I2b2KnowledgeSourceBackend (AIW i2b2 ETL 2.0-Alpha-12 API)

java.lang.Object
- org.protempa.backend.AbstractBackend<org.protempa.backend.KnowledgeSourceBackendUpdatedEvent>
- - org.protempa.backend.ksb.AbstractKnowledgeSourceBackend
  - - org.protempa.backend.AbstractCommonsKnowledgeSourceBackend
    - - edu.emory.cci.aiw.i2b2etl.ksb.I2b2KnowledgeSourceBackend

All Implemented Interfaces:

org.protempa.backend.Backend<org.protempa.backend.KnowledgeSourceBackendUpdatedEvent>, org.protempa.backend.ksb.KnowledgeSourceBackend
```
public class I2b2KnowledgeSourceBackend
extends org.protempa.backend.AbstractCommonsKnowledgeSourceBackend
```
Implements using an i2b2 metadata schema to store proposition definitions.

Constructor Summary

Constructors
Constructor and Description

I2b2KnowledgeSourceBackend()

Constructors
Constructor and Description
`I2b2KnowledgeSourceBackend()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`close()`
`Collection<org.protempa.PropositionDefinition>`	`collectPropDefDescendantsUsingAllNarrower(boolean inDataSourceOnly, String[] propIds)`
`Collection<org.protempa.PropositionDefinition>`	`collectPropDefDescendantsUsingInverseIsA(String[] propIds)`
`Collection<String>`	`collectPropIdDescendantsUsingAllNarrower(boolean inDataSourceOnly, String[] propIds)`
`Collection<String>`	`collectPropIdDescendantsUsingInverseIsA(String[] propIds)`
`String`	`getAgeInYearsPropertyName()`
`org.arp.javautil.sql.DatabaseAPI`	`getDatabaseApi()` Returns which Java database API this backend is configured to use.
`String`	`getDatabaseId()`
`String`	`getDateOfBirthPropertyName()`
`String`	`getDateOfDeathPropertyName()`
`String`	`getGenderPropertyName()`
`String`	`getGenderPropertySource()`
`org.protempa.valueset.ValueSet`	`getGenderPropertyValueSet()`
`String`	`getGenderPropertyValueSetDelimiter()`
`Integer`	`getGenderPropertyValueSetDescriptionColumn()`
`Integer`	`getGenderPropertyValueSetDisplayNameColumn()`
`String`	`getGenderPropertyValueSetFile()`
`Boolean`	`getGenderPropertyValueSetHasHeader()`
`Integer`	`getGenderPropertyValueSetIdColumn()`
`String`	`getInoutPropertyName()`
`String`	`getInoutPropertySource()`
`org.protempa.valueset.ValueSet`	`getInoutPropertyValueSet()`
`String`	`getInoutPropertyValueSetDelimiter()`
`Integer`	`getInoutPropertyValueSetDescriptionColumn()`
`Integer`	`getInoutPropertyValueSetDisplayNameColumn()`
`String`	`getInoutPropertyValueSetFile()`
`Boolean`	`getInoutPropertyValueSetHasHeader()`
`Integer`	`getInoutPropertyValueSetIdColumn()`
`Set<String>`	`getKnowledgeSourceSearchResults(String searchKey)`
`String`	`getLanguagePropertyName()`
`String`	`getLanguagePropertySource()`
`org.protempa.valueset.ValueSet`	`getLanguagePropertyValueSet()`
`String`	`getLanguagePropertyValueSetDelimiter()`
`Integer`	`getLanguagePropertyValueSetDescriptionColumn()`
`Integer`	`getLanguagePropertyValueSetDisplayNameColumn()`
`String`	`getLanguagePropertyValueSetFile()`
`Boolean`	`getLanguagePropertyValueSetHasHeader()`
`Integer`	`getLanguagePropertyValueSetIdColumn()`
`String`	`getMaritalStatusPropertyName()`
`String`	`getMaritalStatusPropertySource()`
`org.protempa.valueset.ValueSet`	`getMaritalStatusPropertyValueSet()`
`String`	`getMaritalStatusPropertyValueSetDelimiter()`
`Integer`	`getMaritalStatusPropertyValueSetDescriptionColumn()`
`Integer`	`getMaritalStatusPropertyValueSetDisplayNameColumn()`
`String`	`getMaritalStatusPropertyValueSetFile()`
`Boolean`	`getMaritalStatusPropertyValueSetHasHeader()`
`Integer`	`getMaritalStatusPropertyValueSetIdColumn()`
`String`	`getPassword()`
`String`	`getPatientDetailsDisplayName()`
`String`	`getPatientDetailsPatientIdPropertyName()`
`String`	`getPatientDetailsPropositionId()`
`String`	`getPatientPatientIdPropertyName()`
`String`	`getPatientPropositionId()`
`String`	`getProviderDisplayName()`
`String`	`getProviderNamePropertyName()`
`String`	`getProviderPropositionId()`
`String`	`getRacePropertyName()`
`String`	`getRacePropertySource()`
`org.protempa.valueset.ValueSet`	`getRacePropertyValueSet()`
`String`	`getRacePropertyValueSetDelimiter()`
`Integer`	`getRacePropertyValueSetDescriptionColumn()`
