fix mako_identifier bug if None in parents

if there is a when (which has a None identifier)
on the path to the root then the export failed.

also fix linter errors

Author: bernt-matthias

examples/example_macros.xml

@@ -2,36 +2,38 @@
   <!--This tool descriptor has been generated using galaxyxml.-->
   <token name="ARAGORN_INMACRO"><![CDATA[$flag
 -float $float_section.float
-cond $cond
+#if str($cond.Select) == "bye"
+-some_int $cond.some_int
+#end if
 -i$int_min,$int_max
 
 $posint
 select_local $select_local]]></token>
   <token name="ARAGORN_OUTMACRO"><![CDATA[-output '$output'
 ## TODO CLI for OutputCollection collection]]></token>
   <xml name="aragorn_inmacro">
-    <param label="Flag label" help="Flag help" checked="false" type="boolean" name="flag" argument="-flag" truevalue="-flag" falsevalue=""/>
-    <section title="Float section" name="float_section">
-      <param label="Float label" help="Float help" value="0" type="float" name="float" argument="-float"/>
+    <param name="flag" type="boolean" label="Flag label" help="Flag help" checked="false" truevalue="-flag" falsevalue=""/>
+    <section name="float_section" title="Float section">
+      <param name="float" type="float" value="0" label="Float label" help="Float help"/>
     </section>
-    <conditional label="Conditional" name="cond" argument="cond">
-      <param label="Author did not provide help for this parameter... " type="select" name="Select" argument="Select">
+    <conditional name="cond" label="Conditional">
+      <param name="Select" type="select" label="Author did not provide help for this parameter... ">
         <option value="bye">2</option>
         <option value="hi">1</option>
       </param>
       <when value="hi"/>
       <when value="bye">
-        <param label="Advanced value" value="0" type="integer" name="some_int" argument="-some_int"/>
+        <param name="some_int" type="integer" value="0" label="Advanced value"/>
       </when>
     </conditional>
-    <param label="int_min label" help="int_min help" value="0" type="integer" name="int_min" argument="-int_min"/>
-    <param label="int_max label" help="int_max help" value="0" type="integer" name="int_max" argument="-int_max"/>
-    <param label="posint label" help="posinthelp" value="0" type="integer" name="posint"/>
-    <param label="Author did not provide help for this parameter... " type="select" name="select_local" argument="select_local">
+    <param name="int_min" type="integer" value="0" label="int_min label" help="int_min help"/>
+    <param name="int_max" type="integer" value="0" label="int_max label" help="int_max help"/>
+    <param name="posint" type="integer" value="0" label="posint label" help="posinthelp"/>
+    <param name="select_local" type="select" label="Author did not provide help for this parameter... ">
       <options from_file="loc_file.loc">
-        <column index="0" name="name"/>
-        <column index="1" name="value"/>
-        <filter type="sort_by" column="1" name="sorted"/>
+        <column name="name" index="0"/>
+        <column name="value" index="1"/>
+        <filter name="sorted" type="sort_by" column="1"/>
       </options>
     </param>
   </xml>

examples/tool.xml

@@ -11,21 +11,20 @@
   <expand macro="stdio"/>
   <version_command><![CDATA[aragorn.exe --version]]></version_command>
   <command><![CDATA[aragorn.exe $flag
--float $float
---float-fromarg $float_fromarg
-#if str($Select) == "bye"
--some_int $some_int
+-float $float_section.float
+--float-fromarg $float_section.float_fromarg
+#if str($cond.Select) == "bye"
+-some_int $cond.some_int
 #end if
 -i$int_min,$int_max
 
