AbstractValueSets (Bunsen Parent 0.5.10-SNAPSHOT API)

java.lang.Object
- com.cerner.bunsen.spark.codes.base.AbstractValueSets<T,C>

Type Parameters:

T - the type of the FHIR ValueSet objects being used

C - the type of the subclass of this class being used.

Direct Known Subclasses:

ValueSets
```
public abstract class AbstractValueSets<T extends org.hl7.fhir.instance.model.api.IBaseResource,C extends AbstractValueSets<T,C>>
extends Object
```
This is a partial implementation of logic to manage FHIR ValueSets. It is designed to encapsulate as much functionality as possible while remaining independent of specific FHIR versions. Users should generally not use this class directly, but rather consume the subclass that corresponds to the FHIR version they are using.

Field Summary

Fields
Modifier and Type	Field and Description
`protected ca.uhn.fhir.context.FhirVersionEnum`	`fhirVersion`
`protected org.apache.spark.sql.Dataset<UrlAndVersion>`	`members` URI and Version metadata used to preserve uniqueness among value sets.
`protected org.apache.spark.sql.SparkSession`	`spark`
`protected static Pattern`	`TABLE_NAME_PATTERN`
`protected static org.apache.spark.sql.Encoder<UrlAndVersion>`	`URL_AND_VERSION_ENCODER`
`protected static org.apache.spark.sql.Encoder<Value>`	`VALUE_ENCODER` An encoder for serializing values.
`static String`	`VALUE_SETS_DATABASE` Default database name where the value sets information is stored.
`static String`	`VALUE_SETS_TABLE` Default table name where value sets metadata is stored.
`protected org.apache.spark.sql.Dataset<Value>`	`values`
`static String`	`VALUES_TABLE` Default table name where the expanded values information is stored.
`protected SparkRowConverter`	`valueSetRowConverter`
`protected org.apache.spark.sql.Dataset<org.apache.spark.sql.Row>`	`valueSets`

Constructor Summary

Constructors
Modifier	Constructor and Description
`protected`	`AbstractValueSets(org.apache.spark.sql.SparkSession spark, ca.uhn.fhir.context.FhirVersionEnum fhirVersion, org.apache.spark.sql.Dataset<UrlAndVersion> members, org.apache.spark.sql.Dataset<org.apache.spark.sql.Row> valueSets, org.apache.spark.sql.Dataset<Value> values, SparkRowConverter valueSetRowConverter)`

Method Summary

All Methods Static Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and Description
`protected abstract void`	`addToValueSet(T valueSet, org.apache.spark.sql.Dataset<Value> values)` Adds the given values to the given value set instance.
`org.apache.spark.sql.Dataset<Value>`	`getLatestValues(Set<String> uris, boolean includeExperimental)` Returns a dataset with the latest values for each valueset of the given uris.
`Map<String,String>`	`getLatestVersions(boolean includeExperimental)` Returns the latest version of all value sets.
`Map<String,String>`	`getLatestVersions(Set<String> uris, boolean includeExperimental)` Returns the latest versions of a given set of value sets.
`static org.apache.spark.sql.Encoder<UrlAndVersion>`	`getUrlAndVersionEncoder()` Returns the encoder for UrlAndVersion tuples.
`protected org.apache.spark.sql.Dataset<UrlAndVersion>`	`getUrlAndVersions(org.apache.spark.sql.Dataset<org.apache.spark.sql.Row> valueSets)` Returns a dataset of distinct URL and version tuples.
`static org.apache.spark.sql.Encoder<Value>`	`getValueEncoder()` Returns the encoder for values.
`org.apache.spark.sql.Dataset<Value>`	`getValues()` Returns a dataset of all values in this collection.
`org.apache.spark.sql.Dataset<Value>`	`getValues(Map<String,String> uriToVersion)` Returns a dataset with the values for each element in the map of uri to version.
`org.apache.spark.sql.Dataset<Value>`	`getValues(String uri, String version)` Returns the values for the given URI and version.
`T`	`getValueSet(String uri, String version)` Returns the value set with the given uri and version, or null if there is no such value set.
`org.apache.spark.sql.Dataset<org.apache.spark.sql.Row>`	`getValueSets()` Returns a dataset of value sets to inspect metadata.
`protected boolean`	`hasDuplicateUrlAndVersions(org.apache.spark.sql.Dataset<UrlAndVersion> membersToCheck)` Returns true if the UrlAndVersions if the membersToCheck has any duplicates with the members of this value sets instance.
`protected org.apache.spark.sql.Dataset<org.apache.spark.sql.Row>`	`valueSetDatasetFromDirectory(String path)` Returns a dataset of ValueSet from the content stored at the given directory.
`C`	`withDisjointValueSetsFromDirectory(String path)` Returns all value sets that are disjoint with value sets stored in the default database and adds them to our collection.
`C`	`withDisjointValueSetsFromDirectory(String path, String database)` Returns all value sets that are disjoint with value sets stored in the given database and adds them to our collection.
`abstract C`	`withValueSets(org.apache.spark.sql.Dataset<org.apache.spark.sql.Row> valueSets)` Returns a new ValueSets instance that includes the given value sets.
`C`	`withValueSets(List<T> valueSets)` Returns a new ValueSets instance that includes the given value sets.
`C`	`withValueSets(T... valueSets)` Returns a new ValueSets instance that includes the given value sets.
`C`	`withValueSetsFromDirectory(String path)` Reads all value sets from a given directory and adds them to our collection.
`void`	`writeToDatabase()` Writes the the value sets to the default database "ontologies" using default table names: "values", and "valuesets".
`void`	`writeToDatabase(String database)` Writes the value sets to the given database using default table names: "values", "valuesets", and "ancestors".
`void`	`writeToTables(String valuesTable, String valueSetTable)` Writes value sets to the given tables.

