Reference

usage: ibridges [-h]
                {ls,list,l,pwd,tree,meta-list,meta-add,meta-del,mkcoll,download,upload,search,cd,rm,remove,del,sync,shell,alias,init,setup,gui}
                ...

Positional Arguments

subcommand: Possible choices: ls, list, l, pwd, tree, meta-list, meta-add, meta-del, mkcoll, download, upload, search, cd, rm, remove, del, sync, shell, alias, init, setup, gui

Sub-commands

ls (list, l)

List a collection on iRODS.

ibridges ls [-h] [-m] [-s] [-l] [remote_coll]

Positional Arguments

remote_coll

Path to remote iRODS location starting with ‘irods:’

Default: “.”

Named Arguments

-m, --metadata

Show metadata for each iRODS location.

Default: False

-s, --short

Display available data objects/collections in short form.

Default: False

-l, --long

Display available data objects/collections in long form.

Default: False

Examples:

> ibridges ls > ibridges ls irods:some_collection

pwd

Show current working collection.

ibridges pwd [-h]

Examples:

> ibridges pwd

tree

Show collection/directory tree.

ibridges tree [-h] [--show-max SHOW_MAX] [--ascii] [--depth DEPTH]
              [remote_coll]

Positional Arguments

remote_coll

Path to collection to make a tree of.

Default: “.”

Named Arguments

--show-max

Show only up to this number of dataobject in the same collection, default 10.

Default: 10

--ascii

Print the tree in pure ascii

Default: False

--depth

Maximum depth of the tree to be shown, default no limit.

Examples:

> ibridges tree > ibridges tree irods:some_collection

meta-list

List the metadata of a data object or collection on iRODS.

ibridges meta-list [-h] [remote_path]

Positional Arguments

remote_path

iRODS path for metadata listing, starting with ‘irods:’

Default: “.”

Examples:

> ibridges meta-list > ibridges meta-list irods:remote_collection

meta-add

Add a metadata item to a collection or data object.

ibridges meta-add [-h] remote_path key value [units]

Positional Arguments

remote_path

Path to add a new metadata item to.

key

Key for the new metadata item.

value

Value for the new metadata item.

units

Units for the new metadata item.

Default: “”

Examples:

> ibridges meta-add irods:some_dataobj_or_collection new_key new_value new_units

meta-del

Delete metadata for one collection or data object.

ibridges meta-del [-h] [--key KEY] [--value VALUE] [--units UNITS]
                  [--ignore-blacklist]
                  remote_path

Positional Arguments

remote_path: Path to delete metadata entries from.

Named Arguments

--key

Key for which to delete the entries.

Default: Ellipsis

--value

Value for which to delete the entries.

Default: Ellipsis

--units

Units for which to delete the entries.

Default: Ellipsis

--ignore-blacklist

Ignore the metadata blacklist.

Default: False

Examples:

> ibridges meta-del irods:remote_dataobj_or_coll > ibridges meta-del irods:remote_dataobj_or_coll –key some_key > ibridges meta-del irods:some_obj –key some_key –value some_val –units some_units

mkcoll

Create a new collecion with all its parent collections.

ibridges mkcoll [-h] remote_coll

Positional Arguments

remote_coll: Path to a new collection, should start with ‘irods:’.

Examples:

> ibridges mkcoll irods:~/test

download

Download a data object or collection from an iRODS server.

ibridges download [-h] [--overwrite] [--resource RESOURCE] [--dry-run]
                  [--metadata [METADATA]]
                  remote_path [local_path]

Positional Arguments

remote_path

Path to remote iRODS location starting with ‘irods:’

local_path

Local path to download the data object/collection to.

Default: /home/docs/checkouts/readthedocs.org/user_builds/ibridges/checkouts/v1.5.1/docs/source

Named Arguments

--overwrite

Overwrite the local file(s) if it exists.

Default: False

--resource

Name of the resource from which the data is to be downloaded.

Default: “”

--dry-run

Do not perform the download, but list the files to be updated.

