CHANGELOG.md

Changelog

1.7.0

• updates to infores usage according to Biolink-model changes
• bug fixes for infores auto-mapping

1.6.2

• allow infores to be submitted via input files and via knowledge_sources click parameter
• add some checks for dually submittied primary_knowledge_sources

1.6.1

• minor code clean up, doc clean up and zenodo release

1.6.0

• update provenance to work with Biolink3

1.5.9 (2022-06-13)

• make streaming transform default

1.5.8 (2022-06-02)

• take down logging level for neo4j

1.5.7 (2022-04-15)

• update click utils to use stream for transform in merge command

1.5.6 (2022-03-09)

• upgrade linkml & rdflib
• fix dependencies on black, sphinx, bmt

1.5.5 (2022-01-18)

• upgrade neo4j support to neo4j 4.3.0
• enhance logging support

1.5.3 (2021-09-14)

• remove pystache requirement

1.5.2 (2021-08-23)

• Update to bmt 0.7.4
• add error reporting for empty lines in nt parser

1.5.1 (2021-08-23)

• Keep track of edge properties in owl source

1.5.0 (2021-08-12)

• Support mixins in ancestors hierarchy
• Invalidate mixins as categories
• Maintenance and bug fixes

1.4.0 (2021-07-15)

• This version replaces the previously hard-coded config.yaml Biolink Model release number used in the included Biolink Model Toolkit.
• Users of the KGX 'validate' functionality can also reset the Biolink Model (SemVer) release number at the CLI, and programmatically, with the Validator.set_biolink_model() class method.
• KGX made Biolink Model 2.0++ aware with respect to new provenance slots - knowledge_source and its descendant slot definitions. These slot properties need to be explicitly specified in the Transformer.transform input_args dictionary.
• Some support for heuristic auto-generation of candidate format-compliant CURIES Biolink Model 2.0++ Information Resource ("InfoRes") CURIES. The new code also provides a regular expression and meta-data based rewrite of knowledge source names into such CURIES.
• Some additional clarification in the 'readTheDocs' documentation including for 1.3.0 streaming release features.
• Added tox testing and version support and refactored according to black and flake8 linting reports.

1.3.0 (2021-06-21)

• Add streaming option to validation

1.2.0 (2021-06-17)

• Update BMT to 0.7.2
• Update LinkML to 1.0.0
• Pin some major release versions in requirements.txt

1.1.0 (2021-05-24)

• Migrate to LinkML from BiolinkML

1.2.0 (2021-06-17)

• Update BMT to 0.7.2
• Update LinkML to 1.0.0
• Pin some major release versions in requirements.txt

1.1.0 (2021-05-24)

• Migrate to LinkML from BiolinkML

1.0.0 - (2021-03-16)

• Fix bug with caching records in RdfSource
• Add shortcuts for arguments in all CLI operations
• Fix usage in CLI

1.0.0b0 - (2021-03-11)

• Fixed caching bug in RdfSource
• Fixed bug when setting 'provided_by' for a source

1.0.0a0 - (2021-03-04)

• Added Source implementation for reading from various data stores
• Added Sink implementation for writing to various data stores
• Added a simplified Transformer that is agnostic
• Refactor KGX to make use of Sources and Sinks
• Added ability to stream graphs (Thanks to @gregr for the inspiration)

0.5.0 - (2021-02-23)

• This is the final release on the 0.x.x
• Added ability to assign a default category in SssomTransformer when the incoming category is invalid
• Added the ability to generate different types of graph summary reports

0.4.0 - (2021-02-08)

• Fixed a bug in NtTransformer when parsing malformed triples
• Added a transformer for parsing SSSOM
• Added ability to fold predicates to node properties
• Added ability to unfold node properties to predicates
• Added ability to remove singleton nodes from a graph
• Fixed bug in KGX CLI transform operation that prevented stack trace from showing up
• Unified the way predicates are parsed across different transformers
• Added ability to annotate edges with OWLStar vocabulary in RdfOwlTransformer

0.3.1 - (2021-01-20)

• Fixed a bug that led to import errors
• Fixed column ordering when exporting CSV/TSV
• Added ability to generate a TRAPI knowledge map for a graph
• Fixed bug in ObographJsonTransformer when inferring node category

0.3.0 - (2020-12-21)

• Added Graph API to KGX
• Added compatibility to Biolink Model 1.4.0
• Added the ability to facet on node and edge properties for graph-summary CLI operation
• Fixed a bug where source name defined in YAML was not being used for graph name

0.2.4 - (2020-11-25)

• Fixed bug when handling empty elements returned from bmt
• Fixed bug in CLI when setting property types in RdfTransformer
• Fixed bug when reifying edges on export in RdfTransformer

0.2.3 - (2020-11-04)

• Updated requirements.txt
• Added a Dockerfile

0.2.2 - (2020-11-04)

• Made get_toolkit method configurable
• Use proper input format when parsing OWL via CLI
• Switched default parsing format from CSV to TSV
• Fixed bug with spawning processes when transforming source
• Fixed parsing of xrefs from from OBOGraph JSON

0.2.1 - (2020-11-04)

0.2.0 - (2020-10-20)

• Improved clique merge operation and addded support for strict and relaxed mode
• Fixed a major bug while merging lists during graph merge operation
• Fixed a bug in neo4j-download CLI
• Updated the merge and transform YAML format
• Added support for parsing and exporting jsonlines
• KGX now assigns UUID for edges that don't have and id
• Updated documentation

0.1.0 - (2020-09-10)

• Initial release