Greetings,
I'm using base-2.4.1 (compiled from 2.4.2-src) on tomcat 6.0.14.
I'm stumped on this one. My objective is to parse the output from a
base1 plugin. The output from the plugin is a basefile that looks like
this:
BASEfile
section spots
columns position reporter assayData
assayFields intensity1 intensity2 scaled ch1_sd_pmt_merged
ch2_sd_pmt_merged
assays 70
setExtraFloats scaled ch1_sd_pmt_merged ch2_sd_pmt_merged
%
1 25411 374 385 0 429 331
2 19204 524 583 0 478 343
(much more data here)
The exception I get is below[1].
I went to the 'Extra Value types' administration screen and I see
'ch1_sd_pmt_merged','ch2_sd_pmt_merged', and 'scaled'. When I click on
'scaled' I see 'Permissions on this item: Read, Use, Write, Delete'.
Can anybody offer me some advice on a fix for this?
Thank you!
Chad Matsalla
[1]
net.sf.basedb.core.BaseException: Permission denied: Not allowed to use
Extra value type[id=1; name=scaled]
at
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:429)
at java.lang.Thread.run(Thread.java:595)
Caused by: net.sf.basedb.core.PermissionDeniedException: Permission
denied: Not allowed to use Extra value type[id=1; name=scaled]
at
net.sf.basedb.core.BasicItem.checkPermission(BasicItem.java:110)
at
net.sf.basedb.core.ExtraValue.setExtraValueType(ExtraValue.java:229)
at net.sf.basedb.core.ExtraValue.getNew(ExtraValue.java:83)
at
net.sf.basedb.core.BioAssaySet.getSpotExtraValueBatcher(BioAssaySet.java:924)
at
net.sf.basedb.plugins.Base1PluginExecuter.importData(Base1PluginExecuter.java:1424)
at
net.sf.basedb.plugins.Base1PluginExecuter.run(Base1PluginExecuter.java:698)
at
net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:89)
at
net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:421)
... 1 more
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