[ome-devel] can't find the switch to install OME as a developer

[Bernd Jagla]

Tom,

Why is this not working?

I get
ome=#   select * from configuration where name='import_formats';
 var_id |
value
| configuration_id |      name      
--------+-------------------------------------------------------------------
----------------------------------------------------------------------------
----------------------------------------------------------------------------
----------------------------------------------------------------------------
------------------------------------+------------------+----------------
      5 |
['OME::ImportEngine::OMETIFFreader','OME::ImportEngine::MetamorphHTDFormat',
'OME::ImportEngine::DVreader','OME::ImportEngine::STKreader','OME::ImportEng
ine::BioradReader','OME::ImportEngine::LSMreader','OME::ImportEngine::TIFFre
ader','OME::ImportEngine::BMPreader','OME::ImportEngine::DICOMreader','OME::
ImportEngine::XMLreader'] |                1 | import_formats
(1 row)

I updated using:
ome=# update configuration SET value
='[\'OME::ImportEngine::INCellRunXML\',\'OME::ImportEngine::OMETIFFreader\',
\'OME::ImportEngine::MetamorphHTDFormat\',\'OME::ImportEngine::DVreader\',\'
OME::ImportEngine::STKreader\',\'OME::ImportEngine::BioradReader\',\'OME::Im
portEngine::LSMreader\',\'OME::ImportEngine::TIFFreader\',\'OME::ImportEngin
e::BMPreader\',\'OME::ImportEngine::DICOMreader\',\'OME::ImportEngine::XMLre
ader\']' where name='import_formats';
UPDATE 1

And now it is working....

Isn't this a bug? Can you reproduce this on your end?


Thanks,

Bernd

|-----Original Message-----
|From: Tom Macura [mailto:tm289 at cam.ac.uk]
|Sent: Thursday, August 24, 2006 10:08 PM
|To: Bernd Jagla
|Cc: ome-devel at lists.openmicroscopy.org.uk
|Subject: Re: [ome-devel] can't find the switch to install OME as a
|developer
|
|Hi Bernd,
|
|Do you see your INCellRunXML importer in the DB?
|select * from configuration where name='import_formats';
|If not, manually update the configuration table and see if this fixes your
|import problems.
|
|I am pretty sure the ApacheConfigTask.pm error has nothing to do with your
|importer problem.
|
|Tom
|
|On Aug 24, 2006, at 2:48 PM, Bernd Jagla wrote:
|
|
|	I am sorry, but I can't remember how to get the developer version to
|work.
|
|
|
|	Here is what I have done:
|
|
|
|	I installed OME with all the defaults (including Yes to Apache
|Developer configuration and Web-UI HTML Templates developer configuration).
|I added the line
|
|	OME::ImportEngine::INCellRunXML
|
|	Into CoreDatabasesTablesTasks.pm (first item in list)
|
|
|
|	Reinstalled using -y
|
|	I added line
|
|	print "in INCellRunfile" .  $filename ."\n";
|
|	under getGroups in INCellRunXML.pm
|
|
|
|	Now, all I get is
|
|
|
|	[bernd at BERND-HOME OME]$ ome import -r
|/home/bernd/TestImages/Ai/DrugStudy/041230Plate5_2/041230Plate5_2.xml
|
|	Importing files
|
|	         1/4: [IN PROGRESS] Starting import
|
|	Deleting 041230Plate5_2.xml
|
|	         4/4: [FINISHED] Imported 0 images from 0 files. 1 scanned.
1
|unknown format, 0 duplicates, 0 errors.
|
|	Exiting...
|
|	         4/4: [FINISHED] Imported 0 images from 0 files. 1 scanned.
1
|unknown format, 0 duplicates, 0 errors.
|
|	Exiting...
|
|
|
|
|
|	With no sign that INCellRunXML has ever executed.
|
|
|
|	Then I did a cvs update and install (I had to drop the ome database
|because of errors from moving to the 26 version). But still no luck.
|
|	Now I am a bit frustrated and would really like a hand in this.
|
|
|
|	Thanks a lot
|
|
|
|	Bernd
|
|
|
|	PS. The only clue I found is this:
|
|
|
|	[bernd at BERND-HOME OME]$ !1155
|
|	perl -c src/perl2/OME/Install/CoreDatabaseTablesTask.pm
|
|	Use of uninitialized value in concatenation (.) or string at
|/usr/lib/perl5/site_perl/5.8.6/OME/Install/ApacheConfigTask.pm line 75.
|
|	src/perl2/OME/Install/CoreDatabaseTablesTask.pm syntax OK
|
|
|
|	but I didn't do in ApacheConfigTask.pm.
|
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