I think 3 will be the best. That way I could submit changes easily, and
everyone could get access to versioned code
Pawel
On 22/11/11 14:44, Nicklas Nordborg wrote:
> On 2011-11-22 13:50, Pawel Sztromwasser wrote:
>> Hi Nicklas,
>>
>> I guess the MageTab export plugin is re
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 bundle?
Would you provide a repository dir to pa
pooling of samples (or extracts) and the possibility to have
several "Files[raw]" per RawBioAssay (ex : one cy3 and one cy5)
because we used nimblegen multi-color arrays.
Are you plan to manage that feature ?
Gildas
Le 01/09/2011 14:43, Pawel Sztromwasser a écrit :
Hallo,
I haven
Hallo,
I haven't been to the milestones page for a while, and I didn't know
that work on BASE 3 was in such an advanced state. Great job guys!
Support for sequencing data is excellent news for us.
Anyway, before it is released and before we are ready to migrate, we
will certainly have experime
was wondering if
anyone else is developing or planning to develop a plugin that would
support Mage-Tab?
Regards,
Pawel Sztromwasser
<>--
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Finally, a world-cla
Sorry, wrong mailing list:)
Pawel Sztromwasser wrote:
In BASE it was a Tomcat problem. Hope it helps:
http://www.mail-archive.com/basedb-users@lists.sourceforge.net/msg01838.html
Pawel
<>--
Get a FREE DO
In BASE it was a Tomcat problem. Hope it helps:
http://www.mail-archive.com/basedb-users@lists.sourceforge.net/msg01838.html
Pawel
<>--
Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
user administration c
See my short replies inline.
Nicklas Nordborg wrote:
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, u
yed within BASE), so an
environment that a BASE administrator should have full control over. The
same as external authentication plugins.
Pawel
Nicklas Nordborg wrote:
On 2011-07-26 22:47, Pawel Sztromwasser wrote:
Hello BASE team!
Extending a little on our recent developments reg
, but it is little and
would provide additional way of programmatic interaction with BASE. If
they pass the tests, could you consider including the changes to the
BASE codebase?
Best wishes,
Pawel Sztromwasser
[1]
http://www.mail-archive.com/basedb-devel@lists.sourceforge.net/msg00433.html
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.
I got a bit unexpected behavior of BASE that tried to create a new
account fo
Sorry, just noticed that you mentioned the
...basedb.util.JarClassLoader, not a regular Java class loader as I
initially thought.
On 01/02/11 13:17, Pawel Sztromwasser wrote:
> Thanks for a quick reply. I really wanted to avoid selecting jars and so
> on since BASE has over 50 of the
On 2011-02-01 11:29, Pawel Sztromwasser wrote:s
>> 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 versio
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 same classloading mechanism as for regular
plugins (
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
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;)
All the best,
Pawel
Nicklas Nordborg wrote:
> Pawel Sztromwasser wrote:
>
>>> I
Nicklas Nordborg wrote:
> 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
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 have it done
automatically by the
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 a specific importer for images.
>
> /Nicklas
>
> Pawel Sztr
I have just noticed that the filename I sent has different name then the
class inside. I used ScanImporterNMC name to distinguish from the
original plugin and then renamed the file before sending. Just rename it
back and all will work.
Pawel
Pawel Sztromwasser wrote:
> Hello BASE t
Hello BASE team,
We really enjoy the set of batch uploading plugins and were doing a
little training for our users in Bergen. Everything seemed great except
that they couldn't link freshly created scans with image files. I read
in the example spreadsheet that it is not supported and was very
We experienced that as well. I believe that I have checked these probes
and they were controls, so they can be ignored.
Pawel
Nicklas Nordborg wrote:
> David Waring wrote:
>> I have recently installed the Illumina Plugins and have imported
>> features for several Array Designs. We modified our
Hello,
I found something interesting regarding BASE2 performance on Postgres
(we have 8.3 but I suppose it is valid for previous versions as well).
Recently I was unable to delete ArrayDesign (Illumina Human 8Ref, no
items connected to it, features imported), because database query was
endless
Nicklas Nordborg wrote:
> Pawel Sztromwasser wrote:
>> Totally agree. That makes it much more flexible. Please, feel free to
>> change the code.
>
>
> I have now implemented this feature in the trunk. There are several
> possibilities to specify which 'ServiceF
the constructor?
>
> Eg.
>
> protected AbstractRPCClient(
>String url, String service,
> RPCServiceClientCreator serviceCreator)
> {
> ...
> }
>
> /Nicklas
>
> Pawel Sztromwasser wrote:
>> Hi Nicklas,
>>
>> I had some time and implement
ers for my 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
Hello BASE developers,
We have been recently trying to enable retrieving some data from BASE2
installation directly into our 'home made' analysis tool. We use
webservices for that and have to say that you are doing a great job. We
are really looking forward to use them more extensively.
Recent
best and have a nice Easter,
Pawel
Nicklas Nordborg wrote:
> 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
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 remove value=2 (or
> 1 maybe). T
27;s page.
I checked .jsp sources for these pages and it seems like list-agents.jsp
uses deprecated method to get information about jobs (view-agent.jsp
uses new method introduced in 2.6). I couldn't add a ticket so I am
posting it on the mailing list.
B
Nicklas Nordborg wrote:
> Pawel Sztromwasser wrote:
>> Hi all,
>>
>> I have been trying to optimize the performance of LowessNormalization
>> plugin a little bit lately. It is extremely slow on our Postgres
>> database when using small 'block groups'.
Hi all,
I have been trying to optimize the performance of LowessNormalization
plugin a little bit lately. It is extremely slow on our Postgres
database when using small 'block groups'.
Anyway, I came across something that surprised me. When using
DynamicResultIterator I noticed that hasNext()
Hi,
We are migrating Base1.2.17+ to 2.4.6. The + stands for our local
changes made to satisfy the needs of MAGE-ML exporter. When writing code
to move additional annotations I noticed that information whether
annotation type is required for MIAME is kept in AnnotationType
class/table. This res
why an exception is thrown.
> I didn't find anything about adding dynamic schema to users search_path
> in PostgreSql in Base2 requirements. Some of the code in the same
> 'problem causing' method adds schema prefix when dropping constraints,
> so I consider this issue as
in Base2 requirements. Some of the code in the same
'problem causing' method adds schema prefix when dropping constraints,
so I consider this issue as a bug.
We are looking now for some work-around, like postgres search-path
setting and will post everything useful we find.
Pawel
ny more. Thanks once again for your help.
>
> Pawel Sztromwasser
>
>
> Nicklas Nordborg wrote:
>
>> Nicklas Nordborg wrote:
>>
>>
>>> I am taking this back to the mailing list in the hope that there is some
>>> Postgres expert th
Thank you very much.
I thought about altering database schema somehow to set the constraints
'initially deferred' and check if that works (in small examples it
worked fine), but if a new version makes no trouble it doesn't make
sense any more. Thanks once again for yo
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