Add basic metadata options to CLI

[qubixes]

Adds:

• ibridges meta-show: show the metadata for a collection or dataobject.
• ibridges meta-add: Add one new metadata entry for a collection or dataobject.
• ibridges meta-del: Delete one, multiple or all metadata items using the key/value/units.
• ibridges list --metadata: List the collection, including all metadata of the listed items.
• ibridges list --short: Mimics Unix ls with no options.
• ibridges list --long: Shows checksums and sizes of data objects.
• ibridges ls alias for ibridges list
• ibridges meta alias for ibridges meta-list

Deprecates:

• MetaData.set: I think we should remove this method for 2.0, since the behavior can be easily emulated with two commands (delete/add).

Improvements:

• IrodsPath.walk: Performance with depth==1 should be improved for large collections.

TODO:

• Documentation readthedocs
• CLI help
• New tests

[chStaiger]

To be consistent with the other iRODS clients we should rename show into list.

[qubixes]

Done.

[chStaiger]

Nice PR, I like it. I have nothing to complain about in the code

[qubixes]

Nice PR, I like it. I have nothing to complain about in the code

I have added some more features and a performance improvement for walk with depth==1.

[chStaiger]

Nice!!! Really a good catch!

[qubixes]

@chStaiger Do you understand why the tests fail? I think it's because there are two sessions running at the same time, and there is some timing issue, where the change from the cli doesn't trickle through to the other running session. How do you want to fix this?

[chStaiger]

I think this exception is thrown when you try to delete some metadata that is not there. So there must be some confusion with the metadata as we use it in the metadata tests and the metadata in cli.

from ibridges.path import IrodsPath
from ibridges.interactive import interactive_auth

session = interactive_auth()
irods_path = IrodsPath(session, '~', 'comicbooks')
coll_meta = irods_path.collection.metadata

coll_meta.remove("bogus", "bogus")

CAT_SUCCESS_BUT_WITH_NO_INFO: None

[chStaiger]

I exchanged the assertion in test_cli_meta

irods-client_1 | @mark.parametrize("item_name", ["collection", "dataobject"])
irods-client_1 | def test_meta_cli(item_name, request, pass_opts):
irods-client_1 | item = request.getfixturevalue(item_name)
irods-client_1 | meta = MetaData(item)
irods-client_1 | meta.clear()
irods-client_1 | cli_path = f"irods:{item.path}"
irods-client_1 |
irods-client_1 | ret = subprocess.run(["ibridges", "meta-list", cli_path], capture_output=True, **pass_opts)
irods-client_1 | assert len(ret.stdout.strip("\n").split("\n")) == 1
irods-client_1 |
irods-client_1 | subprocess.run(["ibridges", "meta-add", cli_path, "key", "value", "units"], **pass_opts)
irods-client_1 | assert ("key", "value", "units") in meta
irods-client_1 |
irods-client_1 | subprocess.run(["ibridges", "meta-del", cli_path, "--key", "key"], **pass_opts)
irods-client_1 | > assert ("key", "value", "units") not in meta
irods-client_1 | E AssertionError: assert ('key', 'value', 'units') not in MetaData</tempZone/home/rods/test_collection>
irods-client_1 |
irods-client_1 | test_cli.py:195: AssertionError

So the error seems to be that the metadata item is not removed.

[chStaiger]

I think I found it.

The meta is a snapshot at a time and not updated when the metadata gets changed on the server.
So before all of the asserts we need to fetch the current meta

[chStaiger]

To refresh the meta variable we need the session to fetch the information from the server.

item = IrodsPath(session, <path>).<Obj|Coll>
meta = Metadata(item)
assert ...

[qubixes]

@chStaiger I have added a refresh method to the MetaData class. I think for now this will work fine. We can think of allowing an irodspath at some other time.

[chStaiger]

@chStaiger I have added a refresh method to the MetaData class. I think for now this will work fine. We can think of allowing an irodspath at some other time.

Thanks!!! I agree. Noted down for iBridges 2.0.0 ;)

[chStaiger]

Approved!!!!