---
# System prepended metadata

title: '2023-04-25'
tags: [Tuesday]

---

---
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.


