Pawel Sztromwasser wrote:
> It seems like the plugin is there. Check if this plugin has been shared
> to your user (Administrate->Plugins->Definitions and find the plugin).
> If not, only administrator/superuser can change that. If it is shared to
> you then it should be accessible.
Hi Pawel
Thanks for the reply. I am logging on as the root user.
This was a fresh install of BASE 2.5.0 but the only two plugins I see
under Administrate->Plugins->Defitions are the following 2:
Annotation importer net.sf.basedb.plugins.AnnotationFlatFileImporter
Reporter map importer net.sf.basedb.plugins.ReporterMapFlatFileImporter
However, I took a dump of the database and can see the following rows in
MySQL:
mysql> select * from PluginDefinitions;
+----+---------+---------+------------------+---------------------------------------------------+--------------------------------------------------+----------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------------+--
-----------------------------+---------+-------+------------------------+------+-------------+-----------------+-----------------+-----------------+---------+------------+-----------------+--------------------+------------+---------------+-------+
| id | version | removed | annotationset_id | class_name
| jar_path
| name | description
| version_string |
copyright | contact | email | url
| type | interactive | supports_config | requires_config |
use_permissions | trusted | max_memory | allow_immediate |
use_internal_queue | itemkey_id | projectkey_id | owner |
+----+---------+---------+------------------+---------------------------------------------------+--------------------------------------------------+----------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------------+--
-----------------------------+---------+-------+------------------------+------+-------------+-----------------+-----------------+-----------------+---------+------------+-----------------+--------------------+------------+---------------+-------+
| 1 | 0 | | NULL |
net.sf.basedb.plugins.Base1PluginExecuter | NULL
| Base1PluginExecuter | This
plug-in simulates the plug-in runner from Base 1.2 to enable old
plug-ins to be executed.
| 1.0 | 2006, Base 2 development team | NULL | NULL
| http://base.thep.lu.se | 4 | | |
| | | NULL | |
| NULL | NULL | 1 |
| 2 | 0 | | NULL |
net.sf.basedb.plugins.BioAssaySetExporter | NULL
| Bioassay set file exporter |
Exporter for bioassay sets. Supported formats:
- Tab Delimited, Multiple Sample Files (TDMS Format) for use in MeV
(available from http://www.tm4.org).
- BASEfile
| 2.0
| 2006, Base 2 development team | NULL | NULL |
http://base.thep.lu.se | 2 | | |
| | | NULL | |
| 55 | NULL | 1 |
| 3 | 0 | | NULL |
net.sf.basedb.plugins.FormulaFilter | NULL
| JEP filter plugin | This
plugin is used to filter a bioassay set, creating a new bioassay set
with fewer spots in it. The filter is based on expressions entered by
the user, which are parsed with the JEP package. Thus, the functionality
of this plugin is very flexible.
|
2.0 | 2006, Base 2 development team | NULL | NULL |
http://base.thep.lu.se | 4 | | |
| | | NULL | |
| 55 | NULL | 1 |
| 4 | 0 | | NULL |
net.sf.basedb.plugins.HelpExporter | NULL
| Help texts exporter | This
plugin is used to export a client applications help texts to a XML-file.
The help tests can later be imported by the corresponding import plugin.
| 2.0
| 2006, Base 2 development team | NULL | NULL |
http://base.thep.lu.se | 2 | | |
| | | NULL | |
| NULL | NULL | 1 |
| 5 | 0 | | NULL |
net.sf.basedb.plugins.HelpImporter | NULL
| Help texts importer | This
plugin is used to import help texts from a XML-file to BASE.
|
2.0 | 2006, Base 2 development team | NULL | NULL |
http://base.thep.lu.se | 1 | | |
| | | NULL | |
| NULL | NULL | 1 |
| 6 | 0 | | NULL |
net.sf.basedb.plugins.IntensityCalculatorPlugin | NULL
| Formula intensity calculator | This
plugin is used to calculate intensities from raw data creating an
initial root bioassay set. The intensities are calculated using Formula
objects registered for the experiment's raw data type. Thus, the
functionality of this plugin can be extended by adding more formula
objects to the database.
