Class StandardFieldConverter

    • Constructor Detail

      • StandardFieldConverter

        public StandardFieldConverter​(DbControl dc,
                                      BioAssaySet source)
        Create a new standard field converter.
        Parameters:
        dc - A DbControl to use for database access
        source - The source bioassay set
    • Method Detail

      • getAssayField

        public AssayField getAssayField​(String name,
                                        boolean required)
        Find an assay field. This method will try to locate a field in the following order:
        1. Check if there is an experimental factor with the given name (case-sensitivity depends on the database that is used).
        2. Check if there is an assay-level annotation type with the given name.
        3. If name is 'name', 'description' or another static property (case-insensitive) the corresponding assay value is used.
        Parameters:
        name - The name to find
        required - If TRUE and no field is found this method will throw an ItemNotFoundException
        Returns:
        The field or null
      • getReporterField

        public DynamicField getReporterField​(String name,
                                             boolean required)
        Find a reporter dynamic field. This method will try to locate a field in the following order:
        1. Check if there is an position extra value with the given name (case-sensitivity depends on the database that is used).
        2. Check if there is a formula with the given name (case-sensitivity depends on the database that is used).
        3. If name is 'name', 'externalId', 'description' or another static property (case-insensitive) the corresponding reporter value is used.
        4. Special case for "External ID" and "Internal ID" to simplify pass-throguh to the BFS importer which expects at least one of those columns.
        Parameters:
        name - The name to find
        required - If TRUE and no field is found this method will throw an ItemNotFoundException
        Returns:
        The field or null
      • getSpotField

        public DynamicField getSpotField​(String name,
                                         boolean required)
        Find a spot dynamic field. This method will try to locate a field in the following order:
        1. Check if there is a spot extra value with the given name (case-sensitivity depends on the database that is used).
        2. Check if there is a formula with the given name (case-sensitivity depends on the database that is used).
        3. Check if there is a raw data property that matches the name (case-insensitive)
        4. Special values: Ch 1, Ch2, etc. to get channel intensities (case-insensitive)
        Parameters:
        name - The name to find
        required - If TRUE and no field is found this method will throw an ItemNotFoundException
        Returns:
        The field or null