Open Microscopy Environment

I am testing the functionality of our newly installed OMERO server and OMERO web. Currently i have tried to run a few of the python scripts. However, i am getting an error that says that the process created the image or file, but that it could not be attached. I am not certain what this warning means - but I am able to click on the link and download the file. How can i fix this message so it is not confusing for the user?

Also, i am having trouble understanding where these newly created files are stored on the server. I have tried to look under the the managed data directory, but was unable to find. Could you help point me in the right direction?

Thank you!

Dear Cassie

Thank you very much for contacting us.

The message "Batch export zip created but could not be attached." is caused by the fact that the OMERO user which executed the script is not permitted to annotate/attach files to images of somebody else.
This might occur in situations like
1. Administrator or Group owner in private group tries to Batch image export images of somebody else in that group
2. A member of a read-only group tries to Batch image export images of some other member of that group.

I am not sure we want to suppress tha message, as it is correctly indicating an important fact. We can discuss this point further though if you wish so.

This message will never happen if the user is working on their own data. In that case, a dialog will appear, with a message such as "Batch export zip created and attached to image FURA2-2CH-T.tif." In that message, there will be also 3 icons (not just 2 as in the case with no attachment permitted). If you click on the left-most icon, you will be navigated to the image you tried to export. After this, click on the "Attachments" in the right-hand pane, and see the exported zip attached to that image.
In case the attachment did not happen, the exported file is indeed on the OMERO.server as an OriginalFile, which is not attached to anything. I can give you a query which would help you to find that file via hql if you wish so.

In general, being aware of this problematics with export/download workflows, we came up with omero-downloader. This application can do what the Batch image export can do, but will not produce errors of the kind we are discussing here. Please see https://github.com/ome/omero-downloader/releases and https://github.com/ome/omero-downloader (scroll down to read the README on that page)

Hope this helps

Please do not hesitate to come with any further questions

All the best

Petr

Petr Walczysko

OME Team

Dear Cassie,

Further to what I have written in the previous post.
In your workflow, are you interested more in Export (such as exporting single planes of images as png, jpeg or tiff images, this is what Batch image export script does) ?
Or are you more interested in Downloading the original image files in their original formats (this is what omero-downloader does, and also we have a menu item in the OMERO.web and OMERO.insight clients for this ?

Hope this is not too confusing,

Very happy to continue this discussion

All the best

Petr

Petr Walczysko

OME Team