Merge pull request #57 from lequal/feat-tolerant-of-icode

Fix #55 i-Code exceptions are converted to issues

Author: begarco

.github/ISSUE_TEMPLATE/bug_report.md

@@ -7,27 +7,28 @@ assignees: ''
 
 ---
 
-**Describe the bug**
-A clear and concise description of what the bug is.
+#### Describe the bug
+> _A clear and concise description of what the bug is._
 
-**To reproduce**
-Steps to reproduce the behavior:
+#### To reproduce
+> _Steps to reproduce the behavior._
 1. Go to '...'
 2. Click on '....'
 3. Scroll down to '....'
 4. See error
 
-**Expected behavior**
-A clear and concise description of what you expected to happen.
+#### Expected behavior
+> _A clear and concise description of what you expected to happen._
 
-**Screenshots & log**
-If applicable, add screenshots to help explain your problem. Then, append SonarQube and i-Code log and **do not forget to obfuscate them**.
+#### Screenshots & log
+> _If applicable, add screenshots to help explain your problem. Then, append SonarQube and i-Code log and **do not forget to obfuscate them**._
 
-**User environment (please complete the following information):**
+#### User environment
+> _Please complete the following information._
  - OS: [e.g. Windows 10]
  - Java version: [e.g. 1.8]
  - i-Code version: [e.g. 3.1.0]
  - Plugin version: [e.g. 2.0.0]
 
-**Additional context**
-Add any other context about the problem here.
+#### Additional context
+> _Add any other context about the problem here._

.github/ISSUE_TEMPLATE/feature_request.md

@@ -7,14 +7,14 @@ assignees: ''
 
 ---
 
-**Is your feature request related to a problem? Please describe.**
-> A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+#### Is your feature request related to a problem? Please describe.**
+> _A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]_
 
-**Describe the solution you'd like**
-> A clear and concise description of what you want to happen.
+#### Describe the solution you'd like
+> _A clear and concise description of what you want to happen._
 
-**Describe alternatives you've considered**
-> A clear and concise description of any alternative solutions or features you've considered.
+#### Describe alternatives you've considered
+> _A clear and concise description of any alternative solutions or features you've considered._
 
-**Additional context**
-> Add any other context or screenshots about the feature request here.
+#### Additional context
+> _Add any other context or screenshots about the feature request here._

.github/ISSUE_TEMPLATE/question.md

@@ -7,19 +7,20 @@ assignees: ''
 
 ---
 
-> **Before posting a new question, please read the documentation](https://github.com/lequal/i-CodeCNES/wiki) and check [existing issues](https://github.com/lequal/sonar-icode-cnes-plugin/issues)**
+> _Before posting a new question, please read the documentation](https://github.com/lequal/i-CodeCNES/wiki) and check [existing issues](https://github.com/lequal/sonar-icode-cnes-plugin/issues)_
 
-**Describe what you need to know**
-> A clear and concise description of what your question is.
+#### Describe what you need to know
+> _A clear and concise description of what your question is._
 
-**Screenshots & log**
-> If applicable, add screenshots to help explain your problem. Then, append i-Code log and **do not forget to obfuscate them**.
+#### Screenshots & log
+> _If applicable, add screenshots to help explain your problem. Then, append i-Code log and **do not forget to obfuscate them**._
 
-**User environment (please complete the following information):**
+#### User environment 
+> _Please complete the following information._
  - OS: [e.g. Windows 10]
  - Java version: [e.g. 1.8]
  - i-Code version: [e.g. 3.1.0]
  - Plugin version: [e.g. 2.0.0]
 
-**Additional context**
+#### Additional context
 Add any other context about the problem here.

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,6 +1,6 @@
 ## Proposed changes
 
-> Describe the big picture of your changes here to communicate to the maintainers why we should accept this pull request. If it fixes a bug or resolves a feature request, be sure to link to that issue.
+> _Describe the big picture of your changes here to communicate to the maintainers why we should accept this pull request. If it fixes a bug or resolves a feature request, be sure to link to that issue._
 
 ## Types of changes
 

.travis.yml

@@ -2,13 +2,14 @@ language: java
 sudo: false
 install: true
 
+os: linux
+dist: xenial
+
 addons:
   sonarcloud:
     organization: "lequal"
 
