From 510290feea4bb328566770b636f9f093d00e93b0 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 16 Aug 2016 10:34:57 -0400
Subject: [PATCH 1/4] Add example of regressed 16.04 behavior related to dbkey
 output actions.

---
 test/functional/tools/dbkey_output_action.xml | 24 +++++++++++++++++++
 test/functional/tools/samples_tool_conf.xml   |  1 +
 2 files changed, 25 insertions(+)
 create mode 100644 test/functional/tools/dbkey_output_action.xml

diff --git a/test/functional/tools/dbkey_output_action.xml b/test/functional/tools/dbkey_output_action.xml
new file mode 100644
index 000000000000..89d00c09aff7
--- /dev/null
+++ b/test/functional/tools/dbkey_output_action.xml
@@ -0,0 +1,24 @@
+<tool id="dbkey_output_action" name="dbkey_output_action" version="0.1.0">
+    <command>echo foo > $mapped_reads</command>
+    <inputs>
+        <param name="input" type="data" />
+        <param name="index" type="select" label="Using reference genome">
+          <options from_data_table="test_fasta_indexes">
+            <filter type="data_meta" ref="input" key="dbkey" column="1" />
+            <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
+          </options>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="txt" name="mapped_reads">
+            <actions>
+                <action type="metadata" name="dbkey">
+                    <option type="from_data_table" name="test_fasta_indexes" column="1" offset="0">
+                        <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+                        <filter type="param_value" ref="index" column="0"/>
+                    </option>
+                </action>
+            </actions>
+        </data>
+    </outputs>
+</tool>
\ No newline at end of file
diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
index 669d28ed2fa4..a5dfee0d12d9 100644
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -18,6 +18,7 @@
   <tool file="inputs_as_json.xml" />
   <tool file="dbkey_filter_input.xml" />
   <tool file="dbkey_filter_multi_input.xml" />
+  <tool file="dbkey_output_action.xml" />
   <tool file="composite_output.xml" />
   <tool file="unicode_stream.xml" />
   <tool file="metadata.xml" />

From 88d02dba6e851f0f60758a575920f6e7b130e261 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 16 Aug 2016 12:55:56 -0400
Subject: [PATCH 2/4] Don't fill in a cheetah default if unavailable.

... in metadata hack from #961.
---
 lib/galaxy/tools/actions/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py
index 5cfee0ff06b8..845d86b3322c 100644
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -628,7 +628,7 @@ def set_metadata_defaults( self, output, dataset, tool, on_text, trans, incoming
         """
         if output.actions:
             for action in output.actions.actions:
-                if action.tag == "metadata":
+                if action.tag == "metadata" and action.default:
                     metadata_new_value = fill_template( action.default, context=params ).split(",")
                     dataset.metadata.__setattr__(str(action.name), metadata_new_value)
 

From 0110d5a05a4b1b357a3f321471fce1b2d4960e67 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 16 Aug 2016 14:08:38 -0400
Subject: [PATCH 3/4] Add a test case to dbkey_output_action.xml.

Per @nsoranzo's template and suggestion.
---
 test/functional/tools/dbkey_output_action.xml | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/test/functional/tools/dbkey_output_action.xml b/test/functional/tools/dbkey_output_action.xml
index 89d00c09aff7..9d100105ec5c 100644
--- a/test/functional/tools/dbkey_output_action.xml
+++ b/test/functional/tools/dbkey_output_action.xml
@@ -21,4 +21,16 @@
             </actions>
         </data>
     </outputs>
+    <tests>
+        <test>
+            <param name="input" value="simple_line.txt" dbkey="hg18" />
+            <param name="index" value="hg18"/>
+            <output name="mapped_reads">
+                <metadata name="dbkey" value="hg18" />
+                <assert_contents>
+                    <has_text text="foo" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
 </tool>
\ No newline at end of file

From e06cf9a97802d4c6a2ab97d973a373675e68b751 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 16 Aug 2016 14:12:17 -0400
Subject: [PATCH 4/4] Add None check to fill_template...

... as requested by @nsoranzo.
---
 lib/galaxy/util/template.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/lib/galaxy/util/template.py b/lib/galaxy/util/template.py
index 8e50f8e34d91..ef62853a781c 100644
--- a/lib/galaxy/util/template.py
+++ b/lib/galaxy/util/template.py
@@ -1,7 +1,16 @@
+"""Entry point for the usage of Cheetah templating within Galaxy."""
 from Cheetah.Template import Template
 
 
 def fill_template( template_text, context=None, **kwargs ):
+    """Fill a cheetah template out for specified context.
+
+    If template_text is None, an exception will be thrown, if context
+    is None (the default) - keyword arguments to this function will be used
+    as the context.
+    """
+    if template_text is None:
+        raise TypeError("Template text specified as None to fill_template.")
     if not context:
         context = kwargs
     return str( Template( source=template_text, searchList=[context] ) )