Frequently Asked Questions

When should I use iBridges instead of python-irodsclient/iCommands?

The python-irodsclient and the iCommands are much more powerful and expressive than iBridges. If you are already intimately familiar with either of them, you probably don’t need iBridges, since it doesn’t add any functionality that isn’t already there.

The target audience of iBridges is different: it tries to help researchers/users that are not expert iRODS users. The learning curve of using iBridges is much easier than either of the two alternatives. Additionally, its simplicity and default checks makes it less likely you will end up with bad data.

An advantage compared to the iCommands is that iBridges also works on Mac OS and Windows.

I found a bug or have a feature request, where do I go?

Our development is done on GitHub Look under the Issues section whether the bug or feature request has already been reported. If not, we heartily welcome creating a new issue. We try to get back to you as soon as possible, at least within a few days.

I want to contribute to iBridges, where do I go?

Our development is done on GitHub We are welcoming contributions by pull requests. You can also ask for new features/ideas in our issue tracker.

I have installed iBridges and now get “ibridges: command not found”

This can happen for a variety for reasons, but the most common reason is that your PATH is not setup correctly on your system. Often pip will complain about this when you install ibridges. To solve this, you must first find out where pip installs the ibridges executable. Usually this will be something like /home/your_username/.local/bin, but this is dependent on your system. Then we must add this to the path on the command line: export PATH=”${PATH}:/home/your_username/.local/bin” (change the path according to your system). This should allow your shell to find the ibridges command. You would have to type the previous command every time you start a new shell, which can be inconvenient. To fix this permanently, add the command to your .bashrc or .zshrc file in your home directory at the end of the file (depending on your shell, type echo ${SHELL} to find out).

Help, I’m getting a “NetworkError” while trying to transfer (large) files

This error is most likely to happen if you try to transfer a large file. The default timeout for iBridges is 25000 seconds, which translates to roughly 7 hours. This should not cause issues during the actual transfer. However, if the calculation of the checksum takes more than 7 hours (if the iRODS server is busy for example, or the file is many terabytes), then you will get a network error. The checksum itself should still be created. You can increase the timeout in your irods_environment.json file by adding a new entry with "connection_timeout": <time in seconds>,.

Note, that the maximum number equals to 292 years, i.e. “connection_timeout”: 9208512000,.

During data transfers I receive warnings or errors. How can I steer the verbosity?

iBridges tries to prevent overwriting data by accident. However, sometimes data needs to be overwritten. In those cases iBridges informs the user that data has been overwritten. To steer the behaviour we implemented the flags overwrite and ignore_err in the data transfer functions sync, upload and download:

Data transfer flags
overwrite	ignore_err	Outcome
False	False	Throws FileExistsError if data already exists.
True	False	Overwrite existing data. Other errors are thrown.
False	True	Skip the data which already exists and print a warning.
True	True	Overwrite existing data. All errors are turned into warning.

Warnings can also be switched off through python’s warnings package:

import warnings
warnings.filterwarnings("ignore")

My metadata with keys starting with `org_` do not show up in the iBridges metadata.

By default, iBridges does not show metadata that contain a key starting with the prefix org_. This is due to data security reasons on Yoda systems.

You can omit this by the following code:

from ibridges.meta import MetaData

# collections
meta = MetaData(IrodsPath(session, "~", "my_coll").collection, blacklist=None)
# data objects
meta = MetaData(IrodsPath(session, "~", "my_obj").dataobject, blacklist=None)
print(meta)

How can I list all data I have access to but which does not lie in my home or standard collection?

When data is shared in iRODS it is not always easy to know where the shared data lies. With the CLI search you can list all data you have access to and then use grep to filter or ignore (-v option) certain results. Below we show an example to list all collections you have access to outside of your home-collection:

ibridges search /tempZone/home --item_type collection --path-pattern "%" | grep -v "/tempZone/home/<your_user_name>"

In Python the code to retrieve all collections which are not in your irods_home would look like this:

from ibridges.interactive import interactive_auth
from ibridges import search_data, IrodsPath

session = interactive_auth()
search_res = search_data(session, path="/tempZone/home",  item_type="collection", path_pattern="%")

home_path = IrodsPath(session, session.home)
not_relative = []

for res in search_res:
    try:
        res.relative_to(home_path)   # succeeds only if res is inside home_path
    except ValueError:
        not_relative.append(res)