs to be solved in MeV though.
>>>
>>> I have opened a ticket on the BASE plug-ins site:
>>> http://baseplugins.thep.lu.se/ticket/162
>>>
>>> If anyone has more information please post comments there  
>>> (login=base;
>>> password=base)
>>>
>>> /Nicklas
>>>
>>>
>>> David Waring wrote:
 As best I can tell the current version of Base has MeV support built
 on Version 4.0.01. The current release version of MeV 4.3.01 is much
 improved with a better interface and a more modules. It also has
 webstart support built in.

 I have installed MeV 4.3 on my Base installation. It  required  
 just a
 few tweaks.

 Only one change needed to be made in Base code.
launch_mev.jsp had to be changed to include a few more jars and the
 arguments are different than the current Base implementation of MeV.

 I had to modify two MeV files
FileResourceManager was written to get files via HTTP but choked
 when calling a servlet since is was not passing the query piece  
 of he
 URL. That was easily fixed
HTTPDownloader had a 10 second timeout for reading the file I
 changed it to 100 seconds.

 I will pass the MeV changes on to TIGR and ask them to implement the
 since they are relevant to anyone serving data from a servlet
 In the mean time I include them here for anyone who wants to build
 his own version of MeV


 To implement these changes just:
 1) download the latest MeV
 2) make the changes in the MeV code
 3) go to the build_script directory
 3) ant build-package
 4) ant webstart-package -- you will have to tweak ant to handle the
 jar signing

 5) change launch_mev.jsp
 6) copy all the jars from mev/deploy/webstart/mev/lib/ to the base
 mev directory plugins/org/tigr/microarray/mev

 Thats it, it does not even require a Base compile or even a server
 restart. The only downside is that MeV opens with the the data  
 loaded
 in a dialog box and the users has to select the top-left most data
 cell in the table and then click the load box (just like opening a
 TDMS file) I've written a work around for this if anyone is
 interested.






 Changes

 
 here is the diff for
 mev/source/org/tigr/microarray/mev/resources/ 
 FileResourceManager.java

 252c252,256
 <   File f =
 fd.getTempFile(thisDefURL.getPath());
 ---
>   String path
 = thisDefURL.getPath();
>   String query
 = thisDefURL.getQuery();
>   if (query !=
 null && query.length() > 0)
>   path
 += "?" + query;
>   File f =
 fd.getTempFile(path);

 ###

[basedb-devel] BASE 2.7.2 released. Important bug fix included!

[Jari Häkkinen]

Hi all,

We have released BASE 2.7.2. The release includes important bug fixes
in the LOWESS plug-in shipped as a part of the BASE package. Some
other improvement are also included in the release.

It is highly recommended at all BASE installations where LOWESS is
used as a part of their analysis in BASE are upgraded to this
release. More details on the LOWESS problem is given below.

Note, we have not found any problems with the BASE1 lowess
implementation and analysis made with BASE1 lowess in BASE1 or BASE2
are still valid.

More information about the changes in 2.7.2:
http://base.thep.lu.se/query?milestone=BASE+2.7.2&group=resolution

Download from:
http://base.thep.lu.se/wiki/DownloadPage


We regret any inconvenience that the LOWESS bug may have caused,

The Lund BASE team



Text copied from the installation/upgrade chapter of the BASE
documentation, 
http://base.thep.lu.se/chrome/site/latest/html/admindoc/installation_upgrade/installation_upgrade.upgrade.html

Bug in the LOWESS plug-in affecting BASE version 2.0 -- 2.7.1

This release fixes a serious bug in the LOWESS plug-in shipped as a
part of the BASE package. The bug is found in all BASE versions
between 2.0 and 2.7.1, and has caused incorrect normalization values
to be calculated. All data that has been normalized with the BASE2
LOWESS plug-in prior to BASE 2.7.2 should be considered invalid and
needs to be re-normalized with the fixed version. Downstream analysis
steps that has used the incorrectly normalized data also needs to be
redone. For more information about the bug see
http://base.thep.lu.se/ticket/1077

BASE 2.7.2 includes a utility for finding all experiments/bioassay
sets that includes data normalized with the LOWESS plug-in. An
administrator can use this utility to extract a list of all
experiments/bioassay sets that needs to be fixed. The utility can also
tag the name of the found experiments/bioassay sets with FIX LOWESS to
make it easier to find data that needs to be fixed.

The utility can't see any difference between data normalized with the
old version and the fixed version. It will simply report all data that
has been normalized with the LOWESS plug-in. Only use the utility a
single time right after the upgrade to BASE 2.7.2.

The utility is a command line program that should be executed on the
BASE application (web) server.

cd /bin
./onetimefix.sh lowess_warn -u  -p  -f

We recommend running the utility as the root user. The -f option is
optional. If it is included the found experiments/bioassay sets are
tagged with FIX LOWESS, otherwise only a list with the information is
generated.

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Re: [basedb-devel] Integrating BASE to analysis packages

[Jari Häkkinen]

Aleksi Kallio wrote:
> Hello all,

Hi,


> Currently BASE has an integration to MeV analysis package, which I 
> believe is something that was a custom job by you (ie. it is a modified 
> version of MeV etc.)? We would be interested in implementing a similar 
> integration into our analysis package Chipster (http://chipster.csc.fi).

Chipster would be a nice addition to BASE. Yes, MeV was a custom job,
and not too pretty to be honest. We have (internally) discussed to
change the MeV implementation. MeV support will be moved out from the
core package to become an external plug-in.


