Removed unneeded bits, some cleanup and formatting

Author: dlutz2

src/org/opensextant/howler/abstraction/words/enumerated/DataFacet.java

@@ -7,6 +7,7 @@
 import org.semanticweb.owlapi.model.IRI;
 
 public enum DataFacet implements Word {
+//@formatter:off 
  LENGTH_FACET("length of", Vocabulary.XSDNamespace, "length"),
  MIN_LENGTH_FACET("minimum length of", Vocabulary.XSDNamespace,"minLength"),
  MAX_LENGTH_FACET("maximum length of", Vocabulary.XSDNamespace, "maxLength"),
@@ -19,6 +20,7 @@ public enum DataFacet implements Word {
  FRACTION_DIGITS_FACET("fractional digits of", Vocabulary.XSDNamespace,"fractionDigits"),
  LANG_RANGE_FACET("language range of", Vocabulary.RDFNamespace,"langRange"),
  ERROR_FACET("unknown relation to", Vocabulary.BUILTIN_NS, "error");
+//@formatter:on
 
   private IRI namespace;
   private String logicalform;

src/org/opensextant/howler/abstraction/words/enumerated/PredicateCharacteristic.java

@@ -8,13 +8,15 @@
 import org.semanticweb.owlapi.model.IRI;
 
 public enum PredicateCharacteristic implements Word {
+//@formatter:off  
   FUNCTIONAL("functional"),
   SYMMETRIC("symmetric"),
   ASYMMETRIC("asymmetric"),
   REFLEXIVE("reflexive"),
   TRANSITIVE("transitive"),
   INVERSE_FUNCTIONAL("inverse functional"),
   IRREFLEXIVE("irreflexive");
+//@formatter:on
 
   private final String logicalform;
   private String normalform;
@@ -84,5 +86,5 @@ public String getPrefix() {
   public void setPrefix(String prefix) {
     // ignore
   }
-  
+
 }

src/org/opensextant/howler/abstraction/words/enumerated/Quantifier.java

@@ -7,6 +7,7 @@
 import org.semanticweb.owlapi.model.IRI;
 
 public enum Quantifier implements Word {
+//@formatter:off
   NULL("", false),
   EVERY("every", false),
   SOME("some", false),
@@ -18,6 +19,7 @@ public enum Quantifier implements Word {
   LESS_THAN("less than",true),
   MORE_THAN_OR_EQUAL("at least", true),
   LESS_THAN_OR_EQUAL("at most", true);
+//@formatter:on
 
   private boolean numeric;
   private String normalform;

src/org/opensextant/howler/abstraction/words/enumerated/WordType.java

@@ -7,7 +7,8 @@
 import org.opensextant.howler.utils.TextUtils;
 import org.semanticweb.owlapi.model.IRI;
 
-public enum WordType implements Word { 
+public enum WordType implements Word {
+//@formatter:off
   GENERIC_WORD("generic word",false,false),
   BADWORD("badword",false,false),
   ADJECTIVE("adjective",false,false),
@@ -32,6 +33,7 @@ public enum WordType implements Word {
   PREDICATE("predicate",true,false),
   SCOPE("scope",false,true),
   WORD_TYPE("word type",false,true);
+//@formatter:on
 
   private final String logicalform;
   private String normalForm;

src/org/opensextant/howler/kanban/Kanban.java

@@ -92,10 +92,7 @@ public class Kanban {
 
   // the primary kanban elements indexed by their IDs
   private Map<String, Board> boards = new HashMap<String, Board>();
-  //private Map<String, CardList> lists = new HashMap<String, CardList>();
-  //private Map<String, Card> cards = new HashMap<String, Card>();
   private Map<String, KanbanSentence> sentences = new HashMap<String, KanbanSentence>();
-  //private Map<String, RawText> rawTexts = new HashMap<String, RawText>();
 
   // sentences indexed by their content and board to avoid duplicates
   private Map<String, KanbanSentence> sentencesByText = new HashMap<String, KanbanSentence>();
@@ -161,9 +158,9 @@ public Kanban(Howler howler, String configPath) {
 
   }
 
-  //added a board -> create an ontology
+  // added a board -> create an ontology
   public void addBoard(Board board) {
-    
+
     this.boards.put(board.getId(), board);
     LOGGER.info("Added Board:" + board.getTitle());
 