-jdk:
-- openjdk8
-- openjdk11
+jdk: openjdk11
 
 script:
 - mvn clean org.jacoco:jacoco-maven-plugin:prepare-agent package sonar:sonar
@@ -23,13 +24,13 @@ notifications:
 
 deploy:
   provider: releases
-  api_key: "$GITHUB_TOKEN"
+  token: "$GITHUB_TOKEN"
   file_glob: true
   file: "target/sonar-icode-cnes-plugin-*.jar"
   skip_cleanup: true
-  name: "Sonar i-Code CNES plugin"
+  name: "Sonar i-Code CNES plugin version $TRAVIS_TAG"
   draft: true
   on:
     branch: master
     tags: true
-    jdk: 'openjdk11'
+    jdk: openjdk11

README.md

@@ -21,15 +21,16 @@ You can get i-Code CNES on GitHub: [lequal/i-CodeCNES](https://github.com/lequal
 - Run an analysis with *sonar-scanner*, *maven*, *gradle*, *msbuild*, etc.
 
 #### Run i-Code automatically
-This SonarQube plugin is now able to run automaticcaly an embedded version of i-Code. If you do not specify properties to run i-Code [manually](#run-i-Code-manually) or [from a specific version](#Run-a-specific-i-Code-version-through-sonaricode-plugin), embedded version of i-Code will be executed.
+This SonarQube plugin is now able to run automatically an embedded version of i-Code. If you do not specify properties to run i-Code [manually](#run-i-Code-manually) or [from a specific version](#Run-a-specific-i-Code-version-through-sonaricode-plugin), embedded version of i-Code will be executed.
 
 Here is the compatibility matrix of the plugin:
 
 | sonaricode version | embedded i-Code version | supported SonarQube version |
 |:------------------:|:-----------------------:|:---------------------------:|
 |       < 2.0.0      |           none          |          6.7.x              |
-|        2.0.0       |          4.0.0          |        7.9 -> 8.1           |
-|        2.0.1       |          4.0.0          |        7.9 -> 8.1           |
+|        2.0.0       |          4.0.0          |        7.9 -> 8.2           |
+|        2.0.1       |          4.0.0          |        7.9 -> 8.2           |
+|        2.0.2       |          4.1.0          |        7.9 -> 8.2           |
 
 #### Run i-Code manually
 If you need help to run i-Code please refer to the [official user manual](https://github.com/lequal/i-CodeCNES/wiki/User-Manual) or [i-Code issue tracker](https://github.com/lequal/i-CodeCNES/issues).
@@ -77,6 +78,8 @@ If you experienced a problem with the plugin please open an issue. Inside this i
 
 If you want to do a PR, please put inside of it the reason of this pull request. If this pull request fix an issue please insert the number of the issue or explain inside of the PR how to reproduce this issue.
 
+All details are available in [CONTRIBUTING](https://github.com/lequal/sonar-icode-cnes-plugin/CONTRIBUTING.md).
+
 ### Feedback and Support
 Contact : [email protected]
 

pom.xml

@@ -6,7 +6,7 @@
     <groupId>fr.cnes.sonar.plugins</groupId>
     <artifactId>sonar-icode-cnes-plugin</artifactId>
     <packaging>sonar-plugin</packaging>
-    <version>2.0.1</version>
+    <version>2.0.2</version>
 
     <name>Sonar i-Code CNES plugin</name>
 
@@ -22,7 +22,6 @@
         </license>
     </licenses>
 
-    <!-- optional -->
     <organization>
         <name>CNES</name>
         <url>http://cnes.fr</url>
@@ -52,8 +51,8 @@
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <jdk.version>1.8</jdk.version>
-        <jdk.min.version>1.8</jdk.min.version>
-        <jdk.max.version>1.8</jdk.max.version>
+        <jdk.min.version>11</jdk.min.version>
+        <jdk.max.version>11</jdk.max.version>
         <maven.compiler.source>1.8</maven.compiler.source>
         <maven.compiler.target>1.8</maven.compiler.target>
         <sonar.apiVersion>6.7.7</sonar.apiVersion>
@@ -67,6 +66,7 @@
         <sonar.pluginKey>icode</sonar.pluginKey>
         <sonar.pluginClass>fr.cnes.sonar.plugins.icode.ICodePlugin</sonar.pluginClass>
         <sonar.pluginUrl>https://github.com/lequal/sonar-icode-cnes-plugin</sonar.pluginUrl>
+        <sonar.pluginSourcesUrl>https://github.com/lequal/sonar-icode-cnes-plugin</sonar.pluginSourcesUrl>
         <sonar.pluginOrganizationName>CNES</sonar.pluginOrganizationName>
         <sonar.sources>src/main/java</sonar.sources>
         <sonar.test>src/test/java</sonar.test>
@@ -89,7 +89,7 @@
         <dependency>
             <groupId>com.github.lequal.i-CodeCNES</groupId>
             <artifactId>icode-library</artifactId>
-            <version>4.0.0</version>
+            <version>v4.1.0</version>
         </dependency>
         <dependency>
             <groupId>commons-lang</groupId>

