Removed experimental L2-specific command 'integrate', some todos, etc.

normalizer/src/main/java/org/biopax/paxtools/normalizer/Normalizer.java

@@ -301,7 +301,7 @@ public static String uri(final String xmlBase, String dbName, String idPart,
 		{
 			//for xrefs, always use the simple URI strategy (human-readable)
 			//replace unsafe symbols with underscore
-			localPart = localPart.replaceAll("[^-\\w]", "_");
+			localPart = localPart.replaceAll("[^-\\w]", "_");//todo: e.g. "foo bar" and "foo&bar" result in the same value - can mess things up...
 		} else {
 			//replace the local part with its md5 hash string (32-byte)
 			localPart = ModelUtils.md5hex(localPart);

normalizer/src/test/java/org/biopax/paxtools/normalizer/NormalizerTest.java

@@ -66,7 +66,7 @@ private static Stream<Arguments> uri() {
 				arguments("http://bioregistry.io/pubchem.substance:12345", "", "pubchem-substance", "12345", SmallMoleculeReference.class),
 				//special symbols or spaces in the 'id' part get replaced with underscore in the URI
 				arguments("UX_Foo_Bar", null, null, "Foo Bar", UnificationXref.class),
-				arguments("UX_Foo_Bar", null, null, "Foo&Bar", UnificationXref.class), //todo: no good - makes the same URI, can mess things up...
+				arguments("UX_Foo_Bar", null, null, "Foo&Bar", UnificationXref.class), //todo: the same expected URI as above can be wrong/bug...
 				arguments("uniprot:W0C7J9", "", "UniProt", "W0C7J9", UnificationXref.class),
 				arguments("http://bioregistry.io/ncbitaxon:9606", null, "taxonomy", "9606", BioSource.class),
 				arguments("http://bioregistry.io/ncbitaxon:9606", null, "NCBI Taxonomy", "9606", BioSource.class),

pattern/src/main/java/org/biopax/paxtools/pattern/PatternBox.java

@@ -311,7 +311,7 @@ public static Pattern controlsPhosphorylation()
 	 * Pattern for a Protein controlling a reaction whose participant is a small molecule.
 	 *
 	 * @param blacklist a skip-list of ubiquitous molecules
-	 * @param consumption true/false (TODO explain)
+	 * @param consumption true/false
 	 * @return the pattern
 	 */
 	public static Pattern controlsMetabolicCatalysis(Blacklist blacklist, boolean consumption)

paxtools-console/src/main/java/org/biopax/paxtools/Commands.java

@@ -399,17 +399,6 @@ static void sifnxToSif(String inputFile, String outputFile) throws IOException {
 		writer.close();
 	}
 
-	static void integrate(String[] argv) throws IOException {
-		Model model1 = getModel(io, argv[1]);
-		Model model2 = getModel(io, argv[2]);
-
-		Integrator integrator = new Integrator(SimpleEditorMap.get(model1.getLevel()), model1, model2);
-		integrator.integrate();
-
-		io.setFactory(model1.getLevel().getDefaultFactory());
-		io.convertToOWL(model1, new FileOutputStream(argv[3]));
-	}
-
 	static void merge(String[] argv) throws IOException {
 		Model model1 = getModel(io, argv[1]);
 		Model model2 = getModel(io, argv[2]);

paxtools-console/src/main/java/org/biopax/paxtools/Main.java

@@ -57,9 +57,6 @@ enum Command {
 		toSBGN("<biopax.owl> <output.sbgn> [-nolayout]\n" +
 				"\t- converts model to the SBGN format and applies COSE layout unless optional -nolayout flag is set.")
 				{public void run(String[] argv) throws IOException { toSbgn(argv); } },
-		integrate("<file1> <file2> <output>\n" +
-				"\t- integrates file2 into file1 and writes it into output (experimental)")
-				{public void run(String[] argv) throws IOException{integrate(argv);} },
 		toLevel3("<input> <output> [-psimiToComplexes]\n" +
 				"\t- converts BioPAX level 1 or 2, PSI-MI 2.5 and PSI-MITAB to the level 3 file;\n" +
 				"\t-psimiToComplexes forces PSI-MI Interactions become BioPAX Complexes instead MolecularInteractions.")

paxtools-core/src/main/java/org/biopax/paxtools/controller/Integrator.java

@@ -24,7 +24,13 @@
  * into the <em>target</em>.
  *
  * Please note that this class is in its beta state.
+ *
+ * @author Ozgun Babur
+ * @author Emek Demir
+ *
+ * @deprecated it's experimetal, only for Level2, and seems not tested/maintained
  */
+@Deprecated
 public class Integrator {
 
     private static final Logger log = LoggerFactory.getLogger(Integrator.class);
@@ -48,10 +54,7 @@ public class Integrator {
      * C    |       |       |       |
      * ------------------------------
      */
-    private Map<physicalEntityParticipant,
-                Map<physicalEntityParticipant, Double>> pepScoreMatrix
-                    = new HashMap<physicalEntityParticipant,
-                        Map<physicalEntityParticipant, Double>>();
+    private Map<physicalEntityParticipant, Map<physicalEntityParticipant, Double>> pepScoreMatrix = new HashMap<>();
 
