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h1. {

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Include Page
Menu LexEVS 6.0 CTS2 to Include
Menu LexEVS 6.0 CTS2 to Include

Introduction

LexEVS CTS2 Load API provides capability to load complete or incremental updates of Code System, Value Sets and Association contents. It also provides capability to activate and deactivate loaded contents.

Load Interfaces

There are three major load interfaces proved, each for loading specific content:

  • Code System loader - Provides capability to load complete or partial contents of Code System plus functions to activate and deactivate loaded Code System.
  • Value Sets loader - Provides capability to load Value Sets.
  • Association loader - Provides capability to load Associations.

Each of these interfaces can be accessed using:

Code Block
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h2. Introduction
LexEVS CTS2 Load API provides capability to load complete or incremental updates of Code System, Value Sets and Association contents. It also provides capability to activate and deactivate loaded contents.

h2. Load Interfaces
There are three major load interfaces proved, each for loading specific content:

* Code System loader - Provides capability to load complete or partial contents of Code System plus functions to activate and deactivate loaded Code System.
* Value Sets loader - Provides capability to load Value Sets.
* Association loader - Provides capability to load Associations.

Each of these interfaces can be accessed using:

{code}
org.lexevs.cts2.admin.load.CodeSystemLoadOperation csLoadOp = new org.lexevs.cts2.LexEvsCTS2Impl().getAdminOperation().getCodeSystemLoadOperation();
org.lexevs.cts2.admin.load.ValueSetLoadOperation vsLoadOp = new org.lexevs.cts2.LexEvsCTS2Impl().getAdminOperation().getValueSetLoadOperation();
org.lexevs.cts2.admin.load.AssociationLoadOperation assnLoadOp = new org.lexevs.cts2.LexEvsCTS2Impl().getAdminOperation().getAssociationLoadOperation();
{code}


h3. Code System Loader
{{

Code System Loader

org.lexevs.cts2.admin.load.CodeSystemLoadOperation

...

is

...

the

...

main

...

interface

...

which

...

can

...

be

...

used

...

to

...

load,

...

activate

...

and

...

deactivate

...

Code

...

System.

...

This

...

interface

...

can

...

be

...

accessed

...

using

...

main

...

LexEVSCTS2

...

interface,

...

like:

{
Code Block
}
org.lexevs.cts2.admin.load.CodeSystemLoadOperation csLoadOp = new org.lexevs.cts2.LexEvsCTS2Impl().getAdminOperation().getCodeSystemLoadOperation();
{code}

There are two different methods available to load Code System:

* Loading Code System from a file - This method provides capability to load complete Code System contents that are present in a file system.
* Loading Code System Object - This method provides capability to load supplied Code System Object.

h4. Loading Code System from a File
This function provides the capability to load Code System found in the file using the loader specified.

{{load(URI source, URI metadata, URI manifest, String loaderName, Boolean stopOnErrors, Boolean async, Boolean overwriteMetadata, String versionTag, Boolean activate)}}

|| *Description:* | Loads Code System found in source file using the loader specified. |
|| *Input:* | *  *_java.net.URI source_* - (*Mandatory*) URI corresponding to the code system file.
*  *_java.net.URI metadata_* - (Optional) URI of the XML file containing custom code system meta data. Loads additional data to be maintained and queried as terminology meta-information within the system. All tags and values are interpreted as simple text-based key/value pairs.
*  *_java.net.URI manifest_* - (Optional) URI corresponding to the manifest file. The LexGrid Manifest accommodates the need to supplement or override default information provided by the source.  More specifically, the manifest provides a means to customize the same code system metadata defined by the LexGrid model, since each element of the manifest extends directly from an element used to define the LexGrid coding scheme(aka code system) object. Each extended element allows for the administrator to specify whether the manifest definition replaces or supplements original values provided in the terminology source.  Like the LexGrid Terminology model, the manifest is defined by a formal model mastered as XML Schema.
* *_java.lang.String loaderName_* - (*Mandatory*) Loader to use for loading the code system. Use getSupportedLoaderNames() method to get all the loaders supported by the service.
For example, 'OBOLoader' could be used to load code system source that is in OBO format, 'OWLLoader' for code system source in OWL format, 'LexGrid_Loader' for Code System in LexGrid XML format, etc.
* *_boolean stopOnErrors_* - (Optional) default is false. True means stop if any load error is detected. False means attempt to load what can be loaded if recoverable errors are encountered.
* *_boolean async_* - (Optional) Flag controlling whether load occurs in the calling thread.
If true, the load will occur in a separate asynchronous process.
If false, this method blocks until the load operation completes or fails. Regardless of setting, the getStatus and getLog calls are used to fetch results.
* *_boolean_overwriteMetadata_* - (Optional) If true, existing meta data for the code system will be erased. If false, new meta data will be appended to existing meta data.
* *_java.lang.String versionTag_* - (Optional) The tag (e.g "devel", "production", ...) to be set for the this code system.
* *_boolean activate_* - (Optional) True: activates the code system after the load. |
|| *Output:* |  Array of *_;

There are two different methods available to load Code System:

  • Loading Code System from a file - This method provides capability to load complete Code System contents that are present in a file system.
  • Loading Code System Object - This method provides capability to load supplied Code System Object.

Loading Code System from a File

This function provides the capability to load Code System found in the file using the loader specified.

load(URI source, URI metadata, URI manifest, String loaderName, Boolean stopOnErrors, Boolean async, Boolean overwriteMetadata, String versionTag, Boolean activate)

Description:

Loads Code System found in source file using the loader specified.