| 2.0 | 2006, Base 2 development team | NULL |
NULL | http://base.thep.lu.se | 3 | | |
| | | NULL |
| | 55 | NULL | 1 |
| 7 | 0 | | NULL |
net.sf.basedb.plugins.JepExtraValueCalculator | NULL
| JEP extra value calculator | This
plugin is used to calculate extra values for a bioassay set using
expressions entered by the user. The expressions are parsed with the JEP
package.
| 2.0 | 2006, Base 2 development team | NULL | NULL |
http://base.thep.lu.se | 4 | | |
| | | NULL | |
| 55 | NULL | 1 |
| 8 | 0 | | NULL |
net.sf.basedb.plugins.JepIntensityTransformer | NULL
| JEP intensity transformer | This
plugin is used to transform the intensities of a bioassayset using
expressions entered by the user. The expressions are parsed with the JEP
package.
| 2.0 | 2006, Base 2 development team | NULL | NULL |
http://base.thep.lu.se | 4 | | |
| | | NULL | |
| 55 | NULL | 1 |
| 9 | 0 | | NULL |
net.sf.basedb.plugins.LowessNormalization | NULL
| Normalization: Lowess | This
is an efficient java implementation by Johan Enell of the LOWESS
algorithm. It provides intensity-based normalization.
The window size is the only smoothness parameter available in this
implementation. The higher it is, the smoother the function will be.
Tweaking the other two parameters allows you to gain performance at the
price of a small precision loss. The default values are usually good.
For more info on LOWESS:
Cleveland WS, Devlin SJ: Locally weighted regression: an approach to
regression analysis by local fitting. J Am Stat Assoc 1988, 83:596-610.
Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP:
Normalization for cDNA microarray data: a robust composite method
addressing single and multiple slide systematic variation. Nucleic Acids
Res 2002, 30:e15. | 2.5 | 2006, Base 2 development team |
NULL | NULL | http://base.thep.lu.se | 4 | |
| | | | NULL |
| | 55 | NULL | 1 |
| 10 | 0 | | NULL |
net.sf.basedb.plugins.MedianRatioNormalization | NULL
| Normalization: Median ratio | This
normalizer scales the intensities in such a way that their geometric
mean (sqrt(i1 * i2)) is kept constant but the median of their ratios
(i1/i2) is shifted to 1.
The normalizer lets you exclude a percentage of the highest and lowest
intensities as well as all spots with at least one intensity below a
fixed value.
| 2.5 |
2006, Base 2 development team | NULL | NULL | http://base.thep.lu.se
| 4 | | | |
| | NULL | | |
55 | NULL | 1 |
| 11 | 0 | | NULL |
net.sf.basedb.plugins.PlateFlatFileImporter | NULL
| Plate importer | This
plugin is used to import plates from a simple flat file.
|
2.0 | 2006, Base 2 development team | NULL | NULL |
http://base.thep.lu.se | 1 | | |
| | | NULL | |
| NULL | NULL | 1 |
| 12 | 0 | | NULL |
net.sf.basedb.plugins.PlateMappingExporter | NULL
| Plate mapping exporter | This
plugin is used to export plate mappings, which maps the coordinates of
one or more source plates to coordinates on one or more destination
plates.
| 2.0 | 2006, Base 2 development team | NULL | NULL |
http://base.thep.lu.se | 2 | | |
| | | NULL | |
| NULL | NULL | 1 |
| 13 | 0 | | NULL |
net.sf.basedb.plugins.PlateMappingImporter | NULL
| Plate mapping importer | This
plugin is used to import plate mappings, which maps the coordinates of
one or more source plates to coordinates on one or more destination
plates.
