Bacting 1.0.4

Minor release updating various dependencies, including CDK 2.10 and BridgeDb 3.1.4, Apache Jena 5.2, Log4j 2.24.3, Guava 33.4, and more. New functionality includes the below method and the ability to read TRIG files.

Semweb managers

• rdf.saveRDF(IRDFStore store, String, String) for saving RDF in XML, N-TRIPLES, or Notation3

Full Changelog: bacting-1.0.3...bacting-1.0.4

Bacting 1.0.3

Minor update release, with BridgeDb 3.1.3 and fixed handling empty SPARQL results.

Full Changelog: bacting-1.0.2...bacting-1.0.3

Bacting 1.0.1

Minor release which updates the Eclipse version, multiple plugin updates, and new functionality:

Bioinformatics managers

• gpml.loadModel(String) load a GPML model from file
• gpml.saveModelAsGPML2013a(String) saves a GPML model to file

Semweb managers

• wikidata.getEntityIDsForWorksOfAuthor(String) taking a QID of an author and returning the Wikidata QIDs of their works
• wikidata.getDOIsForWorksOfAuthor(String) taking a QID of an author and returning the DOIs of their works
• wikidata.getEntityIDsForWorksOfVenue(String) taking a QID of a venue and returning the Wikidata QIDs of its works
• wikidata.getDOIsForWorksOfVenue(String) taking a QID of an venue and returning the DOIs of its works

Full Changelog: bacting-1.0.0...bacting-1.0.1

Bacting 1.0.0

Major release which completes the original goal: to have the basic Bioclipse 2.6 functionality available on the command line. Includes a bug fix by setting the expected content type of returned SPARQL query results. New functionality includes additional ported CDKDebugManager code from Bioclipse, and a new BioclipseManager method for remote SPARQLing with additional HTTP headers. Also updates various dependencies to their latest versions, including CMLXOM, Log4j, Guava, and JSON.

Core managers

• bioclipse.sparqlRemote(endpoint, sparql. headers) to query a SPARQL endpoint and get a raw XML reply

Cheminformatics managers

• cdk.getProperty(IMolecule, Object) and cdk.setProperty(IMolecule, Object. Object)
• chemspider.loadCompound(csid, target) to download the chemical structure of a ChemSpider record

Semweb managers

• rdf.allClasses(store)
• rdf.allPredicates(store)
• xml.validate(file)

Full Changelog: bacting-0.5.2...bacting-1.0.0

Bacting 0.5.2

Bug fix release, fixing the dependencies of the new mwmbl manager and adding the missing rdf manager dependency on commons-logging. Also updates various dependencies, including CMLXOM 4.8.

Full Changelog: bacting-0.5.1...bacting-0.5.2

Bacting 0.5.1

Minor release with JavaDoc updates and some more Java 17 building patches. New functionality includes additional ported CDKDebugManager code from Bioclipse, and a new manager for the Mwmbl search engine API.

Cheminformatics managers

• perceiveSybylAtomTypes(IMolecule) which returns a String with the list of perceived Sybyl atom types
• debug(IMolecule) which returns a string representation of the molecule
• listReaderOptions(IChemFormat)
• listWriterOptions(IChemFormat)

Search managers

• mwmbl.search(query) which returns a list of strings of webpage URLs

Full Changelog: bacting-0.5.0...bacting-0.5.1

Bacting 0.5.0

Major release, now requiring Java 17 or higher (and hence the bump to 0.5), as do recent Eclipse releases. It updates dependencies to Guava 33 and BridgeDb 3.1.1 and multiple Maven plugin updates for development. It also has a few new (ported) methods, completing porting of the JSoupManager:

Core managers

• jsoup.parse(file) which returns a JSoup Document of the workspace file

Semantic Web managers

• wikidata.getEntityID(doi) which returns the matching Wikidata entity
• wikidata.getEntityIDsForDOIs(List<doi>) which returns the matching Wikidata entities
• wikidata.getEntityIDsForType(type) which takes a Q-identifier and looks up everything P31
• wikidata.isValidQIdentifier(id)

Full Changelog: bacting-0.4.1...bacting-0.5.0

Bacting 0.4.1

Update release with several dependency updates: CMLXOM 4.7, BridgeDb 3.0.25, JSoup 1.17.1, JUnit 5.10.1 and Apache's log4 2.22, commons.io 2.15.1, and POI 5.2.5.

Full Changelog: bacting-0.4.0...bacting-0.4.1

Bacting 0.4.0

Update release with several dependency updates: Guave 32.1.3, Apache POI 5.2.4, Commons 2.14, and Jena 4.10, OPSIN 2.8, and org.json 20231013.

Full Changelog: bacting-0.3.6...bacting-0.4.0

Bacting 0.3.6

Update release with several dependency updates: BioJava 1.9.7, Guava 31.1.2, slf4j 2.0.9, and CMLXOM 4.6.

Full Changelog: bacting-0.3.5...bacting-0.3.6