Bacting - Bacting 1.0.7

Major update release, fixing queries against Wikidata for the graph split, important updates including Apache HttpClient5, Oscar 5.3, NanoJava 2.0.5 and jQUDT 1.5.1.

Cheminformatics managers * opsin.parseIUPACNameAsTokens(String) returns a List of Strings with the tokens * opsin.createVariations(String, List<List<String>>, boolean) which create IUPAC name variations , max 5000 * opsin.createVariations(String, List<List<String>>, int, boolean) which create IUPAC name variations

Full Changelog: https://github.com/egonw/bacting/compare/bacting-1.0.6...bacting-1.0.7

Scientific Software - Peer-reviewed - Java
Published by egonw 6 months ago

Bacting - Bacting 1.0.6

This release updates for the Wikidata graph split, updates various depedencies, importantly Apache Jena 5.4 and CMLXOM 4.13, and adds new functionality.

Semweb managers * wikidata.getDOIsForWorksForPeopleAtEvent(String) for returning DOIs of works by people attending the event

Full Changelog: https://github.com/egonw/bacting/compare/bacting-1.0.5...bacting-1.0.6

Scientific Software - Peer-reviewed - Java
Published by egonw 6 months ago

Bacting - Bacting 1.0.5

Update release with CMLXOM 4.11, CDK 2.11, Jena 5.3, JNA-InChI 1.3.1, and JSoup 1.19.

Full Changelog: https://github.com/egonw/bacting/compare/bacting-1.0.4...bacting-1.0.5

Scientific Software - Peer-reviewed - Java
Published by egonw 11 months ago

Bacting - 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: https://github.com/egonw/bacting/compare/bacting-1.0.3...bacting-1.0.4

Scientific Software - Peer-reviewed - Java
Published by egonw about 1 year ago

Bacting - Bacting 1.0.3

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

Full Changelog: https://github.com/egonw/bacting/compare/bacting-1.0.2...bacting-1.0.3

Scientific Software - Peer-reviewed - Java
Published by egonw about 1 year ago

Bacting - 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: https://github.com/egonw/bacting/compare/bacting-1.0.0...bacting-1.0.1

Scientific Software - Peer-reviewed - Java
Published by egonw over 1 year ago

Bacting - 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: https://github.com/egonw/bacting/compare/bacting-0.5.2...bacting-1.0.0

Scientific Software - Peer-reviewed - Java
Published by egonw almost 2 years ago

Bacting - 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: https://github.com/egonw/bacting/compare/bacting-0.5.1...bacting-0.5.2

Scientific Software - Peer-reviewed - Java
Published by egonw about 2 years ago

Bacting - 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: https://github.com/egonw/bacting/compare/bacting-0.5.0...bacting-0.5.1

Scientific Software - Peer-reviewed - Java
Published by egonw about 2 years ago

Bacting - 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: https://github.com/egonw/bacting/compare/bacting-0.4.1...bacting-0.5.0

Scientific Software - Peer-reviewed - Java
Published by egonw about 2 years ago

Bacting - 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: https://github.com/egonw/bacting/compare/bacting-0.4.0...bacting-0.4.1

Scientific Software - Peer-reviewed - Java
Published by egonw about 2 years ago

Bacting - 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: https://github.com/egonw/bacting/compare/bacting-0.3.6...bacting-0.4.0

Scientific Software - Peer-reviewed - Java
Published by egonw over 2 years ago

Bacting - 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: https://github.com/egonw/bacting/compare/bacting-0.3.5...bacting-0.3.6

Scientific Software - Peer-reviewed - Java
Published by egonw over 2 years ago

Bacting - 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: https://github.com/egonw/bacting/compare/bacting-0.3.4...bacting-0.3.5

Scientific Software - Peer-reviewed - Java
Published by egonw over 2 years ago

Bacting - 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: https://github.com/egonw/bacting/compare/bacting-0.3.3...bacting-0.3.4

Scientific Software - Peer-reviewed - Java
Published by egonw over 2 years ago

Bacting - 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: https://github.com/egonw/bacting/compare/bacting-0.3.2...bacting-0.3.3

Scientific Software - Peer-reviewed - Java
Published by egonw over 2 years ago

Bacting - Bacting 0.3.2

Minor update release updating dependency version to CMLXOM 4.5, slf4j 2.0.7, JSoup 1.15.4, NanoJava 2.0.2, log4j 2.20.0, and woodstox-core 6.4.0 (for OPSIN).

