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LexEVS 6.5.1

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Release Highlights Include:

Note: This release includes all LexEVS 6.5.0 changes.

 

Features of this Release

Efficient Value Set Resolution using Source Asserted Value Sets

  • The
New features in this release focus on updates of the value set loading system.  Since the
  • source of value sets
it
  • is the NCI Thesaurus (NCIt), and since the NCIt contains logical, computable assertions about what value sets are in
it’s
  • its system, business logic has moved towards direct access to the code system rather than external defining files.
 This
  •   This has been a collaborative effort with NCIt curators and has resulted in improved loading efficiency of value set definitions and resolved value set coding schemes.
 

Detection of Value Set Updates

  • An additional API that detects value set updates has also been made available.
 This
  •   This represents an additional efficiency for value set loading.
 
  •   

Representation of Value Set Hierarchy

  • Other assertions made in the NCIt about the hierarchical style storage of value sets also now have an API as well.
 This
  •   This is specific to the NCIt source at this time.  
This release will also contain a prototype of a direct to source value set resolution and search service, based on the kind of assertions the NCIt makes about it’s value sets.  Terminologies that make similar assertions my also make use of this API.  It should make some earlier value set API’s obsolete while retaining the ability of users to define and load their own value sets.

Fully Dynamic Source Asserted Value Set Resolution

  • Source asserted value set API can fully resolve directly against the source coding scheme.

Source Asserted Value Set Search

  • New search API implemented against Value Sets

LexEVS Services Support for Source Asserted Value Sets

  • LexEVS Distributed API and LexEVS REST services updated to fully support Source Asserted Value Sets 

Enhanced Loaders

  • Continued enhancement of existing LexEVS Loaders
    • Notably, expanded OWL2 and RRF support for MED-RT 
Some value set querying mechanisms are better optimized based on additional methods that provide more tailored object contents for methods requiring a list of value sets without resolving other attributes that may slow performance.

Issues Fixed in this Release

Many issues were reported with the large amount of new code written around value set loading and access.  This includes fixes to resolving value set function as well as value set hierarchy functions.  This also contains fixes to long standing history load issues, some tree extension issues and simple search api problems.  We updated an outdated tracking policy artifact in this release as well — removing a couple of failing value sets that were placeholders for issues that should be resolved.  This allows continuous integration to be more accurate and precise without any expected failures that can be ignored.  

Migration Notes

LexEVS 6.5.1 - Features Implemented

  • Numerous fixes were included.   

 

LexEVS 6.5.1 - Features Implemented (43)

FeatureSummary
FeatureSummaryType
LEXEVS-3509I would like to add a value set to the VS hierarchy implementation from an outside sourceImprovement
LEXEVS-3694Change the coding scheme name in ResolvedConceptReference returned by both search and resolution API. Improvement
LEXEVS-3781Increase memory on LoadMetaBatch scriptImprovement
LEXEVS-3640Place value set nodes in value set hierarchy using contributing source.New Feature
LEXEVS-3406I would like to have a value set service that runs directly against the NCItNew Feature
LEXEVS-3524Allow VS Hiearchy to be resolved from Source Asserted VS APINew Feature
LEXEVS-3475Write controller/business logic layer for Source Asserted VS APINew Feature
LEXEVS-3476Implement Source Asserted Value Set APINew Feature
LEXEVS-3540Implement Resolved Value Set Style API for Asserted Value SetsNew Feature
LEXEVS-3545Update the Resolved Value Set API to include access to Asserted Value SetsNew Feature
LEXEVS-3565Update and Verify Asserted Value Set Service API for Remote APINew Feature
LEXEVS-3564Update and Verify Asserted Value Set Search Service for Remote APINew Feature
LEXEVS-3639Change the URI in ResolvedConceptReference returned by Value Set Search and Resolution methods.New Feature
LEXEVS-3642Support search against a specific value set or any collection of value sets.New Feature
LEXEVS-3301I would like LexEVSTreeItem attributes to be made public or publicly accessibleNew Feature
LEXEVS-2961VS Workflow:
  key
Remove Dependency on value set definition files for NCIt defined Value Sets
JirashowSummaryfalseserverNCI Trackercolumnskey,summary,type,created,updated,due,assignee,reporter,priority,status,resolutionserverId7954a81f-12da-3366-a0ef-97c806660e7c
New Feature
LEXEVS-2962VS Workflow:
 
