subparsers that are a parent are macros

each subparser that is a parent of another is becomes
a two macros (in/out) and a token (commandline).

implemented in MacrosTool

Author: bernt-matthias

galaxyxml/tool/__init__.py

@@ -2,7 +2,14 @@
 import logging
 from lxml import etree
 from galaxyxml import Util, GalaxyXML
-from galaxyxml.tool.parameters import XMLParam
+from galaxyxml.tool.parameters import (
+    Import,
+    Inputs,
+    Macro,
+    Macros,
+    Outputs,
+    XMLParam
+)
 
 VALID_TOOL_TYPES = ('data_source', 'data_source_async')
 VALID_URL_METHODS = ('get', 'post')
@@ -15,8 +22,9 @@ class Tool(GalaxyXML):
 
     def __init__(self, name, id, version, description, executable, hidden=False,
                  tool_type=None, URL_method=None, workflow_compatible=True,
-                 interpreter=None, version_command='interpreter filename.exe --version'):
-
+                 interpreter=None, version_command='interpreter filename.exe --version',
+                 macros=None):
+        self.id = id
         self.executable = executable
         self.interpreter = interpreter
         kwargs = {
@@ -53,6 +61,15 @@ def __init__(self, name, id, version, description, executable, hidden=False,
 
         description_node = etree.SubElement(self.root, 'description')
         description_node.text = description
+        if macros:
+            self.macros = Macros()
+            if isinstance(macros, list):
+                for m in macros:
+                    self.macros.append(Import(m))
+            else:
+                self.macros.append(Import(macros))
+        self.inputs = Inputs()
+        self.outputs = Outputs()
 
     def add_comment(self, comment_txt):
         comment = etree.Comment(comment_txt)
@@ -80,8 +97,11 @@ def clean_command_string(self, command_line):
         return '\n'.join(clean)
 
     def export(self, keep_old_command=False):  # noqa
-
         export_xml = copy.deepcopy(self)
+        try:
+            export_xml.append(export_xml.macros)
+        except Exception:
+            pass
 
         try:
             export_xml.append(export_xml.edam_operations)
@@ -108,6 +128,7 @@ def export(self, keep_old_command=False):  # noqa
             command_line.append(export_xml.inputs.cli())
         except Exception as e:
             logger.warning(str(e))
+            raise
 
         try:
             command_line.append(export_xml.outputs.cli())
@@ -165,3 +186,55 @@ def export(self, keep_old_command=False):  # noqa
             pass
 
         return super(Tool, export_xml).export()
+
+
+class MacrosTool(Tool):
+
+    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)
+
+        try:
+            for child in export_xml.macros:
+                export_xml.append(child)
+        except Exception:
+            pass
+
+        command_line = []
+        try:
+            command_line.append(export_xml.inputs.cli())
+        except Exception as e:
+            logger.warning(str(e))
+
+        # Add command section
+        command_node = etree.SubElement(export_xml.root, 'token', {"name": "%s_INMACRO" % self.id.upper()})
+        actual_cli = "%s" % (export_xml.clean_command_string(command_line))
+        command_node.text = etree.CDATA(actual_cli.strip())
+
+        command_line = []
+        try:
+            command_line.append(export_xml.outputs.cli())
+        except Exception:
+            pass
+        command_node = etree.SubElement(export_xml.root, 'token', {"name": "%s_OUTMACRO" % self.id.upper()})
+        actual_cli = "%s" % (export_xml.clean_command_string(command_line))
+        command_node.text = etree.CDATA(actual_cli.strip())
+
+        try:
+            export_xml.append(export_xml.inputs)
+        except Exception:
+            pass
+
+        try:
+            export_xml.append(export_xml.outputs)
+        except Exception:
+            pass
+
+        return super(Tool, export_xml).export()

galaxyxml/tool/parameters/__init__.py

@@ -52,7 +52,8 @@ class Macros(XMLParam):
     name = "macros"
 
     def acceptable_child(self, child):
-        return isinstance(child, Macro)
+        return isinstance(child, Macro) \
+               or isinstance(child, Import)
 
 
 class Macro(XMLParam):
@@ -62,7 +63,19 @@ def __init__(self, name):
         params = Util.clean_kwargs(locals().copy())
         passed_kwargs = {}
         passed_kwargs['name'] = params['name']
-        super(Expand, self).__init__(**passed_kwargs)
+        super(Macro, self).__init__(**passed_kwargs)
+
+    def acceptable_child(self, child):
+        return issubclass(type(child), XMLParam) \
+               and not isinstance(child, Macro)
+
+
+class Import(XMLParam):
+    name = "import"
+
+    def __init__(self, value):
+        super(Import, self).__init__()
+        self.node.text = value
 
     def acceptable_child(self, child):
         return issubclass(type(child), XMLParam) \
@@ -81,6 +94,13 @@ def __init__(self, macro):
         passed_kwargs['macro'] = params['macro']
         super(Expand, self).__init__(**passed_kwargs)
 
+    def command_line(self):
+        """
+        need to define empty command line contribution
+        since Expand can be child of Inputs/Outputs
+        """
+        return ""
+
 
 class ExpandIO(Expand):
     """
@@ -182,7 +202,6 @@ def acceptable_child(self, child):
         return issubclass(type(child), EdamTopic) \
                or isinstance(child, Expand)
 
-
     def has_topic(self, edam_topic):
         """
         Check the presence of a given edam_topic.
@@ -369,7 +388,6 @@ def acceptable_child(self, child):
                or isinstance(child, Expand)
 
 
-
 class Repeat(InputParameter):
     name = 'repeat'
 
@@ -401,7 +419,7 @@ def __init__(self, name, **kwargs):
         super(Conditional, self).__init__(**params)
 
     def acceptable_child(self, child):
-        return (issubclass(type(child), InputParameter) \
+        return (issubclass(type(child), InputParameter)
                 and not isinstance(child, Conditional)) \
                or isinstance(child, Expand)