`Integer`	`getRacePropertyValueSetDisplayNameColumn()`
`String`	`getRacePropertyValueSetFile()`
`Boolean`	`getRacePropertyValueSetHasHeader()`
`Integer`	`getRacePropertyValueSetIdColumn()`
`String`	`getReligionPropertyName()`
`String`	`getReligionPropertySource()`
`org.protempa.valueset.ValueSet`	`getReligionPropertyValueSet()`
`String`	`getReligionPropertyValueSetDelimiter()`
`Integer`	`getReligionPropertyValueSetDescriptionColumn()`
`Integer`	`getReligionPropertyValueSetDisplayNameColumn()`
`String`	`getReligionPropertyValueSetFile()`
`Boolean`	`getReligionPropertyValueSetHasHeader()`
`Integer`	`getReligionPropertyValueSetIdColumn()`
`String`	`getTargetTable()`
`String`	`getUsername()`
`String`	`getVisitAgePropertyName()`
`String`	`getVisitDisplayName()`
`String`	`getVisitPropositionId()`
`String`	`getVitalStatusPropertyName()`
`void`	`initialize(org.protempa.backend.BackendInstanceSpec config)`
`void`	`parseDatabaseApi(String databaseApiString)` Configures which Java database API to use (`DriverManager` or `DataSource` by parsing a `DatabaseAPI`'s name.
`void`	`parseGenderPropertyValueSet(String valueSetStr)`
`void`	`parseInoutPropertyValueSet(String valueSetStr)`
`void`	`parseLanguagePropertyValueSet(String valueSetStr)`
`void`	`parseMaritalStatusPropertyValueSet(String valueSetStr)`
`void`	`parseRacePropertyValueSet(String valueSetStr)`
`void`	`parseReligionPropertyValueSet(String valueSetStr)`
`String[]`	`readAbstractedInto(String propId)`
`org.protempa.AbstractionDefinition`	`readAbstractionDefinition(String id)`
`List<org.protempa.AbstractionDefinition>`	`readAbstractionDefinitions(String[] ids)`
`org.protempa.ContextDefinition`	`readContextDefinition(String id)`
`List<org.protempa.ContextDefinition>`	`readContextDefinitions(String[] toArray)`
`String[]`	`readInduces(String propId)`
`String[]`	`readIsA(String propId)`
`org.protempa.PropositionDefinition`	`readPropositionDefinition(String id)`
`List<org.protempa.PropositionDefinition>`	`readPropositionDefinitions(String[] ids)`
`String[]`	`readSubContextOfs(String propId)`
`org.protempa.TemporalPropositionDefinition`	`readTemporalPropositionDefinition(String id)`
`List<org.protempa.TemporalPropositionDefinition>`	`readTemporalPropositionDefinitions(String[] ids)`
`org.protempa.valueset.ValueSet`	`readValueSet(String id)`
`void`	`setAgeInYearsPropertyName(String ageInYearsPropertyName)`
`void`	`setDatabaseApi(org.arp.javautil.sql.DatabaseAPI databaseApi)` Configures which Java database API to use (`DriverManager` or `DataSource`.
`void`	`setDatabaseId(String databaseId)`
`void`	`setDateOfBirthPropertyName(String dateOfBirthPropertyName)`
`void`	`setDateOfDeathPropertyName(String dateOfDeathPropertyName)`
`void`	`setGenderPropertyName(String genderPropertyName)`
`void`	`setGenderPropertySource(String genderPropertySource)`
`void`	`setGenderPropertyValueSet(org.protempa.valueset.ValueSet genderPropertyValueSet)`
`void`	`setGenderPropertyValueSetDelimiter(String genderPropertyValueSetDelimiter)`
`void`	`setGenderPropertyValueSetDescriptionColumn(Integer genderPropertyValueSetDescriptionColumn)`
`void`	`setGenderPropertyValueSetDisplayNameColumn(Integer genderPropertyValueSetDisplayNameColumn)`
`void`	`setGenderPropertyValueSetFile(String genderPropertyValueSetFile)`
`void`	`setGenderPropertyValueSetHasHeader(Boolean genderPropertyValueSetHasHeader)`
`void`	`setGenderPropertyValueSetIdColumn(Integer genderPropertyValueSetIdColumn)`
`void`	`setInoutPropertyName(String inoutPropertyName)`
`void`	`setInoutPropertySource(String inoutPropertySource)`
`void`	`setInoutPropertyValueSet(org.protempa.valueset.ValueSet inoutPropertyValueSet)`
`void`	`setInoutPropertyValueSetDelimiter(String inoutPropertyValueSetDelimiter)`
`void`	`setInoutPropertyValueSetDescriptionColumn(Integer inoutPropertyValueSetDescriptionColumn)`
`void`	`setInoutPropertyValueSetDisplayNameColumn(Integer inoutPropertyValueSetDisplayNameColumn)`
`void`	`setInoutPropertyValueSetFile(String inoutPropertyValueSetFile)`
`void`	`setInoutPropertyValueSetHasHeader(Boolean inoutPropertyValueSetHasHeader)`
