Hello Reader, here is this month’s iRODS news and developments!

If you’re facing an issue with iRODS you’re not sure how to solve, please do drop me a line; if I’ve come across a solution or seen something relevant elsewhere, I’ll do my best to let you know. Or just drop me a mail to say ‘Hi’. Always nice to hear from people, particularly in these pandemic times!

I’d love your thoughts and feedback on how this newsletter could be better for you.

News

RENCI have been hard at work this month! Lots of releases!

iRODS S3 Resource Plugin v4.2.11.2 is released

​v4.2.11.2.

​changes​

iRODS UGM 2021 Proceedings now available online and in print.

142pp. 40 talks. 11 papers.

​amazon link​

Association of Biomolecular Resource Facilities Annual Meeting

"Join iRODS Executive Director Terrell Russell in-person or virtually at the ABRF 2022 Annual Meeting held March 27 - 30, where attendees will gather to celebrate science, community + resiliency through various workshops + presentations!"

​Association of Biomolecular Resource Facilities Annual Meeting ​

iRODS Automated Ingest v0.4.0 is released

​v0.4.0 inc changelog​

"This release abstracts the scanners, eases deployment by putting the event handler in redis, provides better SSL support, and now requires Python 3.7+."

Python iRODS Client v1.1.2 is released

​v1.1.2​

Big changes I can see is parallel transfer to/from S3 resources and allowing users to change own password, but there are more that might be germane to your use case!.

Reminder - Registration is open for the 2022 iRODS UGM

I shall be there, likely giving a talk, hope to see list readers also! Why not come up and say hi?

​Registration link (MailChimp)​

iRODS C++ REST API v0.9.1 is released

​v0.9.1​

​changes​

Seems to be mainly adding support for changing passwords and ensuring they don’t get accidentally logged anywhere.

iRODS Zone Management Tool (ZMT) v0.2.0 is released

​v0.2.0​

​changes​

Lots of work on this, including health check dashboard (interesting…). I confess I’ve not spun this up yet, probably should. Anyone using it in live/production?

TRiRODS: MinIO-Gateway for iRODS

​Video posted from February TriRODS​

Main Repository Activity

Open Issues

​setup of iRODS with existing non-local service account​

This is AD based, hadn’t hit my installations which are LDAP backed, but then I didn’t try and install fresh and/or with the latest version. Wonder if this will hit when I upgrade?

​rodsadmin user renames folder, orphaning contents​

EEK. Being investigated…

​Remove ASSERT_ERROR and ASSERT_PASS​

​Recursive iget with connection renewal flag set does the opposite of the intended behaviour.​

TL;DR; -T drops the connection, but is probably not required for post 4.2.9(?) installs as they send all data over 1249, so the connection is kept open and renewed.

​irule –test, -t does not enable test mode​

​Can’t execute a long python rule by irule​

Python Rule engine, obvs.

​Database load from mass ingest of files on PostgreSQL​

TL;DR - Ingest of files into a collection with Inherit ACL’s set means a non-optimised (for PostgreSQL at least) query can cause the database to do more work than needed, which can add up when you do lots of uploads.

​Reorganization: split lib/core​

"Post-#6201, we build three sets of targets from lib/core:
irods_common_core - an object library target.
irods_plugin_dependencies - a shared library
    irods_plugin_dependencies_obj - an object library target
irods_lib_core_client/irods_lib_core_server - two object library targets compiled using the same source files with different defines.
Given that these targets have a substantial number of source files, we should split these up into their own directories. "

​Add config option to irods_environment.json that defines default number of threads to request​

"This would be the equivalent of manually setting -N for iput/iget.
Option name: irods_default_number_of_transfer_threads"

​add delay server memory usage, default to server_config.json on upgrade​

If I am reading this correctly, if you upgrade to 4.2.11, the upgrade script doesn’t set (It should have a default value of 0 (unlimited)). When not set, this produces an error in the rodsLog.

So something to be aware of if you are upgrading to 4.2.11.

​Weird packaging message for CentOS 7​

4.2.12 in-progress build artefact for RPM’s.

