Release 1.0.1. Fix #2.

JULIELab · Nov 20, 2022 · a3ae317 · a3ae317
1 parent 9024cf7
commit a3ae317
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Showing 4 changed files with 4 additions and 22 deletions.
diff --git a/pom.xml b/pom.xml
@@ -5,7 +5,7 @@
     <groupId>de.julielab</groupId>
     <artifactId>julielab-gnormplus</artifactId>
     <packaging>jar</packaging>
-    <version>1.0.1-SNAPSHOT</version>
+    <version>1.0.1</version>
     <name>JULIE Lab GNormPlus</name>
     <url>https://www.ncbi.nlm.nih.gov/research/bionlp/Tools/gnormplus/</url>
 

diff --git a/src/GNormPluslib/BioCDoc.java b/src/GNormPluslib/BioCDoc.java
@@ -299,7 +299,7 @@ public void BioC2PubTator(String input, String output) throws IOException, XMLSt
 								}
 							}
 						} else {
-							Annoid = annotation.getInfon("Identifier").get();
+							Annoid = annotation.getInfon("Identifier").orElse(null);
 						}
 					} else if (Annotype.equals("Species") || Annotype.equals("Genus") || Annotype.equals("Strain")) {
 						if (annotation.getInfons().containsKey("NCBI Taxonomy")) {
@@ -563,7 +563,6 @@ public void BioCReader(String input) throws IOException, XMLStreamException {
 			PassageOffsets.add(PassageOffset);
 			Annotations.add(AnnotationInPMID);
 		}
-		System.out.println("[BioCReader] PMCIDs.size(): " + PMIDs.size() + ", " + PMIDs);
 	}
 
 	public void BioCReaderWithAnnotation(String input) throws IOException, XMLStreamException {
@@ -678,8 +677,6 @@ public void BioCReaderWithAnnotation(String input) throws IOException, XMLStream
 			PassageOffsets.add(PassageOffset);
 			Annotations.add(AnnotationInPMID);
 		}
-		System.out.println("[BioCReaderWithAnnotation] PMCIDs.size(): " + PMIDs.size()+ ", " + PMIDs + "; Annotations: " + Annotations.size());
-
 	}
 
 	public void BioCOutput(String input, String output, ArrayList<ArrayList<ArrayList<String>>> Annotations, boolean Final, boolean RemovePreviousAnno) throws IOException, XMLStreamException {

diff --git a/src/GNormPluslib/GN.java b/src/GNormPluslib/GN.java
@@ -912,23 +912,7 @@ public void GeneIDRecognition(String Filename, String FilenameBioC) throws IOExc
                     String mention = anno[2].toLowerCase();
                     mention = mention.replaceAll("[\\W\\-\\_]+", "");
                     if (GNormPlus.GeneIDs_hash.containsKey(mention)) {
-                        try {
-                            data.getBioCDocobj().Annotations.get(i).get(j).add(locations.get(k) + "\tGeneID:" + GNormPlus.GeneIDs_hash.get(mention)); //paragraph
-                        } catch (Exception e) {
-                            System.out.println("i: " + i);
-                            System.out.println("j: " + j);
-                            System.out.println("Number of PMIDs: " + data.getBioCDocobj().PMIDs.size());
-                            System.out.println("Number of annotation lists: " + data.getBioCDocobj().Annotations.size());
-//                            final String pmid = i < data.getBioCDocobj().PMIDs.size() ? data.getBioCDocobj().PMIDs.get(i) : "i too large: i=" + i + ", data.getBioCDocobj().PMIDs.size()=" + data.getBioCDocobj().PMIDs.size();
-//                            System.out.println("PMID: " + pmid);
-//                            System.out.println("data.getBioCDocobj().Annotations.size(): " + data.getBioCDocobj().Annotations.size());
-//                            if (i < data.getBioCDocobj().Annotations.size()) {
-//                                System.out.println("data.getBioCDocobj().Annotations.get(i).size(): " + data.getBioCDocobj().Annotations.get(i).size());
-//                            } else {
-//                                System.out.println("i too large: i=" + i + ", data.getBioCDocobj().Annotations.size()=" + data.getBioCDocobj().Annotations.size());
-//                            }
-                            System.out.println("[GNormPlus:GN#GeneIDRecognition] Warning: Skipping GeneIDMatch for document number " + i + " with ID " + data.getBioCDocobj().PMIDs.get(i) + " because of an internal consistency issue");
-                        }
+                        data.getBioCDocobj().Annotations.get(i).get(j).add(locations.get(k) + "\tGeneID:" + GNormPlus.GeneIDs_hash.get(mention)); //paragraph
                     }
                 }
             }

diff --git a/src/GNormPluslib/SR.java b/src/GNormPluslib/SR.java
@@ -563,6 +563,7 @@ public void SpeciesAssignment(String Filename,String FilenameBioC) throws IOExce
 		// When we only reset the annotations, GN#GeneIDRecognition fails because the PMIDs are added anyway
 		// and then there are more PMIDs than annotations.
 //		data.getBioCDocobj().Annotations = new ArrayList();
+//		data.getBioCDocobj().PMIDs = new ArrayList();
 		data.resetBioCDocobj();
 		data.getBioCDocobj().BioCReaderWithAnnotation(Filename);