@@ -190,52 +187,16 @@ public void addBoard(Board board) {
     }
 
   }
-  /*
-   * private Board getBoard(String id) { return this.boards.get(id); }
-   */
-  
+
   public void addList(CardList list) {
     // add the list to the board it is part of
     this.boards.get(list.getBoardId()).addList(list);
-    LOGGER.info("Added List:" + list.getTitle() + " to board " + this.boards.get(list.getBoardId()).getTitle() );
-  }
-  
-  /*
-   * private CardList getList(String id) { return this.lists.get(id); }
-   */
-  /*
-  public void addCard(Card card) {
-   // this.cards.put(card.get_id(), card);
-    // add the card to the board it is part of
-    boards.get(card.getBoardId()).addCard(card);
-    this.cardsByKey.put(card.getKey(), card);
-    // add the card to the list it is part of
-    lists.get(card.getListId()).addCard(card);
-    LOGGER.info("Added Card:" + card.getTitle());
+    LOGGER.info("Added List:" + list.getTitle() + " to board " + this.boards.get(list.getBoardId()).getTitle());
   }
-*/
-  /*
-   * private Card getCard(String id) { return this.cards.get(id); } private Card getCardByKey(String key) { return
-   * this.cardsByKey.get(key); } private KanbanSentence getSentence(String id) { return sentences.get(id); }
-   */
-  /*
-  private void addSentence(KanbanSentence sentence) {
-    
-    LOGGER.info("Added Sentence:" + sentence.getText());
-    // create any cards needed to match words used in sentence
-    this.addCards(sentence);
-    // create axiom(s) that corresponds to sentence and add to ontology
-    this.addAxioms(sentence);
 
-  }
-  */
-  
-  /*
-   * private RawText getRawText(String id) { return rawTexts.get(id); }
-   */
   public void addRawText(RawText rawText) {
 
-    //rawTexts.put(rawText.get_id(), rawText);
+    // rawTexts.put(rawText.get_id(), rawText);
 
     // rawtext to abstraction Document
     Document doc = howler.convertText("dummy", rawText.getText());
@@ -279,7 +240,8 @@ public void addRawText(RawText rawText) {
       for (Word w : sent.getWords()) {
         WordType wt = w.getWordType();
         // dont create cards for generic, quantifiers or WordTypes
-        if (!wt.equals(WordType.GENERIC_WORD) && !wt.equals(WordType.QUANTIFIER) && !wt.equals(WordType.NEGATIVE) && !wt.equals(WordType.WORD_TYPE)) {
+        if (!wt.equals(WordType.GENERIC_WORD) && !wt.equals(WordType.QUANTIFIER) && !wt.equals(WordType.NEGATIVE)
+            && !wt.equals(WordType.WORD_TYPE)) {
           if (w instanceof Predicate) {
             Predicate pred = (Predicate) w;
             // don't create card for builtin predicates
@@ -296,21 +258,19 @@ public void addRawText(RawText rawText) {
         this.addCard(wrd, rawText.getBoardId(), rawText.getSwimlaneId(), rawText.getUserId());
         kbSent.addKey(wrd.getKey().toString());
       }
-     
+
       // add sentence to index
       this.sentences.put(kbSent.get_id(), kbSent);
-      
+
       // add inferences
       this.addAxioms(kbSent);
-      
+
       kbSents.add(kbSent);
     }
 
     // send the sentences to the Wekan system
     this.sendSentences(kbSents, false);
 
-
-    
     // remove the rawtext
     client.collectionDelete("rawtext", rawText.get_id());
 
@@ -328,11 +288,6 @@ private void addToOntology(Document doc, OWLOntology onto) {
 
   }
 
-  /*
-  private boolean isSynched() {
-    return synched;
-  }
-*/
   private void setSynched(boolean synched) {
     this.synched = synched;
     if (synched) {
@@ -437,49 +392,6 @@ private void addCard(Word wrd, String boardID, String swimlaneID, String userID)
 
   }
 
-  /*
-  // create any new cards needed to represent words used in the sentence
-  private void addCards(KanbanSentence sent) {
-
-    String userID = sent.getUserId();
-    String boardID = sent.getBoardId();
-
-    for (String key : sent.getKeys()) {
-
-      // seen key before?
-      if (!this.cardsByKey.keySet().contains(key)) {
-
-        // keys look like:logicalForm|WordType|boardID
-        String[] pieces = key.split("\\|");
-
-        // title is the words logical form with part of speech following
-        String title = pieces[0].replaceAll("_", " ") + " (" + pieces[1].toLowerCase() + ")";
-
-        // create and populate new card
-        Card card = new Card();
-
-        card.setTitle(title);
-        card.setKey(key);
-        card.setEntityType(WordType.valueOf(pieces[1]));
-        card.setBoardId(boardID);
-        // TODO list selected is first list in board. Better choice?
-        card.setListId(boards.get(boardID).getLists().get(0).getId());
-        card.setUserid(userID);
-
-        // create field map and send to Wekan
-        String json = gson.toJson(card);
-        Map<String, Object> fields = gson.fromJson(json, Map.class);
-
-        int id = client.collectionInsert("cards", fields);
-        LOGGER.info("Inserting new Card. ID=" + id + ". " + card.getTitle());
-
-        this.cardsByKey.put(key, card);
-      }
-
-    }
-  }
-*/
-
   // create a axiom(s) from a sentence and add to appropriate ontology
   private void addAxioms(KanbanSentence sent) {
 

