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java.lang.Objectedu.mayo.informatics.lexgrid.convert.directConversions.UmlsCommon.UMLSBaseCode
@Deprecated public class UMLSBaseCode
Common Code for RRF/UMLS based loaders. Here are the table use details for the UMLS converter Used tables: MRCONSO.RRF MRREL.RRF MRSAB.RRF MRDEF.RRF MRSTY.RRF MRSAT.RRF MRDOC.RRF MRRANK.RRF MRHIER.RRF Conditionally referenced: MRHIER.RRF (for contextual links) Unused tables: AMBIGLUI.RRF AMBIGSUI.RRF MRAUI.RRF MRCOC.RRF MRCOLS.RRF MRCUI.RRF MRCXT.RRF MRFILES.RRF MRHIST.RRF MRMAP.RRF MRSMAP.RRF MRXNS_ENG.RRF MRXNW_ENG.RRF MRXW_BAQ.RRF MRXW_CZE.RRF MRXW_DAN.RRF MRXW_DUT.RRF MRXW_ENG.RRF MRXW_FIN.RRF MRXW_FRE.RRF MRXW_GER.RRF MRXW_HEB.RRF MRXW_HUN.RRF MRXW_ITA.RRF MRXW_JPN.RRF MRXW_NOR.RRF MRXW_POR.RRF MRXW_RUS.RRF MRXW_SPA.RRF MRXW_SWE.RRF There are a couple of unused tables that I probably should be using - but I'm just not loading that info yet - such as the history. I'm not sure about the map tables - I'll need to look into them more at some future point. Here is the breakdown for the NCI MetaThesaurus: Used tables: MRCONSO.RRF MRREL.RRF MRSAB.RRF MRDEF.RRF MRSTY.RRF MRRANK.RRF Unused tables: MRCOC.RRF MRCOLS.RRF MRDOC.RRF MRFILES.RRF Here, I think that the only one that I'm not using that I maybe should be is the MRCOC file - I'll have to look at this again at some point. Differences/issues I can remember (though there may have been more): While loading from the UMLS: For most terminologies, I could get the Language from the LAT column in the MRCONSO file. In Snomed, I had to do a query on the MRSAT table and pull the language out of the ATV column. In the UMLS - when we load things, we are loading based on terminology concept codes, not CUI's - so to get the preferred text for a code in a terminology (per language) required reading all presentations for a code from a terminology, and then doing a sort taking into account 4 different columns, each with various values that mean preferred in different terminologies In the NCI MetaThesaurus, since we are loading it using the CUI's as the concept codes, I can just use the IsPref column to determine the preferred text. I think that all of the other differences in the UMLS loader versus the NCI MetaThesaurus loader are due to loading based on CUI's instead of concept codes.
Nested Class Summary | |
---|---|
class |
UMLSBaseCode.Association
Deprecated. |
class |
UMLSBaseCode.AssociationQualification
Deprecated. |
class |
UMLSBaseCode.AssociationSorter
Deprecated. |
class |
UMLSBaseCode.CodeHolder
Deprecated. |
class |
UMLSBaseCode.ConceptPresentation
Deprecated. |
class |
UMLSBaseCode.ConceptPresentationSorter
Deprecated. |
class |
UMLSBaseCode.SABString
Deprecated. Inner class defining a string optionally qualified by SAB and providing corresponding equality methods, etc, to support use and comparison in various collections. |
Field Summary | |
---|---|
protected java.util.HashSet |
associationQualifierRUI_
Deprecated. |
protected org.apache.commons.collections.map.LRUMap |
auiToCodeCache_
Deprecated. |
protected int |
batchSize
Deprecated. |
protected java.lang.String |
defaultLanguage_
Deprecated. |
protected static int |
entryStateId_
Deprecated. |
protected java.sql.PreparedStatement |
getAllAssocQualifiersFromRRF_
Deprecated. |
protected java.sql.PreparedStatement |
getAssocInstance_
Deprecated. |
protected java.sql.PreparedStatement |
getAssocQualifier_
Deprecated. |
protected java.sql.PreparedStatement |
getAssocQualifierFromRRF_
Deprecated. |
protected java.sql.PreparedStatement |
getAUIFromPresentation_
Deprecated. |
protected java.sql.PreparedStatement |
getCodeForCUI_
Deprecated. |
protected java.sql.PreparedStatement |
getCodeForCUINoAUI_
Deprecated. |
protected java.sql.PreparedStatement |
getPresentationRank_
Deprecated. |
protected java.sql.PreparedStatement |
getPropIds_
Deprecated. |
protected java.sql.PreparedStatement |
getSource_
Deprecated. |
protected java.sql.PreparedStatement |
getUMLSRoot_
Deprecated. |
protected java.sql.PreparedStatement |
insertIntoAssociations
Deprecated. |
protected java.sql.PreparedStatement |
insertIntoCodingScheme
Deprecated. |
protected java.sql.PreparedStatement |
insertIntoCodingSchemeMultiAttributes
Deprecated. |
protected java.sql.PreparedStatement |
insertIntoCodingSchemeSupportedAttributes
Deprecated. |
protected java.sql.PreparedStatement |
insertIntoConceptsMultiAttributes
Deprecated. |
protected java.sql.PreparedStatement |
insertIntoEntities
