Modified: uima/ruta/trunk/ruta-ep-textruler/src/main/java/org/apache/uima/ruta/textruler/learner/trabal/TrabalLearner.java URL: http://svn.apache.org/viewvc/uima/ruta/trunk/ruta-ep-textruler/src/main/java/org/apache/uima/ruta/textruler/learner/trabal/TrabalLearner.java?rev=1853491&r1=1853490&r2=1853491&view=diff ============================================================================== --- uima/ruta/trunk/ruta-ep-textruler/src/main/java/org/apache/uima/ruta/textruler/learner/trabal/TrabalLearner.java (original) +++ uima/ruta/trunk/ruta-ep-textruler/src/main/java/org/apache/uima/ruta/textruler/learner/trabal/TrabalLearner.java Wed Feb 13 11:24:19 2019 @@ -139,9 +139,7 @@ public class TrabalLearner extends TextR this.additionalFolderPath = additionalFolderPath; } - /** - * Main method. Starts the algorithm. - */ + @Override protected void doRun() { try { getAnalysisEngine(); @@ -155,7 +153,8 @@ public class TrabalLearner extends TextR sendStatusUpdateToDelegate("Comparing documents...", TextRulerLearnerState.ML_RUNNING, true); for (int i = 0; i < algorithmIterations; i++) { actualResult += "BLOCK(Iteration_" + (i + 1) + ") Document{} {\n"; - sendStatusUpdateToDelegate("Comparing documents...", TextRulerLearnerState.ML_RUNNING, true); + sendStatusUpdateToDelegate("Comparing documents...", TextRulerLearnerState.ML_RUNNING, + true); idf = createIDF(); Map<String, List<AnnotationError>> errorGrps = createErrorGroups(); List<TrabalRule> rules = runAlgorithm(errorGrps); @@ -241,14 +240,6 @@ public class TrabalLearner extends TextR return result; } - /** - * Compares the training data to the additional data and creates a mapping of the contained - * errors, where the key is a combination of the error type and the names of the concerned - * annotations, and the values are lists of errors that can be corrected through the same type of - * rule. - * - * @return map of errors - */ private Map<String, List<AnnotationError>> createErrorGroups() { errors = createErrorList(); Collections.sort(errors); @@ -300,9 +291,6 @@ public class TrabalLearner extends TextR return result; } - /** - * Creates a list of annotation pairs and the fitting type of transformation action. - */ private List<AnnotationError> createErrorList() { positiveExamples = new HashMap<String, RankedList>(); List<AnnotationError> result = new ArrayList<AnnotationError>(); @@ -341,8 +329,9 @@ public class TrabalLearner extends TextR if (shouldAbort()) break; exampleIndex++; - sendStatusUpdateToDelegate("Comparing documents " + (i + 1) + " of " + goldStandard.size() - + ": example " + exampleIndex + " of " + gold.size(), + sendStatusUpdateToDelegate( + "Comparing documents " + (i + 1) + " of " + goldStandard.size() + ": example " + + exampleIndex + " of " + gold.size(), TextRulerLearnerState.ML_RUNNING, false); a = iterator.next(); docIterator = docs.iterator(); @@ -508,13 +497,6 @@ public class TrabalLearner extends TextR return result; } - /** - * Is called by doRun(). Creates and tests rules for a given list of error groups created by - * createErrorGroups(). - * - * @param errorGrps - * @return The best found list of correction rules. - */ private List<TrabalRule> runAlgorithm(Map<String, List<AnnotationError>> errorGrps) { removeBasics(); inducedRules.clear(); @@ -534,8 +516,8 @@ public class TrabalLearner extends TextR if (basicRules.size() > maxNumberOfBasicRules) { basicRules = basicRules.subList(0, maxNumberOfBasicRules); } - sendStatusUpdateToDelegate("Testing basic rules: " + status, - TextRulerLearnerState.ML_RUNNING, false); + sendStatusUpdateToDelegate("Testing basic rules: " + status, TextRulerLearnerState.ML_RUNNING, + false); basicRules = testTrabalRulesOnDocumentSet(basicRules, exampleDocuments, additionalDocuments, "basic rules (" + i + " of " + errorGrps.size() + ")"); if (basicRules.size() > 0) { @@ -543,8 +525,8 @@ public class TrabalLearner extends TextR bestRulesForStatus.add(basicRules.get(0)); } result = actualResult + getRuleStrings(bestRulesForStatus); - sendStatusUpdateToDelegate("Testing basic rules: " + status, - TextRulerLearnerState.ML_RUNNING, true); + sendStatusUpdateToDelegate("Testing basic rules: " + status, TextRulerLearnerState.ML_RUNNING, + true); List<TrabalRule> learntRules = new ArrayList<TrabalRule>(); for (TrabalRule rule : basicRules) { if (rule.getCoveringStatistics().getCoveredPositivesCount() > 0 @@ -638,12 +620,6 @@ public class TrabalLearner extends TextR return learntRules; } - /** - * Chooses the best final rules from the results of runAlgorithm(). - * - * @param rules - * @return A non redundant list of correction rules. - */ private List<TrabalRule> getBest(List<TrabalRule> rules) { List<TrabalRule> result = new ArrayList<TrabalRule>(); Collections.sort(rules, enhancedComparator); @@ -713,12 +689,6 @@ public class