From cf25f7dcec6f7f7b13aac93a18ced291d5e74444 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 3 Dec 2018 09:31:59 +0100
Subject: [PATCH 1/2] Fix nesting of repeats and error when repeat is provided
 literally.

This fixex #7048, where in addition to repeat values
('repeat_0|param: some_value') there are also values
for the repeat param itself ('repeat': []).
---
 lib/galaxy/tools/parameters/meta.py | 20 ++++++++++++--------
 1 file changed, 12 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/tools/parameters/meta.py b/lib/galaxy/tools/parameters/meta.py
index d5fb5f53590..7440b1bf64c 100644
--- a/lib/galaxy/tools/parameters/meta.py
+++ b/lib/galaxy/tools/parameters/meta.py
@@ -72,26 +72,30 @@ def expand_workflow_inputs(inputs):
     return params, params_keys
 
 
-def process_key(incoming_key, d):
+def process_key(incoming_key, incoming_value, d):
     key_parts = incoming_key.split('|')
     if len(key_parts) == 1:
         # Regular parameter
-        d[incoming_key] = object()
+        d[incoming_key] = incoming_value
     elif key_parts[0].rsplit('_', 1)[-1].isdigit():
         # Repeat
         input_name_index = key_parts[0].rsplit('_', 1)
         input_name, index = input_name_index
+        index = int(index)
         if input_name not in d:
             d[input_name] = []
-        subdict = {}
-        d[input_name].append(subdict)
-        process_key("|".join(key_parts[1:]), d=subdict)
+        if len(d[input_name]) > index:
+            subdict = d[input_name][index]
+        else:
+            subdict = {}
+            d[input_name].append(subdict)
+        process_key("|".join(key_parts[1:]), incoming_value=incoming_value, d=subdict)
     else:
         # Section / Conditional
         input_name = key_parts[0]
         subdict = {}
         d[input_name] = subdict
-        process_key("|".join(key_parts[1:]), d=subdict)
+        process_key("|".join(key_parts[1:]), incoming_value=incoming_value, d=subdict)
 
 
 def expand_meta_parameters(trans, tool, incoming):
@@ -113,9 +117,9 @@ def expand_meta_parameters(trans, tool, incoming):
     # according to tool.inputs (which is ordered).
     incoming_copy = incoming.copy()
     nested_dict = {}
-    for incoming_key in incoming_copy:
+    for incoming_key, incoming_value in incoming_copy.items():
         if not incoming_key.startswith('__'):
-            process_key(incoming_key, d=nested_dict)
+            process_key(incoming_key, incoming_value=incoming_value, d=nested_dict)
 
     reordered_incoming = OrderedDict()
 

From 3a93fd4f2321bf141b2ccf34ea80c42ee517b33d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 3 Dec 2018 09:31:36 +0100
Subject: [PATCH 2/2] Add test for proper nesting in process_keys

and a unit test for https://github.com/galaxyproject/galaxy/issues/7048
---
 test/unit/tools/test_parameter_parsing.py | 24 +++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/test/unit/tools/test_parameter_parsing.py b/test/unit/tools/test_parameter_parsing.py
index 79b3ac35afd..047222a26be 100644
--- a/test/unit/tools/test_parameter_parsing.py
+++ b/test/unit/tools/test_parameter_parsing.py
@@ -3,10 +3,34 @@ from xml.etree.ElementTree import XML
 
 from galaxy import model
 from galaxy.tools.parameters import basic
+from galaxy.tools.parameters.meta import process_key
 from galaxy.util import bunch
 from ..tools_support import UsesApp
 
 
+def test_process_key():
+    nested_dict = {}
+    d = {
+        'repeat_0|inner_repeat_0|data_table_column_value': u'bla',
+        'repeat_1|inner_repeat_1|data_table_column_value': u'bla2',
+    }
+    for key, value in d.items():
+        process_key(key, value, nested_dict)
+    assert len(nested_dict) == 1
+
+
+def test_process_key_2():
+    nested_dict = {}
+    d = {
+        'data_tables_0|columns_0|data_table_column_value': 'Amel_HAv3.1',
+        'data_tables': [],
+        'directory_content': [],
+    }
+    for key, value in d.items():
+        process_key(key, value, nested_dict)
+    assert len(nested_dict) == 2
+
+
 class BaseParameterTestCase(TestCase, UsesApp):
 
     def setUp(self):