Re: [basedb-devel] How to extend and override BioAssaySetExporterand Base1PluginExecuter?

2007-08-29 Thread Nicklas Nordborg
Adam Ameur wrote: Hi, I would like to extend some methods in the Base1PluginExecuter for another purpose. I think we need to be careful about this. The Base1PluginExecuter and BioAssaySetExporter was designed and implemented to solve ONE specific problem: Being able to run plug-ins

Re: [basedb-devel] How to extend and overrideBioAssaySetExporterand Base1PluginExecuter?

2007-09-03 Thread Nicklas Nordborg
Gregory Vincic wrote: Hi, consider the possibility where future plugins would like to use code from both of the suggested Abstract classes - AbstractPluginExecuter - AbstractBioAssaySetExporter as you can only extend on of the abstract classes the problem remains. This is not a

Re: [basedb-devel] Bug in how Base1PluginExecuter handles the stdin.txt file.

2007-09-05 Thread Nicklas Nordborg
vegard nygaard wrote: When working with my BASE1 plug-in in BASE2 the Transformation page was suddenly broken. I think this happened when upgrading to 2.4 but I am not sure. After some investigation I found the reason to be that the stdin.txt file was missing in the database. It was not in

Re: [basedb-devel] How to extend and overrideBioAssaySetExporterandBase1PluginExecuter?

2007-09-05 Thread Nicklas Nordborg
vegard nygaard wrote: Hi. I have now modified my BASE2.4 code to the Abstract version, laid out earlier by Nicklas. I got it to work and it will do very well for my needs, that is if I understood what the plan really was. It would be nice if Lund put it into the next version. But verify that

[basedb-devel] Comments wanted about new feature in BASE 2.5: Store data in files instead of in the database

2007-09-21 Thread Nicklas Nordborg
Hello all, We are currently working on the issue of keeping data (ie. raw data, array design data and possible analyzed data) in files instead of importing it into the database. It is alread possible to do that for Affymetrix experiments, but the solution can't be used to give the same

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

2007-09-24 Thread Nicklas Nordborg
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

Re: [basedb-devel] Managing Units for Annotation Type in BASE

2007-09-27 Thread Nicklas Nordborg
Philippe wrote: Hi Nicklas, base-developpers, Dominic an myself are currently working on a MAGE-TAB*(http://www.mged.org/mage-tab/) importer for BASE2. The format allows specifying Units to qualify descriptors such as protocol parameter, experimental factors, biomaterial descriptors. I

Re: [basedb-devel] Getting normalized data out Base

2007-09-27 Thread Nicklas Nordborg
Peter Mertens wrote: Dear list, again i have another question for you. I have developed a normalization plugin for Base. But now i want this normalized data back out of base to use it in another application. I wanted to do this using the webservices, since this is, according to me, the

Re: [basedb-devel] How to delete a Job that is in Executing mode.

2007-09-27 Thread Nicklas Nordborg
vegard nygaard wrote: I have some jobs I want to delete, but I am not allowed to. I think the reason is that they are still in Executing mode, according to the job list. In reality they are not executing, this is just old trial and error runs of plug-ins that apparently failed in unexpected

Re: [basedb-devel] hyb to l.extract (and onwards) with API

2007-10-04 Thread Nicklas Nordborg
Hmmm... I was a bit puzzled at first... The query seemed to be a valid query. However, I found that the problem is that the creationEvent.sources is a Map collection where the LabeledExtract is the key and the used quantity is the value part. Unfortunately it seems like the expression

Re: [basedb-devel] File URL

2007-10-08 Thread Nicklas Nordborg
Peter Mertens wrote: Hi, I'm willing to use the solution, to store the files on the server (temporarily, until the user logs out) if nothing else works. I cannot understand why one can reach his files over http when logged in to the base2 webclient and not when logged in to my

Re: [basedb-devel] File URL

2007-10-08 Thread Nicklas Nordborg
Peter Mertens wrote: I searched in the base servlet code and the mev code, but i can't find how they manage the download. Could you provide more info? http://base.thep.lu.se/browser/trunk/src/clients/web/net/sf/basedb/clients/web/servlet/Download.java Line 89-123: Parse the request URL to