TrabalLearner extends TextR return result; } - /** - * Is called from getBest(). Applies the chosen rules to the additional documents, so the learner - * can ignore the already corrected errors in the next interation. - * - * @param rule - */ private void updateDocumentData(TrabalRule rule) { try { sendStatusUpdateToDelegate("Writing rules...", TextRulerLearnerState.ML_RUNNING, false); @@ -737,12 +707,6 @@ public class TrabalLearner extends TextR } } - /** - * Creates basic rules for the given types of errors. - * - * @param errors - * @return list of basic rules - */ public List<TrabalRule> createBasicRules(List<AnnotationError> errors) { List<TrabalRule> result = new ArrayList<TrabalRule>(); for (AnnotationError each : errors) { @@ -766,12 +730,6 @@ public class TrabalLearner extends TextR return getBestBasicRule(result); } - /** - * Chooses the rules which are expected to be the best. - * - * @param rules - * @return list of best basic rules - */ private List<TrabalRule> getBestBasicRule(List<TrabalRule> rules) { if (rules.size() < maxNumberOfBasicRules) return rules; @@ -821,12 +779,6 @@ public class TrabalLearner extends TextR return result; } - /** - * Creates basic rules for shifting type errors. - * - * @param error - * @return list of shifting rules - */ private List<TrabalRule> createShiftingRules(AnnotationError each) { List<TrabalRule> result = new ArrayList<TrabalRule>(); TextRulerExample error = each.getError(); @@ -848,15 +800,6 @@ public class TrabalLearner extends TextR return result; } - /** - * Creates basic rules for shifting errors, where both borders are shiftet to the same side or the - * size of the annotation is reduced. - * - * @param error - * The error example - * @param truth - * The truth example - */ private List<TrabalRule> createShiftAllRules(TextRulerExample error, TextRulerExample truth) { List<TrabalRule> result = new ArrayList<TrabalRule>(); TextRulerExampleDocument document = error.getDocument(); @@ -907,13 +850,6 @@ public class TrabalLearner extends TextR return result; } - /** - * Creates basic rules for expansion type errors. - * - * @param error - * @param truth - * @return list of expansion rules - */ private List<TrabalRule> createExpansionRules(TextRulerExample error, TextRulerExample truth) { List<TrabalRule> result = new ArrayList<TrabalRule>(); TextRulerExampleDocument document = error.getDocument(); @@ -939,17 +875,11 @@ public class TrabalLearner extends TextR return result; } - /** - * Creates basic rules for annotation type errors. - * - * @param error - * @return list of annotation rules - */ private List<TrabalRule> createAnnotationRules(AnnotationError each) { List<TrabalRule> result = new ArrayList<TrabalRule>(); TextRulerExample truth = each.getTruth(); - TextRulerExampleDocument document = additionalDocuments.getDocuments().get( - exampleDocuments.getDocuments().indexOf(truth.getDocument())); + TextRulerExampleDocument document = additionalDocuments.getDocuments() + .get(exampleDocuments.getDocuments().indexOf(truth.getDocument())); CAS cas = document.getCAS(); List<TrabalRuleItem> truthLeftBorder = getBorderOfExample(truth, document, cas, true); List<TrabalRuleItem> truthRightBorder = getBorderOfExample(truth, document, cas, false); @@ -967,12 +897,6 @@ public class TrabalLearner extends TextR return result; } - /** - * Creates basic rules for deletion type errors. - * - * @param error - * @return list of deletion rules - */ private List<TrabalRule> createDeletionRules(AnnotationError each) { List<TrabalRule> result = new ArrayList<TrabalRule>(); TextRulerExample error = each.getError(); @@ -982,12 +906,6 @@ public class TrabalLearner extends TextR return result; } - /** - * Creates basic rules for correction type errors. - * - * @param error - * @return list of correction rules - */ private List<TrabalRule> createCorrectionRules(AnnotationError each) { List<TrabalRule> result = new ArrayList<TrabalRule>(); TextRulerExample error = each.getError(); @@ -998,16 +916,6 @@ public class TrabalLearner extends TextR return result; } - /** - * Examines the border of an example annotation and returns all annotations before and on that - * border if looking at the left border or returns all annotations on and after the example if - * looking at the right border. - * - * @param example - * The example that should be examined - * @param examineLeftBorder - * set true for the left border or false for the right border to be examined - */ private List<TrabalRuleItem> getBorderOfExample(TextRulerExample example, TextRulerExampleDocument document, CAS cas, boolean examineLeftBorder) { List<TrabalRuleItem> result = new ArrayList<TrabalRuleItem>(); @@ -1055,12 +963,6 @@ public class TrabalLearner extends TextR return result; } - /** - * Creates conditions for a given rule. - * - * @param