Fix some quality flaws

sonar-batch-protocol/src/main/java/org/sonar/batch/protocol/input/issues/PreviousIssueHelper.java

@@ -30,6 +30,7 @@
 import java.io.Reader;
 import java.io.Writer;
 import java.util.Iterator;
+import java.util.NoSuchElementException;
 
 public class PreviousIssueHelper {
 
@@ -47,7 +48,6 @@ public static interface Function<F, T> {
   }
 
   public <G> void streamIssues(Writer out, Iterable<G> issues, Function<G, PreviousIssue> converter) {
-    Gson gson = GsonHelper.create();
     try {
       JsonWriter writer = new JsonWriter(out);
       writer.setIndent("  ");
@@ -101,6 +101,13 @@ public boolean hasNext() {
 
     @Override
     public PreviousIssue next() {
+      try {
+        if (!jsonreader.hasNext()) {
+          throw new NoSuchElementException();
+        }
+      } catch (IOException e) {
+        throw new IllegalStateException("Unable to iterate over JSON file ", e);
+      }
       return gson.fromJson(jsonreader, PreviousIssue.class);
     }
 

sonar-batch-protocol/src/main/java/org/sonar/batch/protocol/input/issues/package-info.java

@@ -0,0 +1,24 @@
+/*
+ * SonarQube, open source software quality management tool.
+ * Copyright (C) 2008-2014 SonarSource
+ * mailto:contact AT sonarsource DOT com
+ *
+ * SonarQube is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 3 of the License, or (at your option) any later version.
+ *
+ * SonarQube is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+ */
+@ParametersAreNonnullByDefault
+package org.sonar.batch.protocol.input.issues;
+
+import javax.annotation.ParametersAreNonnullByDefault;
+

sonar-batch-protocol/src/main/java/org/sonar/batch/protocol/output/ReportHelper.java

@@ -19,14 +19,14 @@
  */
 package org.sonar.batch.protocol.output;
 
-import org.sonar.batch.protocol.output.component.ReportComponents;
-
 import com.google.gson.Gson;
 import com.google.gson.stream.JsonReader;
 import com.google.gson.stream.JsonWriter;
+import org.apache.commons.io.Charsets;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.sonar.batch.protocol.GsonHelper;
+import org.sonar.batch.protocol.output.component.ReportComponents;
 import org.sonar.batch.protocol.output.issue.ReportIssue;
 
 import java.io.BufferedInputStream;
@@ -39,6 +39,7 @@
 import java.io.InputStreamReader;
 import java.io.OutputStreamWriter;
 import java.util.Iterator;
+import java.util.NoSuchElementException;
 
 public class ReportHelper {
 
@@ -71,7 +72,6 @@ public void saveComponents(ReportComponents components) {
   }
 
   public void saveIssues(long componentBatchId, Iterable<ReportIssue> issues) {
-    Gson gson = GsonHelper.create();
     File issuesFile = getIssuesFile(componentBatchId);
     try (OutputStreamWriter out = new OutputStreamWriter(new BufferedOutputStream(new FileOutputStream(issuesFile)), "UTF-8")) {
 
@@ -127,7 +127,7 @@ private final class ReportIssueIterator implements Iterator<ReportIssue> {
 
     public ReportIssueIterator(File issuesFile) {
       try {
-        reader = new JsonReader(new InputStreamReader(new BufferedInputStream(new FileInputStream(issuesFile))));
+        reader = new JsonReader(new InputStreamReader(new BufferedInputStream(new FileInputStream(issuesFile)), Charsets.UTF_8));
         reader.beginArray();
       } catch (IOException e) {
         throw new IllegalStateException("Unable to read " + issuesFile, e);
@@ -151,6 +151,13 @@ public boolean hasNext() {
 
     @Override
     public ReportIssue next() {
+      try {
+        if (!reader.hasNext()) {
+          throw new NoSuchElementException();
+        }
+      } catch (IOException e) {
+        throw new IllegalStateException("Unable to iterate over JSON file ", e);
+      }
       return gson.fromJson(reader, ReportIssue.class);
     }
 

sonar-batch-protocol/src/main/java/org/sonar/batch/protocol/output/package-info.java

@@ -0,0 +1,24 @@
+/*
+ * SonarQube, open source software quality management tool.
+ * Copyright (C) 2008-2014 SonarSource
+ * mailto:contact AT sonarsource DOT com
+ *
+ * SonarQube is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 3 of the License, or (at your option) any later version.
+ *
+ * SonarQube is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+ */
+@ParametersAreNonnullByDefault
+package org.sonar.batch.protocol.output;
+
+import javax.annotation.ParametersAreNonnullByDefault;
+

sonar-batch/src/main/java/org/sonar/batch/components/TimeMachineConfiguration.java

