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National Cancer Institute Center for Bioinformatics
Product LexEVS 5.0 Release Notes
May 08 2009
Product Changes
- New Feature: Removed convenience methods for codeToName
EVS:CF#15222 - New Feature: Update to work with SDK 4.1
EVS:CF#15942 - New Feature: Javadocs should open in new window
EVS:CF#16686 - New Feature: LexBIG GUI launch support for OSX environment
EVS:CF#16989 - New Feature: Import RRF Representation of Relationship Groups
EVS:CF#17019 - New Feature: CodingSchemeId not present in exported LexGrid XML
EVS:CF#17183 - New Feature: OWL Loader Enhancements
EVS:CF#17233 - New Feature: Finalize BDA for 5.0 release
EVS:CF#17508 - New Feature: Model revisions & readiness for Silver/Gold Compatibility
(scope modified & approved 1/14/09)
EVS:CF#17509 - New Feature: 5.0 Data Services/SDK
EVS:CF#17511 - New Feature: 2009/01 model changes
(please see Gforge tracker for more detail on the nature of the changes and further descriptions)
EVS:CF#18449 - New Feature: Add 'namespace' to the Lucene Indexes
EVS:CF#19883 - New Feature: Change name of ProtegeFramesLoader to RadlexProtegeFramesLoader
EVS:CF#19888 - New Feature: Rename getParentsOf() and getChildrenOf()
EVS:CF#19889 - New Feature: Support query of non-concept entities
EVS:CF#19890 - New Feature: Creation of XSL stylesheets for transformation of LexBig data to n-1 LexBig versions
EVS:CF#20043
- Bug: Implement getAssociation for EVS API web service
EVS:CF#15091 - Bug: Two constructors create ConceptReferenceList methods throw exceptions
EVS:CF#15976 - Bug: Example to dump/query auxiliary metadata
EVS:CF#16508 - Bug: Better error handling for invalid search criteria in http interface
EVS:CF#16579 - Bug: Users should have the ability to request Search results be sorted
EVS:CF#17161 - Bug: Remove JUnit test dependency on 'Automobiles' vocab for LexEVS Grid Services
EVS:CF#17405 - Bug: Change -nf option to -fe (fail on error)
EVS:CF#17410 - Bug: EntityDescription not assigned to the NCI PT (rdfs:label) using Scrubber output
EVS:CF#17421 - Bug: LexBIG History 'getEditActionList' Error
EVS:CF#19411 - Bug: Owl loader fails when duplicate objectProperty is loaded from two namespaces
EVS:CF#19462 - Bug: Supported Coding Scheme default is set even when coding scheme name is specified in manifest
EVS:CF#19484 - Bug: Applying manifest with only an association forward/reverse name receives 'String index out of range' exception.
EVS:CF#19485 - Bug: CodedNodeGraph not resolving across ontology boundary
EVS:CF#19492 - Bug: Entity 'isActive' not being indexed correctly on Postgresql and MS Access
EVS:CF#19573 - Bug: Problem applying supportedNamespace
EVS:CF#19586 - Bug: Unable to load NCIT v9.01d and other large ontologies
EVS:CF#19600 - Bug: Equivalent CodingScheme on SupportedNamespace default value not being set correctly.
EVS:CF#19628 - Bug: Relationships not resolving that contain a Namespace that has a localId that does not match the CodingScheme.
EVS:CF#19629 - Bug: CodingSchemeProperties not being persisted to the database.
EVS:CF#19702 - Bug: LexBIG property behavior does not match EA model
EVS:CF#19716 - Bug: Transitivity Table not being built
EVS:CF#19741 - Bug: Supported Hierarchies not being fully populated in 2.3 - 5.0 Compatibility Test
EVS:CF#19864 - Bug: LexBIG 2.3 xml import command fails
EVS:CF#19900 - Bug: Metathesaurus history accessing wrong column name
EVS:CF#20032 - Bug: Owl loader ClassCast Exception while loading OWLObjectProperties
EVS:CF#20037 - Bug: Lucene Indexer fails with empty EntityDescription
EVS:CF#20068 - Bug: EMF loaders fail while inserting CodingScheme Properties
EVS:CF#20070 - Bug: Exception entering null into BIGINT column on PostgreSQL database.
