include corpus name and function parameters in the url. change bucket name in the report

src/main/java/de/uni_hamburg/corpora/server/CorpusChecker.java

@@ -5,6 +5,8 @@ import java.io.File;
 import java.io.FileWriter;
 import java.io.IOException;
 import java.lang.Thread;
+
+import com.fasterxml.jackson.databind.JsonNode;
 import jakarta.ws.rs.GET;
 import jakarta.ws.rs.Path;
 import jakarta.ws.rs.Produces;
@@ -17,12 +19,16 @@ import jakarta.ws.rs.core.Response;
 
 import java.lang.reflect.InvocationTargetException;
 import java.net.URISyntaxException;
+import java.net.URL;
+import java.time.LocalDateTime;
+import java.time.format.DateTimeFormatter;
 import java.util.*;
 
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import de.uni_hamburg.corpora.*;
 
+import org.apache.commons.io.FileUtils;
 import org.exmaralda.partitureditor.jexmaralda.JexmaraldaException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -30,7 +36,7 @@ import org.xml.sax.SAXException;
 
 /**
  * @author bba1792 Dr. Herbert Lange
- * @version 20210708
+ * @version 20220405
  * Worker thread for the corpus checker
  */
 class CorpusThread extends Thread {
@@ -38,6 +44,7 @@ class CorpusThread extends Thread {
     private final Logger logger = LoggerFactory.getLogger(this.getClass().getName());
 
     de.uni_hamburg.corpora.Report report = new de.uni_hamburg.corpora.Report();
+    String corpusName;
     String inFile ;
     String functionNames;
     String outFile;
@@ -45,8 +52,9 @@ class CorpusThread extends Thread {
     String token; // Identifier to be sent back to the server to identify and authorize task
     String callbackUrl; // URL to be called when the task is done, giving an empty string means skipping the callback
 
-    CorpusThread(String infile, String outfile, String functions, Properties properties, String token,
+    CorpusThread(String name, String infile, String outfile, String functions, Properties properties, String token,
                  String callbackUrl) {
+        this.corpusName=name;
         if (infile.equals("tmp"))
             this.inFile = System.getProperty("java.io.tmpdir") + "/corpus-files";
         else
@@ -59,17 +67,28 @@ class CorpusThread extends Thread {
             this.outFile = outfile;
         this.token = token ;
         this.callbackUrl = callbackUrl ;
+        logger.info("Input: " + this.inFile + " output: " + this.outFile + " functions: " + functions + " params: " +
+                this.props + " token: " + this.token + " callback: " + this.callbackUrl);
     }
 
     public void run() {
         ArrayList<String> functionList = new ArrayList<>(Arrays.asList(functionNames.split(",")));
         Set<String> allFunctions = CorpusServices.getCorpusFunctions() ;
         CorpusIO cio = new CorpusIO();
+        report.addNote("CorpusWebServices","Starting run at " +
+                DateTimeFormatter.ofPattern("yyyy/MM/dd HH:mm:ss").format(LocalDateTime.now()));
 
         try {
             // Create corpus from given input file/folder
-            Corpus corpus = new Corpus(cio.read(new File(inFile).toURI().toURL(),report)) ;
+            Corpus corpus;
+            if (corpusName != null && !corpusName.isEmpty()) {
+                URL baseUrl = new File(inFile).toURI().toURL();
+                corpus = new Corpus(corpusName,baseUrl,cio.read(baseUrl,report)) ;
+            }
+            else
+                corpus = new Corpus(cio.read(new File(inFile).toURI().toURL(),report)) ;
             logger.info("Loaded " + corpus.getCorpusData().size() + " corpus files");
+            logger.info("Got report: " + report.getFullReports());
             // For all functions to be applied, get their canonical name and create an object for them
             Set<CorpusFunction> functions = new HashSet<>() ;
             for (String function : functionList) {
@@ -84,24 +103,24 @@ class CorpusThread extends Thread {
                         }
                         catch (IllegalArgumentException | NoSuchMethodException | InstantiationException | InvocationTargetException | IllegalAccessException e) {
                             logger.warn("Error creating {}", canonical);
-                            report.addWarning("CorpusService", "Test " + function + " cannot be created");
+                            report.addWarning("CorpusWebServices", "Test " + function + " cannot be created");
 //                            e.printStackTrace();
                         }
                     }
                 }
                 if (!found) {
                     // Warn if we could not find the function
-                    report.addWarning("CorpusService", "Test " + function + " is not available");
+                    report.addWarning("CorpusWebServices", "Test " + function + " is not available");
                     logger.warn("Function {} is not available in corpus services", function);
 
                 }
             }
             for (CorpusFunction f : functions) {
                 logger.warn("Running function {}", f.getFunction());
-                report.addNote("CorpusService", "Run test " + f.getFunction());
+                report.addNote("CorpusWebServices", "Run test " + f.getFunction());
                 de.uni_hamburg.corpora.Report result = f.execute(corpus);
                 report.merge(result);
-                report.addNote("CorpusService", "Finish test " + f.getFunction());
+                report.addNote("CorpusWebServices", "Finish test " + f.getFunction());
                 logger.warn("Done with function {}", f.getFunction());
             }
         } catch (URISyntaxException | ClassNotFoundException | IOException | SAXException | JexmaraldaException e) {
@@ -109,7 +128,8 @@ class CorpusThread extends Thread {
         }
 
         logger.info("Done with all functions");
-        report.addNote("CorpusService","Finished all tests");
+        report.addNote("CorpusWebServices","Finished all tests at " +
+                DateTimeFormatter.ofPattern("yyyy/MM/dd HH:mm:ss").format(LocalDateTime.now()));
         logger.info("Creating report");
         // Get summary
         HashMap<ReportItem.Severity,Integer> summary = CorpusServices.generateSummary(report);
@@ -181,7 +201,8 @@ public class CorpusChecker {
 
     @GET
     @Produces(MediaType.TEXT_PLAIN)
-    public Response checkCorpus(@QueryParam("input") String input,
+    public Response checkCorpus(@QueryParam("name") String name,
+                                @QueryParam("input") String input,
                                 @QueryParam("output") String output,
                                 @QueryParam("functions") String functions,
                                 @QueryParam("params") String paramStr,
@@ -220,11 +241,25 @@ public class CorpusChecker {
             return Response.status(400).entity("400 - " + errorMsg).build();
         }
         Properties params = new Properties();
-        if (paramStr != null) {
+        if (paramStr != null && !paramStr.equals("{}")) {
             ObjectMapper mapper = new ObjectMapper();
-            params.putAll(mapper.convertValue(paramStr,Map.class));
+            try {
+                JsonNode node = mapper.readTree(paramStr);
+                // Copy the jason data into the properties
+                for (Iterator<Map.Entry<String, JsonNode>> it = node.fields(); it.hasNext(); ) {
+                    Map.Entry<String, JsonNode> e = it.next();
+                    params.put(e.getKey(),e.getValue().textValue());
+                }
+                logger.info(params.toString());
+                //params.putAll(mapper.convertValue(paramStr,Map.class));
+            } catch (JsonProcessingException e) {
+                e.printStackTrace();
+            }
+        }
+        else {
+            params = new Properties();
         }
-        CorpusThread ct = new CorpusThread(input,output,functions,params,token,callbackUrl);
+        CorpusThread ct = new CorpusThread(name,input,output,functions,params,token,callbackUrl);
         ct.start();
         Main.addThread(ct);
         return Response.ok().entity("Executing " + functions + " on " + input +