Merge pull request #10703 from jmchilton/null_handling_2

Null handling and optional values for integers, floats, and text params.

lib/galaxy/tools/parameters/basic.py

@@ -302,12 +302,16 @@ class SimpleTextToolParameter(ToolParameter):
     def __init__(self, tool, input_source):
         input_source = ensure_input_source(input_source)
         super().__init__(tool, input_source)
-        self.value = ''
+        self.optional = input_source.get_bool('optional', False)
+        if self.optional:
+            self.value = None
+        else:
+            self.value = ''
 
     def to_json(self, value, app, use_security):
         """Convert a value to a string representation suitable for persisting"""
         if value is None:
-            rval = ''
+            rval = '' if not self.optional else None
         else:
             rval = unicodify(value)
         return rval
@@ -346,6 +350,7 @@ class TextToolParameter(SimpleTextToolParameter):
         d = super().to_dict(trans)
         d['area'] = self.area
         d['datalist'] = self.datalist
+        d['optional'] = self.optional
         return d
 
 

lib/galaxy/tools/parameters/wrapped_json.py

@@ -86,7 +86,10 @@ def _json_wrap_input(input, value_wrapper, profile, handle_files="skip"):
             return SKIP_INPUT
         raise NotImplementedError()
     elif input_type in ["text", "color", "hidden"]:
-        json_value = _cast_if_not_none(value_wrapper, str)
+        if getattr(input, "optional", False) and value_wrapper is not None and value_wrapper.value is None:
+            json_value = None
+        else:
+            json_value = _cast_if_not_none(value_wrapper, str)
     elif input_type == "float":
         json_value = _cast_if_not_none(value_wrapper, float, empty_to_none=True)
     elif input_type == "integer":

test/functional/tools/expression_null_handling_float.xml

@@ -0,0 +1,22 @@
+<tool name="expression_null_handling_float" id="expression_null_handling_float"
+	  version="0.1.0" tool_type="expression">
+    <expression type="ecma5.1">
+        {return {'float_out': $job.float_input};}
+    </expression>
+    <inputs>
+        <param type="float" label="Float input." name="float_input" optional="true" />
+    </inputs>
+    <outputs>
+        <output type="float" name="float_out" from="float_out" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="float_input" value_json="7.2" />
+            <output name="float_out" value_json="7.2" />
+        </test>
+        <test>
+            <param name="float_input" value_json="null" />
+            <output name="float_out" value_json="null" />
+        </test>
+    </tests>
+</tool>

test/functional/tools/expression_null_handling_integer.xml

@@ -0,0 +1,22 @@
+<tool name="expression_null_handling_integer" id="expression_null_handling_integer"
+	  version="0.1.0" tool_type="expression">
+    <expression type="ecma5.1">
+        {return {'int_out': $job.int_input};}
+    </expression>
+    <inputs>
+        <param type="integer" label="Integer input." name="int_input" optional="true" />
+    </inputs>
+    <outputs>
+        <output type="integer" name="int_out" from="int_out" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="int_input" value_json="7" />
+            <output name="int_out" value_json="7" />
+        </test>
+        <test>
+            <param name="int_input" value_json="null" />
+            <output name="int_out" value_json="null" />
+        </test>
+    </tests>
+</tool>

test/functional/tools/expression_null_handling_text.xml

@@ -0,0 +1,32 @@
+<tool name="expression_null_handling_text" id="expression_null_handling_text"
+	  version="0.1.0" tool_type="expression">
+    <expression type="ecma5.1">
+        {return {'text_out': $job.text_input};}
+    </expression>
+    <inputs>
+        <param type="text" label="Text input." name="text_input" optional="true" />
+    </inputs>
+    <outputs>
+        <output type="text" name="text_out" from="text_out" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="text_input" value_json="&quot;foo bar&quot;" />
+            <output name="text_out" value_json="&quot;foo bar&quot;" />
+        </test>
+        <test>
+            <param name="text_input" value_json="&quot;null&quot;" />
+            <output name="text_out" value_json="&quot;null&quot;" />
+        </test>
+        <!-- Bug with the following test on postgres.
+        <test>
+            <param name="text_input" value_json="&quot;&quot;" />
+            <output name="text_out" value_json="&quot;&quot;" />
+        </test>
+        -->
+        <test>
+            <param name="text_input" value_json="null" />
+            <output name="text_out" value_json="null" />
+        </test>
+    </tests>
+</tool>

test/functional/tools/samples_tool_conf.xml

@@ -175,6 +175,9 @@
   <tool file="expression_parse_int.xml" />
   <tool file="expression_log_line_count.xml" />
   <tool file="expression_null_handling_boolean.xml" />
+  <tool file="expression_null_handling_integer.xml" />
+  <tool file="expression_null_handling_float.xml" />
+  <tool file="expression_null_handling_text.xml" />
   <tool file="cheetah_casting.xml" />
   <tool file="cheetah_problem_unbound_var.xml" />
   <tool file="cheetah_problem_unbound_var_input.xml" />