diff --git a/karma-commands/commands-alignment-openrdf/.factorypath b/karma-commands/commands-alignment-openrdf/.factorypath
new file mode 100644
index 000000000..262a26f93
--- /dev/null
+++ b/karma-commands/commands-alignment-openrdf/.factorypath
@@ -0,0 +1,121 @@
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diff --git a/karma-commands/commands-alignment/.factorypath b/karma-commands/commands-alignment/.factorypath
new file mode 100644
index 000000000..83206d262
--- /dev/null
+++ b/karma-commands/commands-alignment/.factorypath
@@ -0,0 +1,94 @@
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diff --git a/karma-commands/commands-bloom/.factorypath b/karma-commands/commands-bloom/.factorypath
new file mode 100644
index 000000000..bc0b84e19
--- /dev/null
+++ b/karma-commands/commands-bloom/.factorypath
@@ -0,0 +1,158 @@
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diff --git a/karma-commands/commands-common/.factorypath b/karma-commands/commands-common/.factorypath
new file mode 100644
index 000000000..13a1a2b20
--- /dev/null
+++ b/karma-commands/commands-common/.factorypath
@@ -0,0 +1,78 @@
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diff --git a/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/history/CommandHistoryUtil.java b/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/history/CommandHistoryUtil.java
index 549587ff5..bb36175fa 100644
--- a/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/history/CommandHistoryUtil.java
+++ b/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/history/CommandHistoryUtil.java
@@ -10,7 +10,8 @@
import java.util.Map;
import java.util.Set;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
import org.json.JSONArray;
import edu.isi.karma.controller.command.Command;
@@ -36,7 +37,7 @@ public class CommandHistoryUtil {
private Workspace workspace;
private String worksheetId;
Map commandFactoryMap;
- static Logger logger = Logger.getLogger(CommandHistoryUtil.class);
+ static Logger logger = LogManager.getLogger(CommandHistoryUtil.class.getName());
public CommandHistoryUtil(List commands, Workspace workspace, String worksheetId) {
this.worksheetId = worksheetId;
diff --git a/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/history/HistoryJSONEditor.java b/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/history/HistoryJSONEditor.java
index 48f3cd59a..e7b46b3f1 100644
--- a/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/history/HistoryJSONEditor.java
+++ b/karma-commands/commands-common/src/main/java/edu/isi/karma/controller/history/HistoryJSONEditor.java
@@ -5,7 +5,8 @@
import java.util.List;
import java.util.Set;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
import org.json.JSONArray;
import org.json.JSONObject;
@@ -18,7 +19,7 @@ public class HistoryJSONEditor {
private JSONArray historyJSON;
private Workspace workspace;
private String worksheetId;
- static Logger logger = Logger.getLogger(HistoryJSONEditor.class);
+ static Logger logger = LogManager.getLogger(HistoryJSONEditor.class.getName());
public HistoryJSONEditor(JSONArray historyJSON, Workspace workspace, String worksheetId) {
this.worksheetId = worksheetId;
this.workspace = workspace;
diff --git a/karma-commands/commands-import/import-avro/.factorypath b/karma-commands/commands-import/import-avro/.factorypath
new file mode 100644
index 000000000..047935c5a
--- /dev/null
+++ b/karma-commands/commands-import/import-avro/.factorypath
@@ -0,0 +1,78 @@
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diff --git a/karma-commands/commands-import/import-common/.factorypath b/karma-commands/commands-import/import-common/.factorypath
new file mode 100644
index 000000000..047935c5a
--- /dev/null
+++ b/karma-commands/commands-import/import-common/.factorypath
@@ -0,0 +1,78 @@
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diff --git a/karma-commands/commands-import/import-csv/.factorypath b/karma-commands/commands-import/import-csv/.factorypath
new file mode 100644
index 000000000..047935c5a
--- /dev/null
+++ b/karma-commands/commands-import/import-csv/.factorypath
@@ -0,0 +1,78 @@
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diff --git a/karma-commands/commands-import/import-database/.factorypath b/karma-commands/commands-import/import-database/.factorypath
new file mode 100644
index 000000000..2ee36cd2c
--- /dev/null
+++ b/karma-commands/commands-import/import-database/.factorypath
