Change log

Release History

VersionDateDescription
1.4.12014-07-18Git tag.
1.4.02014-06-26Dependency updates (new Rhea data model)
1.3.202014-03-13Enzyme synonyms in JSON; RHEA: prefix for xrefs
1.3.192013-10-17Bug fix
1.3.182013-09-06JSON exporter
1.3.172013-06-04Dependency updates
1.3.162012-11-30IUBMB flags
1.3.152012-11-16Fixed IntEnzXML validation issue
1.3.142012-11-14Urgent update to fix CML issue
1.3.132012-11-14Rhea reactions in CML for IntEnzXML
1.3.122012-10-08Dependencies update
1.3.112012-10-03Methods gone public; bug fix; dependencies update
1.3.102012-05-22Bug fix, dependencies update
1.3.92011-05-20
1.3.82010-11-26Bug fix
1.3.72010-11-25KEGG enzyme format
1.3.62010-10-07Bug fix
1.3.52010-05-10Bug fix
1.3.42010-04-15Bug fix
1.3.32010-04-14Dependencies update
1.3.22009-12-01Cross references to Rhea from IntEnzXML
1.3.12009-10-12Preliminary EC numbers in IntEnzXML
1.32009-09-30Preliminary EC numbers
1.2.12009-06-25Updated dependencies
1.22009-05-07Added BioPAX export
1.12009-01-19Fixed xchars export
1.0.42008-08-19Updated dependencies
1.0.32008-04-22Updated dependency
1.0.22008-03-28Updated dependency

Release 1.4.1 - 2014-07-18

TypeChangesBy
fixJust a tag created with git, containing the whole code tree.rafalcan

Release 1.4.0 - 2014-06-26

TypeChangesBy
updateUpdated to intenz-core-4.3.3, intenz-mapper-4.6.0, intenz-biopax-1.0.6, intenz-database-1.1.5, rhea-domain-1.8.1, rhea-mapper-3.8.3 and biobabel-core-0.18.rafalcan

Release 1.3.20 - 2014-03-13

TypeChangesBy
addAdded synonyms to the JSON returned for a serial EC number.rafalcan
addAdded RHEA: prefix to the accession_number of Rhea links in IntEnzXML.rafalcan
updateUpdated to intenz-translator-1.0.12.rafalcan

Release 1.3.19 - 2013-10-17

TypeChangesBy
fixRestablished exception catching removed by mistake in the previous release, which allows going on with other entries if there is some problem during XML marshalling.rafalcan
updateUpdated to latest versions of rhea-mapper and biobabel-core.rafalcan
addAdded cml schema to the output directory (script).rafalcan

Release 1.3.18 - 2013-09-06

TypeChangesBy
addAdded interface IntenzExporter for exporters, and a new implementation JsonExporter to be used by webapps.rafalcan
removeDeprecated methods from XmlExporter taking release number and date as parameters, as they don't conform to the interface and are not needed for every exporter implementation. In this case, they can be set using the accessor methods.rafalcan
fixMoved dependency on Oracle driver to the apps profile and test scope, avoiding its inclusion in the jar package.rafalcan

Release 1.3.17 - 2013-06-04

TypeChangesBy
updateUpdated to latest version of parent, intenz-core, intenz-mapper, intenz-translator, rhea-mapper and javax.mail.rafalcan
removeRemoved unused files from the jar file, including a log4j.xml which produced a rogue log file from the web services in the server.rafalcan
addAdded an 'apps' profile to use for releases (the packaged jar artifact is also used by the web services, but does not need any log4j or database configuration files).rafalcan

Release 1.3.16 - 2012-11-30

TypeChangesBy
updateUpdated to latest version of intenz-mapper, intenz-biopax and intenz-xml - which add IUBMB flags - and intenz-translator.rafalcan
addAdded IUBMB flag to IntEnzXML (as attribute for plain text reactions, or as label for Rhea reactions exported as CMLReact).rafalcan

Release 1.3.15 - 2012-11-16

TypeChangesBy
updateUpdated to latest versions of intenz-xml, which fixes issue with IntEnzXML validation in LDCs.rafalcan

Release 1.3.14 - 2012-11-14

TypeChangesBy
updateUpdated to latest versions of rhea-cml, which avoids troublesome formulae (non compliant with CMLReact schema).rafalcan

Release 1.3.13 - 2012-11-14

TypeChangesBy
addAdded Rhea reactions as CML.rafalcan
updateUpdated to latest versions of intenz-xml - which allows reactions to be included as CML -, intenz-mapper and intenz-translator.rafalcan
addAdded dependency on rhea-cml to export Rhea reactions as CMLReact within IntEnzXML.rafalcan

