Merge branch 'master' of https://github.com/DeepPhe/dphe-stream

DeepPhe · Aug 26, 2021 · 6f03a5a · 6f03a5a
2 parents 30a75b2 + 3765e61
commit 6f03a5a
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Showing 4 changed files with 12 additions and 9 deletions.
diff --git a/src/main/java/org/healthnlp/deepphe/nlp/ae/NonGraphedRelationFinder.java b/src/main/java/org/healthnlp/deepphe/nlp/ae/NonGraphedRelationFinder.java
@@ -272,7 +272,8 @@ public void process( final JCas jCas ) throws AnalysisEngineProcessException {
                findMetastasis( jCas, neoplasmList, metastasisList );
             }
             if ( !allBreastTumors.isEmpty() ) {
-               findAllStatus( jCas, paragraph, allMassNeoplasmList, allBreastTumors );
+               // We now use BiomarkerFinder for all biomarkers including the brca receptor status
+//               findAllStatus( jCas, paragraph, allMassNeoplasmList, allBreastTumors );
                // if there are breast sites then there may be breast site modifiers
 //               final Collection<IdentifiedAnnotation> breasts
 //                     = Neo4jOntologyConceptUtil.getAnnotationsByUriBranch( jCas, paragraph, UriConstants.BREAST );

diff --git a/src/main/java/org/healthnlp/deepphe/summary/concept/ConceptAggregateHandler.java b/src/main/java/org/healthnlp/deepphe/summary/concept/ConceptAggregateHandler.java
@@ -115,9 +115,9 @@ static public Map<String, Collection<ConceptAggregate>> createUriConceptAggregat
 
 
 
-               LOGGER.info( "Created " + chain.size() + "mention ConceptAggregate " + concept.getUri() + " " + concept.getId() + " "
-                                             + "scored:"
-                            + " " + concept.getUriScore() );
+//               LOGGER.info( "Created " + chain.size() + "mention ConceptAggregate " + concept.getUri() + " " + concept.getId() + " "
+//                                             + "scored:"
+//                            + " " + concept.getUriScore() );
 //               uriRoots.forEach( (k,v) -> LOGGER.info( "URI " + k + " with -unordered- root URIs (" + String.join( ",", v ) + ")" ) );
 
 
@@ -146,7 +146,7 @@ static public Map<String, Collection<ConceptAggregate>> createUriConceptAggregat
                            Collections.singletonList( mentionNoteId.getKey() ) ) ) );
 
 
-         LOGGER.info( "Created Simple ConceptAggregate of " + bestUri );
+//         LOGGER.info( "Created Simple ConceptAggregate of " + bestUri );
 
 
       }
@@ -155,8 +155,8 @@ static public Map<String, Collection<ConceptAggregate>> createUriConceptAggregat
       addRelations( conceptAggregates.values(), patientRelations );
 
 
-      LOGGER.info( "\n!!!     All Concept Aggregates:" );
-      conceptAggregates.values().stream().flatMap( Collection::stream ).forEach( c -> LOGGER.info( c + "\n" ) );
+//      LOGGER.info( "\n!!!     All Concept Aggregates:" );
+//      conceptAggregates.values().stream().flatMap( Collection::stream ).forEach( c -> LOGGER.info( c + "\n" ) );
 
 
 

diff --git a/src/main/java/org/healthnlp/deepphe/util/MentionUtil.java b/src/main/java/org/healthnlp/deepphe/util/MentionUtil.java
@@ -434,8 +434,8 @@ static public Map<String, Collection<String>> getAssociatedSiteUriMap( final Col
       final Map<String, String> bestRoots = UriUtil.getBestRoots( uris );
 
 
-      LOGGER.info( "Best Root URIs for Site URIs: " );
-      bestRoots.forEach( (k,v) -> LOGGER.info( k + " " + v ) );
+//      LOGGER.info( "Best Root URIs for Site URIs: " );
+//      bestRoots.forEach( (k,v) -> LOGGER.info( k + " " + v ) );
 
 
       final Map<String, Collection<String>> rootChildrenMap = new HashMap<>();

diff --git a/src/main/resources/pipeline/DpheXn.piper b/src/main/resources/pipeline/DpheXn.piper
@@ -1,5 +1,6 @@
 //cli OverwriteGraph=n
 cli StartNeo4j=n
+cli StopNeo4j=e
 cli Neo4jUri=r
 cli Neo4jUser=user
 cli Neo4jPass=pass
@@ -173,5 +174,6 @@ addLast PatientSummaryCleaner
 
 //  Alert User that the pipeline is Finished.
 package org.apache.ctakes.core.util.log
+addLast Neo4jServerShutdownAe
 addLast FinishedLogger
 addLast PipelineStopper