org.LexGrid.LexBIG.Extensions.Load
Interface UMLS_Loader

All Superinterfaces:
Extendable, Loader, java.io.Serializable, StatusReporter

public interface UMLS_Loader
extends Loader

Load one or more coding schemes from UMLS RRF format stored in a SQL database. This requires that RRF source generation tool be set up to "output versionless source abbreviations" for any given subset of the UMLS.


Method Summary
 void load(java.net.URI source, LocalNameList targetTerminologies, boolean stopOnErrors, boolean async)
          Load content from RRF files.
 void load(java.net.URI source, java.lang.String uid, java.lang.String pwd, java.lang.String driver, LocalNameList targetTerminologies, boolean stopOnErrors, boolean async)
          Load content from a database repository.
 void load(java.net.URI source, java.lang.String uid, java.lang.String pwd, java.lang.String driver, LocalNameList targetTerminologies, int hierarchyOpt, boolean stopOnErrors, boolean async)
          Load content from a database repository.
 void loadSemnet(java.net.URI source, boolean stopOnErrors, boolean async)
          Load content for the UMLS semantic network from files distributed by the NLM (see http://semanticnetwork.nlm.nih.gov/Download/index.html).
 void validate(java.net.URI source, LocalNameList targetTerminologies, int validationLevel)
          Validate content from RRF files.
 void validate(java.net.URI source, LocalNameList targetTerminologies, int hierarchyOpt, int validationLevel)
          Validate content from RRF files.
 void validate(java.net.URI source, java.lang.String uid, java.lang.String pwd, java.lang.String driver, LocalNameList targetTerminologies, int validationLevel)
          Validate content for a candidate resource without performing a load.
 void validate(java.net.URI source, java.lang.String uid, java.lang.String pwd, java.lang.String driver, LocalNameList targetTerminologies, int hierarchyOpt, int validationLevel)
          Validate content for a candidate resource without performing a load.
 void validateSemnet(java.net.URI source, int validationLevel)
          Validate UMLS semantic network files prior to performing a load operation.
 
Methods inherited from interface org.LexGrid.LexBIG.Extensions.Load.Loader
clearLog, getCodingSchemeManifest, getCodingSchemeManifestURI, getCodingSchemeReferences, getLoaderPreferences, getLog, getOntologyFormat, getOptions, getStatus, load, setCodingSchemeManifest, setCodingSchemeManifestURI, setLoaderPreferences, setLoaderPreferences
 
Methods inherited from interface org.LexGrid.LexBIG.Extensions.Extendable
getDescription, getName, getProvider, getVersion
 

Method Detail

load

void load(java.net.URI source,
          java.lang.String uid,
          java.lang.String pwd,
          java.lang.String driver,
          LocalNameList targetTerminologies,
          int hierarchyOpt,
          boolean stopOnErrors,
          boolean async)
          throws LBException
Load content from a database repository. This will also result in implicit generation of standard indices required by the LexBIG runtime.

An exception is raised if resources cannot be accessed or another load operation is already in progress.

Parameters:
source - Location of the source database. Typically this is specified in the form of a URL that indicates the database server, port, name, and optional properties. An example (items in square brackets are optional) is as follows: jdbc:mysql://[host][,failoverhost...][:port]/[database] [?propertyName1][=propertyValue1][&propertyName2][=propertyValue2]...
uid - User ID for authenticated access, if required and not specified as part of the database URL parameters.
pwd - Password for authenticated access, if required and not specified as part of the database URL parameters.
driver - Name of the JDBC driver to use when accessing the database.
targetTerminologies - The list of UMLS terminologies to load. If null, all available terminologies will be loaded. The terminology name should be the SAB name of the terminology - or values from the RSAB column of the MRSAB file.
hierarchyOpt - Process hierarchical relationships stored by the MRHIER file. Supported values are: 0 = Do not process information from MRHIER; basic associations are calculated from MRREL without adding atom-specific contexts. 1 = Process atom chains that have been tagged with context identifiers (HCD). The HCD value is assigned to participating text properties and associations in the LexGrid repository. If not specified, this is the assumed default.
stopOnErrors - True means stop if any load error is detected. False means attempt to load what can be loaded if recoverable errors are encountered.
async - 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.
Throws:
LBException

load

void load(java.net.URI source,
          java.lang.String uid,
          java.lang.String pwd,
          java.lang.String driver,
          LocalNameList targetTerminologies,
          boolean stopOnErrors,
          boolean async)
          throws LBException
Load content from a database repository. This will also result in implicit generation of standard indices required by the LexBIG runtime.

An exception is raised if resources cannot be accessed or another load operation is already in progress.

Parameters:
source - Location of the source database. Typically this is specified in the form of a URL that indicates the database server, port, name, and optional properties. An example (items in square brackets are optional) is as follows: jdbc:mysql://[host][,failoverhost...][:port]/[database] [?propertyName1][=propertyValue1][&propertyName2][=propertyValue2]...
uid - User ID for authenticated access, if required and not specified as part of the database URL parameters.
pwd - Password for authenticated access, if required and not specified as part of the database URL parameters.
driver - Name of the JDBC driver to use when accessing the database.
targetTerminologies - The list of UMLS terminologies to load. If null, all available terminologies will be loaded. The terminology name should be the SAB name of the terminology - or values from the RSAB column of the MRSAB file.
stopOnErrors - True means stop if any load error is detected. False means attempt to load what can be loaded if recoverable errors are encountered.
async - 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.
Throws:
LBException

load

void load(java.net.URI source,
          LocalNameList targetTerminologies,
          boolean stopOnErrors,
          boolean async)
          throws LBException
Load content from RRF files. This will also result in implicit generation of standard indices required by the LexBIG runtime.

An exception is raised if resources cannot be accessed or another load operation is already in progress.

