TypeExample-Genome.yaml

# This specification describes how a Workspace Genome object is transformed into a document that is
# indexed by the KBaseSeachEngine.

# The name of the type in the search system.
global-object-type: Genome
# The data source of the objects, in this case the Workspace.
storage-type: WS
# The name of the type in the data source.
storage-object-type: KBaseGenomes.Genome

# IMPORTANT NOTE: Once a type version is established in the search system, the type version
# CANNOT be changed or given a new version number (i.e. by changing the ordering of the versions)
# without dropping the ElasticSearch indexes for the type.

# This list contains different versions of the parsing rules used to parse the specified
# storage-object-type. The list is ordered by version number. Each parsing rule version results
# in a corresponding search type version. The mapping between the source storage-object-type
# version and the target search type version is specified by the type mappings.
# If no type mapping is specified for this type, the latest version is used.
versions:
    -
        # The following rules describe which fields are extracted from the source object and
        # transforms performed upon said fields.
        indexing-rules:
            -
                # Extract a keyword from the /id path. The key name will be id.
                path: id
                keyword-type: keyword
            -
                # Extract a keyword from the /domain path. The key name will be domain.
                path: domain
                keyword-type: keyword
            -
                # Extract a full-text search field from the /taxonomy path. A full-text field is
                # parsed into tokens which can be searched on individually, as opposed to a keyword
                # field which is an opaque block and must be matched in its entirety.
                # The key name will be taxonomy.
                path: taxonomy
                full-text: true
            -
                # Extract a full-text search field from the /scientific_name path.
                # The key name will be scientific_name.
                path: scientific_name
                full-text: true
            -
                # for sorting by scientific name we need a keyword form
                path: scientific_name
                key-name: scientific_name_keyword
                keyword-type: keyword
            -
                # Extract the number of features from a list at the /features path. The special
                # {size} element directs the parser to return the size of a list or mapping. Since
                # this number will be an integer, the keyword type is set as such.
                # The key name is explicitly set to features, rather than implicitly set by the
                # first section of the path.
                path: features/{size}
                keyword-type: integer
                key-name: feature_count
            -
                path: cdss/{size}
                keyword-type: integer
                key-name: cds_count
                ui-name: CDSs
            -
                path: mrnas/{size}
                keyword-type: integer
                key-name: mrna_count
                ui-name: mRNAs
            -
                path: num_contigs
                keyword-type: integer
                key-name: contig_count
            -
                path: source
                keyword-type: keyword
            -
                path: source_id
                keyword-type: keyword
            -
                # Extract a reference to an Assembly object and transform it into a Globally
                # Unique ID (GUID).
                # The reference is at the /assembly_ref path.
                path: assembly_ref
                # The reference will be transformed into a GUID.
                transform: guid
                # The expected type of the object to which the reference refers is an Assembly.
                # This is a search system type, not a data source type.
                target-object-type: Assembly
                target-object-type-version: 1
                # If there is no value at the path location, substitute an empty list instead.
                optional-default-value: []
                # Index the transformed GUID as a keyword.
                keyword-type: keyword
                # The key for the transformed GUID in the search document will be assembly_guid.
                key-name: assembly_guid
                # Don't show the guid in any UI context when displaying search data.
                ui-hidden: true