Generate all NCIt sourced resolved value set coding schemes from NCIt source in LexEVS
JiraserverNCI Trackercolumnskey,summary,type,created,updated,due,assignee,reporter,priority,status,resolutionserverId7954a81f-12da-3366-a0ef-97c806660e7c
New Feature
LEXEVS-3058Value Set: Value Set Hierarchy will be defined from that in the NCIt and returned in a performant mannerNew Feature
LEXEVS-2967Value Set - (Browser) Efficient search by code or name - query for value set that this concept matchesNew Feature
key
LEXEVS-2966Value Set - (Browser) Efficient retrieval VS definition metadata resolution calls. Faster queries against the definitions themselves.New Feature
LEXEVS-
2967
3170Provide ability to add Non-NCIt value sets to asserted vs hierarchyNew Feature
Value Set - (Browser) Efficient search by code or name - query for value set that this concept matches
LEXEVS-3057Value Set - Definition for LexEVS Value Set Definition Asserted Source TaskNew Feature
LEXEVS-
3058
3074Value Set:
  Value Set Hierarchy will be defined from that in the NCIt and returned in a performant manner
Create User Defined property name parameter for Concept Domain New Feature
LEXEVS-3063Implement Value Set Tree Integration for Browser API
LEXEVS-3074Value Set:  Create User Defined property name parameter for Concept Domain 
New Feature
LEXEVS-3165Implement simpler approach to resolving a list of all value sets
LEXEVS-3170Provide ability to add Non-NCIt value sets to asserted vs hierarchy
New Feature
LEXEVS-3203Value Set - Update Resolved Value Set Query Mechanism for Optimized SearchNew Feature
LEXEVS-3220Determine if a NCIt Asserted Value Set has changedNew Feature
LEXEVS-
3301
3494Follow up code cleanup test expansion for Asserted Value Set IndexingNew Feature
LEXEVS-3474I would like
LexEVSTreeItem attributes to be made public or publicly accessibleLEXEVS-3406
an index access layer to be written for the source asserted value set searchNew Feature
LEXEVS-3339Modularize the full system test to allow individual modules to be runNew Feature
LEXEVS-3473I would like
to have
an Index creation layer to be written for Source Asserted Value SetsNew Feature
LEXEVS-3477Create Full Unit test suite for the APINew Feature
LEXEVS-3547Create and support a value set
service that runs directly against the NCIt
iterator that pages from the data baseNew Feature
LEXEVS-3603Iterators for Assserted Value Sets need to be adjusted for RMINew Feature
LEXEVS-3617Update AssertedValueSet Search Extension to work with RMINew Feature
LEXEVS-3518I would like to include external value sets in NCIt asserted value set indexNew Feature
LEXEVS-3517I would like to include Neoplasm Tree value set entities in asserted VS indexNew Feature
LEXEVS-3135Default page for lexevsapi6 needs to be updatedImprovement
LEXEVS-3749Update lexgrid.org to be localImprovement
LEXEVS-3789Services don't start up when asserted value sets are not present.Improvement
LEXEVS-3587Update Lexevs value set loader to work for CTS2 in memory testsImprovement
LEXEVS-3655Update to support CTS2 asserted resolved value set read Improvement
LEXEVS-3739Add ability to determine if Asserted Value Sets exist before requesting themImprovement

LexEVS 6.5.1 - Defects Fixed (29)