@@ -0,0 +1,82 @@
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diff --git a/karma-commands/commands-import/import-excel/.factorypath b/karma-commands/commands-import/import-excel/.factorypath
new file mode 100644
index 000000000..047935c5a
--- /dev/null
+++ b/karma-commands/commands-import/import-excel/.factorypath
@@ -0,0 +1,78 @@
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diff --git a/karma-commands/commands-import/import-file/.factorypath b/karma-commands/commands-import/import-file/.factorypath
new file mode 100644
index 000000000..047935c5a
--- /dev/null
+++ b/karma-commands/commands-import/import-file/.factorypath
@@ -0,0 +1,78 @@
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diff --git a/karma-commands/commands-import/import-json/.factorypath b/karma-commands/commands-import/import-json/.factorypath
new file mode 100644
index 000000000..cf5abcfc7
--- /dev/null
+++ b/karma-commands/commands-import/import-json/.factorypath
@@ -0,0 +1,94 @@
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diff --git a/karma-commands/commands-import/import-ontology/.factorypath b/karma-commands/commands-import/import-ontology/.factorypath
new file mode 100644
index 000000000..6bef6a3d9
--- /dev/null
+++ b/karma-commands/commands-import/import-ontology/.factorypath
@@ -0,0 +1,78 @@
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diff --git a/karma-commands/commands-import/import-service/.factorypath b/karma-commands/commands-import/import-service/.factorypath
new file mode 100644
index 000000000..047935c5a
--- /dev/null
+++ b/karma-commands/commands-import/import-service/.factorypath
@@ -0,0 +1,78 @@
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diff --git a/karma-commands/commands-import/import-spatial/.factorypath b/karma-commands/commands-import/import-spatial/.factorypath
new file mode 100644
index 000000000..d9f3f5024
--- /dev/null
+++ b/karma-commands/commands-import/import-spatial/.factorypath
@@ -0,0 +1,102 @@
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diff --git a/karma-commands/commands-import/import-xml/.factorypath b/karma-commands/commands-import/import-xml/.factorypath
new file mode 100644
index 000000000..047935c5a
--- /dev/null
+++ b/karma-commands/commands-import/import-xml/.factorypath
@@ -0,0 +1,78 @@
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diff --git a/karma-commands/commands-publish-alignment-openrdf/.factorypath b/karma-commands/commands-publish-alignment-openrdf/.factorypath
new file mode 100644
index 000000000..a32d55bef
--- /dev/null
+++ b/karma-commands/commands-publish-alignment-openrdf/.factorypath
@@ -0,0 +1,121 @@
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diff --git a/karma-commands/commands-publish-jdbc/.factorypath b/karma-commands/commands-publish-jdbc/.factorypath
new file mode 100644
index 000000000..3e5d1f109
--- /dev/null
+++ b/karma-commands/commands-publish-jdbc/.factorypath
@@ -0,0 +1,82 @@
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diff --git a/karma-commands/commands-publish/.factorypath b/karma-commands/commands-publish/.factorypath
new file mode 100644
index 000000000..ddf5abff1
--- /dev/null
+++ b/karma-commands/commands-publish/.factorypath
@@ -0,0 +1,79 @@
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diff --git a/karma-commands/commands-python/.factorypath b/karma-commands/commands-python/.factorypath
new file mode 100644
index 000000000..63a6f7a48
--- /dev/null
+++ b/karma-commands/commands-python/.factorypath
@@ -0,0 +1,94 @@
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diff --git a/karma-commands/commands-update-jdbc/.factorypath b/karma-commands/commands-update-jdbc/.factorypath
new file mode 100644
index 000000000..dfd44518d
--- /dev/null
+++ b/karma-commands/commands-update-jdbc/.factorypath
@@ -0,0 +1,81 @@
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diff --git a/karma-commands/commands-update/.factorypath b/karma-commands/commands-update/.factorypath
new file mode 100644
index 000000000..13a1a2b20
--- /dev/null
+++ b/karma-commands/commands-update/.factorypath
@@ -0,0 +1,78 @@
+
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diff --git a/karma-commands/commands-worksheet/.factorypath b/karma-commands/commands-worksheet/.factorypath
new file mode 100644
index 000000000..c2ab0289c
--- /dev/null
+++ b/karma-commands/commands-worksheet/.factorypath
@@ -0,0 +1,94 @@