Release 1.3.12 - 2012-10-08

TypeChangesBy
updateUpdated to latest version of intenz-biopax - which uses latest rhea-biopax, fixing an issue with BioPAX export related to the citations data model.rafalcan

Release 1.3.11 - 2012-10-03

TypeChangesBy
fixXmlExporter constructor is now public, usable from other packages. Also, ExporterApp.getDescriptions is now public and static, with one parameter.rafalcan
fixAmpershands are now escaped in link elements.rafalcan
updateUpdated to latest version of intenz-mapper - which fixes a bug resulting in failed exports for EC numbers with modified versions -, intenz-database, rhea-domain, rhea-mapper, biobabel-db, log4j and junit.rafalcan

Release 1.3.10 - 2012-05-22

TypeChangesBy
fixClosing output stream for every XML file avoids the "too many open files" error.rafalcan
updateUpdated to latest version of intenz-mapper, intenz-xml (which adds ChEBI IDs to cofactors), intenz-translator, intenz-biopax (which uses proper URIs for RDF IDs), intenz-database, rhea-domain and rhea-mapper.rafalcan
fixFixed script (compression of exported files).rafalcan

Release 1.3.9 - 2011-05-20

TypeChangesBy
updateUpdated to latest version of parent (intenz), intenz-mapper, intenz-translator, rhea-domain, rhea-mapper and biobabel-db.rafalcan
fixReinstated method to get back xchars markup instead of escaped text.rafalcan
fixRelease number and date are taken from the database now, instead of the properties file.rafalcan
fixOutput directories are created if not there.rafalcan
fixThis module is now deployed to the repository.rafalcan

Release 1.3.8 - 2010-11-26

TypeChangesBy
fixFixed bug which left unescaped ampershands in the XML file, by using non-deprecated API.rafalcan

Release 1.3.7 - 2010-11-25

TypeChangesBy
addAdded exporter for KEGG enzyme flat file.rafalcan
addAdded command line options to ExporterApp.rafalcan
updateUpdated to latest version of dependencies.rafalcan

Release 1.3.6 - 2010-10-07

TypeChangesBy
fixRemoved links to Rhea when the reaction is not public.rafalcan
updateUpdated to latest version of intenz (parent), intenz-mapper, rhea-domain, rhea-mapper, biobabel-db, xercesImpl, javax.mail, log4j and junit.rafalcan

Release 1.3.5 - 2010-05-10

TypeChangesBy
fixFixed addition of links to XML (no 'links' element added when there are none to add).rafalcan
updateUpdated to latest version of intenz-mapper, rhea-domain and rhea-mapper.rafalcan

Release 1.3.4 - 2010-04-15

TypeChangesBy
updateUpdated to latest version of intenz-xml, which fixes a bug in the generation of the whole-tree XML.rafalcan

Release 1.3.3 - 2010-04-14

TypeChangesBy
updateUpdated to latest versions of intenz-biopax, rhea-domain, rhea-mapper and biobabel-db modules.rafalcan
fixFixed script for SQL dump.rafalcan

Release 1.3.2 - 2009-12-01

TypeChangesBy
addAdded cross references to Rhea from IntEnzXML.rafalcan
updateUpdated to latest versions of domain and xml modules.rafalcan

Release 1.3.1 - 2009-10-12

TypeChangesBy
updateUpdated dependencies on rhea-mapper - which fixes potential issue with the new ChEBI database server layout -, intenz-xml - which adds a new attribute to better distinguish preliminary EC numbers - and intenz-biopax - which fixes issue with missing EC numbers.rafalcan
fixFixed direction symbol in XCHARS export.rafalcan

Release 1.3 - 2009-09-30

TypeChangesBy
addAdded support for preliminary EC numbers in exported files.rafalcan
updateUpdated dependencies on rhea.domain, rhea.mapper, intenz.mapper and biobabel.db modules.rafalcan
removeMoved XML schema and generated code to a new independent module (intenz-xml).rafalcan

Release 1.2.1 - 2009-06-25

TypeChangesBy
updateUpdated dependencies on rhea.domain, rhea.mapper, intenz.mapper and biobabel.db modules.rafalcan

Release 1.2 - 2009-05-07

TypeChangesBy
addAdded BioPAX export.rafalcan

Release 1.1 - 2009-01-19

TypeChangesBy
fixFixed export of fields containing xchars markup: it is not enclosed in CDATA sections anymore, and xchars tags take their namespace prefix.rafalcan

Release 1.0.4 - 2008-08-19

TypeChangesBy
updateUpdated dependency to latest mapper, translator and biobabel.db modules.rafalcan

Release 1.0.3 - 2008-04-22

TypeChangesBy
updateUpdated dependencies to latest mapper (and domain) module.rafalcan

Release 1.0.2 - 2008-03-28

TypeChangesBy
updateUpdated dependency to latest mapper module.rafalcan