From 647ba8531acdf576cfefea71bc7bb73a89ed7a0a Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 6 Jun 2018 18:38:49 +0200
Subject: [PATCH] Add test tool and workflow for mapping over with mapping
 output

This doesn't quite work because of the dynamic output collection,
which fails with:

```
galaxy.tools.parameters.output_collect DEBUG 2018-06-06 18:40:38,784 (3) Add dynamic collection datasets to history for output [reverse] (171.970 ms)
galaxy.tools.parameters.output_collect ERROR 2018-06-06 18:40:38,839 Problem gathering output collection.
Traceback (most recent call last):
  File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/output_collect.py", line 340, in collect_dynamic_outputs
    collection_builder.populate()
  File "/Users/mvandenb/src/galaxy/lib/galaxy/dataset_collections/builder.py", line 88, in populate
    elements = self.build_elements()
  File "/Users/mvandenb/src/galaxy/lib/galaxy/dataset_collections/builder.py", line 59, in build_elements
    new_elements[identifier] = element.build()
AttributeError: 'HistoryDatasetAssociation' object has no attribute 'build'
```

This seems to happen because the inner collection is wrongly detected as
nested. In general I doubt that mapping over colleciton output works
with dynamically discovered output collections.
---
 test/api/test_workflows.py                    | 20 +++++++++++++++++++
 .../tools/collection_type_source_map_over.xml | 16 +++++++++++++++
 test/functional/tools/samples_tool_conf.xml   |  1 +
 3 files changed, 37 insertions(+)
 create mode 100644 test/functional/tools/collection_type_source_map_over.xml

diff --git a/test/api/test_workflows.py b/test/api/test_workflows.py
index 47067be026e..ccc046a4f55 100644
--- a/test/api/test_workflows.py
+++ b/test/api/test_workflows.py
@@ -1359,6 +1359,26 @@ test_data:
 """, history_id=history_id, wait=True)
             self.assertEqual("0\n", self.dataset_populator.get_history_dataset_content(history_id))
 
+    @skip_without_tool("collection_type_source_map_over")
+    def test_mapping_and_subcollection_mapping(self):
+        with self.dataset_populator.test_history() as history_id:
+            jobs_summary = self._run_jobs("""
+class: GalaxyWorkflow
+steps:
+  - label: text_input1
+    type: input_collection
+  - tool_id: collection_type_source_map_over
+    state:
+      input_collect:
+        $link: text_input1
+test_data:
+  text_input1:
+    type: "list:paired"
+        """, history_id=history_id)
+            hdca = self.dataset_populator.get_history_collection_details(history_id=jobs_summary.history_id, hid=5)
+            assert hdca['collection_type'] == 'list:paired'
+            assert len(hdca['elements'][0]['object']["elements"]) == 2
+
     @skip_without_tool("empty_list")
     @skip_without_tool("count_multi_file")
     @skip_without_tool("random_lines1")
diff --git a/test/functional/tools/collection_type_source_map_over.xml b/test/functional/tools/collection_type_source_map_over.xml
new file mode 100644
index 00000000000..cf008421275
--- /dev/null
+++ b/test/functional/tools/collection_type_source_map_over.xml
@@ -0,0 +1,16 @@
+<tool id="collection_type_source_map_over" name="collection_type_source_map_over" version="0.1.0">
+  <command>
+    mkdir output;
+    #for $key in $input_collect.keys()#
+    cat "$input_collect[$key]" >> output/"$key";
+    #end for#
+  </command>
+  <inputs>
+    <param name="input_collect" type="data_collection" collection_type="list,paired" label="Input Collect" help="Input collection..." />
+  </inputs>
+  <outputs>
+    <collection name="list_output" type_source="input_collect" label="Duplicate List">
+      <discover_datasets pattern="__name__" directory="output" visible="true" />
+    </collection>
+  </outputs>
+</tool>
diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
index 116b3ac34a0..97e6c48bd74 100644
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -125,6 +125,7 @@
   <tool file="collection_creates_dynamic_nested_from_json_elements.xml" />
   <tool file="collection_creates_dynamic_list_of_pairs.xml" />
   <tool file="collection_type_source.xml" />
+  <tool file="collection_type_source_map_over.xml" />
   <tool file="collection_creates_list_fail.xml" />
   <tool file="collection_creates_dynamic_nested_fail.xml" />
   <tool file="cheetah_casting.xml" />