Mercurial > repos > iuc > map_param_value

changeset 1:a01f088d0e5e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/map_param_value commit 49eab9a9d601cccd50401e5a0221264b5681b64d
author iuc
date Wed, 19 Oct 2022 11:37:19 +0000
parents 43d7b3642a30
children 5ac8a4bf7a8d
files map_param_value.xml
diffstat 1 files changed, 144 insertions(+), 24 deletions(-) [+]
line wrap: on
line diff
--- a/map_param_value.xml	Sun Oct 16 08:05:37 2022 +0000
+++ b/map_param_value.xml	Wed Oct 19 11:37:19 2022 +0000
@@ -1,10 +1,16 @@
-<tool name="Map parameter value" id="map_param_value" version="0.1.0" tool_type="expression" profile="22.01">
+<tool name="Map parameter value" id="map_param_value" version="0.1.1" tool_type="expression" profile="22.01">
     <macros>
         <xml name="when_element" tokens="type_selection">
-            <param name="input_param" type="@TYPE_SELECTION@" optional="true" label="Map this parameter value to a different value"/>
+            <param name="input_param" type="@TYPE_SELECTION@" optional="true" label="Value to map">
+                <sanitizer sanitize="false"/>
+            </param>
             <repeat name="mappings" label="Add value mapping">
-                <param name="from" type="@TYPE_SELECTION@" optional="true" label="Map from this value"></param>
-                <param name="to" type="text" label="to this value" help="This value must be coercable to the selected output parameter type"></param>
+                <param name="from" type="@TYPE_SELECTION@" optional="true" label="Map from this value">
+                    <sanitizer sanitize="false"/>
+                </param>
+                <param name="to" type="text" optional="true" label="to this value" help="This value must be coercable to the selected output parameter type">
+                    <sanitizer sanitize="false"/>
+                </param>
             </repeat>
         </xml>
     </macros>
@@ -30,12 +36,12 @@
 }
 
 for ( var i = 0; i < mappings.length; i++ ) {
-    if ( String(mappings[i].from) == source ) {
+    if ( String(mappings[i].from) == String(source) ) {
         return { output: coerceToOutput(mappings[i].to) };
     }
 }
 if ( $job.unmapped.on_unmapped == "fail" ) {
-    return { __error_message: `text_param ${source} not found in mapping values.` };
+    return { __error_message: `input_param ${source} not found in mapping values.` };
 } else if ( $job.unmapped.on_unmapped == "default" ) {
     return { output: coerceToOutput($job.unmapped.default_value) };
 }
@@ -63,14 +69,8 @@
                 <expand macro="when_element" type_selection="boolean"/>
             </when>
         </conditional>
-        <param name="output_param_type" type="select" label="Select type of parameter to output">
-            <option value="text">Text</option>
-            <option value="integer">Integer</option>
-            <option value="float">Float</option>
-            <option value="boolean">Boolean</option>
-        </param>
         <conditional name="unmapped">
-            <param name="on_unmapped" type="select" label="Select how">
+            <param name="on_unmapped" type="select" label="Select how to handle unmapped values">
                 <option value="input">Use unmodified input parameter value if input parameter value not found in mappings</option>
                 <option value="fail">Fail if input parameter value not found in mappings</option>
                 <option value="default">Provide a default value to use if input parameter value not found in mappings</option>
@@ -81,6 +81,12 @@
                 <param name="default_value" type="text" label="Use this value if the input parameter value was not found in mappings"/>
             </when>
         </conditional>
+        <param name="output_param_type" type="select" label="Select type of parameter to output">
+            <option value="text">Text</option>
+            <option value="integer">Integer</option>
+            <option value="float">Float</option>
+            <option value="boolean">Boolean</option>
+        </param>
     </inputs>
     <outputs>
         <output type="text" name="output_param_text" from="output">
@@ -98,6 +104,7 @@
     </outputs>
     <tests>
         <test expect_num_outputs="1">
+            <!-- map string A to string B -->
             <conditional name="input_param_type">
                 <param name="type" value="text"/>
                 <param name="input_param" value="A" />
@@ -109,6 +116,19 @@
             <output name="output_param_text" value_json="&quot;B&quot;" />
         </test>
         <test expect_num_outputs="1">
+            <!-- test that mapping works in the presence of usually sanitized characters -->
+            <conditional name="input_param_type">
+                <param name="type" value="text"/>
+                <param name="input_param" value="echo $abc &gt; 1" />
+                <repeat name="mappings">
+                    <param name="from" value="echo $abc &gt; 1" />
