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

Bacting 0.3.5

Update release with several dependency updates: CDK 2.9, Guava 32.1.1, Apache Jena 4.9, Commons IO 2.13, and BridgeDb 3.0.23.

Full Changelog: bacting-0.3.4...bacting-0.3.5

Bacting 0.3.4

Update release with a new sitemap manager and new methods in the xml manager, and several dependency updates: JSON 20230618 and BioJava 1.9.6.

Search managers

• sitemap.parse(url) which returns a list of URL strings

Semantic Web managers

• xml.readValid(filename) which returns a XOM Document
• xml.readWellFormed(filename) which returns a XOM Document
• xml.readValidString(string) which returns a XOM Document
• xml.readString(string) which returns a XOM Document

Full Changelog: bacting-0.3.3...bacting-0.3.4

Bacting 0.3.3

Update release with a new zenodo manager and several dependency updates: Woordstox 6.5.1, JSoup 1.16.1, commons-io 2.12.0, and XOM 1.3.9.

Search managers

• zenodo.getOAIPMHData(doi)

Full Changelog: bacting-0.3.2...bacting-0.3.3