`void`	`setInoutPropertyValueSetIdColumn(Integer inoutPropertyValueSetIdColumn)`
`void`	`setLanguagePropertyName(String languagePropertyName)`
`void`	`setLanguagePropertySource(String languagePropertySource)`
`void`	`setLanguagePropertyValueSet(org.protempa.valueset.ValueSet languagePropertyValueSet)`
`void`	`setLanguagePropertyValueSetDelimiter(String languagePropertyValueSetDelimiter)`
`void`	`setLanguagePropertyValueSetDescriptionColumn(Integer languagePropertyValueSetDescriptionColumn)`
`void`	`setLanguagePropertyValueSetDisplayNameColumn(Integer languagePropertyValueSetDisplayNameColumn)`
`void`	`setLanguagePropertyValueSetFile(String languagePropertyValueSetFile)`
`void`	`setLanguagePropertyValueSetHasHeader(Boolean languagePropertyValueSetHasHeader)`
`void`	`setLanguagePropertyValueSetIdColumn(Integer languagePropertyValueSetIdColumn)`
`void`	`setMaritalStatusPropertyName(String maritalStatusPropertyName)`
`void`	`setMaritalStatusPropertySource(String maritalStatusPropertySource)`
`void`	`setMaritalStatusPropertyValueSet(org.protempa.valueset.ValueSet maritalStatusPropertyValueSet)`
`void`	`setMaritalStatusPropertyValueSetDelimiter(String maritalStatusPropertyValueSetDelimiter)`
`void`	`setMaritalStatusPropertyValueSetDescriptionColumn(Integer maritalStatusPropertyValueSetDescriptionColumn)`
`void`	`setMaritalStatusPropertyValueSetDisplayNameColumn(Integer maritalStatusPropertyValueSetDisplayNameColumn)`
`void`	`setMaritalStatusPropertyValueSetFile(String maritalStatusPropertyValueSetFile)`
`void`	`setMaritalStatusPropertyValueSetHasHeader(Boolean maritalStatusPropertyValueSetHasHeader)`
`void`	`setMaritalStatusPropertyValueSetIdColumn(Integer maritalStatusPropertyValueSetIdColumn)`
`void`	`setPassword(String password)`
`void`	`setPatientDetailsDisplayName(String patientDetailsDisplayName)`
`void`	`setPatientDetailsPatientIdPropertyName(String patientDetailsPatientIdPropertyName)`
`void`	`setPatientDetailsPropositionId(String patientDetailsPropositionId)`
`void`	`setPatientPatientIdPropertyName(String patientPatientIdPropertyName)`
`void`	`setPatientPropositionId(String patientPropositionId)`
`void`	`setProviderDisplayName(String providerDisplayName)`
`void`	`setProviderNamePropertyName(String providerNamePropertyName)`
`void`	`setProviderPropositionId(String providerPropositionId)`
`void`	`setRacePropertyName(String racePropertyName)`
`void`	`setRacePropertySource(String racePropertySource)`
`void`	`setRacePropertyValueSet(org.protempa.valueset.ValueSet racePropertyValueSet)`
`void`	`setRacePropertyValueSetDelimiter(String racePropertyValueSetDelimiter)`
`void`	`setRacePropertyValueSetDescriptionColumn(Integer racePropertyValueSetDescriptionColumn)`
`void`	`setRacePropertyValueSetDisplayNameColumn(Integer racePropertyValueSetDisplayNameColumn)`
`void`	`setRacePropertyValueSetFile(String racePropertyValueSetFile)`
`void`	`setRacePropertyValueSetHasHeader(Boolean racePropertyValueSetHasHeader)`
`void`	`setRacePropertyValueSetIdColumn(Integer racePropertyValueSetIdColumn)`
`void`	`setReligionPropertyName(String religionPropertyName)`
`void`	`setReligionPropertySource(String religionPropertySource)`
`void`	`setReligionPropertyValueSet(org.protempa.valueset.ValueSet religionPropertyValueSet)`
`void`	`setReligionPropertyValueSetDelimiter(String religionPropertyValueSetDelimiter)`
`void`	`setReligionPropertyValueSetDescriptionColumn(Integer religionPropertyValueSetDescriptionColumn)`
`void`	`setReligionPropertyValueSetDisplayNameColumn(Integer religionPropertyValueSetDisplayNameColumn)`
`void`	`setReligionPropertyValueSetFile(String religionPropertyValueSetFile)`
`void`	`setReligionPropertyValueSetHasHeader(Boolean religionPropertyValueSetHasHeader)`
`void`	`setReligionPropertyValueSetIdColumn(Integer religionPropertyValueSetIdColumn)`
`void`	`setTargetTable(String tableName)`
`void`	`setUsername(String username)`
`void`	`setVisitAgePropertyName(String visitAgePropertyName)`
`void`	`setVisitDisplayName(String visitDisplayName)`
`void`	`setVisitPropositionId(String visitPropositionId)`
`void`	`setVitalStatusPropertyName(String vitalStatusPropertyName)`

