ICAT Project


ICAT Collaboration Meeting - 29th June 2023


  • Patrick
  • Nicolas Soler
  • Rolf Krahl
  • Louise
  • Allan Pinto
  • Alexander
  • Alejandra
  • Marjolaine


  • Alex de Maria (ESRF)
  • Andy Goetz (ESRF)
  • Kevin
  • Malik
  • Gabriel Preuß

Site Updates

ESRF (Marjolaine):

Busy with 3-days visit from DLS people on Thursday

  • Spoke a lot about data management

Alex spoke at ispyb collab meeting about putting their data into ICAT DB Working on generic sample tracking for all beamlines (merging ISPyB and ICAT sample tracking) Had corrupted Etherpad files, have removed from frontend and placed it on standby (deployed, but hidden from users)

HZB (Rolf):

Cyber attack two weeks ago, "everything is down" (including email)

  • Lots of Windows PCs have been infected, encrypting files
  • No known instances of Linux machines being affected - confident about the data infrastructure
    • But no way to check
  • Forensic experts are currently investigation, rumoured to be a matter of weeks before bringing things back

Would be interested in meeting re: logbooks

ALBA (Nicolas)

In process of implementing ICAT on beamline Desigining the metadata that should be uploaded to ICAT Also exploring the logbook (will need ICAT+ API)

Sirius (Allan)

Not too much to report Deciding on data format for tomographic beamlines (already have it for other domain) Then will begin ingest, play around with project and try to understand the components Want to test:

  • Kubernetes (hope to have feedback by next meeting) - looking at ALBA's solution


Don't think Will Taylor has been able to work on this recently


Effort migrating tape archive from castor to CTA Pre-prod installation for Payara6

  • Alan has been making releases for this

ICAT 6 / Payara 6

  • Want to encourage adoption of Payara6 (for security concerns and to avoid having to support multiple versions)
    • HZB: soonish
    • ESRF: no plan yet, TBD
    • Sirius: using 5
    • ALBA: don't know
  • Deadline for moving? TBD via mailing list or in future meeting

Component Updates


More or less ready for 1.1 release:

  • Provides an IngestReader, which was implemented in HZB specific code before and is now moved into main python-icat codebase
  • Few minor fixes

Q: Do we want a snapshot, or release outright (do not expect compatibility issues)?

  • DG-API pins the version, so we can test afterwards
  • Direct release is fine

Expect tomorrow or next week

Logbooks (timestamped version)

Interest from multiple facilities HZB working on making it suitable for multiple facilities

  • Ideally want to push changes upstream to ESRF
    • Need to tweak things which are "hardcoded" to ESRF logic, this is the main effort currently, making them configurable
  • Using the DataHub verson, not the standalone version

ESRF working on the DataPortal version too, one item of the plan is to make it standalone version (not clear when)

Notebooks (Etherpad version)

STFC student has been adapting the permissions and work on endpoint, use DG-API or speak with ICAT server. Concerns of the corruptions of pads, under investigation. Other concern is suitability of Etherpad due to the lack of updates. There has been some activitiy in the repository. There are some alternatives:

Permissions would be configurable. ESRF - they haven't had time to investigate a lot but scientists complain because when they entered images or tables, it wasn't working.


Sample tracking

Question from Allan - information per sample might be different for each group wanting to implement sample tracking, is it better to implement a standalone solution?

  • ESRF have ICAT(+) (for all beamlines) and ispyb (for MX) and are trying to merge these
  • Have a configuration (processing plan) for each beamline
  • Interface retrieves config and displays the relevant column
  • Generic (configurable) solution

Currently collating the information from the three interested groups, will reach out in the future.


Availability for July/August meetings?