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

- Field Detail
  - VALUE_ENCODER
```
protected static final org.apache.spark.sql.Encoder<Value> VALUE_ENCODER
```
    An encoder for serializing values.
  - URL_AND_VERSION_ENCODER
```
protected static final org.apache.spark.sql.Encoder<UrlAndVersion> URL_AND_VERSION_ENCODER
```
  - TABLE_NAME_PATTERN
```
protected static final Pattern TABLE_NAME_PATTERN
```
  - VALUE_SETS_DATABASE
```
public static final String VALUE_SETS_DATABASE
```
    Default database name where the value sets information is stored.
    
    See Also:
    
    Constant Field Values
  - VALUES_TABLE
```
public static final String VALUES_TABLE
```
    Default table name where the expanded values information is stored.
    
    See Also:
    
    Constant Field Values
  - VALUE_SETS_TABLE
```
public static final String VALUE_SETS_TABLE
```
    Default table name where value sets metadata is stored.
    
    See Also:
    
    Constant Field Values
  - spark
```
protected final org.apache.spark.sql.SparkSession spark
```
  - fhirVersion
```
protected final ca.uhn.fhir.context.FhirVersionEnum fhirVersion
```
  - members
```
protected final org.apache.spark.sql.Dataset<UrlAndVersion> members
```
    URI and Version metadata used to preserve uniqueness among value sets.
  - values
```
protected final org.apache.spark.sql.Dataset<Value> values
```
  - valueSets
```
protected final org.apache.spark.sql.Dataset<org.apache.spark.sql.Row> valueSets
```
  - valueSetRowConverter
```
protected final SparkRowConverter valueSetRowConverter
```
- Constructor Detail
  - AbstractValueSets
```
protected AbstractValueSets(org.apache.spark.sql.SparkSession spark,
                            ca.uhn.fhir.context.FhirVersionEnum fhirVersion,
                            org.apache.spark.sql.Dataset<UrlAndVersion> members,
                            org.apache.spark.sql.Dataset<org.apache.spark.sql.Row> valueSets,
                            org.apache.spark.sql.Dataset<Value> values,
                            SparkRowConverter valueSetRowConverter)
```
- Method Detail
  - getUrlAndVersionEncoder
```
public static org.apache.spark.sql.Encoder<UrlAndVersion> getUrlAndVersionEncoder()
```
    Returns the encoder for UrlAndVersion tuples.
    
    Returns:
    
    the encoder for UrlAndVersion tuples.
  - getValueEncoder
```
public static org.apache.spark.sql.Encoder<Value> getValueEncoder()
```
    Returns the encoder for values.
    