Methods inherited from class org.protempa.backend.AbstractCommonsKnowledgeSourceBackend
getDisplayName, getId, nameForErrors, setId

Methods inherited from class org.protempa.backend.ksb.AbstractKnowledgeSourceBackend
fireKnowledgeSourceBackendUpdated, getPropositionsByTerm, getPropositionsByTermSubsumption

Methods inherited from class org.protempa.backend.AbstractBackend
addBackendListener, fireBackendUpdated, fireUnrecoverableError, getConfigurationsId, removeBackendListener

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.protempa.backend.Backend
addBackendListener, getConfigurationsId, removeBackendListener

Constructor Detail
- I2b2KnowledgeSourceBackend
```
public I2b2KnowledgeSourceBackend()
```

Method Detail

getDatabaseApi
```
public org.arp.javautil.sql.DatabaseAPI getDatabaseApi()
```
Returns which Java database API this backend is configured to use.

Returns:

a DatabaseAPI. The default value is DatabaseAPI.DRIVERMANAGER

setDatabaseApi
```
public void setDatabaseApi(org.arp.javautil.sql.DatabaseAPI databaseApi)
```
Configures which Java database API to use (DriverManager or DataSource. If null, the default is assigned (DatabaseAPI.DRIVERMANAGER).

Parameters:

databaseApi - a DatabaseAPI.

getTargetTable
```
public String getTargetTable()
```

setTargetTable

public void setTargetTable(String tableName)

parseDatabaseApi
```
public void parseDatabaseApi(String databaseApiString)
```
Configures which Java database API to use (DriverManager or DataSource by parsing a DatabaseAPI's name. Cannot be null.

Parameters:

databaseApiString - a DatabaseAPI's name.

getDatabaseId
```
public String getDatabaseId()
```

setDatabaseId

public void setDatabaseId(String databaseId)

getUsername
```
public String getUsername()
```

setUsername

public void setUsername(String username)

getPassword
```
public String getPassword()
```

setPassword

public void setPassword(String password)

getPatientPatientIdPropertyName

public String getPatientPatientIdPropertyName()

setPatientPatientIdPropertyName

public void setPatientPatientIdPropertyName(String patientPatientIdPropertyName)

getPatientDetailsPatientIdPropertyName

public String getPatientDetailsPatientIdPropertyName()

setPatientDetailsPatientIdPropertyName

public void setPatientDetailsPatientIdPropertyName(String patientDetailsPatientIdPropertyName)

getPatientPropositionId

public String getPatientPropositionId()

setPatientPropositionId

public void setPatientPropositionId(String patientPropositionId)

getPatientDetailsPropositionId

public String getPatientDetailsPropositionId()

setPatientDetailsPropositionId

public void setPatientDetailsPropositionId(String patientDetailsPropositionId)

getPatientDetailsDisplayName

public String getPatientDetailsDisplayName()

setPatientDetailsDisplayName

public void setPatientDetailsDisplayName(String patientDetailsDisplayName)

getVisitPropositionId
```
public String getVisitPropositionId()
```

setVisitPropositionId

public void setVisitPropositionId(String visitPropositionId)

getVisitDisplayName
```
public String getVisitDisplayName()
```

setVisitDisplayName

public void setVisitDisplayName(String visitDisplayName)

getProviderPropositionId

public String getProviderPropositionId()

setProviderPropositionId

public void setProviderPropositionId(String providerPropositionId)

getProviderDisplayName

public String getProviderDisplayName()

setProviderDisplayName

public void setProviderDisplayName(String providerDisplayName)

getProviderNamePropertyName

public String getProviderNamePropertyName()

setProviderNamePropertyName

public void setProviderNamePropertyName(String providerNamePropertyName)

getInoutPropertyName
```
public String getInoutPropertyName()
```

setInoutPropertyName

public void setInoutPropertyName(String inoutPropertyName)

getInoutPropertySource

public String getInoutPropertySource()

setInoutPropertySource

public void setInoutPropertySource(String inoutPropertySource)

getInoutPropertyValueSet

public org.protempa.valueset.ValueSet getInoutPropertyValueSet()

setInoutPropertyValueSet

public void setInoutPropertyValueSet(org.protempa.valueset.ValueSet inoutPropertyValueSet)

parseInoutPropertyValueSet

public void parseInoutPropertyValueSet(String valueSetStr)

getInoutPropertyValueSetFile

public String getInoutPropertyValueSetFile()

setInoutPropertyValueSetFile

public void setInoutPropertyValueSetFile(String inoutPropertyValueSetFile)

getInoutPropertyValueSetHasHeader

public Boolean getInoutPropertyValueSetHasHeader()

setInoutPropertyValueSetHasHeader

public void setInoutPropertyValueSetHasHeader(Boolean inoutPropertyValueSetHasHeader)

getInoutPropertyValueSetDelimiter

public String getInoutPropertyValueSetDelimiter()

setInoutPropertyValueSetDelimiter

public void setInoutPropertyValueSetDelimiter(String inoutPropertyValueSetDelimiter)

getInoutPropertyValueSetIdColumn

public Integer getInoutPropertyValueSetIdColumn()

setInoutPropertyValueSetIdColumn

public void setInoutPropertyValueSetIdColumn(Integer inoutPropertyValueSetIdColumn)

getInoutPropertyValueSetDisplayNameColumn

public Integer getInoutPropertyValueSetDisplayNameColumn()

