[ome-users] Problem with ome command-line administration: annotate spreadsheet

[Hicks, Bryson]

Hey all,
 
Sort of a small problem, but this is what happened:  When I try to do
"ome annotate spreadsheet -n "ImportSpreadsheetTemplateCG-1.xls" the
prompt actually creates the annotations, rather than just displaying
what would be created.  On the OME website's System administration page,
it says that the "-n" and the "--noop" options will "not create any
annotations, just report what would be created"
(http://www.openmicroscopy.org.uk/system-admin/docs/annotate_spreadsheet
.html).

I then tried to verify that -n and --noop are commands by typing "ome
annotate spreadsheet help" but this did not work.  When I did so, the
response I got was:
 
[hicks at ome Brunn's Nest]$ ome annotate spreadsheet help
\1 better written as $1 at
/usr/lib/perl5/site_perl/5.8.5/ome/Web/Search.pm line 678.
Use of uninitialized value in pattern match (m//) at
/usr/lib/perl5/5.8.5/Getopt/Long.pm line 315.
Use of uninitialized value in string eq at
/usr/lib/perl5/5.8.5/Getopt/Long.pm line 317.
Use of uninitialized value in pattern match (m//) at
/usr/lib/perl5/5.8.5/Getopt/Long.pm line 686.
Please login to OME:
Username? hicks
Password?
Great, you're in.
 
Couldn't open help for reading: No such file or directory at
/usr/lib/perl5/site_perl/5.8.5/OME/Util/Annotate/SpreadsheetReader.pm
line 248, <STDIN> line 2.
 
Also, when I tried importing the spreadsheet, the response I got was:
 
[hicks at ome Brunn's Nest]$ ome annotate spreadsheet help
\1 better written as $1 at
/usr/lib/perl5/site_perl/5.8.5/ome/Web/Search.pm line 678.
Use of uninitialized value in pattern match (m//) at
/usr/lib/perl5/5.8.5/Getopt/Long.pm line 315.
Use of uninitialized value in string eq at
/usr/lib/perl5/5.8.5/Getopt/Long.pm line 317.
Use of uninitialized value in pattern match (m//) at
/usr/lib/perl5/5.8.5/Getopt/Long.pm line 686.
Please login to OME:
Username? hicks
Password?
Great, you're in.
 
Finished annotating:
Spreadsheet Identifier: '189'
        Image ID: 189
        Classifications:
                \_ 'Camera' : '3.3ug_per_mL'
                \_ 'Concentration_of_Primary' : 'DC200'
                ...(this continues.  It describes all of the annotations
for each image.  Also, all of these annotations are wrong, because the
Categories are made under the wrong Category Groups).
 
If I then go into the OME web browser and search for Module Extensions,
it turns out that the Spreadsheet Global Import truly was created, and
that all of the annotations were made.  Does this make sense to anyone?
 
Thanks for the help,
--Bryson Hicks

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