Deprecated. |
protected java.sql.PreparedStatement |
insertIntoEntityAssociationsToEntity
Deprecated. |
protected java.sql.PreparedStatement |
insertIntoEntityAssociationsToEntityQualifier
Deprecated. |
protected java.sql.PreparedStatement |
insertIntoEntityProperty
Deprecated. |
protected java.sql.PreparedStatement |
insertIntoEntityPropertyLinks
Deprecated. |
protected java.sql.PreparedStatement |
insertIntoEntityPropertyMultiAttributes
Deprecated. |
protected java.sql.PreparedStatement |
insertIntoEntityType
Deprecated. |
protected java.sql.PreparedStatement |
insertIntoEntryState
Deprecated. |
protected java.sql.PreparedStatement |
insertIntoRelations
Deprecated. |
protected java.util.Hashtable |
isoMap
Deprecated. |
protected java.util.HashSet |
loadedAssociations_
Deprecated. |
protected LoaderPreferences |
loadPrefs_
Deprecated. |
protected static org.apache.log4j.Logger |
log
Deprecated. |
protected java.net.URI |
manifestLocation_
Deprecated. |
boolean |
manifestNameChange_
Deprecated. |
protected LgMessageDirectorIF |
messages_
Deprecated. |
protected java.util.Hashtable |
mrconsoRepresentationalMap_
Deprecated. |
protected java.util.HashMap |
MRRANK_
Deprecated. |
protected java.util.Hashtable |
sabToCodeSystem_
Deprecated. |
protected java.util.Map |
schemeToHierNames_
Deprecated. |
protected java.sql.Connection |
sqlConnection_
Deprecated. |
protected GenericSQLModifier |
sqlModifier_
Deprecated. |
protected SQLTableUtilities |
sqlTableUtility_
Deprecated. |
protected SQLTableConstants |
stc_
Deprecated. |
protected java.util.HashSet |
supportedAssociationQualifiers_
Deprecated. |
protected UMLSBaseCode.Association[] |
supportedAssociations_
Deprecated. |
protected java.util.HashSet |
supportedCodingSchemes_
Deprecated. |
protected java.util.HashSet |
supportedHierarchies_
Deprecated. |
protected java.util.HashSet |
supportedLanguages_
Deprecated. |
protected java.util.HashSet |
supportedPropertyLinks_
Deprecated. |
protected java.util.HashSet |
supportedPropertyQualifiers_
Deprecated. |
protected java.util.HashSet |
supportedPropertyTypes_
Deprecated. |
protected java.util.HashSet |
supportedSources_
Deprecated. |
protected java.sql.Connection |
umlsConnection_
Deprecated. |
protected java.sql.Connection |
umlsConnection2_
Deprecated. |
protected GenericSQLModifier |
umlsSqlModifier_
Deprecated. |
Constructor Summary | |
---|---|
UMLSBaseCode()
Deprecated. |
Method Summary | |
---|---|
protected void |
addAssociationToAssociations(java.lang.String codingSchemeName,
java.lang.String relationName,
java.lang.String association,
java.lang.String forwardName,
java.lang.String reverseName,
java.lang.String inverse,
java.lang.Boolean isNavigable,
java.lang.Boolean isTransitive,
java.lang.Boolean isAntiTransitive,
java.lang.Boolean isSymmetric,
java.lang.Boolean isAntiSymmetric,
java.lang.Boolean isReflexive,
java.lang.Boolean isAntiReflexive,
java.lang.Boolean isFunctional,
java.lang.Boolean isReverseFunctional,
java.lang.Boolean isTranslationAssociation,
java.lang.String targetCodingScheme,
java.lang.String entityDescription)
Deprecated. |
protected void |
addConceptToConcepts(java.lang.String codingSchemeName,
java.lang.String conceptCode,
java.lang.Boolean firstRelease,
java.lang.Boolean modifiedInRelease,
java.lang.Boolean deprecated,
java.lang.Boolean isActive,
java.lang.Boolean isDefined,
java.lang.Boolean isInferred,
java.lang.String conceptStatus,
java.lang.Boolean isAnonymous,
java.lang.String entityDescription)
Deprecated. |
protected void |
addConceptToConceptsMultiAttributes(java.lang.String codingSchemeName,
java.lang.String conceptCode,
java.lang.String attributeName,
java.lang.String attributeValue)
Deprecated. |
protected void |
addConceptToEntityPropertyMultiAttributes(java.lang.String codingSchemeName,
java.lang.String entityType,
java.lang.String conceptCode,
java.lang.String propertyId,
java.lang.String typeName,
java.lang.String attributeValue,
java.lang.String val1,
java.lang.String val2)
Deprecated. |
protected void |
addEntityAssociationQualifierToEntityAssociation(java.lang.String codingSchemeName,
java.lang.String multiAttributesKey,
java.lang.String qualifierName,
java.lang.String qualifierValue)
Deprecated. |
protected void |
addEntityAssociationToEntity(java.lang.String codingSchemeName,
java.lang.String sourceCodingSchemeName,
java.lang.String sourceEntityType,
java.lang.String sourceConceptCode,
java.lang.String relationName,
java.lang.String association,
java.lang.String targetCodingSchemeName,
