cleanup elton reporting format

globalbioticinteractions · Sep 5, 2018 · 28f8d20 · 28f8d20
1 parent c62bd8c
commit 28f8d20
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Showing 3 changed files with 10 additions and 12 deletions.
diff --git a/src/main/java/org/globalbioticinteractions/elton/cmd/CmdCheck.java b/src/main/java/org/globalbioticinteractions/elton/cmd/CmdCheck.java
@@ -17,6 +17,7 @@
 import org.eol.globi.service.DatasetFinder;
 import org.eol.globi.service.DatasetFinderGitHubArchiveMaster;
 import org.eol.globi.service.DatasetFinderProxy;
+import org.eol.globi.util.CSVTSVUtil;
 import org.globalbioticinteractions.elton.util.NodeFactoryNull;
 import org.globalbioticinteractions.elton.util.SpecimenNull;
 
@@ -77,7 +78,7 @@ private void addUntilFull(String message, Set<String> msgs) {
             }
 
             String msgForRepo(String message) {
-                return "[" + repoName + "]: [" + message + "]";
+                return repoName + "\t" + message;
             }
         });
 
@@ -87,10 +88,11 @@ String msgForRepo(String message) {
                 throw new StudyImporterException(getResultMsg(repoName, warnings, errors) + ", please check your log.");
             }
         } finally {
-            infos.forEach(LOG::info);
-            warnings.forEach(LOG::warn);
-            errors.forEach(LOG::error);
-            System.out.println("\n" + getResultMsg(repoName, warnings, errors));
+            infos.forEach(System.out::println);
+            warnings.forEach(System.out::println);
+            errors.forEach(System.out::println);
+            System.out.println(repoName + "\t" + errors.size() + " error(s)");
+            System.out.println(repoName + "\t" + warnings.size() + " warning(s)");
         }
     }
 
@@ -111,10 +113,10 @@ private static class NodeFactoryLogging extends NodeFactoryNull {
             @Override
             public void interactsWith(Specimen target, InteractType type, Location centroid) {
                 if (counter.get() > 0 && counter.get() % 1000 == 0) {
-                    System.out.println();
+                    System.err.println();
                 }
                 if (counter.get() % 10 == 0) {
-                    System.out.print(".");
+                    System.err.print(".");
                 }
                 counter.getAndIncrement();
             }

diff --git a/src/main/java/org/globalbioticinteractions/elton/cmd/CmdLine.java b/src/main/java/org/globalbioticinteractions/elton/cmd/CmdLine.java
@@ -27,9 +27,6 @@ public static void run(String[] args) throws Throwable {
             CmdLine.run(jc.getCommands().get(jc.getParsedCommand()));
         } catch (Throwable ex) {
             LOG.error("unexpected exception", ex);
-            StringBuilder out = new StringBuilder();
-            jc.usage(out);
-            System.err.append(out.toString());
             throw ex;
         }
     }

diff --git a/src/main/resources/log4j.properties b/src/main/resources/log4j.properties
@@ -7,5 +7,4 @@ log4j.appender.stdout=org.apache.log4j.ConsoleAppender
 log4j.appender.stdout.Target=System.err
 log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
 
-# Print the date in ISO 8601 format
-log4j.appender.stdout.layout.ConversionPattern=%d [%t] %-5p %c - %m%n
+log4j.appender.stdout.layout.ConversionPattern=%m%n