Full Changelog: https://github.com/egonw/bacting/compare/bacting-0.3.1...bacting-0.3.2

Scientific Software - Peer-reviewed - Java
Published by egonw almost 3 years ago

Bacting - Bacting 0.3.1

Minor release with dependency updates for BridgeDb, slf4j, Apache Jena, and org.json. Now compiled and tested with Java 11, 17, and 19, removing testing for Java 14.

Full Changelog: https://github.com/egonw/bacting/compare/bacting-0.3.0...bacting-0.3.1

Scientific Software - Peer-reviewed - Java
Published by egonw almost 3 years ago

Bacting - Bacting 0.3.0

Minor release with dependency updates for BirdgeDb, slf4j, and HttpClient. Bumped the minor release, reflecting two new papers where Bacting is used or functionality described.

Scientific Software - Peer-reviewed - Java
Published by egonw about 3 years ago

Bacting - Bacting 0.1.2

Another release with dependency updates: Guava version harmonization and various Maven plugin updates.

Scientific Software - Peer-reviewed - Java
Published by egonw over 3 years ago

Bacting - Bacting 0.1.1

This release updates a number of dependencies: XOM, org.json, Log4j, Apache POI, CMLXOM, and NanoJava.

Scientific Software - Peer-reviewed - Java
Published by egonw over 3 years ago

Bacting - Bacting 0.1.0

The release brings in the first bump of the minor version, reflecting a first article where Bioclipse scripts are used that can be run with Bacting. The release also brings in the rename of the git default branch to main. Otherwise, various dependency updates (CDK 2.8, Apache Jena 2.6.1, and Eclipse).

Full Changelog: https://github.com/egonw/bacting/compare/bacting-0.0.44...bacting-0.1.0

Scientific Software - Peer-reviewed - Java
Published by egonw over 3 years ago

Bacting - Bacting 0.0.45

Security update for the jSoup dependency.

Scientific Software - Peer-reviewed - Java
Published by egonw over 3 years ago

Bacting - Bacting 0.0.44

Minor release, bringing in some dependency updates (OPSIN 2.7.0) and some dependency cleanup.

Scientific Software - Peer-reviewed - Java
Published by egonw over 3 years ago

Bacting - Bacting 0.0.43

Release with various updates (jQUDT 1.5.0, BridgeDb 3.0.17) and a new manager for nanomaterials.

Cheminformatics managers * nm.listMaterialTypes() * nm.newMaterial() * nm.newMaterial(String), taking a type as input * nm.newMaterial(String, String), taking a type and a label as input * nm.generateInChI(), see this paper

Scientific Software - Peer-reviewed - Java
Published by egonw over 3 years ago

Bacting - Bacting 0.0.40

Release that only updated dependencies. Bacting-Bioclipse 2.0.16 (with updated Eclipse libraries), Oscar4 5.2.0, and several smaller dependency updates. No new or changed APIs.

Scientific Software - Peer-reviewed - Java
Published by egonw over 3 years ago

Bacting - Bacting 0.0.39

API-breaking release, tho only of a method introduced in Bacting 0.0.38. It also brings in two helper managers to get CSL-JSON for PubMed and DOI identifiers.

Bioinformatics managers * bridgedb.curie(String) (was bridgedb.compactIdentier(String))

Other managers * pubmed.fetchInfo(String) which a JSONObject with CSL-JSON for a PubMed identifier * doi.fetchInfo(String) which a JSONObject with CSL-JSON for a DOI

Scientific Software - Peer-reviewed - Java
Published by egonw over 3 years ago

Bacting - Bacting 0.0.36

Minor bugfix release of Bacting 0.0.35 fixing an Log4j dependency and now uses a released Bacting-Bioclipse 2.8 release.