@@ -25,7 +25,6 @@
 import org.sonar.api.BatchExtension;
 import org.sonar.api.database.DatabaseSession;
 import org.sonar.api.database.model.Snapshot;
-import org.sonar.api.resources.Project;
 import org.sonar.api.resources.Qualifiers;
 
 import javax.annotation.CheckForNull;
@@ -39,15 +38,13 @@ public class TimeMachineConfiguration implements BatchExtension {
   private static final Logger LOG = LoggerFactory.getLogger(TimeMachineConfiguration.class);
 
   private final DatabaseSession session;
-  private Project project;
   private final PeriodsDefinition periodsDefinition;
 
   private List<Period> periods;
   private List<PastSnapshot> modulePastSnapshots;
 
-  public TimeMachineConfiguration(DatabaseSession session, Project project, PeriodsDefinition periodsDefinition) {
+  public TimeMachineConfiguration(DatabaseSession session, PeriodsDefinition periodsDefinition) {
     this.session = session;
-    this.project = project;
     this.periodsDefinition = periodsDefinition;
     initModulePastSnapshots();
   }

sonar-batch/src/main/java/org/sonar/batch/index/ResourcePersister.java

@@ -93,26 +93,27 @@ private void persist(BatchResource batchResource) {
       return;
     }
     BatchResource parentBatchResource = batchResource.parent();
+    Snapshot s;
     if (parentBatchResource != null) {
       persist(parentBatchResource);
+      s = persist(findModule(parentBatchResource), batchResource.resource(), parentBatchResource.resource());
+    } else {
+      // Root project
+      s = persistProject((Project) batchResource.resource(), null);
     }
-    Snapshot s = persist(findParentModule(batchResource), batchResource.resource(), parentBatchResource != null ? parentBatchResource.resource() : null);
     batchResource.setSnapshot(s);
     if (ResourceUtils.isPersistable(batchResource.resource())) {
       graph.addComponent(batchResource.resource(), batchResource.snapshotId());
     }
   }
 
   @CheckForNull
-  private Project findParentModule(BatchResource batchResource) {
-    if (batchResource != null && batchResource.parent() != null) {
-      if (batchResource.parent().resource() instanceof Project) {
-        return (Project) batchResource.parent().resource();
-      } else {
-        return findParentModule(batchResource.parent());
-      }
+  private Project findModule(BatchResource batchResource) {
+    if (batchResource.resource() instanceof Project) {
+      return (Project) batchResource.resource();
+    } else {
+      return findModule(batchResource.parent());
     }
-    return null;
   }
 
   private Snapshot persistProject(Project project, @Nullable Project parent) {
@@ -158,18 +159,14 @@ Snapshot persist(Project project, Resource resource, @Nullable Resource parent)
     if (resource instanceof Project) {
       // should not occur, please use the method saveProject()
       snapshot = persistProject((Project) resource, (Project) parent);
-
-    } else if (resource instanceof Library) {
-      snapshot = persistLibrary(project.getAnalysisDate(), (Library) resource);
-
     } else {
       snapshot = persistFileOrDirectory(project, resource, parent);
     }
 
     return snapshot;
   }
 
-  private Snapshot persistLibrary(Date analysisDate, Library library) {
+  Snapshot persistLibrary(Date analysisDate, Library library) {
     ResourceModel model = findOrCreateModel(library, null);
     model = session.save(model);
     // TODO to be removed

sonar-batch/src/main/java/org/sonar/batch/phases/DefaultPhaseExecutor.java

@@ -46,7 +46,7 @@
 
 public final class DefaultPhaseExecutor implements PhaseExecutor {
 
-  public static final Logger LOGGER = LoggerFactory.getLogger(DefaultPhaseExecutor.class);
+  private static final Logger LOGGER = LoggerFactory.getLogger(DefaultPhaseExecutor.class);
 
   private final EventBus eventBus;
   private final Phases phases;

sonar-batch/src/main/java/org/sonar/batch/phases/PreviewPhaseExecutor.java

@@ -23,7 +23,6 @@
 import org.slf4j.LoggerFactory;
 import org.sonar.api.batch.SensorContext;
 import org.sonar.api.resources.Project;
-import org.sonar.batch.bootstrap.AnalysisMode;
 import org.sonar.batch.events.BatchStepEvent;
 import org.sonar.batch.events.EventBus;
 import org.sonar.batch.index.DefaultIndex;
@@ -36,7 +35,7 @@
 
 public final class PreviewPhaseExecutor implements PhaseExecutor {
 
-  public static final Logger LOGGER = LoggerFactory.getLogger(PreviewPhaseExecutor.class);
+  private static final Logger LOGGER = LoggerFactory.getLogger(PreviewPhaseExecutor.class);
 