setInoutPropertyValueSetDisplayNameColumn

public void setInoutPropertyValueSetDisplayNameColumn(Integer inoutPropertyValueSetDisplayNameColumn)

getInoutPropertyValueSetDescriptionColumn

public Integer getInoutPropertyValueSetDescriptionColumn()

setInoutPropertyValueSetDescriptionColumn

public void setInoutPropertyValueSetDescriptionColumn(Integer inoutPropertyValueSetDescriptionColumn)

getVisitAgePropertyName

public String getVisitAgePropertyName()

setVisitAgePropertyName

public void setVisitAgePropertyName(String visitAgePropertyName)

getGenderPropertyName
```
public String getGenderPropertyName()
```

setGenderPropertyName

public void setGenderPropertyName(String genderPropertyName)

getGenderPropertyValueSet

public org.protempa.valueset.ValueSet getGenderPropertyValueSet()

setGenderPropertyValueSet

public void setGenderPropertyValueSet(org.protempa.valueset.ValueSet genderPropertyValueSet)

parseGenderPropertyValueSet

public void parseGenderPropertyValueSet(String valueSetStr)

getGenderPropertySource

public String getGenderPropertySource()

setGenderPropertySource

public void setGenderPropertySource(String genderPropertySource)

getGenderPropertyValueSetFile

public String getGenderPropertyValueSetFile()

setGenderPropertyValueSetFile

public void setGenderPropertyValueSetFile(String genderPropertyValueSetFile)

getGenderPropertyValueSetHasHeader

public Boolean getGenderPropertyValueSetHasHeader()

setGenderPropertyValueSetHasHeader

public void setGenderPropertyValueSetHasHeader(Boolean genderPropertyValueSetHasHeader)

getGenderPropertyValueSetDelimiter

public String getGenderPropertyValueSetDelimiter()

setGenderPropertyValueSetDelimiter

public void setGenderPropertyValueSetDelimiter(String genderPropertyValueSetDelimiter)

getGenderPropertyValueSetIdColumn

public Integer getGenderPropertyValueSetIdColumn()

setGenderPropertyValueSetIdColumn

public void setGenderPropertyValueSetIdColumn(Integer genderPropertyValueSetIdColumn)

getGenderPropertyValueSetDisplayNameColumn

public Integer getGenderPropertyValueSetDisplayNameColumn()

setGenderPropertyValueSetDisplayNameColumn

public void setGenderPropertyValueSetDisplayNameColumn(Integer genderPropertyValueSetDisplayNameColumn)

getGenderPropertyValueSetDescriptionColumn

public Integer getGenderPropertyValueSetDescriptionColumn()

setGenderPropertyValueSetDescriptionColumn

public void setGenderPropertyValueSetDescriptionColumn(Integer genderPropertyValueSetDescriptionColumn)

getRacePropertyName
```
public String getRacePropertyName()
```

setRacePropertyName

public void setRacePropertyName(String racePropertyName)

getRacePropertyValueSet

public org.protempa.valueset.ValueSet getRacePropertyValueSet()

setRacePropertyValueSet

public void setRacePropertyValueSet(org.protempa.valueset.ValueSet racePropertyValueSet)

parseRacePropertyValueSet

public void parseRacePropertyValueSet(String valueSetStr)

getRacePropertyValueSetFile

public String getRacePropertyValueSetFile()

setRacePropertyValueSetFile

public void setRacePropertyValueSetFile(String racePropertyValueSetFile)

getRacePropertyValueSetHasHeader

public Boolean getRacePropertyValueSetHasHeader()

setRacePropertyValueSetHasHeader

public void setRacePropertyValueSetHasHeader(Boolean racePropertyValueSetHasHeader)

getRacePropertyValueSetDelimiter

public String getRacePropertyValueSetDelimiter()

setRacePropertyValueSetDelimiter

public void setRacePropertyValueSetDelimiter(String racePropertyValueSetDelimiter)

getRacePropertyValueSetIdColumn

public Integer getRacePropertyValueSetIdColumn()

setRacePropertyValueSetIdColumn

public void setRacePropertyValueSetIdColumn(Integer racePropertyValueSetIdColumn)

getRacePropertyValueSetDisplayNameColumn

public Integer getRacePropertyValueSetDisplayNameColumn()

setRacePropertyValueSetDisplayNameColumn

public void setRacePropertyValueSetDisplayNameColumn(Integer racePropertyValueSetDisplayNameColumn)

getRacePropertyValueSetDescriptionColumn

public Integer getRacePropertyValueSetDescriptionColumn()

setRacePropertyValueSetDescriptionColumn

public void setRacePropertyValueSetDescriptionColumn(Integer racePropertyValueSetDescriptionColumn)

getRacePropertySource
```
public String getRacePropertySource()
```

setRacePropertySource

public void setRacePropertySource(String racePropertySource)

getLanguagePropertyName

public String getLanguagePropertyName()

setLanguagePropertyName

public void setLanguagePropertyName(String languagePropertyName)

getLanguagePropertyValueSet

public org.protempa.valueset.ValueSet getLanguagePropertyValueSet()

