monarch-initiative/owlsim-v3

[#58] get data from biolink

[#78] allow labels to be loaded as tsvs

Merge pull request #73 from monarch-initiative/72-ontomatch-single-en… …

…tity

[#72] added service for single entity

Merge pull request #76 from monarch-initiative/issue-75 …

Implemented prefix filter,

Implemented prefix filter, #75

Merge branch 'master' into 72-ontomatch-single-entity

[#72] provide a resolveIri method in the KB

Issue #57 changed uses of 'data' to 'individualAssociations' in conte… …

…xt of the Ontology/OntologySourceData/OwlKnowledgebase in order to be more specific.

[#72] added service for single entity

Issue #57 Added methods to enable adding individuals to the Ontology … …

…via the OwlKnowledgeBase and the OntologyDataSource.

Issue #57 Added static owlLoader() method to BMKnowledgebase to make … …

…API more self-explanatory.

Added log info and made getOWLNamedIndividual private.

Tidied-up Entity and Attribute classes - made immutable value objects… …

…, added toString.

Issue #57 - Changed OwlKnowledgeBase from abstract to final class.

Issue #57 - Added new OwlKnowledgeBase class as a main entry point fo… …

…r creating a BMKnowledgeBaseOWLAPIImpl - @deprecated OWLLoader.

Added new supporting classes Ontology and OntologyDataSource, OntologyLoadException to help the OwlKnowledgeBase do its thing.
OWLLoader is only partially removed from the tests at present.
Removed overly verbose logging from FilterEngine.
Added commented-out clean-up of KnowledgeBaseModule - server still fails to start with ot without this.

Added back missing code from bungled merge.

Changed Optional from Guava to Java.util version.

Merge branch 'master' of https://github.com/monarch-initiative/owlsim-v3 …

 into 57-loader_refactor

# Conflicts:
#	owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java

[#62] we still need the the inject indicator for guice. We can the ma… …

…tcher package through java reflection and let the injector construct the objects.

Updated BMKnowledgeBaseOWLAPIImpl to use java.util.Optional as now pr… …

…oduced from CurieUtil.

Removed useless right-hand class types from collection initialisation. e.g. = new ArrayList<String>() -> new ArrayList<>();

Bumped curie-util version to 0.0.2.

Merge branch 'master' into 62-guice

typos

[#62] moved guice modules away from core

reducing logging

reducing logging

fixing typo in property name

first pass at frequency-awareness, issue #56

tests

adding missing

docs for NB3state

documentation and formatting

documentation and formatting fixes

change method-name converIndexSetToBitmap to convertIndexSetToBitmap

When converting Curie to IRI, return the original string if no conver… …

…sion is found