java.lang.String targetEntityType,
java.lang.String targetConceptCode,
java.lang.String multiAttributesKey,
java.lang.Boolean firstVersion,
java.lang.Boolean lastVersion)
Deprecated. |
protected void |
addEntityType(java.lang.String codingSchemeName,
java.lang.String entityCodeNamespace,
java.lang.String entityCode,
java.lang.String entityType)
Deprecated. |
protected void |
addEntryState(int entryStateId,
java.lang.String entryType,
java.lang.String owner,
java.lang.String status,
java.lang.String effectiveDate,
java.lang.String expirationDate,
java.lang.String revisionId,
java.lang.String prevRevisionId,
java.lang.String changeType,
int relativeOrder)
Deprecated. |
protected void |
addRelationToRelations(java.lang.String codingSchemeName,
java.lang.String relationName,
java.lang.Boolean isNative,
java.lang.String entityDescription)
Deprecated. |
protected void |
addToCodingScheme(java.lang.String codingSchemeName,
java.lang.String registeredName,
java.lang.String representsVersion,
java.lang.String formalName,
java.lang.String language,
int approxNumConcepts,
java.lang.Boolean isActive,
int entryStateId,
java.lang.String releaseURI,
java.lang.String entityDescription,
java.lang.String copyright)
Deprecated. |
protected void |
addToEntityProperty(java.lang.String codingSchemeName,
java.lang.String entityType,
java.lang.String conceptCode,
java.lang.String propertyId,
java.lang.String propertyType,
java.lang.String propertyName,
java.lang.String language,
java.lang.String presentationFormat,
java.lang.Boolean isPreferred,
java.lang.String degreeOfFidelity,
java.lang.Boolean matchIfNoContext,
java.lang.String representationForm,
java.lang.String propertyValue)
Deprecated. |
protected void |
buildRootNode(java.lang.String codingSchemeName,
boolean isMeta,
UMLSBaseCode.SABString[] dirNames,
java.lang.String lgRelationContainerName)
Deprecated. Build relations to an artificial root ('@') or tail ('@@') node to assist with navigation of one or more associations. |
protected void |
closeConnections()
Deprecated. |
protected void |
closeLoadStatements()
Deprecated. |
protected java.lang.String |
generateUniqueKey(int seed)
Deprecated. Generates a unique but random key, using the given integer as seed. |
protected java.lang.String |
generateUniqueKey(java.lang.String[] basis)
Deprecated. Generates a unique but reproducible key based on the given base of string values. |
protected java.lang.String |
get5DigitRandom()
Deprecated. |
protected java.lang.String |
getCodingSchemeNameFromManifest(java.lang.String defaultCodingSchemeName)
Deprecated. Helper method to check if the Coding Scheme Name is changed in the Manifest. |
protected java.lang.String |
getExpandedForm(java.lang.String rrfName,
java.lang.String rrfField)
Deprecated. Return the detailed name of the given RRF name; null if not available. |
protected java.lang.String[] |
getHierAssocNames(java.lang.String codeSystemName)
Deprecated. Returns the names of the hierarchical associations in use for the LexGrid code system of the given name. |
protected UMLSBaseCode.SABString[] |
getHierRelas()
Deprecated. Relation names in the RRF (RELA field) for hierarchical associations specific to the source distribution. |
protected UMLSBaseCode.SABString[] |
getHierRels()
Deprecated. Standard names (REL field in the RRF) for hierarchical associations in the UMLS. |
static java.util.Hashtable |
getIsoMap()
Deprecated. |
protected java.lang.String |
getISOString(java.lang.String UMLSCodingSchemeName)
Deprecated. |
protected java.lang.String |
getRegisteredNameFromManifest(java.lang.String defaultRegisteredName)
Deprecated. Helper method to check if the Registered name is changed in the Manifest. |
protected UMLSBaseCode.SABString[] |
getRelaNames(UMLSBaseCode.SABString[] relNames)
Deprecated. Resolve source-assigned relation names corresponding to the given array of standard UMLS relation names (e.g. resolve 'part_of' for 'PAR'). |
protected java.lang.String |
getRelationInverseName(java.lang.String rrfName,
java.lang.String rrfField)
Deprecated. Return the inverse name of the given RRF-based relation; null if not available. |
protected UMLSBaseCode.SABString[] |
getRelationSABs(java.lang.String[] rrfNames,
java.lang.String rrfField)
Deprecated. Resolve UMLS source abbreviations corresponding to the given array of source-defined relation names (e.g. resolved from MRREL). |
protected java.security.MessageDigest |
getSHA1()
Deprecated. Returns a message digest to be used for fixed-length key generation. s |
