[ome-users] OME XML export and import

[Josiah Johnston]

The problem most likely is that the experimenters on your second  
machine have different LSIDs than the experimenters on the first. When  
you import the images into the second machine, the owner is recorded as  
the owner in the first.

It's a very similar problem to file permissions on NFS mounts. If your  
user id is different between two *nix machines that mount the same  
network drive, then you can have permission to read on one machine and  
not on the other. The usual solution for this problem is to synchronize  
the uid's and gid's between machines.

The simple solution is the same for both problems. If you want to use  
more than one machine, synchronize your LSIDs between installations.  
You can find the LSID of your experimenter in your exported file. Look  
for something like:
	<Experimenter ID = "urn:lsid:foo.bar.com:Experimenter:123456">
You'll need to wipe the imported data from the second machine before  
doing this next step.
On your second machine, type

[siah-tibook:OME/src/xml] josiah% psql ome
Welcome to psql, the PostgreSQL interactive terminal.

Type:  \copyright for distribution terms
        \h for help with SQL commands
        \? for help on internal slash commands
        \g or terminate with semicolon to execute query
        \q to quit

ome=# select * from experimenters where ome_name = 'josiah';
  attribute_id | firstname |          data_dir          | group_id |  
institution |          email           | ome_name | lastname |    
password    | module_execution_id
--------------+-----------+----------------------------+---------- 
+-------------+--------------------------+----------+---------- 
+---------------+---------------------
             1 | Josiah    | /Users/josiah/OME/Datasets |        2 |      
         | josiah at siah-tibook.local | josiah   | Johnston |  
WyDnmgluTbozE |                   1
(1 row)

ome=# insert into lsid_object_map (object_id, namespace, lsid) values  
(1, 'Experimenter', 'urn:lsid:foo.bar.com:Experimenter:123456' );
INSERT 462419 1

Now the second machine has my account registered with the LSID from the  
first machine.



There's a larger question of, "What is appropriate behavior for OME  
when you import someone else's data?" Presumably, OME should preserve a  
recording of original ownership of the data, and allow you to look at  
it. In the current state of access control, this would be most easily  
accomplished using groups.

-Josiah

On Sep 20, 2005, at 6:29 AM, gerhard wrote:

> So here's another question to the OME-XML File. I used the OME
> XML-Export feature and imported than the .ome file to another OME
> server. The dataset in which I saved the .ome file states ...has 5
> Images. But going into dataset detail it states ..Images:(none). Is
> there no convertion back from OME-XML file into the original file (for
> example tiff) on the server.
> If there is no convertion back what I can I do with a dataset  
> containing
> XML Files. I can't even run analyses on them.
>
> Thanks in advance
> gerhard
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