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NEWS
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Changes in sssom-java-1.0.0
---------------------------
* sssom-core:
* Library split in two components: sssom-core and sssom-ext.
* SSSOM/T:
* Add filter and callback functions.
* Add support for optional, named arguments in function calls.
* Add the possibility to define variables.
* Add placeholder substitution in function arguments.
* Add experimental support for URI Expressions.
* SSSOM/T-OWL:
* Add the exists and is_a filter functions.
* Add the annotate function.
Changes in sssom-java-0.9.0
---------------------------
* sssom-core:
* Add support for sssom:NoTermFound.
* Add support for renamed semantic_similarity_* slots.
* Add support for literal mappings.
* Accept date and time values when a date is expected (reading only).
* SSSOM/T:
* Allow filtering on empty slots.
* sssom-cli:
* Accept positional arguments as input files.
Changes in sssom-java-0.8.0
---------------------------
* Add JSON read/write support in the library and CLI tool.
* Enforce [0,1.0] range of double-typed slots.
Changes in sssom-java-0.7.9
---------------------------
* Support writing metadata into a separate file.
* Better control for sssom-cli's --update-from-ontology option.
Changes in sssom-java-0.7.8
---------------------------
* SSSOM/TSV writer
* Use YAML plain-style for scalar values whenever possible.
* Fix incorrect handling of missing extension values.
* Allow disabling condensation of propagatable slots.
* SSSOM/TSV parser
* Fix parsing of unquoted scalar values.
* Allow disabling propagation of propagatable slots.
* sssom-cli:
* New options --no-condensation and --no-propagation.
Changes in sssom-java-0.7.7
---------------------------
* SSSOM/TSV writer:
* Align the format of floating numbers with SSSOM-Py.
* Remove propagated values from set-level metadata.
* xref-extract:
* Fill the subject_source field with the ontology IRI.
* Accept multiple spaces in the --map-prefix-to-predicate option.
* sssom-cli:
* New --update-from-ontology option.
Changes in sssom-java-0.7.6
---------------------------
* sssom-core:
* Ignore empty lines when reading a SSSOM/TSV file.
* sssom-cli:
* Added convenience --include and --exclude options.
* Write non-standard metadata by default.
Changes in sssom-java-0.7.5
---------------------------
* New experimental support for non-standard metadata.
* Allow to use non-standard metadata to annotate OWL axioms.
* Write TSV headers when writing an empty set.
* Fix backward compatibility with 'match_term_type' slot.
Changes in sssom-java-0.7.4
---------------------------
* Fix the SSSOM/TSV writer to write escaped values as needed.
* Experimental support for non-standard metadata.
Changes in sssom-java-0.7.3
---------------------------
* sssom-core:
* Added support for Extended Prefix Maps.
* sssom-inject:
* New option --use-input-prefix-map.
* sssom-cli:
* New output option --split.
* Support "reconciliating" a set against an Extended Prefix Map.
* New options to control the metadata of the result set.
* New options to control the output prefix map.
Changes in sssom-java-0.7.2
---------------------------
* SSSOM/T:
* New function "assign()" to edit mapping slots with fixed values.
* New function "replace()" to perform replacement on slot values.
* Previously introduced function "edit()" obsoleted.
* sssom-inject:
* New option --error-on-unshortenable-iris.
Changes in sssom-java-0.7.1
---------------------------
* Fix missing optional argument in SSSOM/T-OWL "direct" function.
Changes in sssom-java-0.7.0
---------------------------
* New ROBOT command to rename entities in a OWL ontology.
* New SSSOM/T preprocessing function to edit mappings on the fly.
Changes in sssom-java-0.6.2
---------------------------
* Fix erroneous inversion of object_source slot.
* sssom-cli:
* Provide a self-executable Jar file (Unix only).
* Add the --rule option to specify a single SSSOM/T rule.
* sssom-inject:
* Allow to create annotated axioms using mapping metadata.
Changes in sssom-java-0.6.1
---------------------------
* TSV writer:
* Write out a default license value if no license is set.
* Write out an automically generated ID if no ID is set.
* SSSOM/T:
* Fix filtering on mapping cardinality.
* xref-extract:
* Try to infer mapping ID and license from the source ontology.
* New options --set-id and --set-license.
* sssom-inject:
* Renamed to "inject".
Changes in sssom-java 0.6.0
---------------------------
* SSSOM/T can now filter on all available slots.
* Changes to the TSV reader:
* Silently ignore unknown slots.
* Recognise and convert slots from older versions.
* Propagate slots down to individual mappings.
* Changes to the TSV Writer:
* Condense slots up to the level of the mapping set.
* SSSOM-to-OWL:
* Exclude mapping_cardinality from OWL serialisation.
* Use dc/terms rather dc/elements/1.1 for dispatch table metadata.
* Addition of sssom-cli, a command-line tool to manipulate sets.
Changes in sssom-java 0.5.0
---------------------------
* Fix sssom-inject crash when using --direct option.
* Fix parsing of multi-valued slots in mappings.
* Make TSVWriter output fully predictable:
* Sort mapping set metadata by "spec order".
* Sort Curie map entries by alphabetical order.
* Sort mappings using all available slots.
* Write the effective Curie map only.
* Add SlotVisitor interface.
* Add test suite.
Changes in sssom-java 0.4.3
---------------------------
* Update model to sssom-0.15.
* Fix writing of date fields.
* Fix bogus computation of mapping cardinality.
* xref-extract:
* Ignore obsolete classes when extracting cross-references.
* Allow reusing an existing mapping set (or its metadata).
Changes in sssom-java 0.4.2
---------------------------
* Allow filtering on mapping cardinality.
* Add option --drop-duplicates to xref-extract.
* Allow to set default ontology ID/version in a dispatch table.
* Dispatch table filenames are relative to the table filename.
Changes in sssom-java 0.4.1
---------------------------
* New options in sssom-inject:
* --invert to invert the mapping set.
* --no-default-prefixes to ignore ROBOT's known prefixes.
* --bridge-iri to specify the ontology IRI of the bridge.
* --only-subject-in to filter mappings on their subject ID.
* --only-object-in to filter mappings on their object ID.
Changes in sssom-java 0.4.0
---------------------------
* SSSOM/T-OWL:
* New preprocessing functions check_(subject|object)_existence.
* New function set_var to declare mapping-dependent variables.
* New ROBOT command xref-extract to get mappings from xrefs.
* sssom-inject:
* Allow loading multiple mapping sets by repeating --sssom option.
* New option --extract to get a mapping set from ontology xrefs.
* New add-axiom key in dispatch table entries.
Changes in sssom-java 0.3.1
---------------------------
* Fix missing dependency in ROBOT plugin artifact.
Changes in sssom-java 0.3.0
---------------------------
* Project artifacts now split between sssom-core and sssom-robot.
* Fix parsing of date fields.
* Support for arbitrary functions in SSSOM/Transform.
* New interface to specialise the SSSOM/Transform parser.
* New options for the sssom-inject ROBOT command:
* --create, to create a new ontology from mappings;
* --hasdbxref, to create OBO-style cross-references.
Changes in sssom-java 0.2.0
---------------------------
* Report all undeclared prefixes once parsing is over, instead of
erroring out on the first undeclared prefix.
* Support inversion of mappings.
* Support filtering on many more fields.
* New options for the sssom-inject ROBOT command:
* --dispatch-table, to write generated axioms to different files;
* --include-rule, to selectively enable only some rules;
* --exclude-rule, to selectively disable some rules;
* --direct, to generate direct OWL serialisation of mappings.