    Returns:
    
    the encoder for values.
  - getLatestVersions
```
public Map<String,String> getLatestVersions(boolean includeExperimental)
```
    Returns the latest version of all value sets.
    
    Parameters:
    
    includeExperimental - whether to include value sets marked as experimental
    
    Returns:
    
    a map of value set URIs to the latest version for them.
  - getLatestVersions
```
public Map<String,String> getLatestVersions(Set<String> uris,
                                            boolean includeExperimental)
```
    Returns the latest versions of a given set of value sets.
    
    Parameters:
    
    uris - a set of URIs for which to retrieve the latest versions, or null to load them all
    
    includeExperimental - whether to include value sets marked as experimental
    
    Returns:
    
    a map of value set URIs to the latest versions for them.
  - getLatestValues
```
public org.apache.spark.sql.Dataset<Value> getLatestValues(Set<String> uris,
                                                           boolean includeExperimental)
```
    Returns a dataset with the latest values for each valueset of the given uris.
    
    Parameters:
    
    uris - URIs for the value sets
    
    includeExperimental - whether to include value sets marked as experimental
    
    Returns:
    
    a dataset of the latest mappings for them.
  - getValues
```
public org.apache.spark.sql.Dataset<Value> getValues()
```
    Returns a dataset of all values in this collection. This is generally used for inspection and debugging of values.
    
    Returns:
    
    a dataset of all values.
  - getValues
```
public org.apache.spark.sql.Dataset<Value> getValues(String uri,
                                                     String version)
```
    Returns the values for the given URI and version.
    
    Parameters:
    
    uri - the uri of the value set for which we get values
    
    version - the version of the value set for which we get values
    
    Returns:
    
    a dataset of values for the given URI and version.
  - getValues
```
public org.apache.spark.sql.Dataset<Value> getValues(Map<String,String> uriToVersion)
```
    Returns a dataset with the values for each element in the map of uri to version.
    
    Parameters:
    
    uriToVersion - a map of value set URI to the version to load
    
    Returns:
    
    a dataset of values for the given URIs and versions.
  - getValueSets
```
public org.apache.spark.sql.Dataset<org.apache.spark.sql.Row> getValueSets()
```
    Returns a dataset of value sets to inspect metadata. Since the value sets themselves can be quite large, the values in this dataset do not contain them. Instead, users should use the getValues() method to query values in depth.
    
    Returns:
    
    a dataset of value sets that do not contain concept values.
  - getValueSet
```
public T getValueSet(String uri,
                     String version)
```
    Returns the value set with the given uri and version, or null if there is no such value set.
    
    Parameters:
    
    uri - the uri of the value set to return
    
    version - the version of the value set to return
    
    Returns:
    
    the specified value set.
  - addToValueSet
```
protected abstract void addToValueSet(T valueSet,
                                      org.apache.spark.sql.Dataset<Value> values)
```
    Adds the given values to the given value set instance.
    
    Parameters:
    
    valueSet - the value set to add.
    
    values - the values to add.
  - getUrlAndVersions
```
protected org.apache.spark.sql.Dataset<UrlAndVersion> getUrlAndVersions(org.apache.spark.sql.Dataset<org.apache.spark.sql.Row> valueSets)
```
    Returns a dataset of distinct URL and version tuples.
    
    Parameters:
    
    valueSets - valueSets to scan for the URL and version.
    
    Returns:
    
    the distinct URL and versions for the value sets.
  - hasDuplicateUrlAndVersions
```
protected boolean hasDuplicateUrlAndVersions(org.apache.spark.sql.Dataset<UrlAndVersion> membersToCheck)
```
    Returns true if the UrlAndVersions if the membersToCheck has any duplicates with the members of this value sets instance.
    
    Parameters:
    
    membersToCheck - the members to check for duplicates
    
    Returns:
    
    true if there are duplicate URL and versions, false otherwise.
  - withValueSets
```
public abstract C withValueSets(org.apache.spark.sql.Dataset<org.apache.spark.sql.Row> valueSets)
```
    Returns a new ValueSets instance that includes the given value sets.
    
    Parameters:
    
    valueSets - the value sets to add to the returned collection.
    