rules - * @return ranked list of conditions - */ public RankedList createConditions(List<TrabalRule> rules) { if (rules.size() == 0) return new RankedList(idf); @@ -1075,12 +977,12 @@ public class TrabalLearner extends TextR error.addAll(createConditions(rule.getAnnotation())); truth.addAll(createConditions(rule.getTargetAnnotation())); } - result = error.subtract(truth.unite(getPositiveExamplesFor(rules.get(0) - .getTargetAnnotation().getType()))); + result = error.subtract( + truth.unite(getPositiveExamplesFor(rules.get(0).getTargetAnnotation().getType()))); setNegative(result); - result.addAll(truth.cut( - getPositiveExamplesFor(rules.get(0).getTargetAnnotation().getType())).subtract( - error)); + result.addAll( + truth.cut(getPositiveExamplesFor(rules.get(0).getTargetAnnotation().getType())) + .subtract(error)); return result; case CORRECTION: for (TrabalRule rule : rules) { @@ -1090,9 +992,9 @@ public class TrabalLearner extends TextR truth.unite(getPositiveExamplesFor(rules.get(0).getTargetAnnotation().getType()))); setNegative(result); if (getPositiveExamplesFor(rules.get(0).getTargetAnnotation().getType()).size() > 0) { - result.addAll(truth.cut( - getPositiveExamplesFor(rules.get(0).getTargetAnnotation().getType())).subtract( - getPositiveExamplesFor(rules.get(0).getAnnotation().getType()))); + result.addAll(truth + .cut(getPositiveExamplesFor(rules.get(0).getTargetAnnotation().getType())) + .subtract(getPositiveExamplesFor(rules.get(0).getAnnotation().getType()))); } else { result.addAll(truth); } @@ -1112,8 +1014,8 @@ public class TrabalLearner extends TextR } result = getPositiveExamplesFor(rules.get(0).getAnnotation().getType()).subtract(error); setNegative(result); - result.addAll(createConditions(rules.get(0).getAnnotation()).subtract( - getPositiveExamplesFor(rules.get(0).getAnnotation().getType()))); + result.addAll(createConditions(rules.get(0).getAnnotation()) + .subtract(getPositiveExamplesFor(rules.get(0).getAnnotation().getType()))); return result; } return null; @@ -1136,19 +1038,11 @@ public class TrabalLearner extends TextR } } - /** - * Creates conditions for a rule given by its boundaries and annotation type. - * - * @param frontBoundary - * @param rearBoundary - * @param truth - * @return ranked list of conditions - */ private RankedList createConditions(TrabalRuleItem frontBoundary, TrabalRuleItem rearBoundary, TrabalAnnotation truth) { RankedList result = new RankedList(idf); - TextRulerExampleDocument doc = additionalDocuments.getDocuments().get( - exampleDocuments.getDocuments().indexOf(truth.getDocument())); + TextRulerExampleDocument doc = additionalDocuments.getDocuments() + .get(exampleDocuments.getDocuments().indexOf(truth.getDocument())); CAS cas = doc.getCAS(); for (TrabalRuleItem item : getTermsBefore(frontBoundary, doc)) { result.add(new Condition(ConditionType.AFTER, item)); @@ -1166,8 +1060,9 @@ public class TrabalLearner extends TextR result.add(new Condition(ConditionType.STARTSWITH, item)); } } else { - for (List<TrabalRuleItem> list : getFirstTermsWithinBounds(frontBoundary.getAnnotation() - .getBegin(), rearBoundary.getAnnotation().getEnd(), doc, cas, 1)) { + for (List<TrabalRuleItem> list : getFirstTermsWithinBounds( + frontBoundary.getAnnotation().getBegin(), rearBoundary.getAnnotation().getEnd(), doc, + cas, 1)) { result.add(new Condition(ConditionType.STARTSWITH, list.get(0))); } } @@ -1176,20 +1071,15 @@ public class TrabalLearner extends TextR result.add(new Condition(ConditionType.ENDSWITH, item)); } } else { - for (List<TrabalRuleItem> list : getLastTermsWithinBounds(rearBoundary.getAnnotation() - .getBegin(), frontBoundary.getAnnotation().getEnd(), doc, cas, 1)) { + for (List<TrabalRuleItem> list : getLastTermsWithinBounds( + rearBoundary.getAnnotation().getBegin(), frontBoundary.getAnnotation().getEnd(), doc, + cas, 1)) { result.add(new Condition(ConditionType.ENDSWITH, list.get(0))); } } return result; } - /** - * Creates conditions for a rule, given by its annotation. - * - * @param error - * @return ranked list of conditions - */ private RankedList createConditions(TrabalAnnotation annotation) { RankedList result = new RankedList(idf); TrabalRuleItem ruleItem = new TrabalRuleItem(annotation); @@ -1221,17 +1111,6 @@ public class TrabalLearner extends TextR return result; } - /** - * Returns all items directly preceding the given example rule item. - * - * @param ruleItem - * Examined rule item - * @param document - * Example document - * @param cas - * The CAS - * @return List of rule items that precede the given example - */ private List<TrabalRuleItem> getTermsBefore(TrabalRuleItem ruleItem, TextRulerExampleDocument document) { List<TrabalRuleItem> result = new ArrayList<TrabalRuleItem>(); @@ -1256,8 +1135,8 @@ public class TrabalLearner extends TextR nextEnd = a.getEnd(); } if (a.getEnd() >= nextEnd && a.getEnd() <= begin) { - TrabalRuleItem term = new TrabalRuleItem(new TrabalAnnotation(a, document, - enableFeatures)); + TrabalRuleItem term = new TrabalRuleItem( + new TrabalAnnotation(a, document, enableFeatures)); result.add(term); } } @@ -1267,17 +1146,6 @@ public class TrabalLearner extends TextR return result; } - /** - * Returns all items directly following the given example rule item. - * - * @param ruleItem - * Examined rule item - * @param document - * Example document - * @param cas - * The CAS - * @return List of rule items that follow the given example - */ private List<TrabalRuleItem> getTermsAfter(TrabalRuleItem ruleItem, TextRulerExampleDocument document) { List<TrabalRuleItem> result = new ArrayList<TrabalRuleItem>(); @@ -1297,8 +1165,8 @@ public class TrabalLearner extends TextR nextBegin = a.getBegin(); } if (a.getBegin() <= nextBegin && a.getBegin() >= end) { - TrabalRuleItem term = new TrabalRuleItem(new TrabalAnnotation(a, document, - enableFeatures)); + TrabalRuleItem term = new TrabalRuleItem( + new TrabalAnnotation(a, document, enableFeatures)); result.add(term); } } @@ -1308,17 +1176,6 @@ public class TrabalLearner extends TextR return result; } - /** - * Gets the left border within the bounds, that means a list of elements that start with the - * border and those that end right before it. - * - * @param startPos - * @param endPos - * @param document - * @param cas - * @param numberOfSideItems - * @return first term - */ private List<List<TrabalRuleItem>> getFirstTermsWithinBounds(int startPos, int endPos, TextRulerExampleDocument document, CAS cas, int numberOfSideItems) { List<List<TrabalRuleItem>> preItems = new ArrayList<List<TrabalRuleItem>>(); @@ -1348,7 +1205,8 @@ public class TrabalLearner extends TextR for (AnnotationFS each : startAs) { List<TrabalRuleItem> startList = new ArrayList<TrabalRuleItem>(); - TrabalRuleItem term = new TrabalRuleItem(new TrabalAnnotation(each, document, enableFeatures)); + TrabalRuleItem term = new TrabalRuleItem( + new TrabalAnnotation(each, document, enableFeatures)); startList.add(term); preItems.add(startList); } @@ -1356,17 +1214,6 @@ public class TrabalLearner extends TextR return preItems; } - /** - * Gets the right border within the bounds, that means a list of elements that end with the border - * and those that start right behind it. - * - * @param startPos - * @param endPos - * @param document - * @param cas - * @param numberOfSideItems - * @return last term - */ private List<List<TrabalRuleItem>> getLastTermsWithinBounds(int startPos, int endPos, TextRulerExampleDocument document, CAS cas, int numberOfSideItems) { List<List<TrabalRuleItem>> postItems = new ArrayList<List<TrabalRuleItem>>(); @@ -1397,7 +1244,8 @@ public class TrabalLearner extends TextR for (AnnotationFS each : endAs) { List<TrabalRuleItem> endList = new ArrayList<TrabalRuleItem>(); - TrabalRuleItem term = new TrabalRuleItem(new TrabalAnnotation(each, document, enableFeatures)); + TrabalRuleItem term = new TrabalRuleItem( + new TrabalAnnotation(each, document, enableFeatures)); endList.add(term); postItems.add(endList); } @@ -1405,17 +1253,6 @@ public class TrabalLearner extends TextR return postItems; } - /** - * Returns a list of rule elements that precede the given elements. - * - * @param lists - * @param till - * @param document - * @param cas - * @param index - * @param maxNumberOfItems - * @return updated list of items - */ private List<List<TrabalRuleItem>> addPreceding(List<List<TrabalRuleItem>> lists, int till, TextRulerExampleDocument document, CAS cas, int index, int maxNumberOfItems) { if (index >= maxNumberOfItems) { @@ -1449,17 +1286,6 @@ public class TrabalLearner extends TextR return result; } - /** - * Returns a list of rule elements that follow on the given elements. - * - * @param lists - * @param till - * @param document - * @param cas - * @param index - * @param maxNumberOfItems - * @return updated list of items - */ private List<List<TrabalRuleItem>> addFollowing(List<List<TrabalRuleItem>> lists, int till, TextRulerExampleDocument document, CAS cas, int index, int maxNumberOfItems) { if (index >= maxNumberOfItems) { @@ -1493,9 +1319,6 @@ public class TrabalLearner extends TextR return result; } - /** - * Returns a list of all items, consuming the given RuleItem. - */ private List<TrabalRuleItem> getConsumingTerms(TrabalRuleItem ruleItem, TextRulerExampleDocument document) { CAS cas = document.getCAS(); @@ -1516,15 +1339,6 @@ public class TrabalLearner extends TextR return result; } - /** - * Returns a list of rule items within the given bounds. - * - * @param begin - * @param end - * @param doc - * @param cas - * @return list of terms - */ private List<TrabalRuleItem> getSingleTermsWithinBounds(int begin, int