IntEnz curator tool change log

Release History

VersionDateDescription
4.3.0Updates for new Rhea data model
4.2.152014-02-19Bug fix
4.2.142013-08-09Bug fixes
4.2.132013-08-07No V$SESSION in auditpackage
4.2.122013-06-12Health check for the curator tool.
4.2.112013-06-11Fixed citations URLs; using WS for ChEBI public data.
4.2.102012-12-03IUBMB flag
4.2.92012-11-05Editing target EC of transferred entries
4.2.82012-11-02Editing notes for already deleted/transferred enzymes
4.2.72011-05-13Bug fix
4.2.62011-05-06Bug fix
4.2.52011-04-07Bug fix
4.2.42010-10-14Oracle 11g.
4.2.32010-03-03Updated dependencies.
4.2.22010-01-19Updated ffwriter.
4.2.12009-12-17Bug fixes.
4.22009-12-11Preliminary EC numbers and maintainable authentication
4.1.32009-01-26Fixed dependency
4.1.22009-01-19Updated dependency
4.1.12009-01-14Fixed bug
4.12009-01-13Cofactor handling
4.0.102008-07-03Xchars update
4.0.92008-06-09Bug fix
4.0.82008-05-30Rheactions colour code, ORed cofactors
4.0.72008-04-25ORed cofactors
4.0.62008-04-23
4.0.52008-04-03Avoiding cofactor loss
4.0.42008-03-31Fixed cofactor handling
4.0.32008-03-12Fixed complex reactions display
4.0.22008-02-21Removed unused code
4.0.12008-02-15Fixed cofactors

Release 4.3.0 -

TypeChangesBy

update

Updated to latest versions of intenz-core, intenz-mapper, intenz-ffwriter and all rhea artifacts (new data model).rafalcan

Release 4.2.15 - 2014-02-19

TypeChangesBy

fix

Extended limit of text field for enzyme names.rafalcan

update

Updated to latest version of parent, intenz-ffwriter, rhea-mapper, rhea-util, rhea-biopax, rhea-find-struts1 and biobabel-core.rafalcan

Release 4.2.14 - 2013-08-09

TypeChangesBy

fix

Inactive preliminary EC numbers can be created now. Fixes 217.rafalcan

fix

UniProt cross references shown also when there are no others. Fixes 186.rafalcan

fix

Cofactors view is now properly shown. Fixes 172.rafalcan

fix

Now the reason of a suggestion or proposal is shown in the entry view and also in the listing of suggested/proposed changes. Fixes 101.rafalcan

fix

Book editions can have values other than integers (ex. '2nd'). Fixes 113.rafalcan

fix

XChars markup can now be properly stored and edited for links. Fixes 114.rafalcan

fix

Cofactors are now properly sorted in SIB preview. Fixes 116.rafalcan

Release 4.2.13 - 2013-08-07

TypeChangesBy

fix

Variable osuser is now set in the database session (auditpackage) when the connection is established, by calling explicitly the method setosuser, which allows removing the reference to V$SESSION from the body of the package (Rhea does not use it, but this explicit call instead).rafalcan

update

Updated dependency on intenz-ffwriter.rafalcan

Release 4.2.12 - 2013-06-12

TypeChangesBy

add

Added filter and JSP to allow health checks from the load balancer without logging them.rafalcan

Release 4.2.11 - 2013-06-11

TypeChangesBy

fix

Fixed URL for bibliographic references (used to be SRS, now is Europe PubMed Central).rafalcan

update

Updated to latest version of parent, intenz-core, intenz-mapper, intenz-ffwriter, rhea-webapp-util - which uses ChEBI web services for ChEBI public data instead of a connection to the database -, rhea-chebiUpdater, biobabel-webapp, biobabel-core, biobabel-citations and log4j.rafalcan

remove

Removed unused database connection to ChEBI public.rafalcan

Release 4.2.10 - 2012-12-03

TypeChangesBy

update

Updated to latest version of intenz-core and intenz-mapper - which implement IUBMB flags for enzyme-reaction associations -, intenz-ffwriter, rhea-domain, rhea-mapper, biobabel-core and biobabel-citations.rafalcan

add

Added controls to manage IUBMB flags for reactions.rafalcan

Release 4.2.9 - 2012-11-05

TypeChangesBy

add

Now it is possible to edit the target EC in already transferred entries. Fixes 2987702.rafalcan

Release 4.2.8 - 2012-11-02

TypeChangesBy

update

Updated to latest versions of intenz-core, intenz-mapper, intenz-ffwriter, rhea-domain, rhea-mapper, rhea-util, rhea-ph, rhea-biopax, rhea-find-struts1, rhea-taglib, rhea-chebiUpdater, biobabel-core, biobabel-db, biobabel-citations (which now uses CiteXplore WS v3) and commons-collections.rafalcan

add

Now it is possible to edit history notes for deleted and transferred entries. Fixes 2987702.rafalcan