Re: [basedb-devel] hql boolean restriction

2007-10-10 Thread Nicklas Nordborg
Bob MacCallum wrote: Hi all, The following works as expected: ItemQueryArrayDesign affyQuery = ArrayDesign.getQuery(); affyQuery.include(Include.SHARED); affyQuery.restrict( Restrictions.eq(Hql.property(affyChip),

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

2007-10-11 Thread Nicklas Nordborg
Thanks Nicklas for the help with boolean queries. Now I'm confused by something else also affy-related. I'm trying to write code to lookup which ArrayDesigns a Reporter is on. For non-Affy arrays this is easy (join via arrayDesignBlocks, features and reporter). For Affy arrays it looks

Re: [basedb-devel] object attributes missing when API used from tomcat servlet

2007-10-25 Thread Nicklas Nordborg
This seems really strange. The only thing I can think of is that the data is coming from different databases. Are you really sure that both base.config files are the same? Do you get the same problem with other array designs? /Nicklas Bob MacCallum wrote: Hi, This one is might odd.

Re: [basedb-devel] object attributes missing when API used from tomcat servlet

2007-10-26 Thread Nicklas Nordborg
Bob MacCallum wrote: Only in ../../apache-tomcat-6.0.14/webapps/GEWebapp/WEB-INF/lib: biojava-ensembl.jar biojava.jar bytecode.jar commons-collections-2.1.jar commons-dbcp-1.1.jar commons-pool-1.1.jar gesol.jar GEWebapp.jar jstl.jar mysql-connector-java-3.0.10-stable-bin.jar standard.jar

Re: [basedb-devel] number of unique reporters on an array

2007-10-28 Thread Nicklas Nordborg
Bob MacCallum wrote: I tried this, but there's no group by possible on a DataQuery (I'm getting and UnsupportedOperationException) DataQueryFeatureData featQuery = baseArray.getFeatures(); featQuery.include(Include.SHARED); featQuery.join(Hql.innerJoin(reporter,

Re: [basedb-devel] JobAgents on multi-processor machine

2007-10-29 Thread Nicklas Nordborg
Paweł Sztromwasser wrote: Hi, I am trying to test the performance of Base2 (2.4.3) installation on our server. It is an 8-processor machine so we thought about running several job agents on it to speed up the plugin execution. You will not gain anything by running multiple job agents on the

Re: [basedb-devel] JobAgents on multi-processor machine

2007-10-31 Thread Nicklas Nordborg
Paweł Sztromwasser wrote: All job agents were configured to run all installed plugins and Everyone group has access to them. In fact each of them is able to run a job, but only if no other job is running. I saw couple of times (on JobAgents tab in web UI), as 4 of jobs were assigned to (let's

Re: [basedb-devel] JobAgents on multi-processor machine - private:)

2007-10-31 Thread Nicklas Nordborg
Pawel Sztromwasser wrote: Nicklas Nordborg wrote: Pawel Sztromwasser wrote: Hey, I came private to not spam others. Could you send me source code of tests you used? I would like to check if this is not me doing something wrong with the API before I get deep into postgreSQL things. I did

Re: [basedb-devel] JobAgents on multi-processor machine

2007-11-01 Thread Nicklas Nordborg
Nicklas Nordborg wrote: I am taking this back to the mailing list in the hope that there is some Postgres expert that can shed some light on this. I found this http://www.thescripts.com/forum/thread174537.html It is about a rather old Postgres version (7.4). I am not sure if the same

Re: [basedb-devel] Index dropping fails with Postgres 7.3.19

2007-11-05 Thread Nicklas Nordborg
Pawel Sztromwasser wrote: I investigated a bit and found out that this index in fact exists. I managed to drop it manually using psql with command: DROP INDEX dynamic.D21886Filtercolumn Command without schema name prefix (DROP INDEX D21886Filtercolumn) doesn't work. I checked the index

[basedb-devel] BASE 2.5 beta has been released

2007-11-07 Thread Nicklas Nordborg
We are happy to announce the release of BASE 2.5 beta. Since we normally don't release beta versions there are a few things that you need to be aware of. * The beta should be used for testing only. Don't install it on production servers. * Make a backup of the BASE database before