protected java.lang.String |
getSourceVersionString(java.lang.String fallbackString)
Deprecated. |
protected void |
initIsoMap()
Deprecated. |
protected void |
initLoadStatements()
Deprecated. |
protected void |
initMRCONSOTTYMAP()
Deprecated. |
protected void |
insertIntoCodingSchemeSupportedAttributes(java.lang.String codingSchemeName,
java.lang.String supportedAttributeTag,
java.lang.String id,
java.lang.String urn,
java.lang.String value,
java.lang.String assemblyRule,
java.lang.String agentRole)
Deprecated. |
protected void |
insertIntoConceptPropertyLinks(java.lang.String codingSchemeName,
java.lang.String entityType,
java.lang.String conceptCode,
java.lang.String sourcePropertyId,
java.lang.String link,
java.lang.String targetPropertyId)
Deprecated. |
protected boolean |
isHierarchicalAssociation(UMLSBaseCode.Association assoc,
java.lang.String codingSchemeName)
Deprecated. Indicates whether the given association is used to represent hierarchical relationships in the source being processed. |
protected boolean |
isHierarchicalName(java.lang.String name,
java.lang.String codeSystemName)
Deprecated. Indicates whether the given name is used to represent hierarchical relationships in the source being processed. |
protected boolean |
isLoaded(java.lang.String name,
java.lang.String codingSchemeName,
java.lang.String relationsContainerName)
Deprecated. Indicates if the given association name matches those currently loaded for the given coding scheme and relations container. |
protected boolean |
isLoaded(UMLSBaseCode.Association assoc,
java.lang.String codingSchemeName,
java.lang.String relationsContainerName)
Deprecated. Indicates if the given association matches those currently loaded for the given coding scheme and relations container. |
protected int |
loadContext(UMLSBaseCode.AssociationQualification aq,
boolean constructHCD,
java.lang.String rela,
int totalCount)
Deprecated. Adds qualification to concepts and associations in the LexGrid repository. |
protected void |
loadDefaultSupportedNamespace(java.lang.String codingSchemeName)
Deprecated. |
protected void |
loadLoaderPreferences()
Deprecated. |
protected void |
loadMRRANK()
Deprecated. |
protected void |
loadSupportedAssociationQualifiers(java.lang.String codingSchemeName)
Deprecated. |
protected void |
loadSupportedLanguages(java.lang.String codingSchemeName)
Deprecated. |
protected void |
loadSupportedProperties(java.lang.String codingSchemeName)
Deprecated. |
protected void |
loadSupportedPropertyLinks(java.lang.String codingSchemeName)
Deprecated. |
protected void |
loadSupportedPropertyQualifiers(java.lang.String codingSchemeName)
Deprecated. |
protected void |
loadSupportedSources(java.lang.String codingSchemeName)
Deprecated. |
protected void |
makeConnections(java.lang.String umlsServer,
java.lang.String umlsDriver,
java.lang.String umlsUserName,
java.lang.String umlsPassword,
java.lang.String sqlServer,
java.lang.String sqlDriver,
java.lang.String sqlUserName,
java.lang.String sqlPassword,
java.lang.String tablePrefix,
boolean enforceIntegrity)
Deprecated. |
protected java.lang.String |
mapCodeSystemNameToSAB(java.lang.String codeSystemName)
Deprecated. Map from the coding scheme name used for identification in the LexGrid model to the UMLS source abbreviation (SAB). |
protected UMLSBaseCode.CodeHolder[] |
mapCUIToCode(java.lang.String cui,
java.lang.String aui,
java.lang.String sab)
Deprecated. |
protected UMLSBaseCode.CodeHolder[] |
mapCUIToCodeWithAUI(java.lang.String cui,
java.lang.String aui)
Deprecated. |
protected java.lang.String |
mapRela(java.lang.String rrfName)
Deprecated. Maps from the given UMLS-provided relationship name to a pre-designated LexGrid association name (e.g. map from 'inverse_isa' to 'hasSubtype'), if available. |
protected java.lang.String |
mapSABToCodeSystemName(java.lang.String sab)
Deprecated. Map from the UMLS source abbreviation (SAB) to the coding scheme name used for identification in the LexGrid model. |
protected UMLSBaseCode.Association |
mapSupportedAssociationsHelper(java.lang.String rrfName,
java.lang.String rrfSAB,
java.lang.String rrfDirFlag,
java.lang.String rrfField,
java.util.Map map)
Deprecated. Map the provided information to a new Association and add, if new, add to the given hashtable. |
protected java.lang.String |
mapVSABtoRSAB(java.lang.String vsab)
Deprecated. |
protected void |
markLoaded(java.lang.String name,
java.lang.String codingSchemeName,