> I have gone through the way MeV is integrated into BASE, and the same 
> approach would work well with Chipster also (and would not need a 
> modified version of the analysis software as with MeV). As adding 
> different analysis packages one by one is a bit of a burden, I would 
> like to suggest that BASE could be modified to allow system manager to 
> configure different Java Web Start based analysis tools to be used. 
> After all, there are quite a few packages out there using Web Start. Of 
> course not only Web Start is required, but the package should also be 
> capable of accepting URL's as arguments and fetch the datafiles pointed 
> by them.
> 
> Would you consider this as a feasible new feature to implement? We would 
> be willing to contribute this kind of integration, with some help from 
> you core developers!

We agree with you, something more general is needed. We have discussed
this issue several times and always postponed it, there is so many
things to do. There is a very non-informative ticket related to this,
http://base.thep.lu.se/ticket/436 but to be honest, to see the
connection you need to join us in our coffee room.

We are working hard for the next milestone here, so we'd like to pick up
this thread after finalization of the milestone (due in two weeks). I
hope this is okay with you. And we appreciate your offer to contribute
to the project.


> All the best,
> Aleksi


Cheers,

Jari

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[basedb-devel] BASE 2.5.1 released

[Jari Häkkinen]

A new version of BASE is available for download at
http://base.thep.lu.se/wiki/DownloadPage

Fixed issues are listed at
http://base.thep.lu.se/query?status=closed&milestone=BASE+2.5.1


The Lund BASE team

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Re: [basedb-devel] Potential problem in plug-in execution

[Jari Häkkinen]

We should fix this through the properties file. The joba agents are 
running on different hosts so the BASE server should not try set the 
temporary directory for another machine. I have added this as a ticket, 
http://base.thep.lu.se/ticket/897


Jari


Nicklas Nordborg skrev:
> Jari Häkkinen wrote:
>>>> Many plug-ins acquire a working directory with code similar to the 
>>>> sample attached below. This is mostly safe but when running more than 
>>>> one BASE server on a host there is a potential clash. A plugin running 
>>>> in the different BASEs may allocate the same temporary directory (since 
>>>> jobids may match).
>>>>
>>>> The java.io.tmpdir returns /tmp on linux irrespective what 
>>>> CATALINA_TMPDIR is set to. /tmp is the Java default on linux and running 
>>>> tomcat CATALINA_TMPDIR is set properly by default. This means that the 
>>>> tmp for running tomcat server is /path/to/tomcat/temp as expected.
>>>>
>>>> So, the BASEcore is proably using the CATALINA_TMPDIR whereas the 
>>>> plugins are using the system default. This must be an effect of how 
>>>> plugins are started by the core. Is it possible to pass the tmp 
>>>> directory to the plug-in running environment?
>>> I am not sure that I understand why using one directory would be better 
>>> than the other. Wouldn't the name clash still happen if 
>>> /path/to/tomcat/temp was used instead of /tmp?
>> I would like to use SEVERAL temporary directories, one for each tomcat 
>> server running. In my setup I have several BASE instances running, each 
>> in they own tomcat instance. I can setup up the tomcats to use different 
>> temporary directories (well, it does that by default so I am not really 
>> doing anything), but the problem occurs as soon as any of the BASE 
>> servers starts a plugin requiring temporary disk space. Independent of 
>> assigned tomcat temporary directories all plugins use /tmp.
>>
>> In the start up of the different tomcat servers, java.io.tmpdir is set 
>> to private tempdirs like
>> /path/to/tomcat1/temp
>> /path/to/tomcat2/temp
>> (logs, conf, and ordinary tomcat stuff are set up similarly). The 
>> problem is that when tomcat/BASE starts a plugin execution the temporary 
>> directory is reset to /tmp. This could be that plugins runs in a ... 
>> jobagent ... which doesn't know anything about the temporary directory 
>> structure ... Hm, this is probably the issue. So, a new question. Can we 
>> tell the jobagents which temporary directory to use? I suppose a 
>> configuration parameter would solve it but dynamically on the fly?
> 
> I guess that this is what is causing it. If a plug-in is executed within 
> Tomcat it will most likely get the same temporary directory as Tomcat is 
> using. The BASE core is not messing with it. Neither is the job agent 
> code, which means that they will all get the system default temporary 
> directory.
> 
> Hmm... maybe the job agent should be messing with the temporary 
> directory the same way as tomcat does... Maybe it can be a configuration 
> property in jobagent.properties, or maybe we can find some way to assign 
> a directory by default, or a combination... Any ideas?

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Re: [basedb-devel] Potential problem in plug-in execution

[Jari Häkkinen]

>> Many plug-ins acquire a working directory with code similar to the 
>> sample attached below. This is mostly safe but when running more than 
>> one BASE server on a host there is a potential clash. A plugin running 
>> in the different BASEs may allocate the same temporary directory (since 
>> jobids may match).
>>
>> The java.io.tmpdir returns /tmp on linux irrespective what 
>> CATALINA_TMPDIR is set to. /tmp is the Java default on linux and running 
>> tomcat CATALINA_TMPDIR is set properly by default. This means that the 
>> tmp for running tomcat server is /path/to/tomcat/temp as expected.
>>
>> So, the BASEcore is proably using the CATALINA_TMPDIR whereas the 
>> plugins are using the system default. This must be an effect of how 
>> plugins are started by the core. Is it possible to pass the tmp 
>> directory to the plug-in running environment?
> 
> I am not sure that I understand why using one directory would be better 
> than the other. Wouldn't the name clash still happen if 
> /path/to/tomcat/temp was used instead of /tmp?

I would like to use SEVERAL temporary directories, one for each tomcat 
server running. In my setup I have several BASE instances running, each 
in they own tomcat instance. I can setup up the tomcats to use different 
temporary directories (well, it does that by default so I am not really 
doing anything), but the problem occurs as soon as any of the BASE 
servers starts a plugin requiring temporary disk space. Independent of 
assigned tomcat temporary directories all plugins use /tmp.