Re: [basedb-devel] BASE 2.5 beta has been released

2007-11-08 Thread Nicklas Nordborg
Bob MacCallum wrote: Interesting stuff - we will try to give the beta a try ASAP. What's the general strategy behind the provision of storage of array designs and data as files rather than in the db? Some reasons I could think of: Is it to handle arbitrary future array technologies

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))

2008-01-11 Thread Nicklas Nordborg
Carl Mäsak wrote: Since I last had my problems getting a web service client to work in mid-December, I've slowly come to the realisation that (1) I should be starting from the web service client examples provided on the home page, and (2) I should really use Java 1.6 and not Java 1.5, as I am

Re: [basedb-devel] Two small questions about webservice clients

2008-01-14 Thread Nicklas Nordborg
Carl Mäsak wrote: Everything now works: the webservice examples, even my Bioclipse plugin. Due to this, I have a few more specific questions: 1. The two experiments contained in My 1st project show up as test and test 0, respectively. I would like them to show up as New experiment and ST

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

2008-01-14 Thread Nicklas Nordborg
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

Re: [basedb-devel] Data Files in a RawBioAssay

2008-01-30 Thread Nicklas Nordborg
Carl Mäsak wrote: I've now come far enough with my BASE2 web services client in Bioclipse that I dare show it to the eventual end user. Due to this, I have a couple of more specific questions: * How do I get the name of a data file contained in a RawBioAssay? You can't with the current web

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

2008-02-21 Thread Nicklas Nordborg
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

Re: [basedb-devel] Base and baseplugins subversion repositories are moving

2008-02-29 Thread Nicklas Nordborg
to readme and installation information like this [source:/plugins/base2/net.sf.basedb.illumina/trunk/README README] We will not automatically fix links pointing to the old locations. /Nicklas Nicklas Nordborg wrote: We are planning to move the subversion repositories for the base and baseplugins

Re: [basedb-devel] Migration transfers deleted items

2008-03-14 Thread Nicklas Nordborg
Pawel Sztromwasser wrote: Hi, While testing migration I found out that items deleted in BASE1 are migrated to BASE2. As I understand from documentation, BASE1 doesn't delete items from the database unless purgeDatabase.php script is executed. They are just flagged as deleted by setting

Re: [basedb-devel] Migration transfers deleted items

2008-03-17 Thread Nicklas Nordborg
Pawel Sztromwasser wrote: We will be still testing migration for some time, because we haven't moved BASE1 to the new server yet. Some additional code was needed to move our local adaptations. They are supposed to be a part of 1.2.18 BASE1 release (if happens), so if anyone ever needs to

[basedb-devel] Base 2.6.1 is released

2008-03-25 Thread Nicklas Nordborg
Hello all, We have now released BASE 2.6.1. The release is a bugfix release, including some critical fixes for the BioAssaySetExporter and a potential out of memory problem. More information about the changes: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.6.1 Download from:

Re: [basedb-devel] extract Annotations from BioAssay: error connection closed

2008-03-31 Thread Nicklas Nordborg
Alessandro De Stasio wrote: Hi, I'm writing a Fold Change Plugin. I need to extract all the Annotations from a list of BioAssay. So When I try: ... DbControl dc = sc.newDbControl(); //From the input BioAssaySet source = getSourceBioAssaySet(dc);

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

2008-04-02 Thread Nicklas Nordborg
. Currently, there are two extension points, one in the menu and one where the MeV Launcher is in the tree of bioassaysets in the analysis. Suggestions for other extension points can be posted to http://base.thep.lu.se/ticket/933 /Nicklas Nicklas Nordborg wrote: We agree with you, something more

Re: [basedb-devel] Problem with multiple parameter values in PluginConfigurationImporter

2008-04-02 Thread Nicklas Nordborg
I think this is a bug in the importer. I have created at ticket for this and will fix it in the 2.6.2 release. Can you upload the exported file that fails so we have something to test with? Use base/base as login/password. The ticket can be found here: http://base.thep.lu.se/ticket/970