Scientific Software - Peer-reviewed - Java
Published by egonw over 3 years ago

Bacting - Bacting 0.0.37

Minor release that updates dependencies of BridgeDb, JSoup, Apache POI, slf4j, and JUnit. No new functionality.

Scientific Software - Peer-reviewed - Java
Published by egonw over 3 years ago

Bacting - Bacting 0.0.38

Release that updates BridgeDb to version 3.0.15 with Bioregistry.io and primary/secondary identifier support. It also has minor JavaDoc improvements.

Bioinformatics managers * bridgedb.getSourceByPrefix(String); returning a DataSource * bridgedb.compactIdentifier(String) returning an Xref * map(String, Xref) to search with a REST service * map(String, Xref, String) to search for a spectic target with a REST service

Scientific Software - Peer-reviewed - Java
Published by egonw over 3 years ago

Bacting - Bacting 0.0.35

Minor release that updates Apache Jena to 4.5.0 and ports four cdk manager methods.

Cheminformatics managers * cdk.mcss(List<IMolecule>) * cdk.newMolecule() * cdk.newMolecule(IChemObjectBuilder) * cdk.newMolecule(IAtomContainer)

Scientific Software - Peer-reviewed - Java
Published by egonw almost 4 years ago

Bacting - Bacting 0.0.34

Release that updates a number of dependencies and ports two methods in the CDKManager:

Cheminformatics managers * cdk.calculateMass(IMolecule) * cdk.calculateMajorIsotopeMass(IMolecule)

Scientific Software - Peer-reviewed - Java
Published by egonw almost 4 years ago

Bacting - Bacting 0.0.33

Bug fix release, fixing a regression in InChI calculation where warnings were now all taken as errors. This regression was introduced in Bacting 0.0.31.

Scientific Software - Peer-reviewed - Java
Published by egonw almost 4 years ago

Bacting - Bacting 0.0.32

This release ports a few old Bioclipse methods and adds some new methods. The UIManager and BioclipseManager are extended with additional methods to download content (allowing passing additional HTTP headers) and working with files in the workspace. This release also ported the JSoupManager and introduces a manager to search in the DuckDuckGo search engine.

Core managers * download(String, String, Map<String,String>) * ui.append(byte[]) * ui.readFile(String) * ui.readFileIntoArray(String) * jsoup.parseString(String) to parse HTML pages * jsoup.select(Element, String) to select content in an HTML page

Other managers * duckduckgo.search(String) which return search hits for the given search string as a List<String>

Scientific Software - Peer-reviewed - Java
Published by egonw almost 4 years ago

Bacting - Bacting 0.0.31

Brings in updated libraries for Apache Jena (4.3.2), BridgeDb (3.0.13) and the CDK (2.7.1). The last adopts jna-inchi with the InChI 1.0.6 library.

Scientific Software - Peer-reviewed - Java
Published by egonw about 4 years ago

Bacting - Bacting 0.0.30

Bigger release, which now compiles with Java 17, introduces a new QUDTManager for quantity conversion, and adds a few more methods:

Core managers * qudt.newQuantity(value, unit) for creating a new quantity object from a double value and a Unit object * qudt.newQuantity(value, symbol) as the previous one, but then with a unit symbol * qudt.findUnits(symbol) for finding units from their symbol (return a list of one or more matches) * qudt.convertTo(quantity, unit) for converting, for example, a quantity in meter into millimeter * qudt.convertTo(quantity, symbol) as the previous one, but then with a unit symbol

Other managers * rdf.validateAllOfType(store, shexFile, shapeURI, type) for validating RDF against a ShEx schema, returning a report * rdf.asString(report) which converts the validation report to a String * bridgedb.search(restServer, query, limit) which allows searching with online BridgeDb REST services

Scientific Software - Peer-reviewed - Java
Published by egonw about 4 years ago

Bacting - Bacting 0.0.29

This release brings in another round of updates: OPSIN 2.6.0. Oscar4 5.1.2, and BridgeDb 3.0.12.

