Open Microscopy Environment

then, if I copy the current etc/grid/config.xml after I unpack the zip file to the corresponding location, and run bin/omero admin start, my server runs correctly without losing any previous data in the server?

BK

Hi BK,

it shouldn't be possible for you to lose any data if you are pointing to the same omero.data.dir (e.g. "/OMERO") and to the same PostgreSQL database ("omero") after the upgrade, which is what config.xml is for.

~Josh.

Hi All,

From our server (4.2.1), I still cannot retrieve images by querying for Attachment.

As I said, I attached an Experiment File ((output001.cpe.xml like the image below 002.jpg) to an image.
That experiment file is like image 003.jpg.

after this, I tried to search by "Glass" (004.jpg), but still could not retrieve anything.
Do you have any Idea?

And it's strange that I cannot find the attachment file in the Experiments nor in the Protocols from Attachments tab). those files are categorized as "Other files".


Best,
BK

Would it be possible to get a database dump and a copy of the experiment file, BK? Also, did you add the file after upgrading to 4.2.1 or before?

~J.

Hi J,

I dont know how to get the database dump. could you tell me how?
I generated that xml file from my local machine and linked it via OMERO.Insight.
Right after that, I could see the file is attached in the "Protocols and Experiments" in the right section of Insight.
However, I could not see the details of the xml file.
So, I open it by clicking the button (a pencil and some dots) and save it as (to server). Then I can found that attachment file as "Experiments" in the "Attachments" tab in the left section of Insight.
And then If I attach that "Experiment" file by selecting from "Uploaded Document", then I now could see the details of the xml file in the "Protocols and Experiments" tab. BUT, as I mentioned before, it does NOT show everything (it shows until some part).

I attached that xml file here.

I added the file after upgrading our server.

BK

Depending on how you connection to your database, you need something like this:

Code: Select all

pg_dump -U omero omero > omero-db.sql


~J.

Hi J,

the size of the dump is too big to upload to here. (15M)
could you tell me other way to send this to you?

BK

Is that 15M compressed, BK? I can probably handle 15M via either email address, but if you could compress it that would be great.

Cheers,
~Josh

I sent you by email after zipping.

BK

Got it. I'll take look and get back to you tomorrow. ~J.