Input:

  • java.net.URI source - (Mandatory) URI corresponding to the code system file.
  • java.net.URI metadata - (Optional) URI of the XML file containing custom code system meta data. Loads additional data to be maintained and queried as terminology meta-information within the system. All tags and values are interpreted as simple text-based key/value pairs.
  • java.net.URI manifest - (Optional) URI corresponding to the manifest file. The LexGrid Manifest accommodates the need to supplement or override default information provided by the source. More specifically, the manifest provides a means to customize the same code system metadata defined by the LexGrid model, since each element of the manifest extends directly from an element used to define the LexGrid coding scheme(aka code system) object. Each extended element allows for the administrator to specify whether the manifest definition replaces or supplements original values provided in the terminology source. Like the LexGrid Terminology model, the manifest is defined by a formal model mastered as XML Schema.
  • java.lang.String loaderName - (Mandatory) Loader to use for loading the code system. Use getSupportedLoaderNames() method to get all the loaders supported by the service.
    For example, 'OBOLoader' could be used to load code system source that is in OBO format, 'OWLLoader' for code system source in OWL format, 'LexGrid_Loader' for Code System in LexGrid XML format, etc.
  • boolean stopOnErrors - (Optional) default is false. True means stop if any load error is detected. False means attempt to load what can be loaded if recoverable errors are encountered.
  • boolean async - (Optional) Flag controlling whether load occurs in the calling thread.
    If true, the load will occur in a separate asynchronous process.
    If false, this method blocks until the load operation completes or fails. Regardless of setting, the getStatus and getLog calls are used to fetch results.
  • boolean_overwriteMetadata - (Optional) If true, existing meta data for the code system will be erased. If false, new meta data will be appended to existing meta data.
  • java.lang.String versionTag - (Optional) The tag (e.g "devel", "production", ...) to be set for the this code system.
  • boolean activate - (Optional) True: activates the code system after the load.

Output:

Array of edu.mayo.informatics.lexgrid.convert.utility.URNVersionPair

...

-

...

URN

...

and

...

Version

...

of

...

the

...

loaded

...

code

...

system

Exception:

org.LexGrid.LexBIG.Exceptions.LBException

...

Sample Call:

  • Step 1: Instantiate CodeSystemLoadOperation if it is not done yet:
    Code Block
    
org.lexevs.cts2.admin.load.CodeSystemLoadOperation csLoadOp = new org.lexevs.cts2.LexEvsCTS2Impl().getAdminOperation().getCodeSystemLoadOperation();

...

  • Step 2:
...
  •  Call 
...
  •  load 
...
  •  method 
...
  •  by 
...
  •  passing 
...
  •  the 
...
  •  inputfile 
...
  •  location 
...
  •  and 
...
  •  other 
...
  •  parameter 
...
  •  values: 
...
  •  Code Block
...
  • 
 URNVersionPair[] csloaded = csLoad.load(new File("resources/testData/fungal_anatomy.obo").toURI(), null, null, "OBOLoader", true, true, true, "DEV", true); 

...
Loading Code System Object
This function provides the capability to load supplied Code System object.
load(CodingScheme codeSystem, URI metadata, Boolean stopOnErrors, Boolean async, Boolean overwriteMetadata, String versionTag, Boolean activate)
 Description: 
 Loads supplied Code System Object. 
 Input: 
  • org.LexGrid.codingSchemes.CodingScheme 
...
  •  codeSystem
...
  •  - 
...
  •  (
...
  • Mandatory
...
  • ) 
...
  •  Code 
...
  •  System 
...
  •  Object 
...
  •  to 
...
  •  be 
...
  •  loaded 
...
  •  into 
...
  •  the 
...
  •  terminology 
...
  •  service.
...
  • java.net.URI 
...
  •  metadata
...
  •  - 
...
  •  (Optional) 
...
  •  URI 
...
  •  of 
...
  •  the 
...
  •  XML 
...
  •  file 
...
  •  containing 
...
  •  custom 
...
  •  code 
...
  •  system 
...
  •  meta 
...
  •  data. 
...
  •  Loads 
...
  •  additional 
...
  •  data 
...
  •  to 
...
  •  be 
...
  •  maintained 
...
  •  and 
...
  •  queried 
...
  •  as 
...
  •  terminology 
...
  •  meta-information 
...
  •  within 
...
  •  the 
...
  •  system. 
...
  •  All 
...
  •  tags 
...
  •  and 
...
  •  values 
...
  •  are 
...
  •  interpreted 
...
  •  as 
...
  •  simple 
...
  •  text-based 
...
  •  key/value 
...
  •  pairs.
...
  • boolean stopOnErrors - (Optional) 
...
  •  default 
...
  •  is 
...
  •  false. 
...
  •  True 
...
  •  means 
...
  •  stop 
...
  •  if 
...
  •  any 
...
  •  load 
...
  •  error 
...
  •  is 
...
  •  detected. 
...
  •  False 
...
  •  means 
...
  •  attempt 
...
  •  to 
...
  •  load 
...
  •  what 
...
  •  can 
...
  •  be 
...
  •  loaded 
...
  •  if 
...
  •  recoverable 
...
  •  errors 
...
  •  are 
...
  •  encountered.
...
  • boolean 
...
  •  async
...
  •  - 
...
  •  (Optional) 
...
  •  Flag 
...
  •  controlling 
...
  •  whether 
...
  •  load 
...
  •  occurs 
...
  •  in 
...
  •  the 
...
  •  calling 
...
  •  thread.
...

  •  If 
...
  •  true, 
...
  •  the 
...
  •  load 
...
  •  will 
...
  •  occur 
...
  •  in 
...
  •  a 
...
  •  separate 
...
  •  asynchronous 
...
  •  process.
...

