command in input json can be a list

tests/tibanna/unicorn/test_ec2_utils.py

@@ -82,7 +82,7 @@ def test_args_parse_input_files2():
     assert args.input_files['file1']['object_key'][1][1] == 'somekey4'
 
 
-def test_args_parse_input_files2():
+def test_args_parse_input_files3():
     input_dict = {'args': {'input_files': {"file1": ["s3://somebucket/somekey1",
                                                      "s3://somebucket/somekey2"]},
                            'output_S3_bucket': 'somebucket',
@@ -101,6 +101,7 @@ def test_args_parse_input_files2():
     assert args.input_files['file1']['object_key'][0] == 'somekey1'
     assert args.input_files['file1']['object_key'][1] == 'somekey2'
 
+
 def test_args_parse_input_files_format_error():
     input_dict = {'args': {'input_files': {"file1": "somerandomstr"},
                            'output_S3_bucket': 'somebucket',
@@ -113,6 +114,7 @@ def test_args_parse_input_files_format_error():
     assert ex
     assert 'S3 url must begin with' in str(ex.value)
 
+
 def test_args_parse_input_files_format_error2():
     input_dict = {'args': {'input_files': {"file1": ["s3://somebucket/somekey1",
                                                      "s3://otherbucket/somekey2"]},
@@ -126,6 +128,18 @@ def test_args_parse_input_files_format_error2():
     assert ex
     assert 'bucket' in str(ex.value)
 
+
+def test_parse_command():
+    input_dict = {'args': {'command': ['command1', 'command2', 'command3'],
+                           'output_S3_bucket': 'somebucket',
+                           'language': 'shell',
+                           'container_image': 'someimage',
+                           'app_name': 'someapp'}}
+    args = Args(**input_dict['args'])
+    args.fill_default()
+    assert args.command == 'command1; command2; command3'
+
+
 def test_config():
     input_dict = {'config': {'log_bucket': 'tibanna-output', 'shutdown_min': 30}}
     cfg = Config(**input_dict['config'])
@@ -213,6 +227,7 @@ def test_execution_benchmark():
     s3.delete_objects(Bucket='tibanna-output',
                       Delete={'Objects': [{'Key': randomstr}]})
 
+
 def test_get_file_size():
     randomstr = 'test-' + create_jobid()
     s3 = boto3.client('s3')
@@ -224,6 +239,7 @@ def test_get_file_size():
     s3.delete_objects(Bucket='tibanna-output',
                       Delete={'Objects': [{'Key': randomstr}]})
 
+
 def test_get_input_size_in_bytes():
     randomstr = 'test-' + create_jobid()
     s3 = boto3.client('s3')
@@ -244,6 +260,7 @@ def test_get_input_size_in_bytes():
     s3.delete_objects(Bucket='tibanna-output',
                       Delete={'Objects': [{'Key': randomstr}]})
 
+
 def test_update_config_ebs_size():
     """ebs_size is given as the 'x' format. The total estimated ebs_size is smaller than 10"""
     randomstr = 'test-' + create_jobid()
@@ -265,6 +282,7 @@ def test_update_config_ebs_size():
     s3.delete_objects(Bucket='tibanna-output',
                       Delete={'Objects': [{'Key': randomstr}]})
 
+
 def test_update_config_ebs_size2():
     """ebs_size is given as the 'x' format. The total estimated ebs_size is larger than 10"""
     randomstr = 'test-' + create_jobid()
@@ -286,6 +304,7 @@ def test_update_config_ebs_size2():
     s3.delete_objects(Bucket='tibanna-output',
                       Delete={'Objects': [{'Key': randomstr}]})
 
+
 def test_unicorn_input_missing_field():
     """app_name that doesn't exist in benchmark, without instance type, mem, cpu info"""
     input_dict = {'args': {'input_files': {}, 'app_name': 'app_name_not_in_benchmark',

tibanna/ec2_utils.py

@@ -187,6 +187,16 @@ def fill_default(self):
             if not self.cwl_directory_local and not self.cwl_directory_url:
                 errmsg = "either %s or %s must be provided in args" % ('cwl_directory_url', 'cwl_directory_local')
                 raise MissingFieldInInputJsonException(errmsg)
+        # reformat command
+        self.parse_command()
+
+    def parse_command(self):
+        """if command is a list, conert it to a string"""
+        if hasattr(self, 'command'):
+            if isinstance(self.command, list):
+                self.command = '; '.join(self.command)
+            elif not isinstance(self.command, str):
+                raise MalFormattedInputJsonException("command must be either a string or a list")
 
     def parse_input_files(self):
         """checking format for input files and converting s3:// style string into