adds expand nodes (macros)

.travis.yml

@@ -9,6 +9,8 @@ script:
 - flake8 galaxyxml --ignore=E2,E3,E4,E5,W3,W505,C901,E501
 - python examples/example.py > tmp.xml
 - xmldiff tmp.xml examples/tool.xml
+- python examples/example_macros.py > tmp.xml
+- xmldiff tmp.xml examples/example_macros.xml
 - nosetests --with-coverage --cover-package=galaxyxml
 deploy:
   provider: pypi

examples/example_macros.py

@@ -0,0 +1,109 @@
+#!/usr/bin/env python
+import galaxyxml.tool as gxt
+import galaxyxml.tool.parameters as gxtp
+
+# examplify the use of MacrosTool
+# 
+
+tool = gxt.MacrosTool(
+    name="aragorn",
+    id="aragorn",
+    version="1.2.36",
+    description="Aragorn is a tRNA finder",
+    executable="aragorn.exe",
+    version_command="aragorn.exe --version",
+)
+
+inputs = tool.inputs
+outputs = tool.outputs
+
+# Add requirements
+requirements = gxtp.Requirements()
+requirements.append(gxtp.Requirement("package", "samtools", version="1.0.0"))
+requirements.append(gxtp.Container("docker", "one_super_image"))
+tool.requirements = requirements
+
+# A parameter
+param = gxtp.BooleanParam("flag", label="Flag label", help="Flag help", num_dashes=1)
+# Yes I know this is rubbish. Please make a PR!!
+param.space_between_arg = " "
+inputs.append(param)
+
+
+# A float in a section
+section = gxtp.Section("float_section", "Float section")
+param = gxtp.FloatParam("float", label="Float label", help="Float help", value=0, num_dashes=1)
+param.space_between_arg = " "
+section.append(param)
+inputs.append(section)
+
+# A conditional
+param = gxtp.Conditional("cond", label="Conditional")
+param.append(gxtp.SelectParam("Select", options={"hi": "1", "bye": "2"}))
+when_a = gxtp.When(value="hi")
+when_b = gxtp.When(value="bye")
+when_b.append(gxtp.IntegerParam("some_int", value=0, num_dashes=1, label="Advanced value"))
+param.append(when_a)
+param.append(when_b)
+inputs.append(param)
+
+# Integer parameters
+param_min = gxtp.IntegerParam("int_min", label="int_min label", help="int_min help", value=0, num_dashes=1)
+param_max = gxtp.IntegerParam("int_max", label="int_max label", help="int_max help", value=0, num_dashes=1)
+
+posint = gxtp.IntegerParam("posint", label="posint label", positional=True, help="posinthelp", value=0, num_dashes=2)
+
+param_min.command_line_override = "-i$int_min,$int_max"
+param_max.command_line_override = ""
+param_min.space_between_arg = " "
+param_max.space_between_arg = " "
+inputs.append(param_min)
+inputs.append(param_max)
+inputs.append(posint)
+
+# Add Select with options from_file with columns and filter
+param = gxtp.SelectParam("select_local")
+options = gxtp.Options(from_file="loc_file.loc")
+column_a = gxtp.Column("name", 0)
+options.append(column_a)
+column_b = gxtp.Column("value", 1)
+options.append(column_b)
+filter_a = gxtp.Filter("sort_by", name="sorted", column="1")
+options.append(filter_a)
+param.append(options)
+inputs.append(param)
+
+# Configfiles
+configfiles = gxtp.Configfiles()
+configfiles.append(gxtp.Configfile(name="testing", text="Hello <> World"))
+configfiles.append(gxtp.ConfigfileDefaultInputs(name="inputs"))
+
+# Outputs
+param = gxtp.OutputData("output", format="tabular", num_dashes=1)
+param.space_between_arg = " "
+outputs.append(param)
+# Collection
+collection = gxtp.OutputCollection("supercollection", label="a small label")
+discover = gxtp.DiscoverDatasets("(?P&lt;designation&gt;.+)\.pdf.fasta", format="fasta")
+collection.append(discover)
+outputs.append(collection)
+
+tool.inputs = inputs
+tool.outputs = outputs
+tool.help = "HI"
+tool.configfiles = configfiles
+
+# Add Tests sections
+tool.tests = gxtp.Tests()
+test_a = gxtp.Test()
+param = gxtp.TestParam("float", value=5.4)
+test_a.append(param)
+test_out = gxtp.TestOutput(name="output", value="file.out")
+test_a.append(test_out)
+tool.tests.append(test_a)
+
+
+# Add comment to the wrapper
+tool.add_comment("This tool descriptor has been generated using galaxyxml.")
+
+print(tool.export())

examples/example_macros.xml

@@ -0,0 +1,47 @@
+<macros>
+  <!--This tool descriptor has been generated using galaxyxml.-->
+  <token name="ARAGORN_INMACRO"><![CDATA[$flag
+-float $float_section.float
+#if str($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 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 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 name="some_int" type="integer" value="0" label="Advanced value"/>
+      </when>
+    </conditional>
+    <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 name="name" index="0"/>
+        <column name="value" index="1"/>
+        <filter name="sorted" type="sort_by" column="1"/>
+      </options>
+    </param>
+  </xml>
+  <xml name="aragorn_outmacro">
+    <data name="output" format="tabular" hidden="false"/>
+    <collection name="supercollection" label="a small label">
+      <discover_datasets pattern="(?P&amp;lt;designation&amp;gt;.+)\.pdf.fasta" format="fasta"/>
+    </collection>
+  </xml>
+</macros>
+