Re: [basedb-devel] setting annotation values programmatically

2008-04-11 Thread Nicklas Nordborg
Micha Bayer wrote: Hi all, I am in the final throes of adding the custom interface to the tab2mage importer plugin but I have one more thing to do before it all works as specified, and that is to set values for the experimental factors on each of the raw bioassays added to the experiment so

[basedb-devel] BASE 2.6.2 has been released

2008-04-17 Thread Nicklas Nordborg
Hello all, We have now released BASE 2.6.2. The release is a bugfix release, including a critical fix for the Base1PluginExector (#957). More information about the changes: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.6.2 Download from: http://base.thep.lu.se/wiki/DownloadPage

Re: [basedb-devel] MEV can't open data files

2008-04-21 Thread Nicklas Nordborg
Ilenia Zara wrote: Hi All, I read the ticket 996 (http://base.thep.lu.se/ticket/996) and I have a similar problem. I have an experiment with 16 raw bioassays on MG_U74Av2. If I export a root bioassayset with more than 12 raw bioassays on MeV, the Slide data loading window is stopping at

[basedb-devel] BASE 2.6.3 has been released

2008-05-09 Thread Nicklas Nordborg
Hello all, We have now released BASE 2.6.3. The release is a bug fix release for some minor bugs only. We expect this to be the last release of the 2.6.x branch. 2.7.0 is scheduled for May 22, but may be released earlier if no more problems show up during testing. More information about the

Re: [basedb-devel] Webservices transport error: 411 Error: Length Required

2008-08-04 Thread Nicklas Nordborg
version and 2.7.1. Just thought, it might be helpful. I hope the code will be useful. Best wishes, Pawel Nicklas Nordborg wrote: Pawel Sztromwasser wrote: Hello BASE developers, We have been recently trying to enable retrieving some data from BASE2 installation directly into our

Re: [basedb-devel] intermittent hibernate errors when using BASE API

2008-08-05 Thread Nicklas Nordborg
for the hint. Will post back when I have a solution. cheers, Bob. Nicklas Nordborg writes: Bob MacCallum wrote: Quick follow up to: http://www.mail-archive.com/basedb-devel@lists.sourceforge.net/msg00316.html The problem seems to be triggered by concurrent access to our BASE

Re: [basedb-devel] Webservices transport error: 411 Error: Length Required

2008-08-20 Thread Nicklas Nordborg
Pawel Nicklas Nordborg wrote: Thanks for the code. It was something like this that I had in mind. The one thing I don't like is to pass the type as an 'int' parameter in the constructor and having a switch statement that creates the actual object to use. This makes it impossible

[basedb-devel] BASE 2.8 has been released

2008-09-08 Thread Nicklas Nordborg
Hello all, We are happy to announce the release of BASE 2.8. This is major release adding several new features. One of the most important is a bunch of batch import/update plug-ins that makes it possible to import data for hundreds of items with a lot less effort than before. More information

[basedb-devel] BASE FTP Server 1.0beta has been released

2008-09-08 Thread Nicklas Nordborg
Hello all, We are happy to announce the release of the FTP Server extension 1.0beta for BASE. This extension makes it possible to upload/download files to/from a BASE installation using regular FTP client software. Download and more information is available on:

[basedb-devel] BASE 2.8.1 has been release

2008-09-10 Thread Nicklas Nordborg
Hello all, We are releasing BASE 2.8.1 to fix a serious bug in the job agent code that caused job agents to be unable to execute plug-ins. BASE installations that doesn't use job agents are not affected by this bug. For a complete list of changes, see:

[basedb-devel] BASE 2.8.3 has been released

2008-10-15 Thread Nicklas Nordborg
We have now released BASE 2.8.3. The release fixes two permission- related problems that may occur when using shared directories in a project and a few other minor bugs. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.8.3 As usual, the program can

Re: [basedb-devel] Performance/delete issues on Postgres

2008-10-16 Thread Nicklas Nordborg
Oh, I didn't know this. We are mainly working with MySQL which implicitly creates an index for every foreign key. I agree that indexes are certainly needed on the big tables. I guess we could make the 'updateindexes.sh' script check that each foreign key definition has an associated index.

