Merge pull request #56 from phyloref/replace-stderr-with-log4j

This PR replaces most of our System.err calls with calls to the SLF4J logging system. This will make it easier to add debugging information in the future, when we can use verbose flags (`-v`, `-vv`) to provide increasingly detailed debugging information (#31). Closes #51.
phyloref · Apr 21, 2020 · 2041cb6 · 2041cb6
2 parents e0162f9 + a273586
commit 2041cb6
Show file tree

Hide file tree

Showing 6 changed files with 47 additions and 27 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,7 @@
 Based on the suggestion at https://keepachangelog.com/en/1.0.0/.
 
 ## [Unreleased]
+- Replaced `System.err` and `System.out` with calls to SLF4J (#51).
 - Display the filename of the input file in the testing output.
 - Added a "resolve" command that resolves phylorefs in input ontologies (in OWL
   or JSON-LD) and returns the result as a JSON string (#52).

diff --git a/src/main/java/org/phyloref/jphyloref/JPhyloRef.java b/src/main/java/org/phyloref/jphyloref/JPhyloRef.java
@@ -15,12 +15,17 @@
 import org.phyloref.jphyloref.helpers.ReasonerHelper;
 import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
 import org.semanticweb.owlapi.util.VersionInfo;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * Main class for JPhyloRef. Contains a list of Commands, as well as the code for determining which
  * Command to execute.
  */
 public class JPhyloRef {
+  /** Set up a logger to use for providing logging. */
+  private static final Logger logger = LoggerFactory.getLogger(JPhyloRef.class);
+
   /** Version of JPhyloRef. */
   public static final String VERSION = "0.2-SNAPSHOT";
 
@@ -51,7 +56,7 @@ public int execute(String[] args) {
     try {
       cmdLine = new DefaultParser().parse(opts, args);
     } catch (ParseException ex) {
-      System.err.println("Could not parse command line options: " + ex);
+      logger.error("Could not parse command line options: {}", ex.toString());
       return 1;
     }
 
@@ -77,7 +82,7 @@ public int execute(String[] args) {
       }
 
       // Could not find any command.
-      System.err.println("Error: command '" + command + "' has not been implemented.");
+      logger.error("Command '{}' has not been implemented.", command);
       return 1;
     }
   }

diff --git a/src/main/java/org/phyloref/jphyloref/commands/ResolveCommand.java b/src/main/java/org/phyloref/jphyloref/commands/ResolveCommand.java
@@ -25,6 +25,8 @@
 import org.semanticweb.owlapi.reasoner.OWLReasoner;
 import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
 import org.semanticweb.owlapi.util.AutoIRIMapper;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * Resolve an ontology of phyloreferences provided on the command line, and report on the resolution
@@ -38,6 +40,9 @@
  * @author Gaurav Vaidya <[email protected]>
  */
 public class ResolveCommand implements Command {
+  /** Set up a logger to use for providing logging. */
+  private static final Logger logger = LoggerFactory.getLogger(ResolveCommand.class);
+
   /**
    * This command is named "resolve". It should be invoked as "java -jar jphyloref.jar resolve ..."
    */
@@ -115,21 +120,21 @@ public int execute(CommandLine cmdLine) throws RuntimeException {
       try {
         inputStreamToReadFrom = new FileInputStream(inputFilename);
       } catch (FileNotFoundException ex) {
-        System.err.println("Could not open input file '" + inputFilename + "': " + ex);
+        logger.error("Could not open input file '{}': {}", inputFilename, ex);
         return 1;
       }
     }
 
     // Report the name of the file being tested.
-    System.err.println("Input: " + inputFilename);
+    logger.info("Input: {}", inputFilename);
 
     // Set up an OWL Ontology Manager to work with.
     OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
 
     // Is purl.obolibrary.org down? No worries, you can access local copies
     // of your ontologies in the 'ontologies/' folder.
     AutoIRIMapper mapper = new AutoIRIMapper(new File("ontologies"), true);
-    System.err.println("Found local ontologies: " + mapper.getOntologyIRIs());
+    logger.info("Found local ontologies: {}", mapper.getOntologyIRIs());
     manager.addIRIMapper(mapper);
 
     // Is this a JSON or JSON-LD file?

