Merge pull request #38 from fubar2/master

 IUC want profile in the <tool> and detect_errors in the <command>

examples/tool.xml

@@ -5,10 +5,6 @@
     <requirement version="1.0.0" type="package">samtools</requirement>
     <container type="docker">one_super_image</container>
   </requirements>
-  <stdio>
-    <exit_code range="1:" level="fatal"/>
-  </stdio>
-  <expand macro="stdio"/>
   <version_command><![CDATA[aragorn.exe --version]]></version_command>
   <command><![CDATA[aragorn.exe $flag
 -float $float_section.float

galaxyxml/__init__.py

@@ -1,7 +1,4 @@
-from builtins import (
-    object,
-    str
-)
+from builtins import object, str
 
 from lxml import etree
 

galaxyxml/tool/__init__.py

@@ -2,15 +2,7 @@
 import logging
 
 from galaxyxml import GalaxyXML, Util
-from galaxyxml.tool.parameters import (
-    Expand,
-    Import,
-    Inputs,
-    Macro,
-    Macros,
-    Outputs,
-    XMLParam
-)
+from galaxyxml.tool.parameters import Expand, Import, Inputs, Macro, Macros, Outputs, XMLParam, Command
 
 from lxml import etree
 
@@ -37,18 +29,21 @@ def __init__(
         version_command="interpreter filename.exe --version",
         command_override=None,
         macros=[],
+        profile=None,
     ):
 
         self.id = id
         self.executable = executable
         self.interpreter = interpreter
         self.command_override = command_override
+        self.profile = profile
         kwargs = {
             "name": name,
             "id": id,
             "version": version,
             "hidden": hidden,
             "workflow_compatible": workflow_compatible,
+            "profile": profile
         }
         self.version_command = version_command
 
@@ -81,6 +76,7 @@ def __init__(
                 self.macros.append(Import(m))
         self.inputs = Inputs()
         self.outputs = Outputs()
+        self.command = Command()
 
     def add_comment(self, comment_txt):
         comment = etree.Comment(comment_txt)
@@ -134,13 +130,11 @@ def export(self, keep_old_command=False):
             stdio_element = export_xml.stdios
         except Exception:
             stdio_element = None
-        if not stdio_element:
-            stdio_element = etree.SubElement(export_xml.root, "stdio")
-            etree.SubElement(stdio_element, "exit_code", range="1:", level="fatal")
-        try:
-            export_xml.append(stdio_element)
-        except Exception:
-            export_xml.append(Expand(macro="stdio"))
+        if stdio_element:
+            try:
+                export_xml.append(stdio_element)
+            except Exception:
+                export_xml.append(Expand(macro="stdio"))
 
         # Append version command
         export_xml.append_version_command()
@@ -158,25 +152,30 @@ def export(self, keep_old_command=False):
                 command_line.append(export_xml.outputs.cli())
             except Exception:
                 pass
-        # Steal interpreter from kwargs
-        command_kwargs = {}
-        if export_xml.interpreter is not None:
-            command_kwargs["interpreter"] = export_xml.interpreter
         # Add command section
-        command_node = etree.SubElement(export_xml.root, "command", **command_kwargs)
+        command_node_text = None
         if keep_old_command:
             if getattr(self, "command", None):
-                command_node.text = etree.CDATA(export_xml.command)
+                command_node_text = etree.CDATA(export_xml.command)
             else:
                 logger.warning("The tool does not have any old command stored. Only the command line is written.")
-                command_node.text = export_xml.executable
+                command_node_text = export_xml.executable
         else:
             if self.command_override:
                 actual_cli = export_xml.clean_command_string(command_line)
             else:
-                actual_cli = "%s %s" % (export_xml.executable, export_xml.clean_command_string(command_line),)
-            command_node.text = etree.CDATA(actual_cli.strip())
-        export_xml.append(command_node)
+                actual_cli = "%s %s" % (
+                    export_xml.executable,
+                    export_xml.clean_command_string(command_line),
+                )
+            command_node_text = actual_cli.strip()
+        export_xml.command_line = command_node_text
+        try:
+            command_element = export_xml.command
+        except Exception:
+            command_element = etree.SubElement(export_xml.root, "command", detect_errors=None)
+        command_element.node.text = etree.CDATA(command_node_text)
+        export_xml.append(command_element)
 
         try:
             export_xml.append(export_xml.configfiles)
@@ -226,13 +225,13 @@ class MacrosTool(Tool):
 
