SSSOM-Java 0.7.8

Changes since version 0.7.7:

• The SSSOM/TSV writer now writes scalar values in YAML “plain style” whenever possible.
• Incorrect parsing of some unquoted scalar values in the metadata block has been fixed.
• Incorrect handling of missing extension values has been fixed.
• The propagation and condensation of “propagatable slots” is now deactivatable. With sssom-cli, new options --no-propagation and --no-condensation have been added to that effect.

SSSOM-Java 0.7.7

Changes since version 0.7.6:

• SSSOM/TSV writer (SSSOM-Core):
  • Align the format of floating point values with SSSOM-Py.
  • When a propagatable metadata is effectively propagated to individual mappings, remove it from the set-level metadata.
• xref-extract (SSSOM-Robot):
  • Fill in the subject_source field with the ontology IRI.
  • Accept multiple spaces in the value of the --map-prefix-to-predicate option.
• SSSOM-CLI:
  • New option --update-from-ontology to check/update a mapping set against a OWL ontology.

SSSOM-Java 0.7.6

Changes since version 0.7.5:

• sssom-core:
  • Ignore empty lines when reading a SSSOM/TSV file.
• sssom-cli:
  • Added convenience options --include and --exclude.
  • Write non-standard metadata by default (--write-extra-metadata now defaults to DEFINED rather than NONE).

SSSOM-Java 0.7.5

Changes since version 0.7.4:

• The support for non-standard metadata has been updated to align with the latest proposition from the SSSOM specification.
• When generating OWL axioms, they can now be annotated with values from non-standard metadata slots in addition to the standard slots.
• When writing a set, if the set is actually empty (contains no mappings), a TSV header line is written. This makes the resulting file readable by the SSSOM/TSV parser.
• Compatibility with the old slot match_term_type has been improved.

SSSOM-Java 0.7.4

Changes since version 0.7.3:

• The SSSOM/TSV writer now correctly escapes strings in the YAML metadata block and in TSV values.
• Experimental support for reading and writing non-standard metadata.

SSSOM-Java 0.7.3

Changes since version 0.7.2:

• SSSOM-Core library:
  • Added support for Extended Prefix Maps.
• SSSOM-Robot plugin:
  • New option --use-input-prefix-map to allow using the prefix map from the input set(s) in SSSOM/T rules.
• SSSOM-CLI tool:
  • New option --split to write the result set in several chunks splitted along the subject and object ID prefixes.
  • New option --mangle-iris to “reconciliate” the IRIs in a mapping set against an extended prefix map.
  • New option --no-metadata-merge to disable merging of multi-valued metadata slots when merging several input sets.
  • New option --output-metadata to set the metadata of the result set from a specific file.
  • New option --prefix-map to set the transform prefix map from the metadata of a specific file.
  • New option --prefix-map-from-input to fill the transform prefix map with the prefixes from the input set(s).
  • New option --output-prefix-map to control which prefix map should be used to write the result set.

SSSOM-Java 0.7.2

Changes since version 0.7.1:

• SSSOM/T:
  • Add a new function assign() to edit mapping slots with fixed values known at compile-time (this replaces the previously introduced edit() function, which is still available for backwards compatibility but is deprecated).
  • Add a new function replace() to edit mapping slots by performing regex-based search-and-replace operations.
• ROBOT inject command:
  • Add a new option --error-on-unshortenable-iris to force the command to error out if some IRIs cannot be shortened when generating annotation axioms.

SSSOM-Java 0.7.1

This is a bugfix release.

The documentation of the SSSOM/T-OWL dialect used by the inject ROBOT command states that all axiom-generating functions accept an optional argument describing how to annotate the generated axioms, but this was not true for the direct() function, which accepted no such argument.

The only change from version 0.7.0 is that the direct() function now accepts the same optional argument as all the other axiom-generating functions. The default behaviour, when the function is called without argument, is still to generate direct axiom annotations for all the mapping metadata except mapping_cardinality.

SSSOM-Java 0.7.0

Changes since version 0.6.2:

• New ROBOT command to rename entities in a OWL ontology, using a mapping set as data source.
• New SSSOM/T preprocessing function to edit mappings on the fly.

SSSOM-Java 0.6.2

Changes since version 0.6.1:

• Fix erroneous inversion of object_source slot when inverting a mapping.
• sssom-cli:
  • Provide a self-executable Jar file (for Unix-like systems only).
  • Add the --rule option to specify a single SSSOM/T rule directly from the command line.
• sssom-inject:
  • Allow to create annotated axioms using the mapping metadata.

Full Changelog: sssom-java-0.6.1...sssom-java-0.6.2