Defect
Summary
jira
Type
serverNCI Tracker
columnskey,summary,type,created,updated,due,assignee,reporter,priority,status,resolution
serverId7954a81f-12da-3366-a0ef-97c806660e7c
keyLEXEVS-2712
MappingExtension.getMappingCodingSchemesEntityParticipatesIn failure.
LEXEVS-3755LoadUmlsBatch fails to load MED-RTBug
LEXEVS-3748Unable to retrieve correct namespace of target entities in a mapping coding scheme.Bug
LEXEVS-3741Core.xsd has a typo in the value set namespace declarationBug
LEXEVS-3137Contains type search breaks on special characters.Bug
LEXEVS-3221Duplicate value sets accessing the same index will fail any queries against either schemeBug
LEXEVS-3376ValueSetDefinition getEntityDescription().getContent() method does not return description.LEXEVS-3377Value sets with a Publish_Value_Set property set to ‘No’ are being loaded as definitions. 
LEXEVS-3067Value Set:
 
Thread management for resolved value set loadsBug
LEXEVS-3071Value Set Publishing Value Needs to be used to determine VS LoadsBug
LEXEVS-3092Hierarchy Source adjustment in LEXEVS-1300 fix creates an unsupported associationBug
LEXEVS-3101Code clean up including refactoring, additional testing, any minor issuesBug
LEXEVS-3121Value Set (Browser) Create initial index for coding schemes (resolved value sets)
LEXEVS-3137Contains type search breaks on special characters.
Bug
LEXEVS-
3221Duplicate value sets accessing the same index will fail any queries against either schemeLEXEVS-
3277Providing support for failing iterator paging on tree service extensionBug
LEXEVS-3299OWL2 Loader -- ChEBI load runs out of memoryBug
LEXEVS-2712MappingExtension.getMappingCodingSchemesEntityParticipatesIn failure.Bug
LEXEVS-3305Loader - Value Set -- SourceAssertedResolvedValueSetLoad overwrites indexes with same nameBug
LEXEVS-3341NCIt History Load fails silently and throws other extraneous errorsBug
LEXEVS-3376ValueSetDefinition getEntityDescription().getContent() method does not return description.Bug
LEXEVS-
3385
3377Value sets with a Publish_Value_Set property set to ‘No’ are being loaded as definitions. Bug
Populate _ns attribute in LexEVSTreeItem with proper namespace
LEXEVS-3386Replace the value of _code (currently, header concept code) by the (source asserted) value set URI. Bug
LEXEVS-3387In the source view value set tree returned by getFullServiceValueSetTree, sort nodes by value set names.Bug
LEXEVS-3388In the terminology view of value set hierarchy returned by getSourceDefinedTree, place the NCIt node first, and then sort the rest of the root nodes by value set names.Bug
LEXEVS-
3463Move Marker for LexEVS issues Kept as Unit tests
3385Populate _ns attribute in LexEVSTreeItem with proper namespaceBug
LEXEVS-
3470Move Marker for LexEVS issues Kept as Unit tests for 6.5 branchLEXEVS-3305Loader - Value Set -- SourceAssertedResolvedValueSetLoad overwrites indexes with same name
Features not yet done
2183Tree Extension: TreeService API returns JSON String containing anonymous nodes.Bug
LEXEVS-3510
LEXEVS-3473
I would like
an Index creation layer to be written for Source Asserted Value SetsLEXEVS-3474I would like an index access layer to be written for the source asserted value set searchLEXEVS-3475Write controller/business logic layer for Source Asserted VS APILEXEVS-3476Implement Source Asserted Value Set APILEXEVS-3477Create Full Unit test suite for the API

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to Implement a service layer for the asserted value set search mechanismBug
LEXEVS-3681Serialization Error against the RMI of Resolved Value Set iteratorBug
LEXEVS-3689AssertedValueset iterator cannot advance over paged next callBug
LEXEVS-3733Search Iterator Regression failure on Source Coding Scheme NameBug
LEXEVS-3779Orphaned Asserted VS Entity Service is not needed Bug
LEXEVS-3783OWL2Loader manifest causes failed update in asserted value set indexBug
LEXEVS-3830Target Namespace in mapping iterator ResolveConceptRefence incorrectBug

