Make the 'USED BY' field say more accurately where used in Stanford NLP.

liblocal/README

@@ -13,34 +13,32 @@ DESCRIPTION: ANTLR runtime, for compiled software
 
 URL: http:https://www.antlr.com
 
-USED BY:
-The Quickcheck library
+USED BY: The Quickcheck library (not directly used in Stanford NLP code)
 
 LAST UPDATE: 2015/10/5
 
 LAST UPDATE BY: Keenon Werling
 
 -----------------------------------------------------------------------
-java-hamcrest.jar
+hamcrest-core.jar
 
-ORIGINAL JAR NAME: java-hamcrest-2.0.0.0.jar
+ORIGINAL JAR NAME: hamcrest-core-1.3.jar
 
-VERSION: 2.0.0.0
+VERSION: 1.3
 
-RELEASE DATE: January 2015
+RELEASE DATE: Jul, 2010
 
 SOURCE AVAILABLE: Maven Central
 
 DESCRIPTION: Hamcrest shennanigans, for JUnit
 
 URL: http:https://www.hamcrest.org
 
-USED BY:
-The JUnit library
+USED BY: The JUnit library (not directly used in Stanford NLP code)
 
-LAST UPDATE: 2016-04-30
+LAST UPDATE: 2015/10/5
 
-LAST UPDATE BY: John Bauer
+LAST UPDATE BY: Keenon Werling
 
 -----------------------------------------------------------------------
 javaruntype.jar
@@ -57,8 +55,7 @@ DESCRIPTION: Something for Quickcheck
 
 URL: http:https://www.javaruntype.org
 
-USED BY:
-The Quickcheck library
+USED BY: The Quickcheck library (not directly used in Stanford NLP code)
 
 LAST UPDATE: 2015/10/5
 
@@ -79,8 +76,7 @@ DESCRIPTION: Quickcheck, runs random inputs and validates outputs
 
 URL: https://github.com/pholser/junit-quickcheck
 
-USED BY:
-The Quickcheck library
+USED BY: loglinear package tests
 
 LAST UPDATE: 2015/10/5
 
@@ -97,7 +93,7 @@ RELEASE DATE: Nov, 2013
 
 SOURCE AVAILABLE: Maven Central
 
-DESCRIPTION: Quickcheck, runs random inputs and validates outputs
+DESCRIPTION: loglinear package tests
 
 URL: https://github.com/pholser/junit-quickcheck
 
@@ -123,8 +119,7 @@ DESCRIPTION: JUnit theories run JUnit against a number of inputs
 
 URL: junit.org
 
-USED BY:
-The Quickcheck library
+USED BY: loglinear package tests
 
 LAST UPDATE: 2015/10/5
 
@@ -145,8 +140,7 @@ DESCRIPTION: Object graph navigation library, used by Quickcheck
 
 URL: https://commons.apache.org/proper/commons-ognl/
 
-USED BY:
-The Quickcheck library
+USED BY: The Quickcheck library (not directly used in Stanford NLP code)
 
 LAST UPDATE: 2015/10/5
 

src/edu/stanford/nlp/graph/DirectedMultiGraph.java

@@ -2,6 +2,7 @@
 
 import java.util.*;
 
+import edu.stanford.nlp.semgraph.SemanticGraphEdge;
 import edu.stanford.nlp.util.CollectionUtils;
 import edu.stanford.nlp.util.Generics;
 import edu.stanford.nlp.util.MapFactory;
@@ -40,9 +41,8 @@ public DirectedMultiGraph(MapFactory<V, Map<V, List<E>>> outerMapFactory, MapFac
  }
 
  /**
- * Creates a copy of the given graph. This will copy the entire data
- * structure (this may be slow!), but will not copy any of the edge
- * or vertex objects.
+ * Creates a copy of the given graph. This will copy the entire data structure (this may be slow!), but will not copy
+ * any of the edge or vertex objects.
  *
  * @param graph The graph to copy into this object.
  */
@@ -477,38 +477,39 @@ public List<Set<V>> getConnectedComponents() {
  /**
  * Deletes all duplicate edges.
  */
- public void deleteDuplicateEdges() {
- for (V vertex : getAllVertices()) {
- for (V vertex2 : outgoingEdges.get(vertex).keySet()) {
- List<E> data = outgoingEdges.get(vertex).get(vertex2);
- Set<E> deduplicatedData = new TreeSet<>(data);
- data.clear();
- data.addAll(deduplicatedData);
- }
- for (V vertex2 : incomingEdges.get(vertex).keySet()) {
- List<E> data = incomingEdges.get(vertex).get(vertex2);
- Set<E> deduplicatedData = new TreeSet<>(data);
- data.clear();
- data.addAll(deduplicatedData);
- }
- }
- }
+
+ public void deleteDuplicateEdges() {
+ for (V vertex : getAllVertices()) {
+ for (V vertex2 : outgoingEdges.get(vertex).keySet()) {
+ List<E> data = outgoingEdges.get(vertex).get(vertex2);
+ Set<E> deduplicatedData = new TreeSet<>(data);
+ data.clear();
+ data.addAll(deduplicatedData);
+ }
+ for (V vertex2 : incomingEdges.get(vertex).keySet()) {
+ List<E> data = incomingEdges.get(vertex).get(vertex2);
+ Set<E> deduplicatedData = new TreeSet<>(data);
+ data.clear();
+ data.addAll(deduplicatedData);
+ }
+ }
+}
 