+                    <param name="to" value="echo $abc &gt; 2" />
+                </repeat>
+            </conditional>
+            <output name="output_param_text" value_json="&quot;echo $abc &gt; 2&quot;" />
+        </test>
+        <test expect_num_outputs="1">
+            <!-- keep unmodified input if no match in mapping values -->
             <conditional name="input_param_type">
                 <param name="input_param" value="C" />
                 <repeat name="mappings">
@@ -118,7 +138,8 @@
             </conditional>
             <output name="output_param_text" value_json="&quot;C&quot;" />
         </test>
-        <test expect_num_outputs="1" expect_failure="true">
+        <test expect_failure="true">
+            <!-- fail job if no mapping found and on_unmapped is set to fail -->
             <conditional name="input_param_type">
                 <param name="input_param" value="C" />
                 <repeat name="mappings">
@@ -131,8 +152,8 @@
             </conditional>
         </test>
         <test expect_num_outputs="1">
+            <!-- map unspecified option text to string default via unmapped default value -->
             <conditional name="input_param_type">
-                <param name="input_param" value="C" />
                 <repeat name="mappings">
                     <param name="from" value="A" />
                     <param name="to" value="B" />
@@ -140,11 +161,12 @@
             </conditional>
             <conditional name="unmapped">
                 <param name="on_unmapped" value="default"/>
-                <param name="default_value" value="D"/>
+                <param name="default_value" value="default"/>
             </conditional>
-            <param name="output_param_text" value_json="&quot;D&quot;" />
+            <output name="output_param_text" value_json="&quot;default&quot;" />
         </test>
         <test expect_num_outputs="1">
+            <!-- map string C to string X via default value -->
             <conditional name="input_param_type">
                 <param name="input_param" value="C" />
                 <repeat name="mappings">
@@ -156,9 +178,10 @@
                 <param name="on_unmapped" value="default"/>
                 <param name="default_value" value="X"/>
             </conditional>
-            <param name="output_param_text" value_json="&quot;X&quot;" />
+            <output name="output_param_text" value_json="&quot;X&quot;" />
         </test>
         <test expect_num_outputs="1">
+            <!-- map string C to string D in presence of multiple mappings -->
             <conditional name="input_param_type">
                 <param name="input_param" value="C" />
                 <repeat name="mappings">
@@ -170,9 +193,10 @@
                     <param name="to" value="D" />
                 </repeat>
             </conditional>
-            <param name="output_param_text" value_json="&quot;D&quot;" />
+            <output name="output_param_text" value_json="&quot;D&quot;" />
         </test>
         <test expect_num_outputs="1">
+            <!-- map integer 42 to integer true value -->
             <conditional name="input_param_type">
                 <param name="type" value="integer" />
                 <param name="input_param" value="42" />
@@ -182,9 +206,10 @@
                 </repeat>
             </conditional>
             <param name="output_param_type" value="boolean"/>
-            <param name="output_param_boolean" value_json="true" />
+            <output name="output_param_boolean" value_json="true" />
         </test>
         <test expect_num_outputs="1">
+            <!-- map float 1.2 to boolean false via unmapped default value -->
             <conditional name="input_param_type">
                 <param name="type" value="float" />
                 <param name="input_param" value="1.2" />
@@ -198,9 +223,10 @@
                 <param name="default_value" value="False"/>
             </conditional>
             <param name="output_param_type" value="boolean"/>
-            <param name="output_param_boolean" value_json="false" />
+            <output name="output_param_boolean" value_json="false" />
         </test>
         <test expect_num_outputs="1">
+            <!-- map integer 1 to float 1.1 -->
             <conditional name="input_param_type">
                 <param name="type" value="integer" />
                 <param name="input_param" value="1" />
@@ -210,11 +236,12 @@
                 </repeat>
             </conditional>
             <param name="output_param_type" value="float"/>
-            <param name="output_param_float" value_json="1.1" />
+            <output name="output_param_float" value_json="1.1" />
         </test>
         <test expect_num_outputs="1">
+            <!-- map string A to integer 2 -->
             <conditional name="input_param_type">
-                <param name="type" value="string" />
+                <param name="type" value="text" />