     TODO all other elements, like requirements are currently ignored
     """
+
     def __init__(self, *args, **kwargs):
         super(MacrosTool, self).__init__(*args, **kwargs)
         self.root = etree.Element('macros')
         self.inputs = Macro("%s_inmacro" % self.id)
         self.outputs = Macro("%s_outmacro" % self.id)
 
-
     def export(self, keep_old_command=False):  # noqa
 
         export_xml = copy.deepcopy(self)

galaxyxml/tool/import_xml.py

@@ -27,7 +27,6 @@ def _init_tool(self, xml_root):
                 description = child.text
             elif child.tag == "command":
                 executable = child.text.split()[0]
-                command = child.text
             elif child.tag == "version_command":
                 version_cmd = child.text
 
@@ -43,7 +42,6 @@ def _init_tool(self, xml_root):
             workflow_compatible=xml_root.attrib.get("workflow_compatible", True),
             version_command=version_cmd,
         )
-        tool.command = command
         return tool
 
     def _load_description(self, tool, desc_root):
@@ -77,21 +75,28 @@ def _load_stdio(self, tool, stdio_root):
         """
         tool.stdios = gxtp.Stdios()
         for std in stdio_root:
-            slevel = std.attrib['level']
-            srange = std.attrib['range']
+            slevel = std.attrib["level"]
+            srange = std.attrib["range"]
             tool.stdios.append(gxtp.Stdio(level=slevel, range=srange))
         logger.info("<stdio> loaded.")
 
-    def _load_command(self, tool, desc_root):
+    def _load_command(self, tool, command_root):
         """
-        <command> is already loaded during initiation.
-
         :param tool: Tool object from galaxyxml.
         :type tool: :class:`galaxyxml.tool.Tool`
         :param desc_root: root of <command> tag.
         :type desc_root: :class:`xml.etree._Element`
         """
-        logger.info("<command> is loaded during initiation of the object.")
+        try:
+            detect_errors = command_root.attrib['detect_errors']
+        except KeyError:
+            detect_errors = None
+        ctext = command_root.text
+        command = gxtp.Command(detect_errors=detect_errors)
+        command.node.text = ctext
+        tool.command_line = ctext
+        tool.command = command
+        tool.executable = ctext.split()[0]
 
     def _load_help(self, tool, help_root):
         """
@@ -727,11 +732,12 @@ def _load_element(self, test_root, element_root):
         :param repeat_root: root of <output_collection> tag.
         :param repeat_root: :class:`xml.etree._Element`
         """
-        test_root.append(gxtp.TestOCElement(
-            name=element_root.attrib.get("name", None),
-            ftype=element_root.attrib.get("ftype", None),
-            file=element_root.attrib.get("file", None)
-        )
+        test_root.append(
+            gxtp.TestOCElement(
+                name=element_root.attrib.get("name", None),
+                ftype=element_root.attrib.get("ftype", None),
+                file=element_root.attrib.get("file", None),
+            )
         )
 
     def _load_repeat(self, test_root, repeat_root):
@@ -747,7 +753,7 @@ def _load_repeat(self, test_root, repeat_root):
             repeat_root.attrib.get("title", None),
             min=repeat_root.attrib.get("min", None),
             max=repeat_root.attrib.get("max", None),
-            default=repeat_root.attrib.get("default", None)
+            default=repeat_root.attrib.get("default", None),
         )
         # Deal with child nodes
         self.load_inputs(repeat, repeat_root)