In the start up of the different tomcat servers, java.io.tmpdir is set 
to private tempdirs like
/path/to/tomcat1/temp
/path/to/tomcat2/temp
(logs, conf, and ordinary tomcat stuff are set up similarly). The 
problem is that when tomcat/BASE starts a plugin execution the temporary 
directory is reset to /tmp. This could be that plugins runs in a ... 
jobagent ... which doesn't know anything about the temporary directory 
structure ... Hm, this is probably the issue. So, a new question. Can we 
tell the jobagents which temporary directory to use? I suppose a 
configuration parameter would solve it but dynamically on the fly?


> 
> As far as I know the core is not using a temporary directory for 
> anything. If it needed to, the core would probably also use the 
> java.io.tmpdir directory.

Yes, but for the core it will be the one set at tomcat start up, 
wouldn't it?


Jari

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[basedb-devel] Potential problem in plug-in execution

[Jari Häkkinen]

Many plug-ins acquire a working directory with code similar to the 
sample attached below. This is mostly safe but when running more than 
one BASE server on a host there is a potential clash. A plugin running 
in the different BASEs may allocate the same temporary directory (since 
jobids may match).

The java.io.tmpdir returns /tmp on linux irrespective what 
CATALINA_TMPDIR is set to. /tmp is the Java default on linux and running 
tomcat CATALINA_TMPDIR is set properly by default. This means that the 
tmp for running tomcat server is /path/to/tomcat/temp as expected.

So, the BASEcore is proably using the CATALINA_TMPDIR whereas the 
plugins are using the system default. This must be an effect of how 
plugins are started by the core. Is it possible to pass the tmp 
directory to the plug-in running environment?


Jari


protected java.io.File getExecDirectory()
{
   if (execDirectory == null) {
 execDirectory = new java.io.File
(System.getProperty("java.io.tmpdir") + java.io.File.separator +
getAbout().getName() + java.io.File.separator + job.getId());
 execDirectory.mkdirs();
   }
   return execDirectory;
}


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Re: [basedb-devel] more trials with getting a web service client to work (Re: strange AxisFault exception when using the example in the docs (Re: Writing an external importer/exporter))

[Jari Häkkinen]

The demo server is now running 2.5.0.

Maybe we should finalize 2.5.1 and not forget to upgrade the demo server?


Jari

Carl Mäsak wrote:
> Nicklas (>), Carl (>>), Nicklas (>>>):
 All examples are included in the source download (is this what you
 downloaded?). To build the examples you need to do (from the root
 directory of the source download):

 ant package.examples

 This will build the examples, and put everything in the
 /examples/webservices directory. Read the README file for further
 instructions.
>>> I did this, and the build failed. Thought you might be interested:
>>>
>>>  
>> Seems like this is a problem with internal dependencies. Or in other
>> words, the different BASE packages are compiled in incorrect order. Try
>> 'ant dev' instead. This will compile everything.
> 
> That worked. Going through the rest of the motions produces the
> AxisFault below, but at least it does that on my computer now, running
> Java 1.5.
> 
>>> I also tried downloading the web service client example tar file from this 
>>> page:
>>>
>>>  
>>>  
>>>
>>> Running it on my own computer (somewhat predictably) produces an
>>> UnsupportedClassVersionError, since I'm running java 1.5.0_07. I
>>> cannot upgrade to 1.6 without upgrading my OS X version to 10.5. But
>>> from reading summaries of what's new in Java 1.6 -- foremost of which
>>> seems to be a better support for web services -- I suppose that the
>>> Java 1.6 dependency is not easily removed from the web service client
>>> code. Am I correct?
>> If you are running Mac OS X you are out of luck. There is no Java 1.6
>> available yet for Mac. I think the problem is that the temporary example
>> package that we put up on the web site is compiled with Java 1.6. We
>> usually compile released packages with 1.5. It never happend in this
>> case since all of us were really busy or on vacation. We'll fix this
>> when we release 2.5.1.
> 
> They way I read that, it would still be possible (though maybe
> increasingly inconvenient) to have a client running on Java 1.5.
> Bioclipse (the application on which I am writing a plugin) is
> currently written in Java 1.5.
> 
>>> Running the client example on a collegue's computer equipped with Java
>>> 1.6 produces the following AxisFault exception:
>>>
>>>  
>>>
>>> The relevant settings in this case were:
>>>
>>>  >> value="http://base2.thep.lu.se/demo/services"; />
>>>  
>>>  
>>>
>>> What have I missed?
>> No, but I think we have!
>>
>> The demo server is still running a 2.5beta version. It needs to be
>> upgraded. We'll fix it as soon as possible.
> 
> Sounds good.
> 
> // Carl


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Re: [basedb-devel] Modifying BASE Affy plugin to use other Affymetrix Power Tools besides apt-probesets-summarize

[Jari Häkkinen]

Collett, James R skrev:
> Happy New Year, BASErs!
> 
> We are developing metagenomic assays using Affy chips with
> custom-designed probe sets. The tools available for analyzing standard
> Affy gene expression data using pm-mm comparisons, however, are not
> relevant to our chip design and analytical approach (we're only using pm
> probes).   
> 

We are aware of the shortcomings of the current plug-in. Unfortunately, 
we currently have no time to extend and improve it. Another reason that 
further slows down the progress is that we do not use the Affymetrix 
platform ourselves. There are many improvements that could be done as 
you point out. There are users who extend the affymetrix plug-in but 
these additions have not become public yet and I am not sure if they 
will be published.


> Accordingly, we would like to adapt the BASE affymetrix.jar plugin to
> use other executables in the Affymetrix Power Tools suite besides just
> the apt-probeset-summarize.  Specifically, we would like to use
> apt-cel-extract within affymetrix.jar to simply extract feature
> intensities, probe IDs, probe set IDs, and XY coordinates from CEL files
> into new root bioassay sets.  I have already used apt-cel-extract on the
> command line to successfully extract these fields from CEL files into
> text files.