Default: False

--metadata

Path for metadata

Examples:

> ibridges download irods:~/test.txt > ibridges download irods:~/some_collection

upload

Upload a data object or collection from an iRODS server.

ibridges upload [-h] [--overwrite] [--resource RESOURCE] [--dry-run]
                [--metadata [METADATA]]
                local_path [remote_path]

Positional Arguments

local_path

Local path to upload the data object/collection from.

remote_path

Path to remote iRODS location starting with ‘irods:’

Default: “.”

Named Arguments

--overwrite

Overwrite the remote file(s) if it exists.

Default: False

--resource

Name of the resource to which the data is to be uploaded.

Default: “”

--dry-run

Do not perform the upload, but list the files to be updated.

Default: False

--metadata

Path for metadata

Examples:

> ibridges upload local_file.txt > ibridges upload local_file.txt irods:remote_collection > ibridges upload local_dir irods:remote_collection

search

Search for dataobjects and collections.

ibridges search [-h] [--path-pattern PATH_PATTERN] [--checksum CHECKSUM]
                [--metadata METADATA [METADATA ...]] [--item_type ITEM_TYPE]
                [remote_path]

Positional Arguments

remote_path

Remote path to search inn. The path itself will not be matched.

Default: “.”

Named Arguments

--path-pattern: Pattern of the path constraint. For example, use ‘%.txt’ to find all data objects and collections that end with .txt. You can also use the name of the item here to find all items with that name.
--checksum: Checksum of the data objects to be found.
--metadata: Constrain the results using metadata, see examples. Can be used multiple times.
--item_type: Use data_object or collection to show only items of that type. By default all items are returned.

Examples:

> ibridges search –path-pattern “%.txt” > ibridges search –checksum “sha2:5dfasd%” > ibridges search –metadata “key” “value” “units” > ibridges search –metadata “key” –metadata “key2” “value2” > ibridges search irods:some_collection –item_type data_object > ibridges search irods:some_collection –item_type collection

cd

Change current working collection for the iRODS server.

ibridges cd [-h] [remote_coll]

Positional Arguments

remote_coll

Path to remote iRODS location.

Default: “~”

Examples:

> ibridges cd > ibridges cd irods:some_collection

rm (remove, del)

Remove collection or data object.

ibridges rm [-h] [-r] remote_path

Positional Arguments

remote_path: Collection or data object to remove.

Named Arguments

-r, --recursive

Remove collections and their content recursively.

Default: False

Examples:

> ibridges rm irods:~/test.txt > ibridges rm -r irods:~/test_collection

sync

Synchronize files/directories between local and remote.

ibridges sync [-h] [--dry-run] [--metadata [METADATA]] source destination

Positional Arguments

source: Source path to synchronize from (collection on irods server or local directory).
destination: Destination path to synchronize to (collection on irods server or local directory).

Named Arguments

--dry-run

Do not perform the synchronization, but list the files to be updated.

Default: False

--metadata

Path for metadata

Examples:

> ibridges sync local_dir irods:remote_collection > ibridges sync irods:remote_collection local_dir

shell

Shell for ibridges commands with autocomplete

ibridges shell [-h]

alias

Print existing aliases or create new ones.

ibridges alias [-h] [--delete] [alias] [env_path]

Positional Arguments

alias: The new alias to be created
env_path: iRODS environment path.

Named Arguments

--delete, -d

Delete the alias.

Default: False

Examples:

> ibridges alias some_alias ~/.irods/irods_environment.json > ibridges alias other_alias –delete

init

Create a cached password for future use.

ibridges init [-h] [irods_env_path_or_alias]

Positional Arguments

irods_env_path_or_alias: The path to your iRODS environment JSON file.

Examples:

> ibridges init > ibridges init ~/.irods/another_env_path.json > ibridges init some_alias

setup

Use templates to create an iRODS environment json.

ibridges setup [-h] [--list] [-o OUTPUT] [--overwrite] [server_name]

Positional Arguments

server_name: Server name to create your irods_environment.json for.

Named Arguments

--list

List all available server names.

Default: False

-o, --output

Store the environment to a file.

Default: /home/docs/.irods/irods_environment.json

--overwrite

Overwrite the irods environment file.

Default: False

Examples:

> ibridges setup some-servername -o ~/.irods/some_server.json

gui

Start the iBridges GUI.

ibridges gui [-h]

Examples:

> ibridges gui gui