diff --git a/src/main/java/org/phyloref/jphyloref/commands/TestCommand.java b/src/main/java/org/phyloref/jphyloref/commands/TestCommand.java
@@ -34,6 +34,8 @@
 import org.semanticweb.owlapi.search.EntitySearcher;
 import org.semanticweb.owlapi.util.AutoIRIMapper;
 import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.tap4j.model.Comment;
 import org.tap4j.model.Directive;
 import org.tap4j.model.Plan;
@@ -54,6 +56,9 @@
  * @author Gaurav Vaidya <[email protected]>
  */
 public class TestCommand implements Command {
+  /** Set up a logger to use for providing logging. */
+  private static final Logger logger = LoggerFactory.getLogger(TestCommand.class);
+
   /** This command is named "test". It should be invoked as "java -jar jphyloref.jar test ..." */
   @Override
   public String getName() {
@@ -119,21 +124,21 @@ public int execute(CommandLine cmdLine) throws RuntimeException {
       try {
         inputStreamToReadFrom = new FileInputStream(inputFilename);
       } catch (FileNotFoundException ex) {
-        System.err.println("Could not open input file '" + inputFilename + "': " + ex);
+        logger.error("Could not open input file '{}': {}", inputFilename, ex);
         return 1;
       }
     }
 
     // Report the name of the file being tested.
-    System.err.println("Input: " + inputFilename);
+    logger.info("Input: {}", inputFilename);
 
     // Set up an OWL Ontology Manager to work with.
     OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
 
     // Is purl.obolibrary.org down? No worries, you can access local copies
     // of your ontologies in the 'ontologies/' folder.
     AutoIRIMapper mapper = new AutoIRIMapper(new File("ontologies"), true);
-    System.err.println("Found local ontologies: " + mapper.getOntologyIRIs());
+    logger.info("Found local ontologies: {}", mapper.getOntologyIRIs());
     manager.addIRIMapper(mapper);
 
     // Is this a JSON or JSON-LD file?
@@ -157,15 +162,15 @@ public int execute(CommandLine cmdLine) throws RuntimeException {
         ontology = manager.loadOntologyFromOntologyDocument(inputStreamToReadFrom);
       }
     } catch (OWLOntologyCreationException ex) {
-      System.err.println("Could not create ontology '" + inputFilename + "': " + ex);
+      logger.error("Could not create ontology '{}': {}", inputFilename, ex);
       return 1;
     } catch (IOException ex) {
-      System.err.println("Could not read and load ontology '" + inputFilename + "': " + ex);
+      logger.error("Could not read and load ontology '{}': {}", inputFilename, ex);
       return 1;
     }
 
     // Ontology loaded.
-    System.err.println("Loaded ontology: " + ontology);
+    logger.info("Loaded ontology: {}", ontology);
 
     // Reason over the loaded ontology -- but only if the user wants that!
     // Set up an OWLReasoner to work with.
@@ -175,7 +180,7 @@ public int execute(CommandLine cmdLine) throws RuntimeException {
 
     // Get a list of all phyloreferences.
     Set<OWLClass> phylorefs = PhylorefHelper.getPhyloreferences(ontology, reasoner);
-    System.err.println("Phyloreferences identified: " + phylorefs);
+    logger.info("Phyloreferences identified: {}", phylorefs);
 
     // Okay, time to start testing! Each phyloreference counts as one test.
     // TAP (https://testanything.org/) can be read by downstream software

diff --git a/src/main/java/org/phyloref/jphyloref/commands/WebserverCommand.java b/src/main/java/org/phyloref/jphyloref/commands/WebserverCommand.java
@@ -36,6 +36,8 @@
 import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
 import org.semanticweb.owlapi.util.AutoIRIMapper;
 import org.semanticweb.owlapi.util.VersionInfo;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * Sets up a webserver that allows reasoning over phyloreferences over HTTP.
@@ -50,6 +52,9 @@
  * @author Gaurav Vaidya <[email protected]>
  */
 public class WebserverCommand implements Command {
+  /** Set up a logger to use for providing logging. */
+  private static final Logger logger = LoggerFactory.getLogger(WebserverCommand.class);
+
   /**
    * This command is named "webserver". It should be invoked as "java -jar jphyloref.jar webserver
    * ..."
@@ -97,7 +102,7 @@ public int execute(CommandLine cmdLine) throws RuntimeException {
       Webserver webserver = new Webserver(this, hostname, port, cmdLine);
       while (webserver.isAlive()) {}
     } catch (IOException ex) {
-      System.err.println("An error occurred while running webserver: " + ex);
+      logger.error("An error occurred while running webserver: {}", ex.toString());
     }
 