src/org/opensextant/howler/kanban/Syncher.java

@@ -100,7 +100,7 @@ public void update(Observable obs, Object msg) {
         KanbanSentence sent = KanbanSentence.fromMap(fields);
         sent.set_id(id);
         LOGGER.debug("Got a " + msgtype + " message for collection " + collName + ":" + sent);
-        //kanban.addSentence(sent);
+        // kanban.addSentence(sent);
         return;
       }
 
@@ -127,7 +127,7 @@ public void update(Observable obs, Object msg) {
         Card card = Card.fromMap(fields);
         card.set_id(id);
         LOGGER.debug("Got a " + msgtype + " message for collection " + collName + ":" + card);
-        //kanban.addCard(card);
+        // kanban.addCard(card);
         return;
       }
 

src/org/opensextant/howler/owl/ToOWL.java

@@ -554,22 +554,22 @@ private List<OWLAxiom> convertObject(FactStatement<ObjectPredicate, ProperNoun>
 
       OWLClassExpression predObjCE = convertObject(predPhrase);
 
-     // OWLClassExpression objCE = convertObject(predPhrase.getObject());
+      // OWLClassExpression objCE = convertObject(predPhrase.getObject());
 
       if (pExp.getPredicate().isBuiltinPredicate()) {
 
         PredicateType predType = pExp.getPredicate().getPredicateType();
 
         if (predType == PredicateType.IS) {
-            axs.add(owlDataFactory.getOWLClassAssertionAxiom(predObjCE, subject, annos));
+          axs.add(owlDataFactory.getOWLClassAssertionAxiom(predObjCE, subject, annos));
         }
 
         if (predType == PredicateType.SAME_AS) {
           OWLObjectOneOf subjOneOf = owlDataFactory.getOWLObjectOneOf(subject);
           axs.add(owlDataFactory.getOWLEquivalentClassesAxiom(subjOneOf, predObjCE, annos));
         }
       } else {// must be VERB type predicate
-          axs.add(owlDataFactory.getOWLClassAssertionAxiom(predObjCE, subject, annos));
+        axs.add(owlDataFactory.getOWLClassAssertionAxiom(predObjCE, subject, annos));
       }
 
       return axs;

src/org/opensextant/howler/test/OWL2Text.java

@@ -33,6 +33,7 @@
 import org.apache.commons.io.filefilter.SuffixFileFilter;
 import org.opensextant.howler.abstraction.WordManager;
 import org.opensextant.howler.owl.FromOWL;
+import org.opensextant.howler.text.DocumentFactory.FileStructure;
 import org.opensextant.howler.text.TextDocument;
 import org.opensextant.howler.text.ToText;
 
@@ -46,7 +47,16 @@ public static void main(String[] args) throws IOException {
 
     File inputDirsFile = new File(args[0]);
     File resultsDir = new File(args[1]);
-    boolean ignoreBadImports = Boolean.valueOf(args[2]);
+    
+    FileStructure outFormat = FileStructure.DOCUMENT_PER_LINE;
+
+     try {
+      outFormat = FileStructure.valueOf(args[2]);
+    } catch (Exception e) {
+      System.err.println("Bad value for format:" + args[2]);
+    }
+
+    boolean ignoreBadImports = Boolean.valueOf(args[3]);
 
     // the to and from converters
     FromOWL fromOWL = new FromOWL(ignoreBadImports);
@@ -91,7 +101,7 @@ public static void main(String[] args) throws IOException {
         // create a name from the input ontology file
         String ontoNameBase = ontoFile.getName().split("\\.")[0];
         File outText = new File(byOntoDir, ontoNameBase + ".txt");
-        FileUtils.writeStringToFile(outText, backText.toString(), "UTF-8");
+        FileUtils.writeStringToFile(outText, backText.toString(outFormat,true), "UTF-8");
       }
     }
 

src/org/opensextant/howler/test/OWL2Text2OWLTest.java

@@ -139,18 +139,21 @@ public static void main(String[] args) throws IOException, OWLOntologyCreationEx
         for (OWLAxiom originalAx : OWLAPIStreamUtils.asList(originalOnto.axioms())) {
           if (!compare(backOnto, originalAx)) {
 