Scientific Software - Peer-reviewed - Java
Published by egonw about 4 years ago

Bacting - Bacting 0.0.28

This release updates to CDK 2.6, Oscar4 5.1.1, Bioclipse 2.8.0.11 (based on the latest Eclipse libraries), and BridgeDb 3.0.11.

Scientific Software - Peer-reviewed - Java
Published by egonw about 4 years ago

Bacting - Bacting 0.0.27

Incremental release fixing a cookie HTTP problem in another place, and updated some dependencies (Oscar4 and BridgeDb).

Scientific Software - Peer-reviewed - Java
Published by egonw about 4 years ago

Bacting - Bacting 0.0.26

Bacting 0.0.26 is a minor release porting on cdk manager function, adding a dependency for convenience, improved documentation a bit, and addressing a Apache HTTPClient cookie issue:

Cheminformatics managers * cdk.getFormats() returning the formats supported for IO

Scientific Software - Peer-reviewed - Java
Published by egonw over 4 years ago

Bacting - Bacting 0.0.25

Bacting 0.0.25 is based on Bioclipse 2.8.0.10 with Apache Jena 4.2.0 and ports a few more methods:

Cheminformatics managers * cdk.totalFormalCharge(IMolecule)

Semantic web managers * wikidata.hasMolecule(InChI) * wikidata.getEntityID(InChI) * wikidata.getMolecule(InChI)

Scientific Software - Peer-reviewed - Java
Published by egonw over 4 years ago

Bacting - Bacting 0.0.24

Bacting 0.0.24 ports a few more methods

Cheminformatics managers * cdk.calculateSMILES(IMolecule) * cdk.loadMolecule(file) * cdk.determineIChemFormat(file) * cdx.diff(ICDKMolecule, ICDKMolecule)

Scientific Software - Peer-reviewed - Java
Published by egonw over 4 years ago

Bacting - Bacting 0.0.23

Bacting 0.0.23 does not migrate or add new Bioclipse functionality, but updates several build dependencies and the poi-ooxml dependency. It also adds a missing BridgeDb dependency needed load local ID mapping databases. Finally, this release comes with a bundle, so that Bacting can be used more easily when multiple managers are needed.

Scientific Software - Peer-reviewed - Java
Published by egonw over 4 years ago

Bacting - Bacting 0.0.22

Bacting 0.0.22 completes the Bioclipse 2.6 PubChem manager and upgrades the RDF manager to use the most recent Apache Jena 4.1.0 library.

Cheminformatics managers * pubchem.loadCompoundRDF() * pubchem.loadCompound() * pubchem.loadCompound3d() * pubchem.download3d() * pubchem.download3dAsString() * pubchem.download(List) * pubchem.download3d(List)

Scientific Software - Peer-reviewed - Java
Published by egonw over 4 years ago

Bacting - Bacting 0.0.21

Bacting 0.0.21 adds a new CDK method to generate SVG, updates to the latest BridgeDb version, but mostly improves the test coverage.

Cheminformatics managers * cdk.asSVG(IMolecule) which returns a String

Scientific Software - Peer-reviewed - Java
Published by egonw over 4 years ago

Bacting - Bacting 0.0.20

Bacting 0.0.20 ports a few methods (see below), disables the chemspider manager because the service was down, improves the test coverage, and the rdf.importURL() method now follows HTTP redirects, improving the usefulness greatly. PS, the paper is out!

Core managers * ui.append(String path, InputStream toWrite)

Cheminformatics managers * cdk.getFormat(format) which returns a IChemFormat * pubchem.download(cid) * pubchem.downloadRDF(cid)

Other managers * rdf.getForPredicate(IRDFStore store, String resourceURI, String predicate) * rdf.allOwlSameAs(IRDFStore store, String resourceURI) * rdf.allOwlEquivalentClass(IRDFStore store, String resourceURI, String predicate)

Scientific Software - Peer-reviewed - Java
Published by egonw over 4 years ago

Bacting - Bacting 0.0.19

Bacting 0.0.19 updates the URLs of the BridgeDb webservice (if you use it, you need to upgrade to this version), and now requires Java 11, as one of the dependencies does.