Release 4.2.7 - 2011-05-13

TypeChangesBy

fix

Fixed NPE when trying to import a new cofactor from ChEBI.rafalcan

Release 4.2.6 - 2011-05-06

TypeChangesBy

fix

Caught errors from citations retrieval: now there is an error message in the form but no blank page.rafalcan

fix

Reaction source is now handled using a Rhea class, not an EnzymeSourceConstant.rafalcan

update

Updated to latest version of intenz-ffwriter and forced to latest biobabel-citations, which fixes issue with jaxws versions.rafalcan

Release 4.2.5 - 2011-04-07

TypeChangesBy

fix

Proper use of the rhea-webapp-util module (missing objects in session/application scope).rafalcan

fix

Removed duplicate jar files from included war artifacts, which caused classpath conflicts (two versions of the same jar file).rafalcan

update

Updated to latest version of most intenz and rhea modules, one of them (rhea-domain) required to deal with reactions cross-referencing EcoCyc.rafalcan

Release 4.2.4 - 2010-10-14

TypeChangesBy

update

Updated database configuration to point to the new 11g instance.rafalcan

update

Updated to latest version of intenz-core, intenz-mapper, intenz-ffwriter, rhea-domain, rhea-mapper, rhea-chebiIdAssigner, rhea-find-struts1, rhea-search-struts1, rhea-chebiUpdater and biobabel-db.rafalcan

Release 4.2.3 - 2010-03-03

TypeChangesBy

update

Updated to latest version of several dependencies, one of them - biobabel-core - fixes a bug in the CAS number validation.rafalcan

Release 4.2.2 - 2010-01-19

TypeChangesBy

update

Updated to latest version of intenz-ffwriter with DE line modifications.rafalcan

Release 4.2.1 - 2009-12-17

TypeChangesBy

update

Updated to latest version of intenz-core and displaytag.rafalcan

fix

Fixed overlay of war dependencies to avoid clashing versions of dependencies (esp. log4j).rafalcan

fix

Removed static links (based on EC number) - which are automatically generated - from the database and the drop-down selector.rafalcan

Release 4.2 - 2009-12-11

TypeChangesBy

add

Added support for preliminary EC numbers: create, amend, transfer, search, list, link to other preliminary ECs.rafalcan

update

Updated dependencies.rafalcan

fix

Refactored authentication: Users identify themselves at login using the method configured in the application container (web.xml or context file), so that their passwords are stored in just one place, not three. All of the users share the database user, but their work is distinguished in the audit tables by their v$session.osuser oracle property (now set when opening the connection).rafalcan

fix

Textual reactions are now stripped of any line feed characters to avoid problems in the exported enzyme.dat.rafalcan

Release 4.1.3 - 2009-01-26

TypeChangesBy

fix

Removed dependency on citations-1.0 which clashed with transitive dependency on citations-1.0.3.rafalcan

Release 4.1.2 - 2009-01-19

TypeChangesBy

update

Updated dependency to biobabel.db to fix an issue related to tnsnames.ora file not found.rafalcan

Release 4.1.1 - 2009-01-14

TypeChangesBy

fix

Fixed bug related to wrong name given to a session attribute.rafalcan

Release 4.1 - 2009-01-13

TypeChangesBy

add

Added list of cofactors in IntEnz to allow their re-mapping.rafalcan

Release 4.0.10 - 2008-07-03

TypeChangesBy

update

Updated to latest version of xchars-config.rafalcan

fix

Excluded xchars jar files from war dependencies, as they accumulated different versions in the WEB-INF/lib directory.rafalcan

Release 4.0.9 - 2008-06-09

TypeChangesBy

fix

Fixed bug introduced in previous release, related to reaction status.rafalcan

Release 4.0.8 - 2008-05-30

TypeChangesBy

fix

Fixed problem with addition of complex cofactors (ANDed/ORed) when the compound name included '+' or parentheses.rafalcan

update

Updated to latest intenz.mapper to use rhea mapper interfaces.rafalcan

update

Updated to latest rhea.search module to use Rhea colour code for reaction status.rafalcan

Release 4.0.7 - 2008-04-25

TypeChangesBy

add

Added functionality to add ORed cofactors.rafalcan

Release 4.0.6 - 2008-04-23

TypeChangesBy

update

Updated to latest rhea modules and intenz.mapper to fix a bug due to new xrefs and update management in rheactions.rafalcan

Release 4.0.5 - 2008-04-03

TypeChangesBy

add

Added check to avoid losing cofactors when committing an entry.rafalcan

update

Updated to latest mapper version.rafalcan

add

Added menu item for curator manual.rafalcan

Release 4.0.4 - 2008-03-31

TypeChangesBy

update

Updated to latest biobabel util package which fixes a bug in the way OperatorSets are parsed from Strings. This made cofactors to disappear in some cases.rafalcan

fix

Fixed display and linking of ORed/ANDed cofactors.rafalcan

Release 4.0.3 - 2008-03-12

TypeChangesBy

fix

Complex reactions are shown properly, that is with their child reactions.rafalcan

Release 4.0.2 - 2008-02-21

TypeChangesBy

remove

Moved unused helper classes to the db-indexing module.rafalcan

Release 4.0.1 - 2008-02-15

TypeChangesBy

fix

Fixed cofactor handling and displaying.rafalcan