end, TextRulerExampleDocument doc, CAS cas) { Set<TrabalRuleItem> result = new HashSet<TrabalRuleItem>(); @@ -1544,16 +1358,6 @@ public class TrabalLearner extends TextR return new ArrayList<TrabalRuleItem>(result); } - /** - * Applies a set of rules to the additional data and compares it to the training data to rate - * them. - * - * @param rules - * @param documents - * @param additionalDocuments - * @param ruleSet - * @return list of rules - */ public List<TrabalRule> testTrabalRulesOnDocumentSet(List<TrabalRule> rules, final TextRulerExampleDocumentSet documents, final TextRulerExampleDocumentSet additionalDocuments, String ruleSet) { @@ -1583,8 +1387,9 @@ public class TrabalLearner extends TextR for (int i = 0; i < goldDocs.size(); i++) { TextRulerExampleDocument goldDoc = goldDocs.get(i); TextRulerExampleDocument additionalDoc = additionalDocs.get(i); - sendStatusUpdateToDelegate("Testing " + ruleSet + ruleInfo + " on document " + (i + 1) - + " of " + goldDocs.size() + " : rule " + counter + " of " + rules.size(), + sendStatusUpdateToDelegate( + "Testing " + ruleSet + ruleInfo + " on document " + (i + 1) + " of " + + goldDocs.size() + " : rule " + counter + " of " + rules.size(), TextRulerLearnerState.ML_RUNNING, false); TextRulerStatisticsCollector sumC = new TextRulerStatisticsCollector(); prepareTestCas(theTestCAS, goldDoc, additionalDoc); @@ -1636,13 +1441,6 @@ public class TrabalLearner extends TextR return ruleInfo; } - /** - * Resets the test CAS and adds the annotations of the additional data. - * - * @param testCas - * @param goldDoc - * @param additionalDoc - */ private void prepareTestCas(CAS testCas, TextRulerExampleDocument goldDoc, TextRulerExampleDocument additionalDoc) { testCas.reset(); @@ -1651,7 +1449,7 @@ public class TrabalLearner extends TextR testCas.setDocumentText(goldCas.getDocumentText()); CasCopier.copyCas(additionalCas, testCas, testCas.getDocumentText() == null); - + // for (AnnotationFS fs : additionalCas.getAnnotationIndex()) { // Type t = testCas.getTypeSystem().getType(fs.getType().getName()); // if (t != null) { @@ -1664,16 +1462,6 @@ public class TrabalLearner extends TextR // } } - /** - * Applies a rule to an element of the additional data and compares the result to the - * corresponding element of the training data. - * - * @param rule - * @param goldDoc - * @param additionalDoc - * @param c - * @param testCas - */ private void testRuleOnDocument(final TrabalRule rule, final TextRulerExampleDocument goldDoc, final TextRulerExampleDocument additionalDoc, final TextRulerStatisticsCollector c, CAS testCas) { @@ -1691,44 +1479,36 @@ public class TrabalLearner extends TextR TextRulerToolkit.writeCAStoXMIFile(testCas, tempDirectory() + "testCasProcessed.xmi"); } if (rule.getAnnotation() != null && rule.getTargetAnnotation() != null) { - compareOriginalDocumentWithTestCAS(goldDoc, additionalDoc, testCas, new TextRulerTarget( - rule.getAnnotation().getType().getName(), this), c, false); + compareOriginalDocumentWithTestCAS(goldDoc, additionalDoc, testCas, + new TextRulerTarget(rule.getAnnotation().getType().getName(), this), c, false); if (rule.getAnnotation().getType() != rule.getTargetAnnotation().getType()) { - compareOriginalDocumentWithTestCAS(goldDoc, additionalDoc, testCas, new TextRulerTarget( - rule.getTargetAnnotation().getType().getName(), this), c, false); + compareOriginalDocumentWithTestCAS(goldDoc, additionalDoc, testCas, + new TextRulerTarget(rule.getTargetAnnotation().getType().getName(), this), c, + false); } } else if (rule.getTargetAnnotation() != null) { - compareOriginalDocumentWithTestCAS(goldDoc, additionalDoc, testCas, new TextRulerTarget( - rule.getTargetAnnotation().getType().getName(), this), c, false); + compareOriginalDocumentWithTestCAS(goldDoc, additionalDoc, testCas, + new TextRulerTarget(rule.getTargetAnnotation().getType().getName(), this), c, + false); } else { - compareOriginalDocumentWithTestCAS(goldDoc, additionalDoc, testCas, new TextRulerTarget( - rule.getAnnotation().getType().getName(), this), c, false); + compareOriginalDocumentWithTestCAS(goldDoc, additionalDoc, testCas, + new TextRulerTarget(rule.getAnnotation().getType().getName(), this), c, false); } } catch (Exception e) { e.printStackTrace(); } } - /** - * Compares two documents to rate the results of an applied rule. - * - * @param goldDoc - * @param additionalDoc - * @param testCas - * @param target - * @param c - * @param collectNegativeExamples - */ private void compareOriginalDocumentWithTestCAS(TextRulerExampleDocument goldDoc, TextRulerExampleDocument additionalDoc, CAS testCas, TextRulerTarget target, TextRulerStatisticsCollector c, boolean collectNegativeExamples) { List<TextRulerExample> goldPositives = goldDoc.createSlotInstancesForCAS(goldDoc.getCAS(), target, true); - List<TextRulerExample> additionalPositives = additionalDoc.createSlotInstancesForCAS( - additionalDoc.getCAS(), target, true); - List<TextRulerExample> testPositives = goldDoc - .createSlotInstancesForCAS(testCas, target, false); + List<TextRulerExample> additionalPositives = additionalDoc + .createSlotInstancesForCAS(additionalDoc.getCAS(), target, true); + List<TextRulerExample> testPositives = goldDoc.createSlotInstancesForCAS(testCas, target, + false); List<TextRulerExample> baseFP = new ArrayList<TextRulerExample>(); for (TextRulerExample e : additionalPositives) { @@ -1740,8 +1520,8 @@ public class TrabalLearner extends TextR } List<TextRulerExample> baseFN = new ArrayList<TextRulerExample>(); for (TextRulerExample e : goldPositives) { - TextRulerExample example = TextRulerToolkit.exampleListContainsAnnotation( - additionalPositives, e.getAnnotation()); + TextRulerExample example = TextRulerToolkit.exampleListContainsAnnotation(additionalPositives, + e.getAnnotation()); if (example == null) { baseFN.add(e); } @@ -1775,8 +1555,8 @@ public class TrabalLearner extends TextR for (TextRulerExample e : baseFN) { TextRulerExample example = TextRulerToolkit.exampleListContainsAnnotation(testFN, e.getAnnotation()); - TextRulerExample coveredExample = TextRulerToolkit.exampleListContainsAnnotation( - goldPositives, e.getAnnotation()); + TextRulerExample coveredExample = TextRulerToolkit + .exampleListContainsAnnotation(goldPositives, e.getAnnotation()); if (example == null) { c.addCoveredPositive(coveredExample); } @@ -1804,22 +1584,10 @@ public class TrabalLearner extends TextR } } - /** - * Removes duplicate rules by their hash value. - * - * @param rules - * @return updated list - */ public static List<TrabalRule> removeDuplicateRules(List<TrabalRule> rules) { return new ArrayList<TrabalRule>(new HashSet<TrabalRule>(rules)); } - /** - * Returns a string, containing the rules of the given list. - * - * @param rules - * @return string representation of given rules - */ public static String getRuleStrings(List<TrabalRule> rules) { String result = ""; for (TrabalRule r : rules) { @@ -1828,12 +1596,6 @@ public class TrabalLearner extends TextR return result; } - /** - * Tests, if the given type is a slot type. - * - * @param type - * @return true, if given type is a slot type - */ public boolean isSlotType(Type type) { for (String slot : slotNames) { if (slot.equals(type.getName())) { @@ -1843,44 +1605,16 @@ public class TrabalLearner extends TextR return false; } + @Override public boolean collectNegativeCoveredInstancesWhenTesting() { return false; } + @Override public String getResultString() { return getFileHeaderString(true) + result; } - // // @Override - // public AnalysisEngine getAnalysisEngine() { - // if (ae == null) { - // String descriptorFile = TextRulerToolkit.getEngineDescriptorFromTMSourceFile(new Path( - // preprocessorTMFile)); - // sendStatusUpdateToDelegate("loading AE...", TextRulerLearnerState.ML_INITIALIZING, false); - // ae = TextRulerToolkit.loadAnalysisEngine(descriptorFile); - // - // // set filters to NO filtering so that we can add it manually with - // // the FILTERTYPE expression! - // String tempRulesFileName = getTempRulesFileName(); - // IPath path = new Path(tempRulesFileName); - // ae.setConfigParameterValue(RutaEngine.MAIN_SCRIPT, path.removeFileExtension() - // .lastSegment()); - // String portableString = path.removeLastSegments(1).toPortableString(); - // ae.setConfigParameterValue(RutaEngine.SCRIPT_PATHS, new String[] { portableString }); - // ae.setConfigParameterValue(RutaEngine.ADDITIONAL_SCRIPTS, new String[0]); - // ae.setConfigParameterValue(RutaEngine.RELOAD_SCRIPT, true); - // ae.setConfigParameterValue(RutaEngine.REMOVE_BASICS, true); - // - // try { - // ae.reconfigure(); - // } catch (ResourceConfigurationException e) { - // TextRulerPlugin.error(e); - // return null; - // } - // } - // return ae; - // } - /** * Return the set of additional documents and initializes it, if needed. */ @@ -1897,7 +1631,7 @@ public class TrabalLearner extends TextR return enableFeatures; } - // @Override + @Override public void setParameters(Map<String, Object> params) { if (TextRulerToolkit.DEBUG) saveParametersToTempFolder(params); @@ -1915,12 +1649,6 @@ public class TrabalLearner extends TextR enableFeatures = (Boolean) params.get(ENABLE_FEATURES_KEY); } - /** - * Creates a file in the *.csv format, containing TraBaL errors (error type, file name, false - * annotation and true annotation). - * - * @throws Exception - */ public void getErrorsAsCSV(String filePath) throws Exception { String result = ""; if (exampleDocuments == null) { @@ -1958,11 +1686,8 @@ public class TrabalLearner extends TextR } } - /** - * Compares trabal rules, disregarding the error rate, so basic rules with maximum number of - * covered