  •  If 
...
  •  false, 
...
  •  this 
...
  •  method 
...
  •  blocks 
...
  •  until 
...
  •  the 
...
  •  load 
...
  •  operation 
...
  •  completes 
...
  •  or 
...
  •  fails. 
...
  •  Regardless 
...
  •  of 
...
  •  setting, 
...
  •  the 
...
  •  getStatus 
...
  •  and 
...
  •  getLog 
...
  •  calls 
...
  •  are 
...
  •  used 
...
  •  to 
...
  •  fetch 
...
  •  results.
...
  • boolean overwriteMetadata_
...
  •  - 
...
  •  (Optional) 
...
  •  If 
...
  •  true, 
...
  •  existing 
...
  •  meta 
...
  •  data 
...
  •  for 
...
  •  the 
...
  •  code 
...
  •  system 
...
  •  will 
...
  •  be 
...
  •  erased. 
...
  •  If 
...
  •  false, 
...
  •  new 
...
  •  meta 
...
  •  data 
...
  •  will 
...
  •  be 
...
  •  appended 
...
  •  to 
...
  •  existing 
...
  •  meta 
...
  •  data.
...
  • java.lang.String 
...
  •  versionTag
...
  •  - 
...
  •  (Optional) 
...
  •  The 
...
  •  tag 
...
  •  (e.g 
...
  •  "devel", 
...
  •  "production", 
...
  •  ...) 
...
  •  to 
...
  •  be 
...
  •  set 
...
  •  for 
...
  •  the 
...
  •  this 
...
  •  code 
...
  •  system.
...
  • boolean 
...
  •  activate
...
  •  - 
...
  •  (Optional) 
...
  •  True: 
...
  •  activates 
...
  •  the 
...
  •  code 
...
  •  system 
...
  •  after 
...
  •  the 
...
  •  load.
...
Output:
...
 Array 
...
 of 
...
edu.mayo.informatics.lexgrid.convert.utility.URNVersionPair
...
 - 
...
 URN 
...
 and 
...
 Version 
...
 of 
...
 the 
...
 loaded 
...
 code 
...
system 
 Exception: 
org.LexGrid.LexBIG.Exceptions.LBException
...
 Sample Call: 
  • Step 1: Instantiate CodeSystemLoadOperation if it is not done yet: 
     Code Block
    
org.lexevs.cts2.admin.load.CodeSystemLoadOperation csLoadOp = new org.lexevs.cts2.LexEvsCTS2Impl().getAdminOperation().getCodeSystemLoadOperation();

...
  • Step 2:
...
  •  Populate 
...
  •  Code 
...
  •  System 
...
  •  Object: 
...
  •  Code Block
...
  • 
org.LexGrid.codingSchemes.CodingScheme cs = new org.LexGrid.codingSchemes.CodingScheme();
cs.setApproxNumConcepts(new Long(4));
cs.setCodingSchemeName("miniautomobiles");
cs.setFormalName("miniautomobiles");
cs.setCodingSchemeURI("11.22.33.44");
org.LexGrid.commonTypes.Text copyright = new org.LexGrid.commonTypes.Text();
copyright.setContent("Copyright Mayo Clinic.");
cs.setCopyright(copyright);
cs.setDefaultLanguage("en");
cs.setMappings(new org.LexGrid.naming.Mappings());
cs.setRepresentsVersion("1.1");

org.LexGrid.naming.SupportedAssociation saHasSubType = edu.mayo.informatics.lexgrid.convert.exporters.xml.lgxml.factory.SupportedAssociationFactory.createSupportedAssociationHasSubType();

cs.getMappings().addSupportedAssociation(saHasSubType);
org.LexGrid.naming.SupportedAssociation saUses = edu.mayo.informatics.lexgrid.convert.exporters.xml.lgxml.factory.SupportedAssociationFactory.createSupportedAssociationUses();
cs.getMappings().addSupportedAssociation(saUses);
        
org.LexGrid.relations.Relations rels = new org.LexGrid.relations.Relations();
rels.setContainerName("asD");
        
org.LexGrid.relations.AssociationPredicate ap = new org.LexGrid.relations.AssociationPredicate();
ap.setAssociationName("hasSubtype");
rels.addAssociationPredicate(ap);

ap = new org.LexGrid.relations.AssociationPredicate();

ap.setAssociationName("uses");
        
rels.addAssociationPredicate(ap);

cs.addRelations(rels);

...
  • Step 3:
...
  •  Call 
...
  •  load 
...
  •  method 
...
  •  by 
...
  •  passing 
...
  •  the 
...
  •  Code 
...
  •  System 
...
  •  Object 
...
  •  and 
...
  •  other 
...
  •  parameter 
...
  •  values: 
...
  •  Code Block
...
  • 
URNVersionPair[] csloaded = csLoad.load(cs, null, true, false, true, "DEV", true);

...
Value Set Loader
Value Set is stored in repository in terms of definitions, in LexEVS, it is known as 'Value Set Definition'. As name indicates, it is a definition of a value set contents, NOT the expanded value set contents that will be loaded. During the runtime, these definitions are resolved against the supplied Code System Version to return expanded Value Set contents. Visit LexEVS 6.0 Value Set and Pick List Definition Guide for detailed information about LexEVS Value Set Definition.
org.lexevs.cts2.admin.load.ValueSetLoadOperation
...
 is 
...
 the 
...
 main 
...
 interface 
...
 which 
...
 can 
...
 be 
...
 used 
...
 to 
...
 load 
...
 Value 
...
 Set 
...
 Definition. 
...
 This 
...
 interface 
...
 can 
...
 be 
...
 accessed 
...
 using 
...
 main 
...
 LexEVSCTS2 
...
 interface, 
...
 like:


{
 Code Block
}
org.lexevs.cts2.admin.load.ValueSetLoadOperation vsLoadOp = new org.lexevs.cts2.LexEvsCTS2Impl().getAdminOperation().getValueSetLoadOperation();
{code}