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diff --git a/karma-common/.factorypath b/karma-common/.factorypath
new file mode 100644
index 000000000..047935c5a
--- /dev/null
+++ b/karma-common/.factorypath
@@ -0,0 +1,78 @@
+
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diff --git a/karma-common/pom.xml b/karma-common/pom.xml
index 5f7ed02e8..06fa4aeee 100644
--- a/karma-common/pom.xml
+++ b/karma-common/pom.xml
@@ -44,8 +44,8 @@
commons-lang3
- log4j
- log4j
+ org.apache.logging.log4j
+ log4j-core
org.slf4j
diff --git a/karma-jdbc/.factorypath b/karma-jdbc/.factorypath
new file mode 100644
index 000000000..312088b69
--- /dev/null
+++ b/karma-jdbc/.factorypath
@@ -0,0 +1,81 @@
+
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diff --git a/karma-jdbc/pom.xml b/karma-jdbc/pom.xml
index 1d71dcb91..90374d018 100644
--- a/karma-jdbc/pom.xml
+++ b/karma-jdbc/pom.xml
@@ -24,8 +24,8 @@
${project.version}
- log4j
- log4j
+ org.apache.logging.log4j
+ log4j-core
org.slf4j
diff --git a/karma-mr/.factorypath b/karma-mr/.factorypath
new file mode 100644
index 000000000..467e68086
--- /dev/null
+++ b/karma-mr/.factorypath
@@ -0,0 +1,311 @@
+
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diff --git a/karma-mr/src/main/java/edu/isi/karma/mapreduce/driver/JSONAvroProcessor.java b/karma-mr/src/main/java/edu/isi/karma/mapreduce/driver/JSONAvroProcessor.java
index 16685c8d7..0aa12a582 100644
--- a/karma-mr/src/main/java/edu/isi/karma/mapreduce/driver/JSONAvroProcessor.java
+++ b/karma-mr/src/main/java/edu/isi/karma/mapreduce/driver/JSONAvroProcessor.java
@@ -1,6 +1,7 @@
package edu.isi.karma.mapreduce.driver;
import java.util.Properties;
+// import java.util.logging.LogManager;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.Path;
@@ -10,8 +11,10 @@
import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;
import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat;
import org.apache.hadoop.util.ToolRunner;
-import org.apache.log4j.Level;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Level;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.core.config.Configurator;
import edu.isi.karma.mapreduce.inputformat.AvroKeyBatchInputFormat;
@@ -42,7 +45,8 @@ public Job configure(Properties p ) throws Exception
public static void main(String[] args) throws Exception {
- Logger.getRootLogger().setLevel(Level.ERROR);
+ LogManager.getRootLogger();
+ Configurator.setRootLevel(Level.ERROR);
System.exit(ToolRunner.run(new Configuration(), new JSONAvroProcessor(), args));
}
diff --git a/karma-mr/src/main/java/edu/isi/karma/mapreduce/driver/JSONCSVProcessor.java b/karma-mr/src/main/java/edu/isi/karma/mapreduce/driver/JSONCSVProcessor.java
index be47398b5..6c87e6a2d 100644
--- a/karma-mr/src/main/java/edu/isi/karma/mapreduce/driver/JSONCSVProcessor.java
+++ b/karma-mr/src/main/java/edu/isi/karma/mapreduce/driver/JSONCSVProcessor.java
@@ -10,8 +10,10 @@
import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;
import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat;
import org.apache.hadoop.util.ToolRunner;
-import org.apache.log4j.Level;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Level;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.core.config.Configurator;
import edu.isi.karma.mapreduce.inputformat.CSVBatchTextInputFormat;
@@ -41,7 +43,8 @@ public Job configure(Properties p ) throws Exception
}
public static void main(String[] args) throws Exception {
- Logger.getRootLogger().setLevel(Level.INFO);
+ LogManager.getRootLogger();
+ Configurator.setRootLevel(Level.INFO);
long start = System.currentTimeMillis();
int status = ToolRunner.run(new Configuration(), new JSONCSVProcessor(), args);
System.out.println((System.currentTimeMillis() - start) + " msec");
diff --git a/karma-mr/src/main/java/edu/isi/karma/mapreduce/driver/JSONIdentityReducerProcessor.java b/karma-mr/src/main/java/edu/isi/karma/mapreduce/driver/JSONIdentityReducerProcessor.java
index 21a0a13b5..dd1d2a89e 100644
--- a/karma-mr/src/main/java/edu/isi/karma/mapreduce/driver/JSONIdentityReducerProcessor.java
+++ b/karma-mr/src/main/java/edu/isi/karma/mapreduce/driver/JSONIdentityReducerProcessor.java
@@ -22,8 +22,8 @@
import org.apache.hadoop.mapreduce.lib.output.TextOutputFormat;
import org.apache.hadoop.util.Tool;
import org.apache.hadoop.util.ToolRunner;
-import org.apache.log4j.Level;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Level;
+import org.apache.logging.log4j.Logger;
