edu.emory.cci.aiw.i2b2etl.dest.metadata

Class Metadata

java.lang.Object

edu.emory.cci.aiw.i2b2etl.dest.metadata.Metadata

public final class Metadata
extends Object

Controls the etl process for extracting data from files and a knowledgeSource(s) for transform and load into an i2b2 instance. It is single-threaded and should be called only once per process.

a data file has a corresponding edu.emory.cci.registry.i2b2datareader handler class. the meta information about the data files also have handlers in edu.emory.cci.registry.i2b2metareader.

currently, meta information is found in both the knowledgeSource AND in the data files. the data is found in the data files created by PROTEMPA and a file created by an SQL that fetches demographics data.

there is a conf.xml file that declares how some of this process works. the database & filesystem nodes point to database and file resources. files, once declared, can be grouped into sets of files. the concept dimensions used in i2b2 are declared in the meta node. each branch under the meta node is created from data from the knowledgeSource, file(s), or de novo (hard-coded in a java class).

the metadatatree node declares how to assemble branches into the final product for i2b2 (the metadata schema).

lastly, the observation node declares what to process into observation_fact entities in i2b2. this, along with the implicit Patient, Provider, Visit & Concept dimensions are laoded into the data schema.

the 'resources' folder in this project contains 'conf.xml' and 'demmeta.zip'. the demmeta file needs pointing to from within the conf.xml file; it holds information necessary to build out the demographics portion of the ontology tree.

the method doETL() orchestrates the entire process. the steps are commented within that method.

as little information as is possible is kept in memory so that the observations get streamed from flat files, matched with in-memory data, and batch-loaded into the database.

Constructor Summary

Constructors

Constructor and Description
Metadata(String sourceSystemCode, org.protempa.KnowledgeSourceCache cache, org.protempa.KnowledgeSource knowledgeSource, org.protempa.PropositionDefinition[] userDefinedPropositionDefinitions, FolderSpec[] folderSpecs, Settings settings, Data dataSection, org.arp.javautil.sql.ConnectionSpec metaConnectionSpec)

Method Summary

Modifier and Type	Method and Description
void	addModifierRoot(Concept concept)
ProviderDimension	addProvider(ProviderDimension providerDimension)
void	addToIdCache(Concept concept)
String[]	extractDerived()
Concept[]	getAllRoots()
Concept	getConceptRoot()
Data	getDataSection()
FolderSpec[]	getFolderSpecs()
ConceptId	getFromConceptIdCache(List<Object> key)
Concept	getFromIdCache(ConceptId conceptId)
Concept	getFromIdCache(String propId, String propertyName, org.protempa.proposition.value.Value value)
Concept[]	getModifierRoots()
org.protempa.PropositionDefinition[]	getPhenotypeDefinitions()
Settings	getSettings()
String	getSourceSystemCode() Returns the source system code used for concepts created by this query results handler.
Concept	newConcept(ConceptId conceptId, String conceptCodePrefix, String sourceSystemCode)
void	putInConceptIdCache(List<Object> key, ConceptId conceptId)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Metadata

public Metadata(String sourceSystemCode,
                org.protempa.KnowledgeSourceCache cache,
                org.protempa.KnowledgeSource knowledgeSource,
                org.protempa.PropositionDefinition[] userDefinedPropositionDefinitions,
                FolderSpec[] folderSpecs,
                Settings settings,
                Data dataSection,
                org.arp.javautil.sql.ConnectionSpec metaConnectionSpec)
         throws OntologyBuildException

Parameters:

sourceSystemCode - source system code String to use for concepts created by this query results handler. It is truncated, if necessary, to 50 characters to fit into the i2b2 database tables. Cannot be null.

cache -

knowledgeSource -

userDefinedPropositionDefinitions -

folderSpecs -

settings -

dataSection -

Throws:

OntologyBuildException

Method Detail

getSettings

public Settings getSettings()

getDataSection

public Data getDataSection()

getConceptRoot

public Concept getConceptRoot()

addModifierRoot

public void addModifierRoot(Concept concept)

getModifierRoots

public Concept[] getModifierRoots()

getAllRoots

public Concept[] getAllRoots()

getPhenotypeDefinitions

public org.protempa.PropositionDefinition[] getPhenotypeDefinitions()

getSourceSystemCode

public String getSourceSystemCode()

Returns the source system code used for concepts created by this query results handler.

Returns:

a String, maximum 50 characters. Guaranteed not null.

getFolderSpecs

public FolderSpec[] getFolderSpecs()

addProvider

public ProviderDimension addProvider(ProviderDimension providerDimension)
                              throws InvalidConceptCodeException,
                                     SQLException

Throws:

InvalidConceptCodeException

SQLException

getFromIdCache

public Concept getFromIdCache(ConceptId conceptId)

getFromIdCache

public Concept getFromIdCache(String propId,
                              String propertyName,
                              org.protempa.proposition.value.Value value)

addToIdCache

public void addToIdCache(Concept concept)

putInConceptIdCache

public void putInConceptIdCache(List<Object> key,
                                ConceptId conceptId)

getFromConceptIdCache

public ConceptId getFromConceptIdCache(List<Object> key)

extractDerived

public String[] extractDerived()
                        throws org.protempa.KnowledgeSourceReadException

Throws:

org.protempa.KnowledgeSourceReadException

newConcept

public Concept newConcept(ConceptId conceptId,
                          String conceptCodePrefix,
                          String sourceSystemCode)
                   throws OntologyBuildException

Throws:

OntologyBuildException