setLanguagePropertyValueSet

public void setLanguagePropertyValueSet(org.protempa.valueset.ValueSet languagePropertyValueSet)

parseLanguagePropertyValueSet

public void parseLanguagePropertyValueSet(String valueSetStr)

getLanguagePropertyValueSetFile

public String getLanguagePropertyValueSetFile()

setLanguagePropertyValueSetFile

public void setLanguagePropertyValueSetFile(String languagePropertyValueSetFile)

getLanguagePropertyValueSetHasHeader

public Boolean getLanguagePropertyValueSetHasHeader()

setLanguagePropertyValueSetHasHeader

public void setLanguagePropertyValueSetHasHeader(Boolean languagePropertyValueSetHasHeader)

getLanguagePropertyValueSetDelimiter

public String getLanguagePropertyValueSetDelimiter()

setLanguagePropertyValueSetDelimiter

public void setLanguagePropertyValueSetDelimiter(String languagePropertyValueSetDelimiter)

getLanguagePropertyValueSetIdColumn

public Integer getLanguagePropertyValueSetIdColumn()

setLanguagePropertyValueSetIdColumn

public void setLanguagePropertyValueSetIdColumn(Integer languagePropertyValueSetIdColumn)

getLanguagePropertyValueSetDisplayNameColumn

public Integer getLanguagePropertyValueSetDisplayNameColumn()

setLanguagePropertyValueSetDisplayNameColumn

public void setLanguagePropertyValueSetDisplayNameColumn(Integer languagePropertyValueSetDisplayNameColumn)

getLanguagePropertyValueSetDescriptionColumn

public Integer getLanguagePropertyValueSetDescriptionColumn()

setLanguagePropertyValueSetDescriptionColumn

public void setLanguagePropertyValueSetDescriptionColumn(Integer languagePropertyValueSetDescriptionColumn)

getLanguagePropertySource

public String getLanguagePropertySource()

setLanguagePropertySource

public void setLanguagePropertySource(String languagePropertySource)

getMaritalStatusPropertyValueSet

public org.protempa.valueset.ValueSet getMaritalStatusPropertyValueSet()

setMaritalStatusPropertyValueSet

public void setMaritalStatusPropertyValueSet(org.protempa.valueset.ValueSet maritalStatusPropertyValueSet)

parseMaritalStatusPropertyValueSet

public void parseMaritalStatusPropertyValueSet(String valueSetStr)

getMaritalStatusPropertyValueSetFile

public String getMaritalStatusPropertyValueSetFile()

setMaritalStatusPropertyValueSetFile

public void setMaritalStatusPropertyValueSetFile(String maritalStatusPropertyValueSetFile)

getMaritalStatusPropertyValueSetHasHeader

public Boolean getMaritalStatusPropertyValueSetHasHeader()

setMaritalStatusPropertyValueSetHasHeader

public void setMaritalStatusPropertyValueSetHasHeader(Boolean maritalStatusPropertyValueSetHasHeader)

getMaritalStatusPropertyValueSetDelimiter

public String getMaritalStatusPropertyValueSetDelimiter()

setMaritalStatusPropertyValueSetDelimiter

public void setMaritalStatusPropertyValueSetDelimiter(String maritalStatusPropertyValueSetDelimiter)

getMaritalStatusPropertyValueSetIdColumn

public Integer getMaritalStatusPropertyValueSetIdColumn()

setMaritalStatusPropertyValueSetIdColumn

public void setMaritalStatusPropertyValueSetIdColumn(Integer maritalStatusPropertyValueSetIdColumn)

getMaritalStatusPropertyValueSetDisplayNameColumn

public Integer getMaritalStatusPropertyValueSetDisplayNameColumn()

setMaritalStatusPropertyValueSetDisplayNameColumn

public void setMaritalStatusPropertyValueSetDisplayNameColumn(Integer maritalStatusPropertyValueSetDisplayNameColumn)

getMaritalStatusPropertyValueSetDescriptionColumn

public Integer getMaritalStatusPropertyValueSetDescriptionColumn()

setMaritalStatusPropertyValueSetDescriptionColumn

public void setMaritalStatusPropertyValueSetDescriptionColumn(Integer maritalStatusPropertyValueSetDescriptionColumn)

getMaritalStatusPropertySource

public String getMaritalStatusPropertySource()

setMaritalStatusPropertySource

public void setMaritalStatusPropertySource(String maritalStatusPropertySource)

getMaritalStatusPropertyName

public String getMaritalStatusPropertyName()

setMaritalStatusPropertyName

public void setMaritalStatusPropertyName(String maritalStatusPropertyName)

getReligionPropertyName

public String getReligionPropertyName()

setReligionPropertyName

public void setReligionPropertyName(String religionPropertyName)

getReligionPropertyValueSet

public org.protempa.valueset.ValueSet getReligionPropertyValueSet()

setReligionPropertyValueSet

public void setReligionPropertyValueSet(org.protempa.valueset.ValueSet religionPropertyValueSet)

parseReligionPropertyValueSet

public void parseReligionPropertyValueSet(String valueSetStr)

getReligionPropertyValueSetFile

public String getReligionPropertyValueSetFile()