import edu.isi.karma.rdf.CommandLineArgumentParser;
import edu.isi.karma.rdf.OfflineRdfGenerator;
diff --git a/karma-mr/src/main/java/edu/isi/karma/mapreduce/driver/JSONProcessor.java b/karma-mr/src/main/java/edu/isi/karma/mapreduce/driver/JSONProcessor.java
index b318d0828..89876663c 100644
--- a/karma-mr/src/main/java/edu/isi/karma/mapreduce/driver/JSONProcessor.java
+++ b/karma-mr/src/main/java/edu/isi/karma/mapreduce/driver/JSONProcessor.java
@@ -11,8 +11,11 @@
import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;
import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat;
import org.apache.hadoop.util.ToolRunner;
-import org.apache.log4j.Level;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Level;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.core.config.Configurator;
+
public class JSONProcessor extends KarmaProcessor {
@@ -41,7 +44,8 @@ public Job configure(Properties p ) throws Exception
public static void main(String[] args) throws Exception {
- Logger.getRootLogger().setLevel(Level.ERROR);
+ LogManager.getRootLogger();
+ Configurator.setRootLevel(Level.ERROR);
long start = System.currentTimeMillis();
int status = ToolRunner.run(new Configuration(), new JSONProcessor(), args);
System.out.println((System.currentTimeMillis() - start) + " msec");
diff --git a/karma-offline/.factorypath b/karma-offline/.factorypath
new file mode 100644
index 000000000..f9285850a
--- /dev/null
+++ b/karma-offline/.factorypath
@@ -0,0 +1,175 @@
+
+
+
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diff --git a/karma-offline/pom.xml b/karma-offline/pom.xml
index fc0e86633..e74705e34 100644
--- a/karma-offline/pom.xml
+++ b/karma-offline/pom.xml
@@ -27,8 +27,8 @@
pom
- log4j
- log4j
+ org.apache.logging.log4j
+ log4j-core
org.slf4j
diff --git a/karma-research/pom.xml b/karma-research/pom.xml
index f3d9bc899..aff6967a7 100644
--- a/karma-research/pom.xml
+++ b/karma-research/pom.xml
@@ -29,8 +29,8 @@
${project.version}
- log4j
- log4j
+ org.apache.logging.log4j
+ log4j-core
org.slf4j
diff --git a/karma-spark/.factorypath b/karma-spark/.factorypath
new file mode 100644
index 000000000..202c23af9
--- /dev/null
+++ b/karma-spark/.factorypath
@@ -0,0 +1,388 @@
+
+
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+
diff --git a/karma-typer/.factorypath b/karma-typer/.factorypath
new file mode 100644
index 000000000..eda5076fd
--- /dev/null
+++ b/karma-typer/.factorypath
@@ -0,0 +1,26 @@
+
+
+
+
+
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+
diff --git a/karma-typer/pom.xml b/karma-typer/pom.xml
index 2fe6e95e2..7a2d7d103 100644
--- a/karma-typer/pom.xml
+++ b/karma-typer/pom.xml
@@ -15,8 +15,8 @@
- log4j
- log4j
+ org.apache.logging.log4j
+ log4j-core
org.slf4j
diff --git a/karma-util/.factorypath b/karma-util/.factorypath
new file mode 100644
index 000000000..fb4467665
--- /dev/null
+++ b/karma-util/.factorypath
@@ -0,0 +1,18 @@
+
+
+
+
+
+
+
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+
+
+
+
+
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+
+
+
diff --git a/karma-util/pom.xml b/karma-util/pom.xml
index db0213f49..12df68950 100644
--- a/karma-util/pom.xml
+++ b/karma-util/pom.xml
@@ -19,8 +19,8 @@
- log4j
- log4j
+ org.apache.logging.log4j
+ log4j-core
org.slf4j
diff --git a/karma-web-services/web-services-publish-es/.factorypath b/karma-web-services/web-services-publish-es/.factorypath
new file mode 100644
index 000000000..1dec2103b
--- /dev/null
+++ b/karma-web-services/web-services-publish-es/.factorypath
@@ -0,0 +1,208 @@
+
+
+
+
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diff --git a/karma-web-services/web-services-rdf/.factorypath b/karma-web-services/web-services-rdf/.factorypath
new file mode 100644
index 000000000..077b42928
--- /dev/null
+++ b/karma-web-services/web-services-rdf/.factorypath
@@ -0,0 +1,192 @@
+
+
+
+
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+
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diff --git a/karma-web/.factorypath b/karma-web/.factorypath
new file mode 100644
index 000000000..4a8efe4e0
--- /dev/null
+++ b/karma-web/.factorypath
@@ -0,0 +1,152 @@
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diff --git a/pom.xml b/pom.xml
index 441578743..b18a6e4a4 100644
--- a/pom.xml
+++ b/pom.xml
@@ -61,7 +61,7 @@
2.0.8
1.5.3
- 1.2.17
+ 2.13.3
1.6.0
4.11
@@ -164,8 +164,8 @@
2.7.2
- log4j
- log4j
+ org.apache.logging.log4j
+ log4j-core
${log4j.version}