Similar 
...
 to 
...
 Code 
...
 System, 
...
 there 
...
 are 
...
 two 
...
 different 
...
 methods 
...
 available 
...
 to 
...
 load 
...
 Value 
...
 Sets:
...
  • Loading 
...
  •  Value 
...
  •  Set 
...
  •  Definition 
...
  •  from 
...
  •  a 
...
  •  file 
...
  •  - 
...
  •  This 
...
  •  method 
...
  •  provides 
...
  •  capability 
...
  •  to 
...
  •  load 
...
  •  Value 
...
  •  Set 
...
  •  Definition(s) 
...
  •  that 
...
  •  are 
...
  •  present 
...
  •  in 
...
  •  a 
...
  •  file 
...
  •  system.
...
  • Loading 
...
  •  Value 
...
  •  Set 
...
  •  Definition 
...
  •  Object 
...
  •  - 
...
  •  This 
...
  •  method 
...
  •  provides 
...
  •  capability 
...
  •  to 
...
  •  load 
...
  •  supplied 
...
  •  Value 
...
  •  Set 
...
  •  Definition 
...
  •  Object.
...
Loading 
...
 Value 
...
 Set 
...
 Definition 
...
 from 
...
 a 
...
 File
...
This 
...
 function 
...
 provides 
...
 the 
...
 capability 
...
 to 
...
 load 
...
 Value 
...
 Set 
...
 Definition(s) 
...
 found 
...
 in 
...
 the 
...
 file 
...
 using 
...
 the 
...
 loader 
...
 specified.
...
load(URI 
...
 source, 
...
 URI 
...
 releaseURI, 
...
 String 
...
 loaderName, 
...
 Boolean 
...
 stopOnErrors)
...
Description:
...
 Loads 
...
 Value 
...
 Set 
...
 Definition(s) 
...
 found 
...
 in 
...
 source 
...
 file 
...
 using 
...
 the 
...
 loader 
...
 specified. 
...
 Input: 
  • java.net.URI 
...
  •  source
...
  •  - 
...
  •  (
...
  • Mandatory
...
  • ) 
...
  •  URI 
...
  •  corresponding 
...
  •  to 
...
  •  the 
...
  •  Value 
...
  •  Set 
...
  •  Definition(s) 
...
  •  file.
...
  • java.net.URI 
...
  •  releaseURI
...
  •  - 
...
  •  (Optional) 
...
  •  Release 
...
  •  URI 
...
  •  the 
...
  •  loaded 
...
  •  contents 
...
  •  belong 
...
  •  to.
...
  • java.lang.String 
...
  •  loaderName
...
  •  - 
...
  •  (
...
  • Mandatory
...
  • ) 
...
  •  Loader 
...
  •  to 
...
  •  use 
...
  •  for 
...
  •  loading 
...
  •  the 
...
  •  Value 
...
  •  Set 
...
  •  Definition. 
...
  •  Use 
...
  •  getSupportedLoaderNames() 
...
  •  method 
...
  •  to 
...
  •  get 
...
  •  all 
...
  •  the 
...
  •  loaders 
...
  •  supported 
...
  •  by 
...
  •  the 
...
  •  service.
...

  •  For 
...
  •  example, 
...
  •  use 
...
  •  'LexGrid_Loader' 
...
  •  to 
...
  •  load 
...
  •  file 
...
  •  containing 
...
  •  Value 
...
  •  Set 
...
  •  Definition(s) 
...
  •  in 
...
  •  LexGrid 
...
  •  XML 
...
  •  format, 
...
  • etc.
  • boolean stopOnErrors - (Optional) 
...
  •  default 
...
  •  is 
...
  •  false. 
...
  •  True 
...
  •  means 
...
  •  stop 
...
  •  if 
...
  •  any 
...
  •  load 
...
  •  error 
...
  •  is 
...
  •  detected. 
...
  •  False 
...
  •  means 
...
  •  attempt 
...
  •  to 
...
  •  load 
...
  •  what 
...
  •  can 
...
  •  be 
...
  •  loaded 
...
  •  if 
...
  •  recoverable 
...
  •  errors 
...
  •  are 
...
  •  encountered.
...
Output:
...
 Array 
...
 of 
...
edu.mayo.informatics.lexgrid.convert.utility.URNVersionPair
...
 - 
...
 URI 
...
 and 
...
 Version 
...
 of 
...
 the 
...
 loaded 
...
 Value 
...
 Set 
...
Definition 
 Exception: 
org.LexGrid.LexBIG.Exceptions.LBException
...
 Sample Call: 
  • Step 1: Instantiate ValueSetLoadOperation if it is not done yet: 
     Code Block
    
org.lexevs.cts2.admin.load.ValueSetLoadOperation vsLoadOp = new org.lexevs.cts2.LexEvsCTS2Impl().getAdminOperation().getValueSetLoadOperation();

...
  • Step 2:
...
  •  Call 
...
  •  load 
...
  •  method 
...
  •  by 
...
  •  passing 
...
  •  the 
...
  •  inputfile 
...
  •  location 
...
  •  and 
...
  •  other 
...
  •  parameter 
...
  •  values: 
...
  •  Code Block
...
  • 
URNVersionPair[] vsloaded = vsLoad.load(new File("resources/testData/vsTestData.xml").toURI(), null, "LexGrid_Loader", true);

