WU-BIMAC / MicroMetaApp-Omero

This is a limited-functionality, beta - implementation of the integration of Micro-Meta App in the OMERO.web client
GNU General Public License v3.0
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Error when trying to attach MMA hardware and setting files to one particular image in OMERO. #44

Open JSDLacoste opened 11 months ago

JSDLacoste commented 11 months ago

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).

stephenogg commented 11 months ago

Image with ID 8371

The web client reports this file to be at: judithlacoste_552/2022-10/14/18-48-56.721/CHUM_CR_R12802_SDTIRF_coreg_2018_05_04_mai_40X_fovB.czi

SSH to the server and listing the files to get ownership and permissions at that location gives me this:

@.***:/OMERO/ManagedRepository/judithlacoste_552/2022-10/14/18-48-56.721$ ls -lsh total 403M 403M -rw-rw-r-- 1 omero-server managed_repo_group 403M Oct 14 2022 CHUM_CR_R12802_SDTIRF_coreg_2018_05_04_mai_40X_fovB.czi

Image with ID 8145

The web client reports this file to be at: judithlacoste_552/2022-10/07/13-23-22.256/CHUM_CR_sdTIRF_2020_04_09_Green_fwhm_100X_emccd_fovB.czi

SSH to the server and listing the files to get ownership and permissions at that location gives me this:

@.***:/OMERO/ManagedRepository/judithlacoste_552/2022-10/07/13-23-22.256$ ls -lsh total 51M 51M -rw-rw-r-- 1 omero-server managed_repo_group 51M Oct 7 2022 CHUM_CR_sdTIRF_2020_04_09_Green_fwhm_100X_emccd_fovB.czi

@Judith @.***> is this the information you require?

Best, Steve

From: Judith LACOSTE @.> Date: Wednesday, 13 December 2023 at 21:56 To: WU-BIMAC/MicroMetaApp-Omero @.> Cc: Stephen C. Ogg @.>, Mention @.> Subject: [EXTERNAL] [WU-BIMAC/MicroMetaApp-Omero] Error when trying to attach MMA hardware and setting files to one particular image in OMERO. (Issue #44)

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). @stephenogghttps://urldefense.com/v3/__https:/github.com/stephenogg__;!!Nmw4Hv0!xOb3F6Urw_lcnUX11PHIEm1ihtHs4RQk5t-orLBTwF_hzNuaTU6Khg0x-KssbuHKrb-Zu6Jix05fKFMdrwZDSEqcMgerAm8$, @atykwonderlandhttps://urldefense.com/v3/__https:/github.com/atykwonderland__;!!Nmw4Hv0!xOb3F6Urw_lcnUX11PHIEm1ihtHs4RQk5t-orLBTwF_hzNuaTU6Khg0x-KssbuHKrb-Zu6Jix05fKFMdrwZDSEqcEjEiqjE$, is it possible for you to access the server and check the actual path of the images? Can you track where are those files? @Akramharhttps://urldefense.com/v3/__https:/github.com/Akramhar__;!!Nmw4Hv0!xOb3F6Urw_lcnUX11PHIEm1ihtHs4RQk5t-orLBTwF_hzNuaTU6Khg0x-KssbuHKrb-Zu6Jix05fKFMdrwZDSEqc-Uo_oy0$ would need to find out if it is a configuration problem of MMA, or something else (e.g. related to Omero version situation).

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Akramhar commented 11 months ago

@JSDLacoste I think the screenshot is missing. @stephenogg yes, thank you very much.

In both cases the plugin report the image to be @ ./ManagedRepository/path-to-the-image and it should be working inside the OMERO directory. Once Judith attaches the screenshot I can double check the path returned by the plugin and see if there is any major difference.

JSDLacoste commented 11 months ago

Screenshot from 2023-12-13 13-36-56_8145 Screenshot from 2023-12-13 13-29-57_8371

JSDLacoste commented 11 months ago

Thanks a lot @stephenogg and @Akramhar, let me know if there is anything else I can do.