collections

API endpoint base: https://pirca.arvadosapi.com/arvados/v1/collections

Object type: 4zz18

Example UUID: zzzzz-4zz18-0123456789abcde

Resource

Collections describe sets of files in terms of data blocks stored in Keep. See Keep – Content-Addressable Storage for details.

Each collection has, in addition to the Common resource fields:

Attribute	Type	Description	Example
name	string
description	text
properties	hash	User-defined metadata, may be used in queries using subproperty filters
portable_data_hash	string	The MD5 sum of the manifest text stripped of block hints other than the size hint.
manifest_text	text
replication_desired	number	Minimum storage replication level desired for each data block referenced by this collection. A value of null signifies that the site default replication level (typically 2) is desired.	2
replication_confirmed	number	Replication level most recently confirmed by the storage system. This field is null when a collection is first created, and is reset to null when the manifest_text changes in a way that introduces a new data block. An integer value indicates the replication level of the least replicated data block in the collection.	2, null
replication_confirmed_at	datetime	When replication_confirmed was confirmed. If replication_confirmed is null, this field is also null.
storage_classes_desired	list	An optional list of storage class names where the blocks should be saved. If not provided, the cluster’s default storage class(es) will be set.	['archival']
storage_classes_confirmed	list	Storage classes most recently confirmed by the storage system. This field is an empty list when a collection is first created.	'archival'], []
storage_classes_confirmed_at	datetime	When storage_classes_confirmed was confirmed. If storage_classes_confirmed is [], this field is null.
trash_at	datetime	If trash_at is non-null and in the past, this collection will be hidden from API calls. May be untrashed.
delete_at	datetime	If delete_at is non-null and in the past, the collection may be permanently deleted.
is_trashed	boolean	True if trash_at is in the past, false if not.
current_version_uuid	string	UUID of the collection’s current version. On new collections, it’ll be equal to the uuid attribute.
version	number	Version number, starting at 1 on new collections. This attribute is read-only.
preserve_version	boolean	When set to true on a current version, it will be persisted. When passing true as part of a bigger update call, both current and newly created versions are persisted.
file_count	number	The total number of files in the collection. This attribute is read-only.
file_size_total	number	The sum of the file sizes in the collection. This attribute is read-only.

Conditions of creating a Collection

The portable_data_hash and manifest_text attributes must be provided when creating a Collection. The cryptographic digest of the supplied manifest_text must match the supplied portable_data_hash.

Side effects of creating a Collection

Referenced blocks are protected from garbage collection in Keep.

Data can be shared with other users via the Arvados permission model.

Methods

See Common resource methods for more information about create, delete, get, list, and update.

Required arguments are displayed in green.

Supports federated get only, which may be called with either a uuid or a portable data hash. When requesting a portable data hash which is not available on the home cluster, the query is forwarded to all the clusters listed in RemoteClusters and returns the first successful result.

create

Create a new Collection.

Arguments:

Argument	Type	Description	Location	Example
collection	object		query

delete

Put a Collection in the trash. This sets the trash_at field to now and delete_at field to now + token TTL. A trashed collection is invisible to most API calls unless the include_trash parameter is true.

Arguments:

Argument	Type	Description	Location	Example
uuid	string	The UUID of the Collection in question.	path

get

Gets a Collection’s metadata by UUID or portable data hash. When making a request by portable data hash, attributes other than portable_data_hash and manifest_text are not returned, even when requested explicitly using the select parameter.

Arguments:

Argument	Type	Description	Location	Example
uuid	string	The UUID or portable data hash of the Collection in question.	path

list

List collections.

See common resource list method.

Argument	Type	Description	Location	Example
include_trash	boolean (default false)	Include trashed collections.	query
include_old_versions	boolean (default false)	Include past versions of the collection(s) being listed, if any.	query

Note: Because adding access tokens to manifests can be computationally expensive, the manifest_text field is not included in results by default. If you need it, pass a select parameter that includes manifest_text.

update

Update attributes of an existing Collection.

Arguments:

Argument	Type	Description	Location	Example
uuid	string	The UUID of the Collection in question.	path
collection	object		query

untrash

Remove a Collection from the trash. This sets the trash_at and delete_at fields to null.

Arguments:

Argument	Type	Description	Location	Example
uuid	string	The UUID of the Collection to untrash.	path
ensure_unique_name	boolean (default false)	Rename collection uniquely if untrashing it would fail with a unique name conflict.	query

provenance

Returns a list of objects in the database that directly or indirectly contributed to producing this collection, such as the container request that produced this collection as output.

The general algorithm is:

1. Visit the container request that produced this collection (via output_uuid or log_uuid attributes of the container request)
2. Visit the input collections to that container request (via mounts and container_image of the container request)
3. Iterate until there are no more objects to visit

Arguments:

Argument	Type	Description	Location	Example
uuid	string	The UUID of the Collection to get provenance.	path

used_by

Returns a list of objects in the database this collection directly or indirectly contributed to, such as containers that takes this collection as input.

The general algorithm is:

1. Visit containers that take this collection as input (via mounts or container_image of the container)
2. Visit collections produced by those containers (via output or log of the container)
3. Iterate until there are no more objects to visit

Arguments:

Argument	Type	Description	Location	Example
uuid	string	The UUID of the Collection to get usage.	path

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