It should probably be straightforward to add more functionality to the 
plug-in using the different Affymetrix tools. In the simple case one 
would just add an option for the user to select which tool to use, and a 
more fancy way would be that the plug-in checks which tools are 
appropriate for the data at hand.


> For now, simply trying to feed our CEL files into the current Affy PLIER
> plugin within BASE 2.5.0 gives (not surprisingly) the following error:
> 
> java.io.IOException: Unexpected exit of PLIER sub-process. Return value:
> 1
> at se.lu.thep.affymetrix.Plier.runBinary(Plier.java:157)
> at
> se.lu.thep.affymetrix.AbstractExternalBinaryPlugin.run(AbstractExternalB
> inaryPlugin.java:262)
> at
> net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.
> java:89)
> at
> net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:
> 435)
> at java.lang.Thread.run(Thread.java:619)
> 
> Are any of you interested in working with us to expand affymetrix.jar to
> include functionalities from apt-cel-extract and perhaps others in the
> the Affy Power Tools suite?  If not, can you give us some suggestions on
> how we might best get started on this, and what kinds of challenges or
> incompatibilities that we might face?

This is a great idea! The different apt tools should be in one single 
package. This will make Affymetrix usage simpler for BASE users (and the 
administrators). So, we are happy to work with you on improving the plugin.

The first steps forward. You already have read access to the source code 
for the plug-in through 
http://baseplugins.thep.lu.se/wiki/se.lu.thep.affymetrix Read the 
instructions on this page on how to check-out the latest development code.


> Thanks, and Congratulations on BASE 2.5.0 - it's been working
> exceedingly well for us!

Thank you,

Jari


> Jim Collett
> 
> James R. Collett, Ph.D.
> Systems Biology Fellow
> Chemical and Biological Process Development Group
> Pacific Northwest National Laboratory

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[basedb-devel] BASE 2.5 released

[Jari Häkkinen]

Hi all,

We are happy to announce the release of BASE 2.5. The packages are added 
to the download area, http://base.thep.lu.se/wiki/DownloadPage

Please send feedback through the mailing lists.

Happy BASEing


The Lund BASE team

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Re: [basedb-devel] some user feedback on data input into BASE2

[Jari Häkkinen]

> Finally I read about KuteBase who have reworked the data upload workflow 
> to BASE and built a batchuploader:
> 
> http://vortex.cs.wayne.edu/taxonomy/term/69

It is always nice to see improvements made to BASE and the plug-in looks 
promising. The KUTE plug-in is claimed to work with BASE 2.0.x. We are 
releasing 2.5 tomorrow and there are no guarantee that the plug-in will 
work so please test the plug-in before using it with 2.5. (We believe 
that the plug-in does not work with anything else than 2.0.x.) Since 
Affymetrix handling has changed internally in BASE it will most 
certainly break.

It seems like source code to KUTE is not available online but hopefully 
the KUTE developers will make the tests and needed modifications for the 
BASE community, and publish their code for everyone to leverage on.


Cheers,

Jari

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[basedb-devel] BASE 2.4.5 available for download

[Jari Häkkinen]

A new version of BASE is available for download at
http://base.thep.lu.se/wiki/DownloadPage

This release contains one fix removing a debug sleep statement. Server 
performance is improved when upgrading to this release.

The Lund BASE team


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[basedb-devel] BASE 2.4.4 released. Please read, important performance issue fixed in this release.

[Jari Häkkinen]

We are happy to announce the release of BASE 2.4.4.

As always you can find the latest release at 
http://base.thep.lu.se/wiki/DownloadPage for download.

This releases contains an important fix that resolves severe performance 
issues, cf. http://base.thep.lu.se/ticket/796. The code is now fixed but 
you will have to update your database, please read 
http://base.thep.lu.se/chrome/site/latest/html/admindoc/installation_upgrade/installation_upgrade.upgrade.html
on how to update your database. We have not detected any data integrity 
problems related to this issue.

The script may take quite some time depending on your database size. Our 
BASE installation took almost 24h to fix, so patience is a virtue here. 
Remember to upgrade BASE before starting the upgrade script and kepp 
BASE shutdown until the script ends.

Happy BASEing,

The Lund BASE team


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Re: [basedb-devel] affymetrix.fusion.cdf.FusionCDFData problem

[Jari Häkkinen]

Nicklas Nordborg wrote:
> Bob MacCallum wrote:
>> Thanks Nicklas.
>>
>> If Java has something like Perl's file based DBM storage (e.g. SDBM_File),
>> then a low cost solution might be to store this lookup in such a file, and
>> attach this to the array design (in BASE 2.5).
> 
> I don't know what exists in the Java world (or in the Perl world 
> either). I bet there is something.
> 
> You still have to look through all array designs/files. A potential 
> problem is that you can only get access to an InputStream object for 
> reading the file, which means that you have to copy/parse the entire 
> file if a reporter is not present before you can know this.
> 
> It would probably be better to store the file on the disk outside of BASE.


... and fetch it with a http request or similar from within BASE?


Jari

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Re: [basedb-devel] A couple of questions about web service access

[Jari Häkkinen]

Carl Mäsak wrote:
> It's been a pleasant experience using the web services so far, but the
> above three details are a bit confusing.
> 

I just want to point out that the web services implementation is being 
reimplemented for BASE 2.5. Please read 
http://base.thep.lu.se/ticket/492 for some details, and also add 
comments for what you'd like to see in the next round of web services 
implementation.


Jari

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Re: [basedb-devel] A couple of questions about web service access

[Jari Häkkinen]

Bob MacCallum wrote:
> This means that the base2 user can see all the other users' email addresses
> and contact details.   Is that desired?