    Returns:
    
    a new ValueSets instance with the added value sets.
  - withValueSets
```
public C withValueSets(T... valueSets)
```
    Returns a new ValueSets instance that includes the given value sets.
    
    Parameters:
    
    valueSets - the value sets to add to the returned collection.
    
    Returns:
    
    a new ValueSets instance with the added value sets.
  - withValueSets
```
public C withValueSets(List<T> valueSets)
```
    Returns a new ValueSets instance that includes the given value sets.
    
    Parameters:
    
    valueSets - the value sets to add to the returned collection.
    
    Returns:
    
    a new ValueSets instance with the added value sets.
  - withValueSetsFromDirectory
```
public C withValueSetsFromDirectory(String path)
```
    Reads all value sets from a given directory and adds them to our collection. The directory may be anything readable from a Spark path, including local filesystems, HDFS, S3, or others.
    
    Parameters:
    
    path - a path from which value sets will be loaded
    
    Returns:
    
    an instance of ValueSets that includes the contents from that directory.
  - withDisjointValueSetsFromDirectory
```
public C withDisjointValueSetsFromDirectory(String path)
```
    Returns all value sets that are disjoint with value sets stored in the default database and adds them to our collection. The directory may be anything readable from a Spark path, including local filesystems, HDFS, S3, or others.
    
    Parameters:
    
    path - a path from which disjoint value sets will be loaded
    
    Returns:
    
    an instance of ValueSets that includes content from that directory that is disjoint with content already contained in the default database.
  - withDisjointValueSetsFromDirectory
```
public C withDisjointValueSetsFromDirectory(String path,
                                            String database)
```
    Returns all value sets that are disjoint with value sets stored in the given database and adds them to our collection. The directory may be anything readable from a Spark path, including local filesystems, HDFS, S3, or others.
    
    Parameters:
    
    path - a path from which disjoint value sets will be loaded
    
    database - the database to check value sets against
    
    Returns:
    
    an instance of ValueSets that includes content from that directory that is disjoint with content already contained in the given database.
  - valueSetDatasetFromDirectory
```
protected org.apache.spark.sql.Dataset<org.apache.spark.sql.Row> valueSetDatasetFromDirectory(String path)
```
    Returns a dataset of ValueSet from the content stored at the given directory.
    
    Parameters:
    
    path - the path containting the value sets
    
    Returns:
    
    a dataframe of loaded value sets in row form.
  - writeToDatabase
```
public void writeToDatabase()
```
    Writes the the value sets to the default database "ontologies" using default table names: "values", and "valuesets".
  - writeToDatabase
```
public void writeToDatabase(String database)
```
    Writes the value sets to the given database using default table names: "values", "valuesets", and "ancestors".
    
    Parameters:
    
    database - the name of the database to which the value sets are saved
  - writeToTables
```
public void writeToTables(String valuesTable,
                          String valueSetTable)
```
    Writes value sets to the given tables.
    Warning: these updates are likely not atomic due to the lack of transactional semantics in the underlying data store. Concurrent users may see previous items removed before new ones are added, or items appear separately than others. This is intended for use in a user-specific sandbox or staging environment.
    
    Parameters:
    
    valuesTable - name of the table to which the value records are saved
    
    valueSetTable - name of the table to which the value set metadata is saved

Class AbstractValueSets<T extends org.hl7.fhir.instance.model.api.IBaseResource,C extends AbstractValueSets<T,C>>

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

VALUE_ENCODER

URL_AND_VERSION_ENCODER

TABLE_NAME_PATTERN

VALUE_SETS_DATABASE

VALUES_TABLE

VALUE_SETS_TABLE

spark

fhirVersion

members

values

valueSets

valueSetRowConverter

Constructor Detail

AbstractValueSets

Method Detail

getUrlAndVersionEncoder

getValueEncoder

getLatestVersions

getLatestVersions

getLatestValues

getValues

getValues

getValues

getValueSets

getValueSet

addToValueSet

getUrlAndVersions

hasDuplicateUrlAndVersions

withValueSets

withValueSets

withValueSets

withValueSetsFromDirectory

withDisjointValueSetsFromDirectory

withDisjointValueSetsFromDirectory

valueSetDatasetFromDirectory

writeToDatabase

writeToDatabase

writeToTables