| 2.0 | 2006, Base 2 development team | NULL | NULL |
http://base.thep.lu.se | 1 | | |
| | | NULL | |
| NULL | NULL | 1 |
| 14 | 0 | | NULL |
net.sf.basedb.plugins.PrintMapFlatFileImporter | NULL
| Print map importer | This
plugin is used to import arraydesign from a print map.
|
2.0 | 2006, Base 2 development team | NULL | NULL |
http://base.thep.lu.se | 1 | | |
| | | NULL | |
| NULL | NULL | 1 |
| 15 | 0 | | NULL |
net.sf.basedb.plugins.RawDataFlatFileImporter | NULL
| Raw data importer | This
plugin is used to import raw data from a simple text file.
|
2.0 | 2006, Base 2 development team | NULL | NULL |
http://base.thep.lu.se | 1 | | |
| | | NULL | |
| 55 | NULL | 1 |
| 16 | 0 | | NULL |
net.sf.basedb.plugins.ReporterFlatFileImporter | NULL
| Reporter importer | This
plugin is used to import reporters from a simple flat file.
|
2.0 | 2006, Base 2 development team | NULL | NULL |
http://base.thep.lu.se | 1 | | |
| | | NULL | |
| 55 | NULL | 1 |
| 17 | 0 | | NULL |
net.sf.basedb.plugins.ReporterMapFlatFileImporter | NULL
| Reporter map importer | This
plugin is used to import features to an ArrayDesign from a simple flat
file.
|
2.0 | 2006, Base 2 development team | NULL | NULL |
http://base.thep.lu.se | 1 | | |
| | | NULL | |
| NULL | NULL | 1 |
| 18 | 0 | | NULL |
net.sf.basedb.plugins.SpotImageCreator | NULL
| Spot images creator |
Converts a full-size scanned image into smaller preview jpg images for
each individual spot.
| 2.0 | 2006, Base 2 development team | NULL | NULL |
http://base.thep.lu.se | 5 | | |
| | | NULL | |
| 55 | NULL | 1 |
| 19 | 0 | | NULL |
net.sf.basedb.plugins.ZipFileUnpacker | NULL
| ZIP file unpacker | This
plugin unpacks a zip file on the BASE file system. It supports zip and
jar files.
|
2.0 | 2006, Base 2 development team | NULL | NULL |
http://base.thep.lu.se | 5 | | |
| | | NULL | |
| 55 | NULL | 1 |
| 20 | 0 | | NULL |
net.sf.basedb.plugins.TarFileUnpacker | NULL
| TAR file unpacker | This
plugin unpacks a tar file on the BASE file system. It also supports TAR
files compressed with the GZIP and BZIP algorithms.
|
2.4 | 2007, Base 2 development team | NULL | NULL |
http://base.thep.lu.se | 5 | | |
| | | NULL | |
| 55 | NULL | 1 |
| 21 | 0 | | NULL |
net.sf.basedb.plugins.PluginConfigurationExporter | NULL
| Plugin configuration exporter | This
plugin is used to export selected plugin configurations to an XML-file.
The plugin configurations can later be imported by the corresponding
import plugin.
|
2.1 | 2006, Base 2 development team | NULL | NULL |
http://base.thep.lu.se | 2 | | |
| | | NULL | |
| 55 | NULL | 1 |
| 22 | 0 | | NULL |
net.sf.basedb.plugins.PluginConfigurationImporter | NULL
| Plugin configuration importer | This
plugin is used to import configuration for a BASE plugin from an
XML-file.
| 2.1 | 2006, Base 2 development team | NULL | NULL
| http://base.thep.lu.se | 1 | | |
| | | NULL | |
| NULL | NULL | 1 |
| 23 | 0 | | NULL |
net.sf.basedb.plugins.CdfFileReporterImporter | NULL
| Affymetrix CDF probeset importer | This
plug-in is used to import probesets from an Affymetrix CDF file as
reporters. It can be used in import mode from the reporter list view and
from the array design view and in verification mode from the array
design view. The plug-in can only set the name and ID of the reporters,
since the CDF file doesn't contains any annotation information.
