org.apache.ctakes.ytex.kernel.dao

Class ConceptDaoImpl

java.lang.Object

org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl

All Implemented Interfaces:

ConceptDao

public class ConceptDaoImpl
extends java.lang.Object
implements ConceptDao

Field Summary

Fields

Modifier and Type	Field and Description
private static java.lang.String	CONCEPT_GRAPH_PATH
private static java.lang.String	DEFAULT_ROOT_ID the default concept id for the root.
private static java.lang.String[]	defaultForbiddenConceptArr ignore forbidden concepts.
private static java.util.Set<java.lang.String>	defaultForbiddenConcepts
private IntrinsicInfoContentEvaluator	intrinsicInfoContentEvaluator
private JdbcTemplate	jdbcTemplate
private static Log	log
private SessionFactory	sessionFactory
private java.util.Properties	ytexProperties

Constructor Summary

Constructors

Constructor and Description
ConceptDaoImpl()

Method Summary

Methods

Modifier and Type	Method and Description
private void	addRelation(ConceptGraph cg, java.util.Set<java.lang.String> roots, java.lang.String childCUI, java.lang.String parentCUI, boolean checkCycle, java.util.Set<java.lang.String> forbiddenConcepts) add the relationship to the concept map
private boolean	checkCycle(ConcRel crPar, ConcRel crChild)
void	createConceptGraph(java.lang.String dir, java.lang.String name, java.lang.String query, boolean checkCycle, java.util.Set<java.lang.String> forbiddenConcepts) create the concept graph with specified name using specified query.
ConceptGraph	getConceptGraph(java.lang.String name) retrieve an existing concept graph.
javax.sql.DataSource	getDataSource(javax.sql.DataSource ds)
java.lang.String	getDefaultConceptGraphDir() use value of org.apache.ctakes.ytex.conceptGraphDir if defined.
IntrinsicInfoContentEvaluator	getIntrinsicInfoContentEvaluator()
SessionFactory	getSessionFactory()
java.util.Properties	getYtexProperties()
private boolean	hasAncestor(ConcRel crPar, ConcRel crChild, java.util.HashSet<java.lang.Integer> visitedNodes) check cycle.
private ConceptGraph	initializeConceptGraph(ConceptGraph cg) replace cui strings in concrel with references to other nodes.
static void	main(java.lang.String[] args) create a concept graph.
private static void	printHelp(Options options)
private ConceptGraph	readConceptGraph(java.lang.String name)
void	setDataSource(javax.sql.DataSource ds)
void	setIntrinsicInfoContentEvaluator(IntrinsicInfoContentEvaluator intrinsicInfoContentEvaluator)
void	setSessionFactory(SessionFactory sessionFactory)
void	setYtexProperties(java.util.Properties ytexProperties)
private java.io.File	urlToFile(java.net.URL url)
private void	writeConceptGraph(java.lang.String dir, java.lang.String name, ConceptGraph cg) write the concept graph, create parent directories as required

Methods inherited from class java.lang.Object

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

Field Detail

CONCEPT_GRAPH_PATH

private static final java.lang.String CONCEPT_GRAPH_PATH

See Also:

Constant Field Values

DEFAULT_ROOT_ID

private static final java.lang.String DEFAULT_ROOT_ID

the default concept id for the root. override with -Dytex.defaultRootId

See Also:

Constant Field Values

defaultForbiddenConceptArr

private static final java.lang.String[] defaultForbiddenConceptArr

ignore forbidden concepts. list Taken from umls-interface. f concept is one of the following just return #C1274012|Ambiguous concept (inactive concept) if($concept=~/C1274012/) { return 1; } #C1274013|Duplicate concept (inactive concept) if($concept=~/C1274013/) { return 1; } #C1276325|Reason not stated concept (inactive concept) if($concept=~/C1276325/) { return 1; } #C1274014|Outdated concept (inactive concept) if($concept=~/C1274014/) { return 1; } #C1274015|Erroneous concept (inactive concept) if($concept=~/C1274015/) { return 1; } #C1274021|Moved elsewhere (inactive concept) if($concept=~/C1274021/) { return 1; } #C1443286|unapproved attribute if($concept=~/C1443286/) { return 1; } #C1274012|non-current concept - ambiguous if($concept=~/C1274012/) { return 1; } #C2733115|limited status concept if($concept=~/C2733115/) { return 1; }

defaultForbiddenConcepts

private static java.util.Set<java.lang.String> defaultForbiddenConcepts

log

private static final Log log

intrinsicInfoContentEvaluator

private IntrinsicInfoContentEvaluator intrinsicInfoContentEvaluator

jdbcTemplate

private JdbcTemplate jdbcTemplate

sessionFactory

private SessionFactory sessionFactory

ytexProperties

private java.util.Properties ytexProperties

Constructor Detail

ConceptDaoImpl

public ConceptDaoImpl()

Method Detail

main

public static void main(java.lang.String[] args)
                 throws ParseException,
                        java.io.IOException

create a concept graph. This expects a property file in the classpath under CONCEPT_GRAPH_PATH/[name].xml

If the properties file is found in a directory, the concept graph will be written there.