+            String axString = originalAx.toString().replaceAll("[\\n\\r\\t]", "<WHITE_SPACE>");
             if (nyi(originalAx)) {
               axiomErrorsNYI++;
-              FileUtils.writeStringToFile(results, ontoName + "\t" + "NYI" + "\t" + originalAx.getAxiomType() + "\t"
-                  + originalAx.toString().replaceAll("[\\n\\r\\t]", "<WHITE_SPACE>") + "\n", "UTF-8", true);
-              FileUtils.writeStringToFile(totalResults, ontoName + "\t" + "NYI" + "\t" + originalAx.getAxiomType()
-                  + "\t" + originalAx.toString().replaceAll("[\\n\\r\\t]", " ") + "\n", "UTF-8", true);
+              FileUtils.writeStringToFile(results,
+                  ontoName + "\t" + "NYI" + "\t" + originalAx.getAxiomType() + "\t" + axString + "\n", "UTF-8", true);
+              FileUtils.writeStringToFile(totalResults,
+                  ontoName + "\t" + "NYI" + "\t" + originalAx.getAxiomType() + "\t" + axString + "\n", "UTF-8", true);
             } else {
               axiomErrorsMissing++;
-              FileUtils.writeStringToFile(results, ontoName + "\t" + "Missing" + "\t" + originalAx.getAxiomType() + "\t"
-                  + originalAx.toString().replaceAll("[\\n\\r\\t]", "<WHITE_SPACE>") + "\n", "UTF-8", true);
-              FileUtils.writeStringToFile(totalResults, ontoName + "\t" + "Missing" + "\t" + originalAx.getAxiomType()
-                  + "\t" + originalAx.toString().replaceAll("[\\n\\r\\t]", "<WHITE_SPACE>") + "\n", "UTF-8", true);
+              FileUtils.writeStringToFile(results,
+                  ontoName + "\t" + "Missing" + "\t" + originalAx.getAxiomType() + "\t" + axString + "\n", "UTF-8",
+                  true);
+              FileUtils.writeStringToFile(totalResults,
+                  ontoName + "\t" + "Missing" + "\t" + originalAx.getAxiomType() + "\t" + axString + "\n", "UTF-8",
+                  true);
             }
           }
         }
@@ -160,11 +163,11 @@ public static void main(String[] args) throws IOException, OWLOntologyCreationEx
         for (OWLAxiom backAx : OWLAPIStreamUtils.asList(backOnto.axioms())) {
           if (!compare(originalOnto, backAx)) {
             axiomErrorsExtra++;
-
-            FileUtils.writeStringToFile(results, ontoName + "\t" + "Extra" + "\t" + backAx.getAxiomType() + "\t"
-                + backAx.toString().replaceAll("[\\n\\r\\t]", "<WHITE_SPACE>") + "\n", "UTF-8", true);
-            FileUtils.writeStringToFile(totalResults, ontoName + "\t" + "Extra" + "\t" + backAx.getAxiomType() + "\t"
-                + backAx.toString().replaceAll("[\\n\\r\\t]", "<WHITE_SPACE>") + "\n", "UTF-8", true);
+            String axString = backAx.toString().replaceAll("[\\n\\r\\t]", "<WHITE_SPACE>");
+            FileUtils.writeStringToFile(results,
+                ontoName + "\t" + "Extra" + "\t" + backAx.getAxiomType() + "\t" + axString + "\n", "UTF-8", true);
+            FileUtils.writeStringToFile(totalResults,
+                ontoName + "\t" + "Extra" + "\t" + backAx.getAxiomType() + "\t" + axString + "\n", "UTF-8", true);
           }
         }
 
@@ -229,7 +232,7 @@ private static boolean compare(OWLOntology onto, OWLAxiom ax) {
       String litString = "";
       if (value.isPresent()) {
         OWLLiteral lit = value.get();
-        litString = lit.getLiteral();
+        litString = lit.getLiteral().replaceAll("\n", " ");;
       } else {
         return false;
       }
@@ -241,7 +244,7 @@ private static boolean compare(OWLOntology onto, OWLAxiom ax) {
       for (OWLAnnotationAssertionAxiom annoAx : annos) {
         if (annoAx.literalValue().isPresent()) {
           OWLLiteral axLit = annoAx.literalValue().get();
-          String axLitString = axLit.getLiteral();
+          String axLitString = axLit.getLiteral().replaceAll("\n", " ");
           if (axLitString.equals(litString)) {
             return true;
           }