     /**
      * This is the pool where the scores and relevant conversions
@@ -114,17 +117,13 @@ public Integrator(EditorMap editorMap, Model target, Model... sources) {
         log.info("Merging finished.");
 
         if( isNormalizeModels() ) {
-            log.info("Normalizing models.");
-
             log.info("Normaling XREFs.");
             normalizeXrefs(target);
             normalizeXrefs(mergedSources);
             log.info("Normaling OCVs.");
             normalizeOpenControlledVocabulary(mergedSources);
             log.info("Normaling cellular locations.");
             normalizeCellularLocations(mergedSources);
-
-            log.info("Normalization completed.");
         }
     }
 
@@ -296,21 +295,18 @@ public List<ConversionScore> integrate(List<ConversionScore> alternativeScores)
          * Instead, we are going to copy them, and modify their copies.
          */
         log.info("Creating a copy of the PEP scores.");
-        Map<physicalEntityParticipant,
-            Map<physicalEntityParticipant, Double>> copyMatrix
-                            = new HashMap<physicalEntityParticipant, Map<physicalEntityParticipant, Double>>();
+        Map<physicalEntityParticipant, Map<physicalEntityParticipant, Double>> copyMatrix = new HashMap<>();
             // Copy the contents of the matrix
         for(physicalEntityParticipant pepKey: pepScoreMatrix.keySet()) {
-            copyMatrix.put(pepKey,
-                    new HashMap<physicalEntityParticipant, Double>(pepScoreMatrix.get(pepKey)));
+            copyMatrix.put(pepKey, new HashMap<>(pepScoreMatrix.get(pepKey)));
         }
         // We want to use the copy now
         pepScoreMatrix = copyMatrix;
         log.info("PEP scores copied.");
 
         similarConversions = (alternativeScores == null)
-                                ? new ArrayList<>(this.similarConversions)
-                                : alternativeScores;
+            ? new ArrayList<>(this.similarConversions)
+            : alternativeScores;
 
         log.info("Conversion scores copied.");
         /* End of copies */
@@ -347,7 +343,7 @@ private void equalizeEntities(List<ConversionScore> similarConversions) {
 
         for(ConversionScore convScore: similarConversions) {
             // Since we sorted the list, we are safe to break
-            // But a continue will also do the trick, mostly
+            // But a "continue;" would also do the trick, mostly
             // requiring little more time
             if( convScore.getScore() < getThreshold() )
                 break;
@@ -420,25 +416,8 @@ private void equalizeEntities(List<ConversionScore> similarConversions) {
         }
     }
 
-    /**
-     * @deprecated setRDFId/setUri is not available anymore
-     */
-    @Deprecated
     private void equalize(BioPAXElement e1, BioPAXElement e2) {
-        // Operation below is enough for the time being
-    	// TODO re-factoring: setRDFId/setUri is not available anymore! (changing URIs directly is dangerous)
-        //e2.setUri(e1.getUri());
-
-    	throw new UnsupportedOperationException("This needs re-factoring: bpe.setUri is not available anymore!");
-
-    	//TODO ? use some alternative way to store that a1 equals e2, e.g., Set<String> matched,
-    	//matched.add(e1.getUri()+e2.getUri()); matched.add(e2.getUri()+e1.getUri());
-    }
-
-    private boolean equals(BioPAXElement a, BioPAXElement b) {
-    	throw new UnsupportedOperationException("not implemented yet.");
-    	// TODO ? implement equals(BioPAXElement a, BioPAXElement b): can be smth. like the following... and use below
-    	//return (a == null) ? b == null : a.equals(b) || matched.contains(a.getUri()+b.getUri());
+        ModelUtils.updateUri(null, e2, e1.getUri());
     }
 
     private void equalizePEP(physicalEntityParticipant controller1, physicalEntityParticipant controller2) {

paxtools-core/src/test/resources/L3/skip.owl

@@ -27,7 +27,7 @@ test data inspired by several humancyc v24 data issues -->
                     <!-- Entity is non-instantiable; also term property value must be a string value,
                     preferably from MI ontology, e.g. "gene product" MI:0251 or "see-also", etc.
                     Right now (after latest code fix to prevent exception here), Entity is not entirely ignored, -
-                    FIXME: its URI "http://biopax.org/tmp#Gene" becomes the value the term property value;
+                    FIXME: its URI "http://biopax.org/tmp#Gene" becomes the term property value;
                     i.e. this is equivalent to <term>http://biopax.org/tmp#Gene</term> ... -->
                     <Entity rdf:ID="Gene">
                         <comment>comment1</comment>