Collection

Class used to represent a collection in MetagenomeDB.

class MetagenomeDB.Collection(properties)

Create a new Collection object.

Parameters:

• properties: properties of this sequence, as a dictionary. Must contain at least a ‘name’ property, or a InvalidObjectError exception is thrown.

Note

Collection names are unique in the database; if attempting to commit a collection while another collection already exists with the same name a DuplicateObjectError exception is thrown.

add_to_collection(collection, relationship=None)

Add this collection to a (super) collection.

Parameters:

• collection: collection to add this collection to.
• relationship: properties of the relationship from this collection to collection, as a dictionary (optional). See Annotations.

Note

• If collection has never been committed to the database a UncommittedObjectError is thrown.
• This collection will need to be committed to the database for the information about its relationship to collection to be stored and queried. See Relationships.

See also

remove_from_collection()

commit()

Commit this object to the database.

Note

• The commit will not be performed if the object has already been committed once and no modification (property manipulation) has been performed since then.
• If an object already exists in the database with the same values for properties flagged as unique a DuplicateObjectError exception is thrown.

See also

is_committed()

classmethod count(filter=None)

Count the number of objects of this type in the database.

Parameters:

• filter: filter for the objects to count (optional); see Queries.

See also

find()

count_related_collections(direction=0, collection_filter=None, relationship_filter=None)

Count all collections this collection is linked to, or have links to it.

Parameters:

• direction: direction of the relationship (optional). If set to Direction.INGOING, will count collections that are linked to this collection (i.e., sub-collections). If set to Direction.OUTGOING, will count collections this collection is linked to (i.e., super-collections). If set to Direction.BOTH (default), all neighboring collections are counted. See Relationships.
• collection_filter: filter for the collections to count (optional). See Queries.
• relationship_filter: filter for the relationships between this collection and neighbor collections (optional). See Queries.

Note

• If direction is set to Direction.BOTH or Direction.OUTGOING, relationship_filter is set and this collection is not committed, a UncommittedObjectError exception is thrown.

See also

list_related_collections()

count_sequences(sequence_filter=None, relationship_filter=None)

Count sequences this collection contains.

Parameters:

• sequence_filter: filter for the sequences to count (optional). See Queries.
• relationship_filter: filter for the relationship linking sequences to this collection (optional). See Queries.

See also

list_sequences()

count_sub_collections(collection_filter=None, relationship_filter=None)

Count all collections that are linked to this collection.

Parameters:

• collection_filter: filter for the sub-collections (optional). See Queries.
• relationship_filter: filter for the relationships linking sub-collections to this collection (optional). See Queries.

See also

list_sub_collections(), list_super_collections(), count_super_collections()

count_super_collections(collection_filter=None, relationship_filter=None)

Count all collections this collection is linked to.

Parameters:

• collection_filter: filter for the super-collections (optional). See Queries.
• relationship_filter: filter for the relationships linking this collection to super-collections (optional). See Queries.

Note

• If this collection is not committed and relationship_filter is set a UncommittedObjectError exception is thrown. See Relationships.

See also

list_super_collections(), list_sub_collections(), count_sub_collections()

classmethod distinct(property)

For each value found in the database for a given property, return the number of objects that have this value.

Parameters:

• property: property to count objects for.

Return:

A dictionary with all values found for this property as keys, and number of objects having this value as values.

classmethod find(filter=None)

Find all objects of this type that match a query.

Parameters:

• filter: filter for the objects to select (optional); see Queries.

Return:

A generator.

See also

count(), find_one()

classmethod find_one(filter)

Find the first (or only) object of this type that match a query.

Parameters:

• filter: filter for the object to select; see Queries.

Return:

An object, or None if no object found.

See also

find()

get_properties()

Return a copy of all of this object’s properties, as a dictionary.

See also

get_property()

get_property(key, default=None)

Return the value for a given property.

Parameters:

• key: property to retrieve; see Annotations.

See also

get_properties()

has_relationships_with(target)

Test if this object has relationship(s) with another object.

Parameters:

• target: object to test for the existence of relationships with.

See also

list_relationships_with()

is_committed()

Test if this object has been committed to the database since

its latest modification.

See also

commit()

list_related_collections(direction=0, collection_filter=None, relationship_filter=None)

List all collections this collection is linked to, or have links to it.

Parameters:

• direction: direction of the relationship (optional). If set to Direction.INGOING, will list collections that are linked to this collection (i.e., sub-collections). If set to Direction.OUTGOING, will list collections this collection is linked to (i.e., super-collections). If set to Direction.BOTH (default), all neighboring collections are listed. See Relationships.
• collection_filter: filter for the collections to list (optional). See Queries.
• relationship_filter: filter for the relationships between this collection and neighbor collections (optional). See Queries.

Note

• If direction is set to Direction.BOTH or Direction.OUTGOING, relationship_filter is set and this collection is not committed, a UncommittedObjectError exception is thrown.

See also

count_related_collections()

list_relationships_with(target)

List relationship(s), if any, from this object to others.

Parameters:

• target: object to list relationships with.

Return:

A list.

See also

has_relationships_with()

list_sequences(sequence_filter=None, relationship_filter=None)

List sequences this collection contains.

Parameters:

• sequence_filter: filter for the sequences to list (optional). See Queries.
• relationship_filter: filter for the relationship linking sequences to this collection (optional). See Queries.

See also

count_sequences()

list_sub_collections(collection_filter=None, relationship_filter=None)

List all collections that are linked to this collection.

Parameters:

• collection_filter: filter for the sub-collections (optional). See Queries.
• relationship_filter: filter for the relationships linking sub-collections to this collection (optional). See Queries.

See also

count_sub_collections(), list_super_collections(), count_super_collections()

list_super_collections(collection_filter=None, relationship_filter=None)

List all collections this collection is linked to.

Parameters:

• collection_filter: filter for the super-collections (optional). See Queries.
• relationship_filter: filter for the relationships linking this collection to super-collections (optional). See Queries.

Note

• If this collection is not committed and relationship_filter is set a UncommittedObjectError exception is thrown. See Relationships.

See also

count_super_collections(), list_sub_collections(), count_sub_collections()

remove()

Remove this object from the database.

Note

• Relationships from and to this object are removed as well.
• The object remains in memory, flagged as uncommitted.

See also

remove_all()

classmethod remove_all()

Remove all objects of this type from the database.

Note

• Relationships from and to these objects are removed as well.
• Instanciated objects remain in memory, flagged as uncommitted.

See also

remove()

remove_from_collection(collection, relationship_filter=None)

Remove this collection from another (super) collection.

Parameters:

• collection: collection to remove this collection from.
• relationship_filter: relationships to remove (optional). If none provided, all relationships linking this collection to collection are removed. See Queries.

Note

• If this collection and collection have no relationship, a MetagenomeDBError exception is thrown.
• If this collection is not committed and relationship_filter is set a UncommittedObjectError exception is thrown. See Relationships.

See also

add_to_collection()