Yes, the base2 user was allowed to read all user information. This is 
now changed so that the base2 user can read everything in the demo 
server except the user information. Good point.

Jari

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Re: [basedb-devel] File URL

[Jari Häkkinen]

Hi,

Unfortunately I am away with a poor connection to the Internet. I have a
couple of pointers:

1) Look at how the MeV plug-in does. The plug-in downloads data from a
BASE server using a download. MeV is a Java web start application where
essential parameters are communicated through the jnlp file. See

- http://trac.thep.lu.se/trac/basehacks/wiki/MeV for info on needed MeV
changes such as auto download of data from BASE
- http://base.thep.lu.se/browser/trunk/www/plugins/org/tigr/microarray/mev
(the JSP files) for implementation of dynamic jnlp file creation.

2) BASE supports filedownload through a servlet (I cannot remember the
details but studying the MeV example above should reveal it).

3) In the web services client
http://baseplugins.thep.lu.se/wiki/se.lu.thep.webservices_clients there is
downloads of cel/cdf files.

Hope this helps you in your quest of improving BASE.


Cheers,

Jari


Peter Mertens wrote:
> Hi,
>
> instead of using a plugin i want to create my own base webservice.
>
> This service is almost working, except for one point. Where i want to get
> the url where the data files are located.
>
> So, i can get the project, experiment and the data from the experiment.
> Now
> i want to send all information about the data:name, id, description and
> the
> url where the client, calling the service, can download the files from.
>
> What i tried is:
>
> public String getCelFiles(int experimentId)
> {
> Experiment experiment = experimentVector.get(experimentId-1);
>
> System.out.println("RawBioAssays of exp: "+experiment.getName());
>
> ItemResultIterator rawBioAssays;
>
> String rbas = "";
>
> try
> {
> dc = sc.newDbControl();
>
> ItemQuery query = experiment.getRawBioAssays();
> System.out.println("nr of raw bioassays: "+query.count(dc));
>
> rawBioAssays = query.iterate(dc);
>
> if (rawBioAssays != null)
> {
> RawBioAssay item = null;
> String name = "";
> String loc ="";
> String url ="";
> int id=0;
> File file = null;
> String path = "";
>
> while (rawBioAssays.hasNext())
> {
> item = rawBioAssays.next();
> name = item.getName();
>
> rbas += "";
> rbas += ""+name+"";
>
> id = item.getId();
> file = Affymetrix.getCelFile(item);
> path = file.getPath().toString();
>
> rbas += ""+id+"";
>
> loc = HTML.urlEncode(path);
> url = fileUrl+"-"+sessionId+"-"+loc;
>
> rbas += ""+url+"";
> rbas += "";
> }
>
> }
> dc.close();
>
> }
> catch(Exception e)
> {
> System.out.println("e:"+e);
> }
> rbas += "";
>
> return rbas;
> }
>
> This returns a the string:
> 1.1_290
> http://nbx8.nugo.org/nutriBASE/filemanager/files/view/-42d47d6797b7b05c-/home/PeterMertens/raw+data/test/1.1_2.CEL
> 1.292
> http://nbx8.nugo.org/nutriBASE/filemanager/files/view/-42d47d6797b7b05c-/home/PeterMertens/raw+data/test/1.2.CEL
> 
>
> If i try to download the files (while the session is still active) using
> the
> url's i get a http 500 response.
> I suppose that the part /filemanager/files/view/ is not correct since the
> fileview.jsp is not loaded, but i don't have a clue how to do it
> correctly.
>
> A possible solution would be to download the files to a folder in the
> webserver's directory and than ... . This is not a very nice solution for
> this problem so i hope somebody can help getting the url of the files on
> the
> base server.
>
> thanks,
>
> Peter
>
>
>
>
> 2007/9/27, Nicklas Nordborg <[EMAIL PROTECTED]>:
>>
>> Peter Mertens wrote:
>> > Dear list,
>> >
>> > i'm working on a plugin that gives the possibility to run the analysis
>> > on another machine (not the one base is installed on).
>>
>> Have you checked out the possiblitity to use Job agents? They can be
>> used to execute any plug-in on a different server. See
>> http://base.thep.lu.se/chrome/site/trunk/html/admindoc/plugin_installation/plugins.jobagents.html
>>
>> for more information.
>>
>> > In order to download the files (cel and cdf) over http, i need the to
>> > retrieve the URL's.
>> > Can somebody tell me how to get this?
>>
>> The file URL depends on the sesssion ID of the logged in user. Plug-ins
>> are executed in a different session with a different ID, so I am not
>> sure it will work since the web server may know about the session ID
>> used by the plug-in. It is not possible for the plug-in to get the
>> session ID for the user. In fact, the user may already have logged out
>> before the plug-in is executed.
>>
>> I think it is better if your 

Re: [basedb-devel] APT probeset summarize plugin

[Jari Häkkinen]

Great,

You are right, there are improvements needed to Plier and RMAExpress.

Yes, we appreciate help on developing and extending BASE and plug-ins. 
I'll grant you subversion write access to you. I'll contact you off-line 
with the details in the afternoon today.