...
Loading Value Set Definition Object
This function provides the capability to load supplied Value Set Definition object.
load(ValueSetDefinition valueSetDefinition, URI releaseURI, Boolean stopOnErrors)
 Description: 
 Loads supplied Value Set Definition Object. 
 Input: 
  • org.LexGrid.valueSets.ValueSetDefinition 
...
  •  valueSetDefinition
...
  •  - 
...
  •  (
...
  • Mandatory
...
  • ) 
...
  •  Value 
...
  •  Set 
...
  •  Definition 
...
  •  Object 
...
  •  to 
...
  •  be 
...
  •  loaded 
...
  •  into 
...
  •  the 
...
  •  terminology 
...
  •  service.
...
  • java.net.URI 
...
  •  releaseURI
...
  •  - 
...
  •  (Optional) 
...
  •  Release 
...
  •  URI 
...
  •  the 
...
  •  loaded 
...
  •  contents 
...
  •  belong 
...
  •  to.
...
  • boolean 
...
  •  stopOnErrors
...
  •  - 
...
  •  (Optional) 
...
  •  default 
...
  •  is 
...
  •  false. 
...
  •  True 
...
  •  means 
...
  •  stop 
...
  •  if 
...
  •  any 
...
  •  load 
...
  •  error 
...
  •  is 
...
  •  detected. 
...
  •  False 
...
  •  means 
...
  •  attempt 
...
  •  to 
...
  •  load 
...
  •  what 
...
  •  can 
...
  •  be 
...
  •  loaded 
...
  •  if 
...
  •  recoverable 
...
  •  errors 
...
  •  are 
...
  •  encountered.
...
Output:
...
java.lang.String
...
 - 
...
 URI 
...
 of 
...
 Value 
...
 Set 
...
 Definition 
...
loaded 
 Exception: 
org.LexGrid.LexBIG.Exceptions.LBException
...
 Sample Call: 
  • Step 1: Instantiate ValueSetLoadOperation if it is not done yet: 
     Code Block
    
org.lexevs.cts2.admin.load.ValueSetLoadOperation vsLoadOp = new org.lexevs.cts2.LexEvsCTS2Impl().getAdminOperation().getValueSetLoadOperation();_

...
  • Step 2:
...
  •  Populate 
...
  •  Code 
...
  •  System 
...
  •  Object: 
...
  •  Code Block
...
  • 
org.LexGrid.valueSets.ValueSetDefinition vsd = new org.LexGrid.valueSets.ValueSetDefinition();
vsd.setValueSetDefinitionURI("SRITEST:JUNIT:TEST:VSD1");
vsd.setValueSetDefinitionName("JUnit test vsd 1");
vsd.setConceptDomain("cd");
vsd.addRepresentsRealmOrContext("context");
vsd.setDefaultCodingScheme("Automobiles");
vsd.setIsActive(false);
vsd.setOwner("cts2");
java.util.List<org.LexGrid.commonTypes.Source> srcList = new ArrayList<org.LexGrid.commonTypes.Source>();
org.LexGrid.commonTypes.Source src = new org.LexGrid.commonTypes.Source();
src.setContent("lexevs");
srcList.add(src);
src = new org.LexGrid.commonTypes.Source();
src.setContent("cts2");
srcList.add(src);
vsd.setSource(srcList);

org.LexGrid.valueSets.DefinitionEntry de = new org.LexGrid.valueSets.DefinitionEntry();
de.setRuleOrder(1L);
de.setOperator(org.LexGrid.valueSets.types.DefinitionOperator.OR);
org.LexGrid.valueSets.CodingSchemeReference csr = new org.LexGrid.valueSets.CodingSchemeReference();
csr.setCodingScheme("Automobiles");
de.setCodingSchemeReference(csr);

vsd.addDefinitionEntry(de);

...
  • Step 3:
...
  •  Call 
...
  •  load 
...
  •  method 
...
  •  by 
...
  •  passing 
...
  •  the 
...
  •  Value 
...
  •  Set 
...
  •  Definition 
...
  •  Object 
...
  •  and 
...
  •  other 
...
  •  parameter 
...
  •  values: 
...
  •  Code Block
...
  • 
String vsdURI = vsLoadOp.load(vsd, null, true);; 

...
Association Loader
org.lexevs.cts2.admin.load.AssociationLoadOperation
...
 is 
...
 the 
...
 main 
...
 interface 
...
 which 
...
 can 
...
 be 
...
 used 
...
 to 
...
 load 
...
 Associations 
...
 with 
...
 in 
...
 a 
...
 Code 
...
 System. 
...
 This 
...
 interface 
...
 can 
...
 be 
...
 accessed 
...
 using 
...
 main 
...
 LexEVSCTS2 
...
 interface, 
...
 like:


{
 Code Block
}
org.lexevs.cts2.admin.load.AssociationLoadOperation assnLoadOp = new org.lexevs.cts2.LexEvsCTS2Impl().getAdminOperation().getAssociationLoadOperation();
{code}