setReligionPropertyValueSetFile

public void setReligionPropertyValueSetFile(String religionPropertyValueSetFile)

getReligionPropertyValueSetHasHeader

public Boolean getReligionPropertyValueSetHasHeader()

setReligionPropertyValueSetHasHeader

public void setReligionPropertyValueSetHasHeader(Boolean religionPropertyValueSetHasHeader)

getReligionPropertyValueSetDelimiter

public String getReligionPropertyValueSetDelimiter()

setReligionPropertyValueSetDelimiter

public void setReligionPropertyValueSetDelimiter(String religionPropertyValueSetDelimiter)

getReligionPropertyValueSetIdColumn

public Integer getReligionPropertyValueSetIdColumn()

setReligionPropertyValueSetIdColumn

public void setReligionPropertyValueSetIdColumn(Integer religionPropertyValueSetIdColumn)

getReligionPropertyValueSetDisplayNameColumn

public Integer getReligionPropertyValueSetDisplayNameColumn()

setReligionPropertyValueSetDisplayNameColumn

public void setReligionPropertyValueSetDisplayNameColumn(Integer religionPropertyValueSetDisplayNameColumn)

getReligionPropertyValueSetDescriptionColumn

public Integer getReligionPropertyValueSetDescriptionColumn()

setReligionPropertyValueSetDescriptionColumn

public void setReligionPropertyValueSetDescriptionColumn(Integer religionPropertyValueSetDescriptionColumn)

getReligionPropertySource

public String getReligionPropertySource()

setReligionPropertySource

public void setReligionPropertySource(String religionPropertySource)

getDateOfBirthPropertyName

public String getDateOfBirthPropertyName()

setDateOfBirthPropertyName

public void setDateOfBirthPropertyName(String dateOfBirthPropertyName)

getAgeInYearsPropertyName

public String getAgeInYearsPropertyName()

setAgeInYearsPropertyName

public void setAgeInYearsPropertyName(String ageInYearsPropertyName)

getDateOfDeathPropertyName

public String getDateOfDeathPropertyName()

setDateOfDeathPropertyName

public void setDateOfDeathPropertyName(String dateOfDeathPropertyName)

getVitalStatusPropertyName

public String getVitalStatusPropertyName()

setVitalStatusPropertyName

public void setVitalStatusPropertyName(String vitalStatusPropertyName)

readPropositionDefinition

public org.protempa.PropositionDefinition readPropositionDefinition(String id)
                                                             throws org.protempa.KnowledgeSourceReadException

Throws:: org.protempa.KnowledgeSourceReadException

readPropositionDefinitions

public List<org.protempa.PropositionDefinition> readPropositionDefinitions(String[] ids)
                                                                    throws org.protempa.KnowledgeSourceReadException

Throws:: org.protempa.KnowledgeSourceReadException

readIsA

public String[] readIsA(String propId)
                 throws org.protempa.KnowledgeSourceReadException

Throws:: org.protempa.KnowledgeSourceReadException

getKnowledgeSourceSearchResults

public Set<String> getKnowledgeSourceSearchResults(String searchKey)
                                            throws org.protempa.KnowledgeSourceReadException

Throws:: org.protempa.KnowledgeSourceReadException

initialize
```
public void initialize(org.protempa.backend.BackendInstanceSpec config)
                throws org.protempa.backend.BackendInitializationException
```
Specified by:

initialize in interface org.protempa.backend.Backend<org.protempa.backend.KnowledgeSourceBackendUpdatedEvent>

Overrides:

initialize in class org.protempa.backend.AbstractCommonsKnowledgeSourceBackend

Throws:

org.protempa.backend.BackendInitializationException

readAbstractionDefinition

public org.protempa.AbstractionDefinition readAbstractionDefinition(String id)
                                                             throws org.protempa.KnowledgeSourceReadException

Throws:: org.protempa.KnowledgeSourceReadException

readAbstractionDefinitions

public List<org.protempa.AbstractionDefinition> readAbstractionDefinitions(String[] ids)
                                                                    throws org.protempa.KnowledgeSourceReadException

Throws:: org.protempa.KnowledgeSourceReadException

readContextDefinition

public org.protempa.ContextDefinition readContextDefinition(String id)
                                                     throws org.protempa.KnowledgeSourceReadException

Throws:: org.protempa.KnowledgeSourceReadException

readContextDefinitions

public List<org.protempa.ContextDefinition> readContextDefinitions(String[] toArray)
                                                            throws org.protempa.KnowledgeSourceReadException

Throws:: org.protempa.KnowledgeSourceReadException

readTemporalPropositionDefinition

public org.protempa.TemporalPropositionDefinition readTemporalPropositionDefinition(String id)
                                                                             throws org.protempa.KnowledgeSourceReadException

Throws:: org.protempa.KnowledgeSourceReadException

readTemporalPropositionDefinitions

public List<org.protempa.TemporalPropositionDefinition> readTemporalPropositionDefinitions(String[] ids)
                                                                                    throws org.protempa.KnowledgeSourceReadException

Throws:: org.protempa.KnowledgeSourceReadException

readAbstractedInto

public String[] readAbstractedInto(String propId)
                            throws org.protempa.KnowledgeSourceReadException