 
  public Iterator<E> incomingEdgeIterator(final V vertex) {
- return new EdgeIterator<>(vertex, incomingEdges, outgoingEdges);
+ return new EdgeIterator<>(incomingEdges, vertex);
  }
 
  public Iterable<E> incomingEdgeIterable(final V vertex) {
- return () -> new EdgeIterator<>(vertex, incomingEdges, outgoingEdges);
+ return () -> new EdgeIterator<>(incomingEdges, vertex);
  }
 
  public Iterator<E> outgoingEdgeIterator(final V vertex) {
- return new EdgeIterator<>(vertex, outgoingEdges, incomingEdges);
+ return new EdgeIterator<>(outgoingEdges, vertex);
  }
 
  public Iterable<E> outgoingEdgeIterable(final V vertex) {
- return () -> new EdgeIterator<>(vertex, outgoingEdges, incomingEdges);
+ return () -> new EdgeIterator<>(outgoingEdges, vertex);
  }
 
  public Iterator<E> edgeIterator() {
@@ -519,40 +520,28 @@ public Iterable<E> edgeIterable() {
  return () -> new EdgeIterator<>(DirectedMultiGraph.this);
  }
 
-
- /**
- * This class handles either iterating over a single vertex's
- * connections or over all connections in a graph.
- */
+
  static class EdgeIterator<V, E> implements Iterator<E> {
- private final Map<V, Map<V, List<E>>> reverseEdges;
- /** when iterating over the whole graph, this iterates over nodes */
- private Iterator<Map.Entry<V, Map<V, List<E>>>> vertexIterator;
- /** for a given node, this iterates over its neighbors */
- private Iterator<Map.Entry<V, List<E>>> connectionIterator;
- /** given the neighbor of a node, this iterates over all its connections */
+ private final Map<V, Map<V, List<E>>> incomingEdges;
+ private Iterator<Map<V, List<E>>> vertexIterator;
+ private Iterator<List<E>> connectionIterator;
  private Iterator<E> edgeIterator;
-
- private V currentSource = null;
- private V currentTarget = null;
- private E currentEdge = null;
+ private E lastRemoved = null;
  private boolean hasNext = true;
 
 
  public EdgeIterator(DirectedMultiGraph<V, E> graph) {
- vertexIterator = graph.outgoingEdges.entrySet().iterator();
- reverseEdges = graph.incomingEdges;
+ vertexIterator = graph.outgoingEdges.values().iterator();
+ incomingEdges = graph.incomingEdges;
  }
 
- public EdgeIterator(V startVertex, Map<V, Map<V, List<E>>> source,
- Map<V, Map<V, List<E>>> reverseEdges) {
- currentSource = startVertex;
+ public EdgeIterator(Map<V, Map<V, List<E>>> source, V startVertex) {
  Map<V, List<E>> neighbors = source.get(startVertex);
  if (neighbors != null) {
  vertexIterator = null;
- connectionIterator = neighbors.entrySet().iterator();
+ connectionIterator = neighbors.values().iterator();
  }
- this.reverseEdges = reverseEdges;
+ incomingEdges = null;
  }
 
  @Override
@@ -566,22 +555,18 @@ public E next() {
  if (!hasNext()) {
  throw new NoSuchElementException("Graph edge iterator exhausted.");
  }
- currentEdge = edgeIterator.next();
- return currentEdge;
+ lastRemoved = edgeIterator.next();
+ return lastRemoved;
  }
 
  private void primeIterator() {
  if (edgeIterator != null && edgeIterator.hasNext()) {
  hasNext = true; // technically, we shouldn't need to put this here, but let's be safe
  } else if (connectionIterator != null && connectionIterator.hasNext()) {
- Map.Entry<V, List<E>> nextConnection = connectionIterator.next();
- edgeIterator = nextConnection.getValue().iterator();
- currentTarget = nextConnection.getKey();
+ edgeIterator = connectionIterator.next().iterator();
  primeIterator();
  } else if (vertexIterator != null && vertexIterator.hasNext()) {
- Map.Entry<V, Map<V, List<E>>> nextVertex = vertexIterator.next();
- connectionIterator = nextVertex.getValue().entrySet().iterator();
- currentSource = nextVertex.getKey();
+ connectionIterator = vertexIterator.next().values().iterator();
  primeIterator();
  } else {
  hasNext = false;
@@ -590,60 +575,22 @@ private void primeIterator() {
 