Cheers,

Jari


Robin Andersson wrote:
> Hi,
> 
> The current implementation of the affymetrix plugin Plier.java relies on 
> the Affymetrix Power Tools binary apt-probeset.summarize (analysis 
> option plier-mm) . However, none of the other options in 
> apt-probeset-summarize are made available for the user.
> 
> I have created a new plugin called APT Summarize that extends Plier.java 
> with other options of transformations, PM intensity adjustments and 
> quantifications. Th plugin relies on AbstractExternalBinaryPlugin.
> 
> Are you interested in me sharing the plugin with the BASE community? If 
> yes, how do I proceed? Can I add the plugin to a new branch of 
> (plug-ins) se.lu.thep.affymetrix?
> 
> Best,
> Robin Andersson
> 
> ---
> Robin Andersson, PhD student
> Linnaeus Centre for Bioinformatics
> Uppsala University
> BMC, Box 598, SE-751 24 Uppsala, Sweden
> phone: +46 18 471 66 86 (admin: 66 90)
> fax: +46 18 471 66 98
> office: BMC, C6:315a
> email: [EMAIL PROTECTED] 
> http://www.lcb.uu.se/~robina/
> 
> 
> 
> 
> 
> 
> 
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[basedb-devel] BASE 2.4.3 released

[Jari Häkkinen]

A new version of BASE is available for download at
http://base.thep.lu.se/wiki/DownloadPage

Fixed issues are listed at
http://base.thep.lu.se/query?status=closed&milestone=BASE+2.4.3


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Re: [basedb-devel] Singel-item view stops working after adding annotations

[Jari Häkkinen]

This is an important fix. If everything is checked in for the fix, I can
make another release tonight.


Jari


Nicklas Nordborg wrote:
> Nicklas Nordborg wrote:
>> Harald Stachelscheid wrote:
>>> Am Montag, 24. September 2007 schrieb Nicklas Nordborg:
 Harald Stachelscheid wrote:
> Hallo,
>
> after I add an annotation to an any type of item I get a blank
> window in the browser when I try to display the Single-item view.
> In contrast editing the item by ctrl+clicking the item in the
> list view works correctly and shows the added annotation. Any
> ideas to solve this problem?
>
> My configuration: BASE 2.4.1, Tomcat 5.5.23 and PostgreSQL 8.0.1.
>
 Can you check the Tomcat log file for information about errors?

 /Nicklas
>>> sorry just noticed that additionally to output in the .log-file the
>>> following is written to the catalina.out log: /Harald
>>
>> It seems to be a limitation in Postgres that we didn't know about and
>> that Hibernate seems unable to help us with. Right now I don't have any
>> workaround, other than to use MySQL instead of Postgres.
>
> Fortunately I was wrong when I said that Hibernate couldn't help us to
> solve this. We just had to give Hibernate a hint. So, this problem and
> another similar problem has now been fixed. The fix will be included in
> the 2.4.3 release. Since we just released 2.4.2 yesterday I don't know
> when 2.4.3 will be released. It should be safe to checkout the source
> code from the 2.4-stable branch on our subversion server. See
> http://base.thep.lu.se/wiki/DownloadPage#BASEstable for instructions.
>
> /Nicklas
>
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[basedb-devel] BASE 2.4.2 released

[Jari Häkkinen]

A new version of BASE is available for download at
http://base.thep.lu.se/wiki/DownloadPage

Fixed issues are listed at
http://base.thep.lu.se/query?status=closed&milestone=BASE+2.4.2


The Lund BASE team


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[basedb-devel] BASE 2.4.1 released

[Jari Häkkinen]

A new version of BASE is available for download at 
http://base.thep.lu.se/wiki/DownloadPage

Fixed issues are listed at 
http://base.thep.lu.se/query?status=closed&milestone=BASE+2.4.1


The Lund BASE team


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Re: [basedb-devel] Base2 & MeV questions

[Jari Häkkinen]

Alessandro De Stasio wrote:
> Hello,
> I'm new in this mailing list.
> I'm an italian developer, and in our team we would to develop some 
> plugins for Base2,
> but also some components for MeV (under Base2).

Great. Maybe you should get the MeV components into the official MeV and 
then we get the code merged into the BASE MeV? I am not trying to 
discourage you but I'd hate to fork the source of MeV.


> I have some question for you:
> - MeV under Base2 is the same of MeV in http://www.tm4.org/mev.html?
> If not, what are the differences? And eventually, is downloadable the 
> source code of MeV?

The MeV used by BASE is a modified version of the official TM4 package. 
The reason for this is that the original code did not work as a Java web 
start application, and also upon start from within the BASE application 
we want to automatically load data into MeV.

The changes made to the official MeV can be browsed at 
http://trac.thep.lu.se/trac/basehacks/wiki/MeV. You will also find 
instructions on how to checkout the BASE tampered MeV source code from 
the subversion repository.


> - I Have a problem when I use MeV. In particular when I upload a script 
> an error occurred:
> file "file:/config/mev_script_dtd.dtd" not found.
> I modify the path of this in the script file, but I have several other 
> validation errors.

Does this problem occur when you run BASE MeV? Or is it the official 
MeV? Can you please supply more details if it is the BASE MeV such as 
operating system and versions of software.


> Thanks in advance
> Best regards
> -- 
> De Stasio Alessandro


Cheers,

Jari


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[basedb-devel] [Fwd: Re: another try - base1pluginexecutor, truncated stdin, tempfiles, the trashcan]

[Jari Häkkinen]

Hi,

Chad Matsalla wrote:
> 
> Greetings!
> 
> I sent this to the basedb-devel mailing list last week but it didn't
> turn up so I'm trying again.
> 
> 
> I'm using BASE-2.4.0 and tomcat 6.0.14. I also tried base-2.4.0 and
> tomcat 5.5.20.
> 
> I'm trying, as usual, to run BASE1 plugins. I was close in BASE-2.3.2 in
> that the only problem seemed to be that the last line of the bioassay
> set wasn't written into the stdin.txt file.
> 
> In BASE-2.4.0, I have several problems.

Don't give up, we have reports from users who run BASE1 plug-ins on a
BASE2 server.


> 1. It seems that a BASE1 plugin runs before the data was successfully
> generated out of the database. (see explanation below)

Hm, this is strange. Can you try to use the resolution to item 2 below
and examine the file in the temporary work directory?