                 <param name="input_param" value="A" />
                 <repeat name="mappings">
                     <param name="from" value="A" />
@@ -222,8 +249,101 @@
                 </repeat>
             </conditional>
             <param name="output_param_type" value="integer"/>
-            <param name="output_param_float" value_json="2" />
+            <output name="output_param_integer" value_json="2" />
+        </test>
+        <test expect_num_outputs="1">A
+            <!-- map string False to boolean false -->
+            <conditional name="input_param_type">
+                <param name="type" value="text" />
+                <param name="input_param" value="False" />
+                <repeat name="mappings">
+                    <param name="from" value="False" />
+                    <param name="to" value="false" />
+                </repeat>
+            </conditional>
+            <conditional name="unmapped">
+                <param name="on_unmapped" value="fail"/>
+            </conditional>
+            <param name="output_param_type" value="boolean"/>
+            <output name="output_param_boolean" value_json="false" />
+        </test>
+        <test expect_num_outputs="1">
+            <!-- map boolean false to boolean true -->
+            <conditional name="input_param_type">
+                <param name="type" value="boolean" />
+                <param name="input_param" value="false" />
+                <repeat name="mappings">
+                    <param name="from" value="false" />
+                    <param name="to" value="true" />
+                </repeat>
+            </conditional>
+            <conditional name="unmapped">
+                <param name="on_unmapped" value="fail"/>
+            </conditional>
+            <param name="output_param_type" value="boolean"/>
+            <output name="output_param_boolean" value_json="true" />
+        </test>
+        <test expect_num_outputs="1">
+            <!-- map integer 0 to boolean false via default value coercion -->
+            <conditional name="input_param_type">
+                <param name="type" value="integer" />
+                <param name="input_param" value="0" />
+            </conditional>
+            <param name="output_param_type" value="boolean"/>
+            <output name="output_param_boolean" value_json="false" />
         </test>
+        <test expect_num_outputs="1">
+            <!-- map null text value to boolean true -->
+            <conditional name="input_param_type">
+                <param name="type" value="text" />
+                <param name="input_param" value_json="null" />
+                <repeat name="mappings">
+                    <param name="from" value_json="null" />
+                    <param name="to" value="true" />
+                </repeat>
+            </conditional>
+            <param name="output_param_type" value="boolean"/>
+            <output name="output_param_boolean" value_json="true" />
+        </test>
+        <test expect_num_outputs="1" doc="map null integer value to boolean true">
+            <!-- map null integer value to boolean true -->
+            <conditional name="input_param_type">
+                <param name="type" value="integer" />
+                <param name="input_param" value_json="null" />
+                <repeat name="mappings">
+                    <param name="from" value_json="null" />
+                    <param name="to" value="true" />
+                </repeat>
+            </conditional>
+            <param name="output_param_type" value="boolean"/>
+            <output name="output_param_boolean" value_json="true" />
+        </test>
+        <test expect_num_outputs="1">
+            <!-- map integer value to null text -->
+            <conditional name="input_param_type">
+                <param name="type" value="integer" />
+                <param name="input_param" value="1" />
+                <repeat name="mappings">
+                    <param name="from" value="1" />
+                    <param name="to" value_json="null" />
+                </repeat>
+            </conditional>
+            <param name="output_param_type" value="text"/>
+            <output name="output_param_text" value_json="null" />
+        </test>
+        <!-- Old Galaxy issue, optional unset text input still recorded as ""
+             We could work around this with a conditional, but no usecase yet
+             and we should better fix this in Galaxy
+            <test expect_num_outputs="1">
+                <conditional name="input_param_type">
+                    <param name="input_param" value="A" />
+                    <repeat name="mappings">
+                        <param name="from" value="A" />
+                    </repeat>
+                </conditional>
+                <output name="output_param_text" value_json="null" />
+            </test>
+        -->
     </tests>
     <help><![CDATA[
 **What it does**