[basedb-devel] BASE 2.8.3 has been released

2008-10-27 Thread Nicklas Nordborg
We have now released BASE 2.8.4, which is a bug fix release for some minor bugs. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.8.4 As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage Installation/upgrade

[basedb-devel] BASE 2.9 has been released

2008-11-26 Thread Nicklas Nordborg
Hello all, We are happy to announce the release of BASE 2.9. This is a major release that adds several new features and bugfixes. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.9 IMPORTANT On important change is that BASE now requires

[basedb-devel] BASE 2.9.1 has been released

2008-12-18 Thread Nicklas Nordborg
We have now released BASE 2.9.1. This is a bug fix release that among other things fixes several filtering-related bugs. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.9.1 As usual, the program can be downloaded from:

[basedb-devel] BASE 2.9.2 has been released

2009-01-08 Thread Nicklas Nordborg
We have now released BASE 2.9.2. This is a bug fix release that fixes some critical bugs in the Base1 plug-in executor only. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.9.2 As usual, the program can be downloaded from:

[basedb-devel] BASE 2.9.3 has been released

2009-02-19 Thread Nicklas Nordborg
We have now released BASE 2.9.3. This is a bug fix release that fixes some minor bugs. We expect this to be the last release in the 2.9.x branch. We hope to release BASE 2.10 next week. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.9.3 As usual,

[basedb-devel] BASE 2.10 has been released

2009-02-24 Thread Nicklas Nordborg
ello all, We are happy to announce the release of BASE 2.10. This is a major release that adds several new features, for example a new Biomaterial LIMS system. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.10 Installation/upgrade instructions:

Re: [basedb-devel] Illumina Bead Summary Files

2009-03-09 Thread Nicklas Nordborg
David Waring wrote: I have recently installed the Illumina Plugins and have imported features for several Array Designs. We modified our config to generate the Bead Summary files and I have imported the data. Oddly have found that the Bead Summary files contain some rows with illumina

Re: [basedb-devel] Batch scan importer

2009-03-12 Thread Nicklas Nordborg
Thanks for the code. I am not sure that I like that it creates a new image every time. I think it should at least check if there is already an image with the specified file. Is there a need for setting the other image properties (preview, format, description)? If so, it might be better to have

Re: [basedb-devel] Batch scan importer

2009-03-12 Thread Nicklas Nordborg
Pawel Sztromwasser wrote: Mainly because image has no life on its own and also because there is actually no image list where one could run batch import. OK, there is a list of images for every scan, but image imports for each and every scan would be laborious. Ahh... yes, I didn't think of

[basedb-devel] BASE 2.11 has been released

2009-03-30 Thread Nicklas Nordborg
Hello all, We are happy to announce the release of BASE 2.11. This is a major release that has mainly targeted performance issues. There are several improvements in the analysis section and in plug-ins but also, for example, in the directory tree, which has been changed to only load

Re: [basedb-devel] External id for protocol

2009-05-12 Thread Nicklas Nordborg
Pawel Sztromwasser wrote: Hello, We have been exporting some experiments lately to ArrayExpress and noticed that protocols need to have their own ArrayExpress IDs. Currently we have to add them manually to export file generated in BASE (Tab2MageExporter), but it would be fairly easy to

Re: [basedb-devel] External id for protocol

2009-05-19 Thread Nicklas Nordborg
Pawel Sztromwasser wrote: Hi Nicklas, That was much quicker then I expected. Patch is attached here: http://base.thep.lu.se/ticket/1310 I just hope that I haven't missed too much lines while copy-pasting your code;) The code is looking good. I have not yet tested it but will do that as

Re: [basedb-devel] External id for protocol

2009-05-19 Thread Nicklas Nordborg
Pawel Sztromwasser wrote: Nicklas Nordborg wrote: Pawel Sztromwasser wrote: Hi Nicklas, That was much quicker then I expected. Patch is attached here: http://base.thep.lu.se/ticket/1310 I just hope that I haven't missed too much lines while copy-pasting your code;) The code is looking

[basedb-devel] BASE 2.11.1 and BASE 2.12 released

2009-05-27 Thread Nicklas Nordborg
Hello all, We are happy to announce the release of BASE 2.11.1 and of BASE 2.12. The first release is fixing some minor bugs in the 2.11 branch. BASE 2.12 includes the same (and more) bug fixes and a lot of new functionality as well. For a complete list of changes, see:

Re: [basedb-devel] Query tracing

2009-06-08 Thread Nicklas Nordborg
Olivier Lefevre wrote: I am developing a service. How can I enable query tracing so that Query.list() appends the SQL or HQL form of the query to one of the Tomcat log files? My 'or' queries (Restrictions.or) seem to work ok but not my 'and' queries and I'd like to see what's going on. This

Re: [basedb-devel] Query tracing

2009-06-08 Thread Nicklas Nordborg
Olivier Lefevre wrote: Thanks. By the way, why were WHERE SQL clauses mapped to the unintuitive Restriction rather than Where, like ORDER was mapped to Order? Restrictions can appear in other places also. For example in queries with GROUP BY expression HAVING restriction /Nicklas

Re: [basedb-devel] Minor API questions

2009-06-09 Thread Nicklas Nordborg
Olivier Lefevre wrote: Why aren't all the methods of ServiceUtil static since it has no state and why does that class sport a method with the signature ItemQueryT getConfiguredItemQuery(ItemQueryT query, QueryOptions qOpt) instead of void configuredItemQuery(ItemQueryT query, QueryOptions

[basedb-devel] BASE 2.12.1 has been released

2009-06-15 Thread Nicklas Nordborg
Hello all, We are happy to announce the release of BASE 2.12.1. This is a bugfix release that among other things fixes some critical bugs related to running BASE 1 plug-ins. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.12.1 Installation/upgrade

Re: [basedb-devel] ServicesUtil not found

2009-06-17 Thread Nicklas Nordborg
Olivier Lefevre wrote: My web service client (i.e., a child of AbstractRPCClient) references a custom class in a completely different package, which is is in its own jar under webapps/base2/WEB-INF/lib That class in turn references net.sf.basedb.ws.server.ServicesUtil Upon trying to run the

Re: [basedb-devel] ServicesUtil not found

2009-06-17 Thread Nicklas Nordborg
The ServicesUtil and other classes in the net.sf.basedb.ws.server package are not found in the WEB-INF/lib/ directory and thus can't be referenced from classes that are there. Axis has it's own class loader implementation and expects to find classes in the WEB-INF/services/ directory in the form

Re: [basedb-devel] ServicesUtil not found

2009-06-17 Thread Nicklas Nordborg
Olivier Lefevre wrote: So it's a class loader issue. Thanks for the explanation. I'll find some arrangement that works; worst case is I just shove everything into net.sf.basedb.ws.server: it's my own code, so I can repackage it. While we are talking about design, I have another quick

Re: [basedb-devel] ServicesUtil not found

2009-06-17 Thread Nicklas Nordborg
Olivier Lefevre wrote: Re. the earlier problem, here is what I found: 1) custom classes in their own package and in their own jar under WEB-INF/lib: ClassNotFoundException 2) custom classes in their own package and in their own jar or aar under WEB-INF/services:

Re: [basedb-devel] Question about (To)Transferables

2009-06-18 Thread Nicklas Nordborg
Olivier Lefevre wrote: Why don't *all* the BasicItem classes for which an info class exists implement ToTransferable? E.g., Annotation (doesn't) vs. Experiment (does). Just trying to understand the API. With annotations there is no one-to-one relationship between Annotation and AnnotationInfo.

[basedb-devel] BASE 2.13 has been released

2009-08-31 Thread Nicklas Nordborg
Hello all, We are happy to announce the release of BASE 2.13. The release fixes several bugs and adds some new features as well. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.13 Installation/upgrade instructions:

[basedb-devel] BASE 2.14 has been released

2009-10-22 Thread Nicklas Nordborg
Hello all, We are happy to announce the release of BASE 2.14. This is a major release that among other things includes: * Performance enhancements related to annotation/experimental factor handling. * New plot functionality and more in experiment explorer. For a complete list of changes,

Re: [basedb-devel] ServicesUtil problem

2009-12-10 Thread Nicklas Nordborg
Woodbridge, Mark R wrote: Hi, I might be misunderstanding the documentation but it appears that the Boolean flags that can be passed to the net.sf.basedb.info.QueryOptions constructor are ignored by net.sf.basedb.ws.server.ServicesUtil, as demonstrated by the failure of the

