clj-irods

A Clojure library wrapping clj-jargon and clj-icat-direct for a unified, hopefully performant, interface to IRODS.

Testing from the REPL

This library is configured to add the path ./repl to the source file search path in REPL mode, so that developers can easily test using the Clojure REPL. To use this feature, first create four files: $HOME/.irods/.qa-db.json and $HOME/.irods/.qa-jargon.json for QA, and $HOME/.irods/.prod-db.json and $HOME/.irods/.prod-jargon.json for production. Note that these files will contain sensitive connection information for iRODS. Be sure to set the file permissions accordingly. The two database configuration files should look like this:

{
    "host": "icat.example.org",
    "port": 5432,
    "user": "somedbuser",
    "password": "somedbpassword"
}

The two Jargon configuration files should look like this:

{
    "host": "somehost.example.org",
    "zone": "example",
    "port": "1247",
    "user": "someuser",
    "password": "S0m3-P@$$w0rd",
    "home": "/example/home",
    "resource": "",
    "max-retries": 10,
    "retry-sleep": 1000,
    "use-trash": true
}

Once you have the files in place, you can easily prepare the REPL for accessing iRODS by calling either init-prod or init-qa from clj-irods.repl-utils:

user=> (require '[clj-irods.repl-utils :as ru])
nil

user=> (def prod-jargon (ru/init-prod))
#'user/prod-jargon

Once the REPL is configured to access iRODS, you can make calls to other functions in clj-irods as usual:

user=> (require '[clj-irods.core :refer :all])
nil

user=> (with-irods {:jargon-cfg prod-jargon} irods
        @(permission irods "a" "example" "/example/home/a"))
;; log output omitted
:own

During testing, it can sometimes be useful to indicate that you explicitly want to use either the ICAT or Jargon. Explicitly using the ICAT is easy; all you have to do is omit the Jargon configuration from the call to with-irods:

user=> (with-irods {} irods
        @(permission irods "a" "example" "/example/home/a"))
;; log output omitted
:own

Explicitly using Jargon requires you to pass a special configuration option to with-irods:

user=> (with-irods {:jargon-cfg prod-jargon :use-icat false} irods
        @(permission irods "a" "example" "/example/home/a"))
;; log output omitted
:own

The repl directory is also included in .gitignore so that you can add additional namespaces to it without having to worry very much about accidentally including them in a commit. This can be very helpful if you have an editor that can interactively run Clojure code.