There 
...
 are 
...
 two 
...
 different 
...
 methods 
...
 available 
...
 to 
...
 load 
...
 Associations:
...
  • Load 
...
  •  Associations 
...
  •  from 
...
  •  a 
...
  •  file 
...
  •  - 
...
  •  This 
...
  •  method 
...
  •  provides 
...
  •  capability 
...
  •  to 
...
  •  load 
...
  •  Associations 
...
  •  from 
...
  •  a 
...
  •  file 
...
  •  system.
...
  • Load 
...
  •  Associations 
...
  •  from 
...
  •  an 
...
  •  Object 
...
  •  - 
...
  •  This 
...
  •  method 
...
  •  provides 
...
  •  capability 
...
  •  to 
...
  •  load 
...
  •  Associations 
...
  •  supplied 
...
  •  with 
...
  •  in 
...
  •  a 
...
  •  Code 
...
  •  System 
...
  •  Object.
...
Loading 
...
 Associations 
...
 from 
...
 a 
...
 File
...
This 
...
 function 
...
 provides 
...
 the 
...
 capability 
...
 to 
...
 load 
...
 Associations 
...
 found 
...
 in 
...
 the 
...
 file 
...
 using 
...
 the 
...
 loader 
...
 specified.
...
importAssociationVersion(URI 
...
 source, 
...
 URI 
...
 metadata, 
...
 URI 
...
 manifest, 
...
 String 
...
 loaderName, 
...
 Boolean 
...
 stopOnErrors, 
...
 Boolean 
...
 async, 
...
 Boolean 
...
 overwriteMetadata, 
...
 String 
...
 versionTag, 
...
 Boolean 
...
 activate)
...
Description:
...
 Loads 
...
 Associations 
...
 found 
...
 in 
...
 source 
...
 file 
...
 using 
...
 the 
...
 loader 
...
 specified. 
...
 Input: 
  • java.net.URI 
...
  •  source
...
  •  - 
...
  •  (
...
  • Mandatory
...
  • ) 
...
  •  URI 
...
  •  corresponding 
...
  •  to 
...
  •  the 
...
  •  file 
...
  •  that 
...
  •  contains 
...
  •  Associations.
...
  • java.net.URI 
...
  •  metadata
...
  •  - 
...
  •  (Optional) 
...
  •  URI 
...
  •  of 
...
  •  the 
...
  •  XML 
...
  •  file 
...
  •  containing 
...
  •  custom 
...
  •  meta 
...
  •  data 
...
  •  for 
...
  •  the 
...
  •  code 
...
  •  system 
...
  •  that 
...
  •  contains 
...
  •  this 
...
  •  associations. 
...
  •  Loads 
...
  •  additional 
...
  •  data 
...
  •  to 
...
  •  be 
...
  •  maintained 
...
  •  and 
...
  •  queried 
...
  •  as 
...
  •  terminology 
...
  •  meta-information 
...
  •  within 
...
  •  the 
...
  •  system. 
...
  •  All 
...
  •  tags 
...
  •  and 
...
  •  values 
...
  •  are 
...
  •  interpreted 
...
  •  as 
...
  •  simple 
...
  •  text-based 
...
  •  key/value 
...
  •  pairs.
...
  • java.net.URI 
...
  •  manifest
...
  •  - 
...
  •  (Optional) 
...
  •  URI 
...
  •  corresponding 
...
  •  to 
...
  •  the 
...
  •  manifest 
...
  •  file. 
...
  •  The 
...
  •  LexGrid 
...
  •  Manifest 
...
  •  accommodates 
...
  •  the 
...
  •  need 
...
  •  to 
...
  •  supplement 
...
  •  or 
...
  •  override 
...
  •  default 
...
  •  information 
...
  •  provided 
...
  •  by 
...
  •  the 
...
  •  source. 
...
  •  More 
...
  •  specifically, 
...
  •  the 
...
  •  manifest 
...
  •  provides 
...
  •  a 
...
  •  means 
...
  •  to 
...
  •  customize 
...
  •  the 
...
  •  same 
...
  •  code 
...
  •  system 
...
  •  metadata 
...
  •  defined 
...
  •  by 
...
  •  the 
...
  •  LexGrid 
...
  •  model, 
...
  •  since 
...
  •  each 
...
  •  element 
...
  •  of 
...
  •  the 
...
  •  manifest 
...
  •  extends 
...
  •  directly 
...
  •  from 
...
  •  an 
...
  •  element 
...
  •  used 
...
  •  to 
...
  •  define 
...
  •  the 
...
  •  LexGrid 
...
  •  coding 
...
  •  scheme(aka 
...
  •  code 
...
  •  system) 
...
  •  object. 
...
  •  Each 
...
  •  extended 
...
  •  element 
...
  •  allows 
...
  •  for 
...
  •  the 
...
  •  administrator 
...
  •  to 
...
  •  specify 
...
  •  whether 
...
  •  the 
...
  •  manifest 
...
  •  definition 
...
  •  replaces 
...
  •  or 
...
  •  supplements 
...
  •  original 
...
  •  values 
...
  •  provided 
...
  •  in 
...
  •  the 
...
  •  terminology 
...
  •  source. 
...
  •  Like 
...
  •  the 
...
  •  LexGrid 
...
  •  Terminology 
...
  •  model, 
...
  •  the 
...
  •  manifest 
...
  •  is 
...
  •  defined 
...
  •  by 
...
  •  a 
...
  •  formal 
...
  •  model 
...
  •  mastered 
...
  •  as 
...
  •  XML 
...
  •  Schema.
...
  • java.lang.String 
...
  • loaderName - 
...
  •  (
...
  • Mandatory
...
  • ) 
...
  •  Loader 
...
  •  to 
...
  •  use 
...
  •  for 
...
  •  loading 
...
  •  the 
...
  •  associations. 
...
  •  Use 
...
  •  getSupportedLoaderNames() 
...
  •  method 
...
  •  to 
...
  •  get 
...
  •  all 
...
  •  the 
...
  •  loaders 
...
  •  supported 
...
  •  by 
...
  •  the 
...
  •  service.
...

  •  For 
...
  •  example, 
...
  •  'OBOLoader' 
...
  •  could 
...
  •  be 
...
  •  used 
...
  •  to 
...
  •  load 
...
  •  code 
...
  •  system 
...
  •  source 
...
  •  that 
...
  •  is 
...
  •  in 
...
  •  OBO 
...
  •  format, 
...
  •  'OWLLoader' 
...
  •  for 
...
  •  code 
...
  •  system 
...
  •  source 
...
  •  in 
...
  •  OWL 
...
  •  format, 
...
  •  'LexGrid_Loader' 
...
  •  for 
...
  •  Code 
...
  •  System 
...
  •  in 
...
  •  LexGrid 
...
  •  XML 
...
  •  format, 
...
  •  etc.
...
  • boolean 
...
  •  stopOnErrors
...
  •  - 
...
  •  (Optional) 
...
  •  default 
...
  •  is 
...
  •  false. 
...
  •  True 
...
  •  means 
...
  •  stop 
...
  •  if 
...
  •  any 
...
  •  load 
...
  •  error 
...
  •  is 
...
  •  detected. 
...
  •  False 
...
  •  means 
...
  •  attempt 
...
  •  to 
...
  •  load 
...
  •  what 
...
  •  can 
...
  •  be 
...
  •  loaded 
...
  •  if 
...
  •  recoverable 
...
  •  errors 
...
  •  are 
...
  •  encountered.
...
  • boolean 
...
  •  async
...
  •  - 
...
  •  (Optional) 
...
  •  Flag 
...
  •  controlling 
...
  •  whether 
...
  •  load 
...
  •  occurs 
...
  •  in 
...
  •  the 
...
  •  calling 
...
  •  thread.
...

