wu-bimac / micrometaapp-omero Goto Github PK

Saving does not work

After performing some snap in place accurately the function fails
See attached link for an example video

https://www.dropbox.com/s/ps2qtp6pc5jqick/Snap%20in%20place%20failure_2020-11-22%20at%2021.26.28.mov?dl=0

Under the hardware explorer the menu for "Cameras" missing at all tier level.

The same issue I was observing earlier today on Electron is now on the OMERO version.
Was it updated?

Is your feature request related to a problem? Please describe.

The current behavior does not allow the distinction between the activity of Microscopy Users vs. Microscopy Custodians.
Thus while Microscopy Custodians should be allowed to create and edit Microscope.JSON files (i.e. hardware configurations), in most cases regular Microscope Users should not be allowed to modify the hardware configuration of a given microscope they are using.
In this scenario, it would be useful to introduce a feature that would allow us to distinguish between a read-only vs a read-and-write behavior of Manage Instrument.

Describe the solution you'd like
Ideally, regular Microscope Users would have only access to a "read-only" version of Manage Instrument while Microscope Custodians would have access to a "read and write" version.
This could be achieved by introducing an initial window offering the option of entering the App in Editor mode vs. Viewer mode.

Describe alternatives you've considered
Another alternative would be to take advantage of OMERO permissions and allow regular users access to Manage Instrument only in read-only mode while administrators would have access to a read-and-write mode.

Describe the bug
A member of a "read-only" group where Microscope.json files are kept to be made available to all users of a facility or a lab, is able to see the read-only group in the "Save in group:" list and is able to successfully save in the group.

Expected behavior
Desired behavior is that members of a "read-only" group where Microscope.json files are kept to be made available to all users of a facility or a lab, should not be able to have write access to the group to avoid over-writing and messing up a given microscope configuration.

To Reproduce
Steps to reproduce the behavior:

• Created "UMMS_PMM_BIG_Microscopy" as a "Read-Only" group

• Created "Microscope_User_Test_Group1" as a full-fledged "Read-Write" group.
• Created "Microscope User1" as a member of both UMMS_PMM_BIG_Microscopy and Microscope_User_Test_Group1 (NOT OWNER).
• Logged in as Microscope_User1
• Launch Manage Instrument in MMA
• Both groups are available as "Load from group" and "Save in group"

• Microscope.json file can apparently be saved in read-only group

When performing

Manage Instrument >> Modality Selector

Create from Scratch and Load from File appear readily but Load from Repository appears wth delay and only after several repeated clicks

I am working on the CBI-Omero instance, which has the MMA plugin installed. The attached screenshots are the errors I get when I attempt to do this linking. I tried with two different images (IDs 8371 and 8145). @stephenogg, @atykwonderland, is it possible for you to access the server and check the actual path of the images? Can you track where are those files? @Akramhar would need to find out if it is a configuration problem of MMA, or something else (e.g. related to Omero version situation).

Is your feature request related to a problem? Please describe.
Currently, if a user attempts to save a Microscope a new MMA_Microscope Project will be created and a copy of the Microscope.JSON file will be created with the same name and ID in the Group.
This will create a conflict with other Microscope.JSON files with the same name that has to be saved by other users.

Describe the solution you'd like
Ideally we will have a SINGLE SHARED Project visible by all users in the group. This would avoid duplication.
In the absence of this provision (which might not be possible in OMERO), one solution is to issue an error upon Save to let Users know that another Microscope with the same name and ID is already available in the Group.

One could even go as far as tell the user that such new file cannot be saved.

Describe alternatives you've considered
Another solution is that Microscope.JSON files are kept outside OMERO in a dedicated repository.

Hi Alex,
Head's up: https://www.openmicroscopy.org/2022/02/18/omeroweb-django-upgrade.html

But hopefully you may not have to do too much to use the updated omero-web when it is released (e.g. see changes for iviewer ome/omero-iviewer#399).

Hi Alex,

thanks for the updated Omero package. I tried to integrate the new version today into our Omero system, but am really struggling with this. I think there are some naming inconsistencies, that might be a problem. I'm again installing the module with "pip install " as I did before.

• the main dir is called "omero_microMetaApp" but the directories below "static" and "templates" are called "microMetaAppOmero" (instead "microMetaApp")
• within apps.py and __init__.py you refer to "omero_microMetaApp" instead "omero_microMetaAppOmero"
• urls.py points to "microMetaAppOmero_index" again
• no matter which of both module names I used for the pip installation, Omero is not started (e.g. omero[7508]: ModuleNotFoundError: No module named 'omero_microMetaApp')

When I changed everything consistent to "omero_microMetaAppOmero" manually, Omero started again, but the MicroMetaApp page keeps blank without any error. @will-moore Do you maybe have a hint for me, how to debug this within Omero to get more information about why the page keeps blank?

Did I miss here something? Any hints on how to get this run again are much appreciated.

BR, Anna

Describe the bug
Not able to open image in OMERO.MMA

To Reproduce
Steps to reproduce the behavior:
Launch Micro-Meta App in OMERO
Select Manage Settings
Enter ID 65753
Continue
Select Microscope
Continue
Select "Load image from repository"
Error (see screen shot + console report

Expected behavior
Open image and proceed

Screenshots

Desktop (please complete the following information):

• OS: [e.g. iOS]: MacOS
• Browser [e.g. chrome, safari]: Firefox
• Version [e.g. 22]: ???

Additional context
Popper: modifier "popoverArrowMargins" provided an invalid "fn" property, expected "function" but got "undefined" 2 validateModifiers.js:42:21
onLoadMetadata micro-meta-app:278:17
Object { Error: "/mnt/BFR/omero/ManagedRepository/riganoa_102/2021-01/22/16-52-27.798/FSWT-6hVirus-10minFIX-stk_4-EPI.ome.tif does not exists." }
micro-meta-app:279:17
Warning: Each child in a list should have a unique "key" prop.

Check the render method of MicroscopeLoader. See https://fb.me/react-warning-keys for more information.
in div (created by MicroscopeLoader)
in MicroscopeLoader (created by MicroMetaAppReact)
in div (created by MicroMetaAppReactContainer)
in MicroMetaAppReactContainer (created by MicroMetaAppReact)
in MicroMetaAppReact (at app.js:1124)
in div (at app.js:1164)
in MicroMetaAppOmeroContainer (at app.js:1118)
in MicroMetaAppOmero react.development.js:276:32
Popper: modifier "popoverArrowMargins" provided an invalid "fn" property, expected "function" but got "undefined" validateModifiers.js:42:21

Change the name of this repository to MicroMetaApp-Omero

When tesm_mma_el_103019.json that had been saved in v0016-1 in Electron was imported into OMERO the positions of components were distributed onto an enormous canvas all over the places

Micro-Meta App on
//omero.tim2023.de/webclient/

When attempting to load image in "Manage Settings":

ERROR
FSWT_6hVirus_10minFIX_stk_4_EPI.tif.ome.tif
Error: /ManagedRepository/caterinas_1078/Blitz-0-Ice.ThreadPool.Server-69/2023-03/20/11-42-38.654/FSWT_6hVirus_10minFIX_stk_4_EPI.tif.ome.tif does not exists.
Select a different image or skip.

Was fixed using a Simulink

So the problem is in the path
it starts from the absolute path of the image repository

MMA generated .JSON files that are attached to images, datasets or projects when downloaded are saved as .csv.
Should be saved as .json or with no extension.

File was deleted from "Microscopes" dataset list.

However, it appears as available on the list of available Microscopes under the "Other" manufacturer list.