Package org.incenp.obofoundry.sssom

Class SSSOMReader

java.lang.Object
org.incenp.obofoundry.sssom.SSSOMReader
Direct Known Subclasses:
JSONReader, RDFReader, TSVReader
public abstract class SSSOMReader extends Object
Base class to read a mapping set from any of the supported serialisation formats.

This class should be derived into specialised classes that implement a precise serialisation format.

  • Field Details

  • Constructor Details

    • SSSOMReader

      public SSSOMReader()

  • Method Details

    • setExtraMetadataPolicy

      public void setExtraMetadataPolicy(ExtraMetadataPolicy policy)
      Sets the policy to deal with non-standard metadata in the input file.
      Parameters:
      policy - The policy instructing the parser about what to do when encountering non-standard metadata. The default policy is ExtraMetadataPolicy.NONE.

    • setPropagationEnabled

      public void setPropagationEnabled(boolean enabled)
      Enables or disables the propagation of "propagatable slots".
      Parameters:
      enabled - False to disable propagation; it is enabled by default.

    • setAssumedVersion

      public void setAssumedVersion(Version version)
      Sets the version of the SSSOM specification that the reader should assume the set is compliant with, if the set does not have a sssom_version slot. The default is to assume that the set is compliant with version 1.0, as mandated by the specification.

      This parameter has no effect if the set does have a sssom_version slot: in that case, the set will be expected to be compliant with the version indicated in that slot.

      Parameters:
      version - The SSSOM version a set is assumed to be compliant with.

    • setValidationEnabled

      public void setValidationEnabled(boolean enabled)
      Enables or disables post-parsing validation of mappings.
      Parameters:
      enabled - False to disable validation; it is enabled by default.

    • setValidation

      public void setValidation(ValidationLevel validationType)
      Controls whether a mapping set should be validated after it has been parsed, and how.

      This method provides a finer control than setValidationEnabled(boolean), which simply enables full validation or disables validation entirely.

      Parameters:
      validationType - The level of validation to use; set to ValidationLevel.DISABLED to disable validation entirely; the default is ValidationLevel.FULL.

    • fillPrefixMap

      public void fillPrefixMap(Map<String,String> map)
      Declares all prefix names in the specified map. Prefix names declared here complement the declarations from the file’s own prefix map, allowing the reader to parse a file with an incomplete prefix map.

      It is up to concrete implementations to actually do something with that map. Some of them may ignore it.

      Parameters:
      map - The prefix map to use.

    • read

      public abstract MappingSet read() throws SSSOMFormatException, IOException
      Reads a mapping set from the source file.
      Returns:
      A complete SSSOM mapping set.
      Throws:
      SSSOMFormatException - If encountering invalid SSSOM data.
      IOException - If any kind of non-SSSOM-related I/O error occurs.

    • validate

      protected void validate(MappingSet mappingSet) throws SSSOMFormatException
      Validates a mapping set. This method performs all post-parsing checks to ensure the mapping set is valid according to the SSSOM specification.
      Parameters:
      mappingSet - The set to validate. It should be called by the read method in concrete derived classes.
      Throws:
      SSSOMFormatException - If the mapping set is invalid.