Mercurial > hg > anteater

changeset 7:0c7cf517ff2d

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
linnaeus results
author jdamerow
date Fri, 09 Nov 2012 16:11:08 -0700
parents 50aeb96a8ee9
children 05b2ad41e8f0
files src/de/mpiwg/anteater/results/impl/ScientificNameResultFinder.java src/de/mpiwg/anteater/results/impl/ScientificNameResultManager.java src/de/mpiwg/anteater/xml/impl/AnalysisXMLManager.java
diffstat 3 files changed, 6 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/src/de/mpiwg/anteater/results/impl/ScientificNameResultFinder.java	Thu Nov 01 13:23:25 2012 -0700
+++ b/src/de/mpiwg/anteater/results/impl/ScientificNameResultFinder.java	Fri Nov 09 16:11:08 2012 -0700
@@ -66,7 +66,7 @@
 			for (Integer type : nameExtractionsByType.keySet()) {
 				for (Integer textId : nameExtractionsByType.get(type).keySet()) {
 					List<ScientificNamesExtraction> nameExtractions = nameExtractionsByType.get(type).get(textId);
-					List<PlacesExtraction> placesExtractions = placeExtractionsByType.get(type).get(textId);
+					List<PlacesExtraction> placesExtractions = placeExtractionsByType.get(type).get(textId) != null ? placeExtractionsByType.get(type).get(textId) : new ArrayList<PlacesExtraction>();
 					
 					List<Integer> placeIndices = new ArrayList<Integer>();
 					
--- a/src/de/mpiwg/anteater/results/impl/ScientificNameResultManager.java	Thu Nov 01 13:23:25 2012 -0700
+++ b/src/de/mpiwg/anteater/results/impl/ScientificNameResultManager.java	Fri Nov 09 16:11:08 2012 -0700
@@ -12,7 +12,8 @@
 public class ScientificNameResultManager extends AResultManager<SpeciesScientificResult> {
 
 	public final static String SCIENTIFIC_NAME_TAG_Start = "<species_scientific name=\"";
-	public final static String SCIENTIFIC_NAME_TAG_End = "\">";
+	public final static String SCIENTIFIC_NAME_ID_ATTR = "\" ncbiID=\"";
+	public final static String SCIENTIFIC_NAME_TAG_End = "\" >";
 	public final static String SCIENTIFIC_NAME_TAG_CLOSE = "</species_scientific>";
 	public final static String TAG_TYPE = "scientific_name";
 	
@@ -45,7 +46,7 @@
 
 
 		for (SpeciesScientificResult name : namesOfSum) {
-			tags.add(new AnnotationTag(SCIENTIFIC_NAME_TAG_Start + name.getFinding().getScientificName() + SCIENTIFIC_NAME_TAG_End, name.getFinding().getStart(), SCIENTIFIC_NAME_TAG_CLOSE, name.getFinding().getStart()
+			tags.add(new AnnotationTag(SCIENTIFIC_NAME_TAG_Start + name.getFinding().getScientificName() + SCIENTIFIC_NAME_ID_ATTR + (name.getFinding().getNcbiId() != null ? name.getFinding().getNcbiId() : "") + SCIENTIFIC_NAME_TAG_End, name.getFinding().getStart(), SCIENTIFIC_NAME_TAG_CLOSE, name.getFinding().getStart()
 					+ name.getFinding().getLength(), TAG_TYPE));
 		}
 
--- a/src/de/mpiwg/anteater/xml/impl/AnalysisXMLManager.java	Thu Nov 01 13:23:25 2012 -0700
+++ b/src/de/mpiwg/anteater/xml/impl/AnalysisXMLManager.java	Fri Nov 09 16:11:08 2012 -0700
@@ -47,11 +47,11 @@
 	}
 	
 	public List<String> getSummaryCommonNamesResults() {
-		return getResults("/analysis/commonNames/summaries");
+		return getResults("/analysis/commonNames/summaries/linnaeus");
 	}
 	
 	public List<String> getSupplementaryInfoCommonNamesResults() {
-		return getResults("/analysis/commonNames/supplementary_information");
+		return getResults("/analysis/commonNames/supplementary_information/linnaeus");
 	}
 	
 	public List<String> getSummaryPlacesResults() {