java.lang.String relationsContainerName)
Deprecated. Sets an indication that the given association has been loaded for the given coding scheme and relations container. |
protected void |
markLoaded(UMLSBaseCode.Association assoc,
java.lang.String codingSchemeName,
java.lang.String relationsContainerName)
Deprecated. Sets an indication that the given association has been loaded for the given coding scheme and relations container. |
protected void |
qualifyConceptPresentation(java.lang.String code,
java.lang.String aui,
java.lang.String codingSchemeName,
java.lang.String qualifierName,
java.lang.String qualifierValue)
Deprecated. Add context qualifiers to text presentations for matching concepts. |
protected java.lang.String |
toCommaDelimitedWithQuotes(java.lang.String[] strings)
Deprecated. Converts the given string array to a single string, separating each value by comma and embedding quotes before and after each value. |
protected void |
updateApproxNumberOfConcepts(int count,
java.lang.String codingSchemeName)
Deprecated. |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
---|
protected static org.apache.log4j.Logger log
protected java.sql.Connection umlsConnection_
protected java.sql.Connection umlsConnection2_
protected java.sql.Connection sqlConnection_
protected SQLTableUtilities sqlTableUtility_
protected SQLTableConstants stc_
protected GenericSQLModifier umlsSqlModifier_
protected GenericSQLModifier sqlModifier_
protected final int batchSize
protected java.util.Hashtable isoMap
protected java.util.HashSet loadedAssociations_
protected java.util.HashSet supportedCodingSchemes_
protected UMLSBaseCode.Association[] supportedAssociations_
protected java.util.HashSet supportedAssociationQualifiers_
protected java.util.HashSet supportedPropertyTypes_
protected java.util.HashSet supportedPropertyLinks_
protected java.util.HashSet supportedPropertyQualifiers_
protected java.util.HashSet supportedSources_
protected java.util.HashSet supportedLanguages_
protected java.util.HashSet supportedHierarchies_
protected java.util.HashSet associationQualifierRUI_
protected java.util.HashMap MRRANK_
protected java.lang.String defaultLanguage_
protected java.util.Hashtable mrconsoRepresentationalMap_
protected java.util.Hashtable sabToCodeSystem_
protected java.sql.PreparedStatement insertIntoCodingScheme
protected java.sql.PreparedStatement insertIntoCodingSchemeMultiAttributes
protected java.sql.PreparedStatement insertIntoEntityProperty
protected java.sql.PreparedStatement insertIntoEntityPropertyMultiAttributes
protected java.sql.PreparedStatement insertIntoEntities
protected java.sql.PreparedStatement insertIntoEntryState
protected java.sql.PreparedStatement insertIntoEntityType
protected java.sql.PreparedStatement insertIntoConceptsMultiAttributes
protected java.sql.PreparedStatement insertIntoRelations
protected java.sql.PreparedStatement insertIntoAssociations
protected java.sql.PreparedStatement insertIntoEntityAssociationsToEntity
protected java.sql.PreparedStatement insertIntoEntityAssociationsToEntityQualifier
protected java.sql.PreparedStatement insertIntoEntityPropertyLinks
protected java.sql.PreparedStatement insertIntoCodingSchemeSupportedAttributes
protected java.sql.PreparedStatement getCodeForCUI_
protected java.sql.PreparedStatement getCodeForCUINoAUI_
protected java.sql.PreparedStatement getSource_
protected java.sql.PreparedStatement getUMLSRoot_
protected java.sql.PreparedStatement getAssocInstance_
protected java.sql.PreparedStatement getAssocQualifier_
protected java.sql.PreparedStatement getAllAssocQualifiersFromRRF_
protected java.sql.PreparedStatement getAssocQualifierFromRRF_
protected java.sql.PreparedStatement getAUIFromPresentation_
protected java.sql.PreparedStatement getPresentationRank_
protected java.sql.PreparedStatement getPropIds_
protected org.apache.commons.collections.map.LRUMap auiToCodeCache_
protected LgMessageDirectorIF messages_
protected LoaderPreferences loadPrefs_
protected java.net.URI manifestLocation_
public boolean manifestNameChange_
protected static int entryStateId_
protected java.util.Map schemeToHierNames_
Constructor Detail |
---|
public UMLSBaseCode()
Method Detail |
---|
protected void makeConnections(java.lang.String umlsServer, java.lang.String umlsDriver, java.lang.String umlsUserName, java.lang.String umlsPassword, java.lang.String sqlServer, java.lang.String sqlDriver, java.lang.String sqlUserName, java.lang.String sqlPassword, java.lang.String tablePrefix, boolean enforceIntegrity) throws java.lang.Exception
