Greetings,
I'm using BASE-2.4.0 and tomcat 6.0.14. I also tried base-2.4.0 and tomcat
5.5.20.
I'm trying, as usual, to run BASE1 plugins. I was close in BASE-2.3.2 in
that the only problem seemed to be that the last line of the bioassay set
wasn't written into the stdin.txt file.
In BASE-2.4.0, I have several problems.
1. It seems that a BASE1 plugin runs before the data was successfully
generated out of the database. (see explanation below)
2. The basefile is generated into a tomcat temp directory and is unlinked
before I can analyze it.
3. I can't empty the trash
Plugin runs before data is generated
------------------------------------
I call a perl executable on the server - this executable reads the stdout
from the base server and then calls R. Because of problem (2) (described
above), I've modified the perl program to also write the output to /tmp.
In /tmp I see a file containing:
BASEfile
fname rnormv1.R
norm.method p
do.bgcorr 0
ngrid.r.in 12.0
ngrid.c.in 4.0
nspot.r.in 18.0
(and a whole bunch more stuff that is correct but the last two lines I see
are:)
863 18058 A006151_01 565 398 0 444 282 243 146 0 197
864 85459 At30009369 620 441 0 397 276 248 1
It seems that I'm only seeing the first 864 rows of reporter data and the
last line is obviously truncated.
When I export data from the Bioassay set in the Experiments viewer I get a
proper basefile with 31200 rows of reporter data.
File is deleted before I can Examine It
----------------------------------------
It appears that the stdin.txt file containing the basefile intended for the
Base1PluginExecutor is being written to a tomcat tempfile somewhere. I
looked all through base.userfiles with commands like:
userfiles$ find . -type f -mtime -1 -exec ls -l {} \;
I found the r-debug.txt that the R-program generated (indicating that rows
were missing from the basefile) but no XXXXXXXstdin.txt (where XXXXXXX is
the BASE serial number).
This behavior changed since 2.3.2 and I can't find any information regarding
this change in TRAC. In previous versions checking the 'Leave stdin.txt' in
the plugin Configuration, well, resulted in stdin.tx being left behind.
Emptying the trash
------------------
In my trashcan I have 1.6 gazillion files. I followed the instructions here:
http://base.thep.lu.se/chrome/site/doc/html/userdoc/trashcan/trashcan.viewde
pendencies.html
But whenever I try to delete items using the 'Empty Trash...' command I get:
"0 of xxx items removed. xxx items are used and can't be removed.' xxx is
some number.
This is interesting because if I filter by Item Type 'File', click on the
little icon on the left (looks like a paper document with a piece of a chain
on it) see no indication that it has dependencies.
If I select a single File item from the Trashcan and click 'Delete
Permanently' I get the "can't be removed" message.
If, in the Properties page for the same file I click 'Delete
Permanently....' no error message appears and when I return to the
'Trashcan' page the item is gone and the total count of hits is decremented.
In addition, the command:
userfiles $ find . -type f | wc
returns one less. This indicates that the delete was successful.
Do I have to delete files one at a time?
Summary
-------
Can somebody please help me understand the best way to:
1. Restore the behavior that I saw in previous versions of BASE2 where the
stdin.txt that was intended to be used for a base1 plugin appear on the
filesystem? I can then use it to troublshoot the R program that does my
work.
2. Run base1 plugins? I can't seem to get the entire basefile out of base.
Thank you for any help you can provide.
Chad Matsalla
Plant Biotechnology Institute, National Research Council of Canada
Saskatoon, Saskatchewan
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