 $posint
 select_local $select_local
 #for $i in $repeat:
---data $data
+--data $repeat.data
 #end for
 -output '$output'
-## TODO CLI for OutputCollection collection
-  ]]></command>
+## TODO CLI for OutputCollection collection]]></command>
   <configfiles>
     <configfile name="testing"><![CDATA[Hello <> World]]></configfile>
     <inputs name="inputs"/>

galaxyxml/tool/__init__.py

@@ -153,6 +153,7 @@ def export(self, keep_old_command=False):
                 command_line.append(export_xml.inputs.cli())
             except Exception as e:
                 logger.warning(str(e))
+                raise
             try:
                 command_line.append(export_xml.outputs.cli())
             except Exception:

galaxyxml/tool/parameters/__init__.py

@@ -2,12 +2,16 @@
     str,
     object
 )
+import logging
 
 from galaxyxml import Util
 
 from galaxy.tool_util.parser.util import _parse_name
 from lxml import etree
 
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
 class XMLParam(object):
     name = "node"
 
@@ -160,7 +164,7 @@ def __init__(self, **kwargs):
 
     def acceptable_child(self, child):
         return isinstance(child, RequestParamTranslation) \
-               or isinstance(child, Expand)
+            or isinstance(child, Expand)
 
 
 class RequestParam(XMLParam):
@@ -175,7 +179,7 @@ def __init__(self, galaxy_name, remote_name, missing, **kwargs):
 
     def acceptable_child(self, child):
         return isinstance(child, AppendParam) and self.galaxy_name == "URL" \
-               or isinstance(child, Expand)
+            or isinstance(child, Expand)
 
 
 class AppendParam(XMLParam):
@@ -205,7 +209,7 @@ class EdamOperations(XMLParam):
 
     def acceptable_child(self, child):
         return issubclass(type(child), EdamOperation) \
-               or isinstance(child, Expand)
+            or isinstance(child, Expand)
 
     def has_operation(self, edam_operation):
         """
@@ -232,7 +236,7 @@ class EdamTopics(XMLParam):
 
     def acceptable_child(self, child):
         return issubclass(type(child), EdamTopic) \
-               or isinstance(child, Expand)
+            or isinstance(child, Expand)
 
     def has_topic(self, edam_topic):
         """
@@ -260,8 +264,8 @@ class Requirements(XMLParam):
 
     def acceptable_child(self, child):
         return issubclass(type(child), Requirement) \
-               or issubclass(type(child), Container) \
-               or isinstance(child, Expand)
+            or issubclass(type(child), Container) \
+            or isinstance(child, Expand)
 
 
 class Requirement(XMLParam):
@@ -292,8 +296,8 @@ class Configfiles(XMLParam):
 
     def acceptable_child(self, child):
         return issubclass(type(child), Configfile) \
-               or issubclass(type(child), ConfigfileDefaultInputs) \
-               or isinstance(child, Expand)
+            or issubclass(type(child), ConfigfileDefaultInputs) \
+            or isinstance(child, Expand)
 
 
 class Configfile(XMLParam):
@@ -327,8 +331,8 @@ def __init__(self, action=None, check_value=None, method=None, target=None, ngin
 
     def acceptable_child(self, child):
         return issubclass(type(child), InputParameter) \
-                or issubclass(type(child), Expand) \
-                or issubclass(type(child), ExpandIO)
+            or issubclass(type(child), Expand) \
+            or issubclass(type(child), ExpandIO)
 
 
 class InputParameter(XMLParam):
@@ -406,7 +410,9 @@ def mako_name(self):
         parent_identifiers = []
         p = self.parent
         while p is not None and hasattr(p, "mako_identifier"):
-            parent_identifiers.append(p.mako_identifier)
+            # exclude None identifiers -- e.g. <when> tags
+            if p.mako_identifier is not None:
+                parent_identifiers.append(p.mako_identifier)
             p = p.parent
         if len(parent_identifiers) > 0:
             parent_identifiers.append("")
@@ -432,7 +438,7 @@ def command_line(self):
 
     def acceptable_child(self, child):
         return issubclass(type(child), InputParameter) \
-               or isinstance(child, Expand)
+            or isinstance(child, Expand)
 