Re: [basedb-devel] Prompting for credentials

2009-12-14 Thread Nicklas Nordborg
Olivier Lefevre wrote: Is there a way to make BASE2 automatically prompt for credentials when a user who is not yet logged in clicks on a link pointing to a restricted-access resource? For instance the generic URL for an Experiment is

Re: [basedb-devel] Prompting for credentials

2009-12-15 Thread Nicklas Nordborg
Olivier Lefevre wrote: Hi Nicklas, If you supply a URL like the one above BASE is going to ask you for a login and password. I assume you mean a screen like the attached. If so that is indeed what I get in my own local development instance but the production instance (not managed by

Re: [basedb-devel] Prompting for credentials

2009-12-15 Thread Nicklas Nordborg
Olivier Lefevre wrote: Out of curiosity, this error message implies that session IDs, once allocated, are tied to the remote ID the initial request came from. Is it a security feature? Yes, but a very simple one. The idea is to protect the server from someone guessing an ID that is in use.

Re: [basedb-devel] Setting active project via API

2010-01-06 Thread Nicklas Nordborg
Woodbridge, Mark R wrote: Hi, I’m linking to experiments in BASE from another web application. This works fine, including automatically logging in, as long as the experiment belongs to the user’s active project. I’d like to ensure that the correct project is activated before the

Re: [basedb-devel] Tab2Mage exporter plugin

2010-02-05 Thread Nicklas Nordborg
On 2010-02-05 10:07, Gildas Le Corguillé wrote: 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

[basedb-devel] BASE 2.15 has been released

2010-04-20 Thread Nicklas Nordborg
Hello all, We are happy to announce the release of BASE 2.15. This is a major release which among other things include a new plug-in executor for running external analysis programs. The executor is highly configurable and extendable and it is intended that this should replace the old and

[basedb-devel] BASE 2.16 has been released

2010-11-03 Thread Nicklas Nordborg
Hello all, We are happy to announce the release of BASE 2.16. This is a major release which lots of new functionality and enhancements as well as some bug fixes For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.16group=type Installation/upgrade

[basedb-devel] BASE 2.16.1 has been released

2010-11-21 Thread Nicklas Nordborg
Hello all, We are happy to announce the release of BASE 2.16. This is a bugfix release that fixes mostly minor bugs but also a critical problem that made it impossible to view reporter and raw data information in some places. For a complete list of changes, see:

Re: [basedb-devel] base or hibernate bug?

2011-01-21 Thread Nicklas Nordborg
It used to work on 2.12.x but I'm having trouble reproducing that now because I don't have a database with the correct schema easily to hand (we could dig up an old backup...). After some detective work, I believe it's something to do with http://dev.thep.lu.se/base/ticket/1350 and

Re: [basedb-devel] External authentication

2011-02-01 Thread Nicklas Nordborg
On 2011-02-01 11:29, Pawel Sztromwasser wrote: Hi, I am working on an external authentication plugin for BASE that will use an STS Web service to authenticate users. The plugin uses a bunch of external jars for WS communication, but with different versions then BASE. I was hoping for the

Re: [basedb-devel] External authentication

2011-02-01 Thread Nicklas Nordborg
I added a ticket: http://base.thep.lu.se/ticket/1575 /Nicklas -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download

Re: [basedb-devel] External authentication

2011-02-01 Thread Nicklas Nordborg
On 2011-02-01 13:24, Pawel Sztromwasser wrote: Sorry, just noticed that you mentioned the ...basedb.util.JarClassLoader, not a regular Java class loader as I initially thought. Check the code for DataFileType.getValidator():

[basedb-devel] BASE 2.16.2 has been released

2011-02-18 Thread Nicklas Nordborg
Hello all, We are happy to announce the release of BASE 2.16.2. This is a bugfix release that fixes a few non-critical bugs and is the last 2.16.x release before BASE 2.17 For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.16.2group=type

[basedb-devel] BASE 2.17 has been released

2011-02-23 Thread Nicklas Nordborg
Hello all, We are happy to announce the release of BASE 2.17. This is a major release which include new functionality and enhancements as well as some bug fixes. Worth mentioning is the bioplate events feature which makes it possible to batch edit biomaterial on a bioplate. For a complete list