Else (e.g. if the props file is coming from a jar), the concept graph will be written to the directory specified via the system property/ytex property 'org.apache.ctakes.ytex.conceptGraphDir'

Else if the 'org.apache.ctakes.ytex.conceptGraphDir' property is not defined, the concept graph will be written to the conceptGraph subdirectory relative to ytex.properties (if ytex.properties is in a directory).

Parameters:

args -

Throws:

ParseException

java.io.IOException

printHelp

private static void printHelp(Options options)

addRelation

private void addRelation(ConceptGraph cg,
               java.util.Set<java.lang.String> roots,
               java.lang.String childCUI,
               java.lang.String parentCUI,
               boolean checkCycle,
               java.util.Set<java.lang.String> forbiddenConcepts)

add the relationship to the concept map

Parameters:

conceptMap -

conceptIndexMap -

conceptList -

roots -

conceptPair -

createConceptGraph

public void createConceptGraph(java.lang.String dir,
                      java.lang.String name,
                      java.lang.String query,
                      boolean checkCycle,
                      java.util.Set<java.lang.String> forbiddenConcepts)
                        throws java.io.IOException

Description copied from interface: ConceptDao

create the concept graph with specified name using specified query. Will create a file [name].gz under dir.

Specified by:

createConceptGraph in interface ConceptDao

Parameters:

dir - directory of concept graph (optional). If null will use directory specified by the system property/ytex property org.apache.ctakes.ytex.conceptGraphDir. If the property is not defined, use [directory of ytex.properties]/conceptGraph

name - name of concept graph

query - returns 2 string columns, 1st column is the child concept, 2nd column is the parent concept.

checkCycle - if true will check for cycles and remove them (default true). If this is set to false, then only pagerank can be used on this graph.

forbiddenConcepts - set of concepts whose edges will not be added to the concept graph (optional). By default, this includes umls concepts like C1274012 (Ambiguous concept).

Throws:

java.io.IOException

getConceptGraph

public ConceptGraph getConceptGraph(java.lang.String name)

Description copied from interface: ConceptDao

retrieve an existing concept graph. This attempts to find the concept graph as follows:

• classpath: attempt to load org/apache/ctakes/ytex/conceptGraph/[name].gz
• relative to org.apache.ctakes.ytex.conceptGraphDir: if that fails then relative to the directory defined by the system property/ytex property org.apache.ctakes.ytex.conceptGraphDir
• relative to ytex.properties: if the org...conceptGraphDir property is not defined, then look for [directory of ytex.properties]/conceptGraph/[name].gz

Specified by:

getConceptGraph in interface ConceptDao

Parameters:

name - name of concept graph. Will retrieve from classpath/file system. @see #createConceptGraph

Returns:

urlToFile

private java.io.File urlToFile(java.net.URL url)

getDefaultConceptGraphDir

public java.lang.String getDefaultConceptGraphDir()

use value of org.apache.ctakes.ytex.conceptGraphDir if defined. else try to determine ytex.properties location and use the conceptGraph directory there. else return null

Returns:

getDataSource

public javax.sql.DataSource getDataSource(javax.sql.DataSource ds)

getIntrinsicInfoContentEvaluator

public IntrinsicInfoContentEvaluator getIntrinsicInfoContentEvaluator()

getSessionFactory

public SessionFactory getSessionFactory()

getYtexProperties

public java.util.Properties getYtexProperties()

checkCycle

private boolean checkCycle(ConcRel crPar,
                 ConcRel crChild)

hasAncestor

private boolean hasAncestor(ConcRel crPar,
                  ConcRel crChild,
                  java.util.HashSet<java.lang.Integer> visitedNodes)

check cycle.

Parameters:

crPar - parent

crChild - child that should not be an ancestor of parent

visitedNodes - nodes we've visited in our search. keep track of this to avoid visiting the same node multiple times

Returns:

true if crChild is an ancestor of crPar

initializeConceptGraph

private ConceptGraph initializeConceptGraph(ConceptGraph cg)

replace cui strings in concrel with references to other nodes. initialize the concept list

Parameters:

cg -

Returns:

readConceptGraph

private ConceptGraph readConceptGraph(java.lang.String name)

setDataSource

public void setDataSource(javax.sql.DataSource ds)

setIntrinsicInfoContentEvaluator

public void setIntrinsicInfoContentEvaluator(IntrinsicInfoContentEvaluator intrinsicInfoContentEvaluator)

setSessionFactory

public void setSessionFactory(SessionFactory sessionFactory)

setYtexProperties

public void setYtexProperties(java.util.Properties ytexProperties)

writeConceptGraph

private void writeConceptGraph(java.lang.String dir,
                     java.lang.String name,
                     ConceptGraph cg)

write the concept graph, create parent directories as required

Parameters:

name -

cg -