Throws:: org.protempa.KnowledgeSourceReadException

readInduces

public String[] readInduces(String propId)
                     throws org.protempa.KnowledgeSourceReadException

Throws:: org.protempa.KnowledgeSourceReadException

readSubContextOfs

public String[] readSubContextOfs(String propId)
                           throws org.protempa.KnowledgeSourceReadException

Throws:: org.protempa.KnowledgeSourceReadException

close
```
public void close()
```
Specified by:

close in interface org.protempa.backend.Backend<org.protempa.backend.KnowledgeSourceBackendUpdatedEvent>

Overrides:

close in class org.protempa.backend.ksb.AbstractKnowledgeSourceBackend

readValueSet
```
public org.protempa.valueset.ValueSet readValueSet(String id)
                                            throws org.protempa.KnowledgeSourceReadException
```
Specified by:

readValueSet in interface org.protempa.backend.ksb.KnowledgeSourceBackend

Overrides:

readValueSet in class org.protempa.backend.ksb.AbstractKnowledgeSourceBackend

Throws:

org.protempa.KnowledgeSourceReadException

collectPropIdDescendantsUsingAllNarrower

public Collection<String> collectPropIdDescendantsUsingAllNarrower(boolean inDataSourceOnly,
                                                                   String[] propIds)
                                                            throws org.protempa.KnowledgeSourceReadException

Throws:: org.protempa.KnowledgeSourceReadException

collectPropIdDescendantsUsingInverseIsA

public Collection<String> collectPropIdDescendantsUsingInverseIsA(String[] propIds)
                                                           throws org.protempa.KnowledgeSourceReadException

Throws:: org.protempa.KnowledgeSourceReadException

collectPropDefDescendantsUsingAllNarrower

public Collection<org.protempa.PropositionDefinition> collectPropDefDescendantsUsingAllNarrower(boolean inDataSourceOnly,
                                                                                                String[] propIds)
                                                                                         throws org.protempa.KnowledgeSourceReadException

Throws:: org.protempa.KnowledgeSourceReadException

collectPropDefDescendantsUsingInverseIsA

public Collection<org.protempa.PropositionDefinition> collectPropDefDescendantsUsingInverseIsA(String[] propIds)
                                                                                        throws org.protempa.KnowledgeSourceReadException

Throws:: org.protempa.KnowledgeSourceReadException

Class I2b2KnowledgeSourceBackend

Constructor Summary

Method Summary

Methods inherited from class org.protempa.backend.AbstractCommonsKnowledgeSourceBackend

Methods inherited from class org.protempa.backend.ksb.AbstractKnowledgeSourceBackend

Methods inherited from class org.protempa.backend.AbstractBackend

Methods inherited from class java.lang.Object

Methods inherited from interface org.protempa.backend.Backend

Constructor Detail

I2b2KnowledgeSourceBackend

Method Detail

getDatabaseApi

setDatabaseApi

getTargetTable

setTargetTable

parseDatabaseApi

getDatabaseId

setDatabaseId

getUsername

setUsername

getPassword

setPassword

getPatientPatientIdPropertyName

setPatientPatientIdPropertyName

getPatientDetailsPatientIdPropertyName

setPatientDetailsPatientIdPropertyName

getPatientPropositionId

setPatientPropositionId

getPatientDetailsPropositionId

setPatientDetailsPropositionId

getPatientDetailsDisplayName

setPatientDetailsDisplayName

getVisitPropositionId

setVisitPropositionId

getVisitDisplayName

setVisitDisplayName

getProviderPropositionId

setProviderPropositionId

getProviderDisplayName

setProviderDisplayName

getProviderNamePropertyName

setProviderNamePropertyName

getInoutPropertyName

setInoutPropertyName

getInoutPropertySource

setInoutPropertySource

getInoutPropertyValueSet

setInoutPropertyValueSet

parseInoutPropertyValueSet

getInoutPropertyValueSetFile

setInoutPropertyValueSetFile

getInoutPropertyValueSetHasHeader

setInoutPropertyValueSetHasHeader

getInoutPropertyValueSetDelimiter

setInoutPropertyValueSetDelimiter

getInoutPropertyValueSetIdColumn

setInoutPropertyValueSetIdColumn

getInoutPropertyValueSetDisplayNameColumn

setInoutPropertyValueSetDisplayNameColumn

getInoutPropertyValueSetDescriptionColumn

setInoutPropertyValueSetDescriptionColumn

getVisitAgePropertyName

setVisitAgePropertyName

getGenderPropertyName

setGenderPropertyName

getGenderPropertyValueSet

setGenderPropertyValueSet

parseGenderPropertyValueSet

getGenderPropertySource

setGenderPropertySource

getGenderPropertyValueSetFile

setGenderPropertyValueSetFile

getGenderPropertyValueSetHasHeader

setGenderPropertyValueSetHasHeader

getGenderPropertyValueSetDelimiter

setGenderPropertyValueSetDelimiter

getGenderPropertyValueSetIdColumn

setGenderPropertyValueSetIdColumn

getGenderPropertyValueSetDisplayNameColumn

setGenderPropertyValueSetDisplayNameColumn