EVS:CF#20193 - Bug: Blank description in the Service Context on grid portal
EVS:CF#20419
Important Remaining Issues
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:title} {panel:title=Contents} {toc:minLevel=2} {panel} National Cancer Institute Center for Bioinformatics \\ Product LexEVS 5.0 Release Notes \\ May 08 2009 h2. Product Changes * *New Feature:* Removed convenience methods for codeToName [EVS:CF#15222 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=15222&group_id=491&atid=1904] * *New Feature:* Update to work with SDK 4.1 [EVS:CF#15942 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=15942&group_id=491&atid=1853] * *New Feature:* Javadocs should open in new window [EVS:CF#16686 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=16686&group_id=491&atid=1904] * *New Feature:* LexBIG GUI launch support for OSX environment [EVS:CF#16989 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=16989&group_id=491&atid=1853] * *New Feature:* Import RRF Representation of Relationship Groups [EVS:CF#17019 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=17019&group_id=491&atid=1904] * *New Feature:* CodingSchemeId not present in exported LexGrid XML [EVS:CF#17183 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=17183&group_id=491&atid=1904] * *New Feature:* OWL Loader Enhancements [EVS:CF#17233 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=17233&group_id=491&atid=1904] * *New Feature:* Finalize BDA for 5.0 release [EVS:CF#17508 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=17508&group_id=491&atid=1904] * *New Feature:* Model revisions & readiness for Silver/Gold Compatibility (scope modified & approved 1/14/09) [EVS:CF#17509 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=17509&group_id=491&atid=1904] * *New Feature:* 5.0 Data Services/SDK [EVS:CF#17511 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=17511&group_id=491&atid=1904] * *New Feature:* 2009/01 model changes (please see Gforge tracker for more detail on the nature of the changes and further descriptions) [EVS:CF#18449 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=18449&group_id=491&atid=1904] * *New Feature:* Add 'namespace' to the Lucene Indexes [EVS:CF#19883 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=19883&group_id=491&atid=1853] * *New Feature:* Change name of ProtegeFramesLoader to RadlexProtegeFramesLoader [EVS:CF#19888 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=19888&group_id=491&atid=1853] * *New Feature:* Rename getParentsOf() and getChildrenOf() [EVS:CF#19889 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=19889&group_id=491&atid=1853] * *New Feature:* Support query of non-concept entities [EVS:CF#19890 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=19890&group_id=491&atid=1853] * *New Feature:* Creation of XSL stylesheets for transformation of LexBig data to n-1 LexBig versions [EVS:CF#20043 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=20043&group_id=491&atid=1853] * *Bug:* Implement getAssociation for EVS API web service [EVS:CF#15091 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=15091&group_id=491&atid=1904] * *Bug:* Two constructors create ConceptReferenceList methods throw exceptions [EVS:CF#15976 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=15976&group_id=491&atid=1904] * *Bug:* Example to dump/query auxiliary metadata [EVS:CF#16508 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=16508&group_id=491&atid=1904] * *Bug:* Better error handling for invalid search criteria in http interface [EVS:CF#16579 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=16579&group_id=491&atid=1904] * *Bug:* Users should have the ability to request Search results be sorted [EVS:CF#17161 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=17161&group_id=491&atid=1904] * *Bug:* Remove JUnit test dependency on 'Automobiles' vocab for LexEVS Grid Services [EVS:CF#17405 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=17405&group_id=491&atid=1904] * *Bug:* Change \-nf option to \-fe (fail on error) [EVS:CF#17410 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=17410&group_id=491&atid=1904] * *Bug:* EntityDescription not assigned to the NCI PT (rdfs:label) using Scrubber output [EVS:CF#17421 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=17421&group_id=491&atid=1904] * *Bug:* LexBIG History 'getEditActionList' Error [EVS:CF#19411 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=19411&group_id=491&atid=1850] * *Bug:* Owl loader fails when duplicate objectProperty is loaded from two namespaces [EVS:CF#19462 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=19462&group_id=491&atid=1850] * *Bug:* Supported Coding Scheme default is set even when coding scheme name is specified in manifest [EVS:CF#19484 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=19484&group_id=491&atid=1850] * *Bug:* Applying manifest with only an association forward/reverse name receives 'String index out of range' exception. [EVS:CF#19485 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=19485&group_id=491&atid=1850] * *Bug:* CodedNodeGraph not resolving across ontology boundary [EVS:CF#19492 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=19492&group_id=491&atid=1850] * *Bug:* Entity 'isActive' not being indexed correctly on Postgresql and MS Access [EVS:CF#19573 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=19573&group_id=491&atid=1850] * *Bug:* Problem applying supportedNamespace [EVS:CF#19586 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=19586&group_id=491&atid=1850] * *Bug:* Unable to load NCIT v9.01d and other large ontologies [EVS:CF#19600 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=19600&group_id=491&atid=1850] * *Bug:* Equivalent CodingScheme on SupportedNamespace default value not being set correctly. [EVS:CF#19628 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=19628&group_id=491&atid=1850] * *Bug:* Relationships not resolving that contain a Namespace that has a localId that does not match the CodingScheme. [EVS:CF#19629 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=19629&group_id=491&atid=1850] * *Bug:* CodingSchemeProperties not being persisted to the database. [EVS:CF#19702 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=19702&group_id=491&atid=1850] * *Bug:* LexBIG property behavior does not match EA model [EVS:CF#19716 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=19716&group_id=491&atid=1850] * *Bug:* Transitivity Table not being built [EVS:CF#19741 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=19741&group_id=491&atid=1850] * *Bug:* Supported Hierarchies not being fully populated in 2.3 - 5.0 Compatibility Test [EVS:CF#19864 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=19864&group_id=491&atid=1850] * *Bug:* LexBIG 2.3 xml import command fails [EVS:CF#19900 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=19900&group_id=491&atid=1850] * *Bug:* Metathesaurus history accessing wrong column name [EVS:CF#20032 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=20032&group_id=491&atid=1850] * *Bug:* Owl loader ClassCast Exception while loading OWLObjectProperties [EVS:CF#20037 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=20037&group_id=491&atid=1850] * *Bug:* Lucene Indexer fails with empty EntityDescription [EVS:CF#20068 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=20068&group_id=491&atid=1850] * *Bug:* EMF loaders fail while inserting CodingScheme Properties [EVS:CF#20070 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=20070&group_id=491&atid=1850] * *Bug:* Exception entering null into BIGINT column on PostgreSQL database. [EVS:CF#20193 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=20193&group_id=491&atid=1850] * *Bug:* Blank description in the Service Context on grid portal [EVS:CF#20419 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=20419&group_id=491&atid=1850] h2. Important Remaining Issues Make use of logging consistent - eliminate system out. We will address this if time permits [EVS:CF#14971 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=14971&group_id=491&atid=1853] The NCI_Thesaurus association Has_Salt_Form and Has_Free_Acid_Or_Base needs reverse name. We will address this if time permits. [EVS:CF#15975 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=15975&group_id=491&atid=1853] gov.nih.nci.evs.domain.Atom.getLUI does not return value. We will address this if time permits. |
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[EVS:CF#15667 |
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| https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=15667&group_id=491&atid=1850] Serializer Exception on org.apach.lucene.search.regenex. We will address this if time permits. |
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[EVS:CF#16678 |
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CORE Product Dependencies
Refer to the CORE Product Dependency Matrix for the caCORE SDK and other software technologies on which this release of this product relies.
Release History
Release | Date |
---|---|
LexEVS 5.0 | 12 May 2009 |
LexEVS 4.2.1 | 30 January 2009 |
LexEVS 4.2 | 05 November 2008 |
EVS API 4.1.1 | 08 August 2008 |
EVS API 4.1 | 27 June 2008 |
EVS API 4.0 | 07 November 2007 |
caCORE 3.2 | 22 December 2006 |
caCORE 3.1 | 27 March 2006 |
caCORE 3.0.1.3 | 12 December 2006 |
caCORE 3.0.1.2 | 18 October 2005 |
caCORE 3.0.1.1 | 30 August 2005 |
caCORE 3.0.1 | 22 July 2005 |
caCORE 3.0 | 31 March 2005 |
caCORE 2.1 | 28 May 2004 |
caCORE 2.0.1 | 19 December 2003 |
caCORE 2.0 | 31 October 2003 |
caCORE 1.2 | 13 June 2003 |
caCORE 1.1 | 07 February 2003 |
caCORE 1.0 | 29 August 2002 |
...
| https://gforge.nci.nih.gov/tracker/?func=detail&group_id=491&aid=16678&atid=1850]
Results not Deserializing Properly when using QueryModifiers on CQL Queries
[EVS:CF#19406 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=19406&group_id=491&atid=1850]
Root concepts found by ListHierarchyMetaBySource when running against NCI MetaThesaurus with source set to NCI are different from root concepts in NCI Thesaurus.
[EVS:CF#20354 | https://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=20354&group_id=491&atid=1850]
h2. CORE Product Dependencies
Refer to the [CORE Product Dependency Matrix|https://wiki.nci.nih.gov/x/hIx8] for the caCORE SDK and other software technologies on which this release of this product relies.
h2. Release History
|| Release || Date ||
| LexEVS 5.0 \\ | 12 May 2009 \\ |
| LexEVS 4.2.1 \\ | 30 January 2009 \\ |
| LexEVS 4.2 \\ | 05 November 2008 \\ |
| EVS API 4.1.1 \\ | 08 August 2008 \\ |
| EVS API 4.1 \\ | 27 June 2008 \\ |
| EVS API 4.0 \\ | 07 November 2007 \\ |
| caCORE 3.2 \\ | 22 December 2006 \\ |
| caCORE 3.1 \\ | 27 March 2006 \\ |
| caCORE 3.0.1.3 \\ | 12 December 2006 \\ |
| caCORE 3.0.1.2 | 18 October 2005 \\ |
| caCORE 3.0.1.1 | 30 August 2005 \\ |
| caCORE 3.0.1 | 22 July 2005 \\ |
| caCORE 3.0 \\ | 31 March 2005 \\ |
| caCORE 2.1 \\ | 28 May 2004 \\ |
| caCORE 2.0.1 \\ | 19 December 2003 \\ |
| caCORE 2.0 \\ | 31 October 2003 \\ |
| caCORE 1.2 \\ | 13 June 2003 \\ |
| caCORE 1.1 \\ | 07 February 2003 \\ |
| caCORE 1.0 \\ | 29 August 2002 \\ |
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