java.lang.Exception
protected void initMRCONSOTTYMAP()
protected void addToCodingScheme(java.lang.String codingSchemeName, java.lang.String registeredName, java.lang.String representsVersion, java.lang.String formalName, java.lang.String language, int approxNumConcepts, java.lang.Boolean isActive, int entryStateId, java.lang.String releaseURI, java.lang.String entityDescription, java.lang.String copyright) throws java.sql.SQLException
java.sql.SQLException
protected void addToEntityProperty(java.lang.String codingSchemeName, java.lang.String entityType, java.lang.String conceptCode, java.lang.String propertyId, java.lang.String propertyType, java.lang.String propertyName, java.lang.String language, java.lang.String presentationFormat, java.lang.Boolean isPreferred, java.lang.String degreeOfFidelity, java.lang.Boolean matchIfNoContext, java.lang.String representationForm, java.lang.String propertyValue) throws java.sql.SQLException
java.sql.SQLException
protected void addConceptToEntityPropertyMultiAttributes(java.lang.String codingSchemeName, java.lang.String entityType, java.lang.String conceptCode, java.lang.String propertyId, java.lang.String typeName, java.lang.String attributeValue, java.lang.String val1, java.lang.String val2) throws java.sql.SQLException
java.sql.SQLException
protected void addConceptToConceptsMultiAttributes(java.lang.String codingSchemeName, java.lang.String conceptCode, java.lang.String attributeName, java.lang.String attributeValue) throws java.sql.SQLException
java.sql.SQLException
protected void addAssociationToAssociations(java.lang.String codingSchemeName, java.lang.String relationName, java.lang.String association, java.lang.String forwardName, java.lang.String reverseName, java.lang.String inverse, java.lang.Boolean isNavigable, java.lang.Boolean isTransitive, java.lang.Boolean isAntiTransitive, java.lang.Boolean isSymmetric, java.lang.Boolean isAntiSymmetric, java.lang.Boolean isReflexive, java.lang.Boolean isAntiReflexive, java.lang.Boolean isFunctional, java.lang.Boolean isReverseFunctional, java.lang.Boolean isTranslationAssociation, java.lang.String targetCodingScheme, java.lang.String entityDescription) throws java.sql.SQLException
java.sql.SQLException
protected void addEntityAssociationToEntity(java.lang.String codingSchemeName, java.lang.String sourceCodingSchemeName, java.lang.String sourceEntityType, java.lang.String sourceConceptCode, java.lang.String relationName, java.lang.String association, java.lang.String targetCodingSchemeName, java.lang.String targetEntityType, java.lang.String targetConceptCode, java.lang.String multiAttributesKey, java.lang.Boolean firstVersion, java.lang.Boolean lastVersion) throws java.sql.SQLException
java.sql.SQLException
protected void addEntityAssociationQualifierToEntityAssociation(java.lang.String codingSchemeName, java.lang.String multiAttributesKey, java.lang.String qualifierName, java.lang.String qualifierValue) throws java.sql.SQLException
java.sql.SQLException
protected void addRelationToRelations(java.lang.String codingSchemeName, java.lang.String relationName, java.lang.Boolean isNative, java.lang.String entityDescription) throws java.sql.SQLException
java.sql.SQLException
protected void addConceptToConcepts(java.lang.String codingSchemeName, java.lang.String conceptCode, java.lang.Boolean firstRelease, java.lang.Boolean modifiedInRelease, java.lang.Boolean deprecated, java.lang.Boolean isActive, java.lang.Boolean isDefined, java.lang.Boolean isInferred, java.lang.String conceptStatus, java.lang.Boolean isAnonymous, java.lang.String entityDescription) throws java.sql.SQLException
java.sql.SQLException
protected void addEntityType(java.lang.String codingSchemeName, java.lang.String entityCodeNamespace, java.lang.String entityCode, java.lang.String entityType) throws java.sql.SQLException
java.sql.SQLException
protected void addEntryState(int entryStateId, java.lang.String entryType, java.lang.String owner, java.lang.String status, java.lang.String effectiveDate, java.lang.String expirationDate, java.lang.String revisionId, java.lang.String prevRevisionId, java.lang.String changeType, int relativeOrder) throws java.sql.SQLException
java.sql.SQLException
public static java.util.Hashtable getIsoMap() throws java.lang.Exception
java.lang.Exception
protected void initIsoMap()
protected void updateApproxNumberOfConcepts(int count, java.lang.String codingSchemeName)