Scientific Software - Peer-reviewed - Java
Published by egonw over 4 years ago

Bacting - JOSS paper v3

Second revision, applying some editorial text suggestions.

Scientific Software - Peer-reviewed - Java
Published by egonw over 4 years ago

Bacting - Bacting 0.0.18

Bacting 0.0.18 updated the dependencies to CDK 2.5 and BridgeDb 3.0.4. It also ports the OscarManager with the below functionality:

Other managers * oscar.findNamedEntities(String) which returns a list of strings * oscar.findResolvedNamedEntities() which returns a list of IMolecules * oscar.extractText() which takes a HTML string and extract the text content

Scientific Software - Peer-reviewed - Java
Published by egonw almost 5 years ago

Bacting - Bacting 0.0.17

Minor release that adds documentation on how to use Bacting in Python with scyjava and removes a duplicate plugin declaration in the pom.xml.

Scientific Software - Peer-reviewed - Java
Published by egonw almost 5 years ago

Bacting - Bacting 0.0.16

This release fixes a few JavaDoc issues, and adds two methods that needed to be ported to allow comparing chemical structures from the new CAS Common Chemistry with Wikidata (doi:10.5281/zenodo.4682767).

Cheminformatics managers * cdk.isValidCAS(String) * cdk.partition(IMolecule molecule) (which returns a List<IAtomContainer>)

Scientific Software - Peer-reviewed - Java
Published by egonw almost 5 years ago

Bacting - Bacting 0.0.15

This release mostly improved test coverage and adds some further documentation. It adds an initial Biojava manager (based on version 1.9.4) with a minimal amount of ported functionality and fixed an issues in that bridgedb.guessIdentifierType() did not always provide expected output. The following new functionality was ported in this release, along with the Bioclipse domain objects IDNA, ISequence, IProtein, and IRNA:

Bioinformatics managers * biojava.DNAfromPlainSequence(dnaString) * biojava.DNAfromPlainSequence(dnaString, name) * biojava.proteinFromPlainSequence(proteinString) * biojava.proteinFromPlainSequence(proteinString, name)

Cheminformatics managers * pubchem.downloadAsString() * inchi.options() * inchi.generate(molecule, options)

Scientific Software - Peer-reviewed - Java
Published by egonw about 5 years ago

Bacting - Bacting 0.0.14

This release mostly improved documentation, adds test coverage with JaCoCo, and updates versions of dependencies:

• Eclipse Core Runtime (3.20.0) and Resources (3.13.900)
• BridgeDb 2.3.10
• OPSIN 2.5.0

Furthermore, it fixes a few small issues:

• reported manager names of the pubchem and cdx managers
• BridgeDb mapping with the REST webservice

Scientific Software - Peer-reviewed - Java
Published by egonw about 5 years ago

Bacting - Bacting 0.0.13

This releases adds a method to export a report as Markdown and ports three xml manager methods to explore XML files.

Core managers * report.asMarkdown(IReport report) * xml.isWellFormed(String file) * xml.isValid(String file) * xml.listNamespaces(String file)

Scientific Software - Peer-reviewed - Java
Published by egonw over 5 years ago

Bacting - Bacting 0.0.12

This releases adds JavaDoc and unit tests for all managers. It also updates the dependencies on BridgeDb (now 2.3.8) and the XOM library (now 1.2.5). It ports the ui.newProject() method and fixes the return value of ui.newFile(). This release now requires Java 8 and has been tested against Java 11 and Java 14.

Core managers * ui.newProject(String projectName)

Scientific Software - Peer-reviewed - Java
Published by egonw over 5 years ago

Bacting - Bacting 0.0.11

This releases ports several more methods, one to determine the file format of some content, and parse the content of a string in to a molecule object. Also, two methods to download content from ChemSpider are added.