  •  If 
...
  •  true, 
...
  •  the 
...
  •  load 
...
  •  will 
...
  •  occur 
...
  •  in 
...
  •  a 
...
  •  separate 
...
  •  asynchronous 
...
  •  process.
...

  •  If 
...
  •  false, 
...
  •  this 
...
  •  method 
...
  •  blocks 
...
  •  until 
...
  •  the 
...
  •  load 
...
  •  operation 
...
  •  completes 
...
  •  or 
...
  •  fails. 
...
  •  Regardless 
...
  •  of 
...
  •  setting, 
...
  •  the 
...
  •  getStatus 
...
  •  and 
...
  •  getLog 
...
  •  calls 
...
  •  are 
...
  •  used 
...
  •  to 
...
  •  fetch 
...
  •  results.
...
  • boolean overwriteMetadata_
...
  •  - 
...
  •  (Optional) 
...
  •  If 
...
  •  true, 
...
  •  existing 
...
  •  meta 
...
  •  data 
...
  •  for 
...
  •  the 
...
  •  code 
...
  •  system 
...
  •  will 
...
  •  be 
...
  •  erased. 
...
  •  If 
...
  •  false, 
...
  •  new 
...
  •  meta 
...
  •  data 
...
  •  will 
...
  •  be 
...
  •  appended 
...
  •  to 
...
  •  existing 
...
  •  meta 
...
  •  data.
...
  • java.lang.String 
...
  •  versionTag
...
  •  - 
...
  •  (Optional) 
...
  •  The 
...
  •  tag 
...
  •  (e.g 
...
  •  "devel", 
...
  •  "production", 
...
  •  ...) 
...
  •  to 
...
  •  be 
...
  •  set 
...
  •  for 
...
  •  the 
...
  •  the 
...
  •  code 
...
  •  system 
...
  •  that 
...
  •  contains 
...
  •  this 
...
  •  associations.
...
  • boolean 
...
  •  activate
...
  •  - 
...
  •  (Optional) 
...
  •  True: 
...
  •  activates 
...
  •  the 
...
  •  code 
...
  •  system 
...
  •  that 
...
  •  contains 
...
  •  this 
...
  •  association 
...
  •  after 
...
  •  the 
...
  •  load.
...
Output:
...
 None 
 Exception: 
org.LexGrid.LexBIG.Exceptions.LBException
...
 Sample Call: 
  • Step 1: Instantiate AssociationLoadOperation if it is not done yet: 
     Code Block
    
org.lexevs.cts2.admin.load.AssociationLoadOperation assnLoadOp = new org.lexevs.cts2.LexEvsCTS2Impl().getAdminOperation().getAssociationLoadOperation();

...
  • Step 2:
...
  •  Call 
...
  •  load 
...
  •  method 
...
  •  by 
...
  •  passing 
...
  •  the 
...
  •  inputfile 
...
  •  location 
...
  •  and 
...
  •  other 
...
  •  parameter 
...
  •  values: 
...
  •  Code Block
...
  • 
assnLoad.importAssociationVersion(new File("resources/testData/fungal_anatomy.obo").toURI(), null, null, "OBOLoader", true, true, true, "DEV", true);

...
Loading Associations from an Object
This function provides the capability to load Associations supplied with in a Code System object.
importAssociationVersion(CodingScheme codeSystem, URI metadata, Boolean stopOnErrors, Boolean async, Boolean overwriteMetadata, String versionTag, Boolean activate)
 Description: 
 Loads Associations supplied with in Code System Object. 
 Input: 
  • org.LexGrid.codingSchemes.CodingScheme 
...
  •  codeSystem
...
  •  - 
...
  •  (
...
  • Mandatory
...
  • ) 
...
  •  Code 
...
  •  System 
...
  •  Object 
...
  •  that 
...
  •  contains 
...
  •  Associations 
...
  •  to 
...
  •  be 
...
  •  loaded 
...
  •  into 
...
  •  the 
...
  •  terminology 
...
  •  service.
...
  • java.net.URI 
...
  •  metadata
...
  •  - 
...
  •  (Optional) 
...
  •  URI 
...
  •  of 
...
  •  the 
...
  •  XML 
...
  •  file 
...
  •  containing 
...
  •  custom 
...
  •  meta 
...
  •  data 
...
  •  of 
...
  •  code 
...
  •  system 
...
  •  that 
...
  •  contains 
...
  •  this 
...
  •  associations. 
...
  •  Loads 
...
  •  additional 
...
  •  data 
...
  •  to 
...
  •  be 
...
  •  maintained 
...
  •  and 
...
  •  queried 
...
  •  as 
...
  •  terminology 
...
  •  meta-information 
...
  •  within 
...
  •  the 
...
  •  system. 
...
  •  All 
...
  •  tags 
...
  •  and 
...
  •  values 
...
  •  are 
...
  •  interpreted 
...
  •  as 
...
  •  simple 
...
  •  text-based 
...
  •  key/value 
...
  •  pairs.
...
  • boolean 
...
  •  stopOnErrors
...
  •  - 
...
  •  (Optional) 
...
  •  default 
...
  •  is 
...
  •  false. 
...
  •  True 
...
  •  means 
...
  •  stop 
...
  •  if 
...
  •  any 
...
  •  load 
...
  •  error 
...
  •  is 
...
  •  detected. 
...
  •  False 
...
  •  means 
...
  •  attempt 
...
  •  to 
...
  •  load 
...
  •  what 
...
  •  can 
...
  •  be 
...
  •  loaded 
...
  •  if 
...
  •  recoverable 
...
  •  errors 
...
  •  are 
...
  •  encountered.
...
  • boolean 
...
  •  async
...
  •  - 
...
  •  (Optional) 
...
  •  Flag 
...
  •  controlling 
...
  •  whether 
...
  •  load 
...
  •  occurs 
...
  •  in 
...
  •  the 
...
  •  calling 
...
  •  thread.
...