protected java.lang.String getISOString(java.lang.String UMLSCodingSchemeName) throws java.sql.SQLException
java.sql.SQLException
protected java.lang.String mapVSABtoRSAB(java.lang.String vsab) throws java.sql.SQLException
java.sql.SQLException
protected void loadSupportedPropertyLinks(java.lang.String codingSchemeName) throws java.sql.SQLException
java.sql.SQLException
protected void loadSupportedProperties(java.lang.String codingSchemeName) throws java.sql.SQLException
java.sql.SQLException
protected void loadSupportedPropertyQualifiers(java.lang.String codingSchemeName) throws java.sql.SQLException
java.sql.SQLException
protected void loadSupportedAssociationQualifiers(java.lang.String codingSchemeName) throws java.sql.SQLException
java.sql.SQLException
protected void loadSupportedSources(java.lang.String codingSchemeName) throws java.sql.SQLException
java.sql.SQLException
protected void loadSupportedLanguages(java.lang.String codingSchemeName) throws java.sql.SQLException
java.sql.SQLException
protected void insertIntoConceptPropertyLinks(java.lang.String codingSchemeName, java.lang.String entityType, java.lang.String conceptCode, java.lang.String sourcePropertyId, java.lang.String link, java.lang.String targetPropertyId) throws java.sql.SQLException
java.sql.SQLException
protected void insertIntoCodingSchemeSupportedAttributes(java.lang.String codingSchemeName, java.lang.String supportedAttributeTag, java.lang.String id, java.lang.String urn, java.lang.String value, java.lang.String assemblyRule, java.lang.String agentRole) throws java.sql.SQLException
java.sql.SQLException
protected void initLoadStatements() throws java.sql.SQLException
java.sql.SQLException
protected void qualifyConceptPresentation(java.lang.String code, java.lang.String aui, java.lang.String codingSchemeName, java.lang.String qualifierName, java.lang.String qualifierValue) throws java.sql.SQLException
code
- The code of the concept to qualify.aui
- The AUI identifying specific context text to be matched.codingSchemeName
- The coding scheme container the code to be qualified.qualifierName
- The qualifier name (e.g. 'HCD').qualifierValue
- The qualifier value.
java.sql.SQLException
protected int loadContext(UMLSBaseCode.AssociationQualification aq, boolean constructHCD, java.lang.String rela, int totalCount) throws java.sql.SQLException
aq
- Qualification information from the UMLS source.constructHCD
- Indicates whether artificial context values should be
constructed if not provided in the UMLS information.rela
- The relationship attribute defined by UMLS (can be empty or
null).totalCount
- The total number of context links qualified previously.
java.sql.SQLException
protected UMLSBaseCode.CodeHolder[] mapCUIToCode(java.lang.String cui, java.lang.String aui, java.lang.String sab) throws java.sql.SQLException
java.sql.SQLException
protected UMLSBaseCode.CodeHolder[] mapCUIToCodeWithAUI(java.lang.String cui, java.lang.String aui) throws java.sql.SQLException
java.sql.SQLException
protected java.lang.String getSourceVersionString(java.lang.String fallbackString)
protected void closeLoadStatements() throws java.sql.SQLException
java.sql.SQLException
protected void closeConnections() throws java.sql.SQLException
java.sql.SQLException
protected void buildRootNode(java.lang.String codingSchemeName, boolean isMeta, UMLSBaseCode.SABString[] dirNames, java.lang.String lgRelationContainerName) throws java.sql.SQLException
codingSchemeName
- The LexGrid code system name being loaded.isMeta
- True if the LexGrid code system is to represent multiple UMLS
ontologies, acting as a single meta-ontology; false if the
code system represents a single UMLS ontology. If true,
LexGrid concept codes and association references are defined
in terms of UMLS CUI instead of native codes from the source
ontology. In addition, relations for meta distributions are
interpreted as intra-scheme, whereas relations for individual
coding systems are allowed to cross coding scheme boundaries.dirNames
- The names of UMLS directional relations to be evaluated,
optionally qualified by SAB. Roots are evaluated for
participation as source or target for the given names.lgRelationContainerName
- The LexGrid relations container defining the associations to
be evaluated, or null to match any relations for the code
system.
java.sql.SQLException
protected java.lang.String getExpandedForm(java.lang.String rrfName, java.lang.String rrfField) throws java.sql.SQLException
rrfName
- The UMLS relation name.rrfField
- The UMLS field (e.g. 'RELA' or 'REL').