 
 class Repeat(InputParameter):
@@ -448,7 +454,7 @@ def __init__(self, name, title, min=None, max=None, default=None, **kwargs):
 
     def acceptable_child(self, child):
         return issubclass(type(child), InputParameter) \
-               or isinstance(child, Expand)
+            or isinstance(child, Expand)
 
     def command_line_actual(self):
         lines = []
@@ -499,7 +505,7 @@ def __init__(self, value):
 
     def acceptable_child(self, child):
         return issubclass(type(child), InputParameter) \
-                          or isinstance(child, Expand)
+            or isinstance(child, Expand)
 
 
 class Param(InputParameter):
@@ -520,8 +526,8 @@ def __init__(self, name, argument=None, value=None, optional=None, label=None, h
 
     def acceptable_child(self, child):
         return issubclass(type(child), InputParameter) \
-                          or isinstance(child, ValidatorParam) \
-                          or isinstance(child, Expand)
+            or isinstance(child, ValidatorParam) \
+            or isinstance(child, Expand)
 
 
 class TextParam(Param):
@@ -627,8 +633,8 @@ def __init__(
 
     def acceptable_child(self, child):
         return issubclass(type(child), SelectOption) \
-                          or issubclass(type(child), Options) \
-                          or isinstance(child, Expand)
+            or issubclass(type(child), Options) \
+            or isinstance(child, Expand)
 
 
 class SelectOption(InputParameter):
@@ -655,8 +661,8 @@ def __init__(self, from_dataset=None, from_file=None, from_data_table=None, from
 
     def acceptable_child(self, child):
         return issubclass(type(child), Column) \
-                          or issubclass(type(child), Filter) \
-                          or isinstance(child, Expand)
+            or issubclass(type(child), Filter) \
+            or isinstance(child, Expand)
 
 
 class Column(InputParameter):
@@ -713,9 +719,9 @@ class Outputs(XMLParam):
 
     def acceptable_child(self, child):
         return isinstance(child, OutputData) \
-                          or isinstance(child, OutputCollection) \
-                          or isinstance(child, Expand) \
-                          or isinstance(child, ExpandIO)
+            or isinstance(child, OutputCollection) \
+            or isinstance(child, Expand) \
+            or isinstance(child, ExpandIO)
 
 
 class OutputData(XMLParam):
@@ -763,9 +769,9 @@ def flag(self):
 
     def acceptable_child(self, child):
         return isinstance(child, OutputFilter) \
-                          or isinstance(child, ChangeFormat) \
-                          or isinstance(child, DiscoverDatasets) \
-                          or isinstance(child, Expand)
+            or isinstance(child, ChangeFormat) \
+            or isinstance(child, DiscoverDatasets) \
+            or isinstance(child, Expand)
 
 
 class OutputFilter(XMLParam):
@@ -790,7 +796,7 @@ def __init__(self, **kwargs):
 
     def acceptable_child(self, child):
         return isinstance(child, ChangeFormatWhen) \
-                          or isinstance(child, Expand)
+            or isinstance(child, Expand)
 
 
 class ChangeFormatWhen(XMLParam):
@@ -840,16 +846,16 @@ class Tests(XMLParam):
 
     def acceptable_child(self, child):
         return issubclass(type(child), Test) \
-                          or isinstance(child, Expand)
+            or isinstance(child, Expand)
 
 
 class Test(XMLParam):
     name = "test"
 
     def acceptable_child(self, child):
         return isinstance(child, TestParam) \
-                          or isinstance(child, TestOutput) \
-                          or isinstance(child, Expand)
+            or isinstance(child, TestOutput) \
+            or isinstance(child, Expand)
 
 
 class TestParam(XMLParam):
@@ -886,7 +892,7 @@ class Citations(XMLParam):
 
     def acceptable_child(self, child):
         return issubclass(type(child), Citation) \
-                          or isinstance(child, Expand)
+            or isinstance(child, Expand)
 
     def has_citation(self, type, value):
         """