  •  If 
...
  •  true, 
...
  •  the 
...
  •  load 
...
  •  will 
...
  •  occur 
...
  •  in 
...
  •  a 
...
  •  separate 
...
  •  asynchronous 
...
  •  process.
...

  •  If 
...
  •  false, 
...
  •  this 
...
  •  method 
...
  •  blocks 
...
  •  until 
...
  •  the 
...
  •  load 
...
  •  operation 
...
  •  completes 
...
  •  or 
...
  •  fails. 
...
  •  Regardless 
...
  •  of 
...
  •  setting, 
...
  •  the 
...
  •  getStatus 
...
  •  and 
...
  •  getLog 
...
  •  calls 
...
  •  are 
...
  •  used 
...
  •  to 
...
  •  fetch 
...
  •  results.
...
  • *
...
  • boolean
...
  •  overwriteMetadata 
...
  •  - 
...
  •  (Optional) 
...
  •  If 
...
  •  true, 
...
  •  existing 
...
  •  meta 
...
  •  data 
...
  •  for 
...
  •  the 
...
  •  code 
...
  •  system 
...
  •  will 
...
  •  be 
...
  •  erased. 
...
  •  If 
...
  •  false, 
...
  •  new 
...
  •  meta 
...
  •  data 
...
  •  will 
...
  •  be 
...
  •  appended 
...
  •  to 
...
  •  existing 
...
  •  meta 
...
  •  data.
...
  • java.lang.String 
...
  •  versionTag
...
  •  - 
...
  •  (Optional) 
...
  •  The 
...
  •  tag 
...
  •  (e.g 
...
  •  "devel", 
...
  •  "production", 
...
  •  ...) 
...
  •  to 
...
  •  be 
...
  •  set 
...
  •  for 
...
  •  the 
...
  •  code 
...
  •  system 
...
  •  that 
...
  •  contains 
...
  •  this 
...
  •  associations.
...
  • boolean 
...
  •  activate
...
  •  - 
...
  •  (Optional) 
...
  •  True: 
...
  •  activates 
...
  •  the 
...
  •  code 
...
  •  system 
...
  •  that 
...
  •  contains 
...
  •  this 
...
  •  associations 
...
  •  after 
...
  •  the 
...
  •  load.
...
Output:
...
 None 
 Exception: 
org.LexGrid.LexBIG.Exceptions.LBException
...
 Sample Call: 
  • Step 1: Instantiate AssociationLoadOperation if it is not done yet: 
     Code Block
    
org.lexevs.cts2.admin.load.AssociationLoadOperation assnLoadOp = new org.lexevs.cts2.LexEvsCTS2Impl().getAdminOperation().getAssociationLoadOperation(); 

...
  • Step 2:
...
  •  Populate 
...
  •  Code 
...
  •  System 
...
  •  Object: 
...
  •  Code Block
...
  • 
org.LexGrid.codingSchemes.CodingScheme cs = new org.LexGrid.codingSchemes.CodingScheme();
cs.setApproxNumConcepts(new Long(4));
cs.setCodingSchemeName("miniautomobiles");
cs.setFormalName("miniautomobiles");
cs.setCodingSchemeURI("11.22.33.44");
org.LexGrid.commonTypes.Text copyright = new org.LexGrid.commonTypes.Text();
copyright.setContent("Copyright Mayo Clinic.");
cs.setCopyright(copyright);
cs.setDefaultLanguage("en");
cs.setMappings(new org.LexGrid.naming.Mappings());
cs.setRepresentsVersion("1.1");

org.LexGrid.naming.SupportedAssociation saHasSubType = edu.mayo.informatics.lexgrid.convert.exporters.xml.lgxml.factory.SupportedAssociationFactory.createSupportedAssociationHasSubType();

cs.getMappings().addSupportedAssociation(saHasSubType);
org.LexGrid.naming.SupportedAssociation saUses = edu.mayo.informatics.lexgrid.convert.exporters.xml.lgxml.factory.SupportedAssociationFactory.createSupportedAssociationUses();
cs.getMappings().addSupportedAssociation(saUses);
        
org.LexGrid.relations.Relations rels = new org.LexGrid.relations.Relations();
rels.setContainerName("asD");
        
org.LexGrid.relations.AssociationPredicate ap = new org.LexGrid.relations.AssociationPredicate();
ap.setAssociationName("hasSubtype");
rels.addAssociationPredicate(ap);

ap = new org.LexGrid.relations.AssociationPredicate();

ap.setAssociationName("uses");
        
rels.addAssociationPredicate(ap);
        
cs.addRelations(rels);

...
  • Step 3:
...
  •  Call 
...
  •  load 
...
  •  method 
...
  •  by 
...
  •  passing 
...
  •  the 
...
  •  Code 
...
  •  System 
...
  •  Object 
...
  •  and 
...
  •  other 
...
  •  parameter 
...
  •  values: 
...
  •  Code Block
...
  • 
assnLoad.importAssociationVersion(cs, null, true, false, true, "DEV", true);


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