---
tags: Tuesday
---

# 2023-04-25

Attending: Will, Frances, Jean-Marie, Andeas, David, Jason, Maadhav, Khaled, Dominik, Melissa, Kyle, Seb, Susanne Kunis, Dom, Petr, Chris, Erin,

Start: 2:00 pm UK

Intros:
Maadhav Kothari - Glencoe, formerly at Zeiss
Susanne - Osnabruk, I3D:bio

## Accepting minutes from [last meeting](https://github.com/ome/meeting-minutes)

## Project Status

(2-3 minutes each)

- IDR (Frances):
- testing data for next submissions, working with authors
- David looking at series ordering in ZarrReader
- converting idr0033 idr0036 and others to NGFF
- Khaled: will present search later (see below)
- [GCDR](https://globalbiodata.org/scientific-activities/global-core-biodata-resources/gcbr-selection-2023/) submission in preparation - see https://drive.google.com/drive/u/0/folders/1bf4xAR7IK4RZCCMRowzWpylDIdlT_V8s

- OMERO (JM):
- migrating repos to remove python 3.7 support
- replace custom portalocker with dependency - failing on Windows
- Andreas: reviewing old PRs
- Will: will need to upgrade node.js on merge-ci at some point, needed for some js upgrades (e.g. omero-parade)
- Seb: Kevin's histogram PR on big images, needs to support old data
- JM: release process should allow anybody to release as needed

- Bio-Formats (David)
- ZarrReader needs few days work to support Fileset swapping
- 6.13 milestone nearly done. Release on Thursday. Lots of dependency updates

- NGFF
- [ngff-histo](https://docs.google.com/document/d/1afMmTqqo1EoUGX76UR7CeknQ4lgcuG2z5m6sVMIScWo/edit#) paper "last call"
- Will: [new script](https://github.com/IDR/idr-utils/pull/54) to create symlinks after in-place import to support import without chunks.

- GerBI
- JM: watched presentation on OMERO at TIM2023 - was success - likely to be adopted elsewhere

- Glencoe (Chris)
- Maadhav started - see above
- Preparing for update to Django 4.2
- Changes are compatible with current Django 3.2
- ABRF meeting - will have booth

- Community (Petr)
- EastBio workshop yesterday - good feedback
- NEUBIAS - 8th May Porto
- Ongoing planning Japan & US trips
- Richard Acton (Developer from HDBR) - preparing workshop setup with Renku
- Jason: UK Digital Reasearch Infrastructure meetings

## AOB

(5 min. max; tech. Discussion should be highlighted to relevant people and rescheduled)

## Main Topic

(20-25 minutes plus 15 minutes questions max)

Khaled search-engine access permissions:

- Elasticsearch indexes key/value pairs
- Currently no authentication - suitable for public data eg. IDR
- Public user Access
- configure public user before indexing
- other data is private
- Auth App
- JSON Web Token (JWT) used for auth
- Token is digitally signed
- JSON payload specifies user_id, user_groups etc.
- Auth App logs into OMERO with user/password
- Creates the JWT with user/groups info
- SearchEngine with Auth App
- Uses the JWT created by Auth App
- Client gets JWT from Auth App and sends it with query to Search Engine
- Implementation
- prototype of Auth app with Flask framework

Discussions:

Chris: with microservices we integrated with OMERO.web to allow single login etc.
Implementation with JWT is hard to maintain security.