Cheminformatics managers * cdk.determineIChemFormatOfString(String fileContent) which returns the file format * cdk.fromString(String molstring) which returns an IMolecule * chemspider.downloadAsString(Integer csid) which returns a String * chemspider.download(Integer csid) which returns an IMolecule

Scientific Software - Peer-reviewed - Java
Published by egonw over 5 years ago

Bacting - Bacting 0.0.10

This releases migrated four additional methods from the rdf manager to add triples, and one method to set prefixes.

Other managers * rdf.addPrefix(IRDFStore store, String prefix, String namespace) * rdf.addObjectProperty(IRDFStore store, String subject, String property, String object) * rdf.addDataProperty(IRDFStore store, String subject, String property, String object) * rdf.addTypedDataProperty(IRDFStore store, String subject, String property, String object, String dataType) * rdf.addPropertyInLanguage(IRDFStore store, String subject, String property, String value, String language)

Scientific Software - Peer-reviewed - Java
Published by egonw over 6 years ago

Bacting - Bacting 0.0.9

This releases updates to Bacting-Bioclipse 2.8.0.6 which introduces the IBioclipseManager extended by the new IBactingManager. Each manager now implements two new methods: getName() (inherited from Bioclipse 2.6 and before) and the new doi() which has been introduced to mimicked the doi <manager> command in Bioclipse 2, which is hard to reproduce(r) in Groovy. Furthermore, this release ports the cdk.appendToSDF() method and add a new UIManager method ui.renewFile(file) which creates a new file if it did not exist yet, or empties the existing file.

Core managers * ui.renewFile(String file)

Cheminformatics managers * cdk.appendToSDF(String sdFile, ICDKMolecule molecule)

Scientific Software - Peer-reviewed - Java
Published by egonw over 6 years ago

Bacting - Bacting 0.0.8

This releases updates to CDK 2.3 and ported a few rdf manager methods.

Other managers * rdf.importURL(IRDFStore store, String url) which returns an IRDFStore * rdf.importURL(IRDFStore store, String url, Map<String, String> extraHeaders) which does the same but with the option to add additional HTTP headers * rdf.asRDFN3(IRDFStore store) which returns the triples as Notation3 * rdf.asTurtle(IRDFStore store) which returns the triples as Turtle * rdf.asRDF(IRDFStore store, String type) which returns the triples as RDF/XML

Scientific Software - Peer-reviewed - Java
Published by egonw over 6 years ago

Bacting - Bacting 0.0.7

First release after 0.0.5 and the second one available from Maven Central. This release ported a first method from the chemspider manager, the bridgedb manager with BridgeDb, and the report manager. For searching in ChemSpider, identifier mapping, and creating HTML reports.

Core managers * bioclipse.version() * report.createReport() * report.asHTML(IReport report)

Cheminformatics managers * chemspider.resolve(String inchiKey)

Other managers * bridgedb.getSource(String source) * bridgedb.getSourceFromName(String name) * bridgedb.listAllSources() * bridgedb.listAllOrganisms() * bridgedb.search(IDMapper database, String query, int limit) * bridgedb.guessIdentifierType(String identifier) * bridgedb.map(String restService, String identifier, String source) * bridgedb.map(IDMapper database, String identifier, String source) * bridgedb.map(String restService, String identifier, String source, String target) * bridgedb.map(IDMapper database, String identifier, String source, String target) * bridgedb.map(IDMapper database, Xref source) * bridgedb.map(IDMapper database, Xref source, String target)

Scientific Software - Peer-reviewed - Java
Published by egonw over 6 years ago

Bacting - Bacting 0.0.5

Major release as it is the first one available from OSSRH, simplying the use. This release changed the groupId to accomodate for this. In Groovy you can now use:

groovy @GrabResolver(name='ossrh', root='https://oss.sonatype.org/content/groups/public') @Grab(group='io.github.egonw.bacting', module='managers-cdk', version='0.0.5')

This release also introduces a new manager, excel, which allows reading of Excel files. Otherwise, it ported a few more methods from Bioclipse 2.6.