Re: [basedb-devel] External authentication

2011-03-01 Thread Nicklas Nordborg
On 2011-03-01 12:58, Pawel Sztromwasser wrote: Hi Nicklas, I changed the Application.getAuthenticator() to use a separate classloader for external login plugin (attached a diff to the ticket #1575) and I was able to verify user's credentials using an STS service. Thanks for the patch. It

[basedb-devel] BASE 2.17.2 has been released

2011-06-17 Thread Nicklas Nordborg
Hello all, We are happy to announce the release of BASE 2.17.2. This is a bugfix release that fixes a few minor bugs. For a complete list of changes, see: http://base.thep.lu.se/query?status=closedmilestone=BASE+2.17.2group=type Installation/upgrade instructions:

Re: [basedb-devel] Programmatic login using a token

2011-08-01 Thread Nicklas Nordborg
On 2011-07-26 22:47, Pawel Sztromwasser wrote: Hello BASE team! Extending a little on our recent developments regarding external authentication in BASE [1], I am working now on a Web service interface to BASE that will authenticate users based on secure tokens issued by a trusted STS. The

Re: [basedb-devel] Programmatic login using a token

2011-08-01 Thread Nicklas Nordborg
On 2011-08-01 10:51, Pawel Sztromwasser wrote: Hi Nicklas, Thanks for the suggestions. Maybe I am missing something but wouldn't it be possible to send the username and password to the STS as part of the BASE login? Or, use an empty password string? I should have explained the use case

[basedb-devel] BASE 3.0-alfa has been released

2011-09-15 Thread Nicklas Nordborg
Hello all, Today we are happy to announce the relase of BASE 3.0-alfa. If all goes well the final 3.0 release is expected in a couple of months. This release contains major changes which are mainly targeted at supporting sequencing experiments with expression like data. Do not use this

[basedb-devel] BASE 3.0-beta has been released

2011-10-12 Thread Nicklas Nordborg
Hello all, Today we are happy to announce the release of BASE 3.0-beta. If all goes well the final 3.0 release is expected within the near future. This release should contain all new functionality that is needed for supporting sequencing experiments with expression like data, but there may still

[basedb-devel] BASE 3.0.1 has been released

2011-11-10 Thread Nicklas Nordborg
Hello all, We have released BASE 3.0.1 today. It fixes a critical issue related to upgrading from BASE 2.17 to BASE 3. We recommend that all servers that has been upgraded are upgraded to BASE 3.0.1 as soon as possible. The issue doesn't affect fresh BASE 3.0 installations. More information

Re: [basedb-devel] MageTab export plugin

2011-11-22 Thread Nicklas Nordborg
On 2011-11-22 13:50, Pawel Sztromwasser wrote: Hi Nicklas, I guess the MageTab export plugin is ready for submission. I followed instructions for plugin developers (http://baseplugins.thep.lu.se/wiki/PluginSubmitReq), so all the documentation bits should be in place. How could I send you the

[basedb-devel] BASE 3.0.2 has been released

2012-01-25 Thread Nicklas Nordborg
Hello all, We have released BASE 3.0.2 today. This is a bugfix release that fixes a few minor bugs. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.0.2group=type Installation/upgrade instructions:

[basedb-devel] BASE 3.0.3 has been released

2012-02-22 Thread Nicklas Nordborg
Hello all, We have released BASE 3.0.3 today. This is a bugfix release that fixes an annoying Internet Explorer issue with popup windows. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.0.3group=type Installation/upgrade instructions:

[basedb-devel] BASE 3.0.4 has been released

2012-03-05 Thread Nicklas Nordborg
Hello all, We have released BASE 3.0.4 today. This is a bugfix release that fixes a few minor bugs. For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.0.4group=type Installation/upgrade instructions:

[basedb-devel] BASE 3.1 has been released

2012-03-19 Thread Nicklas Nordborg
Hello all, We are happy to announce the release of BASE 3.1. It is a new major release that among other things include: * A new and improved user interface * Possibility to clone reporter information to a local copy per experiment * A migration script for moving a BASE installation

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