examples/tool.xml

@@ -8,19 +8,20 @@
   <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
---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
+#for $i_repeat in $repeat
+--data $i_repeat.data
 #end for]]></command>
   <configfiles>
     <configfile name="testing"><![CDATA[Hello <> World]]></configfile>
@@ -69,5 +70,6 @@ select_local $select_local
     </test>
   </tests>
   <help><![CDATA[HI]]></help>
+  <expand macro="citations"/>
 </tool>
 

galaxyxml/__init__.py

@@ -1,5 +1,7 @@
-from builtins import object
-from builtins import str
+from builtins import (
+    str,
+    object
+)
 
 from lxml import etree
 
@@ -15,7 +17,12 @@ def export(self):
 class Util(object):
     @classmethod
     def coerce(cls, data, kill_lists=False):
-        """Recursive data sanitisation
+        """
+        Recursive data sanitisation
+
+        - recurse into lists, dicts, OrderedDict
+        - remove dict/OrderedDict entries with None value
+        - kill_lists: True -> replace lists by their first element
         """
         if isinstance(data, dict):
             return {k: cls.coerce(v, kill_lists=kill_lists) for k, v in list(data.items()) if v is not None}

galaxyxml/tool/__init__.py

@@ -2,7 +2,15 @@
 import logging
 
 from galaxyxml import GalaxyXML, Util
-from galaxyxml.tool.parameters import XMLParam
+from galaxyxml.tool.parameters import (
+    Expand,
+    Import,
+    Inputs,
+    Macro,
+    Macros,
+    Outputs,
+    XMLParam
+)
 
 from lxml import etree
 
@@ -28,8 +36,10 @@ def __init__(
         interpreter=None,
         version_command="interpreter filename.exe --version",
         command_override=None,
+        macros=[],
     ):
 
+        self.id = id
         self.executable = executable
         self.interpreter = interpreter
         self.command_override = command_override
@@ -65,6 +75,12 @@ def __init__(
 
         description_node = etree.SubElement(self.root, "description")
         description_node.text = description
+        if len(macros) > 0:
+            self.macros = Macros()
+            for m in macros:
+                self.macros.append(Import(m))
+        self.inputs = Inputs()
+        self.outputs = Outputs()
 
     def add_comment(self, comment_txt):
         comment = etree.Comment(comment_txt)
@@ -88,12 +104,15 @@ def clean_command_string(self, command_line):
         for x in command_line:
             if x is not [] and x is not [""]:
                 clean.append(x)
-
         return "\n".join(clean)
 
     def export(self, keep_old_command=False):
         # see lib/galaxy/tool_util/linters/xml_order.py
         export_xml = copy.deepcopy(self)
+        try:
+            export_xml.append(export_xml.macros)
+        except Exception:
+            pass
 
         try:
             export_xml.append(export_xml.edam_operations)
@@ -108,7 +127,7 @@ def export(self, keep_old_command=False):
         try:
             export_xml.append(export_xml.requirements)
         except Exception:
-            pass
+            export_xml.append(Expand(macro="requirements"))
 
         # Add stdio section - now an XMLParameter
         try:
@@ -118,7 +137,10 @@ def export(self, keep_old_command=False):
         if not stdio_element:
             stdio_element = etree.SubElement(export_xml.root, "stdio")
             etree.SubElement(stdio_element, "exit_code", range="1:", level="fatal")
-        export_xml.append(stdio_element)
+        try:
+            export_xml.append(export_xml.stdio)
+        except Exception:
+            export_xml.append(Expand(macro="stdio"))
 
         # Append version command
         export_xml.append_version_command()
@@ -131,6 +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:
@@ -172,14 +195,82 @@ def export(self, keep_old_command=False):
         try:
             export_xml.append(export_xml.tests)
         except Exception:
-            pass
+            export_xml.append(Expand(macro="%s_tests" % self.id))
 
         help_element = etree.SubElement(export_xml.root, "help")
         help_element.text = etree.CDATA(export_xml.help)
         export_xml.append(help_element)
 
         try:
             export_xml.append(export_xml.citations)
+        except Exception:
+            export_xml.append(Expand(macro="citations"))
+
+        return super(Tool, export_xml).export()
+
+
+class MacrosTool(Tool):
+    """
+    creates a <macros> tag containing macros and tokens
+    for the inputs and outputs:
+
+    for the inputs
+
+    - a macro `<xml name="ID_inmacro">` containing all the inputs
+    - a token `<token name="ID_INMACRO">` containing the CLI for the inputs
+
+    where ID is the id used in initialization.
+
+    analogously for the outputs `ID_outmacro` and `ID_OUTMACRO`
+    are created.
+
+    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)
+
+        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))
+            raise
+
+        # 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