Parameters:
source - URI corresponding to the directory containing the RRF files as provided by the NLM or pruned through MetamorphoSys.
targetTerminologies - The list of UMLS terminologies to load. If null, all available terminologies will be loaded. The terminology name should be the SAB name of the terminology - or values from the RSAB column of the MRSAB file.
stopOnErrors - True means stop if any load error is detected. False means attempt to load what can be loaded if recoverable errors are encountered.
async - 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.
Throws:
LBException

loadSemnet

void loadSemnet(java.net.URI source,
                boolean stopOnErrors,
                boolean async)
                throws LBException
Load content for the UMLS semantic network from files distributed by the NLM (see http://semanticnetwork.nlm.nih.gov/Download/index.html). This will also result in implicit generation of standard indices required by the LexBIG runtime.

An exception is raised if resources cannot be accessed or another load operation is already in progress.

Parameters:
source - URI corresponding to the directory containing the semantic network files.
stopOnErrors - True means stop if any load error is detected. False means attempt to load what can be loaded if recoverable errors are encountered.
async - 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.
Throws:
LBException

validate

void validate(java.net.URI source,
              java.lang.String uid,
              java.lang.String pwd,
              java.lang.String driver,
              LocalNameList targetTerminologies,
              int hierarchyOpt,
              int validationLevel)
              throws LBException
Validate content for a candidate resource without performing a load.

Returns without exception if validation succeeds.

Parameters:
source - Location of the source database. Typically this is specified in the form of a URL that indicates the database server, port, name, and optional properties. An example (items in square brakets are optional) is as follows: jdbc:mysql://[host][,failoverhost...][: port]/[database][?propertyName1][=propertyValue1][&propertyName2][=propertyValue 2]...
uid - User ID for authenticated access, if required and not specified as part of the source URI parameters.
pwd - Password for authenticated access, if required and not specified as part of the source URI parameters.
driver - Name of the JDBC driver to use when accessing the database.
targetTerminologies - The list of UMLS terminologies to load. If null, all available terminologies will be loaded.
hierarchyOpt - Process hierarchical relationships stored by the MRHIER file. Supported values are: 0 = Do not process information from MRHIER; basic associations are calculated from MRREL without adding atom-specific contexts. 1 = Process atom chains that have been tagged with context identifiers (HCD). The HCD value is assigned to participating text properties and associations in the LexGrid repository. If not specified, this is the assumed default.
validationLevel - Loader-specific level of validation; 0 = verify that the database and target terminologies are present and accessible.
Throws:
LBException

validate

void validate(java.net.URI source,
              java.lang.String uid,
              java.lang.String pwd,
              java.lang.String driver,
              LocalNameList targetTerminologies,
              int validationLevel)
              throws LBException
Validate content for a candidate resource without performing a load.

Returns without exception if validation succeeds.

Parameters:
source - Location of the source database. Typically this is specified in the form of a URL that indicates the database server, port, name, and optional properties. An example (items in square brakets are optional) is as follows: jdbc:mysql://[host][,failoverhost...][: port]/[database][?propertyName1][=propertyValue1][&propertyName2][=propertyValue 2]...
uid - User ID for authenticated access, if required and not specified as part of the source URI parameters.
pwd - Password for authenticated access, if required and not specified as part of the source URI parameters.
driver - Name of the JDBC driver to use when accessing the database.
targetTerminologies - The list of UMLS terminologies to load. If null, all available terminologies will be loaded.
validationLevel - Loader-specific level of validation; 0 = verify that the database and target terminologies are present and accessible.
Throws:
LBException

validate

void validate(java.net.URI source,
              LocalNameList targetTerminologies,
              int hierarchyOpt,
              int validationLevel)
              throws LBException
Validate content from RRF files. This will also result in implicit generation of standard indices required by the LexBIG runtime.

Returns without exception if validation succeeds.

Parameters:
source - URI corresponding to the directory containing the RRF files as provided by the NLM or pruned through MetamorphoSys.
targetTerminologies - The list of UMLS terminologies to load. If null, all available terminologies will be validated. The terminology name should be the SAB name of the terminology - or values from the RSAB column of the MRSAB file.
hierarchyOpt - Process hierarchical relationships stored by the MRHIER file. Supported values are: 0 = Do not process information from MRHIER; basic associations are calculated from MRREL without adding atom-specific contexts. 1 = Process atom chains that have been tagged with context identifiers (HCD). The HCD value is assigned to participating text properties and associations in the LexGrid repository. If not specified, this is the assumed default.
validationLevel - Loader-specific level of validation; 0 = verify all files are present for the target terminologies and conform to the anticipated format.
Throws:
LBException

validate

void validate(java.net.URI source,
              LocalNameList targetTerminologies,
              int validationLevel)
              throws LBException
Validate content from RRF files. This will also result in implicit generation of standard indices required by the LexBIG runtime.

Returns without exception if validation succeeds.

Parameters:
source - URI corresponding to the directory containing the RRF files as provided by the NLM or pruned through MetamorphoSys.
targetTerminologies - The list of UMLS terminologies to load. If null, all available terminologies will be validated. The terminology name should be the SAB name of the terminology - or values from the RSAB column of the MRSAB file.
validationLevel - Loader-specific level of validation; 0 = verify all files are present for the target terminologies and conform to the anticipated format.
Throws:
LBException

validateSemnet

void validateSemnet(java.net.URI source,
                    int validationLevel)
                    throws LBException
Validate UMLS semantic network files prior to performing a load operation.

Returns without exception if validation succeeds.

Parameters:
source - URI corresponding to the directory containing the semantic network files.
validationLevel - Loader-specific level of validation; 0 = verify all files are present for the target terminologies and conform to the anticipated format.
Throws:
LBException

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