ii

ii - Command line utilities for iRODS

Summary

ii is a collection of commandline utilities for iRODS. The current version is a functional prototype, in the sense that the interface is still subject to change and that it hasn't been tested extensively yet.

Requirements and installation

ii supports Python 3.6 and higher. It has currently been tested with iRODS 4.2.7. The eventual goal is to support all recent iRODS versions.

If you want to try it out, you can install it in a virtualenv:

virtualenv --no-site-packages --python /usr/bin/python3 venv
source venv/bin/activate
pip3 install --upgrade git+https://github.com/UtrechtUniversity/ii.git

Commands

ii cd

Equivalent to the icd command in the iCommands. Changes the current working directory. If no argument is given, it goes back to the home directory.

usage: ii cd [-h] [--verbose] [directory]

positional arguments:
  directory      Directory to change to

optional arguments:
  -h, --help     show this help message and exit
  --verbose, -v  Print verbose information for troubleshooting

ii find

Finds data objects, and returns names of data objects matching the specified properties. The basic idea is similar to the Unix find command.

usage: ii find [-h] [--verbose] [--print0] [--dname DNAME]
               [--owner-name OWNER_NAME] [--owner-zone OWNER_ZONE]
               [--resc-name RESC_NAME] [--minsize MINSIZE] [--maxsize MAXSIZE]
               [--size SIZE]
               [queries [queries ...]]

positional arguments:
  queries               Collection, data object or data object wildcard

optional arguments:
  -h, --help            show this help message and exit
  --verbose, -v         Print verbose information for troubleshooting
  --print0, -0          Use 0 byte delimiters between results
  --dname DNAME         Wildcard filter for data object name
  --owner-name OWNER_NAME
                        Filter for data object owner name (excluding zone)
  --owner-zone OWNER_ZONE
                        Filter for data object owner zone
  --resc-name RESC_NAME
                        Filter for data object resource
  --minsize MINSIZE     Filter for minimum data object size (you can
                        optionally use human-readable sizes, like "2g" for 2
                        gigabytes)
  --maxsize MAXSIZE     Filter for maximum data object size (you can
                        optionally use human-readable sizes, like "2g" for 2
                        gigabytes)
  --size SIZE           Filter for (exact) data object size (you can
                        optionally use human-readable sizes, like "2g" for 2
                        gigabytes)

ii ls

Equivalent to the ils command in the iCommands. Lists data objects or collections.

usage: ii ls [-h] [--verbose] [-m {plain,json,csv,yaml}]
             [-s {name,ext,size,date,unsorted}] [-H {default,yes,no}]
             [--recursive] [-l] [-L]
             [queries [queries ...]]

positional arguments:
  queries               Collection, data object or data object wildcard

optional arguments:
  -h, --help            show this help message and exit
  --verbose, -v         Print verbose information for troubleshooting
  -m {plain,json,csv,yaml}, --format {plain,json,csv,yaml}
                        Output format
  -s {name,ext,size,date,unsorted}, --sort {name,ext,size,date,unsorted}
                        Propery to use for sorting
  -H {default,yes,no}, --hr-size {default,yes,no}
                        Whether to print human-readable sizes
                        [yes,no,default].By default, enable human-readable for
                        text output, disable for other formats.
  --recursive, -r       Include contents of subcollections
  -l                    Display replicas with size, resource, owner, date
  -L                    like -l, but also display checksum and physical path

ii pwd

Equivalent to the ipwd command in the iCommands. Prints the current working directory.

usage: ii pwd [-h] [--verbose]

optional arguments:
  -h, --help     show this help message and exit
  --verbose, -v  Print verbose information for troubleshooting

Known limitations

• ls command: sorting only has effect for the contents of collection arguments (e.g. ii ls .), but not for other arguments (e.g. ii ls "*" or ii ls foo.dat bar.dat baz.dat).
• ls command: human-readable output is not yet supported for JSON and YAML output.
• ls command: this command currently supports dataobject-only wildcards (e.g. *.dat), but not yet wildcards with collection names (e.g. foo/*.dat or */foo.dat).