PostgresPatientStore (HIStream : i2b2 0.14.1 API)

java.lang.Object
- de.sekmi.histream.i2b2.PostgresExtension<I2b2Patient>
- - de.sekmi.histream.i2b2.PostgresPatientStore

All Implemented Interfaces:

PatientStore, Extension<I2b2Patient>, Closeable, AutoCloseable
```
public class PostgresPatientStore
extends PostgresExtension<I2b2Patient>
implements PatientStore, Closeable
```
Patient cache which synchronizes with i2b2 patient_dimension and patient_mapping tables. Required non-null columns are patient_num, update_date.
The method open(Connection, String, DataDialect) will load all patients (relevant to the selected project) into a memory structure based on a hash table.
Some optional columns are used: vital_status_cd, birth_date, death_date, sex_cd, download_date, sourcesystem_cd
The store should be separate from the extension? E.g. I2b2PatientExtension which can operate on PostgresStore, OracleStore, etc. HistreamPatientExtension can also operate on I2b2PostgresStore?
The patient_mapping table is used to map actual (source) patient_ide to internal patient_num for facts. The patient_mapping table is also used to store patient merge events (eg. different patient_ide referring to the same patient_num The Observation stream will still use the actual source patient_ide and encounter_ide
In the patient_mapping table, patient_ide_status can assume values Active, Inactive, Deleted, Merged. The 'Active' patient_mapping for the selected project is used as primary patient id, all other rows are used as alias ids.

Author:

marap1

Constructor Summary

Constructors
Constructor and Description

PostgresPatientStore()

Constructors
Constructor and Description
`PostgresPatientStore()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`close()`
`I2b2Patient`	`createInstance(Object... args)`
`I2b2Patient`	`createInstance(Observation fact)`
`void`	`deleteWhereSourceId(String sourceId)`
`void`	`flush()` Write updates to disk.
`String[]`	`getAliasIds(Patient patient)`
`Iterable<Class<? super I2b2Patient>>`	`getInstanceTypes()`
`I2b2Patient`	`lookupPatientNum(Integer patient_num)`
`void`	`merge(Patient patient, String additionalId, ExternalSourceType source)`
`void`	`open(Connection connection, String projectId, DataDialect dialect)`
`protected void`	`prepareStatements()`
`void`	`purge(String id)`
`I2b2Patient`	`retrieve(String id)`
`int`	`size()` Returns the number of patients which are currently available in memory.

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

- Constructor Detail
  - PostgresPatientStore
```
public PostgresPatientStore()
```
- Method Detail
  - open
```
public void open(Connection connection,
                 String projectId,
                 DataDialect dialect)
          throws SQLException
```
    Throws:
    
    SQLException
  - lookupPatientNum
```
public I2b2Patient lookupPatientNum(Integer patient_num)
```
  - prepareStatements
```
protected void prepareStatements()
                          throws SQLException
```
    Specified by:
    
    prepareStatements in class PostgresExtension<I2b2Patient>
    
    Throws:
    
    SQLException
  - size
```
public int size()
```
    Returns the number of patients which are currently available in memory. The number might grow as more patients are loaded from the database.
    
    Returns:
    
    number of patients.
  - createInstance
```
public I2b2Patient createInstance(Observation fact)
```
    Specified by:
    
    createInstance in interface Extension<I2b2Patient>
  - getInstanceTypes
```
public Iterable<Class<? super I2b2Patient>> getInstanceTypes()
```
    Specified by:
    
    getInstanceTypes in interface Extension<I2b2Patient>
  - createInstance
```
public I2b2Patient createInstance(Object... args)
                           throws IllegalArgumentException
```
    Specified by:
    
    createInstance in interface Extension<I2b2Patient>
    
    Throws:
    
    IllegalArgumentException
  - retrieve
```
public I2b2Patient retrieve(String id)
```
    Specified by:
    
    retrieve in interface PatientStore
  - merge
```
public void merge(Patient patient,
                  String additionalId,
                  ExternalSourceType source)
```
    Specified by:
    
    merge in interface PatientStore
  - getAliasIds
```
public String[] getAliasIds(Patient patient)
```
    Specified by:
    
    getAliasIds in interface PatientStore
  - deleteWhereSourceId
```
public void deleteWhereSourceId(String sourceId)
                         throws SQLException
```
    Specified by:
    
    deleteWhereSourceId in class PostgresExtension<I2b2Patient>
    
    Throws:
    
    SQLException
  - flush
```
public void flush()
```
    Description copied from class: PostgresExtension
    
    Write updates to disk.
    
    Specified by:
    
    flush in class PostgresExtension<I2b2Patient>
  - purge
```
public void purge(String id)
```
    Specified by:
    
    purge in interface PatientStore
  - close
```
public void close()
           throws IOException
```
    Specified by:
    
    close in interface Closeable
    
    Specified by:
    
    close in interface AutoCloseable
    
    Throws:
    
    IOException

Class PostgresPatientStore

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

PostgresPatientStore

Method Detail

open

lookupPatientNum

prepareStatements

size

createInstance

getInstanceTypes

createInstance

retrieve

merge

getAliasIds

deleteWhereSourceId

flush

purge

close