The problem of saving stdin.txt is reported as a bug and will be
resolved in 2.4.1 (cf. http://base.thep.lu.se/ticket/739)


> 2. The basefile is generated into a tomcat temp directory and is
> unlinked before I can analyze it.

The temporary directory is automatically deleted after a successful end
of the plug-in. Successful in this context means that the plug-in either
finalizes its tasks or makes an graceful exit if an exception is
encountered. If you remove the deleteDir() call in the plugin (line 682,
http://base.thep.lu.se/browser/trunk/src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java#L682)
all files generated during plugin execution will remain in tomcats temp
directory.


> 3. I can't empty the trash

Sorry, no resolution on this item from me. Someone else might have a clue.



> Plugin runs before data is generated
> 
> I call a perl executable on the server - this executable reads the
> stdout from the base server and then calls R. Because of problem (2)
> (described above), I've modified the perl program to also write the
> output to /tmp.
> 
> In /tmp I see a file containing:
> 
> BASEfile
> fname rnormv1.R
> norm.methodp
> do.bgcorr 0
> ngrid.r.in 12.0
> ngrid.c.in 4.0
> nspot.r.in 18.0
> (and a whole bunch more stuff that is correct but the last two lines I
> see are:)
> 863  18058 A006151_01 565  398  0444  282  243  146  0 197
> 864  85459 At30009369 620  441  0397  276  248  1
> 
> It seems that I'm only seeing the first 864 rows of reporter data and
> the last line is obviously truncated.
> 
> When I export data from the Bioassay set in the Experiments viewer I get
> a proper basefile with 31200 rows of reporter data.
> 
> 
> File is deleted before I can Examine It
> 
> It appears that the stdin.txt file containing the basefile intended for
> the Base1PluginExecutor is being written to a tomcat tempfile somewhere.
> I looked all through base.userfiles with commands like:
> 
> userfiles$ find . -type f -mtime -1 -exec ls -l {} \;
> 
> I found the r-debug.txt that the R-program generated (indicating that
> rows were missing from the basefile) but no XXXstdin.txt (where
> XXX is the BASE serial number).
> 
> This behavior changed since 2.3.2 and I can't find any information
> regarding this change in TRAC. In previous versions checking the 'Leave
> stdin.txt' in the plugin Configuration, well, resulted in stdin.txt being
> left behind.
> 
> 
> Emptying the trash
> --
> In my trashcan I have 1.6 gazillion files. I followed the instructions
> here:
> http://base.thep.lu.se/chrome/site/doc/html/userdoc/trashcan/trashcan.viewdependencies.html
>  
> 
> But whenever I try to delete items using the 'Empty Trash...' command I
> get: "0 of xxx items removed. xxx items are used and can't be removed.'
> xxx is some number.
> 
> This is interesting because if I filter by Item Type 'File', click on
> the little icon on the left (looks like a paper document with a piece of
> a chain on it) see no indication that it has dependencies.
> 
> If I select a single File item from the Trashcan and click 'Delete
> Permanently' I get the "can't be removed" message.
> 
> If, in the Properties page for the same file I click 'Delete
> Permanently' no error message appears and when I return to the
> 'Trashcan' page the item is gone and the total count of hits is
> decremented.
> 
> In addition, the command:
> userfiles $ find . -type f | wc
> returns one less. This indicates that the delete was successful.
> 
> Do I have to delete files one at a time?
> 
> 
> Summary
> ---
> 
> Can somebody please help me understand the best way to:
> 
> 1. Restore the behavior that I saw in previous versions of BASE2 where
> the stdin.txt that was intended to be used for a base1 plugin appear on
> the filesystem? I can then use it to troublshoot the R program that does
> my work.
> 
> 2. Run base1 plugins? I can't seem to get the entire basefile out of
> base.
> 
> 3. Empty my trash.
> 
> 
> Thank you for any help you can provide.
> 
> Chad Matsalla
> Plant Biote

Re: [basedb-devel] Run script in plugin

[Jari Häkkinen]

Yes it is possible to run non-Java code and scripts from a plug-in. Your 
code below is correctish ... are you sure you are running the script in 
the correct directory in the server? The Affymetrix plug-in at 
http://baseplugins.thep.lu.se/wiki/se.lu.thep.affymetrix uses external 
programs to perform the calculations and the code in that plug-in should 
be usable for you to copy. In function runBinary in 
http://baseplugins.thep.lu.se/browser/trunk/se/lu/thep/affymetrix/RMAExpress.java
there is a call to Runtime.exec but with another list of arguments than 
your example code.


Cheers,

Jari


Peter Mertens wrote:
> Dear list,
> 
> is it possible to run a script from within the plugin?
> 
> Then i have something like this in the "run" method:
> 
> public void run(...)
> {
>  ...
>  Runtime runtime = Runtime.getRuntime ();
>  Process process = runtime.exec("./scirpt PluginRunner arg1 arg2");
>  int exitValue = process.waitFor();
>  ...
> }
> 
> Is this possible because?
> I keep getting errors and it's quite hard to get the exceptionmessages 
> from the Runtime-error to the stacktrace.
> 
> gr.
> 
> Peter


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Re: [basedb-devel] Writing an external importer/exporter

[Jari Häkkinen]

Hi,

I checked the test.pl from the repository and it works (revision 415, 
new version where port 8080 is removed). Can you please try the client 
once more and report back.