positives are chosen. - */ protected Comparator<TrabalRule> basicComparator = new Comparator<TrabalRule>() { + @Override public int compare(TrabalRule o1, TrabalRule o2) { // coveredPositives if (o1.getCoveringStatistics().getCoveredPositivesCount() > o2.getCoveringStatistics() @@ -1988,19 +1713,17 @@ public class TrabalLearner extends TextR } }; - /** - * Compares trabal rules, starting with the error rate. - */ protected Comparator<TrabalRule> enhancedComparator = new Comparator<TrabalRule>() { + @Override public int compare(TrabalRule o1, TrabalRule o2) { // positives - negatives - if (o1.getCoveringStatistics().getCoveredPositivesCount() - - o1.getCoveringStatistics().getCoveredNegativesCount() > o2.getCoveringStatistics() - .getCoveredPositivesCount() - o2.getCoveringStatistics().getCoveredNegativesCount()) + if (o1.getCoveringStatistics().getCoveredPositivesCount() - o1.getCoveringStatistics() + .getCoveredNegativesCount() > o2.getCoveringStatistics().getCoveredPositivesCount() + - o2.getCoveringStatistics().getCoveredNegativesCount()) return -1; - if (o1.getCoveringStatistics().getCoveredPositivesCount() - - o1.getCoveringStatistics().getCoveredNegativesCount() < o2.getCoveringStatistics() - .getCoveredPositivesCount() - o2.getCoveringStatistics().getCoveredNegativesCount()) + if (o1.getCoveringStatistics().getCoveredPositivesCount() - o1.getCoveringStatistics() + .getCoveredNegativesCount() < o2.getCoveringStatistics().getCoveredPositivesCount() + - o2.getCoveringStatistics().getCoveredNegativesCount()) return 1; // coveredPositives if (o1.getCoveringStatistics().getCoveredPositivesCount() > o2.getCoveringStatistics()
Modified: uima/ruta/trunk/ruta-maven-plugin/src/main/java/org/apache/uima/ruta/maven/RutaGenerateDescriptorMojo.java URL: http://svn.apache.org/viewvc/uima/ruta/trunk/ruta-maven-plugin/src/main/java/org/apache/uima/ruta/maven/RutaGenerateDescriptorMojo.java?rev=1853491&r1=1853490&r2=1853491&view=diff ============================================================================== --- uima/ruta/trunk/ruta-maven-plugin/src/main/java/org/apache/uima/ruta/maven/RutaGenerateDescriptorMojo.java (original) +++ uima/ruta/trunk/ruta-maven-plugin/src/main/java/org/apache/uima/ruta/maven/RutaGenerateDescriptorMojo.java Wed Feb 13 11:24:19 2019 @@ -87,15 +87,15 @@ public class RutaGenerateDescriptorMojo private static final String RUTA_NATURE = "org.apache.uima.ruta.ide.nature"; - @Parameter( defaultValue = "${project}", readonly = true ) + @Parameter(defaultValue = "${project}", readonly = true) private MavenProject project; @Component private BuildContext buildContext; - @Parameter( defaultValue = "${session}", readonly = true ) + @Parameter(defaultValue = "${session}", readonly = true) private MavenSession session; - + /** * The source files for the multi tree word list. */ @@ -198,6 +198,7 @@ public class RutaGenerateDescriptorMojo @Parameter(required = false) private String[] buildPaths; + @Override public void execute() throws MojoExecutionException, MojoFailureException { if (!typeSystemOutputDirectory.exists()) { @@ -212,8 +213,7 @@ public class RutaGenerateDescriptorMojo this.project.addCompileSourceRoot(this.typeSystemOutputDirectory.getPath()); this.project.addCompileSourceRoot(this.analysisEngineOutputDirectory.getPath()); - - + String[] files = null; if (scriptFiles != null) { try { @@ -239,18 +239,18 @@ public class RutaGenerateDescriptorMojo List<File> filesToBuild = new ArrayList<File>(); for (String each : files) { File file = new File(each); - + // TODO should check the correct package! List<File> possibleDescriptors = getPossibleDescriptors(file); - if(possibleDescriptors == null) { + if (possibleDescriptors == null) { filesToBuild.add(file); continue; } - + long scriptModified = file.lastModified(); for (File eachDescriptor : possibleDescriptors) { long descModified = eachDescriptor.lastModified(); - if(scriptModified > descModified) { + if (scriptModified > descModified) { filesToBuild.add(file); break; } @@ -262,8 +262,6 @@ public class RutaGenerateDescriptorMojo return; } - - RutaDescriptorFactory factory = new RutaDescriptorFactory(); if (typeSystemTemplate != null) { try { @@ -292,8 +290,7 @@ public class RutaGenerateDescriptorMojo List<String> extensions = getExtensionsFromClasspath(classloader); options.setLanguageExtensions(extensions); - - + if (maxBuildRetries == -1) { maxBuildRetries = filesToBuild.size() * 3; } @@ -322,9 +319,8 @@ public class RutaGenerateDescriptorMojo getLog().warn("Failed to parse UIMA Ruta script: " + scriptName, re); } catch (IOException ioe) { toBuild.add(descriptorInformation); - getLog().warn( - "Tried to build " + scriptName - + ", but failed (dependency probably not yet build): " + ioe.getMessage()); + getLog().warn("Tried to build " + scriptName + + ", but failed (dependency probably not yet build): " + ioe.getMessage()); count++; } catch (SAXException saxe) { getLog().warn("Failed to write descriptor: " + scriptName, saxe); @@ -376,7 +372,6 @@ public class RutaGenerateDescriptorMojo return result; } - private List<String> getExtensionsFromClasspath(ClassLoader classloader) { List<String> result = new ArrayList<String>(); @@ -398,18 +393,18 @@ public class RutaGenerateDescriptorMojo } private void createDescriptors(RutaDescriptorFactory factory, RutaBuildOptions options, - RutaDescriptorInformation descriptorInformation) throws IOException, - RecognitionException, InvalidXMLException, ResourceInitializationException, - URISyntaxException, SAXException { + RutaDescriptorInformation descriptorInformation) throws IOException, RecognitionException, + InvalidXMLException, ResourceInitializationException, URISyntaxException, SAXException { String packageString = ""; if (!StringUtils.isBlank(descriptorInformation.getPackageString())) { packageString = descriptorInformation.getPackageString().replaceAll("[.]", "/").concat("/"); } - String engineOutput = new File(analysisEngineOutputDirectory, packageString - + descriptorInformation.getScriptName() + analysisEngineSuffix + ".xml") - .getAbsolutePath(); - String typeSystemOutput = new File(typeSystemOutputDirectory, packageString - + descriptorInformation.getScriptName() + typeSystemSuffix + ".xml").getAbsolutePath(); + String engineOutput = new File(analysisEngineOutputDirectory, + packageString + descriptorInformation.getScriptName() + analysisEngineSuffix + ".xml") + .getAbsolutePath(); + String typeSystemOutput = new File(typeSystemOutputDirectory, + packageString + descriptorInformation.getScriptName() + typeSystemSuffix + ".xml") + .getAbsolutePath(); Pair<AnalysisEngineDescription, TypeSystemDescription> descriptions = factory .createDescriptions(engineOutput, typeSystemOutput, descriptorInformation, options, scriptPaths, descriptorPaths, resourcePaths); @@ -434,10 +429,6 @@ public class RutaGenerateDescriptorMojo } } - /** - * Create a class loader which covers the classes compiled in the current project and all - * dependencies. - */ public static URLClassLoader getClassloader(MavenProject project, Log aLog) throws MojoExecutionException { @@ -446,12 +437,12 @@ public class RutaGenerateDescriptorMojo for (String element : project.getCompileSourceRoots()) { try { urls.add(new File(element).toURI().toURL()); - if(aLog != null) { + if (aLog != null) { aLog.debug("Classpath entry: " + element); } } catch (MalformedURLException e) { - throw new MojoExecutionException("Unable to assemble classpath: " - + ExceptionUtils.getRootCauseMessage(e), e); + throw new MojoExecutionException( + "Unable to assemble classpath: " + ExceptionUtils.getRootCauseMessage(e), e); } } @@ -459,31 +450,31 @@ public class RutaGenerateDescriptorMojo try { String directory = element.getDirectory(); urls.add(new File(directory).toURI().toURL()); - if(aLog != null) { + if (aLog != null) { aLog.debug("Classpath entry: " + directory); } } catch (MalformedURLException e) { - throw new MojoExecutionException("Unable to assemble classpath: " - + ExceptionUtils.getRootCauseMessage(e), e); + throw new MojoExecutionException( + "Unable to assemble classpath: " + ExceptionUtils.getRootCauseMessage(e), e); } } try { for (Object object : project.getCompileClasspathElements()) { String path = (String) object; - if(aLog != null) { + if (aLog != null) { aLog.debug("Classpath entry: " + object); } urls.add(new File(path).toURI().toURL()); } } catch (IOException e) { - throw new MojoExecutionException("Unable to assemble classpath: " - + ExceptionUtils.getRootCauseMessage(e), e); + throw new MojoExecutionException( + "Unable to assemble classpath: " + ExceptionUtils.getRootCauseMessage(e), e); } catch (DependencyResolutionRequiredException e) { - throw new MojoExecutionException("Unable to resolve dependencies: " - + ExceptionUtils.getRootCauseMessage(e), e); + throw new MojoExecutionException( + "Unable to resolve dependencies: " + ExceptionUtils.getRootCauseMessage(e), e); } - Set<Artifact> artifacts = (Set<Artifact>) project.getDependencyArtifacts(); + Set<Artifact> artifacts = project.getDependencyArtifacts(); if (artifacts != null) { for (Artifact dep : artifacts) { try { @@ -491,9 +482,9 @@ public class RutaGenerateDescriptorMojo // Unresolved file because it is in the wrong scope (e.g. test?) continue; } - if(aLog != null) { - aLog.debug("Classpath entry: " + dep.getGroupId() + ":" + dep.getArtifactId() + ":" - + dep.getVersion() + " -> " + dep.getFile()); + if (aLog != null) { + aLog.debug("Classpath entry: " + dep.getGroupId() + ":" + dep.getArtifactId() + ":" + + dep.getVersion() + " -> " + dep.getFile()); } urls.add(dep.getFile().toURI().toURL()); } catch (Exception e) {