Probesets already in BASE will not be affected by the import
| 2.4 | 2007, Base 2 development team | NULL |
NULL | http://base.thep.lu.se | 1 | | |
| | | NULL |
| | NULL | NULL | 1 |
| 24 | 0 | | NULL |
net.sf.basedb.plugins.PackedFileExporter | NULL
| Packed file exporter | This
plugin is used to pack one or more files/directories into a single file.
Items should be selected before starting the plug-in and they must all
be located in the same parent directory. The compressed file can be
downloaded immediately or stored in the BASE file system. The user can
choose to have the selected files and directories removed after they've
been packed.
|
2.4 | 2007, Base 2 development team | NULL | NULL |
http://base.thep.lu.se | 2 | | |
| | | NULL | |
| 55 | NULL | 1 |
| 25 | 0 | | NULL |
net.sf.basedb.plugins.AnnotationFlatFileImporter | NULL
| Annotation importer | This
plugin is used to import annotations to any annotatable items.
|
2.4 | 2007, Base 2 development team | NULL | NULL |
http://base.thep.lu.se | 1 | | |
| | | NULL | |
| 55 | NULL | 1 |
| 26 | 0 | | NULL |
net.sf.basedb.plugins.IlluminaRawDataImporter | NULL
| Illumina raw data importer | This
plugin is used to import raw data from Illumina data files. The plug-in
can be executed from the list of raw bioassays and will then only create
new raw bioassays, or from within an experiment, in which case the
imported data will also be associated with the experiment.
|
2.4 | 2007, Base 2 development team | NULL | NULL |
http://base.thep.lu.se | 1 | | |
| | | NULL | |
| 55 | NULL | 1 |
| 27 | 0 | | NULL |
net.sf.basedb.clients.web.plugins.SimpleExport | NULL
| Table exporter |
Export all table listings in the web interface as tab-separated text
files or as XML. This plugin only works from within the web client,
since it depends on context and table information.
| 2.0 | 2006, Base 2 development team | NULL |
NULL | http://base.thep.lu.se | 2 | | |
| | | NULL |
| | 55 | NULL | 1 |
| 28 | 0 | | NULL |
net.sf.basedb.exampleplugins.ExampleImporter |
/usr/local/base-2.5.0/plugins/ExamplePlugins.jar | Example importer
| An example plugin that pretends to import samples. It
can't be configured, but will ask for a file to import from and if
existing samples should be updated or not. It won't actually import any
samples, but will report that a few samples has been imported.
| 2.0 | 2006, Base 2 development team
| NULL | NULL | http://base.thep.lu.se | 1 | |
| | | | NULL |
| | NULL | 57 | 1 |
| 29 | 0 | | NULL |
net.sf.basedb.exampleplugins.ExampleAnalyzer |
/usr/local/base-2.5.0/plugins/ExamplePlugins.jar | Copy spot intensity
| An example analysis plugin that creates a new bioassay
set by multiplying each intensitity value with the same factor,
filtering out intensities below a cutoff value.
| 2.0 | 2006, Base 2 development
team | NULL | NULL | http://base.thep.lu.se | 4 | |
| | | |
NULL | | | NULL | 57
| 1 |
+----+---------+---------+------------------+---------------------------------------------------+--------------------------------------------------+----------------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+----------------+--
-----------------------------+---------+-------+------------------------+------+-------------+-----------------+-----------------+-----------------+---------+------------+-----------------+--------------------+------------+---------------+-------+
Weird. Any ideas?
Cheers
Nick.
-------------------------------------------------------------------------
This SF.net email is sponsored by: Microsoft
Defy all challenges. Microsoft(R) Visual Studio 2008.
http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
_______________________________________________
The BASE general discussion mailing list
basedb-users@lists.sourceforge.net
unsubscribe: send a mail with subject "unsubscribe" to
[EMAIL PROTECTED]