   private final EventBus eventBus;
   private final Phases phases;
@@ -50,15 +49,14 @@ public final class PreviewPhaseExecutor implements PhaseExecutor {
   private final DefaultModuleFileSystem fs;
   private final QProfileVerifier profileVerifier;
   private final IssueExclusionsLoader issueExclusionsLoader;
-  private final AnalysisMode analysisMode;
   private final JsonReport jsonReport;
 
   public PreviewPhaseExecutor(Phases phases,
     MavenPluginsConfigurator mavenPluginsConfigurator, InitializersExecutor initializersExecutor,
     SensorsExecutor sensorsExecutor,
     SensorContext sensorContext, DefaultIndex index,
     EventBus eventBus, ProjectInitializer pi, FileSystemLogger fsLogger, JsonReport jsonReport, DefaultModuleFileSystem fs, QProfileVerifier profileVerifier,
-    IssueExclusionsLoader issueExclusionsLoader, AnalysisMode analysisMode) {
+    IssueExclusionsLoader issueExclusionsLoader) {
     this.phases = phases;
     this.mavenPluginsConfigurator = mavenPluginsConfigurator;
     this.initializersExecutor = initializersExecutor;
@@ -72,7 +70,6 @@ public PreviewPhaseExecutor(Phases phases,
     this.fs = fs;
     this.profileVerifier = profileVerifier;
     this.issueExclusionsLoader = issueExclusionsLoader;
-    this.analysisMode = analysisMode;
   }
 
   /**

sonar-batch/src/main/java/org/sonar/batch/scan/ProjectReactorValidator.java

@@ -76,12 +76,10 @@ public void validate(ProjectReactor reactor) {
   }
 
   private void preventAutomaticProjectCreationIfNeeded(ProjectReactor reactor) {
-    if (resourceDao != null) {
-      if (settings.getBoolean(CoreProperties.CORE_PREVENT_AUTOMATIC_PROJECT_CREATION)) {
-        String projectKey = reactor.getRoot().getKeyWithBranch();
-        if (resourceDao.findByKey(projectKey) == null) {
-          throw new SonarException(String.format("Unable to scan non-existing project \"%s\"", projectKey));
-        }
+    if (resourceDao != null && settings.getBoolean(CoreProperties.CORE_PREVENT_AUTOMATIC_PROJECT_CREATION)) {
+      String projectKey = reactor.getRoot().getKeyWithBranch();
+      if (resourceDao.findByKey(projectKey) == null) {
+        throw new SonarException(String.format("Unable to scan non-existing project \"%s\"", projectKey));
       }
     }
   }

sonar-batch/src/main/java/org/sonar/batch/scan/measure/MeasureValueCoder.java

@@ -37,7 +37,7 @@ class MeasureValueCoder implements ValueCoder {
   private final MetricFinder metricFinder;
   private final TechnicalDebtModel techDebtModel;
 
-  public MeasureValueCoder(MetricFinder metricFinder, TechnicalDebtModel techDebtModel) {
+  public MeasureValueCoder(MetricFinder metricFinder, @Nullable TechnicalDebtModel techDebtModel) {
     this.metricFinder = metricFinder;
     this.techDebtModel = techDebtModel;
   }

sonar-batch/src/main/java/org/sonar/batch/sensor/DefaultSensorStorage.java

@@ -95,14 +95,15 @@ public void store(Measure newMeasure) {
     org.sonar.api.measures.Measure measureToSave = new org.sonar.api.measures.Measure(m);
     setValueAccordingToMetricType(newMeasure, m, measureToSave);
     measureToSave.setFromCore(measure.isFromCore());
-    if (newMeasure.inputFile() != null) {
+    InputFile inputFile = newMeasure.inputFile();
+    if (inputFile != null) {
       Formula formula = newMeasure.metric() instanceof org.sonar.api.measures.Metric ?
         ((org.sonar.api.measures.Metric) newMeasure.metric()).getFormula() : null;
       if (formula instanceof SumChildDistributionFormula
         && !Scopes.isHigherThanOrEquals(Scopes.FILE, ((SumChildDistributionFormula) formula).getMinimumScopeToPersist())) {
         measureToSave.setPersistenceMode(PersistenceMode.MEMORY);
       }
-      File sonarFile = getFile(newMeasure.inputFile());
+      File sonarFile = getFile(inputFile);
       if (coverageExclusions.accept(sonarFile, measureToSave)) {
         sonarIndex.addMeasure(sonarFile, measureToSave);
       }

