ICAT Project


Meeting 116 – 26th April 2018


Brian (BR), Chris (CP), Silvie (SR), Stuart (SP), Rolf (RK), Milan (M), Andy (AG), Maxime (MC)

Actions from previous

102.2 – BR still working on this.

113.1 – Stuart hasn’t managed to do this. Is having issues with python script used to test performance of IDS queries.

113.2 – Catherine to organise the topcat development meeting, Stuart will follow up on this.

115.1 – Stuart didn’t see any pressing issues, i.e. issues that are causing significant problems and need fixing immediately.

115.2 – Brian has closed many tickets, most of them no were longer required.

115.3 – Schema changes timetable not done but discussion in this meeting about two smaller changes.

ICAT Components

Server (SP) – Alex reported timer issue in glassfish which required redeployment. Brian found configuration setting in Payara that means the timers would be restarted rather than expunged if they fail. Stuart will test this configuration change to Payara actually fixes the issue and will add it to the setup-glassfish.py script. Stuart also notes that the setup-glassfish script isn’t in version control so he will be adding this.

Topcat (BR) – Brian created 2.4.0 snapshot that he would like testing. The only change since then is missing lang.json.example items. Stuart will test on Diamond pre-production and Jamie will test on ISIS pre-production. Brian notes to be aware of the changes to topcat.properties  when upgrading.

IJP (BR) – Brian reviewed in-progress issues in waffle.io and closed most of them. Reports that ** **IJP job to SCARF no longer works due to problem with platform LSF.

IDS (RK) – Snapshot released and no feedback received yet. Waiting for Stuart to test the database performance.

Site Updates

Diamond (CP) – Double the volume of diamond user recalls over the last two weeks has caused problems. Issue with recalls taking too long to complete, timing out and falling into an expired state. Also because the IDS’s are under heavy load with CPU and disk usage being very high the test they run every 20 minutes is failing. Andy Gotz expressed interest in Diamonds test script so Stuart says he will share it as it may be useful for others.

ESRF (AG and MC) – Only issue has been topcat download/timer issue already discussed. ESRF have DOI landing pages now but asked about anonymous downloads. Rolf explains anonymous auth plugin, rules and topcat config of anonymous plugin is all that’s required. MC has written up requirements for logbook that will work closely with ICAT and will share when complete. AG also reports that their cyroEM is fully integrated into ICAT.

Waffle.IO tickets

‘Ready’ tickets should be for issues that are ready to be worked on. If an issue is ‘In progress’ the ticket assignee should be prepared to talk about it at the next monthly meeting.

Stuart has added two new issues to Ready. Adding setup-glassfish script into version control and testing the Payara configuration option to stop timers being expunged.

Silvia reported she made some changes to the IDS specific to Diamond. Rolf says she can create a PR to be reviewed.

Stuart asked about python 2.7 end of life, Rolf confirms that python-icat works with python 3. Stuart says he will look at getting the setup scripts python 3 compatible.

Schema Changes

Stuart reported he’s going to start with non-controversial additive changes, their presence shouldn’t affect anyone who doesn’t want to use them.

No one objected to adding persistent identifiers to Instruments. Stuart asked if 255 characters are enough, Rolf has never seen a persistent identifier that is longer than 255. Stuart asked what the update should be called and it’s agreed to at least be a minor number change since it’s a schema change.

There’s some discussion regarding the creation of an optional shift to instrument relation but the meeting is cut short so no firm decision is made.


Item Description Assigned
102.2 Produce new releases of IJP components Brian Ritchie
113.1 Look at Rolfs IDS Server and IDS Plugin pull request Stuart Pullinger
113.2 Organise a meeting for thediscussion of a Topcat replacement Catherine Jones
115.3 Create a timetable for discussions of schema changes Stuart Pullinger
116.1 Test Topcat 2.4.0 snapshot on ISIS and diamond Jamie and Stuart
116.2 Share diamond download test script. Stuart
116.3 Look at converting setup scripts to python 3 Stuart

Next meeting scheduled for Thursday 24th May, 3pm UK time.