Merge pull request #1 from maximilianiKIT/dev

Fixed problems with python

Author: maximiliani

src/main/java/edu/kit/datamanager/python/util/PythonUtils.java

@@ -149,6 +149,7 @@ public static int run(String pythonLocation, String scriptLocation, OutputStream
 
     int result = 4711;
     try {
+
       ProcessBuilder pb = new ProcessBuilder(command.toArray(new String[]{}));
       Process p = pb.start();
 

src/main/resources/application.properties

@@ -96,7 +96,7 @@ repo.audit.enabled:true
 # Absolute path to the local python interpreter
 repo.plugin.gemma.pythonLocation:/usr/local/bin/python3
 # Absolute path to the local gemma mapping script mapping_single.py' 
-repo.plugin.gemma.gemmaLocation:/Users/pfeil/git/gemma/mapping_single.py
+repo.plugin.gemma.gemmaLocation:/Users/maximilian/Documents/GitHub/mapping-service/src/test/resources/python/mapping_single.py
 # Absolute path to the local gemma mappings folder
 repo.plugin.gemma.mappingsLocation:/Users/pfeil/git/gemma-plugin/mappings
 # List of schema mappings containing the content type as key in squared brackets and the 

src/test/java/edu/kit/datamanager/indexer/mapping/MappingUtilTest.java

@@ -71,6 +71,7 @@ public static void setUpClass() throws IOException {
     }
     System.out.println("Location of python: " + pythonExecutable);
     PYTHON_EXECUTABLE = new File(pythonExecutable.trim()).getAbsoluteFile().toURI().toURL();
+//    PYTHON_EXECUTABLE = new File("/opt/homebrew/bin/python3".trim()).getAbsoluteFile().toURI().toURL();
     GEMMA_CLASS = new URL("file:src/test/resources/python/mapping_single.py");
   }
 

src/test/resources/python/invalid.py

@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/python3
 
 
 print "Not allowed"

src/test/resources/python/mapping_single.py

@@ -17,8 +17,5 @@
 output_filename = sys.argv[3] 
 #output_filename = "output.json" 
 
-
 print("\n \n \n MAPPING DOCUMENT: {} \n \n \n".format(input_file))
-mapping_functions.map_response(schema, input_file, output_filename)
-
-
+mapping_functions.map_response(schema, input_file, output_filename)

src/test/resources/python/printOutput.py

@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/python3
 import time
 import sys
 

src/test/resources/python/sleep.py

@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/python3
 import time
 
 print ("Sleep for 3 seconds")

src/test/resources/test-config/application-test.properties

@@ -35,6 +35,7 @@ metastore.indexer.mappingsLocation:file:///tmp/metastore2/mapping
 ########################    Configuration for GEMMA    #########################
 # Absolute path to the local python interpreter
 metastore.indexer.gemma.pythonLocation:file:///usr/bin/python3
+
 # Path to the local gemma mapping script mapping_single.py' (may be absolute or relative)
 metastore.indexer.gemma.gemmaLocation:file:src/test/resources/python/mapping_single.py