src/main/java/fr/cnes/sonar/plugins/icode/ICodePlugin.java

@@ -28,8 +28,6 @@
 
 /**
  * This class is the entry point for all extensions.
- * 
- * @author lequal
  */
 public class ICodePlugin implements Plugin {
 

src/main/java/fr/cnes/sonar/plugins/icode/check/ICodeSensor.java

@@ -18,7 +18,6 @@
 
 import fr.cnes.icode.Analyzer;
 import fr.cnes.icode.data.CheckResult;
-import fr.cnes.icode.exception.JFlexException;
 import fr.cnes.icode.services.languages.LanguageService;
 import fr.cnes.sonar.plugins.icode.exceptions.ICodeException;
 import fr.cnes.sonar.plugins.icode.languages.Fortran77Language;
@@ -75,7 +74,7 @@ public void describe(final SensorDescriptor sensorDescriptor) {
         sensorDescriptor.onlyOnLanguages(ShellLanguage.KEY, Fortran77Language.KEY, Fortran90Language.KEY);
 
         // Defines sensor name
-        sensorDescriptor.name(getClass().getName());
+        sensorDescriptor.name("Sonar i-Code");
 
         // Only main files are concerned, not tests.
         sensorDescriptor.onlyOnFileType(InputFile.Type.MAIN);
@@ -130,13 +129,13 @@ protected void executeExternalResultsImport(final SensorContext sensorContext) {
         final ActiveRules activeRules = sensorContext.activeRules();
 
         // Report files found in file system and corresponding to SQ property.
-        final List<String> reportFiles = getReportFiles(config, fileSystem);
+        final List<File> reportFiles = getReportFiles(config, fileSystem);
 
         // If exists, unmarshal each xml result file.
-        for(final String reportPath : reportFiles) {
+        for(final File reportFile : reportFiles) {
             try {
-                // Unmarshall the xml.
-                final FileInputStream file = new FileInputStream(reportPath);
+                // Unmarshal the xml.
+                final FileInputStream file = new FileInputStream(reportFile);
                 final AnalysisProject analysisProject = (AnalysisProject) XmlHandler.unmarshal(file, AnalysisProject.class);
                 // Retrieve file in a SonarQube format.
                 final Map<String, InputFile> scannedFiles = getScannedFiles(fileSystem, analysisProject);
@@ -178,34 +177,30 @@ private void executeEmbeddedICode(final SensorContext sensorContext) {
         final HashSet<File> files = new HashSet<>();
         final HashMap<String,InputFile> filesMap = new HashMap<>();
 
-        try {
-            // Gather all files in a Set.
-            for(final InputFile inputFile : inputFiles) {
-                files.add(inputFile.file());
-                filesMap.put(inputFile.file().getPath(), inputFile);
-            }
+        // Gather all files in a Set.
+        for(final InputFile inputFile : inputFiles) {
+            files.add(new File(inputFile.uri()));
+            filesMap.put(inputFile.uri().getPath(), inputFile);
+        }
 
-            // Run all checkers on all files.
-            final List<CheckResult> results = analyzer.stableCheck(files, LanguageService.getLanguagesIds(), null);
-
-            // Add each issue to SonarQube.
-            for(final CheckResult result : results) {
-                if(isRuleActive(activeRules, result.getName())) { // manage active rules
-                    saveIssue(sensorContext, result);
-                } else if (ICodeMetricsProcessor.isMetric(result.getName())) { // manage trivial measures
-                    ICodeMetricsProcessor.saveMeasure(sensorContext, result);
-                } else { // log ignored data
-                    LOGGER.info(String.format(
-                            "An issue for rule '%s' was detected by i-Code but this rule is deactivated in current analysis.",
-                            result.getName()));
-                }
+        // Run all checkers on all files.
+        final List<CheckResult> results = analyzer.stableCheck(files, LanguageService.getLanguagesIds(), null);
+
+        // Add each issue to SonarQube.
+        for(final CheckResult result : results) {
+            if(isRuleActive(activeRules, result.getName())) { // manage active rules
+                saveIssue(sensorContext, result);
+            } else if (ICodeMetricsProcessor.isMetric(result.getName())) { // manage trivial measures
+                ICodeMetricsProcessor.saveMeasure(sensorContext, result);
+            } else { // log ignored data
+                LOGGER.info(String.format(
+                        "An issue for rule '%s' was detected by i-Code but this rule is deactivated in current analysis.",
+                        result.getName()));
             }
+        }
 