LexEVS Remote API 6.5.1 - Features Implemented (10)

FeatureSummary
LEXEVS-3135Default page for lexevsapi6 needs to be updated
Type
LEXEVSREM-
145
149Updating Codebase to allow Full
Support for
Value Set Hierarchy
in LexEVS Remote API
UseImprovement
LEXEVSREM-147Updating API to provide high performance resolution of value setsImprovement
LEXEVSREM-148Create/Improve/Configure for Distributed Complete set of Resolved Value Set TestsImprovement
LEXEVSREM-
149
153Updating
Codebase to allow Full Value Set Hierarchy Use
Tests and Configuration to support LEXEVS-3221Improvement
LEXEVSREM-145Support for Value Set Hierarchy in LexEVS Remote APINew Feature
LEXEVSREM-169I would like to have Source Asserted Values in Resolved VS work in RMINew Feature
LEXEVSREM-179Unit testing and any adapatations for RMI Asserted VS SearchNew Feature
LEXEVSREM-213Expand Iterator Tests for Asserted Value SetsNew Feature
LEXEVSREM-178Remote Service Requires updates to LexEVS source and testsImprovement
LEXEVSREM-198Fix remote API tests not runningNew Feature

LexEVS Remote API 6.5.1 - Defects Fixed (5)

DefectSummaryType
LEXEVSREM-60Tree Extension: TreeExtension ChildTreeNodeIterator method throws exceptions.Bug
LEXEVSREM-146Test jars from LexEVS need to be updated to reflect current tests.Bug
LEXEVSREM-194Update Tests for Distributed Service For Asserted VS SearchBug
LEXEVSREM-228Search on uri for value set failsBug
LEXEVSREM-232Distributed Tests need updates to accommodate new Hierarchy featuresBug  

LexEVS Remote Client 6.5.1 - Features Implemented

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LexEVS Remote Client 6.5.1 - Defects Fixed 

DefectSummary
  

LexEVS CTS2 Service 1.6.1 - Features Implemented (13)

FeatureSummaryType
LEXEVSCTS2-200CTS2 Service: Test/Update service with no access to lexgrid.orgNew Feature
LEXEVSCTS2-156Remove dependcies that are no longer used/needed.Improvement
LEXEVSCTS2-251Update service to work with asserted value set changesNew Feature
LEXEVSCTS2-164Remove references to remote API in the POM and codeImprovement
LEXEVSCTS2-191Upgrade Apache Commons Collections to v3.2.2Improvement
LEXEVSCTS2-205Update lexevs-service with latest 6.5.1 jar and fix existing issuesImprovement
LEXEVSCTS2-224Adjust in Memory load to include load of Asserted Value Set SchemeNew Feature
LEXEVSCTS2-216Adjust Loader for test to include Asserted Value Set Index LoadNew Feature
LEXEVSCTS2-228Update CTS2 Framework version of maven-surefire-plugin Improvement
LEXEVSCTS2-217Update CTS2 for asserted resolved value set read inclusionNew Feature
LEXEVSCTS2-235Update URLs of WSDLs from http to httpsImprovement
LEXEVSCTS2-236Update test and version of lexevsNew Feature
LEXEVSCTS2-243Update to support CTS2 framework version with local XSDSImprovement

LexEVS CTS2 Service 1.6.1 - Defects Fixed  

DefectSummary
  

LexEVS CTS2 Framework 1.

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4.0 - Features Implemented (3)

FeatureSummaryType
CTS2FW-78Update URLs of WSDLs from http to httpsImprovement
CTS2FW-36CTS2 Framework: Remove Soap Implementation and testing from this ForkImprovement
CTS2FW-74Update XSD references and code to be localImprovement  

LexEVS CTS2 Framework 1.

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4.0 - Defects Fixed

DefectSummary
  

 

URI Resolver 1.1.0 - Features Implemented 

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