Package org.cytoscape.jobs

Interface CyJobDataService

  • public interface CyJobDataService
    The main interface for the marshalling and unmarshalling of data to be exchanged with remote services. Implementations of this interface will often be independent of the remote service (e.g. a JSON implementation of CyJobDataService may be used for multiple backend services). Not all of the methods will be provided by every implementation (see the default methods below).

    Module: jobs-api

    To use this in your app, include the following dependency in your POM:

    <dependency>
    <groupId>org.cytoscape</groupId>
    <artifactId>jobs-api</artifactId>
</dependency>

    Cytoscape Backwards Compatibility (SPI Interface): We expect that this interface will be implemented. Therefore to maintain backwards compatibility this interface will only be modified for major version updates.

    • Method Detail

      • getServiceName

        String getServiceName()
        The name of the service. This is usually the classname and is the name that should be registered with OSGi.
        Returns:
        the service name

      • getDataInstance

        CyJobData getDataInstance()
        Returns an empty instance of CyJobData that may be used with this service. Note that implementations of CyJobData are not meant to be compatible even though they implement a small common subset of methods.
        Returns:
        an empty CyJobData

      • addData

        CyJobData addData​(CyJobData data,
                  String key,
                  Map<Object,​Object> mapData)
        Add generic key, value pairs to a CyJobData item. If the data argument is null, create a new CyJobData object initialized with mapData.
        Parameters:
        data - if not null, add mapData to this data object.
        key - a key string used to retrieve the data
        mapData - the data to add.
        Returns:
        data if provided, else a new CyJobData object

      • addData

        CyJobData addData​(CyJobData data,
                  String key,
                  Object mapData)
        Add a single data item to a CyJobData object. If the data argument is null, create a new CyJobData object initialized with mapData.
        Parameters:
        data - if not null, add item to this data object.
        key - a key string used to retrieve the data
        item - the data to add.
        Returns:
        data if provided, else a new CyJobData object

      • addData

        default CyJobData addData​(CyJobData data,
                          String key,
                          CyNetwork network,
                          List<? extends CyIdentifiable> nodesAndEdges,
                          List<String> nodeColumns,
                          List<String> edgeColumns)
        An optional method to add network data to a CyJobData item. If the data argument is null, create a new CyJobData object initialized with the network data. If the list of nodes and edges (nodesAndEdges is provided, the network data will be restricted to this list. The list of nodeColumns and edgeColumns will restrict the attributes to those columns. For implementations that intent to use a column other than the SUID to map the data back, by convention the key column should be the first column in the list and the list should not be empty.
        NOTE: it is important that implementations of this method deal with the mapping of network, node, and edge SUIDs, which will change across sessions. Typically, this will be done by adding a new column in the appropriate HIDDEN_ATTRS table with the name or id of the job. A utility class SUIDUtil is provided to support one possible mechanism to do this
        Parameters:
        data - if not null, add the model data to this data object.
        key - a key string used to retrieve the data
        network - the CyNetwork to extract the data from.
        nodesAndEdges - the list of org.cytoscape.modelCyNodes and org.cytoscape.modelCyEdges to encode. If null or empty, the entire network will be added
        nodeColumns - the list of columns to include for node data
        edgeColumns - the list of columns to include for edge data
        Returns:
        data if provided, else a new CyJobData object

      • addData

        default CyJobData addData​(CyJobData data,
                          String key,
                          CyTable table,
                          List<CyRow> rows,
                          List<String> columns)
        An optional method to add table data to a CyJobData item. If the data argument is null, create a new CyJobData object initialized with the table data. If the list of CyRows (rows is is provided, the table data will be restricted to these rows. The list of columns will restrict the data to those columns. For implementations that intent to use a column other than the SUID to map the data back, by convention the key column should be the first column in the list and the list should not be empty.
        NOTE: it is important that implementations of this method deal with the mapping of SUIDs, which will change across sessions. Typically, this will be done by adding a new column in the appropriate HIDDEN_ATTRS table with the name or id of the job. A utility class SUIDUtil is provided to support one possible mechanism to do this
        Parameters:
        data - if not null, add the model data to this data object.
        key - a key string used to retrieve the data
        table - the CyTable to extract the data from.
        rows - the list of CyRows to encode. If null or empty, the entire table will be added
        columns - the list of columns to include from table
        Returns:
        data if provided, else a new CyJobData object

      • addData

        default CyJobData addData​(CyJobData data,
                          String key,
                          CyNetworkView networkView,
                          List<? extends CyIdentifiable> nodesAndEdges,
                          List<VisualProperty<?>> properties)
        An optional method to add network view data to a CyJobData item. If the data argument is null, create a new CyJobData object initialized with the network view data. If the list of nodes and edges (nodesAndEdges is provided, the view data will be restricted to this list. The list of properties will restrict the VisualPropertys to only those in the list. NOTE: it is important that implementations of this method deal with the mapping of network, node, and edge SUIDs, which will change across sessions. Typically, this will be done by adding a new column in the appropriate HIDDEN_ATTRS table with the name or id of the job. A utility class SUIDUtil is provided to support one possible mechanism to do this
        Parameters:
        data - if not null, add the model data to this data object.
        key - a key string used to retrieve the data
        networkView - the CyNetworkView to extract the data from.
        nodesAndEdges - the list of CyNodes and CyEdges to encode. If null or empty, the entire network view will be added
        properties - the list of visual properties to include
        Returns:
        data if provided, else a new CyJobData object

      • getData

        Object getData​(CyJobData data,
               String key)
        Extract data from a CyJobData object.
        Parameters:
        data - the CyJobData object that has the data
        key - the key that accesses the data
        Returns:
        the untyped data, or null if the data doesn't exist. Note that it is up to the consumer to determine if this object is of the correct type.

      • getMapData

        Map<Object,​Object> getMapData​(CyJobData data,
                                    String key)
        Extract a map from a CyJobData object.
        Parameters:
        data - the CyJobData object that has the map
        key - the key that accesses the map
        Returns:
        the map itself, or null if the data doesn't exist.

      • getNetworkData

        default CyNetwork getNetworkData​(CyJobData data,
                                 String key)
        Optional method to extract network data from a CyJobData object.
        Parameters:
        data - the CyJobData object that has the CyNetwork
        key - the key that accesses the network
        Returns:
        the returned network or null if it doesn't exist. This should include any nodes, edges, and network tables that were included

      • getTableData

        default CyTable getTableData​(CyJobData data,
                             String key)
        Optional method to extract table data (usually not model associated tables) from a CyJobData object.
        Parameters:
        data - the CyJobData object that has the CyTable
        key - the key that accesses the table
        Returns:
        the returned table or null if it doesn't exist. This should include any rows and columns that were included.

      • getViewData

        default CyNetworkView getViewData​(CyJobData data,
                                  String key)
        Optional method to extract data for a CyNetworkView from a CyJobData object.
        Parameters:
        data - the CyJobData object that has the CyNetworkView
        key - the key that accesses the table
        Returns:
        the returned view or null if it doesn't exist. Note that this will only include view data for the nodes and edges specified in the CyJobData store. All VisualProperty values will be default unless explicitly included, in which case they will be overrides.