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Step 7: Copying data

Copy an entire Collection (or one file)

Copy data

You can copy files or directories within irods with the icp command: 

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icp -r /WCDSacc/courses/11032025/your_username/iris_data/ /WCDSacc/courses/11032025/your_username/iris_data_copy
Extra assignment: Check what the difference is between copying from /WCDSacc/courses/11032025/your_username/iris_data/ or from /WCDSacc/courses/11032025/your_username/iris_data

Or just copy one file: 

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icp /WCDSacc/courses/11032025/your_username/iris_data/iris.data /WCDSacc/courses/11032025/your_username/iris_data/iris.data_copy

Copying data inside irods is not possible with iBridges. You need to upload the files again to a new folder.

You can copy a directory with the following command: 

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gocmd cp -r /WCDSacc/courses/11032025/your_username/iris_data/ /WCDSacc/courses/11032025/your_username/iris_data_copy

You can copy a single specific file with the following command: 

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gocmd cp -r /WCDSacc/courses/11032025/your_username/iris_data/iris.data /WCDSacc/courses/11032025/your_username/iris_data/iris.data_copy

Copy a single file: 

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from connect import connect_to_irods
from irods.exception import CollectionDoesNotExist

session = connect_to_irods()


def copy(copy_path, paste_path):
    return session.data_objects.copy(copy_path, paste_path)


# Example
copy('/WCDSacc/courses/11032025/your_username/iris_data/iris.data', '/WCDSacc/courses/11032025/your_username/iris_data/iris.data_copy')
...

or copy an entire collection (and the data structure). 

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def get_or_create_collection(collection):
    try:
        return session.collections.get(collection)
    except CollectionDoesNotExist:
        print(f'CollectionDoesNotExist {collection}')
        return session.collections.create(collection)


def copy_coll(collection, dest_collection):
    get_or_create_collection(dest_collection)
    src_coll = session.collections.get(collection)
    try:
        print(f'1. create coll: {dest_collection}')

        for cur_coll, sub_colls, data_objs in src_coll.walk():
            print(f'current coll: {cur_coll.name} {cur_coll.path}')
            aa = cur_coll.path.removeprefix(src_coll.path) + '/'
            print(f'removeprefix: {aa}')
            print(f'sub colls: {sub_colls}')
            for col in sub_colls:
                print(f'creating coll: {dest_collection}{aa}{col.name} {type(col)}')
                session.collections.create(f'{dest_collection}{aa}{col.name}')

            print(f'data_objs: {data_objs}')
            for obj in data_objs:
                paste_path = dest_collection + aa + obj.name
                print(f'copy obj: {obj.name} to {paste_path} . {obj.path}')
                copy(obj.path, paste_path)
    except Exception as e:
        print(f'Error: {e}')    


# Example
copy_coll('/WCDSacc/courses/11032025/your_username/iris_data', '/WCDSacc/courses/11032025/your_username/iris_data_copy')