Thursday, 2024/03/21
10:00 am ET
Terrell Russell, Alan King, Judith Lacoste (MIA Cellavie), Nirav Merchant (CyVerse / UArizona), Tobias Gottschall (NFDI4bioimage @ Leibniz Institute for Neurobiology Magdeburg), Caterina Strambio-De-Castillia (UMass Medical School), Mike Conway (NIEHS)
- Serialization of OMERO to (and from!) iRODS via PRC
- https://github.com/irods-contrib/irods_working_group_imaging/pull/30/files
- Save/Export
- Added overwrite protection
- Confirmed Exceptions are logged by OMERO
- Added as_user proxy to script
- Need to use a mapping file instead
- OMERO users -> iRODS users
- Need to use a mapping file instead
- Load/Import
- Added transfer_from_irods
- Don't know the OMERO call/syntax for writing, yet
- AbsorbRawFile
- Would have to go through the bioformats importer®
- parse/identify the file itself and header information
- Haven't done this yet
- Expect this to 'just work' for small files
- Large files would take more temporary/staging space / impossible
- Would have to go through the bioformats importer®
- Guillaume repository/project
- https://gitlab.in2p3.fr/fbi-data/omero-quay
- Potentially launching soon
- Syncing still in the pictures - NFSRODS
- Testing
- Tobias - irodsfs (fuse) mounted into the OMERO container
- Easy to set up - but did not solve the use cases since there are still two databases tracking the file information
- OMERO still has its own copy of the data (duplicate from what is in the iRODS logical paths)
- Tobias - irodsfs (fuse) mounted into the OMERO container
- Tobias - Question - regarding user mapping
- why not have both systems use a similar database - do the matching in SQL
- Ground truth is in LDAP and via shibboleth (the 'easy' case)
- Tobias - working to store PIDs to allow external/agnostic LIMs systems
- https://www.elabftw.net/
- https://www.researchspace.com/ - recently open sourced
- https://github.com/open-lims/open-lims
- Next Meeting
- April 2024