​Non-admins should not be allowed to run iadmin lg​

Hmm. Yes, but also, since once can get the same information from an iquest…

Closed Issues

Closed on - 2022-02-24 14:49:18 ils -A on a data object does not include g: prefix for groups​

This will be fixed in 4.1.12, and was working in 4.1.10, so perhaps broke in 4.1.11 or 4-2-stable branch?

Closed on - 2022-02-24 14:47:04 rx_atomic_apply_acl_operations() does not consider group permissions​

Closed on - 2022-02-24 14:46:39 rx_atomic_apply_metadata_operations() does not consider group permissions​

Closed on - 2022-02-23 15:26:46 Deprecate and all APIs that support it​

"After imeta grows support for the admin mode option (-M), the subcommand adda will not be needed because imeta -M add accomplishes the same thing."

Closed on - 2022-02-21 19:07:35 functionality can be invoked by non-admins](https://github.com/irods/irods/issues/6183)

It’s probably fine, but… :-)

Closed on - 2022-02-21 22:12:18 does not support relative paths](https://github.com/irods/irods/issues/6174)

Closed on - 2022-02-21 19:17:13 Add admin flag (-M) to imeta​

Closed on - 2022-02-21 19:04:43 Cannot remove expiration time from ticket (possible regression)​

Not clear when this was a regression - 4-2-stable seems likely.

Closed on - 2022-02-21 19:10:19 Creation of 64 byte user names is allowed, even though they cause issues​

Closed on - 2022-02-18 14:46:52 Prevent checksum verification in sync-to-archive operations​

Closed on - 2022-02-21 19:10:10 itree fails with exception on relative path ‘..’ or ‘../some/path’​

Closed on - 2022-02-23 20:25:31 Resource redirect is wrong if resource hostname contains current hostname as substring ​

Closed on - 2022-02-28 13:10:41 irods breaks MySQL 8 GTID replication​

If you use MySQL GTID replication and are affected by this, and can’t wait for 4.2.12, the ticket author also pointed to how they were able to patch it - but it sounds like it requires rebuilding iRODS.

Closed on - 2022-03-10 14:00:45 remove iphybun​

Marked for deprecation, and gone in 4.3.0.

Closed on - 2022-02-23 21:42:05 add -r option to ireg​

Python iRODS Client Activity

Closed Issues

Closed on - 2022-03-09 17:35:29 Fix possible infinite loop in _recv_message_in_len()​

Closed on - 2022-03-07 19:24:01 anonymous cannot access APIs if logged in without environment​

Closed on - 2022-03-10 23:52:18 Update connection disconnect logic. ​

Closed on - 2022-02-28 13:36:57 allow parallel transfer to/from S3 storage​

A biggie if you have an S3 Resource back end!

Closed on - 2022-02-19 03:42:05 Use ‘-R’ to identify resource type and ‘-C’ to identify collection in AVU operations​

Closed on - 2022-03-03 14:24:31 Allow a rodsuser to change passwords à la “ipasswd”​

Closed on - 2022-02-18 15:39:47 Trailing slash in path gives python irods error while the same path works using icommands​

Closed on - 2022-03-07 19:22:47 Exception ignored upon iRODSSession clean-up​

NFSRODS Activity

None this month.

icommands Activity

Open Issues

​iquest reads query from stdin​

"When scripting with iquest in bash, it would be nice to be able to use iquest with heredocs. This allows complex queries to span multiple lines without having to add a lot of escape characters. This improves readability."

​iquest silent when no results​

"It would be nice if iquest were silent when the query yields no results. At the moment, it responds with CAT_NO_ROWS_FOUND: Nothing was found matching your query/ This makes it hard to script with iquest. When iterating over a result set, this value needs to be filtered out to prevent the script from failing in a weird way when the result set is empty."

​iquest parses queries with tabs in the where clause incorrectly.​

"Where there is a horizontal tab in the where clause of a generalized query, iquest doesn't return any results. "

​some rule file tests failing​

externals Activity

Closed Issues

Closed on - 2022-03-13 02:11:42 update libs3 for timeout after slow multipart​

YODA Activity

Closed Issues

Closed on - 2022-02-24 09:55:37 [BUG] error message when you click on the “Update” button of a group without changing anything​

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