Core managers * bioclipse.version() * bioclipse.requireVersion("2.8.0.2")

Other managers * rdf.sparql(IRDFStore store, String sparql) * rdf.size(IRDF store) * rdf.importFile(IRDFStore store, String rdfFile, String format) * rdf.importFromStream(IRDFStore store, InputStream rdfStream, String format) * rdf.importFromString(IRDFStore store, String rdfContent, String format)

Scientific Software - Peer-reviewed - Java
Published by egonw over 6 years ago

Bacting - Bacting 0.0.4

Not that many updates, since the current set of methods already runs a good many of the methods I seem to be using and also of the A lot of Bioclipse Scripting Language examples booklet. This release includes two new methods which help with populating Wikidata with clean structures, which are not yet ported back to Bioclipse (pending a bit more testing). This release also depends on a newer Eclipse library version.

Cheminformatics managers * cdk.getAtomsWithDefinedStereo(IMolecule) * cdk.getAtomsWithUndefinedStereo(IMolecule)

Other managers * rdf.createStore(String tripleStoreDirectoryPath) (which creates an on disk store using Apache Jena's TDB)

Scientific Software - Peer-reviewed - Java
Published by egonw almost 7 years ago

Bacting - Bacting 0.0.3

Exposed a more APIs (see below), introducing the opsin manager. If you have used an earlier version, please note that the group and artifacts identifiers have changed.

Core managers * bioclipse.download(String url) * bioclipse.download(String url, String mimetype) * bioclipse.downloadAsFile(String url, String filename) * bioclipse.downloadAsFile(String url, String mimetype, String filename) * bioclipse.downloadAsFile(String url, String mimetype, String filename, Map<String,String> extraHeaders)

Cheminformatics managers * opsin.parseIUPACName(String name) * opsin.parseIUPACNameAsCML(String name) * opsin.parseIUPACNameAsSMILES(String name)

Scientific Software - Peer-reviewed - Java
Published by egonw almost 7 years ago

Bacting - Bacting 0.0.2

Exposed a few more APIs, introducing the cdx manager and a few more methods. The combination of bioclipse.sparqlRemote() and rdf.processSPARQLXML() skips the Jena parsing of the SPARQL:

Core managers * bioclipse.sparqlRemote(String serviceURL, String sparqlQueryString) * ui.open(String file) (does not do anything)

Cheminformatics managers * cdk.fromCml(String molstring) * cdk.asCDKMolecule(IMolecule) * cdk.loadMolecule(InputStream, IChemFormat) * cdx.perceiveCDKAtomTypes(IMolecule)

Other managers * rdf.processSPARQLXML(byte[] queryResults, String originalQuery)

Scientific Software - Peer-reviewed - Java
Published by egonw almost 7 years ago

Bacting - Bacting 0.0.1

First release of Bacting, a first working prototype for running Bioclipse scripts in on the command line with a regular Groovy installation. This version allows me to run an extended script to convert a SMILES to Wikidata content. The following manager APIs are supported:

Core managers * bioclipse.fullPath(String file) (uses a workspace-relative file path) * bioclipse.assumeOnline() * bioclipse.isOnline() * ui.fileExists(String file) * ui.newFile(String file) * ui.newFile(String file, String content) * ui.remove(String file) * ui.append(String file, String content)

Cheminformatics managers * cdk.createMoleculeList() (which returns a List<ICDKMolecule>) * cdk.fromSMILES(String smiles) * cdk.molecularFormulaObject(ICDKMolecule mol) (returns a IMolecularFormula) * cdk.molecularFormula(ICDKMolecule mol) (returns a string) * inchi.generate(IMolecule molecule) (returns a InChI object) * inchi.check(String inchi) * inchi.checkStrict(String inchi) * pubchem.search(String query) (which returns a List<Integer>)

Other managers * rdf.createInMemoryStore() (which returns a IRDFStore) * rdf.createInMemoryStore(boolean ontologyModel) (which returns a IRDFStore) * rdf.sparqlRemote(String serviceURL, String sparqlQueryString) (which returns a StringMatrix)

Scientific Software - Peer-reviewed - Java
Published by egonw almost 7 years ago