-            ICodeMetricsProcessor.saveExtraMeasures(sensorContext, filesMap, results);
+        ICodeMetricsProcessor.saveExtraMeasures(sensorContext, filesMap, results);
 
-        } catch (final JFlexException e) {
-            LOGGER.warn(e.getMessage(), e);
-        }
     }
 
     /**
@@ -220,7 +215,7 @@ private void executeExternalICode(final SensorContext sensorContext) {
         final FilePredicates predicates = fileSystem.predicates();
         final Iterable<InputFile> inputFiles = fileSystem.inputFiles(predicates.hasType(InputFile.Type.MAIN));
         final StringBuilder files = new StringBuilder();
-        inputFiles.forEach(file -> files.append(file.file().getPath()).append(" "));
+        inputFiles.forEach(file -> files.append(file.uri().getPath()).append(" "));
         final String executable = config.get(ICodePluginProperties.ICODE_PATH_KEY).orElse(ICodePluginProperties.ICODE_PATH_DEFAULT);
         final String outputFile = config.get(ICodePluginProperties.REPORT_PATH_KEY).orElse(ICodePluginProperties.REPORT_PATH_DEFAULT);
         final String outputPath = Paths.get(sensorContext.fileSystem().baseDir().toString(),outputFile).toString();
@@ -263,7 +258,9 @@ static void saveIssue(final SensorContext sensorContext, final CheckResult resul
         final FileSystem fileSystem = sensorContext.fileSystem();
         final FilePredicates predicates = fileSystem.predicates();
         final NewIssue issue = sensorContext.newIssue();
-        final InputFile file = fileSystem.inputFile(predicates.hasPath(result.getFile().getPath()));
+        final String fileToFind = result.getFile().getPath();
+        final FilePredicate predicate = predicates.or(predicates.hasPath(fileToFind), predicates.hasRelativePath(fileToFind));
+        final InputFile file = fileSystem.inputFile(predicate);
         if(Objects.nonNull(file)) {
             final String repositoryKey = ICodeRulesDefinition.getRepositoryKeyForLanguage(file.language());
             final RuleKey ruleKey = RuleKey.of(repositoryKey, result.getName());
@@ -335,41 +332,39 @@ protected Map<String, InputFile> getScannedFiles(final FileSystem fileSystem, fi
         // Looks for each file in file system, print an error if not found.
         for(final AnalysisFile file : files) {
             // Checks if the file system contains a file with corresponding path (relative or absolute).
-            FilePredicate predicate = fileSystem.predicates().hasPath(file.getFileName());
-            InputFile inputFile = fileSystem.inputFile(predicate);
+            final String fileToFind = new File(fileSystem.baseDir(), file.getFileName()).getPath();
+            final FilePredicate predicate = fileSystem.predicates().hasRelativePath(fileToFind);
+            final InputFile inputFile = fileSystem.inputFile(predicate);
             if(inputFile!=null) {
                 result.put(file.getFileName(), inputFile);
             } else {
-                LOGGER.error(String.format(
-                        "The source file '%s' was not found.",
-                        file.getFileName()
-                ));
+                LOGGER.error(String.format("The source file '%s' was not found.", file.getFileName()));
             }
         }
 
         return result;
     }
 
     /**
-     * Returns a list of processable result file's path.
+     * Returns a list of processable result files.
      *
      * @param config Configuration of the analysis where properties are put.
      * @param fileSystem The current file system.
      * @return Return a list of path 'findable' in the file system.
      */
-    private List<String> getReportFiles(final Configuration config, final FileSystem fileSystem) {
+    protected List<File> getReportFiles(final Configuration config, final FileSystem fileSystem) {
         // Contains the result to be returned.
-        final List<String> result = new ArrayList<>();
+        final List<File> result = new ArrayList<>();
 
         // Retrieves the non-verified path list from the SonarQube property.
         final String[] pathArray = config.getStringArray(ICodePluginProperties.REPORT_PATH_KEY);
 
         // Check if each path is known by the file system and add it to the processable path list,
         // otherwise print a warning and ignore this result file.
-        for(String path : pathArray) {
+        for(final String path : pathArray) {
             final File file = new File(fileSystem.baseDir(), path);
             if(file.exists() && file.isFile()) {
-                result.add(path);
+                result.add(file);
                 LOGGER.info(String.format("Results file %s has been found and will be processed.", path));
             } else {
                 LOGGER.warn(String.format("Results file %s has not been found and wont be processed.", path));