  @Override
  public void remove() {
- if (currentEdge != null) {
- reverseEdges.get(currentTarget).get(currentSource).remove(currentEdge);
- edgeIterator.remove();
-
- if (reverseEdges.get(currentTarget).get(currentSource) != null &&
- reverseEdges.get(currentTarget).get(currentSource).size() == 0) {
- connectionIterator.remove();
- reverseEdges.get(currentTarget).remove(currentSource);
- // TODO: may not be necessary to set this to null
- edgeIterator = null;
- }
+ if (incomingEdges == null) {
+ throw new UnsupportedOperationException("remove() is only valid if iterating over entire graph (Gabor was too lazy to implement the general case...sorry!)");
  }
- }
- }
-
- /**
- * Topological sort of the graph.
- * <br>
- * This method uses the depth-first search implementation of
- * topological sort.
- * Topological sorting only works if the graph is acyclic.
- *
- * @return A sorted list of the vertices
- * @throws IllegalStateException if this graph is not a DAG
- */
- public List<V> topologicalSort() {
- List<V> result = Generics.newArrayList();
- Set<V> temporary = outerMapFactory.newSet();
- Set<V> permanent = outerMapFactory.newSet();
- for (V vertex : getAllVertices()) {
- if (!temporary.contains(vertex)) {
- topologicalSortHelper(vertex, temporary, permanent, result);
- }
- }
- Collections.reverse(result);
- return result;
- }
-
- private void topologicalSortHelper(V vertex, Set<V> temporary, Set<V> permanent, List<V> result) {
- temporary.add(vertex);
- Map<V, List<E>> neighborMap = outgoingEdges.get(vertex);
- if (neighborMap != null) {
- for (V neighbor : neighborMap.keySet()) {
- if (permanent.contains(neighbor)) {
- continue;
- }
- if (temporary.contains(neighbor)) {
- throw new IllegalStateException("This graph has cycles. Topological sort not possible: " + this.toString());
+ if (lastRemoved != null) {
+ if (lastRemoved instanceof SemanticGraphEdge) {
+ SemanticGraphEdge edge = (SemanticGraphEdge) lastRemoved;
+ //noinspection unchecked
+ incomingEdges.get((V) edge.getDependent()).get((V) edge.getGovernor()).remove((E) edge);
+ edgeIterator.remove();
+ } else {
+ // TODO(from gabor): This passes the tests, but actually leaves the graph in an inconsistent state.
+ edgeIterator.remove();
+// throw new UnsupportedOperationException("remove() is only valid if iterating over semantic graph edges (Gabor was too lazy to implement the general case...sorry!)");
  }
- topologicalSortHelper(neighbor, temporary, permanent, result);
  }
  }
- result.add(vertex);
- permanent.add(vertex);
  }
 
  /**

src/edu/stanford/nlp/pipeline/demo/corenlp-brat.js

@@ -1,9 +1,8 @@
 // Takes Stanford CoreNLP JSON output (var data = ... in data.js)
 // and uses brat to render everything.
 
-//var serverAddress = 'http:https://localhost:9000';
-//var serverAddress = 'http:https://corenlp.run';
-var serverAddress = '';
+//var serverAddress = 'http:https://localhost:9000/'
+var serverAddress = 'http:https://corenlp.run'
 
 // Load Brat libraries
 var bratLocation = 'https://storage.googleapis.com/corenlp/js/brat';
@@ -121,7 +120,7 @@ function nerColor(nerTag) {
  */
 function annotators() {
  var annotators = "tokenize,ssplit"
- $('#annotators').find('option:selected').each(function () {
+ $('#annotators option:selected').each(function () {
  annotators += "," + $(this).val();
  });
  return annotators;
@@ -669,7 +668,7 @@ function renderSemgrex(data) {
  */
 $(document).ready(function() {
  // Some initial styling
- $('.chosen-select').chosen();
+ $(".chosen-select").chosen();
  $('.chosen-container').css('width', '100%');
 
  // Submit on shift-enter
@@ -795,7 +794,7 @@ $(document).ready(function() {
  // Make ajax call
  $.ajax({
  type: 'POST',
- url: serverAddress + '/tokensregex?pattern=' + encodeURIComponent(pattern.replace("&", "\\&").replace('+', '\\+')),
+ url: serverAddress + 'tokensregex?pattern=' + encodeURIComponent(pattern.replace("&", "\\&").replace('+', '\\+')),
  data: currentQuery,
  success: function(data) {
  $('.tokensregex_error').remove(); // Clear error messages
@@ -827,7 +826,7 @@ $(document).ready(function() {
  // Make ajax call
  $.ajax({
  type: 'POST',
- url: serverAddress + '/semgrex?pattern=' + encodeURIComponent(pattern.replace("&", "\\&").replace('+', '\\+')),
+ url: serverAddress + 'semgrex?pattern=' + encodeURIComponent(pattern.replace("&", "\\&").replace('+', '\\+')),
  data: currentQuery,
  success: function(data) {
  $('.semgrex_error').remove(); // Clear error messages