sonar-batch/src/main/java/org/sonar/batch/sensor/coverage/CoverageConstants.java

@@ -27,6 +27,9 @@
 
 public class CoverageConstants {
 
+  private CoverageConstants() {
+  }
+
   public static final Collection<Metric> COVERAGE_METRICS = ImmutableList.<Metric>of(CoreMetrics.LINES_TO_COVER, CoreMetrics.UNCOVERED_LINES, CoreMetrics.NEW_LINES_TO_COVER,
     CoreMetrics.NEW_UNCOVERED_LINES, CoreMetrics.CONDITIONS_TO_COVER, CoreMetrics.UNCOVERED_CONDITIONS,
     CoreMetrics.NEW_CONDITIONS_TO_COVER, CoreMetrics.NEW_UNCOVERED_CONDITIONS);

sonar-batch/src/main/java/org/sonar/batch/sensor/coverage/package-info.java

@@ -0,0 +1,21 @@
+/*
+ * SonarQube, open source software quality management tool.
+ * Copyright (C) 2008-2014 SonarSource
+ * mailto:contact AT sonarsource DOT com
+ *
+ * SonarQube is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 3 of the License, or (at your option) any later version.
+ *
+ * SonarQube is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+ */
+@javax.annotation.ParametersAreNonnullByDefault
+package org.sonar.batch.sensor.coverage;

sonar-batch/src/test/java/org/sonar/batch/components/TimeMachineConfigurationTest.java

@@ -22,7 +22,6 @@
 import org.junit.Before;
 import org.junit.Test;
 import org.sonar.api.database.model.Snapshot;
-import org.sonar.api.resources.Project;
 import org.sonar.jpa.test.AbstractDbUnitTestCase;
 
 import java.util.Date;
@@ -51,7 +50,7 @@ public void get_project_past_snapshot() {
 
     when(periodsDefinition.getRootProjectPastSnapshots()).thenReturn(newArrayList(projectPastSnapshot));
 
-    TimeMachineConfiguration timeMachineConfiguration = new TimeMachineConfiguration(getSession(), (Project) new Project("my:project"), periodsDefinition);
+    TimeMachineConfiguration timeMachineConfiguration = new TimeMachineConfiguration(getSession(), periodsDefinition);
     assertThat(timeMachineConfiguration.periods()).hasSize(1);
     assertThat(timeMachineConfiguration.periods().get(0).getDate()).isNotNull();
     assertThat(timeMachineConfiguration.getProjectPastSnapshots()).hasSize(1);
@@ -67,7 +66,7 @@ public void get_module_past_snapshot() {
 
     when(periodsDefinition.getRootProjectPastSnapshots()).thenReturn(newArrayList(projectPastSnapshot));
 
-    TimeMachineConfiguration timeMachineConfiguration = new TimeMachineConfiguration(getSession(), (Project) new Project("my:module"), periodsDefinition);
+    TimeMachineConfiguration timeMachineConfiguration = new TimeMachineConfiguration(getSession(), periodsDefinition);
     assertThat(timeMachineConfiguration.periods()).hasSize(1);
     assertThat(timeMachineConfiguration.periods().get(0).getDate()).isNotNull();
     assertThat(timeMachineConfiguration.getProjectPastSnapshots()).hasSize(1);
@@ -86,7 +85,7 @@ public void complete_past_snapshot_from_project_past_snapshot() {
 
     when(periodsDefinition.getRootProjectPastSnapshots()).thenReturn(newArrayList(projectPastSnapshot));
 
-    TimeMachineConfiguration timeMachineConfiguration = new TimeMachineConfiguration(getSession(), (Project) new Project("my:project").setId(1), periodsDefinition);
+    TimeMachineConfiguration timeMachineConfiguration = new TimeMachineConfiguration(getSession(), periodsDefinition);
     assertThat(timeMachineConfiguration.getProjectPastSnapshots()).hasSize(1);
     assertThat(timeMachineConfiguration.getProjectPastSnapshots().get(0).getProjectSnapshot().getId()).isEqualTo(1010);
     assertThat(timeMachineConfiguration.getProjectPastSnapshots().get(0).getIndex()).isEqualTo(1);
@@ -103,7 +102,7 @@ public void get_no_date_on_new_project() {
 
     when(periodsDefinition.getRootProjectPastSnapshots()).thenReturn(newArrayList(projectPastSnapshot));
 
-    TimeMachineConfiguration timeMachineConfiguration = new TimeMachineConfiguration(getSession(), new Project("my:project"), periodsDefinition);
+    TimeMachineConfiguration timeMachineConfiguration = new TimeMachineConfiguration(getSession(), periodsDefinition);
     assertThat(timeMachineConfiguration.periods()).hasSize(1);
     assertThat(timeMachineConfiguration.periods().get(0).getDate()).isNull();
   }