Hey, Could you check if you are not using any filters in plugins view that could narrow results?
Pawel Nick Loman wrote: > 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] -- Pawel Sztromwasser Computational Biology Unit Bergen Center for Computational Science ------------------------------------------------------------------------- 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]