     return 0;
@@ -128,15 +133,12 @@ public Webserver(WebserverCommand cmd, String hostname, int port, CommandLine cm
       this.cmdLine = cmdLine;
 
       start(NanoHTTPD.SOCKET_READ_TIMEOUT, false);
-      System.out.println(
-          "Webserver started with reasoner "
-              + ReasonerHelper.getReasonerNameAndVersion(
-                  ReasonerHelper.getReasonerFactoryFromCmdLine(cmdLine))
-              + ". Try accessing it at http://"
-              + hostname
-              + ":"
-              + port
-              + "/");
+      logger.info(
+          "Webserver started with reasoner {}. Try accessing it at http://{}:{}/",
+          ReasonerHelper.getReasonerNameAndVersion(
+              ReasonerHelper.getReasonerFactoryFromCmdLine(cmdLine)),
+          hostname,
+          port);
     }
 
     /** Respond to a request for reasoning over a JSON-LD file (/reason). */
@@ -150,7 +152,7 @@ public JSONObject serveReason(File jsonldFile)
       // Is purl.obolibrary.org down? No worries, you can access local copies
       // of your ontologies in the 'ontologies/' folder.
       AutoIRIMapper mapper = new AutoIRIMapper(new File("ontologies"), true);
-      System.err.println("Found local ontologies: " + mapper.getOntologyIRIs());
+      logger.info("Found local ontologies: {}", mapper.getOntologyIRIs());
       manager.addIRIMapper(mapper);
 
       // Setup ready; parse the file!
@@ -204,7 +206,7 @@ public JSONObject serveReason(File jsonldFile)
       reasoner.dispose();
 
       // Log reasoning results.
-      System.err.println("Phyloreferencing reasoning results: " + nodesPerPhylorefAsString);
+      logger.info("Phyloreferencing reasoning results: {}", nodesPerPhylorefAsString);
 
       // Record phyloreferences and matching nodes in JSON response.
       response.put("phylorefs", nodesPerPhylorefAsString);
@@ -267,7 +269,7 @@ public Response serve(IHTTPSession session) {
       String path = session.getUri();
       Map<String, List<String>> params = session.getParameters();
 
-      System.out.println(">> Request received to '" + path + "': " + params);
+      logger.info(">> Request received to '{}': {}", path, params);
 
       if (path.equals("/reason")) {
         // If it is an OPTIONS request, it's probably someone wanting a

diff --git a/src/test/java/org/phyloref/jphyloref/AppTest.java b/src/test/java/org/phyloref/jphyloref/AppTest.java
@@ -73,7 +73,9 @@ void phylorefCommandLineUnknown() {
 
     try {
       assertEquals("", output.toString("UTF-8"));
-      assertEquals("Error: command 'unknown' has not been implemented.\n", error.toString("UTF-8"));
+      assertEquals(
+          "[main] ERROR org.phyloref.jphyloref.JPhyloRef - Command 'unknown' has not been implemented.\n",
+          error.toString("UTF-8"));
     } catch (UnsupportedEncodingException ex) {
       throw new RuntimeException("'UTF-8' is not supported as an encoding: " + ex);
     }
@@ -89,7 +91,7 @@ void phylorefCommandLineMalformed() {
     try {
       assertEquals("", output.toString("UTF-8"));
       assertEquals(
-          "Could not parse command line options: org.apache.commons.cli.UnrecognizedOptionException: Unrecognized option: ----\n",
+          "[main] ERROR org.phyloref.jphyloref.JPhyloRef - Could not parse command line options: org.apache.commons.cli.UnrecognizedOptionException: Unrecognized option: ----\n",
           error.toString("UTF-8"));
     } catch (UnsupportedEncodingException ex) {
       throw new RuntimeException("'UTF-8' is not supported as an encoding: " + ex);