Cheers,

Jari


Carl Mäsak wrote:
> Carl (>), Nicklas (>>):
>>> If you want webservices you will have to do most of the work yourself.
>>> We have been experimenting with this and there is a prototype branch and
>>> a perl library for using it:
>>> http://lev.thep.lu.se/trac/baseplugins/wiki/se.lu.thep.webservices_clients
>>> It provides functionality for listing Affymetrix experiments and
>>> downloading associated CEL and CDF files.
>> Excellent. This will most likely get me started on a prototype client.
> 
> Hm, the perl test script worked when I originally tried it, but now it
> gives the following errors:
> 
> $ perl test.pl
> Session ID = b87213332421d6bc
> getProjects error: Operation Not found EPR is
> http://base2.thep.lu.se/demo/services/Session and WSA Action =
> http://server.ws.basedb.sf.net/xsd#getProjects
> List of Projects:
> setActiveProject error: Operation Not found EPR is
> http://base2.thep.lu.se/demo/services/Session and WSA Action =
> http://server.ws.basedb.sf.net/xsd#setActiveProject
> getExperiment error: Operation Not found EPR is
> http://base2.thep.lu.se/demo/services/Session and WSA Action =
> http://server.ws.basedb.sf.net/xsd#getExperiments
> List of Experiments:
> 
> I imagine it might recently have gone out-of-date as per 2.4.0. What
> need I change/update locally to make it work?
> 
> // Carl


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Re: [basedb-devel] untarring the 2.4 source

[Jari Häkkinen]

Thanks for the nice feedback.


Bob MacCallum wrote:
> thanks Jari - the svn route sounds less hassle, although I'll have to live
> with 'base-2.4.1pre' as a version name.

The version number will always have an pre attached to it except in the 
tags branch in the repository. The code is always changed to the 
better;-) However, using a minor branch such as 2.4 should be safe since 
we only fix bugs and important changes in minor branches. If you don't 
like the 1pre you can change it in the build.xml file (which I do not 
recommend since it show where the version you are using is coming from).



> The source built fine from the dodgy tar file.

I'll check out the suggestion posted earlier in the mailing list. Maybe 
the problem dissappears in the next release.


> I'm becoming an expert BASE upgrader...  (merging in config and migrate
> patches, keeping plugins working [jars now outside the main base directory])

Me too, I am keeping several BASE installations somewhat up to date. 
someday my update script might end up in the BASE distro. Having jars 
outside the main BASE directory should probably be highlighted in the 
docs. This also allows several BASE applications to use the same plug-in 
directory structure and only configurations have to be added to the 
different applications.


> And it's nice to see a few of my feature requests in there now (switched user
> can stay on same page, JDK6 now supported).

Feature requests are welcome and we'll add them to the application if we 
think they are useful for a larger audience.


Cheers,

Jari


> 
> keep up the good work,
> 
> cheers,
> Bob.
> 
> Jari Häkkinen writes:
>  > Hi,
>  > 
>  > The warning is annoying but harmless. I have not been able to trace the 
>  > problem. The warning message appears when I create the packages on my 
>  > linux box whereas my mac does create clean tar file. I am using the same 
>  > packages on both machines?!
>  > 
>  > So, it should be safe to use the tar but please report any problems.
>  > 
>  > Maybe you should consider to checkout the 2.4 branch from the 
>  > repository? All 2.4.x patches will be applied to the 2.4 branch so you 
>  > will be just a 'svn update' away from fixes;
>  > 
>  > 'svn checkout http://lev.thep.lu.se/repository/base/branches/2.4-stable 
>  > base-2.4'
>  > 
>  > 
>  > Cheers,
>  > 
>  > Jari
>  > 
>  > 
>  > Bob MacCallum wrote:
>  > > Hi,
>  > > 
>  > > The MD5 sum matches for the base-2.4.0-src.tar.gz I downloaded,
>  > > but when I unpack it I get this warning:
>  > > 
>  > >  tar: A lone zero block at 178336
>  > > 
>  > > (SUSE 10.1 Linux)
>  > > 
>  > > It looks (from a 2 min Google search) like this is something to do with 
> ant's
>  > > tar task, but I can't find a definitive explanation of the problem.  I'll
>  > > press on with building BASE and let you know if it doesn't work.
>  > > 
>  > > cheers,
>  > > Bob.
>  > > 
>  > 
>  > 
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-- 
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Complex Systems Divisionmailto:[EMAIL PROTECTED]
Department of Theoretical Physics   phone: +46 (0)46 2229347
Lund University fax:   +46 (0)46 2229686
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Re: [basedb-devel] untarring the 2.4 source

[Jari Häkkinen]

Hi,

The warning is annoying but harmless. I have not been able to trace the 
problem. The warning message appears when I create the packages on my 
linux box whereas my mac does create clean tar file. I am using the same 
packages on both machines?!

So, it should be safe to use the tar but please report any problems.

Maybe you should consider to checkout the 2.4 branch from the 
repository? All 2.4.x patches will be applied to the 2.4 branch so you 
will be just a 'svn update' away from fixes;

'svn checkout http://lev.thep.lu.se/repository/base/branches/2.4-stable 
base-2.4'


Cheers,

Jari


Bob MacCallum wrote:
> Hi,
> 
> The MD5 sum matches for the base-2.4.0-src.tar.gz I downloaded,
> but when I unpack it I get this warning:
> 
>  tar: A lone zero block at 178336
> 
> (SUSE 10.1 Linux)
> 
> It looks (from a 2 min Google search) like this is something to do with ant's
> tar task, but I can't find a definitive explanation of the problem.  I'll
> press on with building BASE and let you know if it doesn't work.
> 
> cheers,
> Bob.
> 


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[basedb-devel] BASE 2.4 released

[Jari Häkkinen]

Hi all,

We are happy to announce BASE 2.4. The packages are added to the 
download area, http://base.thep.lu.se/wiki/DownloadPage

Please send feedback through the mailing lists.

Happy BASEing

The Lund BASE team

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[basedb-devel] web services branch is patched and is working again

[Jari Häkkinen]

Hi,

Due to some unknown reasons merges from the main development trunk to 
the web services branch has failed. The web service branch is now up to 
date and should work properly. Please report any problems through the 
mailing list.


Jari


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