java.sql.SQLException
protected UMLSBaseCode.SABString[] getHierRelas() throws java.sql.SQLException
java.sql.SQLException
- If an error occurs resolving from the source.protected UMLSBaseCode.SABString[] getHierRels() throws java.sql.SQLException
java.sql.SQLException
- If an error occurs resolving from the source.protected java.lang.String[] getHierAssocNames(java.lang.String codeSystemName) throws java.sql.SQLException
codeSystemName
-
java.sql.SQLException
- If an error occurs resolving from the source.protected UMLSBaseCode.SABString[] getRelaNames(UMLSBaseCode.SABString[] relNames) throws java.sql.SQLException
relNames
- SABString[]
java.sql.SQLException
- If an error occurs resolving from the source.protected UMLSBaseCode.SABString[] getRelationSABs(java.lang.String[] rrfNames, java.lang.String rrfField) throws java.sql.SQLException
rrfNames
- String[]rrfField
- 'RELA' or 'REL'.
java.sql.SQLException
- If an error occurs resolving from the source.protected java.lang.String getRelationInverseName(java.lang.String rrfName, java.lang.String rrfField) throws java.sql.SQLException
rrfName
- The UMLS relation name.rrfField
- 'RELA' or 'REL'.
java.sql.SQLException
protected boolean isHierarchicalAssociation(UMLSBaseCode.Association assoc, java.lang.String codingSchemeName) throws java.sql.SQLException
assoc
- Association object to check; not null.codingSchemeName
- Name of the LexGrid coding scheme containing the association;
null to match any coding scheme.
java.sql.SQLException
- If an error occurs resolving from the source.protected boolean isHierarchicalName(java.lang.String name, java.lang.String codeSystemName) throws java.sql.SQLException
dirName
- Directional name of the association to check.codeSystemName
- Name of the LexGrid coding scheme containing the association;
null to match any coding scheme.
java.sql.SQLException
- If an error occurs resolving from the source.protected boolean isLoaded(UMLSBaseCode.Association assoc, java.lang.String codingSchemeName, java.lang.String relationsContainerName) throws java.sql.SQLException
assoc
- codingSchemeName
- relationsContainerName
-
java.sql.SQLException
protected boolean isLoaded(java.lang.String name, java.lang.String codingSchemeName, java.lang.String relationsContainerName) throws java.sql.SQLException
name
- codingSchemeName
- relationsContainerName
-
java.sql.SQLException
protected void markLoaded(UMLSBaseCode.Association assoc, java.lang.String codingSchemeName, java.lang.String relationsContainerName) throws java.sql.SQLException
assoc
- codingSchemeName
- relationsContainerName
-
java.sql.SQLException
protected void markLoaded(java.lang.String name, java.lang.String codingSchemeName, java.lang.String relationsContainerName) throws java.sql.SQLException
name
- codingSchemeName
- relationsContainerName
-
java.sql.SQLException
protected java.lang.String mapSABToCodeSystemName(java.lang.String sab) throws java.sql.SQLException
sab
-
java.sql.SQLException
protected java.lang.String mapCodeSystemNameToSAB(java.lang.String codeSystemName) throws java.sql.SQLException
codeSystemName
-
java.sql.SQLException
protected UMLSBaseCode.Association mapSupportedAssociationsHelper(java.lang.String rrfName, java.lang.String rrfSAB, java.lang.String rrfDirFlag, java.lang.String rrfField, java.util.Map map) throws java.sql.SQLException
rrfName
- The name of the relationship as provided by the UMLS.rrfSAB
- The source abbreviation of the UMLS code system.rrfDirFlag
- The UMLS directional flag. Y indicates that this is the
direction of the RELA relationship in its source; N indicates
that it is not; otherwise indicates that it is not important
or has not yet been determined. (If blank RELA, we interpret
as 'N', based on empirical review of meta files).rrfField
- Indicates whether the association name is defined as a
standard UMLS relation ('REL') or source-provided label
('RELA').map
- A Map of Associations, keyed by SAB-qualified name.
java.sql.SQLException
protected java.lang.String mapRela(java.lang.String rrfName)
rrfName
-
protected java.lang.String toCommaDelimitedWithQuotes(java.lang.String[] strings)
strings
-
protected java.security.MessageDigest getSHA1()
protected java.lang.String generateUniqueKey(java.lang.String[] basis)
components
-
java.sql.SQLException
protected java.lang.String generateUniqueKey(int seed)
seed
-
protected java.lang.String get5DigitRandom()
protected void loadLoaderPreferences()
protected java.lang.String getRegisteredNameFromManifest(java.lang.String defaultRegisteredName)
defaultRegisteredName
- The default to return if the manifest does not override it
protected java.lang.String getCodingSchemeNameFromManifest(java.lang.String defaultCodingSchemeName)
defaultCodingSchemeName
- The default to return if the manifest does not override it
protected void loadMRRANK()
protected void loadDefaultSupportedNamespace(java.lang.String codingSchemeName) throws java.sql.SQLException
java.sql.SQLException
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