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public interface UMLS_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 |
---|
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
An exception is raised if resources cannot be accessed or another load operation is already in progress.
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.
LBException
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
An exception is raised if resources cannot be accessed or another load operation is already in progress.
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.
LBException
void load(java.net.URI source, LocalNameList targetTerminologies, boolean stopOnErrors, boolean async) throws LBException
An exception is raised if resources cannot be accessed or another load operation is already in progress.
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.
LBException
void loadSemnet(java.net.URI source, boolean stopOnErrors, boolean async) throws LBException
An exception is raised if resources cannot be accessed or another load operation is already in progress.
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.
LBException
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
Returns without exception if validation succeeds.
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.
LBException
void validate(java.net.URI source, java.lang.String uid, java.lang.String pwd, java.lang.String driver, LocalNameList targetTerminologies, int validationLevel) throws LBException
Returns without exception if validation succeeds.
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.
LBException
void validate(java.net.URI source, LocalNameList targetTerminologies, int hierarchyOpt, int validationLevel) throws LBException
Returns without exception if validation succeeds.
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.
LBException
void validate(java.net.URI source, LocalNameList targetTerminologies, int validationLevel) throws LBException
Returns without exception if validation succeeds.
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.
LBException
void validateSemnet(java.net.URI source, int validationLevel) throws LBException
Returns without exception if validation succeeds.
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.
LBException
|
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